Psychiatric polygenic risk as a predictor of COVID-19 risk and severity: insight into the genetic overlap between schizophrenia and COVID-19

Despite the high contagion and mortality rates that have accompanied the coronavirus disease-19 (COVID-19) pandemic, the clinical presentation of the syndrome varies greatly from one individual to another. Potential host factors that accompany greater risk from COVID-19 have been sought and schizophrenia (SCZ) patients seem to present more severe COVID-19 than control counterparts, with certain gene expression similarities between psychiatric and COVID-19 patients reported. We used summary statistics from the last SCZ, bipolar disorder (BD), and depression (DEP) meta-analyses available on the Psychiatric Genomics Consortium webpage to calculate polygenic risk scores (PRSs) for a target sample of 11,977 COVID-19 cases and 5943 subjects with unknown COVID-19 status. Linkage disequilibrium score (LDSC) regression analysis was performed when positive associations were obtained from the PRS analysis. The SCZ PRS was a significant predictor in the case/control, symptomatic/asymptomatic, and hospitalization/no hospitalization analyses in the total and female samples; and of symptomatic/asymptomatic status in men. No significant associations were found for the BD or DEP PRS or in the LDSC regression analysis. SNP-based genetic risk for SCZ, but not for BD or DEP, may be associated with higher risk of SARS-CoV-2 infection and COVID-19 severity, especially among women; however, predictive accuracy barely exceeded chance level. We believe that the inclusion of sexual loci and rare variations in the analysis of genomic overlap between SCZ and COVID-19 will help to elucidate the genetic commonalities between these conditions.

Population structure and relatedness estimates in a Mexican sample

Population stratification (PS) is a confounding factor in genome-wide association studies (GWASs) and also an interesting process itself. Latin American populations have mixed genetic ancestry, which may account for PS. We have analyzed the relatedness, by means of the identity-by-descent (IBD) estimations, in a sample of 1805 individuals and 1.006.703 autosomal mutations from a case-control study of colorectal cancer in Mexico. When using the recommended protocol for quality control assessment, 402 should have been removed due to relatedness. Our purpose was to analyze this value in the context of an admixed population. For that aim, we reanalyzed the sample using two software designed for admixed populations, obtaining estimates of 110 and 70 related individuals to remove. The results showed that the first estimation of relatedness was an effect of the higher Native American contribution in part of the data samples, being a confounding factor for IBD estimations. We conclude in the importance of considering PS and genetic ancestry in order to avoid spurious results, not only in GWAS but also in relatedness analysis.

Abstract P2-08-04: HMGA1 negatively regulates the expression of PRRX1 in triple negative breast cancer cells, which favors the progression to metastasis

Background: Triple negative breast cancer (TNBC) presents a very aggressive behavior with a high rate of metastasis. Overexpression of HMGA1 has been reported in TNBC and has been associated with the induction of the Epithelial-Mesenchymal transition (EMT) and metastasis. Therefore, HMGA1 is considered a master regulator of tumor progression in TNBC. The objective of this work was to know which genes are directly or indirectly regulated by HMGA1 to better understand their participation in EMT and their role in aggressive TNBC.

Methods: We performed the silencing of the HMGA1 gene using siRNA Silencer® Select Pre-designed (s6667 HMGA1, 4390849 GAPDH, 4390843 Negative control, all from Thermo Fisher, MA, USA) in two TNBC cell lines, HCC-1395 and MDA-MB-231, and we observed the effect of this gene inhibition by microarray global expression analysis using GeneChip Human Genome U133 Plus 2.0 (Affymetrix, CA, USA), comparing the conditions of inhibition versus their own control without inhibition. After the microarray data mining, results for the HMGA1 and PRRX1 genes were validated by qPCR using the Prime Time® Primers for HMGA1 (Hs.PT.58.38699366), PRRX1 (Hs.PT.58.2820749), and GAPDH as endogenous gene (Hs.PT.39a.22214836) with SybrGreen reagent (Roche, Basel, Switzerland). The level of expression of the HMGA1 and PRRX1 proteins was analyzed by Western blot in nuclear protein extracts of each cell line before and after gene silencing. Finally, we performed an in silico analysis using the "Gene 2 promoter" tool in the Genomatix platform to search the promoters and binding proteins of the PRRX1 gene.

Results: The silencing of HMGA1 in a non-metastatic TNBC-cell line, HCC-1395, showed deregulation of genes associated with cell proliferation and angiogenesis. Meanwhile the silencing in a TNBC-metastatic cell line, MDA-MB-231, resulted in the deregulation of genes involved in the formation and organization of the cytoskeleton, including the overexpression of PRRX1. Validation of the expression changes of HMGA1 and PRRX1 by qPCR and Western blot was performed and HMGA1 was confirmed to negatively regulate the PRRX1 gene expression. Through in silico studies, we identified several binding sites of HMGA1 to the PRRX1 promoter.

