Novel TECPR2 variant in two cases of hereditary sensory and autonomic neuropathy type 9: insights from genetic characterization and comprehensive literature review

Abstract

Background

Hereditary sensory and autonomic neuropathy type 9 (HSAN9) is a rare genetic disorder caused by genetic alterations in the TECPR2 locus and is characterized by developmental and intellectual disability, respiratory dysfunction, gastroesophageal reflux disease (GERD), and sensory and autonomic dysfunction, which are shared among the HSAN family.

Methods

Whole-exome sequencing (WES) was performed on samples from both probands, and the relevant genetic variants were confirmed in their families using Sanger sequencing. Additionally, a comprehensive literature review was conducted on previously reported cases of HSAN9, and the clinical and genetic data were assessed to provide insight into the genetic and clinical characteristics of the disease.

Results

We identified two new cases of HSAN9 with a shared novel variant of TECPR2 (NM_014844.5), c.1568del: p.Ser523PhefsTer12, classified as pathogenic according to ACMG guidelines. The probands showed characteristics of GERD, respiratory dysfunction, gait abnormalities, and developmental and speech delay, and both cases were deceased as a result of severe respiratory infection. The results of the literature review included 34 cases from 9 studies, revealing a wide range of genetic and clinical characteristics.

Conclusions

Our study identified two new cases of HSAN9 with a novel variant in TECPR2, confirmed by WES. The clinical characteristics of the patients as well as the conduction of a comprehensive literature review are crucial in the early diagnosis and management of the disease and establishment of genotype-phenotype correlations.

Introduction

Genetic alterations in the tectonin β-propeller repeat containing protein 2 (TECPR2) locus, a protein component of autophagy, are associated with the incidence of hereditary sensory and autonomic neuropathy type IX (HSAN9, OMIM #615031). HSANs are a heterogeneous family of genetic disorders characterized by progressive dysfunction of autonomic and sensory components of the peripheral nervous system (PNS). HSAN9, primarily known as hereditary spastic paraplegia 49 (HSP49), is an autosomal recessive disorder with intellectual disability, global developmental delay, and respiratory dysfunction in addition to the aforementioned shared characteristics of HSAN disorders [1,2,3,4]. This disease was first identified in 2012 by Oz-Levi et al. in five patients from three families with intellectual disability, gastroesophageal reflux disease (GERD), central apnea, areflexia, and facial dysmorphism [1].

Due to the heterogeneous manifestations of HSAN9 patients, as well as the limited number of confirmed cases, the identification of new cases and genetic variants is crucial in the clinical understanding of the disease and establishing genotype-phenotype correlations.

The aim of this study is to provide a comprehensive literature review on HSAN9, a rare disorder characterized by peripheral neuropathy. This review explores the clinical manifestations, genetic basis, and management strategies associated with HSAN9. Additionally, this study reports two new cases of HSAN9 in an Iranian population, characterized by a shared novel variant of TECPR2 (c.1568del: p.Ser523PhefsTer12). By combining the literature review with the introduction of these new cases, this study aims to explore the genotype-phenotype correlation of HSAN9 and contribute to the understanding and recognition of this condition in various populations.

Case presentation

Case 1

The patient was a three-year-old girl and the result of a full-term cesarean section delivery, with a birth weight of 4 kg (z-score = 1.6, <+2SD), born to healthy, first-cousin parents. The proband had a familial history of Down syndrome in a paternal uncle, as well as history of speech delay in another paternal uncle. However, there was no family history of HSAN9 present. The disease onset occurred at birth, with a presentation of recurrent milk aspiration. The patient showed signs of failure to thrive (FTT), microcephaly, and hearing loss with no findings suggestive of vision impairment, facial dysmorphism, or tooth abnormality in the head and neck regions. She experienced swallowing difficulty resulting in recurrent hospital admissions due to aspiration, respiratory dysfunction, pneumonia, and severe GERD. However, there were no signs of impaired bowel habits. Specific cutaneous or hair abnormalities were not observed. Nevertheless, the patient experienced dermatitis lesions all over her face as well as symmetrically on her upper and lower limbs. She also experienced severe allergic reactions in response to the consumption of egg whites.

Regarding the child’s developmental milestones, unassisted walking was delayed, and she never achieved running, displaying signs of ataxic-like gait. In addition, the patient had speech impairment, and despite the use of simple two-syllabic words at the age of 1, she eventually lost the ability to speak entirely. Signs of intellectual disability and reduced sensitivity to pain were also present. However, no signs of autistic features were detected.

The patient passed away at the age of three due to severe respiratory infection.

