Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA)

Mitochondrial myopathy and sideroblastic anemia (MLASA) is a rare, autosomal recessive oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Linkage analysis and homozygosity testing of two families with MLASA localized the candidate region to 1.2 Mb on 12q24.33. Sequence analysis of each of the six known genes in this region, as well as four putative genes with expression in bone marrow or muscle, identified a homozygous missense mutation in the pseudouridine synthase 1 gene (PUS1) in all patients with MLASA from these families. The mutation is the only amino acid coding change in these 10 genes that is not a known polymorphism, and it is not found in 934 controls. The amino acid change affects a highly conserved amino acid, and appears to be in the catalytic center of the protein, PUS1p. PUS1 is widely expressed, and quantitative expression analysis of RNAs from liver, brain, heart, bone marrow, and skeletal muscle showed elevated levels of expression in skeletal muscle and brain. We propose deficient pseudouridylation of mitochondrial tRNAs as an etiology of MLASA. Identification of the pathophysiologic pathways of the mutation in these families may shed light on the tissue specificity of oxidative phosphorylation disorders.

De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias

Developmental and epileptic encephalopathies (DEEs) are severe neurodevelopmental disorders often beginning in infancy or early childhood that are characterized by intractable seizures, abundant epileptiform activity on EEG, and developmental impairment or regression. CACNA1E is highly expressed in the central nervous system and encodes the α₁-subunit of the voltage-gated Ca_V2.3 channel, which conducts high voltage-activated R-type calcium currents that initiate synaptic transmission. Using next-generation sequencing techniques, we identified de novo CACNA1E variants in 30 individuals with DEE, characterized by refractory infantile-onset seizures, severe hypotonia, and profound developmental impairment, often with congenital contractures, macrocephaly, hyperkinetic movement disorders, and early death. Most of the 14, partially recurring, variants cluster within the cytoplasmic ends of all four S6 segments, which form the presumed Ca_V2.3 channel activation gate. Functional analysis of several S6 variants revealed consistent gain-of-function effects comprising facilitated voltage-dependent activation and slowed inactivation. Another variant located in the domain II S4-S5 linker results in facilitated activation and increased current density. Five participants achieved seizure freedom on the anti-epileptic drug topiramate, which blocks R-type calcium channels. We establish pathogenic variants in CACNA1E as a cause of DEEs and suggest facilitated R-type calcium currents as a disease mechanism for human epilepsy and developmental disorders.

Mitochondrial myopathy, sideroblastic anemia, and lactic acidosis: an autosomal recessive syndrome in Persian Jews caused by a mutation in the PUS1 gene

We report the seventh case of autosomal recessive inherited mitochondrial myopathy, lactic acidosis, and sideroblastic anemia The patient, a product of consanguineous Persian Jews, had the association of mental retardation, dysmorphic features, lactic acidosis, myopathy, and sideroblastic anemia. Muscle biopsy demonstrated low activity of complexes 1 and 4 of the respiratory chain. Electron microscopy revealed paracrystalline inclusions in most mitochondria. Southern blot of the mitochondrial DNA did not show any large-scale rearrangements. The patient was found to be homozygous for the 656C-->T mutation in the pseudouridine synthase 1 gene (PUS1). Mitochondrial myopathy, lactic acidosis, and sideroblastic anemia is an oxidative phosphorylation disorder causing sideroblastic anemia, myopathy, and, in some cases, mental retardation that is due to mutations in the nuclear-encoded PUS1 gene. This finding provides additional evidence that mitochondrial ribonucleic acid modification impacts the phenotypic expression of oxidative phosphorylation disorders.

Can untreated PKU patients escape from intellectual disability? A systematic review

Background

Phenylketonuria (PKU) is often considered as the classical example of a genetic disorder in which severe symptoms can nowadays successfully be prevented by early diagnosis and treatment. In contrast, untreated or late-treated PKU is known to result in severe intellectual disability, seizures, and behavioral disturbances. Rarely, however, untreated or late-diagnosed PKU patients with high plasma phenylalanine concentrations have been reported to escape from intellectual disability. The present study aimed to review published cases of such PKU patients.

