KRAS, NRAS, and BRAF mutation prevalence, clinicopathological association, and their application in a predictive model in Mexican patients with metastatic colorectal cancer: A retrospective cohort study.

Mutations in KRAS, NRAS, and BRAF (RAS/BRAF) genes are the main predictive biomarkers for the response to anti-EGFR monoclonal antibodies (MAbs) targeted therapy in metastatic colorectal cancer (mCRC). This retrospective study aimed to report the mutational status prevalence of these genes, explore their possible associations with clinicopathological features, and build and validate a predictive model. To achieve these objectives, 500 mCRC Mexican patients were screened for clinically relevant mutations in RAS/BRAF genes. Fifty-two percent of these specimens harbored clinically relevant mutations in at least one screened gene. Among these, 86% had a mutation in KRAS, 7% in NRAS, 6% in BRAF, and 2% in both NRAS and BRAF. Only tumor location in the proximal colon exhibited a significant correlation with KRAS and BRAF mutational status (p-value = 0.0414 and 0.0065, respectively). Further t-SNE analyses were made to 191 specimens to reveal patterns among patients with clinical parameters and KRAS mutational status. Then, directed by the results from classical statistical tests and t-SNE analysis, neural network models utilized entity embeddings to learn patterns and build predictive models using a minimal number of trainable parameters. This study could be the first step in the prediction for RAS/BRAF mutational status from tumoral features and could lead the way to a more detailed and more diverse dataset that could benefit from machine learning methods.

The atorvastatin metabolic phenotype shift is influenced by interaction of drug-transporter polymorphisms in Mexican population: results of a randomized trial.

Atorvastatin (ATV) is a blood cholesterol-lowering drug used to prevent cardiovascular events, the leading cause of death worldwide. As pharmacokinetics, metabolism and response vary among individuals, we wanted to determine the most reliable metabolic ATV phenotypes and identify novel and preponderant genetic markers that affect ATV plasma levels. A controlled, randomized, crossover, single-blind, three-treatment, three-period, and six-sequence clinical study of ATV (single 80-mg oral dose) was conducted among 60 healthy Mexican men. ATV plasma levels were measured using high-performance liquid chromatography mass spectrometry. Genotyping was performed by real-time PCR with TaqMan probes. Four ATV metabolizer phenotypes were found: slow, intermediate, normal and fast. Six gene polymorphisms, SLCO1B1-rs4149056, ABCB1-rs1045642, CYP2D6-rs1135840, CYP2B6-rs3745274, NAT2-rs1208, and COMT- rs4680, had a significant effect on ATV pharmacokinetics (P < 0.05). The polymorphisms in SLCO1B1 and ABCB1 seemed to have a greater effect and were especially important for the shift from an intermediate to a normal metabolizer. This is the first study that demonstrates how the interaction of genetic variants affect metabolic phenotyping and improves understanding of how SLCO1B1 and ABCB1 variants that affect statin metabolism may partially explain the variability in drug response. Notwithstanding, the influence of other genetic and non-genetic factors is not ruled out.

Overexpression of the matrix metalloproteinase 11 gene is a potential biomarker for type 1 endometrial cancer.

Metalloproteinase matrix 11 (MMP11) is a member of the matrix metalloproteinase family, which are able to degrade extracellular matrix components, and may serve a central function in the enhancement of tumor-induced angiogenesis, cell migration, proliferation, apoptosis and connective tissue degradation. In the present study, MMP11 gene expression was investigated using the reverse transcription-polymerase chain reaction in 68 cases of type I endometrial carcinoma, and all data were analyzed in association with clinical characteristics. Overexpression of MMP11 was demonstrated in 75%, and sub-expression was demonstrated in 25%, of endometrial cancer cases. Sub-expression cases were associated with good histological parameters, including low histological grade (G1 and G2), early pathological stage, and absence of vascular invasion, metastasis and recurrence. In total, 76.4% of endometrial cancer cases with sub-expression were identified as early stage 1A and B; however, 23.6% of cases were identified as stage 2, with vascular invasion present in 29.4% of cases. On the other hand, cases which demonstrated overexpression with high ranges (>10 times more than control) were associated with adverse histopathological characteristics, including high grade tumor (G3) and vascular invasion. In conclusion, the increased expression of MMP11 may be used as a prognostic biomarker in patients with type 1 endometrial cancer.

