Papel de la variabilidad genética en las enfermedades mendelianas y multifactoriales.

The first draft of the human genome sequencing published in 2001 reported a large number of single nucleotide polymorphisms (SNPs). Given that these polymorphisms could practically represent all the variability involved in the susceptibility, protection, severity, among other aspects, of various common diseases, as well as in their response to medications, it was thought that they might be "the biomarkers of choice" in personalized genomic medicine. With the new information obtained from the sequencing of a larger number of genomes, we have understood that SNPs are only an important part of the genetic markers involved in these traits. In addition to SNPs, other variants have been identified, such as insertions/deletions (INDELs) and copy number variants (CNVs), which - in addition to classic variable number tandem repeats (VNTRs) and short tandem repeats (STRs) - originate or contribute to the development of diseases. The use of these markers has served to identify regions of the genome involved in Mendelian diseases (one gene-one disease) or genes directly associated with multifactorial diseases. This review has the purpose to describe the role of STRs, VNTRs, SNPs, CNVs and INDELs in linkage and association studies and their role in Mendelian and multifactorial diseases.

El primer borrador de la secuencia del genoma humano, publicado en 2001, reportó gran cantidad de variantes de un solo nucleótido (SNP, single nucleotide polymorphisms). Debido a que estos polimorfismos podrían representar prácticamente toda la variabilidad involucrada en la susceptibilidad, protección, gravedad, etcétera, de diversas enfermedades comunes, así como en la respuesta de estas a los medicamentos, se pensó que podrían ser "los biomarcadores de elección" en la medicina genómica personalizada. Con la nueva información de la secuenciación de un mayor número de genomas hemos comprendido que los SNP son solo una parte importante de los marcadores genéticos involucrados en estos rasgos. Además de los SNP, se han identificado que otras variantes como las inserciones/deleciones (INDEL) y las variantes en el número de copia (CNV), las cuales ­ además de los clásicos repetidos en tándem de número variable (VNTR) y repetidos cortos en tándem (STR)­ originan o contribuyen al desarrollo de enfermedades. El uso de estos marcadores ha servido para identificar regiones del genoma involucradas en enfermedades mendelianas (un gen-una enfermedad) o genes directamente asociados con enfermedades multifactoriales. Esta revisión tiene como objetivo describir el papel de los STR, VNTR, SNP, CNV e INDEL en los estudios de ligamiento y asociación, y su papel en las enfermedades mendelianas y multifactoriales.

Genome sequencing and conservation genomics in the Scandinavian wolverine population.

Genetic approaches have proved valuable to the study and conservation of endangered populations, especially for monitoring programs, and there is potential for further developments in this direction by extending analyses to the genomic level. We assembled the genome of the wolverine (Gulo gulo), a mustelid that in Scandinavia has recently recovered from a significant population decline, and obtained a 2.42 Gb draft sequence representing >85% of the genome and including >21,000 protein-coding genes. We then performed whole-genome resequencing of 10 Scandinavian wolverines for population genomic and demographic analyses. Genetic diversity was among the lowest detected in a red-listed population (mean genome-wide nucleotide diversity of 0.05%). Results of the demographic analyses indicated a long-term decline of the effective population size (Ne ) from 10,000 well before the last glaciation to <500 after this period. Current Ne appeared even lower. The genome-wide FIS level was 0.089 (possibly signaling inbreeding), but this effect was not observed when analyzing a set of highly variable SNP markers, illustrating that such markers can give a biased picture of the overall character of genetic diversity. We found significant population structure, which has implications for population connectivity and conservation. We used an integrated microfluidic circuit chip technology to develop an SNP-array consisting of 96 highly informative markers that, together with a multiplex pre-amplification step, was successfully applied to low-quality DNA from scat samples. Our findings will inform management, conservation, and genetic monitoring of wolverines and serve as a genomic roadmap that can be applied to other endangered species. The approach used here can be generally utilized in other systems, but we acknowledge the trade-off between investing in genomic resources and direct conservation actions.

Role of genes GSTM1, GSTT1, and MnSOD in the development of late-onset Alzheimer disease and their relationship with APOE*4. / Papel de las variantes GSTM1, GSTT1 y MnSOD en el desarrollo de enfermedad de Alzheimer de aparición tardía y su relación con el alelo 4 de APOE.

