Manuel L Gonzalez-Garay
- Research Associate Professor, Medicine
- Associate Director, Applied Genomics - Center for Biomedical Informatic / Biostatistics
I am a seasoned expert in bioinformatics, computational biology, and genetics, and I also have extensive training in biostatistics, cell, and molecular biology. I am strongly motivated to contribute to the understanding of genetic disorders. My initial training was in biostatistics, genetics, cell and molecular biology, however during 1997; I redirected my career towards bioinformatics. Since then, I have been working professionally as a bioinformatician for the last eighteen years. In 1998, I joined a drug discovery company, Lexicon Pharmaceuticals as a Scientific Programmer, few months after joining Lexicon, I become engage in a significant number of projects and very soon I got promoted to create my group. During my time at Lexicon, I managed and created databases and software for multiple projects. Some of them were: Omnibank, Lexvision, Lexgene, the lexicon’s mouse knockout database, a target prioritization program, etc. After the burst of the first biotech bubble, I decide to move back to academia and from 2002 to 2009 I worked at Human Genome Sequencing Center (HGSC), Baylor College of Medicine in Houston. During my employment at HGSC, I developed bioinformatics software like Genboree discovery systems and became integrally involved in multiple projects including the Tumor Sequencing Project (TSP), The Cancer Genome Atlas (TCGA) and the ENCODE project. In 2010, I moved to the Institute of Molecular Medicine (UTHealth), where my laboratory was routinely sequencing genomes, exomes and RNAs using multiple sequencing platforms and perform bioinformatics analysis. During that period, I analyzed the whole genome of patients with rare disorders, whole-exome sequences of hundreds of samples. Consequently, I developed the necessary expertise and software to identify genetic variants efficiently. At the IMM, I directed a project in personalized medicine where I analyzed the genetic components of healthy individuals. During 2012, I led a team of clinicians and graduate students to participate in the Boston Children’s Hospital CLARITY challenge with the goal of developing better standards for the interpretation of clinical genomes. Also, I established multiple collaborations at the IMM where I served as the main bioinformatician in a variety of projects directed toward understanding the molecular mechanisms of complex and monogenetic disorders. In 2016, I moved to the University of Arizona where I have been acting as a bioinformatician and biostatistician in multiple projects directed to understand the molecular mechanisms leading to Lipedema, Dercum's disease, Sarcoidosis and other lung disorders.
- Ph.D. Regulatory Biology, 1996
- University of Texas, GSBS
- B. Biology 1988
- Universidad Autónoma de Nuevo León, México
2016-present Associate Professor, Department of Medicine. University of Arizona MS, Tucson, Arizona
2016-present Associate Director for Applied Genomics. Center for Biomedical Informatics and Biostatistics. University of Arizona MS, Tucson, Arizona
2013-present Affiliated Professor, Medical School, Universidad Autónoma de Nuevo Leon (UANL).
2010-2015 Assistant Professor, The Brown Foundation Institute of Molecular Medicine,The University of Texas Health Science Center, Houston, Texas
2002-2009 Senior Scientific Programmer Lead, Bioinformatics Research Laboratory, Human Genome Sequencing Center, Baylor College of Medicine. Houston, TX
2000-2002 Manager of Bioinformatics, Lexicon Genetics Inc. The Woodlands, TX
1999-2000 Bioinformatics Scientist, Lexicon Genetics Inc. The Woodlands, TX
1998-1999 Scientific Programmer, Lexicon Genetics Inc. The Woodlands, TX
1996-1998 Postdoctoral Fellow, University of Texas, MS, Dept. of Integrative Biology, Houston, TX
1988-1991 Research Assistant, University of Texas, Medical School, Dept. of Pharmacology, Houston
- Ph.D. Cell and Regulatory Biology
- The University of Texas UTHealth Graduate School of Biomedical Sciences, Houston, Texas, United States
- Analysis of the mechanisms that maintain coordinate production of alpha and beta- tubulin in mammalian cells
- B.S. Biology
- Universidad Autónoma de Nuevo Leon, Monterrey, Nuevo Leon, Mexico
- Detection of DNA sequences from Human Papillomavirus type 16 inCervical Cancer
- Research Associate Professor & Associate Director of Applied Genomics, University of Arizona, Tucson, Arizona (2016 - Ongoing)
- Assistant Professor, UThealth, Institute of Molecular Medicine (IMM) (2010 - 2015)
