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1. CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis

Author

Martínez-Hernández, Angélica, Mendoza-Caamal, Elvia C., Mendiola-Vidal, Namibia G., Barajas-Olmos, Francisco, Villafan-Bernal, José Rafael, Jiménez-Ruiz, Juan Luis, Monge-Cazares, Tulia, García-Ortiz, Humberto, Cubas, Cecilia Contreras, Centeno-Cruz, Federico, Alaez-Verson, Carmen, Ortega-Torres, Soraya, Luna-Castañeda, Adriana del C., Baca, Vicente, Lezana, José Luis, and Orozco, Lorena

Published
2024
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3. Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes.

Author

Goodrich, Julia K, Singer-Berk, Moriel, Son, Rachel, Sveden, Abigail, Wood, Jordan, England, Eleina, Cole, Joanne B, Weisburd, Ben, Watts, Nick, Caulkins, Lizz, Dornbos, Peter, Koesterer, Ryan, Zappala, Zachary, Zhang, Haichen, Maloney, Kristin A, Dahl, Andy, Aguilar-Salinas, Carlos A, Atzmon, Gil, Barajas-Olmos, Francisco, Barzilai, Nir, Blangero, John, Boerwinkle, Eric, Bonnycastle, Lori L, Bottinger, Erwin, Bowden, Donald W, Centeno-Cruz, Federico, Chambers, John C, Chami, Nathalie, Chan, Edmund, Chan, Juliana, Cheng, Ching-Yu, Cho, Yoon Shin, Contreras-Cubas, Cecilia, Córdova, Emilio, Correa, Adolfo, DeFronzo, Ralph A, Duggirala, Ravindranath, Dupuis, Josée, Garay-Sevilla, Ma Eugenia, García-Ortiz, Humberto, Gieger, Christian, Glaser, Benjamin, González-Villalpando, Clicerio, Gonzalez, Ma Elena, Grarup, Niels, Groop, Leif, Gross, Myron, Haiman, Christopher, Han, Sohee, Hanis, Craig L, Hansen, Torben, Heard-Costa, Nancy L, Henderson, Brian E, Hernandez, Juan Manuel Malacara, Hwang, Mi Yeong, Islas-Andrade, Sergio, Jørgensen, Marit E, Kang, Hyun Min, Kim, Bong-Jo, Kim, Young Jin, Koistinen, Heikki A, Kooner, Jaspal Singh, Kuusisto, Johanna, Kwak, Soo-Heon, Laakso, Markku, Lange, Leslie, Lee, Jong-Young, Lee, Juyoung, Lehman, Donna M, Linneberg, Allan, Liu, Jianjun, Loos, Ruth JF, Lyssenko, Valeriya, Ma, Ronald CW, Martínez-Hernández, Angélica, Meigs, James B, Meitinger, Thomas, Mendoza-Caamal, Elvia, Mohlke, Karen L, Morris, Andrew D, Morrison, Alanna C, Ng, Maggie CY, Nilsson, Peter M, O'Donnell, Christopher J, Orozco, Lorena, Palmer, Colin NA, Park, Kyong Soo, Post, Wendy S, Pedersen, Oluf, Preuss, Michael, Psaty, Bruce M, Reiner, Alexander P, Revilla-Monsalve, Cristina, Rich, Stephen S, Rotter, Jerome I, Saleheen, Danish, Schurmann, Claudia, Sim, Xueling, Sladek, Rob, and Small, Kerrin S

Subjects
AMP-T2D-GENES Consortia, Humans, Diabetes Mellitus, Type 2, Genetic Predisposition to Disease, Risk Assessment, Genotype, Multifactorial Inheritance, Penetrance, Adult, Dyslipidemias, Exome, Biomarkers, Biological Variation, Population
Abstract

Hundreds of thousands of genetic variants have been reported to cause severe monogenic diseases, but the probability that a variant carrier develops the disease (termed penetrance) is unknown for virtually all of them. Additionally, the clinical utility of common polygenetic variation remains uncertain. Using exome sequencing from 77,184 adult individuals (38,618 multi-ancestral individuals from a type 2 diabetes case-control study and 38,566 participants from the UK Biobank, for whom genotype array data were also available), we apply clinical standard-of-care gene variant curation for eight monogenic metabolic conditions. Rare variants causing monogenic diabetes and dyslipidemias display effect sizes significantly larger than the top 1% of the corresponding polygenic scores. Nevertheless, penetrance estimates for monogenic variant carriers average 60% or lower for most conditions. We assess epidemiologic and genetic factors contributing to risk prediction in monogenic variant carriers, demonstrating that inclusion of polygenic variation significantly improves biomarker estimation for two monogenic dyslipidemias.

Published
2021

4. Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls

Author

Flannick, Jason, Mercader, Josep M, Fuchsberger, Christian, Udler, Miriam S, Mahajan, Anubha, Wessel, Jennifer, Teslovich, Tanya M, Caulkins, Lizz, Koesterer, Ryan, Barajas-Olmos, Francisco, Blackwell, Thomas W, Boerwinkle, Eric, Brody, Jennifer A, Centeno-Cruz, Federico, Chen, Ling, Chen, Siying, Contreras-Cubas, Cecilia, Córdova, Emilio, Correa, Adolfo, Cortes, Maria, DeFronzo, Ralph A, Dolan, Lawrence, Drews, Kimberly L, Elliott, Amanda, Floyd, James S, Gabriel, Stacey, Garay-Sevilla, Maria Eugenia, García-Ortiz, Humberto, Gross, Myron, Han, Sohee, Heard-Costa, Nancy L, Jackson, Anne U, Jørgensen, Marit E, Kang, Hyun Min, Kelsey, Megan, Kim, Bong-Jo, Koistinen, Heikki A, Kuusisto, Johanna, Leader, Joseph B, Linneberg, Allan, Liu, Ching-Ti, Liu, Jianjun, Lyssenko, Valeriya, Manning, Alisa K, Marcketta, Anthony, Malacara-Hernandez, Juan Manuel, Martínez-Hernández, Angélica, Matsuo, Karen, Mayer-Davis, Elizabeth, Mendoza-Caamal, Elvia, Mohlke, Karen L, Morrison, Alanna C, Ndungu, Anne, Ng, Maggie CY, O’Dushlaine, Colm, Payne, Anthony J, Pihoker, Catherine, Post, Wendy S, Preuss, Michael, Psaty, Bruce M, Vasan, Ramachandran S, Rayner, N William, Reiner, Alexander P, Revilla-Monsalve, Cristina, Robertson, Neil R, Santoro, Nicola, Schurmann, Claudia, So, Wing Yee, Soberón, Xavier, Stringham, Heather M, Strom, Tim M, Tam, Claudia HT, Thameem, Farook, Tomlinson, Brian, Torres, Jason M, Tracy, Russell P, van Dam, Rob M, Vujkovic, Marijana, Wang, Shuai, Welch, Ryan P, Witte, Daniel R, Wong, Tien-Yin, Atzmon, Gil, Barzilai, Nir, Blangero, John, Bonnycastle, Lori L, Bowden, Donald W, Chambers, John C, Chan, Edmund, Cheng, Ching-Yu, Cho, Yoon Shin, Collins, Francis S, de Vries, Paul S, Duggirala, Ravindranath, Glaser, Benjamin, Gonzalez, Clicerio, Gonzalez, Ma Elena, Groop, Leif, Kooner, Jaspal Singh, and Kwak, Soo Heon

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Prevention, Biotechnology, Human Genome, Diabetes, 2.1 Biological and endogenous factors, Metabolic and endocrine, Animals, Case-Control Studies, Decision Support Techniques, Diabetes Mellitus, Type 2, Exome, Female, Gene Frequency, Genome-Wide Association Study, Humans, Male, Mice, Mice, Knockout, Exome Sequencing, Broad Genomics Platform, DiscovEHR Collaboration, CHARGE, LuCamp, ProDiGY, GoT2D, ESP, SIGMA-T2D, T2D-GENES, AMP-T2D-GENES, General Science & Technology
Abstract

Protein-coding genetic variants that strongly affect disease risk can yield relevant clues to disease pathogenesis. Here we report exome-sequencing analyses of 20,791 individuals with type 2 diabetes (T2D) and 24,440 non-diabetic control participants from 5 ancestries. We identify gene-level associations of rare variants (with minor allele frequencies of less than 0.5%) in 4 genes at exome-wide significance, including a series of more than 30 SLC30A8 alleles that conveys protection against T2D, and in 12 gene sets, including those corresponding to T2D drug targets (P = 6.1 × 10-3) and candidate genes from knockout mice (P = 5.2 × 10-3). Within our study, the strongest T2D gene-level signals for rare variants explain at most 25% of the heritability of the strongest common single-variant signals, and the gene-level effect sizes of the rare variants that we observed in established T2D drug targets will require 75,000-185,000 sequenced cases to achieve exome-wide significance. We propose a method to interpret these modest rare-variant associations and to incorporate these associations into future target or gene prioritization efforts.

Published
2019

5. Relevant Serum Endoplasmic Reticulum Stress Biomarkers in Type 2 Diabetes and Its Complications: A Systematic Review and Meta-Analysis.