Case 2

The second case involved a seven-year-old girl, the result of a full-term pregnancy with normal vaginal delivery (NVD) and a birth weight of 4200 g (z-score = 1.9, <+2SD) from healthy parents with consanguineous marriage. The patient had no familial history of congenital developmental conditions. The first sign of the disease was manifested with failure to thrive at a young age, although the patient was diagnosed at the age of 2. She had a short stature, standing at 70 centimeters tall at the age of 7 (below the 5th percentile), and lower than normal height throughout life, as well as general muscular atrophy. However, no signs of facial dysmorphism were present. She also had mild bilateral esotropia with no vision impairment. In addition, the morphological characteristics of the front teeth underwent a transformation later in life, manifesting as a change from the typical shape to a fang-like appearance. No other signs of sensory deficit or head and neck abnormalities were present.

The patient experienced swallowing difficulty and was repeatedly admitted due to recurrent aspiration pneumonia and respiratory dysfunction. In her last two years of life, a percutaneous endoscopic gastrostomy (PEG) was provided to assist with feeding. No cutaneous lesions were present. However, she had relatively thin, scarce hair with no signs of patchy hair loss characteristic of alopecia areata. Among the developmental milestones, independent sitting was delayed until the age of 2, and she was not able to walk without assistance. Her speech was impaired and she showed behavioral abnormalities in the form of temper tantrums and self-harm tendencies. She experienced multiple episodes of seizures secondary to COVID-19 infection and was admitted with severe respiratory dysfunction as a result of COVID-19 and passed away at the age of 7.

Methods

Blood samples were collected from the patients and both of their parents, and genomic DNA was extracted from the white blood cells using the standard salting out procedure [5]. In the process of WES, genomic DNA enrichment was conducted using the SureSelectXT V6 + UTRs Kit (Agilent Technologies, Lake Forest, CA, USA), and paired-end sequencing was performed using the NovaSeq 6000 platform abiding by the manufacturer’s protocol (Illumina, San Diego, CA, USA). In the next step, the sequences were aligned to the reference human genome (UCSC hg19, NCBI build 37.1) using the Burrows‒Wheeler Aligner (BWA v 0.5.9) [6]. The duplicates generated by the polymerase chain reaction (PCR) were eliminated using the Picard tool (v 1.118). The test platform examined > 95% of the target regions and offered a sensitivity of > 99% and a 100X mean coverage. The Genome Analysis Toolkit (GATK v 3.7) was used to conduct variant calling [7]. Variant annotation was carried out using the ANNOVAR tool [8]. Identification of variants in the 1000 Genomes Project dbSNP 138, ESP6500 and Iranome (www.iranome.com) was defined by a minor allele frequency < 0.01. Furthermore, they were subjected to additional filtering based on pathogenicity and effect of the mutation, databases of clinically relevant variants, presence in the population, and previously established genotype-phenotype correlations as per existing literature. Variant prioritization was ultimately conducted using phenotype plausibility. Confirmation of the variants involved Sanger sequencing of the patient samples as well as targeted Sanger sequencing of the parental samples. The primers were designed by Gene Runner Software (v 3.05) specifically for exon 9 and the surrounding introns (Table 1).

Table 1 Primer pair for PCR

Gathering Reported Cases of HSAN9 Molecularly and Clinically.

The literature review involved a systematic search of relevant databases such as PubMed, Scopus, Web of Science, and Google Scholar. The search strategy was created using a combination of keywords and Boolean operators to refine the search and capture relevant articles. Inclusion criteria were established to ensure the selection of only peer-reviewed journal articles and conference proceedings written in English, specifically focusing on TECPR2 gene expression, function, regulation, or mechanism. Initial screening of articles was conducted based on titles and abstracts, followed by a full-text assessment for relevance by two independent reviewers, and conflicts were resolved by a third reviewer. Relevant data from the selected articles were extracted using a standardized data extraction form and thematically analyzed to identify key themes, patterns, and trends in the findings. The quality of the included studies was assessed using appropriate tools, and the findings were presented following academic writing guidelines and standards. The TECPR2 review provided insights into the current knowledge of TECPR2 gene expression and function, while the HSAN9 review summarized the reported cases of the condition.

Results

In this study, two new cases of HSAN9 were discussed in an Iranian population with a shared novel variant identified by WES. The results of WES revealed a novel homozygous variant, c.1568del: p.Ser523PhefsTer12, located in exon 9, present in both cases. This variant has not been reported in gnomAD, the 1000 Genome Project, and Iranome and is considered pathogenic based on ACMG guidelines. There is supporting evidence of pathogenicity according to allelic data and it is considered moderately pathogenic according to population data, and strongly pathogenic according to its effect on the protein and the PM3, PM2, and PVS1 ACMG criteria are met, respectively [9]. The pedigree and results of Sanger sequencing in both cases are depicted in Figs. 1 and 2. The schematic structures of the wild-type and mutated TECPR2 proteins are illustrated in Fig. 3.

