An updated examination of the perception of barriers for pharmacogenomics implementation and the usefulness of drug/gene pairs in Latin America and the Caribbean.

Pharmacogenomics (PGx) is considered an emergent field in developing countries. Research on PGx in the Latin American and the Caribbean (LAC) region remains scarce, with limited information in some populations. Thus, extrapolations are complicated, especially in mixed populations. In this paper, we reviewed and analyzed pharmacogenomic knowledge among the LAC scientific and clinical community and examined barriers to clinical application. We performed a search for publications and clinical trials in the field worldwide and evaluated the contribution of LAC. Next, we conducted a regional structured survey that evaluated a list of 14 potential barriers to the clinical implementation of biomarkers based on their importance. In addition, a paired list of 54 genes/drugs was analyzed to determine an association between biomarkers and response to genomic medicine. This survey was compared to a previous survey performed in 2014 to assess progress in the region. The search results indicated that Latin American and Caribbean countries have contributed 3.44% of the total publications and 2.45% of the PGx-related clinical trials worldwide thus far. A total of 106 professionals from 17 countries answered the survey. Six major groups of barriers were identified. Despite the region's continuous efforts in the last decade, the primary barrier to PGx implementation in LAC remains the same, the "need for guidelines, processes, and protocols for the clinical application of pharmacogenetics/pharmacogenomics". Cost-effectiveness issues are considered critical factors in the region. Items related to the reluctance of clinicians are currently less relevant. Based on the survey results, the highest ranked (96%-99%) gene/drug pairs perceived as important were CYP2D6/tamoxifen, CYP3A5/tacrolimus, CYP2D6/opioids, DPYD/fluoropyrimidines, TMPT/thiopurines, CYP2D6/tricyclic antidepressants, CYP2C19/tricyclic antidepressants, NUDT15/thiopurines, CYP2B6/efavirenz, and CYP2C19/clopidogrel. In conclusion, although the global contribution of LAC countries remains low in the PGx field, a relevant improvement has been observed in the region. The perception of the usefulness of PGx tests in biomedical community has drastically changed, raising awareness among physicians, which suggests a promising future in the clinical applications of PGx in LAC.

Effect of CYP3A4, CYP3A5, MDR1 and POR Genetic Polymorphisms in Immunosuppressive Treatment in Chilean Kidney Transplanted Patients.

Cyclosporine (CsA) and tacrolimus (TAC) are immunosuppressant drugs characterized by a narrow therapeutic range and high pharmacokinetic variability. The effect of polymorphisms in genes related to the metabolism and transport of these drugs, namely CYP3A4, CYP3A5, MDR1 and POR genes, has been evaluated in diverse populations. However, the impact of these polymorphisms on drug disposition is not well established in Latin American populations. Using TaqMan® probes, we determined the allelic frequency of seven variants in CYP3A4, CYP3A5, MDR1 and POR in 139 Chilean renal transplant recipients, of which 89 were treated with CsA and 50 with TAC. We tested associations between variants and trough and/or 2-hour concentrations, normalized by dose (C0/D and C2/D) at specific time points post-transplant. We found that CYP3A5*3/*3 carriers required lower doses of TAC. In TAC treated patients, most CYP3A5*3/*3 carriers presented higher C0/D and a high proportion of patients with C0 levels outside the therapeutic range relative to other genotypes. These results reinforce the value of considering CYP3A5 genotypes alongside therapeutic drug monitoring for TAC treated Chilean kidney recipients.

Metals and Metalloids in Feathers of Neotropic Cormorants (Phalacrocorax brasilianus) Nesting in Lake Livingston and Richland Creek, Texas, USA.

