Primary and maternal 3-methylcrotonyl-CoA carboxylase deficiency: insights from the Israel newborn screening program

Newborn screening for 3-methylcrotonyl-CoA carboxylase deficiency in Zhejiang province, China

BACKGROUND

3-Methylcrotonyl-CoA carboxylase deficiency (3-MCCD) is an autosomal recessive inborn defect of leucine catabolism caused by MCCC1 or MCCC2 variants. 3-MCCD is considered to be a relatively benign disorder with favorable outcome. We report the biochemical, clinical, and molecular features of patients with 3-MCCD.

METHODS

From January 2009 to August 2022, 4,402,587 newborns were screened by tandem mass spectrometry. Newborns with increased C5OH concentrations were recalled for repeated testing, urine organic acid analysis and molecular genetic analysis were performed if the second test was still positive.

RESULTS

A total of 53 patients were diagnosed with 3-MCCD. The estimated incidence of 3-MCCD in Zhejiang Province was 1 in 83,068 newborns. All these 53 patients exhibited increased C5OH concentrations in blood. 94 % (50/53) of the patients had markedly increased urinary 3-hydroxyisovaleric acid and 3-methylcrotonylglycine. All these 53 patients did not present any clinical symptom. Twenty-three of 53 patients had secondary carnitine deficiency. Twenty-eight patients had variants in MCCC1 and 25 had variants in MCCC2. Eleven novel variants were found in MCCC1 and MCCC2. The c.639 + 2 T > A and c.1144-1147delinsTTTT were the most common variant in MCCC1 and MCCC2 gene, respectively.

CONCLUSION

We elucidated the incidence of 3-MCCD in Zhejiang province, China. All patients showed asymptomatic and present normal growth and development during follow-up. Eleven novel MCCC1 and MCCC2 variants were identified, which expanded the variant spectrum.

Reproductive genetic carrier screening and inborn errors of metabolism: The voice of the inborn errors of metabolism community needs to be heard

Reproductive genetic carrier screening (RGCS) has a history spanning more than 50 years, but for most of that time has been limited to screening for one or a few conditions in targeted population groups. The advent of massively parallel sequencing has led to rapid growth in screening for panels of up to hundreds of genes. Such panels typically include numerous genes associated with inborn errors of metabolism (IEM). There are considerable potential benefits for families from screening, but there are also risks and potential pitfalls. The IEM community has a vital role to play in guiding gene selection and assisting with the complexities that arise from screening, including interpreting complex biochemical assays and counselling at-risk couples about phenotypes and treatments.

A False-Positive Case of Methylmalonic Aciduria by Tandem Mass Spectrometry Newborn Screening Dependent on Maternal Malnutrition in Pregnancy

Methylmalonic Acidurias (MMAs) are a group of inborn errors of metabolism (IEMs), specifically of propionate catabolism characterized by gastrointestinal and neurometabolic manifestations resulting from a deficiency in the function of methylmalonyl-CoA mutase, methylmalonyl-CoA epimerase, and cobalamin metabolism. In Expanded Newborn Screening (NBS), increased levels of propionylcarnitine (C3) and/or of its ratios by MS/MS analysis of dried blood spots (DBS) samples are suggestive for either Propionic Acidemia or MMAs. C3 elevation is not considered a specific marker for these disorders, resulting in high false-positive rates. The use of analyte ratios improves specificity, but it still cannot resolve the diagnostic issue. Second-tier testing are strongly recommended as confirmation of primary NBS results and for a differential diagnosis. LC-MS/MS analysis allows the quantification of more specific markers of the disorder. Here, we report the case of a newborn with a suspected MMA at Expanded NBS and at second-tier test. Given the urgent situation, in-depth diagnostic investigations were performed. Further investigations surprisingly revealed a Vitamin B12 deficiency due to a maternal malnutrition during pregnancy. This case emphasized that metabolic alterations at NBS may not only be influenced by genome and related to IEMs, but also to external factors and to maternal conditions.