INTRODUCTION: Several studies have reported increased oxidation of lipids, proteins and DNA in the brains of patients with Alzheimer disease (AD). Moreover, these patients display differences in the activity and polymorphisms of the genes encoding the enzymes GST (T1, M1) and MnSOD. For these reasons, we designed a study of the variability in GSTT1, GSTM1, and MnSOD genes in healthy and AD groups from a Venezuelan population. METHODS: We included 179 unrelated Venezuelan subjects classified as either AD patients (n=79) or healthy individuals (n=100). Presence or absence of the GSTT1/GSTM1 genes was determined using PCR-SSP, and polymorphisms of MnSOD and APOE genes were identified with PCR-RFLP. RESULTS: The genotype GSTT1+/GSTM1- seems to favour development of AD (OR=2.06, P=.01). The risk level is higher when it is combined with the ɛ4 allele of the APOE gene: GSTT1+/GSTM1-/ɛ3ɛ4 (OR=3.07, P=.05), GSTT1+/GSTM1-/ɛ4ɛ4 (OR=5.52, P=.02). The Ala-9Val polymorphism does not appear to be related to AD. However, the presence of the Ala/Ala genotype increases the risk provided by the ɛ4 allele of the APOE gene: AlaAla/ɛ3ɛ4 (OR=3.47, P=.03), AlaAla/ɛ4ɛ4 (OR=6.3, P=.01). CONCLUSIONS: The results support the hypothesis that impaired mitochondrial function and increased oxidative damage are involved in the pathogenesis of AD. It is important to study other genes related to oxidative stress and antioxidant pathways which could be involved in susceptibility to AD.

Genetic polymorphisms of interleukin-22 in patients with ulcerative colitis. / Polimorfismos genéticos de interleucina-22 en pacientes con colitis ulcerosa.

BACKGROUND: Ulcerative colitis (UC) is a multifactorial and polygenic disease. Interleukin-22 (IL-22) is an immunomodulatory cytokine that belongs to the IL-10 family. Currently, some IL-22 polymorphisms have been associated with inflammatory processes such as rheumatoid arthritis and psoriasis vulgaris, but there are no studies on UC. AIM: The aim of this work was to study the frequency of polymorphisms of IL-22 in Mexican patients with UC. METHODS: We studied a total of 199 Mexican patients with confirmed UC and 697 healthy controls. All individuals were born in Mexico, at least three family generations earlier. A blood sample was obtained from the UC patients and healthy controls in order to perform DNA extraction and then to determine the frequency of IL-22 polymorphisms (rs2227485, rs2272478, rs2227491). RESULTS: No statistical significance was found in the gene and genotype frequencies of three SNPs of IL-22 (rs2227485, rs2272478, rs2227491) between the UC patients and healthy controls. No association was found between those IL-22 SNPs and clinical features of UC. CONCLUSIONS: There was no association between IL-22 SNPs (rs2227485, rs2272478, rs2227491) and the development of UC in a Mexican population.

Genetic polymorphisms in alcohol dehydrogenase, aldehyde dehydrogenase and alcoholic chronic pancreatitis susceptibility: a meta-analysis.

PURPOSE: This study was aimed to determine the relationship of alcohol-metabolizing enzymes ADH2, ADH3, and ALDH2 polymorphisms with the susceptibility to alcoholic chronic pancreatitis (ACP). METHODS: Meta-analyses that evaluated the association of ADH2, ADH3, and ALDH2 variations with ACP were performed. RESULTS: Eight case-control studies were selected for analysis. The overall data revealed a significant association of ADH2 polymorphism (OR=1.56, 95% CI=1.42-1.72, P=0.000 for dominant model; OR=1.63, 95% CI=1.55-1.71, P=0.000 for homozygote comparison model; OR=1.11, 95% CI=1.01-1.22, P=0.030 for allelic contrast model), ADH3 polymorphism (OR=0.95, 95% CI=0.86-1.06, P=0.389 for dominant; OR=0.64, 95% CI=0.44-0.93, P=0.020 for homozygote comparison; and OR=0.87, 95% CI=0.77-0.99, P=0.039 for allelic contrast model) and ALDH2 polymorphism (OR=0.57, 95% CI=0.40-0.81, P=0.002 for dominant; OR=0.50, 95% CI=0.23-1.08, P=0.079 for homozygote comparison; and OR=0.58, 95% CI=0.41-0.84, P=0.003 for allelic contrast model) with ACP risk. The subgroup analyses suggested that the variant ADH2*2/*2+*1/*2, ADH2*2/*2 genotype and ADH2*2 allele significantly increased ACP risk among Asian individuals; the variant ADH3*2/*2 genotype and ADH3*2 allele significantly decreased ACP risk among non-Asian individuals; and the variant ALDH2*2/*2+*1/*2 genotype and ALDH2*2 allele significantly decreased ACP risk among Asians. CONCLUSIONS: ADH2, ADH3 and ALDH2 polymorphisms may be susceptibility facts of ACP, and it may be ethnic and race-dependent.