Author

Villafan-Bernal, José Rafael, Barajas-Olmos, Francisco, Guzmán-Guzmán, Iris Paola, Martínez-Hernández, Angélica, Contreras-Cubas, Cecilia, García-Ortiz, Humberto, Morales-Rivera, Monserrat I., Martínez-Portilla, Raigam Jafet, and Orozco, Lorena

Subjects
TYPE 2 diabetes, GLYCEMIC control, HEAT shock proteins, DIABETES complications, INSULIN resistance
Abstract

Endoplasmic reticulum stress (ERS) is activated in all cells by stressors such as hyperglycemia. However, it remains unclear which specific serum biomarkers of ERS are consistently altered in type 2 diabetes (T2D). We aimed to identify serum ERS biomarkers that are consistently altered in T2D and its complications, and their correlation with metabolic and anthropometric variables. We performed a systematic review and meta-analysis following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and Meta-Analyses and Systematic Reviews of Observational Studies (MOOSE). The risk of bias was assessed using the Newcastle–Ottawa scale. Random-effects models weighted by the inverse variance were employed to estimate the standardized mean difference and correlations as effect size measures. Indicators of heterogeneity and meta-regressions were evaluated. Of the 1206 identified studies, 22 were finally included, representing 11,953 subjects (2224 with T2D and 9992 non-diabetic controls). Most studies were of high quality. Compared with controls, subjects with T2D had higher circulating levels of heat shock protein 70 (HSP70; SMD: 2.30, 95% CI 1.13–3.46; p < 0.001) and secretagogin (SMD: 0.60, 95%CI 0.19–1.01; p < 0.001). They also had higher serum levels of peroxiredoxin-1, -2, -4, and -6. Secretagogin inversely correlated with HOMA-IR, yet positively correlated with HOMA-B, HbA1c, and FPG. PRX4 negatively correlated with HbA1c and FPG, while HSP70 positively correlated with HbA1c. In conclusion, six ERS biomarkers are consistently elevated in human T2D and correlate with glycemic control, insulin resistance, and β-cell function. Emerging evidence links serum ERS biomarkers to diabetes complications, but further research should evaluate their prognostic implications. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Rare coding variants in 35 genes associate with circulating lipid levels—A multi-ancestry analysis of 170,000 exomes

Author

Hindy, George, Dornbos, Peter, Chaffin, Mark D., Liu, Dajiang J., Wang, Minxian, Selvaraj, Margaret Sunitha, Zhang, David, Park, Joseph, Aguilar-Salinas, Carlos A., Antonacci-Fulton, Lucinda, Ardissino, Diego, Arnett, Donna K., Aslibekyan, Stella, Atzmon, Gil, Ballantyne, Christie M., Barajas-Olmos, Francisco, Barzilai, Nir, Becker, Lewis C., Bielak, Lawrence F., Bis, Joshua C., Blangero, John, Boerwinkle, Eric, Bonnycastle, Lori L., Bottinger, Erwin, Bowden, Donald W., Bown, Matthew J., Brody, Jennifer A., Broome, Jai G., Burtt, Noël P., Cade, Brian E., Centeno-Cruz, Federico, Chan, Edmund, Chang, Yi-Cheng, Chen, Yii-Der I., Cheng, Ching-Yu, Choi, Won Jung, Chowdhury, Rajiv, Contreras-Cubas, Cecilia, Córdova, Emilio J., Correa, Adolfo, Cupples, L. Adrienne, Curran, Joanne E., Danesh, John, de Vries, Paul S., DeFronzo, Ralph A., Doddapaneni, Harsha, Duggirala, Ravindranath, Dutcher, Susan K., Ellinor, Patrick T., Emery, Leslie S., Florez, Jose C., Fornage, Myriam, Freedman, Barry I., Fuster, Valentin, Garay-Sevilla, Ma. Eugenia, García-Ortiz, Humberto, Germer, Soren, Gibbs, Richard A., Gieger, Christian, Glaser, Benjamin, Gonzalez, Clicerio, Gonzalez-Villalpando, Maria Elena, Graff, Mariaelisa, Graham, Sarah E., Grarup, Niels, Groop, Leif C., Guo, Xiuqing, Gupta, Namrata, Han, Sohee, Hanis, Craig L., Hansen, Torben, He, Jiang, Heard-Costa, Nancy L., Hung, Yi-Jen, Hwang, Mi Yeong, Irvin, Marguerite R., Islas-Andrade, Sergio, Jarvik, Gail P., Kang, Hyun Min, Kardia, Sharon L.R., Kelly, Tanika, Kenny, Eimear E., Khan, Alyna T., Kim, Bong-Jo, Kim, Ryan W., Kim, Young Jin, Koistinen, Heikki A., Kooperberg, Charles, Kuusisto, Johanna, Kwak, Soo Heon, Laakso, Markku, Lange, Leslie A., Lee, Jiwon, Lee, Juyoung, Lee, Seonwook, Lehman, Donna M., Lemaitre, Rozenn N., Linneberg, Allan, Liu, Jianjun, Loos, Ruth J.F., Lubitz, Steven A., Lyssenko, Valeriya, Ma, Ronald C.W., Martin, Lisa Warsinger, Martínez-Hernández, Angélica, Mathias, Rasika A., McGarvey, Stephen T., McPherson, Ruth, Meigs, James B., Meitinger, Thomas, Melander, Olle, Mendoza-Caamal, Elvia, Metcalf, Ginger A., Mi, Xuenan, Mohlke, Karen L., Montasser, May E., Moon, Jee-Young, Moreno-Macías, Hortensia, Morrison, Alanna C., Muzny, Donna M., Nelson, Sarah C., Nilsson, Peter M., O’Connell, Jeffrey R., Orho-Melander, Marju, Orozco, Lorena, Palmer, Colin N.A., Palmer, Nicholette D., Park, Cheol Joo, Park, Kyong Soo, Pedersen, Oluf, Peralta, Juan M., Peyser, Patricia A., Post, Wendy S., Preuss, Michael, Psaty, Bruce M., Qi, Qibin, Rao, D.C., Redline, Susan, Reiner, Alexander P., Revilla-Monsalve, Cristina, Rich, Stephen S., Samani, Nilesh, Schunkert, Heribert, Schurmann, Claudia, Seo, Daekwan, Seo, Jeong-Sun, Sim, Xueling, Sladek, Rob, Small, Kerrin S., So, Wing Yee, Stilp, Adrienne M., Tai, E. Shyong, Tam, Claudia H.T., Taylor, Kent D., Teo, Yik Ying, Thameem, Farook, Tomlinson, Brian, Tsai, Michael Y., Tuomi, Tiinamaija, Tuomilehto, Jaakko, Tusié-Luna, Teresa, Udler, Miriam S., van Dam, Rob M., Vasan, Ramachandran S., Viaud Martinez, Karine A., Wang, Fei Fei, Wang, Xuzhi, Watkins, Hugh, Weeks, Daniel E., Wilson, James G., Witte, Daniel R., Wong, Tien-Yin, Yanek, Lisa R., Kathiresan, Sekar, Rader, Daniel J., Rotter, Jerome I., Boehnke, Michael, McCarthy, Mark I., Willer, Cristen J., Natarajan, Pradeep, Flannick, Jason A., Khera, Amit V., and Peloso, Gina M.

Published
2022
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8. The L125F MATE1 variant enriched in populations of Amerindian origin is associated with increased plasma levels of metformin and lactate

Author

Morales-Rivera, Monserrat I., Alemón-Medina, Radamés, Martínez-Hernández, Angélica, Gómez-Garduño, Josefina, Mirzaeicheshmeh, Elaheh, Altamirano-Bustamante, Nelly F., Ilizaliturri-Flores, Ian, Mendoza-Caamal, Elvia C., Pérez-Guillé, María G., García-Álvarez, Raquel, Contreras-Cubas, Cecilia, Centeno-Cruz, Federico, Revilla-Monsalve, Cristina, García-Ortiz, Humberto, Barajas-Olmos, Francisco, and Orozco, Lorena

Published
2021
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9. Deep Multi-OMICs and Multi-Tissue Characterization in a Pre- and Postprandial State in Human Volunteers: The GEMM Family Study Research Design

Author

Bastarrachea, Raul A, Laviada-Molina, Hugo A, Nava-Gonzalez, Edna J, Leal-Berumen, Irene, Escudero-Lourdes, Claudia, Escalante-Araiza, Fabiola, Peschard, Vanessa-Giselle, Veloz-Garza, Rosa A, Haack, Karin, Martínez-Hernández, Angélica, Barajas-Olmos, Francisco M, Molina-Segui, Fernanda, Buenfil-Rello, Fatima A, Gonzalez-Ramirez, Lucia, Janssen-Aguilar, Reinhard, Lopez-Muñoz, Ricardo, Perez-Cetina, Fernanda, Gaytan-Saucedo, Janeth F, Vaquera, Zoila, Cornejo-Barrera, Judith, Castillo-Pineda, Juan Carlos, Murillo-Ramirez, Areli, Diaz-Tena, Sara P, Figueroa-Nuñez, Benigno, González-López, Laura, Salinas-Osornio, Rocío A, Valencia-Rendón, Melesio E, Ángeles-Chimal, José, Tapia, Jesús Santa-Olalla, Remes-Troche, José M, Valdovinos-Chavez, Salvador B, Huerta-Avila, Eira E, Han, Xianlin, Orozco, Lorena, Rodriguez-Ayala, Ernesto, Weintraub, Susan, Gallegos-Cabrales, Esther C, Cole, Shelley A, and Kent, Jack W

Subjects
Biotechnology, Prevention, Nutrition, Aging, Genetics, Obesity, Diabetes, Human Genome, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Cardiovascular, Metabolic and endocrine, Good Health and Well Being, multi-OMICS, GEMM family study, postprandial metabolism, mixed meal challenge
Abstract

Cardiovascular disease (CVD) and type 2 diabetes (T2D) are increasing worldwide. This is mainly due to an unhealthy nutrition, implying that variation in CVD risk may be due to variation in the capacity to manage a nutritional load. We examined the genomic basis of postprandial metabolism. Our main purpose was to introduce the GEMM Family Study (Genetics of Metabolic Diseases in Mexico) as a multi-center study carrying out an ongoing recruitment of healthy urban adults. Each participant received a mixed meal challenge and provided a 5-hours' time course series of blood, buffy coat specimens for DNA isolation, and adipose tissue (ADT)/skeletal muscle (SKM) biopsies at fasting and 3 h after the meal. A comprehensive profiling, including metabolomic signatures in blood and transcriptomic and proteomic profiling in SKM and ADT, was performed to describe tendencies for variation in postprandial response. Our data generation methods showed preliminary trends indicating that by characterizing the dynamic properties of biomarkers with metabolic activity and analyzing multi-OMICS data it could be possible, with this methodology and research design, to identify early trends for molecular biology systems and genes involved in the fasted and fed states.

Published
2018

10. Reconstruction of ancient microbial genomes from the human gut

Author

Wibowo, Marsha C., Yang, Zhen, Borry, Maxime, Hübner, Alexander, Huang, Kun D., Tierney, Braden T., Zimmerman, Samuel, Barajas-Olmos, Francisco, Contreras-Cubas, Cecilia, García-Ortiz, Humberto, Martínez-Hernández, Angélica, Luber, Jacob M., Kirstahler, Philipp, Blohm, Tre, Smiley, Francis E., Arnold, Richard, Ballal, Sonia A., Pamp, Sünje Johanna, Russ, Julia, Maixner, Frank, Rota-Stabelli, Omar, Segata, Nicola, Reinhard, Karl, Orozco, Lorena, Warinner, Christina, Snow, Meradeth, LeBlanc, Steven, and Kostic, Aleksandar D.

Published
2021
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11. Effect of the Complex Allele p.[Ile148Thr;Ile1023_Val1024del] in Cystic Fibrosis and Tracing of a Founder Effect in Mexican Families.

