Muhammad Ayub

The genetic basis of non-syndromic intellectual disability: a review

Intellectual disability (ID), also referred to as mental retardation (MR), is frequently the result of genetic mutation. Where ID is present together with additional clinical symptoms or physical anomalies, there is often sufficient information available for the diagnosing physician to identify a known syndrome, which may then educe the identification of the causative defect. However, where co-morbid features are absent, narrowing down a specific gene can only be done by ‘brute force’ using the latest molecular genetic techniques. Here we attempt to provide a systematic review of genetic causes of cases of ID where no other symptoms or co-morbid features are present, or non-syndromic ID. We attempt to summarize commonalities between the genes and the molecular pathways of their encoded proteins. Since ID is a common feature of autism, and conversely autistic features are frequently present in individuals with ID, we also look at possible overlaps in genetic etiology with non-syndromic ID.

Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders

By analyzing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls and 1,077 trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants in SETD1A and risk for schizophrenia (P = 3.3 × 10−9). We found only two heterozygous LoF variants in 45,376 exomes from individuals without a neuropsychiatric diagnosis, indicating that SETD1A is substantially depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carrying SETD1A LoF variants also had learning difficulties. We further identified four SETD1A LoF carriers among 4,281 children with severe developmental disorders and two more carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations indicate that LoF variants in SETD1A cause a range of neurodevelopmental disorders, including schizophrenia. Combining these data with previous common variant evidence, we suggest that epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, is an important mechanism in the pathogenesis of schizophrenia.

Mutation in NSUN2, which Encodes an RNA Methyltransferase, Causes Autosomal-Recessive Intellectual Disability

Causes of autosomal-recessive intellectual disability (ID) have, until very recently, been under researched because of the high degree of genetic heterogeneity. However, now that genome-wide approaches can be applied to single multiplex consanguineous families, the identification of genes harboring disease-causing mutations by autozygosity mapping is expanding rapidly. Here, we have mapped a disease locus in a consanguineous Pakistani family affected by ID and distal myopathy. We genotyped family members on genome-wide SNP microarrays and used the data to determine a single 2.5 Mb homozygosity-by-descent (HBD) locus in region 5p15.32-p15.31; we identified the missense change c.2035G>A (p.Gly679Arg) at a conserved residue within NSUN2. This gene encodes a methyltransferase that catalyzes formation of 5-methylcytosine at C34 of tRNA-leu(CAA) and plays a role in spindle assembly during mitosis as well as chromosome segregation. In mouse brains, we show that NSUN2 localizes to the nucleolus of Purkinje cells in the cerebellum. The effects of the mutation were confirmed by the transfection of wild-type and mutant constructs into cells and subsequent immunohistochemistry. We show that mutation to arginine at this residue causes NSUN2 to fail to localize within the nucleolus. The ID combined with a unique profile of comorbid features presented here makes this an important genetic discovery, and the involvement of NSUN2 highlights the role of RNA methyltransferase in human neurocognitive development.

CC2D2A, Encoding A Coiled-Coil and C2 Domain Protein, Causes Autosomal-Recessive Mental Retardation with Retinitis Pigmentosa

Autosomal-recessive inheritance is believed to be relatively common in mental retardation (MR), although only four genes for nonsyndromic autosomal-recessive mental retardation (ARMR) have been reported. In this study, we ascertained a consanguineous Pakistani family with ARMR in four living individuals from three branches of the family, plus an additional affected individual later identified as a phenocopy. Retinitis pigmentosa was present in affected individuals, but no other features suggestive of a syndromic form of MR were found. We used Affymetrix 500K microarrays to perform homozygosity mapping and identified a homozygous and haploidentical region of 11.2 Mb on chromosome 4p15.33-p15.2. Linkage analysis across this region produced a maximum two-point LOD score of 3.59. We sequenced genes within the critical region and identified a homozygous splice-site mutation segregating in the family, within a coiled-coil and C2 domain-containing gene, CC2D2A. This mutation leads to the skipping of exon 19, resulting in a frameshift and a truncated protein lacking the C2 domain. Conservation analysis for CC2D2A suggests a functional domain near the C terminus as well as the C2 domain. Preliminary functional studies of CC2D2A suggest a possible role in Ca(2+)-dependent signal transduction. Identifying the function of CC2D2A, and a possible common pathway with CC2D1A, in correct neuronal development and functioning may help identify possible therapeutic targets for MR.