A novel method to detect the Mexican founder mutation BRCA1 ex9­12del associated with breast and ovarian cancer using quantitative polymerase chain reaction and TaqMan® probes.

In 2015, according to the National Institute of Statistics and Geography (INEGI), malignant breast tumors were the first cause of cancer fatality in women (6,273 fatalities) in Mexico, whereas 2,793 fatalities in women were due to ovarian cancer. A total of 5­10% of breast cancer and 10­15% of ovarian cancer cases are caused by a hereditary breast­ovarian cancer syndrome, with mutations predominantly identified in the BRCA1 and BRCA2 genes. Recently, the Mexican founder mutation BRCA1 ex9­12del was identified (deletion of exons 9­12 with recombination between introns 8­12). This is the most frequently reported mutation in hereditary breast/ovarian cancer in Mexico. Current detection methods include end­point polymerase chain reaction (PCR) and Multiplex Ligation­dependent Probe Amplification (MLPA). In the present study a cheap, sensitive and fast detection method was developed based on quantitative PCR and two TaqMan® probes, one to detect the deletion (recombination region between introns 8 and 12), and the other one a region from exon 11. With this assay, 90 samples were able to be analyzed in 2 h using 2.5 ng of DNA/reaction at a cost of ~2­3 USD. This method is capable of detecting positive samples for DNA deletion and excluding negative ones. Therefore, the method proposed may be a useful high­throughput diagnostic option that could be useful in future association or prevalence studies that use large populations.

Understanding the HPV integration and its progression to cervical cancer.

Cervical cancer is one of the main causes of female cancer death worldwide, and human papilloma virus (HPV) its causal agent. To investigate viral oncogenesis several studies have focused on the effects of HPV oncoproteins E6 and E7 and the mechanisms by which these proteins stimulate the cellular transformation process. However, phenomena such as the physical state of the viral genome (episomal or integrated) and the effects of this integration on cell proliferation contribute new clues to understand how HPV infection causes carcinogenesis. New molecular technologies are currently facilitating these discoveries. This paper reviews the tumor development process initiated by HPV, recent findings on the process of viral integration into the host genome, new methods to detect HPV integration, and derived associated effects.

Effect of AGTR1 and BDKRB2 gene polymorphisms on atorvastatin metabolism in a Mexican population.

Discrepancies in the response to drugs are partially due to polymorphisms in genes involved in drug metabolism and transport. The frequency, pattern and impact of these polymorphisms vary among populations. In the present study, the pharmacokinetics and pharmacogenetics of atorvastatin (ATV) in a Mexican population were investigated. The study cohort exhibited differing ATV metabolizing phenotypes, and in subsequent allelic discrimination assays, single nucleotide polymorphisms in the angiotensinogen, angiotensin II type 1 receptor (AGTR1) and bradykinin B2 receptor (BDKRB2) genes were genotyped and their effects on the pharmacokinetic parameters of ATV were assessed. Additionally, association studies were performed to test for a correlation between metabolizing phenotypes and genetic variants. It was observed that carriers of the genotypes A/C and C/T in AGTR1 and BDKRB2 had higher area under the plasma concentration-time curve values from time 0 to the time of the last measurement and from time 0 extrapolated to infinity, and lower values of clearance of the fraction dose absorbed compared with homozygous carriers (P<0.05). Only the C/C genotype of BDKRB2 was associated with the fast metabolizer phenotype. These data suggest that AGTR1 and BDKRB2 are involved in ATV pharmacokinetics; a novel finding that requires confirmation in further studies.