MCCC2 overexpression predicts poorer prognosis and promotes cell proliferation in colorectal cancer

PURPOSES

Recently, Methylcrotonoyl-CoA carboxylase 2 (MCCC2) is reported to be involved in tumor formation and progression. However, MCCC2 has nerve been reported in colorectal cancer. In this study, we aimed to investigate the role of MCCC2 in colorectal cancer.

METHODS

118 colorectal cancer and matched adjacent normal tissues were enrolled in this study. The expression level of MCCC2 was measured by quantificational real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC). The clinical significance of MCCC2 and its influence on cell proliferation was further analyzed.

RESULTS

Results shown that the mRNA levels of MCCC2 in colorectal cancer tissues were significantly increased compared with those in normal tissues (P < .0001). MCCC2 high-expression was observed in 56.8% colorectal cancer tissues, which was significantly higher than those in normal controls (9.3%, P < .0001). MCCC2 high-expression correlated with tumor size, T stage, lymph node metastasis, distant metastasis, clinical stage and differentiation in colorectal cancer (P < .05). Moreover, MCCC2 high-expression predicted poorer prognosis and could be as an independent prognostic factor. In addition, MCCC2 knockdown significantly inhibited cell proliferation compared with these controls, while MCCC2 overexpression could reverse the effect.

CONCLUSION

These data indicate MCCC2 overexpression promotes cell proliferation and predicts poorer prognosis in colorectal cancer.

Expanded Newborn Screening for Inborn Errors of Metabolism by Tandem Mass Spectrometry in Suzhou, China: Disease Spectrum, Prevalence, Genetic Characteristics in a Chinese Population

Expanded newborn screening for inborn errors of metabolism (IEMs) by tandem mass spectrometry (MS/MS) could simultaneously analyze more than 40 metabolites and identify about 50 kinds of IEMs. Next generation sequencing (NGS) targeting hundreds of IMEs-associated genes as a follow-up test in expanded newborn screening has been used for genetic analysis of patients. The spectrum, prevalence, and genetic characteristic of IEMs vary dramatically in different populations. To determine the spectrum, prevalence, and gene mutations of IEMs in newborns in Suzhou, China, 401,660 newborns were screened by MS/MS and 138 patients were referred to genetic analysis by NGS. The spectrum of 22 IEMs were observed in Suzhou population of newborns, and the overall incidence (excluding short chain acyl-CoA dehydrogenase deficiency (SCADD) and 3-Methylcrotonyl-CoA carboxylase deficiency (3-MCCD)) was 1/3,163. The prevalence of each IEM ranged from 1/401,660 to 1/19,128, while phenylketonuria (PKU) (1/19,128) and Mild hyperphenylalaninemia (M-HPA) (1/19,128) were the most common IEMs, followed by primary carnitine uptake defect (PCUD) (1/26,777), SCADD (1/28,690), hypermethioninemia (H-MET) (1/30,893), 3-MCCD (1/33,412) and methylmalonic acidemia (MMA) (1/40,166). Moreover, 89 reported mutations and 51 novel mutations in 25 IMEs-associated genes were detected in 138 patients with one of 22 IEMs. Some hotspot mutations were observed for ten IEMs, including PAH gene c.728G > A, c.611A > G, and c.721C > T for Phenylketonuria, PAH gene c.158G > A, c.1238G > C, c.728G > A, and c.1315+6T > A for M-HPA, SLC22A5 gene c.1400C > G, c.51C > G, and c.760C > T for PCUD, ACADS gene c.1031A > G, c.164C > T, and c.1130C > T for SCAD deficiency, MAT1A gene c.791G > A for H-MET, MCCC1 gene c.639+2T > A and c.863A > G for 3-MCCD, MMUT gene c.1663G > A for MMA, SLC25A13 gene c.IVS16ins3Kb and c.852_855delTATG for cittrullinemia II, PTS gene c.259C > T and c.166G > A for Tetrahydrobiopterin deficiency, and ACAD8 gene c.1000C > T and c.286C > A for Isobutyryl coa dehydrogenase deficiency. All these hotspot mutations were reported to be pathogenic or likely pathogenic, except a novel mutation of ACAD8 gene c.286C > A. These mutational hotspots could be potential candidates for gene screening and these novel mutations expanded the mutational spectrum of IEMs. Therefore, our findings could be of value for genetic counseling and genetic diagnosis of IEMs.