Genetic analysis in APC, KRAS, and TP53 in patients with stomach and colon cancer.

BACKGROUND: Stomach cancer (SC) and colorectal cancer (CRC) present with high rates of incidence and mortality in the worldwide population. These 2 tumors are characterized by great genetic heterogeneity. Up to now, there have been no molecular studies that analyze the mutations in the APC, KRAS, and TP53 genes in the Colombian/Latin American population. OBJECTIVES: To analyze mutations in the APC, KRAS, and TP53 genes through direct sequencing in 59 patients with SC and CRC. PATIENTS AND METHODS: Twenty-nine patients with SC and 30 with CRC were studied. An analysis of the mutations of the 3 genes was carried out using polymerase chain reaction and direct sequencing techniques. RESULTS: A 30.5% total mutation frequency was found. The most frequently mutated gene was APC (15.3%), followed by KRAS (10.1%) and TP53 (5.1%). The CRC samples had a mutation frequency of 46.7% and it was 13.3% in the SC samples (P=.006). No mutations occurred simultaneously in the 3 genes. Mutations in 2 genes were found in only 6 tumor samples (10%). There was also a high frequency of polymorphisms in both types of cancer, the most common of which was the rs41115 polymorphism, located on the APC gene. CONCLUSION: The APC, KRAS, and TP53 gene mutations were more common in CRC than in SC. Our results suggest the existence of different genetic pathways in the carcinogenesis of SC and CRC and they also reveal a particular mutation frequency in the Colombian patients studied; this could be influenced by factors related to the environment, ethnicity, and lifestyle of this population.

Correlation between LHCGR and NR5A1 genes polymorphism and male infertility risk.

INTRODUCTION: Infertility is one of the important phenomena in human reproduction. Genetic factors are the most important cause of male infertility. Here, we aimed to investigate the correlation between idiopathic male infertility and SNPs of the LHCGR (rs2293275) and NR5A1 (rs1057517779) genes in the Iranian-Azeri population. METHODS: This case-control study consisted of 100 males with infertility and 100 healthy males from the Iranian Azeri population. Genomic DNA isolation from whole blood samples and Tetra-primer amplification refractory mutation system-polymerase chain reaction (Tetra-ARMS-PCR) method was used for genotyping. The data analysis was performed by chi-square (χ2) and Fisher's exact tests. RESULTS: Genotyping analysis for LHCGR (rs2293275) polymorphism indicated that the frequency of C in the case group was significantly higher than in the control group (P < .05). Moreover, genotyping analysis for NR5A1 (rs1057517779) polymorphism indicated that the frequencies of the A allele and heterozygote GA genotype in the case group were significantly higher than those in the control group (P < .05). CONCLUSION: Our study demonstrated that the SNPs of LHCGR (rs2293275) and NR5A1 (rs1057517779) genes may play a critical role in male infertility in the Iranian Azeri population. However, further studies on other ethnic origins with larger sample sizes are essential for accessing more accurate results. Moreover, functional experiments might be needed to understand the role of these polymorphisms in the molecular pathways involved in male fertility.

Association of carotid atheroma plaque with IL-18 levels and with polymorphisms in the IL-18 receptor gene in a Mediterranean population. / Asociación de la placa de ateroma carotídea con los niveles plasmáticos de IL-18 y con polimorfismos en el gen del receptor de la IL-18 en la población mediterránea.

BACKGROUND: Atherosclerosis is an inflammatory disease. Interleukin 18 (IL-18) is an inflammatory molecule that has been linked to the development of atherosclerosis and cardiovascular disease. OBJECTIVE: To evaluate the possible relationship between plasma levels of IL-18 and the presence of atherosclerosis evaluated at the carotid level, as well as to analyze the possible modulation by different polymorphisms in a Mediterranean population. MATERIAL AND METHODS: Seven hundred and forty-six individuals from the metropolitan area of Valencia were included, recruited over a period of 2 years. Hydrocarbon and lipid metabolism parameters were determined using standard methodology and IL-18 using ELISA. In addition, carotid ultrasound was performed and the genotype of four SNPs related to the IL-18 signaling pathway was analyzed. RESULTS: Patients with higher plasma levels of IL-18 had other associated cardiovascular risk factors. Elevated IL-18 levels were significantly associated with higher carotid IMT and the presence of atheromatous plaques. The genotype with the A allele of the SNP rs2287037 was associated with a higher prevalence of carotid atheromatous plaque. On the contrary, the genotype with the C allele of the SNP rs2293224 was associated with a lower prevalence of atheromatous plaque. CONCLUSIONS: High levels of IL-18 were significantly associated with a higher carotid IMT and the presence of atheromatous plaques, which appear to be influenced by genetic factors, as evidenced by associations between SNPs in the IL-18 receptor gene and the presence of atheroma plaque.

