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. 2020 Dec 28;15(12):e0243925. doi: 10.1371/journal.pone.0243925

Ethnic variation and the relevance of homozygous RNF 213 p.R4810.K variant in the phenotype of Indian Moya moya disease

Arun K 1, C M Shafeeque 2, Jayanand B Sudhir 3, Moinak Banerjee 2, Sylaja P N 1,*
Editor: Klaus Brusgaard4
PMCID: PMC7769475  PMID: 33370357

Abstract

Background and purpose

Polymorphisms in Ring Finger Protein 213 (RNF 213) gene have been detected to confer genetic susceptibility to Moya moya disease (MMD) in the East Asian population. We investigated the frequency of RNF 213 gene polymorphism and its association with MMD phenotypes in the Indian population.

Materials and methods

A case-control study for RNF 213 polymorphism involving 65 MMD patients, 75 parents, and 120 controls were performed. A total of 21 SNPs were screened, of which 17 SNPs were monomorphic. Allelic and genotypic frequency of all polymorphic SNPs were assessed and its association with MMD phenotypes was evaluated.

Results

The median age of symptom onset was 9 (range 2–17) and 37 years (range 20–58) in paediatric and adult patients respectively. A strong association was observed with RNF 213 rs112735431(p.R4810K) and MMD. Out of 65 patients with MMD, five patients carried the homozygous risk AA genotype. None of the healthy controls carried this homozygous mutation. The mutant allele was detected in MMD patients from Tamil Nadu and North eastern states of India (p = <0.0001). All the patients carrying the mutant allele had an early age of onset (p = <0.0001), higher incidence of bilateral disease (p = <0.002), positive family history (p = 0.03), higher Suzuki angiographic stage (≥3) (p<0.0006) and recurrent neurological events (ischemic strokes and TIAs) (p = <0.009).

Conclusion

The homozygous rs112735431(p.R4810K) variant in RNF 213 variant not only predicts the risk for MMD but can also predict the phenotypic variants.

Introduction

Moya moya disease (MMD) is a rare chronic cerebrovascular disorder characterized by progressive bilateral occlusion of the supra-clinoid internal carotid artery (ICA) and its main branches with associated development of fine collateral networks, adjacent to the site of occlusion in the deep areas of the brain [1]. There is marked heterogeneity in the clinical manifestations of MMD, ranging from asymptomatic patients to those with recurrent strokes and intracranial haemorrhage [2]. There also exist numerous differences in the clinical presentation between young children and adults pointing to a genetic basis for different clinical phenotypes. Besides, a strong regional difference has also been noted, with a high occurrence of MMD in East Asian countries particularly Japan, China, and Korea [1, 3]. Studies have demonstrated that single nucleotide polymorphisms in the RNF 213 gene had a strong association with the onset of MMD in both familial and sporadic cases [4, 5]. In the East Asian population, the founder variant RNF 213 p.R4810K was much more frequently found in MMD patients (Japanese, 90.1%; Korean, 78.9%; Chinese, 23.1%) than the general population (Japanese, 2.5%; Korean, 2.7%; Chinese, 0.9%) [5, 6]. RNF 213 p.R4810K was found to be absent from control individuals as well as Caucasian MMD cases [5, 7]. The homozygous mutation of the p.R4810K was associated with an earlier age of onset and a more severe disease than the heterozygous variant [811]. However, non-p.R4810K mutations have also been identified in the RNF 213 which include D4013N in Caucasian patients and E4950D and A5021V in Chinese patients [5].

The genotypic characteristics of Indian MMD patients have not been studied systematically to date. The study aims to determine the genetic characteristics of Indian MMD patients by sequencing the 17-q.25-ter’ region and to clarify whether RNF 213 is potentially associated with clinical phenotypes.

Materials and methods

Study population

This study was approved by the ethics committee of Sree Chitra Tirunal Institute for Medical Sciences and Technology, India. The IEC number are as follows IEC/1150 dated 26/12/2017. All participants were included in the study only after receiving their written informed consent. Hard copies of the consents are available with the ethics division of our institute. Patients with MMD attending the outpatient or inpatients of Comprehensive stroke care program of the Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum from January to December 2018 were recruited in this study. The MMD diagnosis was confirmed by digital subtraction angiography (DSA), based on the criteria of the Research Committee on the Pathology and Treatment of Spontaneous Occlusion of the Circle of Willis; Health Labour Sciences Research Grant for Research on Measures for Intractable Diseases, Japan. A total of 65 MMD patients, 75 parents, 1 son of the affected person, and 120 controls were enrolled in the study. Twenty-five complete patient trios were available for the study. The family samples were included to interpret the pattern of inheritance of the associated variants. Control participants had no typical MMD symptoms in the form of stroke, TIA or seizures and they were not screened by conventional DSA, MR angiography (MRA), CT angiography(CTA), or other tests. The clinical records of all previously diagnosed cases were examined including hospital charts, clinical notes and imaging studies. The medical history, native place, age of onset, symptoms at onset and angiographic staging were reconfirmed. A detailed family history was taken. Recurrent events were defined as events in the form of ischemic events, seizures or haemorrhagic events that occurred after the initial presentation. The angiographic stage was evaluated according to the Suzuki classification. The study was approved by the Institutional Ethics Committee.