Methylcrotonoyl-CoA carboxylase 2 overexpression predicts an unfavorable prognosis and promotes cell proliferation in breast cancer

Aim: Methylcrotonoyl-CoA carboxylase 2 (MCCC2), a  subunit of 3-Methylcrotonyl-CoA carboxylase (MCC), is reported to be involved in tumor formation and development. However, the role of MCCC2 in breast cancer is unknown. Materials & methods: MCCC2 expression was examined in 138 cases of breast cancer and matched adjacent normal tissues by quantitative reverse transcription PCR and immunohistochemistry. The influence of MCCC2 expression on cell proliferation was evaluated by CCK-8 and colony formation assay. Results: Quantitative reverse transcription PCR results show MCCC2 mRNA levels were significantly greater in breast cancer tissues than normal tissues (p < 0.05). Immunohistochemistry analysis revealed that MCCC2 overexpression was significantly associated with Tumor, Node, Metastasis stage and lymph node metastasis and predicted an unfavorable prognosis (p < 0.05). CCK-8 and colony formation assay indicated that MCCC2 overexpression significantly promoted cell proliferation. Discussion & conclusion: These data indicate MCCC2 overexpression predicts an unfavorable prognosis and promotes cell proliferation in breast cancer, which may serve as a potential prognostic biomarker.

Enhancers in the Peril lincRNA locus regulate distant but not local genes

BACKGROUND

Recently, it has become clear that some promoters function as long-range regulators of gene expression. However, direct and quantitative assessment of enhancer activity at long intergenic noncoding RNA (lincRNA) or mRNA gene bodies has not been performed. To unbiasedly assess the enhancer capacity across lincRNA and mRNA loci, we performed a massively parallel reporter assay (MPRA) on six lincRNA loci and their closest protein-coding neighbors.

RESULTS

For both gene classes, we find significantly more MPRA activity in promoter regions than in gene bodies. However, three lincRNA loci, Lincp21, LincEnc1, and Peril, and one mRNA locus, Morc2a, display significant enhancer activity within their gene bodies. We hypothesize that such peaks may mark long-range enhancers, and test this in vivo using RNA sequencing from a knockout mouse model and high-throughput chromosome conformation capture (Hi-C). We find that ablation of a high-activity MPRA peak in the Peril gene body leads to consistent dysregulation of Mccc1 and Exosc9 in the neighboring topologically associated domain (TAD). This occurs irrespective of Peril lincRNA expression, demonstrating this regulation is DNA-dependent. Hi-C confirms long-range contacts with the neighboring TAD, and these interactions are altered upon Peril knockout. Surprisingly, we do not observe consistent regulation of genes within the local TAD. Together, these data suggest a long-range enhancer-like function for the Peril gene body.

CONCLUSIONS

A multi-faceted approach combining high-throughput enhancer discovery with genetic models can connect enhancers to their gene targets and provides evidence of inter-TAD gene regulation.

Biochemical signatures mimicking multiple carboxylase deficiency in children with mutations in MT-ATP6

