Ancestry component as a major predictor of lithium response in the treatment of bipolar disorder.

BACKGROUND: Bipolar Disorder (BD) represents the seventh major cause of disability life-years-adjusted. Lithium remains as a first-line treatment, but clinical improvement occurs only in 30 % of treated patients. Studies suggest that genetics plays a major role in shaping the individual response of BD patients to lithium. METHODS: We used machine-learning techniques (Advance Recursive Partitioned Analysis, ARPA) to build a personalized prediction framework of BD lithium response using biological, clinical, and demographical data. Using the Alda scale, we classified 172 BD I-II patients as responders or non-responders to lithium treatment. ARPA methods were used to build individual prediction frameworks and to define variable importance. Two predictive models were evaluated: 1) demographic and clinical data, and 2) demographic, clinical and ancestry data. Model performance was assessed using Receiver Operating Characteristic (ROC) curves. RESULTS: The predictive model including ancestry yield the best performance (sensibility = 84.6 %, specificity = 93.8 % and AUC = 89.2 %) compared to the model without ancestry (sensibility = 50 %, Specificity = 94.5 %, and AUC = 72.2 %). This ancestry component best predicted lithium individual response. Clinical variables such as disease duration, the number of depressive episodes, the total number of affective episodes, and the number of manic episodes were also important predictors. CONCLUSION: Ancestry component is a major predictor and significantly improves the definition of individual Lithium response in BD patients. We provide classification trees with potential bench application in the clinical setting. While this prediction framework might be applied in specific populations, the used methodology might be of general use in precision and translational medicine.

Structural Protein Effects Underpinning Cognitive Developmental Delay of the PURA p.Phe233del Mutation Modelled by Artificial Intelligence and the Hybrid Quantum Mechanics-Molecular Mechanics Framework.

A whole-exome capture and next-generation sequencing was applied to an 11 y/o patient with a clinical history of congenital hypotonia, generalized motor and cognitive neurodevelopmental delay, and severe cognitive deficit, and without any identifiable Syndromic pattern, and to her parents, we disclosed a de novo heterozygous pathogenic mutation, c.697_699del p.Phe233del (rs786204835)(ACMG classification PS2, PM1, PM2, PP5), harbored in the PURA gene (MIM*600473) (5q31.3), associated with Autosomal Dominant Mental Retardation 31 (MIM # 616158). We used the significant improvement in the accuracy of protein structure prediction recently implemented in AlphaFold that incorporates novel neural network architectures and training procedures based on the evolutionary, physical, and geometric constraints of protein structures. The wild-type (WT) sequence and the mutated sequence, missing the Phe233, were reconstructed. The predicted local Distance Difference Test (lDDT) for the PURAwt and the PURA-Phe233del showed that the occurrence of the Phe233del affects between 220-320 amino acids. The distortion in the PURA structural conformation in the ~5 Å surrounding area after the p.Phe233del produces a conspicuous disruption of the repeat III, where the DNA and RNA helix unwinding capability occurs. PURA Protein-DNA docking corroborated these results in an in silico analysis that showed a loss of the contact of the PURA-Phe233del III repeat domain model with the DNA. Together, (i) the energetic and stereochemical, (ii) the hydropathic indexes and polarity surfaces, and (iii) the hybrid Quantum Mechanics-Molecular Mechanics (QM-MM) analyses of the PURA molecular models demarcate, at the atomic resolution, the specific surrounding region affected by these mutations and pave the way for future cell-based functional analysis. To the best of our knowledge, this is the first report of a de novo mutation underpinning a PURA syndrome in a Latin American patient and highlights the importance of predicting the molecular effects in protein structure using artificial intelligence algorithms and molecular and atomic resolution stereochemical analyses.

CNV analysis in Tourette syndrome implicates large genomic rearrangements in COL8A1 and NRXN1.