DNA extraction and single nucleotide polymorphism genotyping

After obtaining the informed consent, 10 ml peripheral vein blood was extracted from patients with MMD and normal control participants, placed in EDTA anticoagulant tubes and stored in a freezer at −80°C until analysis. DNA was isolated using the salting-out method [12]. The extracted DNA was spectro-photometrically quantified and checked for purity at an absorbance of 260nm and 280nm. Resequencing of the 17-q.25-ter’ region spanning the RNF 213 region covering 21 SNPs was carried out. The selection of SNPs was based on functional significance, minor allele frequency, and their tagging status. The details of the SNPs selected, PCR primers and in silico functional prediction are shown in “Table 1”. The PCR primers were designed using Primer-BLAST and verified by UCSC in silico PCR and synthesised by Sigma-Genosys. Genotyping was done by Gradient PCR amplification at a temperature of 55–65°C. This was followed up by Sanger sequencing using ABI PRISM Big Dye Terminator v3.1 sequencing kit, (Applied Bio-systems, Foster City, CA, USA) according to the manufacturer’s instructions and was run on ABI PRISM3730 Genetic Analyser (Applied Bio-systems, Foster City, CA, USA). Sequence analysis was done using Applied Bio-systems sequence scanner V.1.1.

Table 1. RNF213 SNPs screened for the study and details from ENSEMBL and dbSNP.

RNF213 SNPs screened Primer 5→3 Annealing Temp Product Size Regulome DB rank RegulomeDB rank prediction Variant Ancestral Allele §MAF
rs6565666 ‡‡(F) TTTGCGTGGGCCAGGAGAAGC 62 254 No Data Intron G A = 0.21
‖‖rs200418091 No Data Intron **C T <0.01
rs370268515 No Data Intron G A <0.01
rs367879018 §§(R) GCTCACGGCTTCAATGATGC 5 TF binding or DNase peak Missense G A <0.01
rs149136204 5 TF binding or DNase peak Missense ††T C <0.01
rs6565681 (F) CACTGGGCATTAAGACTGC 53 243 3a TF binding + any motif + DNase peak 3’ UTR G A = 0.353
rs143047595 2b TF binding + any motif + DNase Footprint + DNase peak 3 prime UTR C T = 0.01
(R) CCAGCTCAACTGTCATAGC
rs185195273 4 TF binding + DNase peak 3 prime UTR G A = 0.01
rs369097124 3a TF binding + any motif + DNase peak 3 prime UTR G A = 0.01
rs4889848 (F) TGAGAAAGTGCAGCGTGC 55 252 1f ***eQTL + TF binding / DNase peak Synonymous T C = 0.35
rs114047543 5 TF binding or DNase peak Intron G A = 0.05
rs368578211 5 TF binding or DNase peak Missense G C<0.01
rs139431747 (R) CCCATTGTTTGGCAGCACTG 5 TF binding or DNase peak Synonymous G A = 0.02
rs145282452 5 TF binding or DNase peak Missense G A = 0.01
rs569181011 NA Synonymous G A<0.01
rs112735431 (F) TGAGGCTGGTAAAGTTCCTG 58 191 5 TF binding or DNase peak Missense G A = 0.0012
rs138228835 5 TF binding or DNase peak Missense G C = 0.02
rs370932670 5 TF binding or DNase peak Missense A G = 0.02
rs61746605 (R) CCTATGCAGTGATCCTTTCG 5 TF binding or DNase peak Missense C G = 0.02
rs75053281 5 TF binding or DNase peak Intron G C = 0.10
rs200776946 5 †††TF binding or DNase peak Intron A G = 0.25

RNF 213-Ring finger protein 213

SNP-Single nucleotide polymorphism

§MAF-Mean allele frequency

UTR- Untranslated region

G-Guanine

**C- Cytosine

††T-Thymine

A-Adenine

‡‡(F)-Forward

§§(R)-Reverse

‖‖rs- Reference SNP

¶¶NA-Not applicable

***eQTL- Expression quantitative trait loci

†††TF binding- Transcription factor binding.

Statistical analysis

Demographic and phenotypic observations were analysed using SPSS 22.0 (SPSS Inc., Chicago, IL) and the continuous variables were presented as means ± standard deviation and categorical variables were presented as proportions. Genotype and allele frequencies were computed using the Graph Pad Prism 5.01, (Graph Pad software Inc. San Diego, CA, USA). A p-value of <0.05 was considered significant in all observations. The test of association for rs112735431 RNF 213 risk AA genotype with various phenotype variables such as clinical symptoms, age at onset, unilateral/bilateral, distribution of vasculopathy, imaging characteristics, and Suzuki classification, was done using Chi Square test. Linkage Disequilibrium (LD) plots for controls and patients were generated using Haploview 4.2 (broad.mit.edu/mpg/haploview/). LD plots in cases and control display how non-random association of alleles at two or more loci may differ in cases and control. Functional prediction of the associated SNPs was assessed in silico using regulomeDB (regulome.stanford.edu), Genotype-Tissue Expression (GTEx) portal (www.gtexportal.org/), HaploReg (www.broadinstitute.org/mammals/haploreg). The functional significance of the SNPs was checked for the RegulomeDB rank to assess the possible regulatory effect. RegulomDB rank is derived from RegulomeDB database that annotates SNPs with known and predicted regulatory elements in the intergenic regions of the H. sapiens genome [13]. Lower scores indicate increasing evidence for a variant to be located in a functional region. Category 1 variants have equivalents in other categories with the additional requirement of expression quantitative trait loci (eQTL) information. RegulomeDB score is computed based on the integration of multiple high-throughput datasets. GTex portal was assessed for possible gene expression of the allelic variants. GTEx database allow the users to view and download computed eQTL results and provide a controlled access system for de-identified individual-level genotype, expression, and clinical data. HaploReg was also used, which is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Interpreted data is presented only with reference to associated risk SNP.

