José Francisco Muñoz-Valle

Pre-Hispanic Mesoamerican Demography Approximates the Present-Day Ancestry of Mestizos Throughout the Territory of Mexico

Over the last 500 years, admixture among Amerindians, Europeans, and Africans, principally, has come to shape the present-day gene pool of Mexicans, particularly Mestizos, who represent about 93% of the total Mexican population. In this work, we analyze the genetic data of 13 combined DNA index system-short tandem repeats (CODIS-STRs) in 1,984 unrelated Mestizos representing 10 population samples from different regions of Mexico, namely North, West, Central, and Southeast. The analysis of molecular variance (AMOVA) test demonstrated low but significant differentiation among Mestizos from different regions (F(ST) = 0.34%; P = 0.0000). Although the spatial analysis of molecular variance (SAMOVA) predicted clustering Mestizo populations into four well-delimited groups, the main differentiation was observed between Northwest when compared with Central and Southeast regions. In addition, we included analysis of individuals of Amerindian (Purepechas), European (Huelva, Spain), and African (Fang) origin. Thus, STRUCTURE analysis was performed identifying three well-differentiated ancestral populations (k = 3). STRUCTURE results and admixture estimations by means of LEADMIX software in Mestizo populations demonstrated genetic heterogeneity or asymmetric admixture throughout Mexico, displaying an increasing North-to-South gradient of Amerindian ancestry, and vice versa regarding the European component. Interestingly, this distribution of Amerindian ancestry roughly reflects pre-Hispanic Native-population density, particularly toward the Mesoamerican area. The forensic, epidemiological, and evolutionary implications of these findings are discussed herein.

TH1/TH2 cytokine profile, metalloprotease-9 activity and hormonal status in pregnant rheumatoid arthritis and systemic lupus erythematosus patients

During the course of rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), several immune and neuroendocrine changes associated with pregnancy may exert positive (amelioration) or negative (exacerbation) effects on the clinical outcome. In order to shed light on the mechanisms underlying these responses, we performed a prospective longitudinal study in RA and SLE pregnant women, including healthy pregnant women as a control group. Cytokine messenger RNA (mRNA) expression assessed by quantitative competitive polymerase chain reaction (PCR) in peripheral blood mononuclear cells (PBMC), cytokine levels and lymphocyte proliferation responses (LPR) following phytohaemagglutinin (PHA) stimulation of PBMC, plasma metalloprotease‐9 activity (MMP‐9) and hormonal status during pregnancy were determined. TNFa was the most abundant cytokine mRNA expressed in PBMC in all groups studied (healthy pregnant women, RA and SLE pregnant patients). However, a general TH2 response reflected by high IL‐10 levels was found in RA, as well as SLE, patients. A significant change in IFN‐γ was observed in RA patients but only during the first trimester of pregnancy. This compared with a major TH1 response in healthy pregnant women. Interestingly, our study showed a homogeneous hormonal pattern in RA and SLE patients. Although decreased cortisol levels were observed in all patients studied, this is possibly related to the remission of disease activity status brought about by steroid treatment before and during pregnancy. In summary, we suggest that complex immune and hormonal networks are involved in pregnancy and that rheumatic diseases are very dynamic immune processes that cannot be described with a clear‐cut cytokine profile. Furthermore, the observations in this study may reflect treatment‐related immune effects more than those associated with disease.

Population structure and paternal admixture landscape on present-day Mexican-Mestizos revealed by Y-STR haplotypes

Mestizos currently represent most of the Mexican population (>90%); they are defined as individuals born in the country having a Spanish‐derived last name, with family antecedents of Mexican ancestors back at least to the third generation. Mestizos are result of 500 years of admixture mainly among Spaniards, Amerindians, and African slaves. Consequently, a complex genetic pattern has been generated throughout the country that has been scarcely studied from the paternal point of view. This fact is important, taking into account that gene flow toward the New World comprised largely males. We analyzed the population structure and paternal admixture of present‐day Mexican‐Mestizo populations based on Y‐STRs. We genotyped at least 12 Y‐STRs in DNA samples of 986 males from five states: Aguascalientes (n = 293); Jalisco (n = 185); Guanajuato (n = 168); Chiapas (n = 170); and Yucatán (n = 170). AmpFℓSTR Y‐filer and Powerplex‐Y® kits were used. Inclusion of North and Central Y‐STR databases in the analyses allowed obtaining a Y‐STR variability landscape from Mexico. Results confirmed the population differentiation gradient previously noted in Mestizos with SNPs and autosomal STRs throughout the Mexican territory: European ancestry increments to the Northwest and, correspondingly, Amerindian ancestry increments to the Center and Southeast. In addition, SAMOVA test and Autocorrelation Index for DNA Analysis autocorrelogram plot suggested preferential gene flow of males with neighboring populations in agreement with the isolation‐by‐distance model. Results are important for disease‐risk studies (principally male‐related) and for human identification purposes, because Y‐STR databases are not available on the majority of Mexican‐Mestizo populations. Am. J. Hum. Biol., 2010.