Genetic predisposition of BDNF (rs6265) gene is susceptible to Schizophrenia: A prospective study and updated meta-analysis.

INTRODUCTION: Genetic polymorphism in the BDNF gene has been found to cause neuronal alterations and has been identified as a causal factor for many neuropsychiatric disorders. Therefore, various neurological case-control studies and meta-analyses have been conducted to find the possible link between BDNF and susceptibility to schizophrenia. METHOD: This meta-analysis gathered data from 25 case-control studies including a total of 8384 patients with schizophrenia and 8821 controls in order to identify the relationship between the rs6265 single nucleotide polymorphism and the disease, evaluating the combined odds ratio and 95% confidence intervals under 5 different genetic models. Validation followed the "Leave one out" method, and we used the Egger test and Begg's funnel plot to identify publication bias. RESULTS: Research into the rs6265 (G/A) polymorphism revealed a non-significant association with schizophrenia in all 5 genetic models; in the subgroup analysis, no association was found between white and Asian populations, with a p value>.05. CONCLUSIONS: Overall, the updated meta-analysis revealed that rs6265 exonic polymorphisms do not increase susceptibility to this disease. However, to better understand the pathogenesis of the disease, there is a need for further case-control studies into the BDNF polymorphism including larger sample sizes and different ethnic groups.

Interaction between angiotensin-converting enzyme gene rs4343 polymorphism, environment factors, and angiotensin II level on susceptibility to knee osteoarthritis.

OBJECTIVES: Osteoarthritis (OA) is a complex multifactorial disease. The association of knee OA risk with ACE gene rs4343 polymorphism, gene environment synergistic effect, and angiotensin II serum level has not been previously examined. Therefore, we investigate the ACE gene rs4343 polymorphism in knee OA, and its association with severity of knee OA, and angiotensin II serum level. METHODS: Using a case-control design, we recruited 200 subjects (100 cases and 100 controls) and all were subjected to genotyping of rs4343 SNP by real-time polymerase chain reaction and assay of serum angiotensin II level by ELISA. RESULTS: G containing genotypes (AG and GG) and G allele frequencies of the ACE rs4343 polymorphism were significantly higher in the case group than that in the control group. There was significant association between ACE rs4343 genotypes and risk of knee OA under the following genetic inheritance models: GG vs. AA (P=0.003), AA vs. GG/AG (P=0.014), AG/AA vs. GG (P=0.037), and G vs. A (P<0.001). Stratified analyses showed ACE rs4343 polymorphism was evidently associated with a significantly increased risk of knee OA among those had BMI≥25% (adjusted OR=3.016; 95% CI 1.052-8.648; P=0.040). Additionally, knee OA patients with GG genotype had greater knee specific WOMAC index, Kellgren score, and serum angiotensin II level than those with AA or GA genotypes. CONCLUSION: The investigated polymorphism in the ACE gene rs4343 may reflect the risk and severity of knee OA in the Egyptian population, particularly with the GG genotype. The interaction between ACE gene rs4343 polymorphism and obesity further increased the risk of knee OA. Moreover, the higher angiotensin II level may be involved in the pathogenesis of knee OA.

[Genetic factors associated with long COVID]. / Factores genéticos asociados a long COVID.

INTRODUCTION: The variability in expression and evolution of COVID is not completely explained by clinical factors. In fact, genetic factors play an important role. Moreover, it is unknown whether the genetic factor that contribute to susceptibility and severity are also involved in the onset and evolution of long-COVID. The objective of this review is to gather information from literature to understand which genetic factors are involved in the onset of persistent COVID. MATERIAL AND METHODS: Systematic review in PubMed and bioRxiv and medRxiv repositories based on MeSH-descriptors and MeSH-terms related to COVID and genetic factors. Using these terms 2715 articles were pooled. An initial screening performed by authors independently, selected 205 articles of interest. A final deeper screening a total of 85 articles were chosen for complete reading and summarized in this review. RESULTS: Although ACE2 and TMPSS6 are involved in COVID susceptibility, their involvement in long-COVID has not been found. On the other hand, the severity of the disease and the onset of long-COVID has been associated with different genes involved in the inflammatory and immune response. Particularly interesting has been the association found with the FOXP4 locus. CONCLUSIONS: Although studies on long-COVID are insufficient to fully comprehend the cause, it is clear that the current identified genetic factors do not fully explain the progression and onset of long-COVID. Other factors such as polygenic action, pleiotropic genes, the microbiota and epigenetic changes must be considered and studied.