Author

Mendiola-Vidal, Namibia Guadalupe, Contreras-Cubas, Cecilia, Barajas-Olmos, Francisco, Villafan-Bernal, José Rafael, Yañez-Felix, Ana Lucia, García-Ortiz, Humberto, Centeno-Cruz, Federico, Mendoza-Caamal, Elvia, Alaez-Verson, Carmen, Jiménez-Ruíz, Juan Luis, Monge-Cázares, Tulia, Lieberman, Esther, Baca, Vicente, Lezana, José Luis, Martínez-Hernández, Angélica, and Orozco, Lorena

Subjects
CYSTIC fibrosis transmembrane conductance regulator, PROTEIN structure, CYSTIC fibrosis, NUCLEOTIDE sequencing, EXOMES
Abstract

Cystic fibrosis (CF) is a rare autosomal recessive disease most commonly affecting the Caucasian population. CF diagnosis can be a challenge due to the large spectrum of pathogenic variants in the CFTR gene and the effects of complex alleles. Next-generation sequencing has improved our understanding of the contribution of these complex alleles to the wide spectrum of CF clinical symptoms and to the response to medications. Herein, we studied nine CF patients from six unrelated families carrying the complex allele p.[Ile148Thr;Ile1023_Val1024del] with a frequency of 0.18%. All patients were from Central Mexico. This complex allele was found in trans with Class I and II pathogenic variants such as p.(Phe508del), and p.(Phe1078Profs*77)]. A targeted search of a dataset of 2217 exomes from healthy individuals revealed that eight individuals (0.18%) carried the p.(Ile148Thr) variant, but only one (0.022%), who was also born in Central Mexico, was a carrier of the complex allele. These findings show an enrichment of this p.[Ile148Thr;Ile1023_Val1024del] complex allele in Mexican CF patients in this region of Mexico. Finally, protein modeling revealed that this complex allele disrupts the secondary structure of the CFTR protein and might alter the ion flow. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Exome Sequence Data of Eight SLC Transporters Reveal That SLC22A1 and SLC22A3 Variants Alter Metformin Pharmacokinetics and Glycemic Control.

Author

Morales-Rivera, Monserrat I., Alemón-Medina, Radamés, Martínez-Hernández, Angélica, Contreras-Cubas, Cecilia, Altamirano-Bustamante, Nelly F., Gómez-Garduño, Josefina, Mendoza-Caamal, Elvia C., Nuñez-González, J. Orlando, García-Álvarez, Raquel, Revilla-Monsalve, Cristina, Valcarcel-Gamiño, José Antonio, Villafan-Bernal, José Rafael, Centeno-Cruz, Federico, García-Ortiz, Humberto, Barajas-Olmos, Francisco, and Orozco, Lorena

Subjects
TYPE 2 diabetes, GLYCEMIC control, MEXICANS, HAPLOTYPES, INDIVIDUALIZED medicine
Abstract

Background: Type 2 diabetes (T2D) is one of the leading causes of mortality and is a public health challenge worldwide. Metformin is the first-choice treatment for T2D; its pharmacokinetics (PK) is facilitated by members of the solute carrier (SLC) superfamily of transporters, it is not metabolized, and it is excreted by the kidney. Although interindividual variability in metformin pharmacokinetics is documented in the Mexican population, its pharmacogenomics is still underexplored. We aimed to identify variants in metformin SLC transporter genes associated with metformin PK and response in Mexican patients. Methods: Using exome data from 2217 Mexican adults, we identified 86 biallelic SNVs in the eight known genes encoding SLC transporters, with a minor allele frequency ≥ 1%, which were analyzed in an inadequate glycemic control (IGC) association study in T2D metformin treated patients. Metformin PK was evaluated in a pediatric cohort and the effect of associated SNVs was correlated. Results: Functional annotation classified two SNVs as pathogenic. The association study revealed two blocks associated with IGC. These haplotypes comprise rs622591, rs4646272, rs4646273, and rs4646276 in SLC22A1; and rs1810126 and rs668871 in SLC22A3. PK profiles revealed that homozygotes of the SLC22A1 haplotype reached lower plasma metformin concentrations 2 h post administration than the other groups. Conclusions: Our findings highlight the potential of pharmacogenomics studies to enhance precision medicine, which may involve dosage adjustments or the exploration of alternative therapeutic options. These hold significant implications for public health, particularly in populations with a high susceptibility to develop metabolic diseases, such as Latin Americans. [ABSTRACT FROM AUTHOR]

Published
2024
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13. Two novel variants in DYRK1B causative of AOMS3: expanding the clinical spectrum

Author

Mendoza-Caamal, Elvia C., Barajas-Olmos, Francisco, Mirzaeicheshmeh, Elaheh, Ilizaliturri-Flores, Ian, Aguilar-Salinas, Carlos A., Gómez-Velasco, Donaji V., Cicerón-Arellano, Isabel, Reséndiz-Rodríguez, Adriana, Martínez-Hernández, Angélica, Contreras-Cubas, Cecilia, Islas-Andrade, Sergio, Zerrweck, Carlos, García-Ortiz, Humberto, and Orozco, Lorena

Published
2021
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14. The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas

Author

García-Ortiz, Humberto, Barajas-Olmos, Francisco, Contreras-Cubas, Cecilia, Cid-Soto, Miguel Ángel, Córdova, Emilio J., Centeno-Cruz, Federico, Mendoza-Caamal, Elvia, Cicerón-Arellano, Isabel, Flores-Huacuja, Marlen, Baca, Paulina, Bolnick, Deborah A., Snow, Meradeth, Flores-Martínez, Silvia Esperanza, Ortiz-Lopez, Rocio, Reynolds, Austin W., Blanchet, Antonio, Morales-Marín, Mirna, Velázquez-Cruz, Rafael, Kostic, Aleksandar David, Galaviz-Hernández, Carlos, García-Zapién, Alejandra Guadalupe, Jiménez-López, José Concepción, León-Reyes, Guadalupe, Salas-Bautista, Eva Gabriela, Lazalde-Ramos, Blanca Patricia, Jiménez-Ruíz, Juan Luis, Salas-Martínez, Guadalupe, Ramos-Madrigal, Jazmín, Mirzaeicheshmeh, Elaheh, Saldaña-Alvarez, Yolanda, del Carmen Abrahantes-Pérez, María, Loeza-Becerra, Francisco, Mojica-Espinosa, Raúl, Sánchez-Quinto, Federico, Rangel-Villalobos, Héctor, Sosa-Macías, Martha, Sánchez-Corona, José, Rojas-Martinez, Augusto, Martínez-Hernández, Angélica, and Orozco, Lorena

Published
2021
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16. Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico

Author

Williams, Amy L, Jacobs, Suzanne BR, Moreno-Macías, Hortensia, Huerta-Chagoya, Alicia, Churchhouse, Claire, Márquez-Luna, Carla, García-Ortíz, Humberto, José Gómez-Vázquez, María, Burtt, Noël P, Aguilar-Salinas, Carlos A, González-Villalpando, Clicerio, Florez, Jose C, Orozco, Lorena, Haiman, Christopher A, Tusié-Luna, Teresa, Altshuler, David, Ripke, Stephan, Manning, Alisa K, Neale, Benjamin, Reich, David, Stram, Daniel O, Fernández-López, Juan Carlos, Romero-Hidalgo, Sandra, Patterson, Nick, Aguilar-Delfín, Irma, Martínez-Hernández, Angélica, Centeno-Cruz, Federico, Mendoza-Caamal, Elvia, Revilla-Monsalve, Cristina, Islas-Andrade, Sergio, Córdova, Emilio, Rodríguez-Arellano, Eunice, Soberón, Xavier, González-Villalpando, María Elena, Henderson, Brian E, Monroe, Kristine, Wilkens, Lynne, Kolonel, Laurence N, Le Marchand, Loic, Riba, Laura, Ordóñez-Sánchez, María Luisa, Rodríguez-Guillén, Rosario, Cruz-Bautista, Ivette, Rodríguez-Torres, Maribel, Muñoz-Hernández, Linda Liliana, Sáenz, Tamara, Gómez, Donají, Alvirde, Ulices, Onofrio, Robert C, Brodeur, Wendy M, Gage, Diane, Murphy, Jacquelyn, Franklin, Jennifer, Mahan, Scott, Ardlie, Kristin, Crenshaw, Andrew T, Winckler, Wendy, Prüfer, Kay, Shunkov, Michael V, Sawyer, Susanna, Stenzel, Udo, Kelso, Janet, Lek, Monkol, Sankararaman, Sriram, MacArthur, Daniel G, Derevianko, Anatoli P, Pääbo, Svante, Gopal, Shuba, Grammatikos, James A, Smith, Ian C, Bullock, Kevin H, Deik, Amy A, Souza, Amanda L, Pierce, Kerry A, Clish, Clary B, Fennell, Timothy, and Farjoun, Yossi

Subjects
Nutrition, Diabetes, Prevention, Genetics, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Alleles, Animals, Asian People, Black People, Cohort Studies, Diabetes Mellitus, Type 2, Endoplasmic Reticulum, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Haplotypes, HeLa Cells, Humans, Indians, North American, Lipid Metabolism, Liver, Male, Mexico, Monocarboxylic Acid Transporters, Neanderthals, Polymorphism, Single Nucleotide, RNA, Messenger, Triglycerides, White People, SIGMA Type 2 Diabetes Consortium, Hela Cells, General Science & Technology
Abstract

Performing genetic studies in multiple human populations can identify disease risk alleles that are common in one population but rare in others, with the potential to illuminate pathophysiology, health disparities, and the population genetic origins of disease alleles. Here we analysed 9.2 million single nucleotide polymorphisms (SNPs) in each of 8,214 Mexicans and other Latin Americans: 3,848 with type 2 diabetes and 4,366 non-diabetic controls. In addition to replicating previous findings, we identified a novel locus associated with type 2 diabetes at genome-wide significance spanning the solute carriers SLC16A11 and SLC16A13 (P = 3.9 × 10(-13); odds ratio (OR) = 1.29). The association was stronger in younger, leaner people with type 2 diabetes, and replicated in independent samples (P = 1.1 × 10(-4); OR = 1.20). The risk haplotype carries four amino acid substitutions, all in SLC16A11; it is present at ~50% frequency in Native American samples and ~10% in east Asian, but is rare in European and African samples. Analysis of an archaic genome sequence indicated that the risk haplotype introgressed into modern humans via admixture with Neanderthals. The SLC16A11 messenger RNA is expressed in liver, and V5-tagged SLC16A11 protein localizes to the endoplasmic reticulum. Expression of SLC16A11 in heterologous cells alters lipid metabolism, most notably causing an increase in intracellular triacylglycerol levels. Despite type 2 diabetes having been well studied by genome-wide association studies in other populations, analysis in Mexican and Latin American individuals identified SLC16A11 as a novel candidate gene for type 2 diabetes with a possible role in triacylglycerol metabolism.