Breast feathers of Neotropic Cormorants (Phalacrocorax brasilianus) from two nesting colonies in Lake Livingston (LALIV) and Richland Creek, Texas, were collected during 2014 and were analyzed for metals and metalloids. Mean concentrations of Al, As, Cr, Cu, Fe, Pb, Sb, and Se were not significantly different in breast feathers of cormorants from the two locations or between sexes. However, mean concentrations of Co, Mn, Ni, and V were significantly greater in feathers of cormorants from Richland Creek than in those from LALIV; and Zn concentrations were greater in cormorants from LALIV than in those from Richland Creek (p < 0.05). Overall, except for a few outliers for Pb, concentrations of heavy metals and metalloids in feathers were similar or lower than those reported in other species of cormorants from all over the world and were below levels of concern for lethal or sublethal effects on the species.

As3MT and GST Polymorphisms Influencing Arsenic Metabolism in Human Exposure to Drinking Groundwater.

The urinary arsenic metabolites may vary among individuals and the genetic factors have been reported to explain part of the variation. We assessed the influence of polymorphic variants of Arsenic-3-methyl-transferase and Glutathione-S-transferase on urinary arsenic metabolites. Twenty-two groundwater wells for human consumption from municipalities of Colombia were analyzed for assessed the exposure by lifetime average daily dose (LADD) (µg/kg bw/day). Surveys on 151 participants aged between 18 and 81 years old were applied to collect demographic information and other factors. In addition, genetic polymorphisms (GSTO2-rs156697, GSTP1-rs1695, As3MT-rs3740400, GSTT1 and GSTM1) were evaluated by real time and/or conventional PCR. Arsenic metabolites: AsIII, AsV, monomethylarsonic acid (MMA), and dimethylarsinic acid (DMA) were measured using HPLC-HG-AFS. The influence of polymorphic variants, LADD and other factors were tested using multivariate analyses. The median of total arsenic concentration in groundwater was of 33.3 µg/L and the median of LADD for the high exposure dose was 0.33 µg/kg bw/day. Univariate analyses among arsenic metabolites and genetic polymorphisms showed MMA concentrations higher in heterozygous and/or homozygous genotypes of As3MT compared to the wild-type genotype. Besides, DMA concentrations were lower in heterozygous and/or homozygous genotypes of GSTP1 compared to the wild-type genotype. Both DMA and MMA concentrations were higher in GSTM1-null genotypes compared to the active genotype. Multivariate analyses showed statistically significant association among interactions gene-gene and gene-covariates to modify the MMA and DMA excretion. Interactions between polymorphic variants As3MT*GSTM1 and GSTO2*GSTP1 could be potential modifiers of urinary excretion of arsenic and covariates as age, LADD, and alcohol consumption contribute to largely vary the arsenic individual metabolic capacity in exposed people.

Genetic polymorphisms as non-modifiable susceptibility factors to laryngeal cancer.

Laryngeal squamous cell carcinoma (LSCC) is a highly disabling disease to the patient, affecting speech, swallowing and respiratory skills. Smoking and alcohol abuse are principal risk factors linked to this disease. Genetic factors can be involved in carcinogenesis by controlling the cell cycle, cell survival, angiogenesis, and invasiveness. Single nucleotide polymorphisms (SNPs) involving specific genes could modulate the risk of LSCC related to known carcinogens by modifying cellular responses, but not all genetic associations are known. In a case-control study, we assess the associations between cyclooxygenase-2 (COX2), epidermal growth factor (EGF), EGF receptor (EGFR), and tumor suppressor P53 SNPs on the risk of LSCC development in the Chilean population. A total of 85 LSCC patients and 95 healthy volunteers were recruited. SNPs genotype were analyzed from genomic DNA by Polymerase Chain Reaction (PCR)-Restriction Fragment Length Polymorphism (RFLP) and associations were estimated by odds ratios (ORs) using unconditional logistic regressions. A significant association between COX2 and TP53 SNP and LSCC risk was found, with an OR = 3.27 for COX2 c.-1329A>G (rs689466) SNP, and an OR = 1.94 for TP53 c.215C>G, Pro72Arg (rs1042522) SNP. These findings suggest that COX2 c.-1329A>G and TP53 c.215C>G (Pro72Arg) SNPs may be risk factors for LSCC. Through this research, we identify two low penetrance genetic variants that may be evaluated as novel biomarkers for this disease, in South American Mestizo populations.

