Chiari 1 malformation and exome sequencing in 51 trios: the emerging role of rare missense variants in chromatin-remodeling genes

Congenital syndromic Chiari-like malformation (CSCM) in Holstein cattle: towards unravelling of possible genetic causes

BACKGROUND

Chiari malformation type II (CMII) was originally reported in humans as a rare disorder characterized by the downward herniation of the hindbrain and towering cerebellum. The congenital brain malformation is usually accompanied by spina bifida, a congenital spinal anomaly resulting from incomplete closure of the dorsal aspect of the spinal neural tube, and occasionally by other lesions. A similar disorder has been reported in several animal species, including cattle, particularly as a congenital syndrome. A cause of congenital syndromic Chiari-like malformation (CSCM) in cattle has not been reported to date. We collected a series of 14 CSCM-affected Holstein calves (13 purebred, one Red Danish Dairy F1 cross) and performed whole-genome sequencing (WGS). WGS was performed on 33 cattle, including eight cases with parents (trio-based; group 1), three cases with one parent (group 2), and three single cases (solo-based; group 3).

RESULTS

Sequencing-based genome-wide association study of the 13 Holstein calves with CSCM and 166 controls revealed no significantly associated genome region. Assuming a single Holstein breed-specific recessive allele, no region of shared homozygosity was detected suggesting heterogeneity. Subsequent filtering for protein-changing variants that were only homozygous in the genomes of the individual cases allowed the identification of two missense variants affecting different genes, SHC4 in case 4 in group 1 and WDR45B in case 13 in group 3. Furthermore, these two variants were only observed in Holstein cattle when querying WGS data of > 5,100 animals. Alternatively, potential de novo mutational events were assessed in each case. Filtering for heterozygous private protein-changing variants identified one DYNC1H1 frameshift variant as a candidate causal dominant acting allele in case 12 in group 3. Finally, the presence of larger structural DNA variants and chromosomal abnormalities was investigated in all cases. Depth of coverage analysis revealed two different partial monosomies of chromosome 2 segments in cases 1 and 7 in group 1 and a trisomy of chromosome 12 in the WDR45B homozygous case 13 in group 3.

CONCLUSIONS

This study presents for the first time a detailed genomic evaluation of CSCM in Holstein cattle and suggests an unexpected genetic and allelic heterogeneity considering the mode of inheritance, as well as the type of variant. For the first time, we propose candidate causal variants that may explain bovine CSCM in a certain proportion of affected calves. We present cattle as a large animal model for human CMII and propose new genes and genomic variants as possible causes for related diseases in both animals and humans.

Broadening the ocular phenotypic spectrum of ultra-rare BRPF1 variants: report of two cases

INTRODUCTION

BRPF1 gene on 3p26-p25 encodes a protein involved in epigenetic regulation, through interaction with histone H3 lysine acetyltransferases KAT6A and KAT6B of the MYST family. Heterozygous pathogenic variants in BRPF1 gene are associated with Intellectual Developmental Disorder with Dysmorphic Facies and Ptosis (IDDDFP), characterized by global developmental delay, intellectual disability, language delay, and dysmorphic facial features. The reported ocular involvement includes strabismus, amblyopia, and refraction errors. This report describes a novel ocular finding in patients affected by variants in the BRPF1 gene.

METHODS

We performed exome sequencing and deep ocular phenotyping in two unrelated patients (P1, P2) with mild intellectual disability, ptosis, and typical facies.

RESULTS

Interestingly, P1 had a Chiari Malformation type I and a subclinical optic neuropathy, which could not be explained by variations in other genes. Having detected a peculiar ocular phenotype in P1, we suggested optical coherence tomography (OCT) for P2; such an exam also detected bilateral subclinical optic neuropathy in this case.

DISCUSSION

To date, only a few patients with BRPF1 variants have been described, and none were reported to have optic neuropathy. Since subclinical optic nerve alterations can go easily undetected, our experience highlights the importance of a more detailed ophthalmologic evaluation in patients with BRPF1 variant.

Human genetics and molecular genomics of Chiari malformation type 1

Chiari malformation type 1 (CM1) is the most common structural brain disorder involving the craniocervical junction, characterized by caudal displacement of the cerebellar tonsils below the foramen magnum into the spinal canal. Despite the heterogeneity of CM1, its poorly understood patho-etiology has led to a 'one-size-fits-all' surgical approach, with predictably high rates of morbidity and treatment failure. In this review we present multiplex CM1 families, associated Mendelian syndromes, and candidate genes from recent whole exome sequencing (WES) and other genetic studies that suggest a significant genetic contribution from inherited and de novo germline variants impacting transcription regulation, craniovertebral osteogenesis, and embryonic developmental signaling. We suggest that more extensive WES may identify clinically relevant, genetically defined CM1 subtypes distinguished by unique neuroradiographic and neurophysiological endophenotypes.