Published
2014

17. Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms

Author

Ng, Maggie C.Y., Shriner, Daniel, Chen, Brian H., Li, Jiang, Chen, Wei-Min, Guo, Xiuqing, Liu, Jiankang, Bielinski, Suzette J., Yanek, Lisa R., Nalls, Michael A., Comeau, Mary E., Rasmussen-Torvik, Laura J., Jensen, Richard A., Evans, Daniel S., Sun, Yan V., An, Ping, Patel, Sanjay R., Lu, Yingchang, Long, Jirong, Armstrong, Loren L., Wagenknecht, Lynne, Yang, Lingyao, Snively, Beverly M., Palmer, Nicholette D., Mudgal, Poorva, Langefeld, Carl D., Keene, Keith L., Freedman, Barry I., Mychaleckyj, Josyf C., Nayak, Uma, Raffel, Leslie J., Goodarzi, Mark O., Chen, Y-D Ida, Taylor, Herman A., Jr., Correa, Adolfo, Sims, Mario, Couper, David, Pankow, James S., Boerwinkle, Eric, Adeyemo, Adebowale, Doumatey, Ayo, Chen, Guanjie, Mathias, Rasika A., Vaidya, Dhananjay, Singleton, Andrew B., Zonderman, Alan B., Igo, Robert P., Jr., Sedor, John R., Kabagambe, Edmond K., Siscovick, David S., McKnight, Barbara, Rice, Kenneth, Liu, Yongmei, Hsueh, Wen-Chi, Zhao, Wei, Bielak, Lawrence F., Kraja, Aldi, Province, Michael A., Bottinger, Erwin P., Gottesman, Omri, Cai, Qiuyin, Zheng, Wei, Blot, William J., Lowe, William L., Pacheco, Jennifer A., Crawford, Dana C., Grundberg, Elin, Rich, Stephen S., Hayes, M. Geoffrey, Shu, Xiao-Ou, Loos, Ruth J.F., Borecki, Ingrid B., Peyser, Patricia A., Cummings, Steven R., Psaty, Bruce M., Fornage, Myriam, Iyengar, Sudha K., Evans, Michele K., Becker, Diane M., Kao, W.H. Linda, Wilson, James G., Rotter, Jerome I., Sale, Michèle M., Liu, Simin, Rotimi, Charles N., Bowden, Donald W., Mercader, Josep M., Huerta-Chagoya, Alicia, García-Ortiz, Humberto, Moreno-Macías, Hortensia, Manning, Alisa, Caulkins, Lizz, Burtt, Noël P., Flannick, Jason, Patterson, Nick, Aguilar-Salinas, Carlos A., Tusié-Luna, Teresa, Altshuler, David, Florez, Jose C., Martínez-Hernández, Angélica, Centeno-Cruz, Federico, Barajas-Olmos, Francisco Martin, Zerrweck, Carlos, Contreras-Cubas, Cecilia, Mendoza-Caamal, Elvia, Revilla-Monsalve, Cristina, Islas-Andrade, Sergio, Córdova, Emilio, Soberón, Xavier, Orozco, Lorena, González-Villalpando, Clicerio, González-Villalpando, María Elena, Haiman, Christopher A., Wilkens, Lynne, Le Marchand, Loic, Monroe, Kristine, Kolonel, Laurence, Arellano-Campos, Olimpia, Ordóñez-Sánchez, Maria L., Rodríguez-Torres, Maribel, Segura-Kato, Yayoi, Rodríguez-Guillén, Rosario, Cruz-Bautista, Ivette, Muñoz-Hernandez, Linda Liliana, Sáenz, Tamara, Gómez, Donají, Alvirde, Ulices, Almeda-Valdés, Paloma, Cortes, Maria L., Rusu, Victor, Hoch, Eitan, Tenen, Danielle E., Gymrek, Melissa, Hartigan, Christina R., DeRan, Michael, von Grotthuss, Marcin, Fontanillas, Pierre, Spooner, Alexandra, Guzman, Gaelen, Deik, Amy A., Pierce, Kerry A., Dennis, Courtney, Clish, Clary B., Carr, Steven A., Wagner, Bridget K., Schenone, Monica, Altshuler, David M., Schreiber, Stuart L., Jacobs, Suzanne B.R., and Lander, Eric S.

Published
2017
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18. Total Antioxidant Capacity in Obese and Non-Obese Subjects and Its Association with Anthropo-Metabolic Markers: Systematic Review and Meta-Analysis

Author

Anaya-Morua, Wendoline, primary, Villafan-Bernal, José Rafael, additional, Ramírez-Moreno, Esther, additional, García-Ortiz, Humberto, additional, Martínez-Portilla, Raigam Jafet, additional, Contreras-Cubas, Cecilia, additional, Martínez-Hernández, Angélica, additional, Centeno-Cruz, Federico, additional, Pedroza-Montoya, Florencia Estefana, additional, Orozco, Lorena, additional, and Barajas-Olmos, Francisco, additional

Published
2023
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23. Ancestry-dependent genetic structure of the Xq28 risk haplotype in the Mexican population and its association with childhood-onset systemic lupus erythematosus

Author

García-Ortiz, Humberto, primary, Barajas-Olmos, Francisco, additional, Flores-Huacuja, Marlen, additional, Morales-Rivera, Monserrat I., additional, Martínez-Hernández, Angélica, additional, Baca, Vicente, additional, Contreras-Cubas, Cecilia, additional, and Orozco, Lorena, additional

Published
2023
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24. Influence of obesity, parental history of diabetes, and genes in type 2 diabetes: A case-control study

Author

Berumen, Jaime, Orozco, Lorena, Betancourt-Cravioto, Miguel, Gallardo, Héctor, Zulueta, Mirella, Mendizabal, Leire, Simon, Laureano, Benuto, Rosa Elba, Ramírez-Campos, Elisa, Marin, Melissa, Juárez, Eligia, García-Ortiz, Humberto, Martínez-Hernández, Angélica, Venegas-Vega, Carlos, Peralta-Romero, Jesús, Cruz, Miguel, and Tapia-Conyer, Roberto

Published
2019
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25. Unraveling Signatures of Local Adaptation among Indigenous Groups from Mexico

Author

García-Ortiz, Humberto, primary, Barajas-Olmos, Francisco, additional, Contreras-Cubas, Cecilia, additional, Reynolds, Austin W., additional, Flores-Huacuja, Marlen, additional, Snow, Meradeth, additional, Ramos-Madrigal, Jazmín, additional, Mendoza-Caamal, Elvia, additional, Baca, Paulina, additional, López-Escobar, Tomás A., additional, Bolnick, Deborah A., additional, Flores-Martínez, Silvia Esperanza, additional, Ortiz-Lopez, Rocio, additional, Kostic, Aleksandar David, additional, Villafan-Bernal, José Rafael, additional, Galaviz-Hernández, Carlos, additional, Centeno-Cruz, Federico, additional, García-Zapién, Alejandra Guadalupe, additional, Monge-Cázares, Tulia, additional, Lazalde-Ramos, Blanca Patricia, additional, Loeza-Becerra, Francisco, additional, Abrahantes-Pérez, María del Carmen, additional, Rangel-Villalobos, Héctor, additional, Sosa-Macías, Martha, additional, Rojas-Martínez, Augusto, additional, Martínez-Hernández, Angélica, additional, and Orozco, Lorena, additional

Published
2022
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26. Frequent copy number variants in a cohort of Mexican-Mestizo individuals

Author

Sánchez, Silvia, primary, Juárez, Ulises, additional, Domínguez, Julieta, additional, Molina, Bertha, additional, Barrientos, Rehotbevely, additional, Martínez-Hernández, Angélica, additional, Carnevale, Alessandra, additional, Grether-González, Patricia, additional, Mayen, Dora Gilda, additional, Villarroel, Camilo, additional, Lieberman, Esther, additional, Yokoyama, Emiy, additional, Castillo, Victoria Del, additional, Torres, Leda, additional, and Frias, Sara, additional

Published
2022
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27. Brain radiotoxicity-related 15CAcBRT gene expression signature predicts survival prognosis of glioblastoma patients

Author

Reyes-González, Jesús, primary, Barajas-Olmos, Francisco, additional, García-Ortiz, Humberto, additional, Magraner-Pardo, Lorena, additional, Pons, Tirso, additional, Moreno, Sergio, additional, Aguirre-Cruz, Lucinda, additional, Reyes-Abrahantes, Andy, additional, Martínez-Hernández, Angélica, additional, Contreras-Cubas, Cecilia, additional, Barrios-Payan, Jorge, additional, Ruiz-Garcia, Henry, additional, Hernandez-Pando, Rogelio, additional, Quiñones-Hinojosa, Alfredo, additional, Orozco, Lorena, additional, and Abrahantes-Pérez, María del Carmen, additional

Published
2022
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29. Exome Sequencing Data Analysis and a Case-Control Study in Mexican Population Reveals Lipid Trait Associations of New and Known Genetic Variants in Dyslipidemia-Associated Loci

Author

Jurado-Camacho, Pedro A., primary, Cid-Soto, Miguel A., additional, Barajas-Olmos, Francisco, additional, García-Ortíz, Humberto, additional, Baca-Peynado, Paulina, additional, Martínez-Hernández, Angélica, additional, Centeno-Cruz, Federico, additional, Contreras-Cubas, Cecilia, additional, González-Villalpando, María Elena, additional, Saldaña-Álvarez, Yolanda, additional, Salas-Martinez, Guadalupe, additional, Mendoza-Caamal, Elvia C., additional, González-Villalpando, Clicerio, additional, Córdova, Emilio J., additional, and Orozco, Lorena, additional

Published
2022
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30. Brain radiotoxicity-related 15CAcBRT gene expression signature predicts survival prognosis of glioblastoma patients.