The role of phase I and II genetic polymorphisms, smoking, alcohol and cancer family history, in the risk of developing testicular cancer.

BACKGROUND: Testicular cancer (TCa) is a malignant tumor with highest incidence and mortality rates in Chile. The genes coding for cytochrome P450, glutathione-S-transferases (GSTs), and UDP glucuronyl transferases (UGT) participate in the biotransformation and detoxification of xenobiotics. Mutations in these genes have been associated with a high incidence of various types of cancer and an increased risk of presenting adverse reactions to drugs. OBJECTIVE: The aim of this study was to relate the presence of genetic polymorphisms in cytochrome P450 1A1 (CYP1A1), CYP3A4, GSTM1, GSTP1, GSTT1, and UGT1A1 genes and nongenetic factors with the risk of developing TCa. METHODS: A total of 276 volunteers from the Chilean general population and 251 Chilean TCa patients were recruited for the study. Genotypic analyses were performed using qPCR and PCR-RFLP. RESULTS: Variant alleles found to increase the risk of developing TCa were CYP1A1*2C (rs1048943), GSTP1 (rs1695), and GSTT1null, especially when in conjunction with a cancer family history and/or a smoking habit. The results of the multivariate analysis showed that the presence of variant alleles of GSTP1 (rs1695) together with a smoking habit and a family history of cancer accounted for a 15.9% risk of developing TCa in the Chilean population. CYP1A1*2C, GSTM1null, GSTT1null, and GSTP1 (rs1695) are statistically related to the risk of appearance of TCa, alone or associated with nongenetic factors. CONCLUSION: Therefore, phase I and II variant alleles might be useful in evaluating susceptibility to TCa in the studied population.

Association Study Among Candidate Genetic Polymorphisms and Chemotherapy-Related Severe Toxicity in Testicular Cancer Patients.

Testicular cancer is one of the most commonly occurring malignant tumors in young men with fourfold higher rate of incidence and threefold higher mortality rates in Chile than the average global rates. Surgery is the initial line of treatment for testicular cancers, and is generally followed by chemotherapy, usually with combinations of bleomycin, etoposide, and cisplatin (BEP). However, the adverse effects of chemotherapy vary significantly among individuals; therefore, the present study explored the association of functionally significant allelic variations in genes related to the pharmacokinetics/pharmacodynamics of BEP and DNA repair enzymes with chemotherapy-induced toxicity in BEP-treated testicular cancer patients. We prospectively recruited 119 patients diagnosed with testicular cancer from 2010 to 2017. Genetic polymorphisms were analyzed using PCR and/or qPCR with TaqMan ®probes. Toxicity was evaluated based on the Common Terminology Criteria for Adverse Events, v4.03. After univariate analyses to define more relevant genetic variants (p < 0.2) and clinical conditions in relation to severe (III-IV) adverse drug reactions (ADRs), stepwise forward multivariate logistic regression analyses were performed. As expected, the main severe ADRs associated with the non-genetic variables were hematological (neutropenia and leukopenia). Univariate statistical analyses revealed that patients with ERCC2 rs13181 T/G and/or CYP3A4 rs2740574 A/G genotypes are more likely to develop alopecia; patients with ERCC2 rs238406 C/C genotype may develop leukopenia, and patients with GSTT1-null genotype could develop lymphocytopenia (III-IV). Patients with ERCC2 rs1799793 A/A were at risk of developing severe anemia. The BLMH rs1050565 G/G genotype was found to be associated with pain, and the GSTP1 G/G genotype was linked infection (p < 0.05). Multivariate analysis showed an association between specific ERCC1/2 genotypes and cumulative dose of BEP drugs with the appearance of severe leukopenia and/or febrile neutropenia. Grades III-IV vomiting, nausea, and alopecia could be partly explained by the presence of specific ERCC1/2, MDR1, GSTP1, and BLMH genotypes (p < 0.05). Hence, we provide evidence for the usefulness of pharmacogenetics as a tool for predicting severe ADRs in testicular cancer patients treated with BEP chemotherapy.

