A Novel CCM3 Mutation Associated with a Severe Clinical Course in a Child with Multiple Cerebral Cavernous Malformations

Abstract

Background: Cerebral cavernous malformations (CCMs) are vascular lesions linked to mutations in the CCM1, CCM2, and CCM3 genes, resulting in angiogenesis dysregulation. This case study highlights the clinical course of a child with severe CCMs and explores the genetic basis of the condition. Methods: We used comprehensive clinical assessment and magnetic resonance imaging (MRI) to monitor the patient’s neurological status and CCM progression and genetic analysis by whole-exome sequencing to identify mutations in CCM-related genes. Results: The patient presented with developmental delays, multiple CCMs, and recurrent hemorrhagic events, requiring five surgical interventions. Genetic analysis revealed a novel frameshift mutation in the PDCD10 gene. Despite surgical efforts, the patient developed significant disability by age 13. Conclusions: This case illustrates the aggressive clinical course associated with CCMs, particularly in patients with CCM3 mutations. It underscores the importance of genetic screening and monitoring in understanding hereditary CCM progression and guiding treatment strategies.

1. Introduction

Cerebral cavernous malformations (CCMs) are vascular lesions comprising enlarged vascular cavities lined with endothelium and filled with blood. These malformations result from dysregulated angiogenesis and vasculogenesis caused by mutations in three genes: CCM1 (KRIT1), CCM2 (malcavernin), and CCM3 (PDCD10). These genes, primarily expressed in endothelial cells, regulate key intracellular processes. Sporadic cases often involve gain-of-function variants in the MAP3K3 gene, which activates downstream signaling pathways implicated in angiogenesis dysregulation [1]. In contrast, hereditary CCMs are typically linked to loss-of-function mutations in the CCM1, CCM2, and CCM3 genes, with these mutations being inherited in an autosomal-dominant manner with incomplete penetrance and variable expressivity [2]. Hereditary cases, accounting for approximately 20%, exhibit autosomal-dominant inheritance with incomplete penetrance and variable gene expression [3,4]. It is hypothesized that mutations in the CCM3 gene are associated with a more severe clinical course of the disease, including a high risk of hemorrhage in childhood [5].

2. Case Report History

A boy born on 21 August 2009 had a delay in psychomotor development. At the age of 6 months, pronounced bilateral convergent strabismus was diagnosed, and later, progressive weakness in the right extremities was observed. The first magnetic resonance imaging (MRI) performed on 7 September 2010 revealed multiple brain lesions. On 28 October 2010, the patient was admitted to the Burdenko Neurosurgical Center (BNC) (first admission). He had severe bilateral convergent strabismus and moderate right-sided hemiparesis and was unable to walk. An MRI on 2 November 2010 showed multiple cerebral cavernous malformations (CCMs) of Zabramski Types 1–4 (Figure 1A–D).

On 10 November 2010, the CCM and hematoma in the left frontal lobe were surgically removed, resulting in partial regression of hemiparesis and strabismus. Over the next four years, clinical examinations revealed the patient to be sociable and mobile, though he continued to exhibit persistent convergent strabismus. Speech development lagged behind age-appropriate milestones. There was no objective weakness in the right extremities, but a noticeable preference for using the left hand was evident. His gait was normal. Follow-up MRIs showed cystic and glial changes at the operation site and a slight increase in the size of the second medial CCM in the left frontal lobe.

On 8 August 2015, the patient developed hyperthermia, followed by weakness in the right extremities, dysphagia, and vomiting. An MRI on 18 August 2015 revealed a large hematoma in the left pons, multiple small lesions in both hemispheres, and gliosis in the left frontal lobe (Figure 2A–E). On 20 August 2015, he was readmitted to the BNC (second admission) with central tetraparesis, more pronounced on the right, along with mild peripheral left facial nerve palsy and bulbar symptoms. The CCM and hematoma in the brainstem were surgically removed on 25 August 2015 with intraoperative cranial nerve (VII, XIX, XII) monitoring (Figure 2D–F).

After the surgery, the neurological status improved significantly.

On 25 July 2017, the patient again developed right-sided hemiparesis and vomiting. An MRI on 1 August 2017 revealed a hemorrhage from the CCM of the left posterior temporal lobe and an enlargement of the left anterior temporal CCM (Figure 3A,B). Temporal CCM and chronic hematoma were surgically removed on 24 August 2017 at the BNC (third admission) (Figure 3C).

The next exacerbation on 30 March 2019 was marked by worsening of the right-sided hemiparesis. MRI revealed a new pontine hematoma and a significant increase in the size of the left anterior temporal CCM. On 30 April 2019, surgical removal of the left pontine and left anterior temporal CCMs was performed at the BNC (fourth admission). Control MRI on 5 May 2021 showed enlargement of the right frontal CCM and the appearance of a new CCM in the cerebellum with signs of hemorrhage (Figure 4B–C).