Results

The clinical and demographic characteristics of 65 patients with MMD and 120 normal controls are summarised in “Table 2”. The median age of the first symptom in the paediatric and adult patients was 9 years (range 2–17) and 37 years (range 20–58) respectively. The female to male ratio was 1.2:1. Ischemic stroke (49.2%) was the most common clinical presentation. One patient presented with an isolated headache only. Recurrent events happened in 78.5%, of which 56.9% had ischemic strokes and TIAs, 37.3% had seizures and 3.9% had haemorrhagic events. Bilateral disease was observed in 92.3%. Suzuki’s angiographic stage 4 or 5 was observed in 78.5% and 73.8% on the left side and right side respectively. The birthplace distribution showed 58.5% originated and continued to live in Tamil Nadu, 26.2% in Kerala, and 15.3% in Northeast India.

Table 2. Demographic characteristics of patients with Moya moya disease and healthy controls.

Clinical features No. of patients
Moya moya Disease 65
††Median age of symptom onset(years) (IQR) 8 (1–52)
**Female: Male 1.2:1
**Domicile
    Kerala 17 (26.2)
    Tamil Nadu 38 (58.5)
    Others 10 (15.4)
**Family history 7(10.8)
**Consanguinity 9 (13.8)
**Age of Onset of symptoms (years)
    0–10 39 (60)
    11–20 9 (13.8)
    21–30 4 (6.2)
    31–40 6 (9.2)
    41–50 5 (7.7)
    51–60 2 (3.1)
Young onset (<18 years) 45 (69.2)
Adult onset (≥18years) 20 (30.8)
**Clinical presentation
    Cerebral Infarction 32(49.2)
TIA 13(20)
    Haemorrhage 6 (9.2)
    Seizure 17 (26.2)
    Headache 20 (30.8)
    Syncope 2 (3.1)
††Median §NIHSS on admission (IQR) 2(15)
††Median m RS on admission (IQR) 1(4)
**Risk Factor profile and associations
    Hypertension 7(10.8)
    Diabetes 4(6.2)
    Hyperlipidaemia 1(1.5)
    Trisomy 21 2(3.1)
    Neurofibromatosis 1(1.5)
    Hereditary Spherocytosis 1(1.5)
    Hypothyroidism 8(12.3)
**Recurrent events 51 (78.5)
**Posterior circulation involvement in DSA 18 (27.7)
**Bilateral disease 60 (92.3)
**Suzuki’s staging Right Left
Stage 1 5 (7.7) 3 (4.6)
Stage 2 0 (0) 2 (3.1)
Stage 3 8 (12.3) 4 (6.2)
Stage 4 13 (20) 18 (27.7)
Stage 5 35 (53.8) 33 (50.8)
Stage 6 2 (3.1) 3 (4.6)
Controls 120
**Female/Male 1.14
††Median age in years (IQR) 31 (20–55)
DSA Not done

IQR-Interquartile range

TIA- Transient ischemic attack

§NIHSS-National Institute of Health Stroke Scale

m RS-Modified Rankin scale

DSA-Digital subtraction angiography.

**Categorical variables are presented as n (%)

††Continuous variables are presented as median (IQR).

A total of 21 SNPs were screened in the study of which 17 SNPs were monomorphic. All the polymorphic SNPs were assessed for their allelic and genotypic frequency and evaluated for their role in association with the disease and its clinical phenotypes. A strong association was observed with RNF 213 variant rs112735431 (p.R4810K) (OR, 36.3; 95% CI, 2.11–626; p = 0.0001) and MMD “Table 3”. None of the other SNPs were found to be associated with MMD. rs6565681 and rs488948 were in complete Linkage Disequilibrium. All the patients who had the rs112735431 (p.R4810K) risk mutant A allele were found to be in homozygous condition. The association with rs112735431 was observed to be significant even after the Bonferroni correction for multiple-comparison correction. No homozygous mutation was detected in the healthy control samples. TDT test could not be carried out due to the small sample size. In our study, only one loci rs112735431 was found to be associated with the risk allele, which was absent in the control population. GTEx data for the associated SNP rs112735431 was not available in the GTEx Biobank portal and therefore, allelic expression variation could not be interpreted. Among the five homozygous probands, the parents were in the heterozygous condition with a clear documented disease history in one parent suggesting that the disease could be transmitted in an autosomal dominant pattern. The ethnic distribution of the patients showed clustering of homozygous mutant allele in Tamil Nadu and in the North eastern states of India with none of the mutant allele noted in MMD patients from Kerala (p = <0.0001). All the patients carrying the homozygous mutant allele of rs112735431 (p.R4810K) were also found to have an early age of onset (≤18 years) (p = <0.0001). These risk genotype individuals have a significantly higher incidence of bilateral disease (p = <0.002) and increased Suzuki angiographic stage (≥3) (p<0.0006) and recurrent neurological events (p = <0.009) (Table 4, Fig 1).