Persistent Organic Pollutants in Livers and Hg in Feathers of Neotropic Cormorants (Phalacrocorax brasilianus) from the Trinity River Watershed (Texas, USA).

The Trinity River (Texas, USA) has been historically known as a polluted river because of its proximity to the Dallas-Fort Worth area and because of known discharges of sewage and agricultural irrigation waters to the river. Surprisingly, there are no studies regarding the presence of legacy contaminants in the river and their impacts to wildlife. The objectives of this study were to determine accumulation and potential impacts of persistent organic pollutants, such as organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs), on Neotropic cormorants (Phalacrocorax brasilianus) nesting along the Trinity River. Adult and first-year cormorants were collected from two sites on the Trinity River Watershed during 2014 and 2015. Tissue sections from liver, spleen, kidneys, and gonads were used for histopathology analysis, and a portion of the liver was analyzed for OCPs, PCBs, and PBDEs. Breast feathers were analyzed for Hg. Surprisingly, all the contaminants were present at low concentrations, p,p'-DDE (2-724 ng/g ww), PCBs (28-851 ng/g ww), PBDEs (1-85 ng/g ww), Hg (1.9-3.4 µg/g dw), and below those that could be associated with adverse effects. Also, histological analysis of liver and kidney samples did not reveal morphologic changes consistent with acute or chronic toxicosis. The majority of the histologic changes were inflammatory and were related to parasitic infestation. Our results suggest that aquatic birds using the Trinity River watershed are not at risk for adverse effects due to the contaminants studied. These results should be useful to wildlife managers regarding concerns over contaminant impacts on wildlife of the Trinity River.

Generalized Kubelka-Munk approximation for multiple scattering of polarized light.

We introduce a new model for multiple scattering of polarized light by statistically isotropic and mirror-symmetric particles, which we call the generalized Kubelka-Munk (gKM) approximation. It is obtained through a linear transformation of the system of equations resulting from applying the double spherical harmonics approximation of order one to the vector radiative transfer equation (vRTE). The result is a 32×32 system of differential equations that is much simpler than the vRTE. We compare numerical solutions of the vRTE with the gKM approximation for the problem in which a plane wave is normally incident on a plane-parallel slab composed of a uniform absorbing and scattering medium. These comparisons show that the gKM approximation accurately captures the key features of the polarization state of multiply scattered light. In particular, the gKM approximation accurately captures the complicated polarization characteristics of light backscattered by an optically thick medium composed of a monodisperse distribution of dielectric spheres over a broad range of sphere sizes.

Extending generalized Kubelka-Munk to three-dimensional radiative transfer.

The generalized Kubelka-Munk (gKM) approximation is a linear transformation of the double spherical harmonics of order one (DP1) approximation of the radiative transfer equation. Here, we extend the gKM approximation to study problems in three-dimensional radiative transfer. In particular, we derive the gKM approximation for the problem of collimated beam propagation and scattering in a plane-parallel slab composed of a uniform absorbing and scattering medium. The result is an 8×8 system of partial differential equations that is much easier to solve than the radiative transfer equation. We compare the solutions of the gKM approximation with Monte Carlo simulations of the radiative transfer equation to identify the range of validity for this approximation. We find that the gKM approximation is accurate for isotropic scattering media that are sufficiently thick and much less accurate for anisotropic, forward-peaked scattering media.

Deriving Kubelka-Munk theory from radiative transport.

We derive Kubelka-Munk (KM) theory systematically from the radiative transport equation (RTE) by analyzing the system of equations resulting from applying the double spherical harmonics method of order one and transforming that system into one governing the positive- and negative-going fluxes. Through this derivation, we establish the theoretical basis of KM theory, identify all parameters, and determine its range of validity. Moreover, we are able to generalize KM theory to take into account general boundary sources and nonhomogeneous terms, for example. The generalized Kubelka-Munk (gKM) equations are also much more accurate at approximating the solution of the RTE. We validate this theory through comparison with numerical solutions of the RTE.