The last exacerbation was on 14 October 2021 followed by vomiting and progressive somnolence. MRI on 9 November 2021 revealed a large hematoma in the left temporal lobe and hydrocephalus (Figure 5A,B). On admission to the BNC (fifth admission) on 2 December 2021, the patient was somnolent. CT showed progressive enlargement of the ventricular system (Figure 5C). This required the placement of an external ventricular drain. Subsequently, a chronic hematoma in the left temporal lobe was removed, and a ventriculo-peritoneal shunt was implanted. Upon discharge, the patient was able to talk and walk with assistance.

Based on the last outpatient examination on 22 October 2024 and MRI on 15 October 2024, it was concluded that the clinical condition had stabilized.

A brief overview of the patient’s radiological progression is presented in

Table 1. Summary of radiological findings.

Admission	Date	Imaging Modality	Key Findings
1st admission	2 November 2010	MRI (Axial T1, SWAN)	Multiple CCMs, large hematoma in the left frontal lobe, small CCM in the left frontal lobe
1st admission	2 November 2010	MRI (Axial T2)	CCM in the left temporal lobe
1st admission	2 November 2010	MRI (Axial SWAN)	CCM in the right occipital lobe
2nd admission	18 August 2015	MRI (Axial T1, Coronal T2)	Large hematoma in the left pons, multiple small lesions in both hemispheres, gliosis in the left frontal lobe
2nd admission	25 August 2015	MRI (Axial FLAIR, Axial SWAN)	Post-surgical removal of pontine hematoma
3rd admission	1 August 2017	MRI (Axial T2)	Hemorrhage from CCM in the left posterior temporal lobe, enlargement of the left anterior temporal CCM
3rd admission	24 August 2017	CT Scan	Post-surgical removal of temporal CCM and hematoma
4th admission	30 April 2019	MRI	New pontine hematoma, enlargement of the left anterior temporal CCM
Follow-up	5 May 2021	MRI (Axial T1, Axial T2)	Enlargement of the right frontal CCM, new CCM in the cerebellum with signs of hemorrhage
5th admission	9 November 2021	MRI (Axial T2)	Large hematoma in the left temporal lobe, hydrocephalus
5th admission	2 December 2021	CT Scan	Progressive enlargement of the ventricular system

. It combines key observations from MRI and CT scans, reducing redundancy in the presented data.

A flow chart summarizing the clinical history and progress clinical trial is presented in Supplementary Figure S1. It provides a visual representation of the key events and interventions throughout the patient’s clinical course.

2.1. Family History

The patient’s grandmother died at the age of 36 due to ICH (no autopsy data are available). The patient’s mother had an ICH at the age of 12, after which the histologically confirmed CCM and temporal lobe hematoma were removed. She died at the age of 21 following a brainstem hemorrhage, also without available autopsy data. The patient’s sister and nephews were asymptomatic at the time of publication. The patient’s other relatives declined to undergo MRI.

2.2. Genetic Analysis

Genetic analysis was conducted in 2019. DNA isolation: DNA was isolated from a blood sample using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations. Genetic analysis: We used whole-exome sequencing for polymorphism analysis. DNA library preparation and exon selection were conducted using the KAPA HyperExome Prep Kit (Roche, Basel, Switzerland). The libraries were sequenced on a NovaSeq 6000 platform (Illumina, San Diago, CA, USA) with paired-end reads (2 × 150 bp). Acquired nucleotide reads were mapped to the reference genome (UCSC hg19; “URL (accessed on 20 October 2019)” https://www.ensembl.org/index.html) using the Bowtie2 package with “very sensitive local” parameters. Variant loci (SNP calling) were identified using the SAMtools v. 0.1.19 and BCFtools v. 1.9 packages.

Whole-exome sequencing identified a novel frameshift mutation, c.583_586delAACC, in the PDCD10 gene. This deletion causes a frameshift starting at amino acid 195, leading to a premature stop codon at position 197 and resulting in a truncated protein. The variant was detected in a heterozygous state. Sequencing depth at this locus was 118×, with an alternative allele frequency of 43%. While this specific mutation has not been previously described in the literature, other mutations at the same nucleotide position have been reported. These include a nonsense mutation c.586C>T (p.Arg196Ter) [rs1057517786; OMIM609118] and a frameshift duplication c.584dupT (p.Asn195fs) [rs1559941903; RCV000696694.5]; both are characterized as “pathogenic” and are associated with hereditary cavernous malformations of the CNS.

The mutation identified in this study (c.583_586delAACC) can be characterized as “probably pathogenic” because the deletion of four nucleotides in the heterozygous state causes a frameshift starting at amino acid 195, leading to a stop codon at position 197. This results in a truncated protein. Given that the PDCD10 protein consists of 202 amino acids, this truncation likely impairs protein function. This assumption is further supported by the inclusion of a similar mutation in the OMIM database: a nucleotide substitution that introduces a stop codon at position 196, has been found in two families and is associated with CCM occurrence. Additionally, no evidence of a second-hit somatic mutation was found in the analyzed samples, reinforcing the likelihood that this germline mutation underlies the patient’s multiple CCMs.

Thus, it is highly probable that the multiple CCMs in this patient are associated with the identified mutation. Preliminary MLPA DNA analysis of this patient did not reveal exon deletions in the CCM genes, confirming the uniqueness of the detected mutation.