Methods

To this purpose, we conducted a literature search in PubMed and EMBASE up to 8th of September 2017 to identify cases with 1) PKU diagnosis and start of treatment after 7 years of age; 2) untreated plasma phenylalanine concentrations ≥1200 μmol/l; and 3) IQ ≥80. Literature search, checking reference lists, selection of articles, and extraction of data were performed by two independent researchers.

Results

In total, we identified 59 published cases of patients with late-diagnosed PKU and unexpected favorable outcome who met the inclusion criteria. Although all investigated patients had intellectual functioning within the normal range, at least 19 showed other neurological, psychological, and/or behavioral symptoms.

Conclusions

Based on the present findings, the classical symptomatology of untreated or late-treated PKU may need to be rewritten, not only in the sense that intellectual dysfunction is not obligatory, but also in the sense that intellectual functioning does not (re)present the full picture of brain damage due to high plasma phenylalanine concentrations. Further identification of such patients and additional analyses are necessary to better understand these differences between PKU patients.

Electronic supplementary material

The online version of this article (10.1186/s13023-018-0890-7) contains supplementary material, which is available to authorized users.

Gene responsible for mitochondrial myopathy and sideroblastic anemia (MSA) maps to chromosome 12q24.33

Mitochondrial myopathy and sideroblastic anemia (MSA) is a rare autosomal recessive disorder of oxidative phosphorylation and iron metabolism. Individuals with MSA present with weakness and anemia in late childhood and may become dependent on blood transfusions. Recently, we reported affected sibling pairs from a Jewish-Iranian kindred living in the US [Casas and Fischel-Ghodsian, 2003]. A genome scan and fine mapping of DNA from this family revealed homozygous alleles in the affected individuals, and a multipoint logarithm of the odds (lod) score of 3.3, within 2.3 mb of chromosome 12q24.33. Previously, Inbal et al. [1995: Am J Med Genet 55:372-378] described siblings with a similar clinical phenotype who lived in Israel but originated from the same Iranian town as the US family. Focused analysis of DNA from the Israeli family confirmed the presence of identical, homozygous alleles in the affected of the US and Israeli families within 1.2 mb of chromosome 12q24.33. Combined multipoint linkage analysis revealed a maximum lod score of 5.41 at the 132 cM position of chromosome 12. Therefore, in these two families of Jewish-Iranian descent, a disease gene for MSA maps to a 1.2 mb region of chromosome 12q24.33. This region contains 6 well described genes (SFRS8, MMP17, ULK1, PUS1, EP400, and GALNT9) and at least 15 additional putative transcripts. The known genes are expressed in multiple tissues and lack a function specific to mitochondria, making none an obvious candidate. The eventual identification of the disease gene in MSA is expected to provide insight into the tissue specificity and phenotypic variability of mitochondrial disease.

De novo three-way chromosome translocation 46,XY,t(4;6;21)(p16;p21.1;q21) in a male with cleidocranial dysplasia

Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia associated with cranial, clavicular, and dental anomalies. It is caused by mutations in the RUNX2 gene, which encodes an osteoblast-specific transcription factor and maps to chromosome 6p21. We report clinical and molecular cytogenetic studies in a patient with clinical features of CCD including wormian bones, delayed fontanel closure, hypoplastic clavicles and pubic rami, and supernumerary dentition. Additional abnormalities of bone growth and connective tissue, including easy bruisability, scarring, bleeding, joint hypermobility, and developmental delay were also observed. Molecular cytogenetic studies identified a de novo apparently balanced three-way translocation 46,XY,t(4;6;21)(p16;p21.1;q21). Further mapping revealed the breakpoint on 6p21 to be ∼50 kb upstream of exon 1 of the RUNX2 gene, with RUNX2 being intact on the derivative chromosome 6. We hypothesize that the proband's CCD has arisen from disruption of the developmentally regulated gene RUNX2 at the 6p21 breakpoint, due to a position effect mutation which may have altered the expression of the gene. Further studies might unravel a new regulatory element for RUNX2.

