Multivariate analysis and model building for classifying patients in the peroxisomal disorders X-linked adrenoleukodystrophy and Zellweger syndrome in Chinese pediatric patients

Zhu et al. Orphanet Journal of Rare Diseases https://doi.org/10.1186/s13023-023-02673-x (2023) 18:102 Orphanet Journal of Rare Diseases Open Access RESEARCH Multivariate analysis and model building for classifying patients in the peroxisomal disorders X-linked adrenoleukodystrophy and Zellweger syndrome in Chinese pediatric patients Zhixing Zhu1, Georgi Z. Genchev2, Yanmin Wang3, Wei Ji3, Xiaofen Zhang3, Hui Lu1,4*, Sira Sriswasdi2* and Guoli Tian3,5* Abstract Background The peroxisome is a ubiquitous single membrane-enclosed organelle with an important metabolic role. Peroxisomal disorders represent a class of medical conditions caused by deficiencies in peroxisome function and are segmented into enzyme-and-transporter defects (defects in single peroxisomal proteins) and peroxisome biogenesis disorders (defects in the peroxin proteins, critical for normal peroxisome assembly and biogenesis). In this study, we employed multivariate supervised and non-supervised statistical methods and utilized mass spectrometry data of neurological patients, peroxisomal disorder patients (X-linked adrenoleukodystrophy and Zellweger syndrome), and healthy controls to analyze the role of common metabolites in peroxisomal disorders, to develop and refine a classification models of X-linked adrenoleukodystrophy and Zellweger syndrome, and to explore analytes with utility in rapid screening and diagnostics. Results T-SNE, PCA, and (sparse) PLS-DA, operated on mass spectrometry data of patients and healthy controls were utilized in this study. The performance of exploratory PLS-DA models was assessed to determine a suitable number of latent components and variables to retain for sparse PLS-DA models. Reduced-features (sparse) PLS-DA models achieved excellent classification performance of X-linked adrenoleukodystrophy and Zellweger syndrome patients. Conclusions Our study demonstrated metabolic differences between healthy controls, neurological patients, and peroxisomal disorder (X-linked adrenoleukodystrophy and Zellweger syndrome) patients, refined classification models *Correspondence: Hui Lu Sira Sriswasdi Guoli Tian Full list of author information is available at the end of the article © The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Zhu et al. Orphanet Journal of Rare Diseases (2023) 18:102 Page 2 of 14 and showed the potential utility of hexacosanoylcarnitine (C26:0-carnitine) as a screening analyte for Chinese patients in the context of a multivariate discriminant model predictive of peroxisomal disorders. Keywords X-linked adrenoleukodystrophy, X-ALD, Zellweger syndrome, Very long chain fatty acids, C26: carnitine, Hexacosanoylcarnitine, Newborn screening, Metabolomic signature, PLS-DA, Sparse PLS-DA, PCA, t-SNE Introduction The peroxisome is a ubiquitous single membraneenclosed organelle which plays important metabolic functions, such as the β-oxidation of very long chain fatty acids, α-oxidation of branched chain fatty acids, synthesis of bile acids and ether-linked phospholipids, and removal of reactive oxygen species [1]. Peroxisomal disorders represent a class of medical conditions caused by defects in peroxisome functions and can be broadly segmented into enzymes and transporter defects (defects in single peroxisomal proteins important for peroxisome function) and peroxisome biogenesis disorders (defects in the peroxins - proteins which are critical for normal peroxisome assembly and biogenesis) [2, 3]. Zellweger syndrome (ZS) (OMIM: 214,100, ICD: Q87.82) is a rare congenital peroxisome biogenesis disorder, the most severe of the four disorders of the Zellweger spectrum, with an estimated prevalence of 1:50,000 [4]. It is characterized by a lack of functioning peroxisomes in the cells of the afflicted individual and is associated with deficient neuronal migration and neuronal positioning, and impairment in the individual’s brain development. The patient may present with high forehead, hypoplastic supraorbital ridges, epicanthal folds, midface hypoplasia, and other craniofacial abnormalities. ZS etiology is due to mutations of the PEX gene family, and the disease has rapid progression and high mortality rate. At present, there are limited options for effective treatment, and treatment options are focused on improvement of quality of life and support. X-linked adrenoleukodystrophy, X-ALD (OMIM: 300,100, ICD: E71.33) is a rare disease with estimated prevalence of 1 in 15,000 individuals caused by mutations in ABCD1 - an X chromosome gene (Xq28) which codes for the ALD protein. Functional deficiencies in this peroxisomal membrane transporter protein causes buildup of saturated very long-chain fatty acids (VLCFA) in plasma and tissues [5]. The clinical disease course of X-ALD in male patients commences with being asymptomatic at birth. Addison’s disease is often the first display of the disorder that can present years before the appearance of neurological symptoms. The cerebral type of X-ALD can manifest in childhood (childhood cerebral ALD, CCALD), adolescence (adolescent cerebral ALD, AdolCALD) or adulthood (adult cerebral ALD, ACALD) and progress rapidly with deteriorating condition of the patient. Nearly all male patients and the majority of female patients who reach adulthood eventually develop adrenomyeloneuropathy (AMN)[6]. Depending on the specific X-ALD phenotype, patients may present with adrenocortical insufficiency, rapid decline in cognitive abilities, hyperactivity, spastic paraparesis and seizures, to name a few. Despite their originally shown promise, Lorenzo’s oil and lovastatin have failed to deliver strong evidence as an effective therapy for AMN] [7–9]. Allogeneic bone marrow transplantation or hematopoietic stem cell transplantation are the most effective treatment in cerebral ALD, which if administered at an early time point before neurological symptom appear, can arrest the progression of X-ALD and stop demyelination. The progno (...truncated)