- Senior Scientific Programmer Lead, Human Genome Sequencing Center, Baylor College of Medicine (2002 - 2009)
- Sr. Manager of Bioinformatics, Lexicon Pharmaceuticals (1998 - 2002)
- Postdoctoral Fellow, University of Texas (1996 - 1998)
Rare Genetic disordersLymphedemaLipedemaDercum's DiseasePulmonary hypertension (PH)Pulmonary Fibrosis
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- Gross, C. M., Kellner, M., Wang, T., Lu, Q., Sun, X., Zemskov, E. A., Noonepalle, S., Kangath, A., Kumar, S., Gonzalez-Garay, M., Desai, A. A., Aggarwal, S., Gorshkov, B., Klinger, C., Verin, A. D., Catravas, J. D., Jacobson, J. R., Yuan, J. X., Rafikov, R., , Garcia, J. G., et al. (2017). LPS Induced Acute Lung Injury Involves the NF-κB-mediated Downregulation of SOX18. American journal of respiratory cell and molecular biology.More infoOne of the early events in the progression of lipopolysaccharide (LPS)-mediated acute lung injury (ALI) in mice is the disruption of the pulmonary endothelial barrier resulting in lung edema. However, the molecular mechanisms by which the endothelial barrier becomes compromised remain unresolved. The SRY-related High Mobility Group box (Sox) group-F family member, Sox18, is a barrier- protective protein through its ability to increase the expression of the tight junction protein, Claudin-5. Thus, the purpose of this study was to determine if down-regulation of the Sox18-Claudin-5 axis plays a role in the pulmonary endothelial barrier disruption associated with LPS exposure. Our data indicate that both Sox18 and Claudin-5 expression is decreased in two models of in vivo LPS exposure (intraperitoneal, intratracheal). A similar down-regulation was observed in cultured human lung microvascular endothelial cells (HLMVECs) exposed to LPS. Sox18 over-expression in HLMVECs or in the mouse lung attenuated the LPS-mediated vascular barrier disruption. Conversely, reduced Claudin-5 expression (siRNA) reduced the HLMVEC barrier protective effects of Sox18 over-expression. The mechanism by which LPS decreases Sox18 expression was identified as transcriptional repression through binding of p65 NF-kB to a Sox18 promoter sequence located between -1082 and -1073 bp with peroxynitrite contributing to LPS-mediated NF-kB activation. We conclude that NFkB-dependent decreases in the Sox18-Claudin 5 axis is essentially involved in the disruption of human EC barrier integrity associated with LPS-mediated ALI.
- Gonzalez-Garay, M. L. (2016). Biomechanisms of Comorbidity: Reviewing Integrative Analyses of Multi-omics Datasets and Electronic Health Records.. Yearb Med Inform, 10(1), 194-206. doi:10.15265/IY-2016-040More infoObjectives: Disease comorbidity is a pervasive phenomenon impacting patients’ health outcomes, disease management, and clinical decisions. This review presents past, current and future research directions leveraging both phenotypic and molecular information to uncover disease similarity underpinning the biology and etiology of disease comorbidity. Methods: We retrieved ~130 publications and retained 59, ranging from 2006 to 2015, that comprise a minimum number of five diseases and at least one type of biomolecule. We surveyed their methods, disease similarity metrics, and calculation of comorbidities in the electronic health records, if present. Results: Among the surveyed studies, 44% generated or validated disease similarity metrics in context of comorbidity, with 60% being published in the last two years. As inputs, 87% of studies utilized intragenic loci and proteins while 13% employed RNA (mRNA, LncRNA or miRNA). Network modeling was predominantly used (35%) followed by statistics (28%) to impute similarity between these biomolecules and diseases. Studies with large numbers of biomolecules and diseases used network models or naïve overlap of disease-molecule associations, while machine learning, statistics, and information retrieval were utilized in smaller and moderate sized studies. Multiscale computations comprising shared function, network topology, and phenotypes were performed exclusively on proteins. Conclusion: This review highlighted the growing methods for identifying the molecular mechanisms underpinning comorbidities that leverage multiscale molecular information and patterns from electronic health records. The survey unveiled that intergenic polymorphisms have been overlooked for similarity imputation compared to their intragenic counterparts, offering new opportunities to bridge the mechanistic and similarity gaps of comorbidity.