Genetic data of 15 autosomal STRs (Identifiler kit) of three Mexican Mestizo population samples from the States of Jalisco (West), Puebla (Center), and Yucatan (Southeast)

We report autosomal STR data (Identifiler PCR amplification kit) of a total sample of 884 unrelated Mestizos from three different regions of Mexico. The population sample included 309, 313 and 262 individuals from the states of Jalisco (West), Puebla (Center) and Yucatan (Southeast), respectively. Allele distribution and forensic statistical parameters are described. Genotype distribution by locus and two-loci combination was in agreement with Hardy-Weinberg expectations for all 15 STRs. Pairwise comparisons including Mexican populations reported in the literature demonstrated a significant differentiation, principally between North/West with regard to Center/Southeast Mexico. These results increase STR data from previously unreported regions of this country, and constitute a valuable guide in forensic casework for choosing an auxiliary STR database in states where it is not available.

Prevalence and distribution of human papillomavirus types in cervical cancer, squamous intraepithelial lesions, and with no intraepithelial lesions in women from Southern Mexico

OBJECTIVE This study was to establish the frequency of HPV infection and which HPV types are circulating in women with cervical cancer (CC), with squamous intraepithelial lesions (SIL), and with no intraepithelial lesion (non-IL) from the State of Guerrero in Southern Mexico. Additionally, we investigated the frequency and distribution of HPV 16 intratypic variants found in this population. METHODS This cross-sectional study was conducted in 4150 women who attended five public health centers seeking cytological screening or for gynecological complaints. Pap smears or biopsies, as appropriate, were obtained for cytological and/or histological diagnosis. HPV detection was done by MY09/11 and GP5+/GP6+ PCR systems and typing by restriction fragment length polymorphism or DNA sequencing. HPV 16 variants were also analyzed. RESULTS HPV was found in 100% of CC, 83.5% in HSIL, 94.5% in LSIL, and 40.9% in non-IL. HR-HPV was the most frequent in all groups. HPV 16 was the most commonly identified HPV genotype in CC and HSIL. HPV 33 was the most frequent in LSIL and non-IL. The highest HPV prevalence was found in the youngest women, HR-HPV and HPV 16 were more frequent in women less than 25 years and more than 55 years of age. The HPV 16 variants E, AA-a and AA-c were found, AA-c was found only in CC. CONCLUSION This study contributes to the knowledge of regional prevalence of HPV types in the whole spectrum of disease, which can be useful in the application of prophylactic vaccines against HPV and in the viral screening methods.

Tumor Necrosis Factor α-308 and -238 Polymorphisms in Rheumatoid Arthritis. Association With Messenger RNA Expression and sTNF-α