Table 3. Comparison of allelic and genotypic frequencies of SNPs of RNF213 in Moya moya patients and controls.

Gene SNPs Group Genotype p Allele p Odds ratio 95%CI
(n/Frequency) (n/Frequency)
value value
GG AG AA G A
rs112735431 Cases 60 0 5 0.004 120 10 0.0001 36.3 2.1–626.0
(0.92) (0.0) (0.08) (0.92) (0.08)
Controls 104 0 0 208 0
(1.0) (0.0) (0.0) (1.0) (0.0)
rs6565681 Cases 20 35 10 0.52 75 55 0.57 1.1 0.7–1.8
(0.31) (0.54) (0.15) (0.58) (0.42)
Controls 40 47 17 127 81
(0.38) (0.45) (0.16) (0.61) (0.39)
rs4889848 Cases 20 35 10 0.52 75 55 0.57 1.1 0.7–1.8
(0.31) (0.54) (0.15) (0.58) (0.42)
Controls 40 47 17 127 81
(0.38) (0.45) (0.16) (0.61) (0.39)
rs6565666 Cases 46 18 1 0.84 110 20 1.0 1.0 0.6–1.9
(0.71) (0.28) (0.02) (0.85) (0.15)
Controls 74 27 3 175 33
(0.69) (0.25) (0.03) (0.84) (0.16)

95%CI-95%confidence interval, Genotype frequency in bracket.

Table 4. Frequency of AA risk genotype RNF 213 variant rs112735431 with clinical phenotype.

Patient characteristics Genotype (frequency%) p-value
GG AG AA
Patients with MMD 60 (92) 0 5 (8) 0.004
Normal controls 104 (100) 0 0
Age at onset Childhood onset (<18 y) 38 (88) 0 5 (12) 0.0004
Adult onset (≥18 y) 18 (100) 0 0
Seizure Yes 14 (87) 0 2 (13) NS
No 42 (93) 0 3 (7)
Stroke Yes 42 (93) 0 3 (7) NS
No 14 (88) 0 2 (13)
Family history Yes 5 (83) 0 1 (17) 0.029
No 51 (93) 0 4 (7)
Circulation Anterior circulation alone 40 (91) 0 4 (9) NS
Anterior and Posterior circulation 16 (94) 0 1 (6)
Vasculopathy Unilateral 6 (100) 0 0 0.0021
Bilateral 50 (91) 0 5 (9)
Recurrent events Yes 9 (82) 0 2 (18) 0.009
No 47 (94) 0 3 (6)
Regional Ethnicity Kerala 17 (100) 0 0 0.004
Tamil Nadu 34 (92) 0 3 (8)
Pan Indian Ethnicity Kerala 17 (100) 0 0 0.0004
Others 38 (88) 0 5 (12)
Suzuki stage right 0–2 12 (100) 0 0 0.0006
3–6 42 (89) 0 5 (11)
Suzuki stage left 0–2 6 (86) 0 1 (14) NS
3–6 48 (92) 0 4 (8)

NS-Not significant.

Fig 1. Frequency of AA risk genotype RNF213 variant rs112735431 (p.R4810K) with clinical phenotypes.

Fig 1

Discussion

The study suggests a significant role of RNF 213 rare variant p.R4810K [rs112735431] in MMD and its clinical phenotypes in Indian patients. Population-specific prevalence of risk variants within the Indian subjects, further highlight the need for identifying the ethnic-specific variation, although a larger nationwide study may further highlight the significance of the observations.

The present study revealed a strong association of MMD with RNF 213 variant rs112735431 (p.R4810K) with mutant A allele and AA genotype. No mutant allele was detected in the healthy control population. Studies have shown a higher occurrence of this founder variant in the East Asian population with MMD [5, 6]. Normal populations have also been found to carry this variation at a frequency of 2.5%, 2.7% and 0.9% among Japanese, Korean, and Chinese respectively [5]. Compared to Japanese and Korean patients, the rate of this mutation in Chinese Han MMD patients is lower [13]. In contrast to these observations, we noted this risk variant to be present in only 8% of the Indian patients while it was completely absent in the healthy individuals. Even in Indian patients, it showed ethnic-specific variation. This RNF 213 rare variant significantly increases MMD risk in Korea, Japan and China with an odds ratios (ORs) of 135.63, 338.94 and 14.70 respectively [6]. The incidence of MMD in Europeans is about 1/10 of that found in Japanese [14], and p.R4810K was not identified in Europeans except in one study [15]. Also, among those MMD patients having different descent living in a similar environment, p.R4810K was found in 56% of Asian while none was found in non-Asian descents [7]. Studies have also demonstrated a potential role of non-p.R4810K mutations in the Caucasian population [5] in the MMD pathogenesis. Thus it can be postulated that a multifactorial process might be involved in the etiopathogenesis which includes additional environmental or genetic determinants rather than a definite trait determinant [16]. Even in South East Asian populations, it showed differential penetration where additional variants in RNF 213 were reported in the Han Chinese population [17]. It is interesting to note that even in the present study population we could find a significant ethnic variation with none of the Malayalam speaking population of Kerala carrying the risk variant while all the risk variants are contributed by the individuals from West Bengal and Tamil Nadu. West Bengal populations are known to have gene flow from East Asian genetic lineage. Based on HLA genotyping we have earlier demonstrated that the populations within the south Indian states i.e. Kerala and Tamil Nadu, have different genetic structure and admixtures among population groups have also been reported between West Bengal and Tamil Nadu [1820]. Although the rs112735431 did not affect the transcriptional levels or ubiquitination activity of RNF 213, it could reduce the angiogenic activities of induced pluripotent stem cells (iPSC)-derived vascular endothelial cells (iPSECs) in MMD patients [21], and increase the risk of genomic instability in the cells [22].