3. Discussion

This case demonstrates an exceptionally severe progression of cerebral cavernous malformations (CCMs). The disease manifested in infancy, with frequent recurrent hemorrhages, progressive growth of existing malformations, and the appearance of new lesions. Each episode was accompanied by significant neurological complications, including the development of hemiparesis, impaired coordination, and a gradual decline in the patient’s overall condition. A total of five surgical interventions were performed to remove the most threatening lesions. Despite these efforts, the patient developed severe disability by the age of 13. This case represents a unique example of aggressive CCM progression, not previously observed among the 65 families with hereditary forms of the disease treated at the BNC.

The patient’s family history highlights the genetic nature of the condition. Both the patient’s mother and grandmother also suffered from CCM and died due to severe intracranial hemorrhages at a relatively young age. This genealogical pattern aligns with the autosomal dominant inheritance with incomplete penetrance characteristic of hereditary CCMs.

The existence of a third gene, in addition to CCM1 and CCM2, associated with the formation of cavernous malformations was proposed in the 1990s [6,7]. Subsequently, this gene was identified as CCM3 (PDCD10), confirming its role in the disease [4]. Unlike CCM1 and CCM2, which primarily participate in the CCM protein complex, CCM3 has broader regulatory functions. It interacts with key signaling molecules, including FAT-H, VEGFR3, and RIPOR1, which are essential for vascular stability, cell orientation, and morphology [8,9].

The mutation identified in this patient represents a novel deletion causing a frameshift and producing a truncated protein. This disrupts critical structural elements, such as the α-helices, necessary for PDCD10’s interactions with other proteins [9]. For example, its interaction with CCM2 through the phosphotyrosine-binding domain is impaired, potentially reducing the stability of vascular walls. Furthermore, PDCD10 stabilizes signals of VEGFR2 (vascular endothelial growth factor receptor 2), which regulates angiogenesis. Disruption of these pathways likely explains the aggressive disease progression observed in this case [8,10,11].

Literature data confirm that CCM3 mutations are less common than those in CCM1 and CCM2 (5–15% versus 40% and 30%, respectively) [12,13,14]. However, clinical manifestations in patients with CCM3 are markedly more severe. Such patients often experience disease onset in childhood, frequent hemorrhages, and worse outcomes, consistent with the observations in this case. Additionally, some studies have noted associations between CCM3 mutations and other pathological conditions, such as meningiomas [1,11,15,16,17,18,19,20,21,22,23,24].

Familial CCMs are typically associated with biallelic loss-of-function variants, wherein a germline mutation is inherited, and a second somatic mutation occurs in affected tissues. In this case, however, only a germline frameshift mutation in the PDCD10 gene was identified, with no evidence of a second-hit somatic mutation. This observation suggests that the identified germline mutation may be particularly deleterious, potentially explaining the aggressive clinical course observed in this patient. Further studies are warranted to elucidate whether additional molecular mechanisms contribute to disease progression in such cases.

Despite significant advances in understanding the molecular mechanisms of CCM, the biological role of these genes in disease development remains incompletely understood. Research indicates that the CCM1, CCM2, and CCM3 proteins function as part of a unified signaling complex interacting with other molecular systems. However, mutations in CCM3 cause the most severe disruptions, possibly due to its broader regulatory roles [23]. For instance, PDCD10 inhibits the BMP-6/ERK1/2 complex, preventing excessive angiogenesis. Its deficiency, conversely, promotes increased vascular growth and a higher number of cavernous malformations.

It is known that familial CCMs generally have a more aggressive course compared to sporadic ones. It should also be noted that CCMs can be found not only in the brain but also in the spinal cord. According to data from our center, spinal cord CMs account for approximately 4% of all CM cases. According to the literature, such cases represent about 9% [25]. It is important that patients with multiple CCMs, especially hereditary forms, should undergo not only head MRI but also spinal MRI. Also, it should be noted that while familial SCMs are strongly associated with germline CCM mutations, sporadic spinal lesions rarely harbor these variants. Instead, somatic mutations in MAP3K3 or PIK3CA have been implicated in isolated cases. Pharmacological therapies targeting hyperactive RhoA/ROCK or MAP3K3 signaling—currently under investigation for cerebral CCMs—may hold promise for spinal lesions, though spinal-specific trials are lacking [26].

This case also highlights the importance of genetic screening in families with hereditary CCMs. Early diagnosis and understanding of genetic features enable better prediction of disease progression and determination of effective treatment strategies. At present, therapeutic options are limited to surgical and radiosurgical interventions, as pharmacological treatments targeting CCM molecular mechanisms have yet to be developed.

4. Conclusions

In conclusion, this case supports the hypothesis that CCM3 mutations lead to more severe disease progression compared to CCM1 and CCM2. Further investigation into the molecular mechanisms of CCM3 mutations and their impact on biological processes may open new opportunities for developing targeted therapeutic strategies that improve outcomes for patients with these mutations. Also, genetic counseling is essential for families with hereditary CCMs to understand the inheritance pattern and assess the risk of disease transmission. Such tests as whole-exome sequencing (WES), multiplex ligation-dependent probe amplification (MLPA), and MRI screening will be very useful for early diagnosis of CCM.