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A case report: Autosomal recessive microcephaly caused by a novel mutation in MCPH1 gene
Gene 571 (2015) 149–150
Contents lists available at ScienceDirect
Gene journal homepage: www.elsevier.com/locate/gene
Letter to the Editor A case report: Autosomal recessive microcephaly caused by a novel mutation in MCPH1 gene☆ Keywords: Microcephaly Sex-influenced MCPH1 New mutation
Autosomal Recessive Primary Microcephaly (MCPH-MIM 251200) is distinguished by congenital decrease in occipito-frontal head circumference (OFC) of at least 2 standard deviations (SD) below the population average in addition to non-progressive mental retardation, without any prominent neurological disorder. Until now, genetic studies of such patients in different populations have revealed mutations in 12 genes (MCPH1, WDR62, CDK5RAP2, CASC5, ASPM, CENPJ, STIL, CEP135, CEP152, ZNF335, PHC1 and CDK6) in these patients (Faheem et al., 2015). MCPH1 encodes the protein microcephalin, also called as BRIT1 for BRCT-Repeat Inhibitor of hTert expression. The phenotypes associated with its loss of function mutations include microcephaly with simplified gyral pattern and premature chromosome condensation with microcephaly and mental retardation (Kaindl et al., 2010).
Here we report a consanguineous Iranian family with 2 children both affected with microcephaly. The first one was an 18-year old female with normal intelligence and no delay in motor milestones or speech, but an OFC of 47 cm which was 5 SD below the population age- and sex-related mean. The second child was a 15-year old boy with severe mental retardation and an OFC of 37 cm which was 12 SD below the population mean. Both were delivered spontaneously after unremarkable pregnancies. Their birth OFCs were 31 cm and 29 cm respectively. Cytogenetic analysis of the male patient showed numerically normal male karyotype without significant increase in the fraction of prophase stage chromosomes. The brain magnetic resonance imaging (MRI) of the male patient was normal, except for a small brain size. The heights of female and male patients were 156 cm and 144 cm respectively. Genomic DNA was extracted from blood samples of the patients after informed consent using the standard salting out method. Whole exome sequencing was performed using Illumina's Genome Analyzer for the male patient with focus on 2752 OMIM disease genes, including 33 genes related with microcephaly (BGI-Clinical Laboratories, Shenzhen, China). A homozygous mutation was detected in intron 4 of MCPH1 gene (c.322-2 ANT) which has not been reported in generalist polymorphism databases (ExaC or exome variant server (EVS)). The results were confirmed by Sanger sequencing in both patients and targeted sequencing on the parents showed that they were both heterozygous for the detected mutation. In order to assess the consequence of this novel
Fig. 1. The homozygous mutation detected in the MCPH1 gene in the patients results in a 15-nucleotide deletion in exon 5 (the cDNA sequencing result by Sanger method is shown).
☆ No conflicts of interests exist.No financial support was utilized in this research.
http://dx.doi.org/10.1016/j.gene.2015.07.058 0378-1119/© 2015 Elsevier B.V. All rights reserved.
150
Letter to the Editor
splice-acceptor site mutation, the full-length MCPH1-cDNA was synthesized from RNAs prepared from lymphocytes and then amplified by PCR. A fragment of amplified cDNA in the region of exons 4–5 were sequenced using the ABI Prism3130 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). This novel splice-acceptor site mutation has been shown to result in an RNA processing defect with a 15nucleotide deletion in exon 5 of the mRNA transcript (r.322_336del15, p.R108_Q112del5) (Fig. 1). Here, we detected a homozygous intronic mutation in MCPH1 gene in a male patient with microcephaly and severe mental retardation in addition to his sister who had microcephaly but normal intelligence. MCPH1 has been the first gene whose mutations were detected in MCPH (Kaindl et al., 2010). Few intronic mutations have been reported in MCPH1 gene (Darvish et al., 2010). Although sex related difference in clinical phenotype of MCPH1 mutations has not been previously reported, some missense alterations in this gene have been shown to cause mild cellular and clinical phenotype (Trimborn et al., 2005). In addition, polymorphisms in this gene have been suggested as possible mechanisms which elucidate the brain volume variation detected in existing human populations. Notably, a gender dependent association has been detected between cranial volume and a polymorphism in this gene which implies that the expression of genetic variations for brain development is different between two sexes (Wang et al., 2008). This difference has been detected even in the early stages of brain development and is thought to be regulated mainly by expression of genes encoded by sex chromosomes. Furthermore, the role of autosome-encoded genes in sexually dimorphic brain development is being elucidated (Weickert et al., 2009). For instance, a sex-limited effect on the penetrance of the pathological neurodevelopmental phenotypes at the 16p13.11 locus has been identified. In addition, a male biased sex ratio has been seen in numerous neurodevelopmental disorders which may be attributed to several factors such as sex-specific variations in gene regulation or sexually dimorphic epigenetic mechanisms (Tropeano et al., 2013). Recently, such differences in methylome and transcriptome have been shown in human prefrontal cortex. Sex-biased DNA methylation and gene expression could be either the cause or outcome of differential brain development between two sexes (Xu et al., 2014). We hypothesize that such mechanisms may partially explain the difference in phenotypes observed in the 2 cases, probably in addition to other mechanisms such as modifier genes.