- Gonzalez-Garay, M. L. (2016). Robust extracellular pH modulation by Candida albicans during growth in carboxylic acids. mBio, 7(6), Published online 2016 Nov 15. doi:10.1128/mBio.01646-16More infoThe opportunistic fungal pathogen Candida albicans thrives within diverse niches in the mammalian host. Among the adaptations that underlie this fitness is an ability to utilize a wide array of nutrients, especially sources of carbon that are disfavored by many other fungi; this contributes to its ability to survive interactions with the phagocytes that serve as key barriers against disseminated infections. We have reported that C. albicans generates ammonia as a byproduct of amino acid catabolism to neutralize the acidic phagolysosome and promote hyphal morphogenesis in a manner dependent on the Stp2 transcription factor. Here, we report that this species rapidly neutralizes acidic environments when utilizing carboxylic acids like pyruvate, α-ketoglutarate (αKG), or lactate as the primary carbon source. Unlike in cells growing in amino acid-rich medium, this does not result in ammonia release, does not induce hyphal differentiation, and is genetically distinct. While transcript profiling revealed significant similarities in gene expression in cells grown on either carboxylic or amino acids, genetic screens for mutants that fail to neutralize αKG medium identified a nonoverlapping set of genes, including CWT1, encoding a transcription factor responsive to cell wall and nitrosative stresses. Strains lacking CWT1 exhibit retarded αKG-mediated neutralization in vitro, exist in a more acidic phagolysosome, and are more susceptible to macrophage killing, while double cwt1Δ stp2Δ mutants are more impaired than either single mutant. Together, our observations indicate that C. albicans has evolved multiple ways to modulate the pH of host-relevant environments to promote its fitness as a pathogen.IMPORTANCE The fungal pathogen Candida albicans is a ubiquitous and usually benign constituent of the human microbial ecosystem. In individuals with weakened immune systems, this organism can cause potentially life-threatening infections and is one of the most common causes of hospital-acquired infections. Understanding the interactions between C. albicans and immune phagocytic cells, such as macrophages and neutrophils, will define the mechanisms of pathogenesis in this species. One such adaptation is an ability to make use of nonstandard nutrients that we predict are plentiful in certain niches within the host, including within these phagocytic cells. We show here that the metabolism of certain organic acids enables C. albicans to neutralize acidic environments, such as those within macrophages. This phenomenon is distinct in several significant ways from previous reports of similar processes, indicating that C. albicans has evolved multiple mechanisms to combat the harmful acidity of phagocytic cells.
- Gonzalez-Garay, M. L., Aldrich, M. B., Rasmussen, J. C., Guilliod, R., Lapinski, P. E., King, P. D., & Sevick-Muraca, E. M. (2016). A novel mutation in CELSR1 is associated with hereditary lymphedema. Vascular cell, 8, 1.More infoBiological evidence reported in the literature supports the role of CELSR1 as being essential for valvular function in murine lymphatics. Yet thus far, there have been no variants in CELSR1 associated with lymphatic dysfunction in humans.