Oligodontia Is Caused by Mutation in LTBP3, the Gene Encoding Latent TGF-β Binding Protein 3

We have identified a consanguineous Pakistani family where oligodontia is inherited along with short stature in an autosomal-recessive fashion. Increased bone density was present in the spine and at the base of the skull. Using high-density single-nucleotide polymorphism microarrays for homozygosity mapping, we identified a 28 Mb homozygous stretch shared between affected individuals on chromosome 11q13. Screening selected candidate genes within this region, we identified a homozygous nonsense mutation, Y774X, within LTBP3, the gene for the latent TGF-beta binding protein 3, an extracellular matrix protein believed to be required for osteoclast function.

Mutations in the Alpha 1,2-Mannosidase Gene, MAN1B1, Cause Autosomal-Recessive Intellectual Disability

We have used genome-wide genotyping to identify an overlapping homozygosity-by-descent locus on chromosome 9q34.3 (MRT15) in four consanguineous families affected by nonsyndromic autosomal-recessive intellectual disability (NS-ARID) and one in which the patients show additional clinical features. Four of the families are from Pakistan, and one is from Iran. Using a combination of next-generation sequencing and Sanger sequencing, we have identified mutations in the gene MAN1B1, encoding a mannosyl oligosaccharide, alpha 1,2-mannosidase. In one Pakistani family, MR43, a homozygous nonsense mutation (RefSeq number NM_016219.3: c.1418G>A [p.Trp473*]), segregated with intellectual disability and additional dysmorphic features. We also identified the missense mutation c. 1189G>A (p.Glu397Lys; RefSeq number NM_016219.3), which segregates with NS-ARID in three families who come from the same village and probably have shared inheritance. In the Iranian family, the missense mutation c.1000C>T (p.Arg334Cys; RefSeq number NM_016219.3) also segregates with NS-ARID. Both missense mutations are at amino acid residues that are conserved across the animal kingdom, and they either reduce k(cat) by ∼1300-fold or disrupt stable protein expression in mammalian cells. MAN1B1 is one of the few NS-ARID genes with an elevated mutation frequency in patients with NS-ARID from different populations.

Prevalence and psychosocial risk factors of PTSD: 18 months after Kashmir earthquake in Pakistan

BACKGROUND On average in a year 939 earthquakes of a magnitude between 5 and 8 on the Richter scale occur around the world. In earthquakes developing countries are prone to large-scale destruction because of poor structural quality of buildings, and preparedness for earthquakes. On 8th October 2005, a major earthquake hit the remote and mountainous region of northern Pakistan and Kashmir. We wanted to find out the rate of PTSD in a randomly selected sample of participants living in earthquake area and the correlates of the PTSD. METHOD The study was conducted 18 months after the earthquake. We selected a sample of men and women living in the houses and tents for interviews. Using well established instruments for PTSD and general psychiatric morbidity we gathered information from over 1200 people in face to face interviews. We gathered information about trauma exposure and loss as well. RESULTS 55.2% women and 33.4% men suffered from PTSD. Living in a joint family was protective against the symptoms of PTSD. Dose of exposure to trauma was associated with the symptoms of PTSD. Living in a tent was associated with general psychiatric morbidity but not with PTSD. LIMITATIONS We used questionnaire instead of interviews to detect the symptoms of psychiatric disorders. CONCLUSIONS The symptoms of PTSD are common 18 months after the earthquake and they are specifically associated with the dose of trauma exposure. This may have implications for rehabilitation of this population.

Preliminary evaluation of culturally sensitive CBT for depression in Pakistan: findings from Developing Culturally-sensitive CBT Project (DCCP).