Mutations in PDLIM5 are rare in dilated cardiomyopathy but are emerging as potential disease modifiers

BACKGROUND

A causal genetic mutation is found in 40% of families with dilated cardiomyopathy (DCM), leaving a large percentage of families genetically unsolved. This prevents adequate counseling and clear recommendations in these families. We aim to identify novel genes or modifiers associated with DCM.

METHODS

We performed computational ranking of human genes based on coexpression with a predefined set of genes known to be associated with DCM, which allowed us to prioritize gene candidates for their likelihood of being involved in DCM. Top candidates will be checked for variants in the available whole-exome sequencing data of 142 DCM patients. RNA was isolated from cardiac biopsies to investigate gene expression.

RESULTS

PDLIM5 was classified as the top candidate. An interesting heterozygous variant (189_190delinsGG) was found in a DCM patient with a known pathogenic truncating TTN-variant. The PDLIM5 loss-of-function (LoF) variant affected all cardiac-specific isoforms of PDLIM5 and no LoF variants were detected in the same region in a control cohort of 26,000 individuals. RNA expression of PDLIM5 and its direct interactors (MYOT, LDB3, and MYOZ2) was increased in cardiac tissue of this patient, indicating a possible compensatory mechanism. The PDLIM5 variant cosegregated with the TTN-variant and the phenotype, leading to a high disease penetrance in this family. A second patient was an infant with a homozygous 10 kb-deletion of exon 2 in PDLIM5 resulting in early-onset cardiac disease, showing the importance of PDLIM5 in cardiac function.

CONCLUSIONS

Heterozygous PDLIM5 variants are rare and therefore will not have a major contribution in DCM. Although they likely play a role in disease development as this gene plays a major role in contracting cardiomyocytes and homozygous variants lead to early-onset cardiac disease. Other environmental and/or genetic factors are probably necessary to unveil the cardiac phenotype in PDLIM5 mutation carriers.

Functional genomics of Down syndrome: a multidisciplinary approach

The availability of the DNA sequence of human chromosome 21 (HSA21) is a landmark contribution that will have an immediate impact on the study of the role of specific genes to Down syndrome (DS). Trisomy 21, full or partial, is a major cause of mental retardation and other phenotypic abnormalities, collectively known as Down syndrome (DS), a disorder affecting 1 in 700 births. The identification of genes on HSA21 and the elucidation of the function of the proteins encoded by these genes have been a major challenge for the human genome project and for research in DS. Over 100 of the estimated 300-500 genes of HSA21 have been identified, but the function of most remains largely unknown. It is believed that the overexpression of an unknown number of HSA21 genes is directly or indirectly responsible for the mental retardation and the other clinical features of DS. For this reason, HSA21 genes that are expressed in tissues affected in DS patients are of special interest.

Pre-analytic decrease of phenylalanine in plasma of patients with phenylketonuria treated with pegvaliase

Treatment of phenylketonuria (PKU) has evolved since the initial introduction of a phenylalanine (Phe) restricted diet. The most recent option for adults affected with PKU is treatment with an alternate enzyme, phenylalanine ammonia lyase (PAL), that metabolizes excess Phe. Proper management of all patients with PKU relies on accurate measurement of Phe levels in blood, to comply with guidance intended to minimize the neurological symptoms. Recently, our laboratory was notified of discrepant results for a patient with PKU who is treated with pegvaliase. Two specimens were collected at the same time but yielded unexpectedly different Phe concentrations. After exclusion of specimen mix-ups or analytical errors, we suspected that there was residual pegvaliase activity in the specimens continuing to degrade Phe after collection. To investigate this possibility, we performed spiking studies that showed the degradation of Phe over time at ambient temperatures. Sample preparation by protein crash appears to deactivate pegvaliase and prevents further Phe degradation. However, because pegvaliase deactivation would be required immediately following blood collection, appropriate mitigation measures must be implemented, including stringent pre-analytical requirements, alternate sample matrices such as dried blood spots, or point of care testing. Until then, health care professionals need to be cautious in their interpretation of Phe levels in their patients with PKU that are treated with pegvaliase.