- Kin, K., Chen, X., Gonzalez-Garay, M., & Fakhouri, W. D. (2016). The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs. Human molecular genetics, 25(8), 1517-27.More infoNon-coding DNA variations play a critical role in increasing the risk for development of common complex diseases, and account for the majority of SNPs highly associated with cancer. However, it remains a challenge to identify etiologic variants and to predict their pathological effects on target gene expression for clinical purposes. Cis-overlapping motifs (COMs) are elements of enhancer regions that impact gene expression by enabling competitive binding and switching between transcription factors. Mutations within COMs are especially important when the involved transcription factors have opposing effects on gene regulation, like P53 tumor suppressor and cMYC proto-oncogene. In this study, genome-wide analysis of ChIP-seq data from human cancer and mouse embryonic cells identified a significant number of putative regulatory elements with signals for both P53 and cMYC. Each co-occupied element contains, on average, two COMs, and one common SNP every two COMs. Gene ontology of predicted target genes for COMs showed that the majority are involved in DNA damage, apoptosis, cell cycle regulation, and RNA processing. EMSA results showed that both cMYC and P53 bind to cis-overlapping motifs within a ChIP-seq co-occupied region in Chr12. In vitro functional analysis of selected co-occupied elements verified enhancer activity, and also showed that the occurrence of SNPs within three COMs significantly altered enhancer activity. We identified a list of COM-associated functional SNPs that are in close proximity to SNPs associated with common diseases in large population studies. These results suggest a potential molecular mechanism to identify etiologic regulatory mutations associated with common diseases.
- Agollah, G. D., Gonzalez-Garay, M. L., Rasmussen, J. C., Tan, I., Aldrich, M. B., Darne, C., Fife, C. E., Guilliod, R., Maus, E. A., King, P. D., & Sevick-Muraca, E. M. (2014). Evidence for SH2 domain-containing 5'-inositol phosphatase-2 (SHIP2) contributing to a lymphatic dysfunction. PloS one, 9(11), e112548.More infoThe lymphatic vasculature plays a critical role in a number of disease conditions of increasing prevalence, such as autoimmune disorders, obesity, blood vascular diseases, and cancer metastases. Yet, unlike the blood vasculature, the tools available to interrogate the molecular basis of lymphatic dysfunction/disease have been lacking. More recently, investigators have reported that dysregulation of the PI3K pathway is involved in syndromic human diseases that involve abnormal lymphatic vasculatures, but there have been few compelling results that show the direct association of this molecular pathway with lymphatic dysfunction in humans. Using near-infrared fluorescence lymphatic imaging (NIRFLI) to phenotype and next generation sequencing (NGS) for unbiased genetic discovery in a family with non-syndromic lymphatic disease, we discovered a rare, novel mutation in INPPL1 that encodes the protein SHIP2, which is a negative regulator of the PI3K pathway, to be associated with lymphatic dysfunction in the family. In vitro interrogation shows that SHIP2 is directly associated with impairment of normal lymphatic endothelial cell (LEC) behavior and that SHIP2 associates with receptors that are associated in lymphedema, implicating its direct involvement in the lymphatic vasculature.
- Braun, M. C., Herring, S. M., Gokul, N., Monita, M., Bell, R., Zhu, Y., Gonzalez-Garay, M. L., Wenderfer, S. E., & Doris, P. A. (2014). Hypertensive renal injury is associated with gene variation affecting immune signaling. Circulation. Cardiovascular genetics, 7(6), 903-10.More infoThe spontaneously hypertensive rat (SHR) strain exists in lines that contrast strongly in susceptibility to renal injury in hypertension. These inbred lines share common ancestry, and only 13% of their genomes arise from different ancestors.
- Brownstein, C. A., Beggs, A. H., Homer, N., Merriman, B., Yu, T. W., Flannery, K. C., DeChene, E. T., Towne, M. C., Savage, S. K., Price, E. N., Holm, I. A., Luquette, L. J., Lyon, E., Majzoub, J., Neupert, P., McCallie, D., Szolovits, P., Willard, H. F., Mendelsohn, N. J., , Temme, R., et al. (2014). An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome biology, 15(3), R53.More infoThere is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance.
- Gonzalez-Garay, M. L. (2014). The road from next-generation sequencing to personalized medicine. Personalized medicine, 11(5), 523-544.More infoMoving from a traditional medical model of treating pathologies to an individualized predictive and preventive model of personalized medicine promises to reduce the healthcare cost on an overburdened and overwhelmed system. Next-generation sequencing (NGS) has the potential to accelerate the early detection of disorders and the identification of pharmacogenetics markers to customize treatments. This review explains the historical facts that led to the development of NGS along with the strengths and weakness of NGS, with a special emphasis on the analytical aspects used to process NGS data. There are solutions to all the steps necessary for performing NGS in the clinical context where the majority of them are very efficient, but there are some crucial steps in the process that need immediate attention.