BACKGROUND There is sufficient research evidence in favour of cognitive therapy in western world. However, only limited research has been carried out on its effectiveness in other countries. It is suggested that adaptations in content, format and delivery are needed before CBT can be employed in non-western cultures. We describe a preliminary evaluation of culturally adapted CBT for depression in Pakistan. AIMS We aimed to evaluate the efficacy of this culturally adapted CBT using a therapist manual. METHOD In a randomized controlled trial we compared combination of CBT and antidepressants with antidepressants alone (treatment as usual) in primary care. Referred patients with ICD-10 diagnosis of depression were invited to participate and randomized to the intervention and control groups. Hospital Anxiety and Depression Scale (HADS) and Bradford Somatic Inventory (BSI) were used to measure changes in depression, anxiety and somatic symptoms. RESULTS Seventeen patients each were randomized to each arms of the trial. Except for financial status there were no differences between the two groups on various demographic variables. Patients receiving CBT showed statistically significant improvement on measures of depression (p < .001), anxiety (p < .001) and somatic symptoms (p < .000) as compared to antidepressant alone group. 82% patients attended six or more sessions of therapy. CONCLUSIONS A culturally sensitive manualized CBT was effective in reducing symptoms of depression and anxiety in Pakistan.

Angry Wives, Abusive Husbands: Relationship Between Domestic Violence and Psychosocial Variables

BACKGROUND A small number of studies conducted in Pakistan have shown high rates of domestic violence. None of the studies, however, discussed associated psychosocial factors. We interviewed a group of women to look at violence and associated psychosocial factors. We wanted to see if self-esteem, quality of relationships, social support, stressful life events, psychiatric symptoms, and different measures of anger were associated with domestic violence. METHODOLOGY In a cross-sectional survey of women presenting to primary care physicians, we used Womens Experience with Battering and Domestic Abuse Checklist to measure domestic violence. The Relationship Assessment Scale, Oslo Social Support Scale, State Trait Anger Inventory, and Evaluative Belief Scale were used to look at the correlates of violence. We used the information in a regression model to identify independent predictors of violence in this sample. RESULTS More than half of the women reported experiencing battering and/or violence. Women in abusive relationships reported unhappiness with their intimate relationships and had high scores on 1 subscale of anger. Living in extended families was protective against violence. CONCLUSIONS We were able to replicate findings that women in abusive relationships are not satisfied with the relationships with their partners. Living in extended families was protective against violence. Community studies may provide a better design to look at the association between abuse and poverty, literacy, self-esteem, and social support.

Brief culturally adapted CBT for psychosis (CaCBTp): A randomized controlled trial from a low income country

Evidence for the effectiveness of Culturally adapted CBT for psychosis in Low And Middle Income Countries (LAMIC) is limited. Therefore, brief Culturally adapted CBT for psychosis (CaCBTp) targeted at symptoms of schizophrenia for outpatients plus treatment as usual (TAU) is compared with TAU. A total of 116 participants with schizophrenia were recruited from 2 hospitals in Karachi, Pakistan, and randomized into two groups with 1:1 allocation (CaCBTp plus TAU=59, TAU=57). A brief version of CaCBTp (6 individual sessions with the involvement of main carer, plus one session for the family) was provided over 4months. Psychopathology was measured using Positive and Negative Syndrome Scale of Schizophrenia (PANSS), Psychotic Symptom Rating Scales (PSYRATS), and the Schedule for Assessment of Insight (SAI) at baseline and end of therapy. Participants in treatment group, showed statistically significant improvement in all measures of psychopathology at the end of the study compared with control group. Participants in treatment group showed statistically significant improvement in Positive Symptoms (PANSS, Positive Symptoms Subscale; p=0.000), Negative Symptoms (PANSS, Negative Symptoms subscales; p=0.000), Delusions (PSYRATS, Delusions Subscale; p=0.000), Hallucinations (PSYRATS, Hallucination Subscale; p=0.000) and Insight (SAI; p=0.007). The results suggest that brief, Culturally adapted CBT for psychosis can be an effective treatment when provided in combination with TAU, for patients with schizophrenia in a LAMIC setting. This is the first trial of CBT for psychosis from outside the western world. These findings need replicating in other low and middle income countries.