Multiple molecular diagnoses identified through genome sequencing in individuals with suspected rare disease

Genome sequencing is a powerful and comprehensive test that detects multiple variants of different types. The interrogation of variants across the genome enables the identification of multiple molecular diagnoses (MMDs) in a single individual. In this retrospective study, we describe individuals in whom MMDs were associated with the proband's indication for testing (IFT), secondary findings, or incidental findings. An MMD is considered where at least one of the findings is associated with the primary IFT and all variants are classified as either likely pathogenic or pathogenic. Clinical genome sequencing was performed for all individuals as part of the iHope program at the Illumina Laboratory Services between September 2017 and December 2023. The iHope cohort included 1,846 affected individuals, with 872 (47.2%) found to have at least one likely pathogenic or pathogenic variant associated with the primary IFT. Of these, 81 (9.3%) individuals had multiple clinically significant molecular findings, including 76 individuals with reported variants associated with 2 different conditions, and 5 individuals with more than 2 molecular findings. A total of 32 individuals (3.7%) had at least 2 molecular diagnoses related to the primary IFT, while in 49 (5.6%) individuals, the variant(s) reported for the second condition constituted a secondary or incidental finding. Our study highlights that among individuals with a likely pathogenic or pathogenic finding identified through genome sequencing, 9% have MMDs, which may have been missed with different testing methods. Of note, approximately 60% of the 81 individuals with an MMD had a potentially actionable secondary or incidental finding.

Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder

PURPOSE

CTR9 is a subunit of the PAF1 complex (PAF1C) that plays a crucial role in transcription regulation by binding CTR9 to RNA polymerase II. It is involved in transcription-coupled histone modification through promoting H3K4 and H3K36 methylation. We describe the clinical and molecular studies in 13 probands, harboring likely pathogenic CTR9 missense variants, collected through GeneMatcher.

METHODS

Exome sequencing was performed in all individuals. CTR9 variants were assessed through 3-dimensional modeling of the activated human transcription complex Pol II-DSIF-PAF-SPT6 and the PAF1/CTR9 complex. H3K4/H3K36 methylation analysis, mitophagy assessment based on tetramethylrhodamine ethyl ester perchlorate immunofluorescence, and RNA-sequencing in skin fibroblasts from 4 patients was performed.

RESULTS

Common clinical findings were variable degrees of intellectual disability, hypotonia, joint hyperlaxity, speech delay, coordination problems, tremor, and autism spectrum disorder. Mild dysmorphism and cardiac anomalies were less frequent. For 11 CTR9 variants, de novo occurrence was shown. Three-dimensional modeling predicted a likely disruptive effect of the variants on local CTR9 structure and protein interaction. Additional studies in fibroblasts did not unveil the downstream functional consequences of the identified variants.

CONCLUSION

We describe a neurodevelopmental disorder caused by (mainly) de novo variants in CTR9, likely affecting PAF1C function.

Assessing Teledentistry versus In-Person Examinations to Detect Dental Caries: A Systematic Review and Meta-analysis

INTRODUCTION

There is no recent consensus on the effectiveness of teledentistry versus in-person examination in the diagnosis of dental caries, especially after the COVID-19 pandemic.

OBJECTIVE

To assess the diagnostic accuracy of teledentistry versus in-person examination for dental caries diagnosis (PROSPERO #CRD42023410962).

METHODS

This systematic review and meta-analysis compared the effectiveness of teledentistry versus in-person examination for dental caries diagnosis. The eligibility criteria were peer-reviewed studies published in English between January 2013 and December 2021 that reported diagnostic parameters (specificity and sensitivity) for caries detection in primary and permanent dentition. Articles were extracted using search strategies from PubMed and CINAHL databases and screened using PRISMA-DTA guidelines, following a review for quality assessment and risk of bias using the QUADAS-2 and JBI Critical Appraisal Checklists. Meta-analysis was conducted in R using the MADA package. A descriptive analysis of the sensitivity, specificity, diagnostic odds ratio, and confidence intervals was performed with respective forest plots. Heterogeneity was assessed using Cochrane Q and Higgins's I2 tests. Univariate measures of diagnostic accuracy were performed based on the DerSimonian-Laird random effect and reported summary diagnostic odds ratios.