- Gonzalez-Garay, M. L., Cranford, S. M., Braun, M. C., & Doris, P. A. (2014). Diversity in the preimmune immunoglobulin repertoire of SHR lines susceptible and resistant to end-organ injury. Genes and immunity, 15(8), 528-33.More infoWe used next-generation sequencing to identify immunoglobulin heavy chain (IGH) genetic variation in two closely related hypertensive rat lines that differ in susceptibility to end-organ disease (SHR-A3 and SHR-B2). The two SHR lines differ extensively at the IGH locus from the rat reference genome sequence and from each other, creating 306 sequence unique IGH genes. Compared with IGH genes mapped in the rat reference genome sequence, 98 are null gene alleles (31 are null in both SHR lines, 45 are null in SHR-A3 only and 23 are null in SHR-B2 only). Of the 306 divergent gene sequences, 126 result in amino acid substitution and, among these, SHR-A3 and SHR-B2 differ from one another at the amino acid level in 96 segments. Twelve pseudogenes in the rat reference genome sequence had changes displacing the stop codon and creating probable functional genes in either or both SHR-A3 and SHR-B2. A further five alleles that encoded functional rat reference genome sequence genes or open reading frames were converted to pseudogenes in either or both SHR-A3 and SHR-B2. These studies reveal that the preimmune immunoglobulin repertoire is highly divergent among SHR lines differing in end-organ injury susceptibility and this may modify immune mechanisms in hypertensive renal injury.
- Burrows, P. E., Gonzalez-Garay, M. L., Rasmussen, J. C., Aldrich, M. B., Guilliod, R., Maus, E. A., Fife, C. E., Kwon, S., Lapinski, P. E., King, P. D., & Sevick-Muraca, E. M. (2013). Lymphatic abnormalities are associated with RASA1 gene mutations in mouse and man. Proceedings of the National Academy of Sciences of the United States of America, 110(21), 8621-6.More infoMutations in gene RASA1 have been historically associated with capillary malformation-arteriovenous malformation, but sporadic reports of lymphatic involvement have yet to be investigated in detail. To investigate the impact of RASA1 mutations in the lymphatic system, we performed investigational near-infrared fluorescence lymphatic imaging and confirmatory radiographic lymphangiography in a Parkes-Weber syndrome (PKWS) patient with suspected RASA1 mutations and correlated the lymphatic abnormalities against that imaged in an inducible Rasa1 knockout mouse. Whole-exome sequencing (WES) analysis and validation by Sanger sequencing of DNA from the patient and unaffected biological parents enabled us to identify an early-frameshift deletion in RASA1 that was shared with the father, who possessed a capillary stain but otherwise no overt disease phenotype. Abnormal lymphatic vasculature was imaged in both affected and unaffected legs of the PKWS subject that transported injected indocyanine green dye to the inguinal lymph node and drained atypically into the abdomen and into dermal lymphocele-like vesicles on the groin. Dermal lymphatic hyperplasia and dilated vessels were observed in Rasa1-deficient mice, with subsequent development of chylous ascites. WES analyses did not identify potential gene modifiers that could explain the variability of penetrance between father and son. Nonetheless, we conclude that the RASA1 mutation is responsible for the aberrant lymphatic architecture and functional abnormalities, as visualized in the PKWS subject and in the animal model. Our unique method to combine investigatory near-infrared fluorescence lymphatic imaging and WES for accurate phenoptyping and unbiased genotyping allows the study of molecular mechanisms of lymphatic involvement of hemovascular disorders.