Author

Reyes-González, Jesús, Barajas-Olmos, Francisco, García-Ortiz, Humberto, Magraner-Pardo, Lorena, Pons, Tirso, Moreno, Sergio, Aguirre-Cruz, Lucinda, Reyes-Abrahantes, Andy, Martínez-Hernández, Angélica, Contreras-Cubas, Cecilia, Barrios-Payan, Jorge, Ruiz-Garcia, Henry, Hernandez-Pando, Rogelio, Quiñones-Hinojosa, Alfredo, Orozco, Lorena, and Abrahantes-Pérez, María del Carmen

Published
2023
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31. Association of a Low-Frequency Variant in HNF1A With Type 2 Diabetes in a Latino Population

Author

Estrada, Karol, Aukrust, Ingvild, Bjørkhaug, Lise, Burtt, Noël P., Mercader, Josep M., García-Ortiz, Humberto, Huerta-Chagoya, Alicia, Moreno-Macías, Hortensia, Walford, Geoffrey, Flannick, Jason, Williams, Amy L., Gómez-Vázquez, María J., Fernandez-Lopez, Juan C., Martínez-Hernández, Angélica, Centeno-Cruz, Federico, Mendoza-Caamal, Elvia, Revilla-Monsalve, Cristina, Islas-Andrade, Sergio, Córdova, Emilio J., Soberón, Xavier, González-Villalpando, María E., Henderson, E., Wilkens, Lynne R., Le Marchand, Loic, Ordóñez-Sánchez, Maria L., Rodríguez-Torres, Maribel, Rodríguez-Guillén, Rosario, Riba, Laura, Najmi, Laeya A., Jacobs, Suzanne B.R., Fennell, Timothy, Gabriel, Stacey, Fontanillas, Pierre, Hanis, Craig L., Lehman, Donna M., Jenkinson, Christopher P., Abboud, Hanna E., Bell, Graeme I., Cortes, Maria L., Boehnke, Michael, González-Villalpando, Clicerio, Orozco, Lorena, Haiman, Christopher A., Tusié-Luna, Teresa, Aguilar-Salinas, Carlos A., Altshuler, David, Njølstad, Pål R., Florez, Jose C., and MacArthur, Daniel G.

Published
2014
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32. Additional file 1 of Two novel variants in DYRK1B causative of AOMS3: expanding the clinical spectrum

Author

Mendoza-Caamal, Elvia C., Barajas-Olmos, Francisco, Mirzaeicheshmeh, Elaheh, Ilizaliturri-Flores, Ian, Aguilar-Salinas, Carlos A., Gómez-Velasco, Donaji V., Cicerón-Arellano, Isabel, Reséndiz-Rodríguez, Adriana, Martínez-Hernández, Angélica, Contreras-Cubas, Cecilia, Islas-Andrade, Sergio, Zerrweck, Carlos, García-Ortiz, Humberto, and Orozco, Lorena

Abstract

Additional file 1. Figure S1. Glucose tolerance curves. Table S1. Variants on DYRK1B in a sample of 968 Mexican Mestizos. Table S2. Pulse wave velocity and other biochemical studies.

Published
2021
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33. Replication of Integrative Data Analysis for Adipose Tissue Dysfunction, Low-Grade Inflammation, Postprandial Responses and OMICs Signatures in Symptom-Free Adults

Author

Gallegos Cabriales, Esther Carlota, Rodríguez Ayala, Ernesto, Laviada Molina, Hugo A., Nava González, Edna Judith, Salinas Osornio, Rocío A., Orozco, Lorena, Leal Berumen, Irene, Castillo Pineda, Juan Carlos, González López, Laura, Escudero Lourdes, Claudia, Cornejo Barrera, Judith, Escalante Araiza, Fabiola, Huerta Ávila, Eira E., Buenfil Rello, Fatima A., Peschard, Vanessa Giselle, Silva, Eliud, Veloz Garza, Rosa A., Martínez Hernández, Angélica, Barajas Olmos, Francisco M., Molina Segui, Fernanda, Gonzalez Ramirez, Lucia, Arjona Villicaña, Ruy D., Hernandez Escalante, Victor M., Gaytan Saucedo, Janeth F., Vaquera, Zoila, Acebo Martinez, Mónica Lucía, Murillo Ramirez, Areli, Diaz Tena, Sara P., Figueroa Nuñez, Benigno, Valencia Rendón, Melesio E., Garzon Zamora, Rafael, Viveros Paredes, Juan Manuel, Valdovinos Chávez, Salvador B., Comuzzie, Anthony G., Haack, Karin, Thorsell, Ashley A., Han, Xianlin, Cole, Shelley A., Bastarrachea, Raúl A., Gallegos Cabriales, Esther Carlota, Rodríguez Ayala, Ernesto, Laviada Molina, Hugo A., Nava González, Edna Judith, Salinas Osornio, Rocío A., Orozco, Lorena, Leal Berumen, Irene, Castillo Pineda, Juan Carlos, González López, Laura, Escudero Lourdes, Claudia, Cornejo Barrera, Judith, Escalante Araiza, Fabiola, Huerta Ávila, Eira E., Buenfil Rello, Fatima A., Peschard, Vanessa Giselle, Silva, Eliud, Veloz Garza, Rosa A., Martínez Hernández, Angélica, Barajas Olmos, Francisco M., Molina Segui, Fernanda, Gonzalez Ramirez, Lucia, Arjona Villicaña, Ruy D., Hernandez Escalante, Victor M., Gaytan Saucedo, Janeth F., Vaquera, Zoila, Acebo Martinez, Mónica Lucía, Murillo Ramirez, Areli, Diaz Tena, Sara P., Figueroa Nuñez, Benigno, Valencia Rendón, Melesio E., Garzon Zamora, Rafael, Viveros Paredes, Juan Manuel, Valdovinos Chávez, Salvador B., Comuzzie, Anthony G., Haack, Karin, Thorsell, Ashley A., Han, Xianlin, Cole, Shelley A., and Bastarrachea, Raúl A.

Abstract

We previously reported preliminary characterization of adipose tissue (AT) dysfunction through the adiponectin/leptin ratio (ALR) and fasting/postprandial (F/P) gene expression in subcutaneous (SQ) adipose tissue (AT) biopsies obtained from participants in the GEMM study, a precision medicine research project. Here we present integrative data replication of previous findings from an increased number of GEMM symptom-free (SF) adults (N = 124) to improve characterization of early biomarkers for cardiovascular (CV)/immunometabolic risk in SF adults with AT dysfunction. We achieved this goal by taking advantage of the rich set of GEMM F/P 5 h time course data and three tissue samples collected at the same time and frequency on each adult participant (F/P blood, biopsies of SQAT and skeletal muscle (SKM)). We classified them with the presence/absence of AT dysfunction: low (1) ALR. We also examined the presence of metabolically healthy (MH)/unhealthy (MUH) individuals through low-grade chronic subclinical inflammation (high sensitivity C-reactive protein (hsCRP)), whole body insulin sensitivity (Matsuda Index) and Metabolic Syndrome criteria in people with/without AT dysfunction. Molecular data directly measured from three tissues in a subset of participants allowed fine-scale multi-OMIC profiling of individual postprandial responses (RNA-seq in SKM and SQAT, miRNA from plasma exosomes and shotgun lipidomics in blood). Dynamic postprandial immunometabolic molecular endophenotypes were obtained to move towards a personalized, patient-defined medicine. This study offers an example of integrative translational research, which applies bench-to-bedside research to clinical medicine. Our F/P study design has the potential to characterize CV/immunometabolic early risk detection in support of precision medicine and discovery in SF individuals.

Published
2021

34. Reconstruction of ancient microbial genomes from the human gut

Author

Wibowo, Marsha C, Yang, Zhen, Borry, Maxime, Hübner, Alexander, Huang, Kun D, Tierney, Braden T, Zimmerman, Samuel, Barajas-Olmos, Francisco, Contreras-Cubas, Cecilia, García-Ortiz, Humberto, Martínez-Hernández, Angélica, Luber, Jacob M, Kirstahler, Philipp, Blohm, Tre, Smiley, Francis E, Arnold, Richard, Ballal, Sonia A, Pamp, Sünje Johanna, Russ, Julia, Maixner, Frank, Rota-Stabelli, Omar, Segata, Nicola, Reinhard, Karl, Orozco, Lorena, Warinner, Christina, Snow, Meradeth, LeBlanc, Steven, Kostic, Aleksandar D, Wibowo, Marsha C, Yang, Zhen, Borry, Maxime, Hübner, Alexander, Huang, Kun D, Tierney, Braden T, Zimmerman, Samuel, Barajas-Olmos, Francisco, Contreras-Cubas, Cecilia, García-Ortiz, Humberto, Martínez-Hernández, Angélica, Luber, Jacob M, Kirstahler, Philipp, Blohm, Tre, Smiley, Francis E, Arnold, Richard, Ballal, Sonia A, Pamp, Sünje Johanna, Russ, Julia, Maixner, Frank, Rota-Stabelli, Omar, Segata, Nicola, Reinhard, Karl, Orozco, Lorena, Warinner, Christina, Snow, Meradeth, LeBlanc, Steven, and Kostic, Aleksandar D

Abstract

Loss of gut microbial diversity1-6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000-2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.

Published
2021

35. Two Novel Variants in DYRK1B causative of AOMS3: Expanding the Clinical Spectrum

Author

Mendoza-Caamal, Elvia Cristina, primary, Barajas-Olmos, Francisco, additional, Mirzaeicheshmeh, Elaheh, additional, Ilizaliturri-Flores, Ian, additional, Aguilar-Salinas, Carlos, additional, Gómez-Velasco, Donaji, additional, Cicerón-Arellano, Isabel, additional, Reséndiz-Rodríguez, Adriana, additional, Martínez-Hernández, Angélica, additional, Contreras-Cubas, Cecilia, additional, Islas-Andrade, Sergio, additional, Zerrweck, Carlos, additional, García-Ortiz, Humberto, additional, and Orozco, Lorena, additional

Published
2020
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37. Metabolic syndrome in indigenous communities in Mexico: a descriptive and cross-sectional study

Author

Mendoza-Caamal, Elvia Cristina, primary, Barajas-Olmos, Francisco, additional, García-Ortiz, Humberto, additional, Cicerón-Arellano, Isabel, additional, Martínez-Hernández, Angélica, additional, Córdova, Emilio J., additional, Esparza-Aguilar, Marcelino, additional, Contreras-Cubas, Cecilia, additional, Centeno-Cruz, Federico, additional, Cid-Soto, Miguel, additional, Morales-Marín, Mirna Edith, additional, Reséndiz-Rodríguez, Adriana, additional, Jiménez-Ruiz, Juan Luis, additional, Salas-Martínez, María Guadalupe, additional, Saldaña-Alvarez, Yolanda, additional, Mirzaeicheshmeh, Elaheh, additional, Rojas-Martínez, María Rosalba, additional, and Orozco, Lorena, additional

Published
2020
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38. Additional file 1 of Metabolic syndrome in indigenous communities in Mexico: a descriptive and cross-sectional study

Author

Mendoza-Caamal, Elvia Cristina, Barajas-Olmos, Francisco, García-Ortiz, Humberto, Cicerón-Arellano, Isabel, Martínez-Hernández, Angélica, Córdova, Emilio J., Esparza-Aguilar, Marcelino, Contreras-Cubas, Cecilia, Centeno-Cruz, Federico, Cid-Soto, Miguel, Morales-Marín, Mirna Edith, Reséndiz-Rodríguez, Adriana, Jiménez-Ruiz, Juan Luis, Salas-Martínez, María Guadalupe, Saldaña-Alvarez, Yolanda, Mirzaeicheshmeh, Elaheh, Rojas-Martínez, María Rosalba, and Orozco, Lorena

Abstract

Additional file 1. Prevalence of Metabolic Syndrome and its components by gender and age group. Description of data: Data are presented as frequency (95% confidence intervals) and prevalences were calculated according to American Heart Association/National Heart, Lung, and Blood Institute Scientific Statement criteria.