References Darvish, H., Esmaeeli-Nieh, S., Monajemi, G.B., et al., 2010. A clinical and molecular genetic study of 112 Iranian families with primary microcephaly. J. Med. Genet. 47 (12), 823–828. Faheem, M., Naseer, M.I., Rasool, M., et al., 2015. Molecular genetics of human primary microcephaly: an overview. BMC Med. Genomics 8 (Suppl. 1), S4. Kaindl, A.M., Passemard, S., Kumar, P., et al., 2010. Many roads lead to primary autosomal recessive microcephaly. Prog. Neurobiol. 90 (3), 363–383. Trimborn, M., Richter, R., Sternberg, N., et al., 2005. The first missense alteration in the MCPH1 gene causes autosomal recessive microcephaly with an extremely mild cellular and clinical phenotype. Hum. Mutat. 26 (5), 496. Tropeano, M., Ahn, J.W., Dobson, R.J., et al., 2013. Male-biased autosomal effect of 16p13.11 copy number variation in neurodevelopmental disorders. PLoS One 8 (4), e61365. Wang, J.K., Li, Y., Su, B., 2008. A common SNP of MCPH1 is associated with cranial volume variation in Chinese population. Hum. Mol. Genet. 17 (9), 1329–1335. Weickert, C.S., Elashoff, M., Richards, A.B., et al., 2009. Transcriptome analysis of male–female differences in prefrontal cortical development. Mol. Psychiatry 14 (6), 558–561. Xu, H., Wang, F., Liu, Y., Yu, Y., Gelernter, J., Zhang, H., 2014. Sex-biased methylome and transcriptome in human prefrontal cortex. Hum. Mol. Genet. 23 (5), 1260–1270.
Soudeh Ghafouri-Fard Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran Majid Fardaei Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran Milad Gholami Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran Mohammad Miryounesi Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran Corresponding author. E-mail address: [email protected]. 15 March 2015
Contents lists available at ScienceDirect
Gene journal homepage: www.elsevier.com/locate/gene
Letter to the Editor A case report: Autosomal recessive microcephaly caused by a novel mutation in MCPH1 gene☆ Keywords: Microcephaly Sex-influenced MCPH1 New mutation
Autosomal Recessive Primary Microcephaly (MCPH-MIM 251200) is distinguished by congenital decrease in occipito-frontal head circumference (OFC) of at least 2 standard deviations (SD) below the population average in addition to non-progressive mental retardation, without any prominent neurological disorder. Until now, genetic studies of such patients in different populations have revealed mutations in 12 genes (MCPH1, WDR62, CDK5RAP2, CASC5, ASPM, CENPJ, STIL, CEP135, CEP152, ZNF335, PHC1 and CDK6) in these patients (Faheem et al., 2015). MCPH1 encodes the protein microcephalin, also called as BRIT1 for BRCT-Repeat Inhibitor of hTert expression. The phenotypes associated with its loss of function mutations include microcephaly with simplified gyral pattern and premature chromosome condensation with microcephaly and mental retardation (Kaindl et al., 2010).
Here we report a consanguineous Iranian family with 2 children both affected with microcephaly. The first one was an 18-year old female with normal intelligence and no delay in motor milestones or speech, but an OFC of 47 cm which was 5 SD below the population age- and sex-related mean. The second child was a 15-year old boy with severe mental retardation and an OFC of 37 cm which was 12 SD below the population mean. Both were delivered spontaneously after unremarkable pregnancies. Their birth OFCs were 31 cm and 29 cm respectively. Cytogenetic analysis of the male patient showed numerically normal male karyotype without significant increase in the fraction of prophase stage chromosomes. The brain magnetic resonance imaging (MRI) of the male patient was normal, except for a small brain size. The heights of female and male patients were 156 cm and 144 cm respectively. Genomic DNA was extracted from blood samples of the patients after informed consent using the standard salting out method. Whole exome sequencing was performed using Illumina's Genome Analyzer for the male patient with focus on 2752 OMIM disease genes, including 33 genes related with microcephaly (BGI-Clinical Laboratories, Shenzhen, China). A homozygous mutation was detected in intron 4 of MCPH1 gene (c.322-2 ANT) which has not been reported in generalist polymorphism databases (ExaC or exome variant server (EVS)). The results were confirmed by Sanger sequencing in both patients and targeted sequencing on the parents showed that they were both heterozygous for the detected mutation. In order to assess the consequence of this novel
Fig. 1. The homozygous mutation detected in the MCPH1 gene in the patients results in a 15-nucleotide deletion in exon 5 (the cDNA sequencing result by Sanger method is shown).