Fig. 1

Familial pedigree and electropherograms of case 1 and her parent (B). Sequencing analysis of case 1 (IV-2) identified a homozygous variant c.1568del (p.Ser523PhefsTer12) in the TECPR2. Segregation analysis revealed parent to be heterozygous

Fig. 2

Familial pedigree (A) and electropherograms of case 2 (IV-1) and her parent (B). Sequencing analysis of case 2 (III-1) identified a homozygous variant c.1568del (p.Ser523PhefsTer12) in the TECPR2. Segregation analysis revealed parent to be heterozygous

Fig. 3

Schematic illustration of (A) wild-type TECPR2 and (B) Mutant TECPR2 with c.1568del; p.Ser523PhefsTer12, resulting in a frameshift and a premature stop codon. Tryptophan-aspartate (WD) repeats, the poly-lysine tract (polyK), and TECPR domains are significant conserved domains in the structure of the wild-type TECPR2

Following the conduction of the literature review, a total of 34 cases from 10 studies, with a variety of missense, nonsense, and truncating variants in the TECPR2 genetic loci (NM_014844.5), were included (Table 2).

Table 2 Summary of 34 cases with variants in the TECPR2 genetic loci from 9 studies

Discussion

In this study, we analyzed a considerably expansive cohort of individuals exhibiting damaging variations in TECPR2. This investigation encompasses a substantial number of participants, providing a strong foundation for exploring the complexities of this condition. Additionally, we have included an extensive literature review of previously reported cases of HSAN9. In total, 34 cases were reviewed, including the two new families presented here, which showcase a diverse clinical and genetic spectrum.

The two novel cases reported in this study are the first patients of HSAN9 of Iranian descent. The discussed probands in this study are two cases of HSAN9, with a shared homozygous novel variant, TECPR2 (NM_014844.5): c.1568del: p.Ser523PhefsTer12, from two distinct families. This variant is considered pathogenic according to the aforementioned ACMG criteria, and due to the resultant loss-of-function, it is implicated in clinical approaches and genetic counseling. In both cases, parents were carriers of the same variant. The patients showed symptoms such as failure to thrive, feeding difficulties, GERD, and recurrent respiratory infections, which were the primary causes of death in both cases. Gait and speech impairments were also observed in both instances. The clinical presentation in both cases aligns with the previously reported clinical features of HSAN9.

TECPR2 is an enhancer of autophagy by binding to human autophagy-related 8 (ATG8) [10]. Autophagy is a cellular process crucial for the digestion of subcellular components through the formation of autophagosomes. The formation of autophagosomes involves two major protein complexes: ULK1 and class III PI3-kinase complex I (PI3KC3-C1). Additionally, ATG9, a transmembrane protein component, plays a role in this process. Upon the activation of these components and downstream proteins of the ATG8 family, WIPI-1 to WIPI-4, and ATG12, various reactions are driven, the hallmark of which is LC3 lipidation, the process of phosphatidylethanolamine attachment to the ATG8/LC3 family. Furthermore, various vesicular trafficking proteins, including COP I, COP II, SNARE, and Rab GTPase, are also involved in autophagy [11]. TECPR2 is likely to be involved in this pathway as a scaffold protein. Its binding to LC3C, a member of the ATG8 family, enables localization to the endomembrane, enhancing its ability to bind to and stabilize the levels of COPII subunit, SEC24D, a cellular trafficking agent, assisting in the formation of SEC24D/SEC23A heterodimer at the assembly site of COP II. Formation of COPII-coated vesicles is involved in membrane exchange between the endoplasmic reticulum and the phagophore [10, 11]. Fig. 4 illustrates the cellular mechanism of autophagy.

Fig. 4

The cellular mechanism of autophagy. This figure was created using the Servier Medical Art Commons Attribution 3.0 Unported License (http://smart.servier.com (accessed 18 August 2023))

Studies have suggested a role for TECPR2 in autophagosome targeting/fusion based on evidence of autophagosome accumulation linked to TECPR2 variants. Additionally, TECPR2 has been associated with homotypic fusion and protein sorting complex (HOPS) and the biogenesis of lysosome-related organelle complex 1 (BLOC-1). TECPR2, in cooperation with lipidated LC3, is also involved in the stabilization of SEC24D, a component of COP II, which is involved in endoplasmic reticulum (ER)-Golgi trafficking at the ER exit site (ERES) [10, 12].

TECPR2 is a relatively large multidomain protein with 1411 residues, containing an amino-terminal domain, a carboxy terminal domain, and an LC3-interacting region (LIR) motif at the carboxy terminal. The N- and C-termini contain a WD (tryptophane-aspartic acid) domain and a TECPR domain, respectively (Fig. 3) [1].