Our study could demonstrate an autosomal dominant pattern of inheritance as evidenced by the presence of a mutant A allele in heterozygous condition in an affected parent while the proband was homozygous. Though a polygenic inheritance combined with environmental factors has been reported in most cases, various Mendelian patterns of transmission have also been suggested in familial MMD and the disease transmission was noted in multiple generations [2326]. Mineharu et al. reported 15 large multigenerational pedigrees consistent with an autosomal dominant pattern of transmission with an incomplete penetrance [23].

The presence of mutant A allele was associated with early age of symptom onset of MMD in our patients. Our data correlate well with the reports from the Chinese population [811]. Similarly, in a case study conducted among MMD twins with homozygous and heterozygous p.R4810K, the age of disease onset in the homozygote sibling was earlier than that of the heterozygote sibling [11]. Thus it can be suggested that the dosage of p.R4810K alleles was strongly associated with clinical phenotype, even in family members sharing a similar genetic background. However, there are reports of homozygous p.R4810K in unaffected control population [6, 27], and identical twins, with the same dosage of p.R4810K alleles but discordant phenotypes [5]. Therefore, it appears that heterogeneity of the MMD phenotype cannot be explained solely by gene dosage effects. Indeed, environmental factors may also play a critical role in phenotype variation.

The presence of mutant A allele was significantly associated with higher incidences of bilateral disease (p = <0.002), positive family history(p = 0.03), higher Suzuki angiographic stage (p<0.0006) and recurrent neurological events (ischemic events and seizures) (p = <0.009). Miyatake et al. reported that the presence of bilateral vasculopathy was significantly associated with the mutant allele [8]. In our study, 9% with bilateral disease showed the mutant A allele and no mutant allele was detected with unilateral disease. Whether unilateral MMD has a common genetic background or it is a separate entity with similar angiographic characteristics as definite MMD needs to be determined. It has been demonstrated that the presence of a positive family history increased the risk by ten times among Japanese and fifty times among Chinese population [28]. Thus, rs112735431 screening could be utilized as a method to identify asymptomatic patients, especially those who have a positive family history of MMD among Asian descent. Sun et al. [18], conducted a meta-analysis and suggested that the rs112735431 variant should be pursued as a diagnostic screening test particularly in the Asian population, especially when the MMD index case is positive in the family. Our study also demonstrated a higher Suzuki stage in those carrying the mutant allele, suggesting more progressive and severe disease in those carrying the allele. Although the exact molecular mechanisms by which RNF 213 regulates angiogenesis and arteriogenesis remains largely unknown, previous studies have suggested several possible processes that involve two different signalling pathways [29, 30]. The first is a process mediated by the hypoxia-inducible factor-1 (HIF-1) [31] and the second possible signalling pathway may function through caveolin-1 [32]. Serum caveolin-1 levels were found to be decreased in MMD patients and were further decreased in those carrying the RNF 213 p.R4810K variant [33]. Similarly, this mutant allele was associated with recurrent events in the form of ischemic strokes and seizures suggesting a more severe disease. Miyatake et al. [8] observed that the homozygous RNF 213 p.R4810K predicted an early-onset and severe form of MMD. Similarly, a recent study also pointed out a more serious form of the disease and unfavourable clinical outcome in association with the mutant allele [10]. All these findings prompt us to consider the role played by genetics in the phenotypic characteristics of MMD and to incorporate the genotyping in the routine evaluation of MMD patients so that early diagnosis and early intervention can be planned.

This study has some limitations. This was a single centre study, so there is a chance for selection bias. We investigated the frequency of RNF 213 polymorphism only, however, since MMD is a complex disease with marked genetic heterogeneity and a single gene focus may not sufficiently elucidate the MMD susceptibility. The strengths of our study include; it is the first study from the Indian subcontinent to report the genetics of MMD. We were able to demonstrate the presence of RNF 213 p.R4810K in the Indian population similar to that of the East Asian population. Though the sample size was small, since the frequency of MMD in the Indian population is less as compared to Japan, China and Korea, this population could be considered a representative of the genetics of Indian MMD.

