DNA Repair Gene (XRCC1) Polymorphism (Arg399Gln) Associated with Schizophrenia in South Indian Population: A Genotypic and Molecular Dynamics Study

Patient iPSC-derived neural progenitor cells display aberrant cell cycle control, p53, and DNA damage response protein expression in schizophrenia

BACKGROUND

Schizophrenia (SCZ) is a severe psychiatric disorder associated with alterations in early brain development. Details of underlying pathomechanisms remain unclear, despite genome and transcriptome studies providing evidence for aberrant cellular phenotypes and pathway deregulation in developing neuronal cells. However, mechanistic insight at the protein level is limited.

METHODS

Here, we investigate SCZ-specific protein expression signatures of neuronal progenitor cells (NPC) derived from patient iPSC in comparison to healthy controls using high-throughput Western Blotting (DigiWest) in a targeted proteomics approach.

RESULTS

SCZ neural progenitors displayed altered expression and phosphorylation patterns related to Wnt and MAPK signaling, protein synthesis, cell cycle regulation and DNA damage response. Consistent with impaired cell cycle control, SCZ NPCs also showed accumulation in the G2/M cell phase and reduced differentiation capacity. Furthermore, we correlated these findings with elevated p53 expression and phosphorylation levels in SCZ patient-derived cells, indicating a potential implication of p53 in hampering cell cycle progression and efficient neurodevelopment in SCZ.

CONCLUSIONS

Through targeted proteomics we demonstrate that SCZ NPC display coherent mechanistic alterations in regulation of DNA damage response, cell cycle control and p53 expression. These findings highlight the suitability of iPSC-based approaches for modeling psychiatric disorders and contribute to a better understanding of the disease mechanisms underlying SCZ, particularly during early development.

Deficient DNA base-excision repair in the forebrain leads to a sex-specific anxiety-like phenotype in mice

Background

Neuropsychiatric disorders, such as schizophrenia (SZ) and autism spectrum disorder (ASD), are common, multi-factorial and multi-symptomatic disorders. Ample evidence implicates oxidative stress, deficient repair of oxidative DNA lesions and DNA damage in the development of these disorders. However, it remains unclear whether insufficient DNA repair and resulting DNA damage are causally connected to their aetiopathology, or if increased levels of DNA damage observed in patient tissues merely accumulate as a consequence of cellular dysfunction. To assess a potential causal role for deficient DNA repair in the development of these disorders, we behaviourally characterized a mouse model in which CaMKIIa-Cre-driven postnatal conditional knockout (KO) of the core base-excision repair (BER) protein XRCC1 leads to accumulation of unrepaired DNA damage in the forebrain.

Results

CaMKIIa-Cre expression caused specific deletion of XRCC1 in the dorsal dentate gyrus (DG), CA1 and CA2 and the amygdala and led to increased DNA damage therein. While motor coordination, cognition and social behaviour remained unchanged, XRCC1 KO in the forebrain caused increased anxiety-like behaviour in males, but not females, as assessed by the light–dark box and open field tests. Conversely, in females but not males, XRCC1 KO caused an increase in learned fear-related behaviour in a cued (Pavlovian) fear conditioning test and a contextual fear extinction test. The relative density of the GABA(A) receptor alpha 5 subunit (GABRA5) was reduced in the amygdala and the dorsal CA1 in XRCC1 KO females, whereas male XRCC1 KO animals exhibited a significant reduction of GABRA5 density in the CA3. Finally, assessment of fast-spiking, parvalbumin-positive (PV) GABAergic interneurons revealed a significant increase in the density of PV+ cells in the DG of male XRCC1 KO mice, while females remained unchanged.

Conclusions

Our results suggest that accumulation of unrepaired DNA damage in the forebrain alters the GABAergic neurotransmitter system and causes behavioural deficits in relation to innate and learned anxiety in a sex-dependent manner. Moreover, the data uncover a previously unappreciated connection between BER deficiency, unrepaired DNA damage in the hippocampus and a sex-specific anxiety-like phenotype with implications for the aetiology and therapy of neuropsychiatric disorders.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01377-1.

The independent and combined effects of selected risk factors and Arg399Gln XRCC1 polymorphism in the risk of colorectal cancer among an Iranian population

Background: Several environmental and genetic factors have contributed to the development of colorectal cancer (CRC). We aimed to investigate the independent and combined effects of some selected risk factors and Arg399Gln XRCC1 polymorphism on CRC.