Elevations of specific acylcarnitines in blood reflect carboxylase deficiencies, and have utility in newborn screening for life-threatening organic acidemias and other inherited metabolic diseases. In this report, we describe a newly-identified association of biochemical features of multiple carboxylase deficiency in individuals harboring mitochondrial DNA (mtDNA) mutations in MT-ATP6 and in whom organic acidemias and multiple carboxylase deficiencies were excluded. Using retrospective chart review, we identified eleven individuals with abnormally elevated propionylcarnitine (C3) or hydroxyisovalerylcarnitine (C5OH) with mutations in MT-ATP6, most commonly m.8993T>G in high heteroplasmy or homoplasmy. Most patients were ascertained on newborn screening; most had normal enzymatic or molecular genetic testing to exclude biotinidase and holocarboxylase synthetase deficiencies. MT-ATP6 is associated with some cases of Leigh disease; clinical outcomes in our cohort ranged from death from neurodegenerative disease in early childhood to clinically and developmentally normal after several years of follow-up. These cases expand the biochemical phenotype associated with MT-ATP6 mutations, especially m.8993T>G, to include acylcarnitine abnormalities mimicking carboxylase deficiency states. Clinicians should be aware of this association and its implications for newborn screening, and consider mtDNA sequencing in patients exhibiting similar acylcarnitine abnormalities that are biotin-unresponsive and in whom other enzymatic deficiencies have been excluded.

Long-term outcome of expanded newborn screening at Boston children's hospital: benefits and challenges in defining true disease

INTRODUCTION

There is no universal consensus of the disorders included in newborn screening programs. Few studies so far, mostly short-term, have compared the outcome of disorders detected by expanded newborn screening (ENBS) to the outcome of the same disorders detected clinically.

METHODS

We compared the clinical and neurodevelopmental outcomes in patients with metabolic disorders detected by ENBS, including biotinidase testing, with those detected clinically and followed at the Metabolism Clinic at Boston Children's Hospital.

RESULTS

One hundred eighty-nine patients came to attention from ENBS and 142 were clinically diagnosed. 3-methylcrotonyl-CoA carboxylase, biotinidase, and carnitine deficiencies were exclusively identified by ENBS and medium chain acyl-CoA dehydrogenase (MCADD) and very long chain acyl-CoA dehydrogenase deficiencies (VLCADD) were predominantly identified by ENBS whereas the organic acid disorders more often came to attention clinically. Only 2% of the ENBS-detected cases had clinically severe outcomes compared to 42% of those clinically detected. The mean IQ score was 103 + 17 for the ENBS-detected cases and 77 + 24 for those clinically detected. Those newly included disorders that seem to derive the greatest benefit from ENBS include the fatty acid oxidation disorders, profound biotinidase deficiency, tyrosinemia type 1, and perhaps carnitine deficiency.

CONCLUSION

Although the NBS-identified and clinically-identified cohorts were not completely comparable, this long-term study shows likely substantial improvement overall in the outcome of these metabolic disorders in the NBS infants. Infants with mild disorders and benign variants may represent a significant number of infants identified by ENBS. The future challenge will be to unequivocally differentiate the disorders most benefitting from ENBS and adjust programs accordingly.

The Risk of Fatty Acid Oxidation Disorders and Organic Acidemias in Children with Normal Newborn Screening

New Zealand has undertaken expanded newborn screening since 2006. During that period there have been no reported cases of fatty acid oxidation disorders or organic acidemias that have been diagnosed clinically that the screening programme missed. However there may have been patients that presented clinically that were not diagnosed correctly or notified.In order to investigate the false-negative screening rate a case-control study was undertaken whereby the clinical coding data and relevant medical records were reviewed for 150 controls and 525 cases. The cases had normal newborn screening but with key analytes and/or ratios just below the notification level for individual disorders and thus in theory were most at risk of having metabolic disease.Two cases had medical histories suggestive of metabolic disease and thus could represent a false-negative screen. One of these had marginally elevated octanoyl carnitine levels and thus possible medium-chain acyl Co-A dehydrogenase deficiency (MCADD) while the other had elevated isovaleryl carnitine and thus may have been a case of isovaleric acidemia (IVA). However, subsequent molecular analysis revealed that the diagnosis of MCADD and IVA was unlikely.Despite relatively high cut-offs the New Zealand Newborn Metabolic Screening Programme does not appear to have missed any confirmed cases of fatty acid oxidation disorders and organic acidemias in its first 8 years of expanded newborn screening. This would suggest a similar low false-negative screening rate in centres with comparable screening protocols and would indicate that the risk of fatty acid oxidation disorders and classical organic acidemias in children who had normal newborn screening is low.