Conclusions: The subexpression of PRRX1 is necessary for EMT to occur. In this study, we present the interesting finding that HMGA1 regulates the subexpression of PRRX1, as supported by the experiments of transcriptional and translational expression presented in this work. To our knowledge, this is the first report describing a regulatory role of HMGA1 on PRRX1, which could explain the metastatic capacity of cancers that overexpress HMGA1.

Key words: Epithelial-Mesenchymal Transition, Triple Negative Breast Cancer, Mesenchymal-Epithelial Transition, Metastasis.

Citation Format: Aguayo-Millán CD, Santuario-Facio SK, Treviño-Alvarado V, Calvo-Anguiano G, Rojas-Martínez A, Camacho-Morales A, Ortíz-López R. HMGA1 negatively regulates the expression of PRRX1 in triple negative breast cancer cells, which favors the progression to metastasis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-08-04.

Delineation of a de novo 7q21.3q31.1 Deletion by CGH-SNP Arrays in a Girl with Multiple Congenital Anomalies Including Severe Glaucoma

In this study, we present a female patient with a constitutional de novo deletion in 7q21.3q31.1 as determined by G-banding and CGH-SNP arrays. She exhibited, among other features, psychomotor retardation, congenital severe bilateral glaucoma, a cleft palate, and heart defect. Microarray assay disclosed a deleted 12.5-Mb region roughly 88 kb downstream the ectrodactyly critical region; thus, the patient's final karyotype was 46,XX.arr 7q21.3q31.1(96,742,140-109,246,085)×1 dn. This girl represents the fourth patient described so far with congenital glaucoma and a deletion encompassing or overlapping the 7q21.3q31.1 region, and confirms the presence of a locus or loci related to such a clinical feature. According to our results, the proneness to ocular defects secondary to 7q intermediate deletions could be caused by co-deletion of TAC1, HBP1, and a small cluster of cytochrome P450 genes (subfamily 3A). This conclusion is supported by their functional roles and expression locations as well as because TAC1 is related to the functional pathway of the MYOC gene whose mutations are linked to glaucoma. Moreover, given that this girl is clinically reminiscent of several phenotypes related to diverse deletions within 7q21q32, our results and observations offer a general overview of the gene content of deletions/phenotypes overlapping 7q21.3q31.1 and confirm that loci distal to DLX genes including the CUX1 gene and potential regulatory elements downstream from DLX5 are unrelated to ectrodactyly.

A de novo sSMC(22) Characterized by High-Resolution Arrays in a Girl with Cat-Eye Syndrome without Coloboma

Cat-eye syndrome (CES) results from trisomy or tetrasomy of proximal 22q originated by a small supernumerary marker chromosome (sSMC). Two critical regions for the major clinical features of CES (CESCRs) have been suggested; however, CES clinical presentation often does not correlate with the sSMC genetic content. We report here a CES girl without coloboma and carrier of a de novo type I sSMC(22) as determined by G- and C-banding, NOR staining and microarrays. This sSMC included 6 distal genes outside the original CESCR and led to a tetrasomy for 22q11.1-22q11.21. The patient's final karyotype was 47,XX,+psu dic(22)(q11.21).arr 22q11.1q11.21(15,250,000-17,035,860)×4 dn. The amplified region outside of CESCR included some genes that may be related to neurologic, heart and renal abnormalities. Conversely, even though the amplification included the CECR2 gene, a major candidate for eye features, there was no coloboma in the patient. The genetic delineation of the present sSMC further strengthens that the CES clinical presentation does not fit completely with the duplicated genetic content and that CES is actually a genomic disorder. Furthermore, since we observed no mosaicism, we believe that other mechanisms might be behind the variability of CES phenotypes as well, mainly those related with functional interactions among amplified genes.

Folate levels and N(5),N(10)-methylenetetrahydrofolate reductase genotype (MTHFR) in mothers of offspring with neural tube defects: a case-control study

BACKGROUND

Neural tube defects (NTDs) have been associated with biochemical factors involved in the conversion of homocysteine to methionine as folate deficiency and the mutation 677T in the N(5),N(10)-methylenetetrahydrofolate reductase gene (MTHFR).

METHODS

A case-control study was performed to detect this mutation in 38 unrelated women with NTD deceased products and 31 mothers without antecedents of NTD offspring. All products were born in Nuevo León (northeastern Mexico) during 1997. Erythrocyte and plasmatic folate levels and the genotype of the 677 polymorphism at the MTHFR locus were analyzed in both groups.