Hereditary sensory and autonomic neuropathies (HSANs) are a group of diverse neurodevelopmental and neurodegenerative conditions with characteristic peripheral sensory and autonomic dysfunction [12]. To date, 16 subtypes have been identified, with HSAN9 being the most recently recognized subtype, an autosomal recessive neurodevelopmental disorder caused by variants in the TECPR2 genetic locus [12].

To date, fewer than 40 cases have been documented, displaying a broad range of phenotypic variations. The clinical and genetic characteristics of the identified cases are summarized in Table 2. The first variant of HSAN was reported by Oz-Levi et al. in 2012 in five patients of Jewish Bukharian heritage and was initially classified as hereditary spastic paraplegia 49 (HSP49). The patients were members of three distinct families and had a homozygous shared variant, c.3416delT, in exon 16 of TECPR2. The clinical manifestations of the disease included spastic paraparesis, intellectual disability, respiratory dysfunction, GERD, dysmorphism, and absent reflexes, as well as signs of progressive brain atrophy in multiple sites in MRI findings [1].

In 2015, Zhu et al. conducted whole exome sequencing analysis on 119 trios of patients with suspected genetic disorders and identified a trio with a homozygous frameshift variant in TECPR2 (c.1319delT). The male patient in this trio, born to parents without a consanguineous marriage history, displayed clinical symptoms such as hypotonia, GERD, respiratory problems, absent reflexes, intellectual disability, encephalopathy, and autonomic dysfunction from infancy [13]. Heimer et al. reported three patients with two novel variants, c.1319delT and c. 566 C > T in TECPR2. In addition to the previously reported disease characteristics, these patients showed significant signs of sensory autonomic neuropathy, such as insensitivity to specific stimuli, hypotonia, absent reflexes, vasomotor dysfunction, temperature abnormality, and episodic reduced arousal. Based on the sensory autonomic findings, Heimer et al. proposed reclassifying such cases as an HSAN subtype in contrast to the previous classification as HSP49 [2]. Two additional patients with similar genotypic and phenotypic characteristics were also identified by Palma et al. in 2021 [14]. Neuser et al. identified 17 patients from 15 distinct families with biallelic variants in TECPR2. The patients showed patterns of intellectual disability, developmental delay, hypotonia, ataxia, brisk reflexes, and respiratory dysfunction [4].

Covone et al. reported a 16-year-old case of motor neuron disease with a compound heterozygote missense variant genotype and classical HSAN9 phenotype as previously mentioned, with normal intellectual abilities. The patient was also positive for a heterozygote missense variant in the SPG7 genetic locus, potentially contributing to the observed phenotype [3]. In addition to the aforementioned studies, several patients with compound heterozygous genotype and clinical presentations of HSAN9 have been reported to date [15,16,17]. The latest reported cases of are two Palestinian siblings with a shared novel homozygous variant, c.745G > A, displaying classical HSAN9 traits, including developmental delay and sensorimotor dysfunction, facial dysmorphism, as well as history of hospitalization due to exacerbation of symptoms and respiratory distress [18].

The patients discussed in this study are both female cases of HSAN9 with a shared homozygous variant, c.1568del: p.Ser523PhefsTer12, located in exon 9 of the TECPR2 genetic locus. Both patients were born from consanguineous marriages between carriers of the same variant. Both probands showed characteristic signs of HSAN9, such as recurrent respiratory infections, gait abnormalities, and developmental delays. The second case displayed strabismus, along with behavioral abnormalities in the form of temper tantrums and self-mutilation. When compared to the known clinical spectrum of previously identified cases, both probands showed both similarities and differences. Similar to most reported cases, the age of onset was early in life. However, some reported cases with a compound heterozygous genotype had a relatively delayed disease onset. Notably, both probands had a relatively high birthweight. While birthweight has not been consistently reported in most previous cases, the cases where it is included in the data do not exhibit such characteristics.

GERD is a frequently observed finding in most cases of HSAN9. Patient 1 in our study showed signs of severe GERD, while patient 2 did not. Patient 2 showed sensory dysfunction in the form of reduced sensitivity to pain, a common trait among HSAN9 cases. Abnormal gait, developmental delay, recurrent aspiration pneumonia, and severe respiratory failure were also among the frequently observed clinical characteristics both in the literature and our cohort. FTT, microcephaly, short stature, hearing loss, strabismus, behavioral signs, and hair and teeth abnormalities were also noted in our study’s probands, consistent with previously reported cases. In addition, the first case showed signs of immunological hypersensitivity reactions, including dermatitis and a severe allergic reaction to egg white.

Conclusion

In this study, we reported two new cases of HSAN9 with a shared novel variant of TECPR2. The comprehensive literature review on the previously reported cases and description of the clinical and genetic characteristics of our probands provides valuable insight into the genetic and clinical landscape of this rare disease. This information can play a crucial role in enhancing our understanding of the genotype-phenotype correlation, aiding in the early detection of suspected cases, and confirming diagnoses through molecular methodologies.