- Schaaf, C. P., Gonzalez-Garay, M. L., Xia, F., Potocki, L., Gripp, K. W., Zhang, B., Peters, B. A., McElwain, M. A., Drmanac, R., Beaudet, A. L., Caskey, C. T., & Yang, Y. (2013). Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism. Nature genetics, 45(11), 1405-8.More infoPrader-Willi syndrome (PWS) is caused by the absence of paternally expressed, maternally silenced genes at 15q11-q13. We report four individuals with truncating mutations on the paternal allele of MAGEL2, a gene within the PWS domain. The first subject was ascertained by whole-genome sequencing analysis for PWS features. Three additional subjects were identified by reviewing the results of exome sequencing of 1,248 cases in a clinical laboratory. All four subjects had autism spectrum disorder (ASD), intellectual disability and a varying degree of clinical and behavioral features of PWS. These findings suggest that MAGEL2 is a new gene causing complex ASD and that MAGEL2 loss of function can contribute to several aspects of the PWS phenotype.
- Ding, L., Getz, G., Wheeler, D. A., Mardis, E. R., McLellan, M. D., Cibulskis, K., Sougnez, C., Greulich, H., Muzny, D. M., Morgan, M. B., Fulton, L., Fulton, R. S., Zhang, Q., Wendl, M. C., Lawrence, M. S., Larson, D. E., Chen, K., Dooling, D. J., Sabo, A., , Hawes, A. C., et al. (2008). Somatic mutations affect key pathways in lung adenocarcinoma. Nature, 455(7216), 1069-75.More infoDetermining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.
- Gonzalez-Garay, M. L. (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455(7216), 1061-8.More infoHuman cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas--the most common type of adult brain cancer--and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.
- Muzny, D. M., Scherer, S. E., Kaul, R., Wang, J., Yu, J., Sudbrak, R., Buhay, C. J., Chen, R., Cree, A., Ding, Y., Dugan-Rocha, S., Gill, R., Gunaratne, P., Harris, R. A., Hawes, A. C., Hernandez, J., Hodgson, A. V., Hume, J., Jackson, A., , Khan, Z. M., et al. (2006). The DNA sequence, annotation and analysis of human chromosome 3. Nature, 440(7088), 1194-8.More infoAfter the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
- Scherer, S. E., Muzny, D. M., Buhay, C. J., Chen, R., Cree, A., Ding, Y., Dugan-Rocha, S., Gill, R., Gunaratne, P., Harris, R. A., Hawes, A. C., Hernandez, J., Hodgson, A. V., Hume, J., Jackson, A., Khan, Z. M., Kovar-Smith, C., Lewis, L. R., Lozado, R. J., , Metzker, M. L., et al. (2006). The finished DNA sequence of human chromosome 12. Nature, 440(7082), 346-51.More infoHuman chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.
- Gibbs, R. A., Weinstock, G. M., Metzker, M. L., Muzny, D. M., Sodergren, E. J., Scherer, S., Scott, G., Steffen, D., Worley, K. C., Burch, P. E., Okwuonu, G., Hines, S., Lewis, L., DeRamo, C., Delgado, O., Dugan-Rocha, S., Miner, G., Morgan, M., Hawes, A., , Gill, R., et al. (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428(6982), 493-521.More infoThe laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
- Boggs, B. A., Gonzalez-Garay, M. L., & Cabral, F. (1996). Significant divergence in nucleotide sequences for beta-tubulin from different laboratory strains of Chinese hamster ovary cells. DNA sequence : the journal of DNA sequencing and mapping, 6(3), 171-4.More infoThe nucleotide sequences for isotype 1 beta-tubulin cDNAs cloned from different laboratory strains of Chinese hamster ovary (CHO) cells were compared and found to contain an unexpected number of sequence differences in both translated and untranslated regions of the gene. The results indicate significant changes in the DNA, but not protein, sequence while the cells have been in culture and reveal sequences in the 5' and 3' untranslated regions that have resisted these changes.