Associations among SNPs in two addictive genes, food addiction, and antioxidant markers in recreationally active young women.

Introduction: Introduction: food addiction is associated with genetic polymorphisms and decreased antioxidant intake. Objectives: this study determined the associations among food addiction, dopamine receptor 2 (DRD2) and toll-interleukin 1 receptor (TIR) domain-containing adaptor protein (TIRAP rs625413) gene polymorphisms, antioxidant capacities, and zinc levels among recreationally active Turkish women. Methods: the Yale Food Addiction Scale was used to evaluate the food addiction status. Serum antioxidant capacities and zinc levels were evaluated by blood analyses. Deoxyribonucleic acid (DNA) extraction was performed using peripheral blood leukocytes, and the polymorphism status of the DRD2 Taq 1A and TIRAP genes was investigated using a commercial kit. Results: the frequencies of the heterozygous genotypes of DRD2 Taq 1A and TIRAP were 23.1 % and 31.4 %, respectively, and the frequency of risk allele homozygous genotypes was 3.2 %. Most participants (94.4 %) had a nonpolymorphic/wild (CC) genotype in both genes; however, 11.5 % of the participants had a food addiction. The differences between serum antioxidant capacities, zinc levels, and body mass indices of those with and without food addiction were statistically significant. However, there were no differences in the serum zinc and antioxidant levels among the different genotypes. Conclusion: food addiction in young Turkish women was not associated with DRD2 Taq 1A or TIRAP polymorphisms but was associated with serum antioxidant capacities and zinc levels. Further studies on different loci of the same genes or genotypes of different genes with larger sample sizes are warranted.

Introducción: Introducción: la adicción a la comida está asociada con polimorfismos genéticos y disminución de la ingesta de antioxidantes. Objetivos: este estudio determinó las asociaciones entre la adicción a la comida, los polimorfismos del gen de la proteína adaptadora que contiene el dominio del receptor de dopamina 2 (DRD2) y del receptor de interleucina 1 (TIR) (TIRAP rs625413), las capacidades antioxidantes y los niveles de zinc entre mujeres turcas recreativamente activas. Métodos: se utilizó la escala de adicción a la comida de Yale para evaluar el estado de adicción a la comida. Las capacidades antioxidantes séricas y los niveles de zinc se evaluaron mediante análisis de sangre. La extracción de ácido desoxirribonucleico (ADN) se realizó a partir de leucocitos de sangre periférica y el estado de polimorfismo de los genes DRD2 Taq 1A y TIRAP se investigó con un kit comercial. Resultados: las frecuencias de los genotipos heterocigotos de DRD2 Taq 1A y TIRAP fueron 23,1 % y 31,4 %, respectivamente, y la frecuencia de genotipos homocigotos de alelos de riesgo fue de 3,2 %. La mayoría de las participantes (94,4 %) tenían un genotipo no polimórfico/salvaje (CC) en ambos genes; sin embargo, el 11,5 % de las participantes tenía adicción a la comida. Las diferencias entre las capacidades antioxidantes séricas, los niveles de zinc y los índices de masa corporal de aquellas con y sin adicción a la comida fueron estadísticamente significativas. Sin embargo, no hubo diferencias en los niveles séricos de zinc y antioxidantes entre los diferentes genotipos. Conclusión: la adicción a la comida en mujeres jóvenes turcas no se asoció con los polimorfismos DRD2 Taq 1A o TIRAP, pero se asoció con las capacidades séricas antioxidantes y los niveles de zinc. Se justifican más estudios sobre diferentes loci de los mismos genes o genotipos de diferentes genes con tamaños de muestra más grandes.

Determination of homeodomain interacting protein kinase 2 polymorphisms rs2058265, rs6464214, and rs7456421 in patients with kidney stone.