Conclusions

The homozygous rs112735431(p.R4810K) variant in RNF 213 variant not only predicts the risk for MMD but can also predict the phenotypic variants.

Data Availability

All relevant data are within the paper.

Funding Statement

This study was funded by Wellcome Trust-Department of Biotechnology (DBT)/India Alliance (IA) as part of Research Training Fellowship. (https://www.indiaalliance.org/) with grant number IA/R/16/2/502992 dated 28/11/2017 received by Arun K. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Decision Letter 0

Klaus Brusgaard

6 Oct 2020

PONE-D-20-24520

Ethnic variation and the relevance of homozygous RNF213 p.R4810.K variant in the phenotype of Indian Moyamoya disease

PLOS ONE

Dear Dr. Sylaja P.N,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

==============================

The manuscript needs additional editing. Especially, table and figures needs proper lables. The "recurrent events" needs to be defined as well as rational for inclusion of patient groups.

The editor comments should be carfully addressed and corrrected accordingly.

==============================

Please submit your revised manuscript by Nov 20 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

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We look forward to receiving your revised manuscript.

Kind regards,

Klaus Brusgaard

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: No

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: No

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Very interesting and relevant study about polymorphism in Ring Finger protein RNF213 and MMD. The tables should be more clear the number of SNPs and controls. The confidence interval 3.11-626 is not consistent with the CI in table 3.

Reviewer #2: Moyamoya disease is rare and this group has provided some important findings in an Indian population. There are several issues with this work however that need to be address prior to publication.

-the authors need to copy edit one final time (spaces, consistency, grammar); lines 207-210 do not make any sense

-need to define 'recurrent events' as they offer data on seizure, stroke and recurrent events - quite confusing

-the authors included syndromic MMD (downs, NF2) and they need to address the rational for including these patients

-if the authors choose to discuss the trio data, there needs to be a table with this data in the manuscript. Does the 'one son of a patient' fit into this data?? Unclear

-Materials and Methods: there needs to be much more included in this section. Simply listing the software packages is not enough - how was the software used? Ref to the salting out method? TDT test? Replicates for PCR and sequencing? Odds ratio, bonferroni? What is the meaning of the pval if bonferroni was performed? Instruments used and suppliers? Who made the pcr primers?

-Table 1: terrible format - should fit the page. What does the bold SNP indicate? What does the Regulome score indicate? What is TM?

-Table 3: what are the two lines of data for? Cases and controls? needs labelling

-Table 4: there seems to be only 104 controls. Kerala is listed twice, numbers don't add up. Again, provide definition of recurrent events vs stroke, seizure.

-figure 1: x axis needs a label, y axis is poor quality, ethnicity (non-Ker) needs to be described

**********

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Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

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Attachment

Submitted filename: Review 08.09.2020 ARL.docx

PLoS One. 2020 Dec 28;15(12):e0243925. doi: 10.1371/journal.pone.0243925.r002

Author response to Decision Letter 0


20 Oct 2020

Response to the academic editor and the reviewer

Dear Editor,

We would like to thank the reviewers for critically reviewing and giving valuable suggestions.

Response to Editorial comments

Comment 1: The study investigates MMD in Indian patients. This genotypic characterization of Indian MMD has not been studied systematically until date according to the article, and it also makes the study relevant.

� We appreciate the positive comment .

Comment 2:The controls were not screened.

� A statement in this regard is already mentioned in the manuscript. Control participants had no typical MMD symptoms in the form of stroke, TIA or seizures, but they were not screened by conventional DSA, MR angiography (MRA), CT angiography(CTA), or other tests, which we understand is a limitation.

Comment 3: 22 SNPs were selected. In table1 there is a list of the SNP’s but it seems that there is only 21.

� We thank the reviewers for pointing this out. In the revised manuscript we have amended this as follows:

� A total of 21 SNPs were screened in the study of which 17 SNPs were monomorphic.

Comment 4: The methods of Sanger Sequencing was performed. More information about the companies of the kits/primers which has been used will be relevant to mention in the article.

� In the revised manuscript we have resolved these issues.

� PCR primers were designed using Primer-BLAST and verified by UCSC In-Silico PCR and sythesised by Sigma-Genosys.

� This was followed up by Sanger sequencing using ABI PRISM Big Dye Terminator v3.1 sequencing kit, (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions and was run on ABI PRISM3730 Genetic Analyzer(Applied Biosystems, Foster City, CA, USA).

Comment 4: Table 3. I need as a reader some explanation about the selection of the SNPs from table 1 compared to table 3.

� The selection of SNPs was based on functional significance, minor allele frequency, and their tagging status. A statement in this regard is mentioned in the manuscript.

� The bolded SNPs were tagged to unbolded SNPs and were also screened using the same set of primers mentioned in the primer column..

� Bolded SNPs were also polymorphic in our population while unbolded SNPs were monomorphic.

� A statement in this regard is already mentioned in the manuscript. “All the polymorphic SNPs were assessed for their allelic and genotypic frequency and evaluated for their role in association with the disease and its clinical phenotypes.”

Comment 5: In table 3 the controls are mentioned but now it is 104 + 1 compared to 120 controls from the abstract - how should that be understood.