Tourette syndrome (TS) is a neuropsychiatric disorder with a strong genetic component. However, the genetic architecture of TS remains uncertain. Copy number variation (CNV) has been shown to contribute to the genetic make-up of several neurodevelopmental conditions, including schizophrenia and autism. Here we describe CNV calls using SNP chip genotype data from an initial sample of 210 TS cases and 285 controls ascertained in two Latin American populations. After extensive quality control, we found that cases (N = 179) have a significant excess (P = 0.006) of large CNV (>500 kb) calls compared to controls (N = 234). Amongst 24 large CNVs seen only in the cases, we observed four duplications of the COL8A1 gene region. We also found two cases with ∼400 kb deletions involving NRXN1, a gene previously implicated in neurodevelopmental disorders, including TS. Follow-up using multiplex ligation-dependent probe amplification (and including 53 more TS cases) validated the CNV calls and identified additional patients with rearrangements in COL8A1 and NRXN1, but none in controls. Examination of available parents indicates that two out of three NRXN1 deletions detected in the TS cases are de-novo mutations. Our results are consistent with the proposal that rare CNVs play a role in TS aetiology and suggest a possible role for rearrangements in the COL8A1 and NRXN1 gene regions.

Genetic make up and structure of Colombian populations by means of uniparental and biparental DNA markers.

Colombia is a country with great geographic heterogeneity and marked regional differences in pre-Columbian native population density and in the extent of past African and European immigration. As a result, Colombia has one of the most diverse populations in Latin America. Here we evaluated ancestry in over 1,700 individuals from 24 Colombian populations using biparental (autosomal and X-Chromosome), maternal (mtDNA), and paternal (Y-chromosome) markers. Autosomal ancestry varies markedly both within and between regions, confirming the great genetic diversity of the Colombian population. The X-chromosome, mtDNA, and Y-chromosome data indicate that there is a pattern across regions indicative of admixture involving predominantly Native American women and European and African men.

Association of DRD2 variants and Gilles de la Tourette syndrome in a family-based sample from a South American population isolate.

Gilles de la Tourette Syndrome (GTS) is a chronic neuropsychiatric disorder characterized by motor and vocal tics. Epidemiological evidence supports the importance of genetic factors in disease susceptibility, whereas pharmacological and neuroimaging studies have suggested a defect in the dopamine system. The dopamine receptor D2 gene (DRD2) has been reported to be associated with GTS and related phenotypes. Here, we evaluate genetic association between DRD2 and GTS in a sample from a South American population isolate (Antioquia, Colombia). We genotyped nine single nucleotide polymorphisms (SNPs) across the DRD2 gene region in 69 GTS patients and their nuclear families and carried out both SNP and haplotype-based transmission distortion analysis. Evidence for association was found for three SNPs (rs6279, rs1079597 and rs4648318) and a five marker-haplotype comprising both rs6279 and rs1079597. Our findings replicate the association of DRD2 and GTS, and are consistent with the proposed connection between the dopamine system and this complex neuropsychiatric disease.

En busqueda de los genes bipolares / Looking for the bipolar genes

Objetivos: Caracterizar una muestra de familias y tríos de una población colombiana aislada para mapear loci involucrados en la vulnerabilidad al Transtorno Bipolar tipo I (TAB-I). Se evaluaron endofenotipos clínicos, neuropsicológicos y moleculares, para acortar el camino entre la identificación de genes y sus expressiones fenotípicas, y luego se realizaron estudios de ligamiento. Métodos: Se recolectaron tríos y genealogías utilizando las entrevistas FIGS-DIGS en miembros de familias y sus posibles afectados. El poder para detectar ligamiento (PDL) se estimó por simulación. Como endofenotipos clínicos comparamos casos de TAB-I con agregación familiar y controles sin agregación. Realizamos una evaluación neuropsicológica comparativa en casos eutímicos y controles sanos. Evaluamos el polimorfismo de longitud del gen del promotor del receptor de serotonina (5HTTLP) y la asociación con el TAB-I. Luego estudiamos el desequilibrio promedio en tríos y familias tamizando los cromosomas 12, 18 y 21.Resultados:Se identificaron 28 familias co TAB-I, asumiendo homogencidad genetica y la evidencia de mestizaje recientemente hallada por nosotros, las simulaciones mostraron PDL significativo de 100 por cento para un LOD-score menor 3. En la población con TAB-I familiar se encontró peor funcionamiento intercrítico, mayor gravedad en episodios depresivos, disfunción neuropsicológica en eutímia y posible evidencia de ligamiento al cromosoma 21 q 22.3. Conclusión : Tenemos un grupo significativo de familias y tríos pertenecientes a una población aislada con un poder para detectar ligamiento al Trastorno Anímico Bipolar. Las características de esta población y los hallazgos actuales en ella sugieren gran probabilidad de encontrar rasgos de expresión clínica y neuropsicológica y genes de susceptibilidad al TAB-I. En el barrido genómico que llevamos a cabo actualmente pretendemos profundizar estos hallazgos.