OBJECTIVE: This study aimed to investigate whether homeodomain interacting protein kinase 2 (HIPK2) polymorphism is associated with renal stone formation in a Turkish population. MATERIALS AND METHODS: A total of 129 patients with calcium nephrolithiasis and 67 sex- and age-matched healthy controls were enrolled in the study. Blood samples were collected into EDTA tubes. The DNA of patients was extracted using a QIAsymphony® automated DNA isolation system. The Chi-square test was applied in the comparisons between the patient and control groups in respect of the differences in the genotype and allele frequencies. RESULTS: No statistically significant difference was found between the groups in terms of single nucleotide polymorphism (SNP) incidence in single allele and double alleles in the rs2058265 and rs6464214 regions (p = 0.13 and 0.37, respectively). The SNP incidence in double alleles in nephrolithiasis patients at rs7456421 was statistically significantly lower than in the control group (p = 0.001). CONCLUSION: Distributions of the genotype and allele of the three polymorphisms (rs2058265, rs6464214, and rs745642 in HIPK2) were not associated with an increased risk of kidney stone in this Turkish population.

OBJETIVO: Investigar si el polimorfismo de la proteína cinasa 2 que interactúa con el homeodominio (HIPK2) está asociado con la formación de cálculos renales en una población turca. MÉTODO: Se inscribieron en el estudio 129 pacientes con nefrolitiasis cálcica y 67 sujetos control sanos, emparejados por sexo y edad. Las muestras de sangre se recogieron en tubos con EDTA. El ADN de los pacientes se extrajo mediante un sistema de aislamiento de ADN automatizado QIAsymphony®. Se aplicó la prueba χ2 en las comparaciones entre los grupos de pacientes y control con respecto a las diferencias de las frecuencias genotípicas y alélicas. RESULTADOS: No se encontraron diferencias estadísticamente significativas entre los grupos en términos de incidencia de polimorfismo de nucleótido simple (PNS) en alelo simple y alelo doble en las regiones rs2058265 y rs6464214 (p = 0.13 y 0.37, respectivamente). La incidencia de PNS en alelos dobles en pacientes con nefrolitiasis en rs7456421 fue menor que en el grupo control, con una diferencia estadísticamente significativa (p = 0.001). CONCLUSIONES: Las distribuciones de genotipo y alelo de los tres polimorfismos (rs2058265, rs6464214 y rs745642 en HIPK2) no se asociaron con un mayor riesgo de cálculos renales en esta población turca.

Effects of serotonin transporter and receptor polymorphisms on depression.

INTRODUCTION: Serotonin is highly implicated in the regulation of emotional state and the execution of cognitive tasks, so much so that the serotonin transporter genes (5-HTT, SLC6A4) and the serotonin receptor genes (HTR1A, HTR1B, HTR2A) have become the perfect candidates when studying the effects that these genes and their polymorphic variations have on depression characteristics. OBJECTIVE: A review of research reports that have studied the effects of variations in the serotonin transporter and receptor genes on different clinical features of depression. METHODS: A search of the Scopus, Web of Science and PubMed databases was conducted using the keywords ("depression" AND "polymorphism"). CONCLUSIONS: According to the review of 54 articles, the short allele of the 5-HTTLPR polymorphism was found to be the most reported risk factor related to the development of depression and its severity. Variations in the genes studied (SLC6A4, HTR1A, HTR2A) can generate morphological alterations of brain structures.

Analysis of KLF7 and KLF5 transcription factors gene variants in coronary artery disease.

INTRODUCTION AND OBJECTIVE: Genetic susceptibility has a key role in the pathogenesis of coronary artery disease (CAD). KLF5 and KLF7 are transcriptional factors essential to cell development and differentiation. Their genetic variants have been associated with the risk of metabolic disorders. The present study aimed to evaluate the possible correlation of KLF5 (rs3812852) and KLF7 (rs2302870) single nucleotide polymorphisms (SNPs) with the risk of CAD for the first time in the world. METHODS: The clinical trial study comprised 150 patients with CAD and 150 control subjects without CAD from the Iranian population. After blood sampling, deoxyribonucleic acid was extracted and genotyped using the Tetra Primer ARMS-PCR method and confirmed by Sanger sequencing. RESULTS: The KLF7 A/C genotypes and C allele frequency were meaningfully higher in the control group compared to the CAD+ group (p<0.05). No obvious association has been observed between KLF5 variants and CAD risk. However, the distribution of the AG genotype of KLF5 was statistically lower in CAD+ patients with diabetes than in CAD+ patients without diabetes (p<0.05). CONCLUSION: This study identified KLF7 SNP as a causative gene contributing to CAD, which presents novel insight into the molecular pathogenesis of the disease. It is, however, unlikely that KLF5 SNP has an essential role in the risk of CAD in the studied population.

Association of rs662799 and rs5070 genetic polymorphisms with hypertriglyceridemia and atherogenic dyslipidemia in pediatric patients in Southeast Mexico.

