Reviewer comments

Title: A phenotypic and molecular spectrum of pyridox(am)ine phosphate oxidase (PNPO) deficiency: a review of 62 cases of PNPO deficiency.

Journal: Clinical Genetics

Manuscript number: CGE-00449-2020

Manuscript type: Review

Authors: Alghamdi et al.

Alghamdi et al report two new patients with PNPO deficiency and literature review. Below are the comments.

General
1. Disease is called pyridoxamine-5’-phosphate oxidase, not pyridox(am)ine or pyridoxine 5’ phosphate oxidase, please correct and use a single name for this disease called with the name of the enzyme pyridoxamine-5’-phosphate oxidase throughout the manuscript.
2. As the literature review included 2002-2019, the below papers are not included and is essential to include into this literature review article. There was a review article in 2015, (Guerin et al., 2015) this study did not mention that review article. In that review article, clinical, EEG, response to pyridoxine, genetic results, patient outcomes, CSF neurotransmitter results of 41 patients reported in the literature up to 2014. The below articles are found in PubMed after a search was initiated as PNPO deficiency from 2013 to 2020:
a. Bagci S, Zschocke J, Hoffmann GF, et al. Pyridoxal phosphate-dependent neonatal epileptic encephalopathy. Arch Dis Child Fetal Neonatal Ed 2008; 93: F151-2. PIMD: 17216302
b. Veerapandiyan A, Winchester SA, Gallentine WB, et al. Electroencephalographic and seizure manifestations of pyridoxal 5'-phosphate-dependent epilepsy. Epilepsy Behav 2011; 20: 494-501. PMID: 21292558
c. Guerin A, Aziz AS, Mutch C, Lewis J, Go CY, Mercimek-Mahmutoglu S. Pyridox(am)ine-5-Phosphate Oxidase Deficiency Treatable Cause of Neonatal Epileptic Encephalopathy With Burst Suppression: Case Report and Review of the Literature. J Child Neurol. 2015 Aug;30(9):1218-25. PMID: 25296925
d. Mohanlal S, Bindu PS, Sureshbabu S, Kumar S. Variable treatment response in a patient with pyridoxal N phosphate oxidase (PNPO) deficiency- understanding the paradox. Epilepsy Behav Rep. 2020 Mar 24;14:100357. doi: 10.1016/j.ebr.2020.100357. eCollection 2020. PMID: 32395712
e. Lugli L, Bariola MC, Ori L, Lucaccioni L, Berardi A, Ferrari F. Further Delineation of Pyridoxine-Responsive Pyridoxine Phosphate Oxidase Deficiency Epilepsy: Report of a New Case and Review of the Literature With Genotype-Phenotype Correlation. J Child Neurol. 2019 Dec;34(14):937-943. doi: 10.1177/0883073819863992. Epub 2019 Aug 9. PMID: 31397616
f. Lloreda-Garcia JM, Fernandez-Fructuoso JR, Martinez-Ferrandez C, Fuentes-Gutierrez C. [Severe fetal anemia and neonatal epileptic encephalopathy caused by a novel PNPO mutation]. Rev Neurol. 2017 Oct 1;65(7):335-336. PMID: 28929476
g. Jaeger B, Abeling NG, Salomons GS, Struys EA, Simas-Mendes M, Geukers VG, Poll-The BT. Pyridoxine responsive epilepsy caused by a novel homozygous PNPO mutation. Mol Genet Metab Rep. 2016 Feb 10;6:60-3. doi: 10.1016/j.ymgmr.2016.01.004. eCollection 2016 Mar. PMID: 27014579
h. Levtova A, Camuzeaux S, Laberge AM, Allard P, Brunel-Guitton C, Diadori P, Rossignol E, Hyland K, Clayton PT, Mills PB, Mitchell GA. Normal Cerebrospinal Fluid Pyridoxal 5'-Phosphate Level in a PNPO-Deficient Patient with Neonatal-Onset Epileptic Encephalopathy. JIMD Rep. 2015;22:67-75. doi: 10.1007/8904_2015_413. Epub 2015 Mar 12. PMID: 25762494
i. Riikonen R, Mankinen K, Gaily E. Long-term outcome in pyridoxine-responsive infantile epilepsy. Eur J Paediatr Neurol. 2015 Nov;19(6):647-51. doi: 10.1016/j.ejpn.2015.08.001. Epub 2015 Aug 18. PMID: 26310861