� Thankyou for the valuable suggestion .In the revised manuscript we have revised the table and now the frequencies are mentioned in bracket. It is not 104 + 1 instead it is genotype number 104 (Frequency is 1.0 i.e 100 percent).

� We had 120 samples but only 104 could provide meaningful genotypes in consensus for all SNPs.

Comment 6: How you calculated the odds ratio? The confidence interval 3.11-626 for rs112735431 is not consistent with the CI in table 3.

� We thank the reviewers for pointing this out. In the revised manuscript we have amended the confidence interval. It is 2.11-626 for rs112735431. Odds Ratio was calculated using GraphPad Prism.

Comment 7: Table 4 just minor things about the seizure and stroke 42 (93) 3(3?).

� We thank the reviewers for the comment. In the revised manuscript we have amended this.

In the revised version the seizure and stroke 42 (93) 3(7).

Comment 8: The discussion is very interesting about the incidence of MMD in populations and that it should be noted that cases of homozygous p.R4810K in unaffected control populations also are reported and that environmental factors may have influence in the phenotype variation.

A very fine section about the limitation of this study with the opportunity to continue working within this very interesting field of polymorphisms in Ring Finger protein RNF213 in MMD diseases.

The conclusion from the reviewer. Very interesting and relevant study about polymorphism in Ring Finger protein RNF213 and MMD. The tables should be more clear as already mentioned (SNP, controls) but I looking forward to following this interesting field.

� We thank the editor for the encouraging remarks.

Response to Reviewers comments

Reviewer #1:

Comment 1: Very interesting and relevant study about polymorphism in Ring Finger protein RNF213 and MMD. The tables should be more clear the number of SNPs and controls. The confidence interval 3.11-626 is not consistent with the CI in table 3.

� In the revised version we have tried to improve the tables to fit in one page. Thanks for pointing the confidence interval issue. We have amended the confidence interval. It is 2.11-626 for rs112735431. Odds Ratio was calculated using GraphPad Prism.

Reviewer #2:

Moyamoya disease is rare and this group has provided some important findings in an Indian population.

Comment 1: -the authors need to copy edit one final time (spaces, consistency, grammar); lines 207-210 do not make any sense

We have made the edits

Comment 2: -need to define 'recurrent events' as they offer data on seizure, stroke and recurrent events - quite confusing

� The data on strokes and seizures mentioned in the manuscript are initial event the patient presented with. Recurrent events are defined as events in the form of ischemic events, seizures or haemorrhagic events which occurred after the initial presentation.

Comment 3: -the authors included syndromic MMD (downs, NF2) and they need to address the rationale for including these patients

� We fully agree with the reviewer that NF2 with moyamoya is considered moyamoya syndrome. But since it has a genetic basis we included that patient. Downs syndrome is mostly reported to coexist with moyamoya disease and is usually not considered moyamoya syndrome.

Comment 4: -if the authors choose to discuss the trio data, there needs to be a table with this data in the manuscript. Does the 'one son of a patient' fit into this data??

� Since the study was conducted using case control association design, therefore only probands and the controls were considered for table 3. Trios or parental samples were used only for evaluating parental genotypes for the risk alleles in probands. A statement in this regard is mentioned.

� For the case control evaluation we have used only the affected son (proband) while affected parent was not used in the study. However, the affected parent sample genotype was evaluated to see the pattern of inheritance. Parental samples wherever could be used were used only to identify the pattern of inheritance.

Comment 5: -Materials and Methods: there needs to be much more included in this section. Simply listing the software packages is not enough - how was the software used? Ref to the salting out method? TDT test? Replicates for PCR and sequencing? Odds ratio, bonferroni? What is the meaning of the pval if bonferroni was performed? Instruments used and suppliers? Who made the pcr primers?

� Overlapping comments have been addressed in response to academic editorial comments. Unaddressed issues are further addressed here.

� All the softwares along with their http links are mentioned in the text. In the revised version all those software that were used for analysis were included and interpreted. (see highlighted text)

� A reference to salting out method is included. “6 Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988;16(3):1215. doi:10.1093/nar/16.3.1215”

� We had mentioned in the text that ”As per Bonferroni correction for multiple comparisons for case control associations for polymorphic variants should be (0.05/4=0.01). The observation obtained in the study with respect to risk SNP is much lower that the 0.01.

� PCR replicates were run randomly and also whenever the sequence or the PCR products gave ambiguous product. Lack of amplification or non-interpretable genotypes were not included in the study.

� In the revised version instruments and suppliers are included wherever applicable. These are further highlighted in the text.

Comment 6: -Table 1: terrible format - should fit the page. What does the bold SNP indicate? What does the Regulome score indicate? What is TM?

� In the revised version we have modified the table for better clarity.

� The selection of SNPs was based on functional significance, minor allele frequency, and their tagging status.

� The bolded SNPs were tagged to unbolded SNPs and were also screened using the same set of primers mentioned in the primer column..