A Novel Craniocervical Junction Compression Severity Index-Based Grading System for Multidirectional Quantification of the Biomechanics at Foramen Magnum of Chiari Malformation Type I

Objective  This study aimed to establish a novel grading system, based on the craniovertebral junction compression severity index (CVJCSI) for multidirectional quantification at the foramen magnum plane for Chiari malformation type I (CMI). Methods  The CVJCSI grading system was established to stratify patients based on the ventral (modified clivoaxial angle < 138°), dorsal (tonsil herniation), and central (brainstem herniation) CVJ (craniovertebral junction) compression, the CVJCSI grading system was established to stratify patients. The optimal surgical method for each grade was recommended by intragroup comparisons regarding the efficacy of the three operations. Finally, according to the CVJCSI grading system, a prospective validation trial was performed and surgically treated for internal validation. Results  Based on the retrospective study ( n  = 310), the CVJCSI included six grades: I: syrinx alone without compression; II: dorsal compression; III: dorsal and central compression; IV: ventral compression; V: dorsal and ventral compression; and VI: ventral, dorsal, and central compression. Among all available variables, only the CVJCSI and surgical methods significantly affected the CCOS. The CCOS scores, overall and for each CVJCSI grade, increased in the prospective cohort ( n  = 42) compared with that in the retrospective analysis. Conclusions  The CVJCSI can be used to stratify CMI patients. The higher the CVJCSI grade, the more severe the CVJ compression and the worse posterior fossa deformity. Meanwhile, the CVJCSI was negatively correlated with the CCOS. The lower the CVJCSI grade, the better the response to surgery, and the less-invasive surgical procedures were warranted. Finally, the prospective cohort study validated the proposed CVJCSI-based surgical protocols.

Evidence for a Pathogenic Role of CSMD1 in Childhood Apraxia of Speech

Childhood apraxia of speech (CAS) is a pediatric motor speech disorder. The genetic etiology of this complex neurological condition is not yet well understood, although some genes have been linked to it. We describe the case of a boy with a severe and persistent motor speech disorder, consistent with CAS, and a coexisting language impairment.Whole exome sequencing in our case revealed a de novo and splicing mutation in the CSMD1 gene.

Chiari Syndrome: Advances in Epidemiology and Pathogenesis: A Systematic Review

Arnold Chiari syndrome is a rare congenital disease of unknown prevalence and whose origin is still under study. It is encompassed within the posterior cranial malformations, showing a wide spectrum of symptomatology that can range from severe headache, dizziness, and paresthesia to complete asymptomatology. It is for this reason that early diagnosis of the disease is difficult, and it is usually diagnosed in adolescence. Treatment is based on remodeling and decompression of the malformed posterior cranial fossa, although the risk of residual symptoms after surgery is high. The aim of this review is to update all the existing information on this pathology by means of an exhaustive analysis covering all the scientific literature produced in the last 5 years. In addition, it has been carried out following the PRISMA model and registered in PROSPERO with code CRD42023394490. One of the main conclusions based on the results obtained in this review is that the origin of the syndrome could have a genetic basis and that the treatment of choice is the decompression of the posterior cerebral fossa.

Congress of Neurological Surgeons Systematic Review and Evidence-Based Guidelines for Patients With Chiari Malformation: Symptoms

BACKGROUND

Chiari I malformation (CIM) is characterized by descent of the cerebellar tonsils through the foramen magnum, potentially causing symptoms from compression or obstruction of the flow of cerebrospinal fluid. Diagnosis and treatment of CIM is varied, and guidelines produced through systematic review may be helpful for clinicians.

OBJECTIVE

To perform a systematic review of the medical literature to answer specific questions on the diagnosis and treatment of CIM.

METHODS

PubMed and Embase were queried between 1946 and January 23, 2021, using the search strategies provided in Appendix I of the full guidelines.

RESULTS

The literature search yielded 430 abstracts, of which 79 were selected for full-text review, 44 were then rejected for not meeting the inclusion criteria or for being off-topic, and 35 were included in this systematic review.

CONCLUSION

Four Grade C recommendations were made based on Class III evidence, and 1 question had insufficient evidence. The full guidelines can be seen online at https://www.cns.org/guidelines/browse-guidelines-detail/2-symptoms .

Chiari I malformation: management evolution and technical innovation

BACKGROUND AND DEFINITION

In recent years thanks to the growing use of radiological assessment, Chiari I malformation became one of the major diseases for a neurosurgeon to deal with. CIM can be classified according to the extent of cerebellar tonsil tip into the foramen magnum being a protrusion over five mm considered pathological. Such a disease is a heterogeneous condition with a multifactorial pathogenetic mechanism that can subdivided into a primary and secondary form. Regardless of the form, it seems that CIM is the result of an imbalance between the volume of the braincase and its content. Acquired CIMs are secondary to conditions causing intracranial hypertension or hypotension while the pathogenesis of primary forms is still controversial.