- Gonzalez-Garay, M. L., & Cabral, F. (1995). Overexpression of an epitope-tagged beta-tubulin in Chinese hamster ovary cells causes an increase in endogenous alpha-tubulin synthesis. Cell motility and the cytoskeleton, 31(4), 259-72.More infoA Chinese hamster beta-tubulin cDNA, engineered to express a 9 amino acid epitope from the influenza hemagglutinin antigen (HA), was transfected into Chinese hamster ovary (CHO) cells. The recombinant protein (HA beta 1-tubulin) appeared to behave normally by the following criteria: immunofluorescence indicated that HA beta 1-tubulin incorporated into all classes of interphase and spindle microtubules as well as microtubule organizing centers. The sensitivity of the cells expressing HA beta 1-tubulin to Colcemid and taxol was unchanged. A 210 kD microtubule associated protein (MAP) remained associated with microtubules that incorporate HA beta 1-tubulin. The synthesis of both endogenous beta-tubulin and HA beta 1-tubulin was repressed by colchicine. The HA beta 1-tubulin incorporated into microtubules to the same extent as the endogenous beta-tubulin, and the overall extent of microtubule assembly in transfected cells was unchanged. Finally, transfected cells had normal growth rates and morphologies. When effects on endogenous tubulin production were measured, it was found that expression of the HA beta 1-tubulin reduced the synthesis of endogenous wild-type beta-tubulin but increased the synthesis of alpha-tubulin. At steady state, a small increase in total tubulin consistent with the increased synthesis of alpha-tubulin was found. The results indicate that expression of excess exogenous beta-tubulin perturbs the synthesis of endogenous alpha-tubulin in a manner that is not easily explained by current models of tubulin regulation. The changes in tubulin synthesis along with degradation of excess tubulin subunits may reflect mechanisms that exist to ensure coordinate levels of alpha- and beta-tubulin for assembly.
- Barlow, S., Gonzalez-Garay, M. L., West, R. R., Olmsted, J. B., & Cabral, F. (1994). Stable expression of heterologous microtubule-associated proteins (MAPs) in Chinese hamster ovary cells: evidence for differing roles of MAPs in microtubule organization. The Journal of cell biology, 126(4), 1017-29.More infoTo study the effects of microtubule-associated proteins (MAPs) on in vivo microtubule assembly, cDNAs containing the complete coding sequences of a Drosophila 205-kD heat stable MAP, human MAP 4, and human tau were stably transfected into CHO cells. Constitutive expression of the transfected genes was low in most cases and had no obvious effects on the viability of the transfected cell lines. High levels of expression, as judged by Western blots, immunofluorescence, and Northern blots, could be induced by treating cells with sodium butyrate. High levels of MAPs were maintained for at least 24-48 h after removal of the sodium butyrate. Immunofluorescence analysis indicated that all three MAPs bound to cellular microtubules, but only the transfected tau caused a rearrangement of microtubules into bundles. Despite high levels of expression of these exogenous MAPs and the bundling of microtubules in cells expressing tau, transfected cells had normal levels of assembled and unassembled tubulin. With the exception of the tau-induced bundles, microtubules in transfected cells showed the same sensitivity as control cells to microtubule depolymerization by Colcemid. Further, all three MAPs were ineffective in reversing the taxol-dependent phenotype of a CHO mutant cell line. The absence of a quantitative effect of any of these heterologous proteins on the assembly of tubulin suggests that these MAPs may have different roles in vivo from those inferred previously from in vitro experiments.
- Barrera Saldaña, H. A., Rojas Martínez, A., Rivera Pérez, J. A., Vázquez Alemán, R. M., & González Garay, M. L. (1992). [The molecular diagnosis of hereditary diseases. In memoriam Dr. Eduardo Aguirre Pequeño]. Gaceta medica de Mexico, 128(6), 613-20; discussion 620-1.More infoAccordingly, we have established in our unit a DNA diagnosis laboratory and have started molecular genetics and epidemiological studies of several inherited diseases. We have started with cystic fibrosis, muscular dystrophy and hemophilia A. We practice the molecular diagnosis with both, Southern transfer and the polymerase chain reaction, using either direct (detection of mutations) or indirect (restriction fragment length polymorphisms) approaches. With the studies we have so far carried out, we have been able to provide genetic counseling and gained valuable information on the type and frequency of mutation associated to these diseases in our region.
- Gonzalez-Garay, M. L., Casanova, N. G., Pauladi, N., Lussier, Y. A., Navarrete, J., Berghout, J., Knox, K., & Garcia, J. G. (2017, May). TNF-α specific PBMC responses in complicated and uncomplicated sarcoidosis by RNA-Seq. American Thoracic Society 2017 Conference. Washington, D.C: ATS.