Methods: A total of 180 patients with CRC and 160 healthy individuals who were matched for sex, age, and place of residence (Northeast of Iran) participated in this case-control study. Before collecting blood samples and filling out questionnaires, a written consent form was obtained from all participants. Genotypes were determined by RFLP-PCR. The comparison of genotype and allele frequencies was performed using p value based on the results of chi-square test. The odds ratios (OR) and 95% confidence intervals (CI) were calculated by employing a logistic regression model. All statistical calculations were performed using SPSS. Each of the 2- sided p values less than 0.05 were considered statistically significant.

Results: The level of literacy, physical activity, consumption of vegetables and fruits, and tea intake of the patients were significantly lower than healthy individuals, but gastrointestinal disorders, family history of cancer, BMI, and fast food consumption were significantly higher in cases than in controls. No significant difference was observed between the 2 groups regarding smoking, opioid addiction, alcohol consumption, diet, fish consumption, and liquid intake, using the kitchen hood, diabetes, and cardiovascular disease. Arg/Gln + Gln/Gln and Arg/Gln genotypes were involved in increased CRC risk (The crude OR =1.781 with a 95% CI of 1.156-2.744 and OR = 1.690 with a 95% CI of 0.787-3.630). Also, Gln/Gln genotype was more frequent in CRC group than in control group. However, none of the risk factors interacted with polymorphism, and thus did not have an effect on CRC.

Conclusion: Some risk factors, such as reducing the consumption of vegetables and fruits or reducing physical activity as well as polymorphism of the XRCC1 Arg399Gln alone, increase the risk of CRC, but they do not interact with each other.

Prioritization of SNPs in y+LAT-1 culpable of Lysinuric protein intolerance and their mutational impacts using protein-protein docking and molecular dynamics simulation studies

Lysinuric protein intolerance (LPI) is a rare, yet inimical, genetic disorder characterized by the paucity of essential dibasic amino acids in the cells. Amino acid transporter y+LAT-1 interacts with 4F2 cell-surface antigen heavy chain to transport the required dibasic amino acids. Mutation in y+LAT-1 is rumored to cause LPI. However, the underlying pathological mechanism is unknown, and, in this analysis, we investigate the impact of point mutation in y+LAT-1's interaction with 4F2 cell-surface antigen heavy chain in causing LPI. Using an efficient and extensive computational pipeline, we have isolated M50K and L334R single-nucleotide polymorphisms to be the most deleterious mutations in y+LAT-1s. Docking of mutant y+LAT-1 with 4F2 cell-surface antigen heavy chain showed decreased interaction compared with native y+LAT-1. Further, molecular dynamic simulation analysis reveals that the protein molecules increase in size, become more flexible, and alter their secondary structure upon mutation. We believe that these conformational changes because of mutation could be the reason for decreased interaction with 4F2 cell-surface antigen heavy chain causing LPI. Our analysis gives pathological insights about LPI and helps researchers to better understand the disease mechanism and develop an effective treatment strategy.

Computational modelling approaches as a potential platform to understand the molecular genetics association between Parkinson's and Gaucher diseases

Gaucher's disease (GD) is a genetic disorder in which glucocerebroside accumulates in cells and specific organs. It is broadly classified into type I, type II and type III. Patients with GD are at high risk of Parkinson's disease (PD), and the clinical and pathological presentation of GD patients with PD is almost identical to idiopathic PD. Several experimental models like cell culture, animal models, and transgenic mice models were used to understand the molecular mechanism behind GD and PD association; however, such mechanism remains unclear. In this context, based on literature reports, we identified the most common mutations K198T, E326K, T369M, N370S, V394L, D409H, L444P, and R496H, in the Glucosylceramidase (GBA) protein that are known to cause GD1, and represent a risk of developing PD. However, to date, no computational analyses have designed to elucidate the potential functional role of GD mutations with increased risk of PD. The present computational pipeline allows us to understand the structural and functional significance of these GBA mutations with PD. Based on the published data, the most common and severe mutations were E326K, N370S, and L444P, which further selected for our computational analysis. PredictSNP and iStable servers predicted L444P mutant to be the most deleterious and responsible for the protein destabilization, followed by the N370S mutation. Further, we used the structural analysis and molecular dynamics approach to compare the most frequent deleterious mutations (N370S and L444P) with the mild mutation E326K. The structural analysis demonstrated that the location of E326K and N370S in the alpha helix region of the protein whereas the mutant L444P was in the starting region of the beta sheet, which might explain the predicted pathogenicity level and destabilization effect of the L444P mutant. Finally, Molecular Dynamics (MD) at 50 ns showed the highest deviation and fluctuation pattern in the L444P mutant compared to the two mutants E326K and N370S and the native protein. This was consistent with more loss of intramolecular hydrogen bonds and less compaction of the radius of gyration in the L444P mutant. The proposed study is anticipated to serve as a potential platform to understand the mechanism of the association between GD and PD, and might facilitate the process of drug discovery against both GD and PD.