[C677T-SNP of methylenetetrahydrofolate reductase gene and breast cancer in Mexican women]. / SNP C677T del gen metilentetrahidrofolatoreductasa y cáncer de mama en mujeres mexicanas.

BACKGROUND: Low-penetrance susceptibility genes such as 5,10-methylenetetrahydrofolate reductase gene (MTHFR) have been considered in the progression of breast cancer (BC). Cancer is a result of genetic, environmental and epigenetic interactions; therefore, these genes should be studied in environmental context, because the results can vary between populations and even within the same country. The objective was to analyze the allelic and genotypic frequencies of the MTHFR C667T SNP in Mexican Mestizo patients with BC and controls from Northeastern Mexico. METHODS: 243 patients and 118 healthy women were studied. The analysis of the polymorphism was performed with a DNA microarray. Once the frequency of the polymorphism was obtained, Hardy-Weinberg equilibrium test was carried out for the genotypes. Chi square test was used to compare the distribution of frequencies. RESULTS: The allele frequency in patients was: C = 0.5406; T = 0.4594 and in controls C = 0.5678, T = 0.4322. Genotype in BC patients was: C / C = 29.9%, C / T = 48.3% and T / T = 21.8. The distribution in controls was: C / C = 31.4%, C / T = 50.8%, T / T = 17.8% (chi squared 0.77, p = 0.6801). CONCLUSIONS: Northeastern Mexican women in this study showed no association between MTFHR C667T SNP and the risk of BC. It seems that the contribution of this polymorphism to BC in Mexico varies depending on various factors, both genetic and environmental.

INTRODUCCIÓN: existen genes de susceptibilidad de baja penentrancia, como el gen de la 5,10-metilentetrahidrofolato reductasa (MTHFR), que participan en la progresión del cáncer de mama (CM). El cáncer es resultado de interacciones genéticas, ambientales y epigenéticas. Estos genes deben ser estudiados en el contexto del medio ambiente, ya que los resultados pueden variar de una población a otra, incluso dentro del mismo país. El objetivo fue analizar las frecuencias alélicas y genotípicas del polimorfismo C667T del gen de la MTHFR en pacientes mestizos mexicanos con CM y controles del noreste de México. MÉTODOS: se estudiaron 243 pacientes y 118 mujeres sanas. El análisis del polimorfismo se realizó con una microarreglo de ADN. Una vez que se obtuvo la fre cuencia del polimorfismo, la prueba de equilibrio de Hardy-Weinberg se llevó a cabo para los genotipos. Se utilizó chi cuadrada para comparar la distribución de frecuencias. RESULTADOS: la frecuencia de los alelos en los pacientes fue: C = 0.5406, T = 0.4594 y en los controles C = 0.5678, T = 0.4322. El genotipo en pacientes con CM fue: C / C = 29.9%, C / T = 48.3% y T / T = 21.8. La distribución en los controles fue: C / C = 31.4%, C / T = 50.8%, T / T = 17.8% (chi cuadrada 0.77, p = 0.6801). CONCLUSIONES: en este estudio no se observó relación entre el SNP MTFHR C667T y el riesgo de CM. Al parecer la contribución de este polimorfismo al CM en México varía dependiendo de varios factores tanto genéticos como ambientales.

Molecular cloning of the myo-inositol oxygenase gene from the kidney of baboons.

The enzyme myo-Inositol oxygenase (MIOX) is also termed ALDRL6. It is a kidney-specific member of the aldo-keto reductase family. MIOX catalyzes the first reaction involved in the myo-inositol metabolism signaling pathway and is fully expressed in mammalian tissues. MIOX catalyzes the oxidative cleavage of myo-Inositol and its epimer, D-chiro-Inositol to D-glucuronate. The dioxygen-dependent cleavage of the C6 and C1 bond in myo-Inositol is achieved by utilizing the Fe2+/Fe3+ binuclear iron center of MIOX. This enzyme has also been implicated in the complications of diabetes, including diabetic nephropathy. The MIOX gene was amplified with reverse transcription-polymerase chain reaction from baboon tissue samples, and the product was cloned and sequenced. MIOX expression in the baboon kidney is described in the present study. The percentages of nucleotide and amino acid similarities between baboons and humans were 95 and 96%, respectively. The MIOX protein of the baboon may be structurally identical to that of humans. Furthermore, the evolutionary changes, which have affected these sequences, have resulted from purifying forces.