BACKGROUND AND AIMS: Triglycerides are the initiators of the metabolic changes that lead to atherogenic dyslipidemia (AD). The APOA5 and APOA1 genes are involved in the response and metabolism of serum lipids and lipoproteins, where single nucleotide polymorphisms (SNP) rs662799 (promoter region) and rs5070 (intronic region) have been associated with the susceptibility to dyslipidemia. Until now, few studies evaluate the association of these polymorphisms with the presentation of hypertriglyceridemia and AD among Mexican children. Therefore, the objective was to determine the association between rs662799 and rs5070 with hypertriglyceridemia and AD in a pediatric population of southeastern Mexico. MATERIALS AND METHODS: A case-control analysis was performed including 268 infants aged 2-16 years, anthropometric, clinical variables, and serum lipid profiles were analyzed. DNA was extracted from blood samples and genotyping of polymorphisms was executed with the TaqMan SNP genotyping assay. Allele and genotypic frequencies were calculated. For genetic association analysis, logistic regression models were fitted according to models of inheritance. RESULTS: The SNP rs662799 (C) was significantly associated with hypertriglyceridemia in the overdominant model (OR=3.89, p=0.001) and AD in the dominant model (OR=4.01, p=0.001). The SNP rs5070 (T) has a protective effect against hypertriglyceridemia in the additive risk model (OR=0.68, p=0.03). CONCLUSION: Polymorphism rs662799 was significantly associated with cases of hypertriglyceridemia and AD in minors in southeastern Mexico. On the other hand, rs5070 polymorphism was not associated with cases of hypertriglyceridemia or AD.

Strong association between angiotensin-converting enzyme gene InDel polymorphism and COVID-19 diseases.

BACKGROUND AND OBJECTIVES: The COVID-19 pandemic that emerged in China in late 2019 and spread rapidly around the world. There is evidence that COVID-19 infection can be influenced by genetic variations in the host. The aim of this study was to investigate the association between ACE InDel polymorphism and COVID-19 in Northern Cyprus. PATIENTS AND METHODS: This study included 250 patients diagnosed with COVID-19 and 371 healthy controls. Genotyping for the ACE InDel gene polymorphism was performed by polymerase chain reaction. RESULTS: The frequency of ACE DD homozygotes was significantly increased in COVID-19 patients compared to the control group (p=0.022). The difference in the presence of the D allele between the patient and control groups was statistically significant (57.2% and 50.67%, respectively, p<0.05). Individuals with the genotype II were found to have a higher risk of symptomatic COVID-19 (p=0.011). In addition, chest radiographic findings were observed more frequently in individuals with the genotype DD compared to individuals with the genotypes ID and II (p=0.005). A statistically significant difference was found when the time of onset of symptoms for COVID-19 and duration of treatment were compared with participants' genotypes (p=0.016 and p=0.014, respectively). The time of onset of COVID-19 was shorter in individuals with the genotype DD than in individuals with the genotype II, while the duration of treatment was longer. CONCLUSION: In conclusion, the ACE I/D polymorphism has the potential to predict the severity of COVID-19.

Association of the rs5186 polymorphism of the AGTR1 gene with decreased eGFR in patients with type 2 diabetes from Mexico City.

