Storage of skin biopsies at -70 degrees C for future fibroblast culture

Integrated multi-omics for rapid rare disease diagnosis on a national scale

Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.

Severe NAD(P)HX Dehydratase (NAXD) Neurometabolic Syndrome May Present in Adulthood after Mild Head Trauma

We have previously reported that pathogenic variants in a key metabolite repair enzyme NAXD cause a lethal neurodegenerative condition triggered by episodes of fever in young children. However, the clinical and genetic spectrum of NAXD deficiency is broadening as our understanding of the disease expands and as more cases are identified. Here, we report the oldest known individual succumbing to NAXD-related neurometabolic crisis, at 32 years of age. The clinical deterioration and demise of this individual were likely triggered by mild head trauma. This patient had a novel homozygous NAXD variant [NM_001242882.1:c.441+3A>G:p.?] that induces the mis-splicing of the majority of NAXD transcripts, leaving only trace levels of canonically spliced NAXD mRNA, and protein levels below the detection threshold by proteomic analysis. Accumulation of damaged NADH, the substrate of NAXD, could be detected in the fibroblasts of the patient. In agreement with prior anecdotal reports in paediatric patients, niacin-based treatment also partly alleviated some clinical symptoms in this adult patient. The present study extends our understanding of NAXD deficiency by uncovering shared mitochondrial proteomic signatures between the adult and our previously reported paediatric NAXD cases, with reduced levels of respiratory complexes I and IV as well as the mitoribosome, and the upregulation of mitochondrial apoptotic pathways. Importantly, we highlight that head trauma in adults, in addition to paediatric fever or illness, may precipitate neurometabolic crises associated with pathogenic NAXD variants.

Expanding the Allelic Heterogeneity of ANO10-Associated Autosomal Recessive Cerebellar Ataxia

Background and Objectives

The term autosomal recessive cerebellar ataxia (ARCA) encompasses a diverse group of heterogeneous degenerative disorders of the cerebellum. Spinocerebellar ataxia autosomal recessive 10 (SCAR10) is a distinct classification of cerebellar ataxia caused by variants in the ANO10 gene. Little is known about the molecular role of ANO10 or its role in disease. There is a wide phenotypic spectrum among patients, even among those with the same or similar genetic variants. This study aimed to characterize the molecular consequences of variants in ANO10 and determine their pathologic significance in patients diagnosed with SCAR10.

Methods

We presented 4 patients from 4 families diagnosed with spinocerebellar ataxia with potential pathogenic variants in the ANO10 gene. Patients underwent either clinical whole-exome sequencing or screening of a panel of known neuromuscular disease genes. Effects on splicing were studied using reverse transcriptase PCR to analyze complementary DNA. Western blots were used to examine protein expression.

Results

One individual who presented clinically at a much earlier age than typical was homozygous for an ANO10 variant (c.1864A > G [p.Met622Val]) that produces 2 transcription products by altering an exonic enhancer site. Two patients, both of Lebanese descent, had a homozygous intronic splicing variant in ANO10 (c.1163-9A > G) that introduced a cryptic splice site acceptor, producing 2 alternative transcription products and no detectable wild-type protein. Both these variants have not yet been associated with SCAR10. The remaining patient was found to have compound heterozygous variants in ANO10 previously associated with SCAR10 (c.132dupA [p.Asp45Argfs*9] and c.1537T > C [p.Cys513Arg]).

Discussion

We presented rare pathogenic variants adding to the growing list of ANO10 variants associated with SCAR10. In addition, we described an individual with a much earlier age at onset than usually associated with ANO10 variants. This expands the phenotypic and allelic heterogeneity of ANO10-associated ARCA.

Pathogenic variants in nucleoporin TPR (translocated promoter region, nuclear basket protein) cause severe intellectual disability in humans

The nuclear pore complex (NPC) is a multi-protein complex that regulates the trafficking of macromolecules between the nucleus and cytoplasm. Genetic variants in components of the NPC have been shown to cause a range of neurological disorders, including intellectual disability and microcephaly. Translocated promoter region, nuclear basket protein (TPR) is a critical scaffolding element of the nuclear facing interior of the NPC. Here, we present two siblings with biallelic variants in TPR who present with a phenotype of microcephaly, ataxia and severe intellectual disability. The variants result in a premature truncation variant, and a splice variant leading to a 12-amino acid deletion respectively. Functional analyses in patient fibroblasts demonstrate significantly reduced TPR levels, and decreased TPR-containing NPC density. A compensatory increase in total NPC levels was observed, and decreased global RNA intensity in the nucleus. The discovery of variants that partly disable TPR function provide valuable insight into this essential protein in human disease, and our findings suggest that TPR variants are the cause of the siblings' neurological disorder.

Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function

Pyridine Nucleotide-Disulfide Oxidoreductase Domain 2 (PYROXD2; previously called YueF) is a mitochondrial inner membrane/matrix-residing protein and is reported to regulate mitochondrial function. The clinical importance of PYROXD2 has been unclear, and little is known of the protein’s precise biological function. In the present paper, we report biallelic variants in PYROXD2 identified by genome sequencing in a patient with suspected mitochondrial disease. The child presented with acute neurological deterioration, unresponsive episodes, and extreme metabolic acidosis, and received rapid genomic testing. He died shortly after. Magnetic resonance imaging (MRI) brain imaging showed changes resembling Leigh syndrome, one of the more common childhood mitochondrial neurological diseases. Functional studies in patient fibroblasts showed a heightened sensitivity to mitochondrial metabolic stress and increased mitochondrial superoxide levels. Quantitative proteomic analysis demonstrated decreased levels of subunits of the mitochondrial respiratory chain complex I, and both the small and large subunits of the mitochondrial ribosome, suggesting a mitoribosomal defect. Our findings support the critical role of PYROXD2 in human cells, and suggest that the biallelic PYROXD2 variants are associated with mitochondrial dysfunction, and can plausibly explain the child’s clinical presentation.

Abnormalities of mitochondrial dynamics and bioenergetics in neuronal cells from CDKL5 deficiency disorder

CDKL5 deficiency disorder (CDD) is a rare neurodevelopmental disorder caused by pathogenic variants in the Cyclin-dependent kinase-like 5 (CDKL5) gene, resulting in dysfunctional CDKL5 protein. It predominantly affects females and causes seizures in the first few months of life, ultimately resulting in severe intellectual disability. In the absence of targeted therapies, treatment is currently only symptomatic. CDKL5 is a serine/threonine kinase that is highly expressed in the brain, with a critical role in neuronal development. Evidence of mitochondrial dysfunction in CDD is gathering, but has not been studied extensively. We used human patient-derived induced pluripotent stem cells with a pathogenic truncating mutation (p.Arg59*) and CRISPR/Cas9 gene-corrected isogenic controls, differentiated into neurons, to investigate the impact of CDKL5 mutation on cellular function. Quantitative proteomics indicated mitochondrial defects in CDKL5 p.Arg59* neurons, and mitochondrial bioenergetics analysis confirmed decreased activity of mitochondrial respiratory chain complexes. Additionally, mitochondrial trafficking velocity was significantly impaired, and there was a higher percentage of stationary mitochondria. We propose mitochondrial dysfunction is contributing to CDD pathology, and should be a focus for development of targeted treatments for CDD.

Mutations in the exocyst component EXOC2 cause severe defects in human brain development

The exocyst, an octameric protein complex, is an essential component of the membrane transport machinery required for tethering and fusion of vesicles at the plasma membrane. We report pathogenic variants in an exocyst subunit, EXOC2 (Sec5). Affected individuals have severe developmental delay, dysmorphism, and brain abnormalities; variability associated with epilepsy; and poor motor skills. Family 1 had two offspring with a homozygous truncating variant in EXOC2 that leads to nonsense-mediated decay of EXOC2 transcript, a severe reduction in exocytosis and vesicle fusion, and undetectable levels of EXOC2 protein. The patient from Family 2 had a milder clinical phenotype and reduced exocytosis. Cells from both patients showed defective Arl13b localization to the primary cilium. The discovery of mutations that partially disable exocyst function provides valuable insight into this essential protein complex in neural development. Since EXOC2 and other exocyst complex subunits are critical to neuronal function, our findings suggest that EXOC2 variants are the cause of the patients’ neurological disorders.

Establishment of primary myoblast cell cultures from cryopreserved skeletal muscle biopsies to serve as a tool in related research & development studies

BACKGROUND

Primary myoblast cell cultures display the phenotypic characteristics and genetic defects of the donor tissue and represent an in vitro model system reflecting the disease pathology. They have been generated only from freshly harvested tissue biopsies. Here, we describe a novel technique to establish myoblast cell cultures from cryopreserved skeletal muscle biopsy tissues that are useful for diagnostic and research purposes.