� Bolded SNPs were also polymorphic in our population while unbolded SNPs were monomorphic. All the polymorphic SNPs were assessed for their allelic and genotypic frequency and evaluated for their role in association with the disease and its clinical phenotypes.” We have added these to the manuscript

� In the revised version we have rephrased the RegulomeDB score as RegulomDB rank. A detail on ranking pattern is explicitly mention in the link. https://www.regulomedb.org/regulome-help/

� In the revised version of the table we have rephrased TM as Annealing temp

Comment 7: -Table 3: what are the two lines of data for? Cases and controls? needs labelling

� In the revised version of the table this has been amended and the second line has been removed and the frequencies are mentioned in bracket

Comment 8: -Table 4: there seems to be only 104 controls. Kerala is listed twice, numbers don't add up. Again, provide definition of recurrent events vs stroke, seizure.

� This has been corrected into regional which refers to south India (Kerala and Tamil Nadu) and Pan Indian ethnicity refers to Non-Malayalam speaking (Non-Ker) population from rest of the country

Comment 9: -figure 1: x axis needs a label, y axis is poor quality, ethnicity (non-Ker) needs to be described

� X and Y axis has been defined in the figure and Non-Ker has been defined in manuscript

Attachment

Submitted filename: Response to academic editor and reviewer.docx

Decision Letter 1

Klaus Brusgaard

19 Nov 2020

PONE-D-20-24520R1

Ethnic variation and the relevance of homozygous RNF213 p.R4810.K variant in the phenotype of Indian Moyamoya disease

PLOS ONE

Dear Dr. Sylaja P.N.,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

==============================

Please carefully adhere to the suggestions and recommendations put forward by reviewer 2 and edit the manuscript accordingly.  

==============================

Please submit your revised manuscript by Jan 03 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Klaus Brusgaard

Academic Editor

PLOS ONE

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: (No Response)

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Partly

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: No

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: No

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: The main issue is what types of stats these authors used in their manuscript - it is NOT enough to simply list the software used. There are many errors in the manuscript and the authors should pay attention to this. Beginning of list: INTRO, 'till date' to 'to date', '17q.25-ter'' to 17-q.25-ter' consistently; M&M, again details of the stats used NOT just the programs, RegulomeDB, the authors really don't describe this; DISCUSSION, 'Kerala carry' to 'Kerala carrying'. 'sample size less' to 'sample size was small', the paragraph starting with 'This study has some limitations...' needs serious editing.

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #2: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2020 Dec 28;15(12):e0243925. doi: 10.1371/journal.pone.0243925.r004

Author response to Decision Letter 1


24 Nov 2020

Dear Editor/ Reviewer,

Thanks for your valuable comments,

1. In the revised manuscript we have revised the ‘Statistical Analysis’ section with explicit explanation of all statistical tests and functional assessments of the SNPs used.

2. We have also included the details on RegulomeDB rank and also presented it in the ‘table 1’ for better clarity.

3. Grammatical errors have been corrected and highlighted in the manuscript.

4. Edits have been made in the paragraph explaining the ‘limitations of the study’.

Statistical Analysis

Demographic and phenotypic observations were analysed using SPSS 22.0 (SPSS Inc., Chicago, IL) and the continuous variables were presented as means ± standard deviation and categorical variables were presented as proportions. Genotype and allele frequencies were computed using the Graph Pad Prism 5.01, (Graph Pad software Inc. San Diego, CA, USA). A p-value of <0.05 was considered significant in all observations. The test of association for rs112735431 RNF 213 risk AA genotype with various phenotype variables such as clinical symptoms, age at onset, unilateral/bilateral, distribution of vasculopathy, imaging characteristics, and Suzuki classification, was done using Chi Square test. Linkage Disequilibrium (LD) plots for controls and patients were generated using Haploview 4.2 (broad.mit.edu/mpg/haploview/). LD plots in cases and control display how non-random association of alleles at two or more loci may differ in cases and control. Functional prediction of the associated SNPs was assessed in-silico using regulomeDB (regulome.stanford.edu), Genotype-Tissue Expression (GTEx) portal (www.gtexportal.org/), HaploReg (www.broadinstitute.org/mammals/haploreg). The functional significance of the SNPs was checked for the RegulomeDB rank to assess the possible regulatory effect. RegulomDB rank is derived from RegulomeDB database that annotates SNPs with known and predicted regulatory elements in the intergenic regions of the H. sapiens genome[13]. Lower scores indicate increasing evidence for a variant to be located in a functional region. Category 1 variants have equivalents in other categories with the additional requirement of expression quantitative trait loci (eQTL) information. RegulomeDB score is computed based on the integration of multiple high-throughput datasets. GTex portal was assessed for possible gene expression of the allelic variants. GTEx database allow the users to view and download computed eQTL results and provide a controlled access system for de-identified individual-level genotype, expression, and clinical data. HaploReg was also used, which is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Interpreted data is presented only with reference to associated risk SNP.

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Decision Letter 2

Klaus Brusgaard

1 Dec 2020

Ethnic variation and the relevance of homozygous RNF213 p.R4810.K variant in the phenotype of Indian Moyamoya disease

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Acceptance letter

Klaus Brusgaard

14 Dec 2020

PONE-D-20-24520R2

Ethnic variation and the relevance of homozygous RNF 213 p.R4810.K variant in the phenotype of Indian Moya moya disease

Dear Dr. P.N.:

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    Supplementary Materials

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    Submitted filename: Response to academic editor and reviewer.docx

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    Data Availability Statement

    All relevant data are within the paper.


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