Background Rheumatoid arthritis (RA) is characterized by a progressive joint damage mediated mainly by tumor necrosis factor α (TNFα). We investigated the relationship of TNFα-308 and -238 polymorphisms with messenger RNA (mRNA) expression and soluble TNFα (sTNFα) in 50 RA and 100 healthy subjects (HS). Methods Clinical and laboratory assessments were performed. Spanish Health Assessment Questionnaire Disability Index, Spanish version of Arthritis Impact Measurement Scales and Disease Activity Score using 28 joint count indices were applied to RA patients. The TNFα-308 and -238 polymorphisms were performed by polymerase chain reaction and restriction fragment length polymorphism techniques. The mRNA expression of TNFα was quantified by real-time polymerase chain reaction. The sTNFα levels were measured by enzyme-linked immunosorbent assay. Results The TNFα-308 polymorphism showed an increased frequency of guanine (G)/adenine (A) genotype in RA versus HS (P = 0.03; 95% confidence interval, 1.05-8.08; odds ratio, 2.9) and also the A allele was more frequent in RA patients versus HS (P = 0.04; 95% confidence interval, 1.01-7.29; odds ratio, 2.7). The G/G genotype and also the G allele were more frequent in HS. No significant difference was observed in TNFα-238 polymorphism. Rheumatoid arthritis patients showed high TNFα mRNA expression (1.33-fold). The G/G genotype was associated with high mRNA and sTNFα levels in both TNFα polymorphisms. The correlation of sTNFα levels with C-reactive protein, erythrocyte sedimentation rate, rheumatoid factor, Spanish Health Assessment Questionnaire Disability Index, and Spanish version of Arthritis Impact Measurement Scales, was observed. Conclusion The TNFα-308 polymorphism is a susceptibility marker to RA. The G/G genotype is associated with a high mRNA and soluble TNFα expression.

Macrophage migration inhibitory factor (MIF): Genetic evidence for participation in early onset and early stage rheumatoid arthritis

Macrophage migration inhibitory factor (MIF) is an upstream pro-inflammatory cytokine that is associated with the pathogenesis of autoimmune inflammatory diseases including rheumatoid arthritis (RA). Two polymorphisms in the upstream region exist in the MIF gene and are associated with RA susceptibility or severity in different populations. In this case-control study, we investigated whether MIF polymorphisms are associated with RA susceptibility or activity in a western Mexican population .The relationship of MIF levels with clinical features of disease also was assessed. Genotyping of the -794 CATT5-8 (rs5844572) and the -173 G>C (rs755622) polymorphisms was performed by PCR and PCR-RFLP respectively on 226 RA patients and 210 healthy subjects. Serum MIF levels were determined by ELISA. We found a significant association between the -794 CATT5-8 6,7 MIF genotype with RA. Moreover, we detected an association between the -794 CATT7 allele with early onset RA. The -794 CATT7 and -173(*)C alleles, which are in linkage disequilibrium, were associated with high disease activity on RA patients. A positive correlation between circulating MIF levels and C-reactive protein, erythrocyte sedimentation rate, rheumatoid factor, anti-citrullinated protein/peptides antibodies and TNFα was detected. MIF levels appear to be associated with disease progression rather than disease activity, which is distinct from the established relationship between disease activity and TNFα levels. In conclusion, the MIF gene and protein are associated with RA in a western Mexican population, with a main contribution onto early onset and early stages of disease.

Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups.

The maternal ancestry (mtDNA) has important applications in different research fields, such as evolution, epidemiology, identification, and human population history. This is particularly interesting in Mestizos, which constitute the main population in Mexico (∼93%) resulting from post-Columbian admixture between Spaniards, Amerindians, and African slaves, principally. Consequently, we conducted minisequencing analysis (SNaPshot) of 11 mitochondrial single-nucleotide polymorphisms in 742 Mestizos of 10 populations from different regions in Mexico. The predominant maternal ancestry was Native American (92.9%), including Haplogroups A, B, C, and D (47, 23.7, 15.9, and 6.2%, respectively). Conversely, European and African ancestries were less frequent (5.3 and 1.9%, respectively). The main characteristics of the maternal lineages observed in Mexican-Mestizos comprised the following: 1) contrasting geographic gradient of Haplogroups A and C; 2) increase of European lineages toward the Northwest; 3) low or absent, but homogeneous, African ancestry throughout the Mexican territory; 4) maternal lineages in Mestizos roughly represent the genetic makeup of the surrounding Amerindian groups, particularly toward the Southeast, but not in the North and West; 5) continuity over time of the geographic distribution of Amerindian lineages in Mayas; and 6) low but significant maternal population structure (FST  = 2.8%; P = 0.0000). The average ancestry obtained from uniparental systems (mtDNA and Y-chromosome) in Mexican-Mestizos was correlated with previous ancestry estimates based on autosomal systems (genome-wide single-nucleotide polymorphisms and short tandem repeats). Finally, the comparison of paternal and maternal lineages provided additional information concerning the gender bias admixture, mating patterns, and population structure in Mestizos throughout the Mexican territory.

The +1858C/T PTPN22 gene polymorphism confers genetic susceptibility to rheumatoid arthritis in Mexican population from the Western Mexico.