METHODS AND RESULTS

This protocol was performed on seven gradually frozen muscle biopsy specimens from various neuromuscular disorders that were stored in dimethylsulfoxide (DMSO)-supplemented freezing media at -80 °C for up to one year. After storage for varying periods of time, primary myoblast cultures were successfully established from all cryopreserved biopsy tissues without any chromosomal abnormality. Desmin immunoreactivity confirmed that the cell cultures contained >90% pure myoblasts. The myoblasts differentiated into multinucleated myotubes successfully. Furthermore, there were no statistically significant differences in cell viability, metabolic activity, population doubling time, and myocyte enhancer factor 2 (MEF2C) expression between cell cultures established from freshly harvested and one year-stored frozen tissue specimens.

CONCLUSIONS

This protocol opens up new horizons for basic research and the pre-clinical studies of novel therapies by using cryopreserved skeletal muscle biopsies stored under suitable conditions in tissue banks.

Analysis of zinc transporter, hZnT4 ( Slc30A4), gene expression in a mammary gland disorder leading to reduced zinc secretion into milk

Zinc deficiency, causing impaired growth and development, may have a nutritional or genetic basis. We investigated two cases of inherited zinc deficiency found in breast-fed neonates, caused by low levels of zinc in the maternal milk. This condition is different from acrodermatitis enteropathica but has similarities to the "lethal milk" mouse, where low levels of zinc in the milk of lactating dams leads to zinc deficiency in pups. The mouse disorder has been attributed to a defect in the ZnT4 gene. Little is known about the expression of the human orthologue, hZnT4 (Slc30A4). Sequence analysis of cDNA, real-time PCR and Western blot analysis of hZnT4, carried out on control cells and cells from unrelated mothers of two infants with zinc deficiency, showed no differences. The hZnT4 gene was highly expressed in mouthwash buccal cells compared with lymphoblasts and fibroblasts. The hZnT4 protein did not co-localise with intracellular free zinc pools, suggesting that hZnT4 is not involved in transport of zinc into vesicles destined for secretion into milk. This observation, combined with phenotypic differences between the "lethal milk" mouse and the human disorder, suggests that the "lethal milk" mouse is not the corresponding model for the human zinc deficiency condition.

Uterine dysfunction and genetic modifiers in centromere protein B-deficient mice

Centromere protein B (CENP-B) binds constitutively to mammalian centromere repeat DNA and is highly conserved between humans and mouse. Cenpb null mice appear normal but have lower body and testis weights. We demonstrate here that testis-weight reduction is seen in male null mice generated on three different genetic backgrounds (denoted R1, W9.5, and C57), whereas body-weight reduction is dependent on the genetic background as well as the gender of the animals. In addition, Cenpb null females show 31%, 33%, and 44% reduced uterine weights on the R1, W9.5, and C57 backgrounds, respectively. Production of "revertant" mice lacking the targeted frameshift mutation but not the other components of the targeting construct corrected these differences, indicating that the observed phenotype is attributable to Cenpb gene disruption rather than a neighbouring gene effect induced by the targeting construct. The R1 and W9.5 Cenpb null females are reproductively competent but show age-dependent reproductive deterioration leading to a complete breakdown at or before 9 months of age. Reproductive dysfunction is much more severe in the C57 background as Cenpb null females are totally incompetent or are capable of producing no more than one litter. These results implicate a further genetic modifier effect on female reproductive performance. Histology of the uterus reveals normal myometrium and endometrium but grossly disrupted luminal and glandular epithelium. Tissue in situ hybridization demonstrates high Cenpb expression in the uterine epithelium of wild-type animals. This study details the first significant phenotype of Cenpb gene disruption and suggests an important role of Cenpb in uterine morphogenesis and function that may have direct implications for human reproductive pathology.