Published
2020
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39. Towards precision medicine: defining and characterizing adipose tissue dysfunction to identify early immunometabolic risk in symptom-free adults from the GEMM family study

Author

Rodríguez Ayala, Ernesto, Gallegos Cabriales, Esther Carlota, González López, Laura, Laviada Molina, Hugo A., Salinas Osornio, Rocío A., Nava González, Edna Judith, Leal Berumen, Irene, Escudero Lourdes, Claudia, Escalante Araiza, Fabiola, Buenfil Rello, Fatima A., Peschard, Vanessa Giselle, Laviada Nagel, Antonio, Silva, Eliud, Veloz Garza, Rosa A., Martínez Hernández, Angélica, Barajas Olmos, Francisco M., Molina Segui, Fernanda, Gonzalez Ramirez, Lucia, Espadas Olivera, Rebeca, Lopez Muñoz, Ricardo, Arjona Villicaña, Ruy D., Hernandez Escalante, Victor M., Rodriguez Arellano, Martha E., Gaytan Saucedo, Janeth F., Vaquera, Zoila, Acebo Martinez, Mónica Lucía, Cornejo Barrera, Judith, Huertas Quintero, Jancy Andrea, Castillo Pineda, Juan Carlos, Murillo Ramirez, Areli, Diaz Tena, Sara P., Figueroa Nuñez, Benigno, Valencia Rendón, Melesio E., Garzon Zamora, Rafael, Viveros Paredes, Juan Manuel, Angeles Chimal, José, Santa Olalla Tapia, Jesús, Remes Troche, José M., Valdovinos Chávez, Salvador B., Huerta Ávila, Eira E., López Alvarenga, Juan Carlos, Comuzzie, Anthony G., Haack, Karin, Han, Xianlin, Orozco, Lorena, Weintraub, Susan, Kent, Jack W., Cole, Shelley A., Bastarrachea, Raúl A., Rodríguez Ayala, Ernesto, Gallegos Cabriales, Esther Carlota, González López, Laura, Laviada Molina, Hugo A., Salinas Osornio, Rocío A., Nava González, Edna Judith, Leal Berumen, Irene, Escudero Lourdes, Claudia, Escalante Araiza, Fabiola, Buenfil Rello, Fatima A., Peschard, Vanessa Giselle, Laviada Nagel, Antonio, Silva, Eliud, Veloz Garza, Rosa A., Martínez Hernández, Angélica, Barajas Olmos, Francisco M., Molina Segui, Fernanda, Gonzalez Ramirez, Lucia, Espadas Olivera, Rebeca, Lopez Muñoz, Ricardo, Arjona Villicaña, Ruy D., Hernandez Escalante, Victor M., Rodriguez Arellano, Martha E., Gaytan Saucedo, Janeth F., Vaquera, Zoila, Acebo Martinez, Mónica Lucía, Cornejo Barrera, Judith, Huertas Quintero, Jancy Andrea, Castillo Pineda, Juan Carlos, Murillo Ramirez, Areli, Diaz Tena, Sara P., Figueroa Nuñez, Benigno, Valencia Rendón, Melesio E., Garzon Zamora, Rafael, Viveros Paredes, Juan Manuel, Angeles Chimal, José, Santa Olalla Tapia, Jesús, Remes Troche, José M., Valdovinos Chávez, Salvador B., Huerta Ávila, Eira E., López Alvarenga, Juan Carlos, Comuzzie, Anthony G., Haack, Karin, Han, Xianlin, Orozco, Lorena, Weintraub, Susan, Kent, Jack W., Cole, Shelley A., and Bastarrachea, Raúl A.

Published
2020

40. Genetic variability of five ADRB2 polymorphisms among Mexican Amerindian ethnicities and the Mestizo population

Author

Salas-Martínez, María Guadalupe, primary, Saldaña-Alvarez, Yolanda, additional, Cordova, Emilio J., additional, Mendiola-Soto, Diana Karen, additional, Cid-Soto, Miguel A., additional, Luckie-Duque, Angélica, additional, Vicenteño-Ayala, Hermenegildo, additional, Barajas-Olmos, Francisco, additional, Contreras-Cubas, Cecilia, additional, García-Ortiz, Humberto, additional, Jiménez-Ruíz, Juan L., additional, Centeno-Cruz, Federico, additional, Martínez-Hernández, Angélica, additional, Mendoza-Caamal, Elvia C., additional, Mirzaeicheshmeh, Elaheh, additional, and Orozco, Lorena, additional

Published
2019
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41. Variation in Actionable Pharmacogenetic Markers in Natives and Mestizos From Mexico

Author

Gonzalez-Covarrubias, Vanessa, primary, Morales-Franco, Marlet, additional, Cruz-Correa, Omar F., additional, Martínez-Hernández, Angélica, additional, García-Ortíz, Humberto, additional, Barajas-Olmos, Francisco, additional, Genis-Mendoza, Alma Delia, additional, Martínez-Magaña, José Jaime, additional, Nicolini, Humberto, additional, Orozco, Lorena, additional, and Soberón, Xavier, additional

Published
2019
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42. Additional file 1 of Altered DNA methylation in liver and adipose tissues derived from individuals with obesity and type 2 diabetes

Author

Barajas-Olmos, Francisco, Centeno-Cruz, Federico, Zerrweck, Carlos, Imaz-Rosshandler, Iván, Martínez-Hernández, Angélica, Cordova, Emilio, Rangel-Escareño, Claudia, Gálvez, Faustino, Castillo, Armando, Maydón, Hernán, Campos, Francisco, Maldonado-Pintado, Diana, and Orozco, Lorena

Abstract

Figure S1. Clustering of methylation data from tissue samples from individuals with obesity. Figure S2. Comparison of methylation averages among tissue types. Figure S3. Comparison of DMCs between different tissues. Figure S4. Differential gene expression. Table S1. List of DMCs in WB in the comparison between the DO and NDO groups. Table S2. List of DMCs in SAT in the comparison between the DO and NDO groups. Table S3. List of DMCs in VAT in the comparison between the DO and NDO groups. Table S4. List of DMCs in LT in the comparison between the DO and NDO groups. Table S5. Gene ontology enrichment analysis using the genes with DMCs in SAT. Table S6. Gene ontology enrichment analysis using the genes with DMCs in VAT. Table S7. Gene ontology enrichment analysis using the genes with DMCs in LT. Table S8. Differential gene expression in WB in the comparison between DO and NDO groups. Table S9. Differential gene expression in SAT in the comparison between DO and NDO groups. Table S10. Differential gene expression in VAT in the comparison between DO and NDO groups. Table S11. Differential gene expression in LT in the comparison between DO and NDO groups. Table S12. List of genes with correlation between alteration of DNA methylation and differential gene expression in WB. Table S13. List of genes with correlation between alteration of DNA methylation and differential gene expression in SAT. Table S14. List of genes with correlation between alteration of DNA methylation and differential gene expression in VAT. Table S15. List of genes with correlation between alteration of DNA methylation and differential gene expression in LT. Table S16. Gene ontology enrichment analysis using the genes with correlation between alteration of DNA methylation and differential gene expression. (PDF 3440 kb)

Published
2018
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43. Program for APOE-E4 allele detection in a Mexican population of older patients with cognitive impairment

Author

Genis-Mendoza, Alma Delia, primary, Martínez-Magaña, José Jaime, additional, Bojórquez, Carolina, additional, Téllez-Martínez, José Alberto, additional, Jiménez-Genchi, Janett, additional, Roche, Andrés, additional, Bojorge, Alexis, additional, Chávez, Mariana, additional, Castañeda, Carlos, additional, Guzmán, Rafael, additional, Zapata, Leonor, additional, Aguilar-Méndez, Dione, additional, Lanzagorta, Nuria, additional, Rebolledo, Ileana, additional, Castro-Chavira, Susana, additional, Fernández, Thalía, additional, Orozco, Lorena, additional, Nicolini, Humberto, additional, and Martínez-Hernández, Angélica Graciela, additional

Published
2019
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44. Gene variants in AKT1, GCKR and SOCS3 are differentially associated with metabolic traits in Mexican Amerindians and Mestizos

Author

Cid-Soto, Miguel A., primary, Martínez-Hernández, Angélica, additional, García-Ortíz, Humberto, additional, Córdova, Emilio J., additional, Barajas-Olmos, Francisco, additional, Centeno-Cruz, Federico, additional, Contreras-Cubas, Cecilia, additional, Mendoza-Caamal, Elvia C., additional, Ciceron-Arellano, Isabel, additional, Morales-Rivera, Monserrat I., additional, Jimenez-Ruiz, Juan L., additional, Salas-Martínez, Guadalupe, additional, Saldaña-Álvarez, Yolanda, additional, Revilla-Monsalve, Cristina, additional, Islas-Andrade, Sergio, additional, and Orozco, Lorena, additional

Published
2018
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45. Programa de detección del alelo APOE-E4 en adultos mayores mexicanos con deterioro cognitivo

Author

Genis-Mendoza, Alma Delia, primary, Martínez-Magaña, José Jaime, additional, Bojórquez, Carolina, additional, Téllez-Martínez, José Alberto, additional, Jiménez-Genchi, Janett, additional, Roche, Andrés, additional, Bojorge, Alexis, additional, Chávez, Mariana, additional, Castañeda, Carlos, additional, Guzmán, Rafael, additional, Zapata, Leonor, additional, Aguilar-Méndez, Dione, additional, Lanzagorta, Nuria, additional, Rebolledo, Ileana, additional, Castro-Chavira, Susana, additional, Fernández, Thalía, additional, Orozco, Lorena, additional, Nicolini, Humberto, additional, and Martínez-Hernández, Angélica Graciela, additional