INTRODUCTION Rheumatoid arthritis (RA) is a common autoimmune disease with a complex genetic background. The PTPN22 gene encodes lymphoid tyrosine phosphatase LYP, a potent negative regulator of T cell activation. Polymorphic variants of this gene have previously been associated with various autoimmune disorders. The +1858C/T single-nucleotide polymorphism (SNP) (rs2476601), in the exon 14 of the PTPN22 gene has been associated with susceptibility to RA in several population. OBJECTIVE The aim of this work was to investigate whether the +1858C/T of the PTPN22 gene is associated with susceptibility to RA in Western Mexico population. METHODS A total of 309 unrelated RA patients, classified according to American College of Rheumatology (ACR) 1987 criteria, as well as 347 controls residents from Western Mexico were recruited for this study. The DNA samples were genotyped for +1858C/T PTPN22 gene SNP using the PCR-RFLP technique. Antibodies to cyclic citrullinated peptides (anti-CCP) were measured by enzyme-linked immunosorbent assay (ELISA). RESULTS The frequency of +1858T risk allele was significantly increased in patients with RA compared with controls (p=0.001, OR=2.83, 95%CI=1.50-5.32). To confirm this results we established a comparison between subjects carrying of CT+TT genotypes versus those carrying CC genotype, between both groups (p=0.004, OR=2.65, 95%CI=1.33-5.36). Nevertheless, we not observed association of the +1858C/T PTPN22 gene SNP with clinical activity and functional disability in RA patients. Likewise, the +1858T variant in RA patients seropositive for anti-CCP antibodies, increased the risk for RA (p=0.008, OR=2.5, 95%CI=1.3-5.0) when we compared with controls; however, in the group of seronegative patients, no was found significant difference (p=0.1, OR=2.5, 95%CI=0.9-7.2). CONCLUSIONS Our results support the association of the +1858T risk allele of the +1858C/T PTPN22 polymorphism with susceptibility to RA and confirm that, in combination with anti-CCP antibodies, this SNP influence the autoimmune processes towards a development of RA in Mexican population.

Distribution of CYP2D6 and CYP2C19 polymorphisms associated with poor metabolizer phenotype in five Amerindian groups and western Mestizos from Mexico.

BACKGROUND The distribution of polymorphisms in the CYP2D6 and CYP2C19 genes allows inferring the potential risk for specific adverse drug reactions and lack of therapeutic effects in humans. This variability shows differences among human populations. The aim of this study was to analyze single-nucleotide polymorphisms related to a poor metabolizer (PM) phenotype in nonpreviously studied Amerindian groups and Mestizos (general admixed population) from Mexico. METHODS We detected by SNaPshot(®) different polymorphisms located in CYP2D6 (*3, *4, *6, *7, and *8) and CYP2C19 (*2, *3, *4 and *5) in western Mestizos (n=145) and five Amerindian groups from Mexico: Tarahumaras from the North (n=88); Purépechas from the Center (n=101); and Tojolabales (n=68), Tzotziles (n=88), and Tzeltales (n=20) from the Southeast. Genotypes were observed by capillary electrophoresis. The genetic relationships among these populations were estimated based on these genes. RESULTS AND DISCUSSION The wild-type allele (*1) of both genes was predominant in the Mexican populations studied. The most widely observed alleles were CYP2C19*2 (range, 0%-31%) and CYP2D6*4 (range, 1.2%-7.3%), whereas CYP2D6*3 was exclusively detected in Mestizos. Conversely, CYP2C19*4 and *5, as well as CYP2D6*3, *6, *7, and *8, were not observed in the majority of the Mexican populations. The Tarahumaras presented a high frequency of the allele CYP2C19*2 (31%) and of homozygotes *2/*2 (10.7%), which represent a high frequency of potentially PM phenotypes in this Amerindian group. The genetic distances showed high differentiation of Tarahumaras (principally for CYP2C19 gene). In general, a relative proximity was observed between most of the Amerindian, Mexican-Mestizo, and Latin-American populations. CONCLUSION In general, the wild-type allele (*1) predominates in Mexican populations, outlining a relatively homogeneous distribution for CYP2C19 and CYP2D6. The exception is the Tarahumara group that displays a potentially increased risk for adverse reactions to CYP2C19-metabolized drugs.