Computational approach to unravel the impact of missense mutations of proteins (D2HGDH and IDH2) causing D-2-hydroxyglutaric aciduria 2

The 2-hydroxyglutaric aciduria (2-HGA) is a rare neurometabolic disorder that leads to the development of brain damage. It is classified into three categories: D-2-HGA, L-2-HGA, and combined D,L-2-HGA. The D-2-HGA includes two subtypes: type I and type II caused by the mutations in D2HGDH and IDH2 proteins, respectively. In this study, we studied six mutations, four in the D2HGDH (I147S, D375Y, N439D, and V444A) and two in the IDH2 proteins (R140G, R140Q). We performed in silico analysis to investigate the pathogenicity and stability changes of the mutant proteins using pathogenicity (PANTHER, PhD-SNP, SIFT, SNAP, and META-SNP) and stability (i-Mutant, MUpro, and iStable) predictors. All the mutations of both D2HGDH and IDH2 proteins were predicted as disease causing except V444A, which was predicted as neutral by SIFT. All the mutants were also predicted to be destabilizing the protein except the mutants D375Y and N439D. DSSP plugin of the PyMOL and Molecular Dynamics Simulations (MDS) were used to study the structural changes in the mutant proteins. In the case of D2HGDH protein, the mutations I147S and V444A that are positioned in the beta sheet region exhibited higher Root Mean Square Deviation (RMSD), decrease in compactness and number of intramolecular hydrogen bonds compared to the mutations N439D and D375Y that are positioned in the turn and loop region, respectively. While the mutants R140Q and R140QG that are positioned in the alpha helix region of the protein. MDS results revealed the mutation R140Q to be more destabilizing (higher RMSD values, decrease in compactness and number of intramolecular hydrogen bonds) compared to the mutation R140G of the IDH2 protein. This study is expected to serve as a platform for drug development against 2-HGA and pave the way for more accurate variant assessment and classification for patients with genetic diseases.

Comparative computational assessment of the pathogenicity of mutations in the Aspartoacylase enzyme

Aspartoacylase (ASPA) is a zinc-dependent abundant enzyme in the brain, which catalyzes the conversion of N-acetyl aspartate (NAA) into acetate and aspartate. Mutations in the ASPA gene are associated with the development of Canavan disease (CD), leading to the deficiency of ASPA activity. Patients with CD were characterized by degeneration of the white matter of the brain. We reported earlier on two patients with severe form of CD that both had two novel missense mutations in the ASPA: c.427 A > G; p. I143V and c.557 T > A; p. V186D (Zaki et al. 2017a), patient 1 harbored both mutations (p.I143V and p.V186D) in a heterozygous form together with four other mutations, and patient 2 had both mutations in homozygous form. Wijayasinghe et al. (2014) crystallized the 3D structures of four different ASPA mutants (p.K213E, p.Y231C, p.E285A, and p.F295S). In this study, we used in silico prediction methods and molecular dynamics simulation (MDS) to understand the structural impact of all these mutations. Moreover, we used molecular docking (MD) to investigate the binding patterns of the NAA substrate to the native and mutant proteins. Among the mutations, p.E285A (crystallized mutant) was predicted to be the most deleterious for the protein function and the least deleteriousness mutant was the p.I143V (novel mutant). Among the novel mutations, p.V186D was observed to be disruptive for both the zinc binding and NAA binding than the p.I143V. This study provides practical insights on the effect of these mutations on the ASPA function and might serve as a platform for drug design for CD treatment.

Attempts to replicate genetic associations with schizophrenia in a cohort from north India