Published
2018
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46. Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms

Author

Massachusetts Institute of Technology. Department of Biology, Altshuler, David M, Lander, Eric Steven, Rusu, Victor, Hoch, Eitan, Mercader, Josep M., Tenen, Danielle E., Gymrek, Melissa, Hartigan, Christina R., DeRan, Michael, von Grotthuss, Marcin, Fontanillas, Pierre, Spooner, Alexandra, Guzman, Gaelen, Deik, Amy A., Pierce, Kerry A., Dennis, Courtney, Clish, Clary B., Carr, Steven A., Wagner, Bridget K., Schenone, Monica, Ng, Maggie C.Y., Chen, Brian H., Centeno-Cruz, Federico, Zerrweck, Carlos, Orozco, Lorena, Schreiber, Stuart L., Florez, Jose C., Jacobs, Suzanne B.R., Shriner, Daniel, Li, Jiang, Chen, Wei-Min, Guo, Xiuqing, Liu, Jiankang, Bielinski, Suzette J., Yanek, Lisa R., Nalls, Michael A., Comeau, Mary E., Rasmussen-Torvik, Laura J., Jensen, Richard A., Evans, Daniel S., Sun, Yan V., An, Ping, Patel, Sanjay R., Lu, Yingchang, Long, Jirong, Armstrong, Loren L., Wagenknecht, Lynne, Yang, Lingyao, Snively, Beverly M., Palmer, Nicholette D., Mudgal, Poorva, Langefeld, Carl D., Keene, Keith L., Freedman, Barry I., Mychaleckyj, Josyf C., Nayak, Uma, Raffel, Leslie J., Goodarzi, Mark O., Chen, Y-D Ida, Taylor, Herman A., Correa, Adolfo, Sims, Mario, Couper, David, Pankow, James S., Boerwinkle, Eric, Adeyemo, Adebowale, Doumatey, Ayo, Chen, Guanjie, Mathias, Rasika A., Vaidya, Dhananjay, Singleton, Andrew B., Zonderman, Alan B., Igo, Robert P., Sedor, John R., Kabagambe, Edmond K., Siscovick, David S., McKnight, Barbara, Rice, Kenneth, Liu, Yongmei, Hsueh, Wen-Chi, Zhao, Wei, Bielak, Lawrence F., Kraja, Aldi, Province, Michael A., Bottinger, Erwin P., Gottesman, Omri, Cai, Qiuyin, Zheng, Wei, Blot, William J., Lowe, William L., Pacheco, Jennifer A., Crawford, Dana C., Grundberg, Elin, Rich, Stephen S., Hayes, M. Geoffrey, Shu, Xiao-Ou, Loos, Ruth J.F., Borecki, Ingrid B., Peyser, Patricia A., Cummings, Steven R., Psaty, Bruce M., Fornage, Myriam, Iyengar, Sudha K., Evans, Michele K., Becker, Diane M., Kao, W.H. Linda, Wilson, James G., Rotter, Jerome I., Sale, Michèle M., Liu, Simin, Rotimi, Charles N., Bowden, Donald W., Huerta-Chagoya, Alicia, García-Ortiz, Humberto, Moreno-Macías, Hortensia, Manning, Alisa, Caulkins, Lizz, Burtt, Noël P., Flannick, Jason, Patterson, Nick, Aguilar-Salinas, Carlos A., Tusié-Luna, Teresa, Altshuler, David, Martínez-Hernández, Angélica, Barajas-Olmos, Francisco Martin, Contreras-Cubas, Cecilia, Mendoza-Caamal, Elvia, Revilla-Monsalve, Cristina, Islas-Andrade, Sergio, Córdova, Emilio, Soberón, Xavier, González-Villalpando, Clicerio, González-Villalpando, María Elena, Haiman, Christopher A., Wilkens, Lynne, Le Marchand, Loic, Monroe, Kristine, Kolonel, Laurence, Arellano-Campos, Olimpia, Ordóñez-Sánchez, Maria L., Rodríguez-Torres, Maribel, Segura-Kato, Yayoi, Rodríguez-Guillén, Rosario, Cruz-Bautista, Ivette, Muñoz-Hernandez, Linda Liliana, Sáenz, Tamara, Gómez, Donají, Alvirde, Ulices, Almeda-Valdés, Paloma, Cortes, Maria L., Massachusetts Institute of Technology. Department of Biology, Altshuler, David M, Lander, Eric Steven, Rusu, Victor, Hoch, Eitan, Mercader, Josep M., Tenen, Danielle E., Gymrek, Melissa, Hartigan, Christina R., DeRan, Michael, von Grotthuss, Marcin, Fontanillas, Pierre, Spooner, Alexandra, Guzman, Gaelen, Deik, Amy A., Pierce, Kerry A., Dennis, Courtney, Clish, Clary B., Carr, Steven A., Wagner, Bridget K., Schenone, Monica, Ng, Maggie C.Y., Chen, Brian H., Centeno-Cruz, Federico, Zerrweck, Carlos, Orozco, Lorena, Schreiber, Stuart L., Florez, Jose C., Jacobs, Suzanne B.R., Shriner, Daniel, Li, Jiang, Chen, Wei-Min, Guo, Xiuqing, Liu, Jiankang, Bielinski, Suzette J., Yanek, Lisa R., Nalls, Michael A., Comeau, Mary E., Rasmussen-Torvik, Laura J., Jensen, Richard A., Evans, Daniel S., Sun, Yan V., An, Ping, Patel, Sanjay R., Lu, Yingchang, Long, Jirong, Armstrong, Loren L., Wagenknecht, Lynne, Yang, Lingyao, Snively, Beverly M., Palmer, Nicholette D., Mudgal, Poorva, Langefeld, Carl D., Keene, Keith L., Freedman, Barry I., Mychaleckyj, Josyf C., Nayak, Uma, Raffel, Leslie J., Goodarzi, Mark O., Chen, Y-D Ida, Taylor, Herman A., Correa, Adolfo, Sims, Mario, Couper, David, Pankow, James S., Boerwinkle, Eric, Adeyemo, Adebowale, Doumatey, Ayo, Chen, Guanjie, Mathias, Rasika A., Vaidya, Dhananjay, Singleton, Andrew B., Zonderman, Alan B., Igo, Robert P., Sedor, John R., Kabagambe, Edmond K., Siscovick, David S., McKnight, Barbara, Rice, Kenneth, Liu, Yongmei, Hsueh, Wen-Chi, Zhao, Wei, Bielak, Lawrence F., Kraja, Aldi, Province, Michael A., Bottinger, Erwin P., Gottesman, Omri, Cai, Qiuyin, Zheng, Wei, Blot, William J., Lowe, William L., Pacheco, Jennifer A., Crawford, Dana C., Grundberg, Elin, Rich, Stephen S., Hayes, M. Geoffrey, Shu, Xiao-Ou, Loos, Ruth J.F., Borecki, Ingrid B., Peyser, Patricia A., Cummings, Steven R., Psaty, Bruce M., Fornage, Myriam, Iyengar, Sudha K., Evans, Michele K., Becker, Diane M., Kao, W.H. Linda, Wilson, James G., Rotter, Jerome I., Sale, Michèle M., Liu, Simin, Rotimi, Charles N., Bowden, Donald W., Huerta-Chagoya, Alicia, García-Ortiz, Humberto, Moreno-Macías, Hortensia, Manning, Alisa, Caulkins, Lizz, Burtt, Noël P., Flannick, Jason, Patterson, Nick, Aguilar-Salinas, Carlos A., Tusié-Luna, Teresa, Altshuler, David, Martínez-Hernández, Angélica, Barajas-Olmos, Francisco Martin, Contreras-Cubas, Cecilia, Mendoza-Caamal, Elvia, Revilla-Monsalve, Cristina, Islas-Andrade, Sergio, Córdova, Emilio, Soberón, Xavier, González-Villalpando, Clicerio, González-Villalpando, María Elena, Haiman, Christopher A., Wilkens, Lynne, Le Marchand, Loic, Monroe, Kristine, Kolonel, Laurence, Arellano-Campos, Olimpia, Ordóñez-Sánchez, Maria L., Rodríguez-Torres, Maribel, Segura-Kato, Yayoi, Rodríguez-Guillén, Rosario, Cruz-Bautista, Ivette, Muñoz-Hernandez, Linda Liliana, Sáenz, Tamara, Gómez, Donají, Alvirde, Ulices, Almeda-Valdés, Paloma, and Cortes, Maria L.

Abstract

Type 2 diabetes (T2D) affects Latinos at twice the rate seen in populations of European descent. We recently identified a risk haplotype spanning SLC16A11 that explains ∼20% of the increased T2D prevalence in Mexico. Here, through genetic fine-mapping, we define a set of tightly linked variants likely to contain the causal allele(s). We show that variants on the T2D-associated haplotype have two distinct effects: (1) decreasing SLC16A11 expression in liver and (2) disrupting a key interaction with basigin, thereby reducing cell-surface localization. Both independent mechanisms reduce SLC16A11 function and suggest SLC16A11 is the causal gene at this locus. To gain insight into how SLC16A11 disruption impacts T2D risk, we demonstrate that SLC16A11 is a proton-coupled monocarboxylate transporter and that genetic perturbation of SLC16A11 induces changes in fatty acid and lipid metabolism that are associated with increased T2D risk. Our findings suggest that increasing SLC16A11 function could be therapeutically beneficial for T2D. Video Abstract [Figure presented] Keywords: type 2 diabetes (T2D); genetics; disease mechanism; SLC16A11; MCT11; solute carrier (SLC); monocarboxylates; fatty acid metabolism; lipid metabolism; precision medicine

Published
2018

47. Deep Multi-OMICs and Multi-Tissue Characterization in a Pre- and Postprandial State in Human Volunteers: The GEMM Family Study Research Design