BACKGROUND: Early biomarkers search for Diabetic Kidney Disease (DKD) in patients with Type 2 Diabetes Mellitus (T2DM), as genetic markers to identify vulnerable carriers of the disease even before Glomerular Filtration Rate (GFR) decline or microalbuminuria development, has been relevant during the last few years. The rs5186 (A116C) polymorphism of the Angiotensin II Receptor Type I gene (AGTR1), has been associated to multiple effects of renal injury risk, commonly detected in patients with Diabetes Mellitus (DM). It has been described that rs5186 could have an effect in stability proteins that assemble Angiotensin II Receptor Type I (AT1), modifying its action, which is why it should be considered as a risk factor for Chronic Kidney Disease (CKD), characterized by a GFR progressive reduction. Even though, the association between rs5186 AGTR1 gene polymorphism and DKD in patients with T2DM has been controversial, inconclusive, and even absent. This disputable issue might be as a result of association studies in which many and varied clinical phenotypes included are contemplated as CKD inductors and enhancers. Although, the sample sizes studied in patients with T2DM are undersized and did not have a strict inclusion criteria, lacking of biochemical markers or KDOQI classification, which have hindered its examination. OBJECTIVE: The aim of our study was to establish an association between rs5186 AGTR1 gene polymorphism and GFR depletion, assessed as a risk factor to DKD development in patients with T2DM. METHODS: We analyzed 297 not related patients with T2DM, divided into 221 controls (KDOQI 1) and 76 cases (KDOQI 2). Arterial pressure, anthropometric and biochemical parameters were measured. rs5186 of AGTR1 genotyping was performed by TaqMan assay real-time PCR method. Allele and genotype frequencies, and Hardy-Weinberg equilibrium were measured. Normality test for data distribution was analyzed by Shapiro-Wilk test, variable comparison by Student's t-test for continuous variables, and Chi-squared test for categorical variables; ANOVA test was used for mean comparison of more than two groups. Effect of rs5186 to DKD was estimated by multiple heritability adjustment models for risk variables of DKD. Statistical significance was indicated by p<0.05. Data was analyzed using Statistical Package STATA v11 software. RESULTS: Dominant and Over-dominant models showed a likelihood ratio to GFR depletion of 1.89 (1.05-3.39, p=0.031) and 2.01 (1.08-3.73, p=0.023) in patients with T2DM. Risk factor increased to 2.54 (1.10-5.89) in women in Over-dominant model. CONCLUSION: In clinical practice, most of nephropathies progress at a slow pace into a total breakdown of renal function, even asymptomatic. This is the first study, reporting that rs5186 polymorphism of AGTR1 gene contribution to GFR depletion, and this could be evaluated as a predisposing factor for DKD in patients with T2DM.

MTHFR-c 677C>T polymorphism and male infertility: An analysis in a cohort of Pakistani men.

OBJECTIVE: To analyze existence of an association between methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism with male infertility. MATERIALS AND METHODS: A case-control study was conducted from June 2017 to August 2018 in which 88 infertile and 40 fertile were recruited. Polymerase chain reaction (PCR) - restriction fragment length polymorphism (RFLP) assay was carried out to study the allelic frequency of C677T polymorphism. The differences in allelic and genotypic frequencies of C677T locus between fertile and infertile groups were evaluated by the Pearson chisquare test. A logistic regression model was used to calculate Odds ratios and 95% confidence intervals, p value<0.05 was considered significant. The Hardy-Weinberg equilibrium was tested using HWE software. RESULTS: In infertile subjects, frequency distribution of CC allele was (60.2%), the CT allele was (30.7%) the TT allele was (9.1%) and in the fertile controls the frequency was CC allele (75%), CT allele (20%) and TT allele (5%) respectively. Analysis revealed MTHFR 677 CC genotype associated significantly with male infertility (p<.046, OR=2.385; 95% CI=1.014-5.608); Frequency of CT (30.7%) and TT (9.1) genotypes were higher in infertile men as compared to CT (20%) TT (5%) in fertile controls but statistically these were not significantly different (p=0.097; OR=0.455; CI=0.179-1.153 and p=0.431; OR=0.526; CI=0.107-2.599 respectively). Significant association of age and BMI with MTHFR genotypes and infertility was observed. CONCLUSION: Our results showed that MTHFR C677T polymorphism is not a risk factor for male infertility in our Pakistani population.

Single nucleotide polymorphisms in 5-HT receptors in the etiology of premature ejaculation.

INTRODUCTION AND OBJECTIVES: Premature ejaculation (PE) is characterized by shorter intravaginal ejaculation latency time than it is acceptable for the patient or partner. It is thought that lifelong PE is a neurobiological dysfunction associated with genetic predisposition and with central serotonin neurotransmission dysfunction in receptors. To contribute to the understanding the genetic etiology of lifelong PE, it was planned to compare the 5-HT2C receptor gene rs3813929, rs518147, 5-HT1A receptor gene rs6295, 5-HT1B receptor gene rs11568817 of lifelong PE patients to healthy controls. MATERIALS AND METHODS: For this purpose, 100 patients with premature ejaculation and 100 healthy controls were included in the study. Blood samples for DNA extraction were obtained. Appropriate procedures were applied to the probes (rs3813929, rs518147, rs6295, rs11568817) suitable for the DNA studied. RESULTS: A statistically significant relationship was found between the rs11568817 polymorphism (p=0.019) in the 5-HT1B receptor gene and the rs518147 polymorphism (p=0.016) in the 5-HT2C receptor gene. Also, no statistically significant relationship was found between 5-HT1A receptor gene rs6295 polymorphism and 5-HT2C receptor gene rs3813929 polymorphism and lifelong PE. CONCLUSIONS: The relationship between rs3813929 and rs11568817 polymorphisms with lifelong PE was confirmed. Repeating the study in larger sample groups could be useful in determining the genetic etiology of PE.