RESULTS

Although no significant differences were found in mean blood folate levels, the percentage of women in the case group with erythrocyte folate levels <160 ng/mL was significantly higher than in the control group (75 vs. 51.2%, p <0.05). The proportion of women with plasma folate levels <3.5 ng/mL was higher in the case group (16.2 vs. 0%, p <0.01). Genotype analysis demonstrated a significantly higher proportion of 677T homozygous mothers with NTD products (39.6 vs. 9.1%, p <0.05). Allele frequencies for the 677T mutation were 0.55 and 0.36 for cases and controls, respectively. The odds ratio (OR) for having a NTD product was 6.1 (95%, CI 1.56-23.6) for homozygous 677T mothers vs. homozygous 677C and heterozygous mothers. Significantly low levels of erythrocyte folate were found in the 677C homozygous case group and in plasma folate in the 677C/677T heterozygous case mothers.

CONCLUSIONS

Our study suggests that folate deficiency and MTHFR unfavorable genotype in mothers are important risk factors for severe NTD phenotype in our population.

[677T mutation of the MTHFR gene in adenomas and colorectal cancer in a population sample from the Northeastern Mexico. Preliminary results]

INTRODUCTION

Adequate intake of folates has been associated to low prevalence of colon cancer. Methylenetetrahydrofolate reductase enzyme (MTHFR) plays an important role in folate metabolism. The role of the 677 mutation at the MTHFR gene in the risk for colorectal cancer remains controversial. A recent report established that this mutation has a high prevalence in the healthy Mexican population.

AIMS

To analyze the prevalence of 677T MTHFR mutation in patients with colorectal cancer and controls without chronic gastrointestinal disorders.

METHODS

Seventy-four colorectal cancer, 32 adenomas and 110 normal samples were analyzed. Patients and controls were matched for sex and age. For each sample, DNA isolation, PCR, and mutation detection by restriction enzyme digestion were performed to determine the allele at the 677 position in the MTHFR gene.

RESULTS

Genotype 677C/677C was found in 18.7, 20.3, and 30.9% in adenomas, cancer lesions and controls, respectively. Frequencies of the 677C/677T genotype were 59.4, 56.7, and 47.3%, in adenomas, cancer lesions, and controls, respectively. Genotype 677T/677T was found in 21.9, 23.0, and 21.8% in adenomas, cancer lesions, and controls, respectively. The odds ratio between genotypes carrying the mutation (T/T and C/T) and normal genotype (CC) was 1.81 (IC 95% 0.97-3.3), chi 2 = 3.5, p = 0.06.

CONCLUSION

Our results showed that persons who carry the 677T mutation at MTHFR locus have a tendency for an increased risk for colorectal cancer. This study supports the basic concept that low levels of folic acid contribute with the colorectal cancer pathogenesis. Our lack of statistic significance may be due to reduced sample size.

[Genetic aspects of asthma]

Asthma is a complex disease associated with bronchial hyperreactivity and atopy, making asthma a disease with a phenotype that has been clinically difficult to define. Despite intense research, prevalence of asthma remain relatively high. The key reason for the high prevalence and morbility is that the fundamental mechanisms predisposing individuals to the development of asthma are not understood. Familial aggregation observed in this pathology has prompted for the search of an involved genetic component. This task is difficult due to the complex nature of asthma. A universally accepted definition for this disease is not available, clinical expression can be modulated by environmental factors, and inheritance does not follow a clear Mendelian pattern. Establishment of more precise clinical and laboratory criteria has improved the design and interpretation of genetic studies. Twin analysis and segregation studies have demonstrated an important genetic component with a probably multifactorial pattern of inheritance. "Sib pair" studies and familial segregation analyses have shown linkage between some chromosomal regions and asthma, including chromosome 5, 6, 7, 11 and 14. The search for major genes in these chromosomal segments has been focused on loci involved in the allergic process. Among these, the loci for IL-9 and IL-13 in chromosome 5 seem to play an important role in the pathogenesis of asthma. Understanding the fundamental gene-environmental interactions in the development of asthma should lead to earlier identification of susceptible individuals and more effective approaches for disease prevention.

CFTR mutations in three Latin American countries

We analyzed 192 cystic fibrosis (CF) alleles in three Latin American countries: Mexico, Colombia, and Venezuela. Mutation screening was performed by polymerase chain reaction (PCR) and a reverse dot blot detection kit that enables determination of 16 of the most common CF mutations worldwide. Mutations were detected in 47.9% of the screened CF alleles. The most prevalent CF allele was DeltaF508 (39. 6%). The remaining 16 non-DeltaF508 detectable mutations represented 8.3% of the CF alleles. Among them, the G542X, N1303K, and 3849+10kb C>T were the most common. Although the frequency of DeltaF508 described here is lower than that reported for Caucasian populations, including in Spain, it is remarkable that mutation prevalences found in this study resemble those observed in Spain. Two of these mutations, G542X and 3849+10kb C>T, that were relevant in this analysis, have a particularly high incidence in Spanish communities. The low frequency of DeltaF508 described here may be explained by the Amerindian, Caucasian, and Black admixture that occurred in Latin America after the discovery of the New World, and also by the probable occurrence of mutations contributed by the original natives, which were undetectable in this analysis.