Prediction of atorvastatin plasmatic concentrations in healthy volunteers using integrated pharmacogenetics sequencing.

AIM: To use variants found by next-generation sequencing to predict atorvastatin plasmatic concentration profiles (AUC) in healthy volunteers. SUBJECTS & METHODS: A total of 60 healthy Mexican volunteers were enrolled in this study. We used variants with a predicted functional effect across 20 genes involved in atorvastatin metabolism to construct a regression model using a support vector approach with a radial basis function kernel to predict AUC refining it afterwards in order to explain a greater extent of the variance. RESULTS: The final support vector regression model using 60 variants (including six novel variants) explained 94.52% of the variance in atorvastatin AUC. CONCLUSION: An integrated analysis of several genes known to intervene in the different steps of metabolism is required to predict atorvastatin's AUC.

Olfactomedin-like 2 A and B (OLFML2A and OLFML2B) expression profile in primates (human and baboon).

BACKGROUND: The olfactomedin-like domain (OLFML) is present in at least four families of proteins, including OLFML2A and OLFML2B, which are expressed in adult rat retina cells. However, no expression of their orthologous has ever been reported in human and baboon. OBJECTIVE: The aim of this study was to investigate the expression of OLFML2A and OLFML2B in ocular tissues of baboons (Papio hamadryas) and humans, as a key to elucidate OLFML function in eye physiology. METHODS: OLFML2A and OLFML2B cDNA detection in ocular tissues of these species was performed by RT-PCR. The amplicons were cloned and sequenced, phylogenetically analyzed and their proteins products were confirmed by immunofluorescence assays. RESULTS: OLFML2A and OLFML2B transcripts were found in human cornea, lens and retina and in baboon cornea, lens, iris and retina. The baboon OLFML2A and OLFML2B ORF sequences have 96% similarity with their human's orthologous. OLFML2A and OLFML2B evolution fits the hypothesis of purifying selection. Phylogenetic analysis shows clear orthology in OLFML2A genes, while OLFML2B orthology is not clear. CONCLUSIONS: Expression of OLFML2A and OLFML2B in human and baboon ocular tissues, including their high similarity, make the baboon a powerful model to deduce the physiological and/or metabolic function of these proteins in the eye.

[Institutional Biobank as a pillar of medical science]. / El Biobanco Institucional como pilar de las ciencias médicas.

A biobank facility is one of the most valuable means that academic medical organizations have to offer researchers for improving the competitiveness of their medical research. We describe the implementation of our institutional biobank. Our efforts focused on the design and equipment of work areas, staff training, quality control, bioethical and regulatory issues, generating research collaborations and developing funding strategies. We implemented an institutional biobank at the School of Medicine of the Autonomous University of Nuevo León, Mexico. The biobank has supported more than a dozen research protocols with over 3 000 individuals enrolled and almost 6 000 sampled biospecimens stored. The institutional biobank has become an essential bridge and effective catalyst for research synergies between basic and clinical sciences and it is on its way to becoming a National Laboratory.

El Biobanco Institucional como pilar de las ciencias médicas / Institutional Biobank as a pillar of medical science

Resumen: Los biobancos constituyen puentes efectivos entre grupos de investigación básicos y clínicos para generar conocimientos y aplicaciones que eleven su competitividad internacional. Se revisaron las tareas realizadas y los logros alcanzados durante la implementación del Biobanco Institucional de la Universidad Autónoma de Nuevo León (UANL). Se abordó el equipamiento, entrenamiento del personal, aspectos bioéticos y regulatorios, y procesos de laboratorio y de gestión de calidad, entre otros. A partir del apoyo a más de una docena de proyectos de investigación, la inscripción de más de 3 000 individuos y la colecta, procesamiento y almacenamiento de casi 6 000 bioespecímenes, el Biobanco Institucional contribuye de manera importante a la integración de las actividades de asistencia, docencia e investigación básica y clínica del Hospital Universitario y de la Facultad de Medicina de la UANL. Se iniciaron planes para transitar del Biobanco Institucional hacia el Laboratorio Nacional.