RESULTS

Twelve studies met the inclusion criteria and were reviewed and included in the meta-analysis. The diagnostic parameters ranged from 45.6% to 88.3% for sensitivity, 55.2% to 98.3% for specificity, 79% to 92% for positive predictive value, 48% to 97% for negative predictive value, and 70% to 96% for accuracy. The κ scores ranged from 0.46 to 0.89 for teledentistry modalities. Tests for equality of sensitivities and specificities were significant (P < 0.001). The studies were not heterogeneous with Cochran's Q: 14.502 (P = 0.206) and Higgins's I2 of 24%. The multivariable analysis showed a diagnostic odds ratio based on the DerSimonian-Laird random effect of 35.14, which indicates that the odds of caries detection via teledentistry is 35 times more true positive (i.e., correctly identifying a positive condition) than false positive.

CONCLUSIONS

Diagnosis of caries via teledentistry is effective and comparable to in-person diagnosis. Remote assessments are consistent in diagnostic accuracy for caries.Knowledge Transfer Statement:This systematic review and meta-analysis added to the evidence about using teledentistry assessment as a diagnostically accurate tool to detect dental caries. Using teledentistry dental practices could promote greater access to dental and oral health care in the absence of in-person assessment.

Multi-center implementation of rapid whole genome sequencing provides additional evidence of its utility in the pediatric inpatient setting

Objective

Multi-center implementation of rapid whole genome sequencing with assessment of the clinical utility of rapid whole genome sequencing (rWGS), including positive, negative and uncertain results, in admitted infants with a suspected genetic disease.

Study design

rWGS tests were ordered at eight hospitals between November 2017 and April 2020. Investigators completed a survey of demographic data, Human Phenotype Ontology (HPO) terms, test results and impacts of results on clinical care.

Results

A total of 188 patients, on general hospital floors and intensive care unit (ICU) settings, underwent rWGS testing. Racial and ethnic characteristics of the tested infants were broadly representative of births in the country at large. 35% of infants received a diagnostic result in a median of 6 days. The most common HPO terms for tested infants indicated an abnormality of the nervous system, followed by the cardiovascular system, the digestive system, the respiratory system and the head and neck. Providers indicated a major change in clinical management because of rWGS for 32% of infants tested overall and 70% of those with a diagnostic result. Also, 7% of infants with a negative rWGS result and 23% with a variant of unknown significance (VUS) had a major change in management due to testing.

Conclusions

Our study demonstrates that the implementation of rWGS is feasible across diverse institutions, and provides additional evidence to support the clinical utility of rWGS in a demographically representative sample of admitted infants and includes assessment of the clinical impact of uncertain rWGS results in addition to both positive and negative results.

Reduction in Newborn Screening False Positive Results Following a New Collection Protocol: a Quality Improvement Project

OBJECTIVE

Premature infants are known to have a higher rate of false positive newborn screening (NBS) results, with TPN as a contributing factor. The purpose of this quality improvement (QI) project is to reduce false positive NBS results via a TPN interruption protocol.

METHODS

A multidisciplinary team reviewed the literature and developed a new NBS collection protocol, which was implemented in 2 periods. In period 1, TPN was interrupted for 4 hours before NBS sample collection and initiation of carnitine supplements was avoided. In period 2, TPN was interrupted for 6 hours for infants birth weight (BW) < 1000 g, carnitine supplementation continued to be avoided. The rates of false positives NBS results were compared pre- and post-interventions in periods 1 and 2.

RESULTS

Four hundred twelve neonates were evaluated prior to implementation of this QI project (July 2013-June 2014) and 414 during period 1 intervention (July 2014-June 2016). False positive results decreased from 20.6% to 11.4% (p < 0.001) among all BW categories following the 4-hour TPN interruption. The rate of false positives was further reduced among infants < 1000 g (p = 0.035) in period 2 (n = 112), including a significant reduction in false positive results with elevated amino acid profiles (p = 0.005).

CONCLUSIONS

The implementation of a strict NBS collection protocol reduced false positive NBS results, which potentially can improve patient care by reducing unnecessary laboratory draws, pain, and parental anxiety. Interruption of TPN for 6 hours was significant in reducing NBS false positive results in neonates < 1000 g.