Cation-dependent uptake of zinc in human fibroblasts

The influence of K+ and Ca2+ on Zn2+ transport into cultured human fibroblasts was investigated. Zn2+ uptake was markedly reduced in the presence of both valinomycin and nigericin (electrogenic and electroneutral K+ ionophores, respectively), and by reduction in the transmembrane K+ gradient produced by replacement of extracellular K+ with Na+, suggesting that Zn2+ may be driven by a Zn2+/K+ counter-transport system. To test the counter-transport hypothesis, we used 86Rb as an analog of K+ for efflux studies. The rate of Rb+ efflux was 3760 times that of Zn2+ uptake, thus the component of K+ involved in the Zn2+ counter-transport system was only a small proportion of the total K+ efflux. In investigating the effect of Ca2+ on Zn2+ uptake, we identified two components: (1) a basal Zn2+ uptake pathway, independent of hormonal or growth factors which does not require extracellular Ca2+ and (2) a Ca(2+)-dependent mechanism. The absence of Ca2+ decreased Zn2+ uptake, while increasing extracellular Ca2+ stimulated Zn2+ uptake. The effect was mediated by Ca2+ influx as the ionophores A23187 and ionomycin also stimulated Zn2+ uptake. We could not ascribe the Ca2+ effect to known Ca2+ influx pathways. We conclude that Zn2+ uptake occurs by a K(+)-dependent process, possibly by Zn2+/K+ counter-transport and that a component of this is also Ca(2+)-dependent.

The cryopreservation of skin biopsies--a technique for reducing workload in a cell culture laboratory

A method is described for the cryopreservation of skin biopsies at -70 degrees C for subsequent possible reculture. Biopsies stored up to 1 year could be successfully recultured without affecting the time to achieve confluence or the culture failure rate. This technique has been in operation in our department for over 3 years and has resulted in a demonstrable reduction in cell culture costs and a greater flexibility in the acceptance of skin biopsies for culture.

A mutation in the epidermal growth factor receptor in waved-2 mice has a profound effect on receptor biochemistry that results in impaired lactation

The mutant mouse waved-2 (wa-2) is strikingly similar to transforming growth factor alpha-deficient mice generated by gene targeting in embryonic stem cells. We confirm that wa-2 is a point mutation (T-->G resulting in a valine-->glycine substitution at residue 743) in the gene encoding the epidermal growth factor (EGF) receptor. wa-2 fibroblastic cells lack high-affinity binding sites for EGF, and the rate of internalization of EGF is retarded. Although the tyrosine kinase activity of wa-2 EGF receptors is significantly impaired, NIH 3T3 cells lacking endogenous EGF receptors but overexpressing recombinant wa-2 EGF receptor cDNA are mitogenically responsive to EGF. While young and adult wa-2 mice are healthy and fertile, 35% of wa-2 mice born of homozygous wa-2 mothers die of malnutrition because of impaired maternal lactation.

Postmortem recognition of fatty acid oxidation disorders

With an appropriate protocol for collection, storage, and sample analysis, it should be possible to ensure correct diagnosis of disorders of fatty acid oxidation presenting to the pathologist. Appropriate counseling of affected families will lead to presymptomatic sibling diagnosis of these frequently treatable disorders, which, in turn, can prevent the catastrophic metabolic consequences of the disorders.

Significance of extracellular zinc-binding ligands in the uptake of zinc by human fibroblasts

Extracellular zinc (Zn)-binding ligands were investigated as vehicles for uptake of Zn by human fibroblasts. The uptake of alpha 2-macroglobulin, a major serum Zn-binding protein proposed to have a function in Zn transport, was less than 1/200 that of the Zn uptake rate. The fibroblast growth medium, BME with 10% FBS, contains several Zn-binding ligands. These were separated into components of MW greater than 30,000 and components of MW less than 30,000 using an Amicon microconcentrator. Cells accumulated Zn from both fractions; however, there was more uptake from the filtrate (MW less than 30,000), containing ligands with low affinity for Zn, hence with greater free Zn concentration. Zn uptake from a number of ligands with a range of affinities for Zn was examined and found to be inversely proportional to the Ka value for the ligands and therefore proportional to the free Zn concentration. When histidine and desferrioxamine, two structurally different Zn-binding ligands were compared, analysis of the concentration curves of calculated free Zn against Zn uptake gave similar Vmax and Km values (+/- S.E.M.) of 373 +/- 6 pmol/micrograms DNA/h and 0.08 +/- 0.004 microM for histidine, and 349 +/- 10 pmol/micrograms DNA/h and 0.06 +/- 0.008 microM for DFO, suggesting that the same transport mechanism was operating in both systems. We conclude that no specific ligands are essential for transport of Zn into fibroblasts, but that "free" Zn is acquired by the cell.