Author

Bastarrachea, Raúl A., Laviada Molina, Hugo A., Nava González, Edna Judith, Leal Berumen, Irene, Escudero Lourdes, Claudia, Escalante Araiza, Fabiola, Peschard, Vanessa Giselle, Veloz Garza, Rosa A., Haack, Karin, Martínez Hernández, Angélica, Barajas Olmos, Francisco M., Molina Segui, Fernanda, Buenfil Rello, Fatima A., Gonzalez Ramirez, Lucia, Janssen Aguilar, Reinhard, Lopez Muñoz, Ricardo, Perez Cetina, Fernanda, Gaytan Saucedo, Janeth F., Vaquera, Zoila, Cornejo Barrera, Judith, Castillo Pineda, Juan Carlos, Murillo Ramirez, Areli, Diaz Tena, Sara P., Figueroa Nuñez, Benigno, González López, Laura, Salinas Osornio, Rocío A., Valencia Rendón, Melesio E., Ángeles Chimal, José, Santa Olalla Tapia, Jesús, Remes Troche, José M., Valdovinos Chávez, Salvador B., Huerta Ávila, Eira E., Han, Xianlin, Orozco, Lorena, Rodríguez Ayala, Ernesto, Weintraub, Susan, Gallegos Cabriales, Esther Carlota, Cole, Shelley A., Kent, Jr., Jack W., Bastarrachea, Raúl A., Laviada Molina, Hugo A., Nava González, Edna Judith, Leal Berumen, Irene, Escudero Lourdes, Claudia, Escalante Araiza, Fabiola, Peschard, Vanessa Giselle, Veloz Garza, Rosa A., Haack, Karin, Martínez Hernández, Angélica, Barajas Olmos, Francisco M., Molina Segui, Fernanda, Buenfil Rello, Fatima A., Gonzalez Ramirez, Lucia, Janssen Aguilar, Reinhard, Lopez Muñoz, Ricardo, Perez Cetina, Fernanda, Gaytan Saucedo, Janeth F., Vaquera, Zoila, Cornejo Barrera, Judith, Castillo Pineda, Juan Carlos, Murillo Ramirez, Areli, Diaz Tena, Sara P., Figueroa Nuñez, Benigno, González López, Laura, Salinas Osornio, Rocío A., Valencia Rendón, Melesio E., Ángeles Chimal, José, Santa Olalla Tapia, Jesús, Remes Troche, José M., Valdovinos Chávez, Salvador B., Huerta Ávila, Eira E., Han, Xianlin, Orozco, Lorena, Rodríguez Ayala, Ernesto, Weintraub, Susan, Gallegos Cabriales, Esther Carlota, Cole, Shelley A., and Kent, Jr., Jack W.

Abstract

Cardiovascular disease (CVD) and type 2 diabetes (T2D) are increasing worldwide. This is mainly due to an unhealthy nutrition, implying that variation in CVD risk may be due to variation in thecapacitytomanageanutritionalload. Weexaminedthegenomicbasisofpostprandialmetabolism. Our main purpose was to introduce the GEMM Family Study (Genetics of Metabolic Diseases in Mexico) as a multi-center study carrying out an ongoing recruitment of healthy urban adults. Each participant received a mixed meal challenge and provided a 5-hours’ time course series of blood, buffy coat specimens for DNA isolation, and adipose tissue (ADT)/skeletal muscle (SKM) biopsies at fasting and 3 h after the meal. A comprehensive profiling, including metabolomic signatures in blood and transcriptomic and proteomic profiling in SKM and ADT, was performed to describe tendencies for variation in postprandial response. Our data generation methods showed preliminary trends indicating that by characterizing the dynamic properties of biomarkers with metabolic activity and analyzing multi-OMICS data it could be possible, with this methodology and research design, to identify early trends for molecular biology systems and genes involved in the fasted and fed states.

Published
2018

48. GSTT1 and GSTM1 null variants in Mestizo and Amerindian populations from northwestern Mexico and a literature review

Author

Palma-Cano, Luz Elena, primary, Córdova, Emilio J., additional, Orozco, Lorena, additional, Martínez-Hernández, Angélica, additional, Cid, Miguel, additional, Leal-Berumen, Irene, additional, Licón-Trillo, Angel, additional, Lechuga-Valles, Ruth, additional, González-Ponce, Mauricio, additional, González-Rodríguez, Everardo, additional, and Moreno-Brito, Verónica, additional

Published
2017
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49. Demographic history and biologically relevant genetic variation of Native Mexicans inferred from whole-genome sequencing

Author

Romero-Hidalgo, Sandra, primary, Ochoa-Leyva, Adrián, additional, Garcíarrubio, Alejandro, additional, Acuña-Alonzo, Victor, additional, Antúnez-Argüelles, Erika, additional, Balcazar-Quintero, Martha, additional, Barquera-Lozano, Rodrigo, additional, Carnevale, Alessandra, additional, Cornejo-Granados, Fernanda, additional, Fernández-López, Juan Carlos, additional, García-Herrera, Rodrigo, additional, García-Ortíz, Humberto, additional, Granados-Silvestre, Ángeles, additional, Granados, Julio, additional, Guerrero-Romero, Fernando, additional, Hernández-Lemus, Enrique, additional, León-Mimila, Paola, additional, Macín-Pérez, Gastón, additional, Martínez-Hernández, Angélica, additional, Menjivar, Marta, additional, Morett, Enrique, additional, Orozco, Lorena, additional, Ortíz-López, Guadalupe, additional, Pérez-Villatoro, Fernando, additional, Rivera-Morales, Javier, additional, Riveros-McKay, Fernando, additional, Villalobos-Comparán, Marisela, additional, Villamil-Ramírez, Hugo, additional, Villarreal-Molina, Teresa, additional, Canizales-Quinteros, Samuel, additional, and Soberón, Xavier, additional

Published
2017
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50. Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms

Author

Rusu, Victor, primary, Hoch, Eitan, additional, Mercader, Josep M., additional, Tenen, Danielle E., additional, Gymrek, Melissa, additional, Hartigan, Christina R., additional, DeRan, Michael, additional, von Grotthuss, Marcin, additional, Fontanillas, Pierre, additional, Spooner, Alexandra, additional, Guzman, Gaelen, additional, Deik, Amy A., additional, Pierce, Kerry A., additional, Dennis, Courtney, additional, Clish, Clary B., additional, Carr, Steven A., additional, Wagner, Bridget K., additional, Schenone, Monica, additional, Ng, Maggie C.Y., additional, Chen, Brian H., additional, Centeno-Cruz, Federico, additional, Zerrweck, Carlos, additional, Orozco, Lorena, additional, Altshuler, David M., additional, Schreiber, Stuart L., additional, Florez, Jose C., additional, Jacobs, Suzanne B.R., additional, Lander, Eric S., additional, Shriner, Daniel, additional, Li, Jiang, additional, Chen, Wei-Min, additional, Guo, Xiuqing, additional, Liu, Jiankang, additional, Bielinski, Suzette J., additional, Yanek, Lisa R., additional, Nalls, Michael A., additional, Comeau, Mary E., additional, Rasmussen-Torvik, Laura J., additional, Jensen, Richard A., additional, Evans, Daniel S., additional, Sun, Yan V., additional, An, Ping, additional, Patel, Sanjay R., additional, Lu, Yingchang, additional, Long, Jirong, additional, Armstrong, Loren L., additional, Wagenknecht, Lynne, additional, Yang, Lingyao, additional, Snively, Beverly M., additional, Palmer, Nicholette D., additional, Mudgal, Poorva, additional, Langefeld, Carl D., additional, Keene, Keith L., additional, Freedman, Barry I., additional, Mychaleckyj, Josyf C., additional, Nayak, Uma, additional, Raffel, Leslie J., additional, Goodarzi, Mark O., additional, Chen, Y-D Ida, additional, Taylor, Herman A., additional, Correa, Adolfo, additional, Sims, Mario, additional, Couper, David, additional, Pankow, James S., additional, Boerwinkle, Eric, additional, Adeyemo, Adebowale, additional, Doumatey, Ayo, additional, Chen, Guanjie, additional, Mathias, Rasika A., additional, Vaidya, Dhananjay, additional, Singleton, Andrew B., additional, Zonderman, Alan B., additional, Igo, Robert P., additional, Sedor, John R., additional, Kabagambe, Edmond K., additional, Siscovick, David S., additional, McKnight, Barbara, additional, Rice, Kenneth, additional, Liu, Yongmei, additional, Hsueh, Wen-Chi, additional, Zhao, Wei, additional, Bielak, Lawrence F., additional, Kraja, Aldi, additional, Province, Michael A., additional, Bottinger, Erwin P., additional, Gottesman, Omri, additional, Cai, Qiuyin, additional, Zheng, Wei, additional, Blot, William J., additional, Lowe, William L., additional, Pacheco, Jennifer A., additional, Crawford, Dana C., additional, Grundberg, Elin, additional, Rich, Stephen S., additional, Hayes, M. Geoffrey, additional, Shu, Xiao-Ou, additional, Loos, Ruth J.F., additional, Borecki, Ingrid B., additional, Peyser, Patricia A., additional, Cummings, Steven R., additional, Psaty, Bruce M., additional, Fornage, Myriam, additional, Iyengar, Sudha K., additional, Evans, Michele K., additional, Becker, Diane M., additional, Kao, W.H. Linda, additional, Wilson, James G., additional, Rotter, Jerome I., additional, Sale, Michèle M., additional, Liu, Simin, additional, Rotimi, Charles N., additional, Bowden, Donald W., additional, Huerta-Chagoya, Alicia, additional, García-Ortiz, Humberto, additional, Moreno-Macías, Hortensia, additional, Manning, Alisa, additional, Caulkins, Lizz, additional, Burtt, Noël P., additional, Flannick, Jason, additional, Patterson, Nick, additional, Aguilar-Salinas, Carlos A., additional, Tusié-Luna, Teresa, additional, Altshuler, David, additional, Martínez-Hernández, Angélica, additional, Barajas-Olmos, Francisco Martin, additional, Contreras-Cubas, Cecilia, additional, Mendoza-Caamal, Elvia, additional, Revilla-Monsalve, Cristina, additional, Islas-Andrade, Sergio, additional, Córdova, Emilio, additional, Soberón, Xavier, additional, González-Villalpando, Clicerio, additional, González-Villalpando, María Elena, additional, Haiman, Christopher A., additional, Wilkens, Lynne, additional, Le Marchand, Loic, additional, Monroe, Kristine, additional, Kolonel, Laurence, additional, Arellano-Campos, Olimpia, additional, Ordóñez-Sánchez, Maria L., additional, Rodríguez-Torres, Maribel, additional, Segura-Kato, Yayoi, additional, Rodríguez-Guillén, Rosario, additional, Cruz-Bautista, Ivette, additional, Muñoz-Hernandez, Linda Liliana, additional, Sáenz, Tamara, additional, Gómez, Donají, additional, Alvirde, Ulices, additional, Almeda-Valdés, Paloma, additional, and Cortes, Maria L., additional

Published
2017
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