PATHOGENESIS AND TREATMENT

There are several theories in the literature but the most accepted one implies an overcrowding due to a small posterior cranial fossa. While asymptomatic CIM do not need treatment, symptomatic ones prompt for surgical management. Several techniques are proposed being the dilemma centered in the need for dural opening procedures and bony decompression ones.

CONCLUSION

Alongside the paper, the authors will address the novelty presented in the literature on management, diagnosis and pathogenesis in order to offer a better understanding of such a heterogeneous pathology.

Optic nerve involvement in CACNA1F-related disease: observations from a multicentric case series

BACKGROUND

Congenital Stationary Night Blindness (CSNB) constitutes a group of non-progressive retinal disorders characterized by disturbances in scotopic vision and/or by a delay in adaptation to darkness, as well as by low visual acuity, myopia, nystagmus, and strabismus. Color vision and fundus appearance tend to be normal. To date, several CACNA1F gene variants have been linked to a CSNB phenotype but only few reports have focused on the optic nerve in this disease.

MATERIALS AND METHODS

Twelve patients underwent standard ophthalmological and genetic evaluation including spectral domain optical coherence tomography (SD-OCT), full-field electroretinography (ffERG), kinetic perimetry, fundus photography, magnetic resonance imaging (MRI), and next-generation sequencing (NGS). Bilateral thinning of the peripapillary nerve fiber layer (pRNFL) and the ganglion cell complex (GCC) supported involvement of the optic nerves. MRI, when available, was assessed for gross intracranial optic pathway abnormalities.

RESULTS

All patients were shown to carry pathogenic variants in the CACNA1F gene, and all showed signs of optic nerve involvement. All patients showed a certain degree of myopic refractive error. Low average pRNFL thickness was evident in all patients. In three of them, pRNFL thickness was evaluated longitudinally and was proven to be stable over time. MRI imaging was unremarkable in all cases.

CONCLUSION

Our data support the hypothesis that CACNA1F could be related to early-onset or congenital optic nerve involvement without any signs of a progressive optic neuropathy. Even though additional data from larger cohorts and longer follow-up periods are needed to further support and confirm our findings, there is a clear significance to our findings in the preparation for future CACNA1F gene therapy trials.

On the association between Chiari malformation type 1, bone mineral density and bone related genes

Background

Chiari malformation type 1 (C1M) is a neurological disease characterized by herniation of the cerebellar tonsils below the foramen magnum. Cranial bone constriction is suspected to be its main cause. To date, genes related to bone development (e.g. DKK1 or COL1A2) have been associated with C1M, while some bone diseases (e.g. Paget) have been found to cosegregate with C1M. Nevertheless, the association between bone mineral density (BMD) and C1M has not been investigated, yet. Here, we systematically investigate the association between C1M and BMD, and between bone related genes and C1M.

Methods

We have recruited a small cohort of C1M patients (12 unrelated patients) in whom we have performed targeted sequencing of an in-house bone-related gene panel and BMD determination through non-invasive DXA.

Results

In the search for association between the bone related genes and C1M we have found variants in more than one C1M patient in WNT16, CRTAP, MYO7A and NOTCH2. These genes have been either associated with craniofacial development in different ways, or previously associated with C1M (MYO7A). Regarding the potential link between BMD and C1M, we have found three osteoporotic patients and one patient who had high BMD, very close to the HBM phenotype values, although most patients had normal BMD.

Conclusions

Variants in bone related genes have been repeatedly found in some C1M cases. The relationship of bone genes with C1M deserves further study, to get a clearer estimate of their contribution to its etiology. No direct correlation between BMD and C1M was observed.

•

We used an in-house bone gene panel to investigate a small cohort of C1M patients.

•

Variants in WNT16, CRTAP, MYO7A and NOTCH2 were found in more than one C1M patient.

•

No clear relationship was found between C1M and BMD in this small C1M cohort.

Dissection of contiguous gene effects for deletions around ERF on chromosome 19

Heterozygous intragenic loss-of-function mutations of ERF, encoding an ETS transcription factor, were previously reported to cause a novel craniosynostosis syndrome, suggesting that ERF is haploinsufficient. We describe six families harboring heterozygous deletions including, or near to, ERF, of which four were characterized by whole-genome sequencing and two by chromosomal microarray. Based on the severity of associated intellectual disability (ID), we identify three categories of ERF-associated deletions. The smallest (32 kb) and only inherited deletion included two additional centromeric genes and was not associated with ID. Three larger deletions (264-314 kb) that included at least five further centromeric genes were associated with moderate ID, suggesting that deletion of one or more of these five genes causes ID. The individual with the most severe ID had a more telomerically extending deletion, including CIC, a known ID gene. Children found to harbor ERF deletions should be referred for craniofacial assessment, to exclude occult raised intracranial pressure.