Methylcrotonoyl-CoA carboxylase 1 potentiates RLR-induced NF-κB signaling by targeting MAVS complex

RNA virus infections are detected by the RIG-I family of receptors, which signal through the adaptor molecule mitochondrial antiviral signaling (MAVS). MAVS then recruits the adaptor’s tumor necrosis factor receptor-associated factor (TRAF) 3 and TRAF6, which in turn activate IRF3 and NF-κB, respectively, to induce interferons (IFNs) and inflammatory responses. Here we show that the biotin-containing enzyme methylcrotonoyl-CoA carboxylase 1 (MCCC1) enhances virus-induced, MAVS-mediated IFN and inflammatory cytokine expression through the NF-κB signaling pathway. MCCC1 knockdown strongly inhibits induction of IFNs and inflammatory cytokines. Furthermore, MCCC1 shows extensive antiviral activity toward RNA viruses, including influenza A virus, human enterovirus 71, and vesicular stomatitis virus. Here, we have elucidated the mechanism underlying MCCC1-mediated inhibition of viral replication. MCCC1 interacts with MAVS and components of the MAVS signalosome and contributes to enhanced production of type I IFNs and pro-inflammatory cytokines by promoting phosphorylation of the IκB kinase (IKK) complex and NF-κB inhibitor-α (IκBα), as well as NF-κB nuclear translocation. This process leads to activation of IFNs and cytokine expression and subsequent activation of IFN-stimulated genes, including double-stranded RNA-dependent protein kinase PKR and myxovirus resistance protein 1. These findings demonstrate that MCCC1 plays an essential role in virus-triggered, MAVS-mediated activation of NF-κB signaling.

3-Methylcrotonyl-CoA carboxylase deficiency: Mutational spectrum derived from comprehensive newborn screening

The deficiency of 3-methycrotonyl-CoA carboxylase (3-MCC; EC 6.4.1.4) is an autosomal recessive organic aciduria that is included in the newborn screening programs of several countries. This study reports data mainly obtained from the Portuguese newborn screening program collected over a ten-year period. Analysis of the MCCC1 and MCCC2 genes yielded 26 previously unreported mutations and a variant of clinically unknown significance. These mutations are discussed in the context of their likely impact on the function of the 3-MCC enzyme, with a view to exploring whether a phenotype-genotype correlation might be discerned. Further, these mutations were analysed in the context of what is known of the MCCC1 and MCCC2 mutational spectra, information that will be useful in both clinical and laboratory practice.

Outcomes of cases with 3-methylcrotonyl-CoA carboxylase (3-MCC) deficiency - Report from the Inborn Errors of Metabolism Information System

INTRODUCTION

3-Methyl crotonyl CoA carboxylase (3MCC) deficiency is an inborn error of leucine metabolism whose detection was increased with the advent of expanded newborn screening. While most NBS-identified infants appear clinically normal, prior studies suggest a possible increased risk for developmental or metabolic abnormalities. As yet, no predictive markers are known that can identify children at risk for biochemical or developmental abnormalities.

METHOD

All available 3-MCC cases diagnosed by newborn screening in the Inborn Errors of Metabolism Information System (IBEM-IS) were reviewed for markers that might be predictive of outcome.

RESULTS

A limited number of cases were identified with traditional biochemical symptoms including acidosis, hyperammonemia or lactic acidosis, and 15% of those with available developmental information had recorded developmental disabilities not clearly attributable to other causes. There was no correlation between newborn screening (NBS) C5OH level and presence of metabolic, newborn, later-life or developmental abnormalities in these cases.

DISCUSSION

This sample, obtained from the IBEM-IS database, attempts to avoid some of the ascertainment bias present in retrospective studies. An increase in developmental abnormalities and in traditionally described metabolic symptoms remains apparent, although no specific biochemical markers appear predictive of outcome. The role that prevention of fasting plays in outcome cannot be ascertained. These data suggest that C5OH level found on newborn screening by itself is not sufficient for diagnostic or predictive purposes.