Abstract: A biobank facility is one of the most valuable means that academic medical organizations have to offer researchers for improving the competitiveness of their medical research. We describe the implementation of our institutional biobank. Our efforts focused on the design and equipment of work areas, staff training, quality control, bioethical and regulatory issues, generating research collaborations and developing funding strategies. We implemented an institutional biobank at the School of Medicine of the Autonomous University of Nuevo León, Mexico. The biobank has supported more than a dozen research protocols with over 3 000 individuals enrolled and almost 6 000 sampled biospecimens stored. The institutional biobank has become an essential bridge and effective catalyst for research synergies between basic and clinical sciences and it is on its way to becoming a National Laboratory.

Structure and evolution of the gorilla and orangutan growth hormone loci.

In primates, the unigenic growth hormone (GH) locus of prosimians expressed primarily in the anterior pituitary, evolved by gene duplications, independently in New World Monkeys (NWM) and Old World Monkeys (OWMs)/apes, to give complex clusters of genes expressed in the pituitary and placenta. In human and chimpanzee, the GH locus comprises five genes, GH-N being expressed as pituitary GH, whereas GH-V (placental GH) and CSHs (chorionic somatomammotropins) are expressed (in human and probably chimpanzee) in the placenta; the CSHs comprise CSH-A, CSH-B and the aberrant CSH-L (possibly a pseudogene) in human, and CSH-A1, CSH-A2 and CSH-B in chimpanzee. Here, the GH locus in two additional great apes, gorilla (Gorilla gorilla gorilla) and orangutan (Pongo abelii), is shown to contain six and four GH-like genes, respectively. The gorilla locus possesses six potentially expressed genes, gGH-N, gGH-V and four gCSHs, whereas the orangutan locus has just three functional genes, oGH-N, oGH-V and oCSH-B, plus a pseudogene, oCSH-L. Analysis of regulatory sequences, including promoter, enhancer and P-elements, shows significant variation; in particular the proximal Pit-1 element of GH-V genes differs markedly from that of other genes in the cluster. Phylogenetic analysis shows that the initial gene duplication led to distinct GH-like and CSH-like genes and that a second duplication provided separate GH-N and GH-V. However, evolution of the CSH-like genes remains unclear. Rapid adaptive evolution gave rise to the distinct CSHs, after the first duplication, and to GH-V after the second duplication. Analysis of transcriptomic databases derived from gorilla tissues establishes that the gGH-N, gGH-V and several gCSH genes are expressed, but the significance of the many CSH genes in gorilla remains unclear.

Draft Genome Sequence of an Atypical Strain of Streptococcus pneumoniae Serotype 19A Isolated from Cerebrospinal Fluid.

We present here the draft genome sequence of ITALIC! Streptococcus pneumoniaestrain MTY32702340SN814 isolated in Monterrey, Mexico, from a girl with bacterial meningitis. The strain belongs to the atypical and multidrug-resistant serogroup 19A. This is the first report in the literature of sequence type 3936 (ST3936) in ITALIC! S. pneumoniaeserotype 19A.