Zinc transport by fibroblasts from patients with acrodermatitis enteropathica

Acrodermatitis enteropathica (AE) is a zinc deficiency disease. To date, the only defect has been demonstrated in the gut. We have investigated zinc uptake in fibroblasts established from four unrelated patients with AE using normal skin fibroblasts as controls. Zinc content of AE and control cells was similar (0.3 fmol/cell). Zinc accumulation over 24 h from a complete culture medium was similar in both normal controls and mutant cells. The fraction of zinc removed by Pronase treatment remained constant at 50 pmol/micrograms DNA, whereas the zinc remaining after Pronase treatment accumulated rapidly for 8 h, then more slowly. Analysis of binding data showed no significant difference between AE and control cells, with apparent Ka values of 4-6 X 10(6) M-1 and between 1 and 2 X 10(8) receptors/cell. Analysis of Pronase resistant data showed no difference between the control and the mutant cells with apparent Km values of 0.2-0.3 microM and Vmax values of 17-19 pmol/micrograms DNA/h. No difference in zinc efflux rates was detected. We conclude that the defect that underlies acrodermatitis enteropathica is either not expressed in fibroblasts or cannot be detected under these experimental conditions.

The effect of tetrathiomolybdate on the metabolism of copper by hepatocytes and fibroblasts

Tetrathiomolybdate (TTM) has been examined for its effect on copper metabolism in mouse hepatocytes in primary culture and human fibroblasts. It decreased the amount of copper inside hepatocytes, decreased the rate of copper uptake by hepatocytes in a concentration dependent manner, and increased the copper efflux from the cells. TTM appeared to remove copper preferentially from the labile pool, but with a lower affinity than cage chelators. In fibroblasts, TTM only had a marginal effect on copper levels below a concentration of 100 microM and had no clear effect on the rate of copper uptake. TTM was not toxic to human fibroblasts, but in some preparations, a concentration of more than 50 microM was toxic to hepatocytes.

Studies on the mechanism of zinc uptake by human fibroblasts

The mechanisms of zinc uptake from a complete culture medium by human fibroblasts have been studied. The metal is accumulated in a biphasic pattern; an initial rapid phase followed by a slower linear phase. We suggest that the former represents binding to carriers or receptors on the cell surface followed by uptake to within the cell, or at least to a compartment inaccessible to proteolytic digestion. The uptake correlates well with estimates of the zinc requirement of a growing fibroblast. The process of uptake is saturable, with an apparent association constant of 1.1 X 10(7) M-1. Interestingly, there appears to be a very large number of binding sites, 2 X 10(7) per cell. No explanation for this observation is immediately apparent. The mechanism of uptake is not dependent on metabolic energy, or at least on ATP levels within the cell, but N-ethyl maleimide does block uptake in a dose-dependent manner. Weak bases and ionophores, apart from nigericin, do not affect uptake. The results suggest that zinc is not taken up by a receptor-mediated endocytic pathway as has been described for transferrin and iron.

Albumin has no role in the uptake of copper by human fibroblasts

The mechanism of copper uptake by cells has been the subject of controversy for some time. This paper examines the possibility of a role for albumin in the uptake of copper by fibroblasts. Although the cells could accumulate copper from a copper-albumin complex, there was no evidence for either copper-albumin or albumin receptors on the cell surface. The possibility of a surface exchange mechanism for copper was examined. While copper uptake showed saturation with increasing concentrations of labelled copper-albumin, adding unlabelled copper to the incubation medium did not inhibit uptake. Adding albumin or histidine to the copper-albumin complex resulted in an inhibition of copper uptake. The results can only be explained by the cell taking up free copper from the incubation medium, with the albumin then releasing its copper to maintain the equilibrium between free and bound metal. Since, in vivo there is essentially no free copper in serum, it is concluded that albumin is most unlikely to play a role in the uptake of copper by fibroblasts.

Neuropathology in cerebral lactic acidosis

The neuropathology in two young infants with cerebral lactic acidosis is presented. Both cases showed microcephaly, ventricular dilatation, absent corpus callosum, absent or extremely hypoplastic pyramids, heterotopic inferior olives, focal neuroglial overgrowth into meninges, focal cystic change with gliosis and recent degenerative changes in the germinal matrix. The cerebellum, basal ganglia, Ammon's horn, inferior colliculi and layering of the cortex were well preserved. The features suggest a continuous damage with very old, relatively old and recent lesions. This striking combination of abnormalities should raise the possibility of a disturbance of lactate/pyruvate metabolism.