Schizophrenia is a chronic, severe, heritable disorder. Genome-wide association studies, conducted predominantly among Caucasians, have indicated > 100 risk alleles, with most significant SNPs on chromosome 6. There is growing interest as to whether these risk alleles are relevant in other ethnic groups as well. Neither an Indian genome-wide association studies nor a systematic replication of GWAS findings from other populations are reported. Thus, we analyzed 32 SNPs, including those associated in the Caucasian ancestry GWAS and other candidate gene studies, in a north Indian schizophrenia cohort (n = 1009 patients; n = 1029 controls) using a Sequenom mass array. Cognitive functioning was also assessed using the Hindi version of the Penn Computerized Neuropsychological Battery in a subset of the sample. MICB (rs6916394) a previously noted Caucasian candidate, was associated with schizophrenia at the p = 0.02 level. One SNP, rs2064430, AHI1 (6q23.3, SZ Gene database SNP) was associated at the p = 0.04 level. Other candidates had even less significance with rs6932590, intergenic (p = 0.07); rs3130615, MICB (p = 0.08); rs6916921, NFKBIL1 (p = 0.08) and rs9273012, HLA-DQA1 (p = 0.06) and haplotypic associations (p = 0.01-0.05) of 6p SNPs were detected. Of note, nominally significant associations with cognitive variables were identified, after covarying for age and diagnostic status. SNPs with p < 0.01 were: rs3130375, with working memory (p = 0.007); rs377763, with sensorimotor (p = 0.004); rs6916921, NFKBIL1 with emotion (p = 0.01). This relative lack of significant positive associations is likely influenced by the sample size and/or differences in the genetic architecture of schizophrenia across populations, encouraging population specific studies to identify shared and unique genetic risk factors for schizophrenia.

POPULATION GENETICS

CAUCASIANS AND INDIANS EXHIBIT GENETIC DISJUNCTION IN SCHIZOPHRENIA: A tenuous link between schizophrenia's genetic basis in Caucasians and Indians calls for more comprehensive research on the latter. Large-scale analyses of the human genome have identified over a hundred genetic variations associated with schizophrenia; however, these have focused largely on European and North American populations. Researchers led by the University of Delhi's BK Thelma, and Smita Deshpande of the Dr. Ram Manohar Lohia Hospital, India, selected 32 gene variations from past studies to look for similar associations in Indians. Many assays met limited success, though the team found significant correlations between certain variations and specific cognitive hallmarks of schizophrenia. Aside from differences in genetic architecture, the lack of adequate and comparable genetic data on schizophrenia in Indians may contribute to this apparent difference to schizophrenia in Caucasian patients. This shows a clear need for more schizophrenia genetic studies in India.

An Integrated Computational Framework to Assess the Mutational Landscape of α-L-Iduronidase IDUA Gene

Mucopolysaccharidosis type I is a lysosomal genetic disorder caused due to the deficiency of the α-L-iduronidase enzyme (IDUA). Mutations associated with IDUA lead to mild to severe forms of diseases characterized by different clinical features. In the present study, we first performed a comprehensive analysis using various in silico prediction tools to screen and prioritize the missense mutations or nonsynonymous SNPs (nsSNPs) associated with IDUA. Subsequently, statistical analysis was empowered to examine the predictive ability and accuracy of the in silico prediction tool results supporting the disease phenotype ranging from mild to severe. Till date, no study has been carried out in IDUA in analyzing the impact of the nsSNPs at the structural level. In this context with the aid of pathogenic and stability prediction in silico tools, we identified nsSNPs R89Q, R89W, and P533R to be most deleterious and disease-causing having impact on the function of the protein. Extensive molecular dynamics analysis was performed using Gromacs to understand the deleterious nature of the mutants. Variations observed between the trajectory files of native and mutants R89Q, R89W, and P533R using Gromacs utilities enabled us to measure the adverse effects on the protein and could be the underlying reasons for the disease pathogenesis. These findings may be helpful in understanding the genotype-phenotype relationship and molecular basis of the disease to design drugs for better treatment. J. Cell. Biochem. 119: 555-565, 2018. © 2017 Wiley Periodicals, Inc.

Chronic oxidative damage together with genome repair deficiency in the neurons is a double whammy for neurodegeneration: Is damage response signaling a potential therapeutic target?

A foremost challenge for the neurons, which are among the most oxygenated cells, is the genome damage caused by chronic exposure to endogenous reactive oxygen species (ROS), formed as cellular respiratory byproducts. Strong metabolic activity associated with high transcriptional levels in these long lived post-mitotic cells render them vulnerable to oxidative genome damage, including DNA strand breaks and mutagenic base lesions. There is growing evidence for the accumulation of unrepaired DNA lesions in the central nervous system (CNS) during accelerated aging and progressive neurodegeneration. Several germ line mutations in DNA repair or DNA damage response (DDR) signaling genes are uniquely manifested in the phenotype of neuronal dysfunction and are etiologically linked to many neurodegenerative disorders. Studies in our lab and elsewhere revealed that pro-oxidant metals, ROS and misfolded amyloidogenic proteins not only contribute to genome damage in CNS, but also impede their repair/DDR signaling leading to persistent damage accumulation, a common feature in sporadic neurodegeneration. Here, we have reviewed recent advances in our understanding of the etiological implications of DNA damage vs. repair imbalance, abnormal DDR signaling in triggering neurodegeneration and potential of DDR as a target for the amelioration of neurodegenerative diseases.