Olfactomedin-like 2 A and B (OLFML2A and OLFML2B) expression profile in primates (human and baboon)

BACKGROUND: The olfactomedin-like domain (OLFML) is present in at least four families of proteins, including OLFML2A and OLFML2B, which are expressed in adult rat retina cells. However, no expression of their orthologous has ever been reported in human and baboon. OBJECTIVE: The aim of this study was to investigate the expression of OLFML2A and OLFML2B in ocular tissues of baboons (Papio hamadryas) and humans, as a key to elucidate OLFML function in eye physiology. METHODS: OLFML2A and OLFML2B cDNA detection in ocular tissues of these species was performed by RT-PCR. The amplicons were cloned and sequenced, phylogenetically analyzed and their proteins products were confirmed by immunofluorescence assays. RESULTS: OLFML2A and OLFML2B transcripts were found in human cornea, lens and retina and in baboon cornea, lens, iris and retina. The baboon OLFML2A and OLFML2B ORF sequences have 96% similarity with their human's orthologous. OLFML2A and OLFML2B evolution fits the hypothesis of purifying selection. Phylogenetic analysis shows clear orthology in OLFML2A genes, while OLFML2B orthology is not clear. CONCLUSIONS: Expression of OLFML2A and OLFML2B in human and baboon ocular tissues, including their high similarity, make the baboon a powerful model to deduce the physiological and/or metabolic function of these proteins in the eye.

Application of Genomic Technologies in Clinical Pharmacology Research.

Technology is the basis of scientific progress and is an essential component for continued competitiveness in industry. The development of a new drug candidate is a long and expensive process, in which a molecule undergoes several stages of research (both pre-clinical and clinical) before being approved for commercialization. Scientific progress has revolutionized the pharmaceutical industry and reshaped the processes by which new drugs are discovered, investigated, and developed. Currently, the influence of genomic variations in drug metabolism must be better understood to predict an individual´s response to a given treatment. Employing genomics tools, an individual's genetic profile may be obtained and used as the basis for prescription of the best treatment option, thus personalizing medicine. In this review, we discuss how current mainstream genomic technologies used in clinical pharmacology research can accelerate the identification of populations that can benefit the most while reducing adverse events.

Technological Evolution in the Development of Therapeutic Antibodies.

Immunotherapy is defined as the use of the immune system or components of it, such as key immune molecules, to fight diseases or invading infectious agents. Modern biotechnology provides industrial versions of immune molecules (components of the immune system) naturally produced by the human body. Immune molecules such as monoclonal antibodies are used as therapeutics in several disease conditions. In recent years a new group of antibody based molecules has been developed to replace monoclonal antibodies, given their ability to overcome some of the limitations of the latter. The first clinical trials with these new molecules have been very encouraging and the promise is that they will be released to the market very soon. This in turn has stimulated more research on new versions of antibody based therapeutics by biotechnological companies supported by the pharmaceutical industry and in many cases in collaboration with academic institutions.

Molecular evolution and expression profile of the chemerine encoding gene RARRES2 in baboon and chimpanzee.

BACKGROUND: Chemerin, encoded by the retinoic acid receptor responder 2 (RARRES2) gene is an adipocytesecreted protein with autocrine/paracrine functions in adipose tissue, metabolism and inflammation with a recently described function in vascular tone regulation, liver, steatosis, etc. This molecule is believed to represent a critical endocrine signal linking obesity to diabetes. There are no data available regarding evolution of RARRES2 in non-human primates and great apes. Expression profile and orthology in RARRES2 genes are unknown aspects in the biology of this multigene family in primates. Thus; we attempt to describe expression profile and phylogenetic relationship as complementary knowledge in the function of this gene in primates. To do that, we performed A RT-PCR from different tissues obtained during necropsies. Also we tested the hypotheses of positive evolution, purifying selection, and neutrality. And finally a phylogenetic analysis was made between primates RARRES2 protein. RESULTS: RARRES2 transcripts were present in liver, lung, adipose tissue, ovary, pancreas, heart, hypothalamus and pituitary tissues. Expression in kidney and leukocytes were not detectable in either species. It was determined that the studied genes are orthologous. CONCLUSIONS: RARRES2 evolution fits the hypothesis of purifying selection. Expression profiles of the RARRES2 gene are similar in baboons and chimpanzees and are also phylogenetically related.