☆ No conflicts of interests exist.No financial support was utilized in this research.
http://dx.doi.org/10.1016/j.gene.2015.07.058 0378-1119/© 2015 Elsevier B.V. All rights reserved.
150
Letter to the Editor
splice-acceptor site mutation, the full-length MCPH1-cDNA was synthesized from RNAs prepared from lymphocytes and then amplified by PCR. A fragment of amplified cDNA in the region of exons 4–5 were sequenced using the ABI Prism3130 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). This novel splice-acceptor site mutation has been shown to result in an RNA processing defect with a 15nucleotide deletion in exon 5 of the mRNA transcript (r.322_336del15, p.R108_Q112del5) (Fig. 1). Here, we detected a homozygous intronic mutation in MCPH1 gene in a male patient with microcephaly and severe mental retardation in addition to his sister who had microcephaly but normal intelligence. MCPH1 has been the first gene whose mutations were detected in MCPH (Kaindl et al., 2010). Few intronic mutations have been reported in MCPH1 gene (Darvish et al., 2010). Although sex related difference in clinical phenotype of MCPH1 mutations has not been previously reported, some missense alterations in this gene have been shown to cause mild cellular and clinical phenotype (Trimborn et al., 2005). In addition, polymorphisms in this gene have been suggested as possible mechanisms which elucidate the brain volume variation detected in existing human populations. Notably, a gender dependent association has been detected between cranial volume and a polymorphism in this gene which implies that the expression of genetic variations for brain development is different between two sexes (Wang et al., 2008). This difference has been detected even in the early stages of brain development and is thought to be regulated mainly by expression of genes encoded by sex chromosomes. Furthermore, the role of autosome-encoded genes in sexually dimorphic brain development is being elucidated (Weickert et al., 2009). For instance, a sex-limited effect on the penetrance of the pathological neurodevelopmental phenotypes at the 16p13.11 locus has been identified. In addition, a male biased sex ratio has been seen in numerous neurodevelopmental disorders which may be attributed to several factors such as sex-specific variations in gene regulation or sexually dimorphic epigenetic mechanisms (Tropeano et al., 2013). Recently, such differences in methylome and transcriptome have been shown in human prefrontal cortex. Sex-biased DNA methylation and gene expression could be either the cause or outcome of differential brain development between two sexes (Xu et al., 2014). We hypothesize that such mechanisms may partially explain the difference in phenotypes observed in the 2 cases, probably in addition to other mechanisms such as modifier genes.
References Darvish, H., Esmaeeli-Nieh, S., Monajemi, G.B., et al., 2010. A clinical and molecular genetic study of 112 Iranian families with primary microcephaly. J. Med. Genet. 47 (12), 823–828. Faheem, M., Naseer, M.I., Rasool, M., et al., 2015. Molecular genetics of human primary microcephaly: an overview. BMC Med. Genomics 8 (Suppl. 1), S4. Kaindl, A.M., Passemard, S., Kumar, P., et al., 2010. Many roads lead to primary autosomal recessive microcephaly. Prog. Neurobiol. 90 (3), 363–383. Trimborn, M., Richter, R., Sternberg, N., et al., 2005. The first missense alteration in the MCPH1 gene causes autosomal recessive microcephaly with an extremely mild cellular and clinical phenotype. Hum. Mutat. 26 (5), 496. Tropeano, M., Ahn, J.W., Dobson, R.J., et al., 2013. Male-biased autosomal effect of 16p13.11 copy number variation in neurodevelopmental disorders. PLoS One 8 (4), e61365. Wang, J.K., Li, Y., Su, B., 2008. A common SNP of MCPH1 is associated with cranial volume variation in Chinese population. Hum. Mol. Genet. 17 (9), 1329–1335. Weickert, C.S., Elashoff, M., Richards, A.B., et al., 2009. Transcriptome analysis of male–female differences in prefrontal cortical development. Mol. Psychiatry 14 (6), 558–561. Xu, H., Wang, F., Liu, Y., Yu, Y., Gelernter, J., Zhang, H., 2014. Sex-biased methylome and transcriptome in human prefrontal cortex. Hum. Mol. Genet. 23 (5), 1260–1270.
Soudeh Ghafouri-Fard Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran Majid Fardaei Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran Milad Gholami Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran Mohammad Miryounesi Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran Corresponding author. E-mail address: [email protected]. 15 March 2015