Reproductive biology and the process of domestication of the columnar cactus Stenocereus Stellatus in Central Mexico

Pollination biology, breeding system, and floral phenology of the columnar cactus Stenocereus stellatus were studied in wild, wild managed in situ and cultivated populations of central Mexico, in order to examine whether these aspects have been modified under domestication and whether they determine reproductive barriers between wild and manipulated individuals. Individuals of both wild and manipulated populations are self-incompatible, indicating that artificial selection has not modified the breeding system. Their pollination biology is also similar. Anthesis is mainly nocturnal, with a peak of nectar production between 0200 and 0400 when the stigma presents maximum turgidity. Nocturnal visitors are the effective pollinators. Nearly 75% of flowers exposed for nocturnal pollination set fruit, while none of the flowers exposed for diurnal pollination produced fruits. The bats Leptonycteris curasoae, L. nivalis, and Choeronycteris mexicana (Glossophaginae) are the most likely pollinators, and their time of foraging is synchronized with the time of nectar production and stigma receptivity in S. stellatus. Bats potentially move pollen over a considerable distance, so there is apparently no spatial isolation to prevent pollen exchange between wild and cultivated populations. Phenological studies showed that there are also no apparent temporal barriers. However, manual cross pollination failed between some domesticated and wild phenotypes, suggesting that gene flow between wild and cultivated populations might be limited by pollen incompatibility.

Analysis of 16 cystic fibrosis mutations in Mexican patients

We carried out molecular analysis of 80 chromosomes from 40 unrelated Mexican patients with a diagnosis of cystic fibrosis. The study was performed in two PCR steps: a preliminary one to identify mutation delta F508, the most frequent cause of cystic fibrosis worldwide, and the second a reverse dot-blot with allele-specific oligonucleotide probes to detect 15 additional common mutations in the Caucasian population. A frequency of 45% for delta F508 was found, making it the most common in our sample of Mexican patients. Another five mutations (G542X, 3,849 + 10 kb C-->T, N1303K, SN549N, and 621 + 1 G-->T) were detected, and those accounted for 11.25%. The remaining mutations (43.75%) were undetectable with the methodology used.

Molecular detection or carriers of hemophilia A in Mexican families

The genomic DNAs of carrier mothers from 20 hemophilia A unrelated Mexican families were analysed by polymerase chain reaction (PCR) amplification of the Bcl I polymorphic region at intron 18 of the factor VIII gene. Eleven women (55%) were found to be informative (Bcl I+/Bcl I-), eight (40%) were Bcl I- homozygotes and one (5%) was a Bcl I+ homozygote. In 18 daughters of the informative families we were able to establish carrier status for eight. The frequency of the Bcl I alleles in the 20 mothers was 0.675 for Bcl I- and 0.325 for Bcl I+ which give a frequency of 44% of heterozygous females in our sample.

[Molecular analysis of hemophilia A in families of Northeastern Mexico]

We analysed DNA through Southern blot and polymerase chain reaction using blood samples of northeastern Mexican families affected by hemophilia A. Our aim was to identify possible carriers of the mutated gene by indirect detection using the Bcl I polymorphism (RFLP) at intron 18 of the factor VIII gene. The sample studied consisted of 43 individuals within eight families with hereditary hemophilia A. Of 17 possible carrier women, three were positive, five were negative, and in the remaining nine, the lack of informativeness (heterozygosity for the polymorphism) of their mothers precluded reaching conclusions. The frequencies found for the Bcl I polymorphism were 63% for the 1.2 kb allelic fragment and 37% for the 0.9 kb allelic fragment. Heterozygote women were found in 48.2% of the families studied. Our results show that probably, the Bcl I RFLP is more useful for HA carrier diagnosis in our sample (northeastern Mexico).

[The molecular genetics of cystic fibrosis: the delta F508 allele in Mexican families]

We have initiated the screening of the delta F508 cystic fibrosis (CF) mutation in our country basing our study on the polymerase chain reaction technique. In a sample of 10 western and a northeastern Mexican families that have at least one CF affected child, we found a delta F508 frequency of 59.1% among CF chromosomes. This frequency is similar to those reported for Spain. Furthermore, we found a correlation between the delta F508 allele and pancreatic insufficiency. This paper points out the advantage of the polymerase chain reaction technology for the analysis of Mendelian disorders.

Poland-Moebius syndrome in a boy and Poland syndrome in his mother

A 4 4/12-year-old boy with the Poland-Moebius syndrome, whose mother had the POland syndrome, is presented. This is the first report of the occurrence of both syndromes in the same family, suggesting that they are expressions of the same autosomal dominant gene.