1. There are important side effects leading to cirrhosis or liver transplantation. This review article did not mention these.
   a. Sudarsanam A, Singh H, Wilcken B, Stormon M, Arbuckle S, Schmitt B, Clayton P, Earl J, Webster R. Cirrhosis associated with pyridoxal 5'-phosphate treatment of pyridoxamine 5'-phosphate oxidase deficiency. JIMD Rep. 2014;17:67-70. doi: 10.1007/8904_2014_338. Epub 2014 Sep 26. PMID: 25256445
   b. Coman D, Lewindon P, Clayton P, Riney K. PNPO Deficiency and Cirrhosis: Expanding the Clinical Phenotype? JIMD Rep. 2016;25:71-75. doi: 10.1007/8904_2015_456. Epub 2015 Jun 25. PMID: 26108646
2. Correct “genetic” to “genotypic”
3. There are conflicting information throughout the manuscript regarding response to treatment or limited response to treatment.
4. It is not clear if the tables include two new patients that the authors included into this study. Throughout the manuscript, there is no section to provide information for the novel two cases that authors report in their study. Please report two novel patients under the section of novel cases to see if anything novel in the new patients diagnosed by authors.

Abstract
7. Describe the phenotypic features instead of “The phenotype results from deficiency of vitamin B6's active form, pyridoxal 5′-phosphate (PLP), which regulates several enzymes in the body.”
8. The following sentence is strong and not correct as some patients can still have seizures on PLP: “The hallmark feature of PNPO deficiency seizure is PLP responsiveness.”
9. What is the percentage of CSF amino acids and neurotransmitters to give a clue of PNPO deficiency? How is PNPO deficiency is differentiated from ALDH7A1 deficiency or PLPBP deficiency?
10. The authors listed what they have done in the abstract, but there is no study result that they report based on their current study. Did authors find any relationship between seizure onset, treatment onset and outcomes? It is not clear what their study results.
11. What is the conclusion of this study based on the extensive literature review?

Introduction
12. Correct “shortage” to “deficiency”.
13. “Can be fatal” should be corrected to “can be fatal, if untreated”
14. “The first case was reported based on a clinical and biochemical profile that was consistent with PLP-responsive neonatal epileptic encephalopathy; aromatic l-amino acid decarboxylase (AADC) deficiency mimics its biochemical profile, as PLP is a cofactor of AADC (Bräutigam et al.,73 2002). These are historic, we have known this deficiency for the last 15 years with the mechanism of AADC deficiency mimickers, this should not be used in a 2020 review article anymore, especially knowing that some patients can present with CSF monoamine neurotransmitter deficiency, but some do not.
15. Unfortunately, authors did not capture all patients published in the literature. This is inadequate review to state that there are 60 cases reported in the literature.
16. Pathophysiology and pathways were recently reported in a review article by three experts, Plecko, Mills and Clayton in the below article. Re-writing all known pathophysiological mechanisms are not novel to be included in this article.
a. Wilson MP, Plecko B, Mills PB, Clayton PT. Disorders affecting vitamin B6 metabolism. J Inherit Metab Dis. 2019 Jul;42(4):629-646. doi: 10.1002/jimd.12060. Epub 2019 Mar 20. PMID: 30671974

Methods
17. This review article should include all cases reported in the literature including 2020.

Results
18. Results are too long with not useful detailed information that should be shortened, such as birth history, urinalysis, plasma and CSF findings, brain MRI etc.
19. How did authors decide for the severity of the phenotype?
20. What is the use of structural analysis in this study?
21. Information in four tables are detailed in the results too. This is duplication of the work, please remove all repeated information.

Figures, tables
22. Figure 1 is not unnecessary, as this is already drawn in several studies, that the author can refer.

Reviewer comments

Title: Phenotypic and molecular spectrum of pyridoxamine-5’- phosphate oxidase (PNPO) deficiency: a scoping review of 87 cases of PNPO deficiency.

Journal: Clinical Genetics

Manuscript number: CGE-00449-2020.R1

Manuscript type: Review

Authors: Alghamdi et al.

Alghamdi et al revised the manuscript for some of the concerns raised by this reviewer. However, there are still open questions that the authors should revise their manuscript accordingly:

1. Despite they included references into their tables, they did not include those references into the reference list. Please add those references in tables into the reference list. All patients summarized in their tables using references, should be in the reference list.
2. Results section should be shortened.