Distribution of Exonic Variants in Glycogen Synthesis and Catabolism Genes in Late Onset Pompe Disease (LOPD)

Round 1

Reviewer 1 Report

The authors state that since, “There is not evidence that environmental factors can modulate the phenotype” in Pompe disease, the “observed clinical variability in [Pompe disease] suggests that genetic variants other than pathogenic GAA mutations influence the mechanisms of muscle damage/repair and the overall clinical picture.”  The authors also suggest that the variability and unpredictability of a patient’s response to enzyme replacement therapy for Pompe disease, might possibly be due to genetic variants other than those of the GAA gene.

The authors set out to search for phenotype modifying genes and propose that such genes might be found among genes encoding proteins that impact glycogen synthesis and catabolism.  The authors performed whole exome sequencing on samples from 30 individuals who carry a diagnosis of late-onset Pompe disease and analyzed the presence of variants of 14 genes involved in glycogen synthesis (10 genes) and catabolism (4 genes).

Interestingly, all the individuals being studied had c.-32-13T>G as one of their pathogenic alleles. The second pathogenic allele varied, and included c.525delT (which is found in some patients with the infantile phenotype) and p.Asp489Asn, and c.2237G>A (also classified as severe) and c.1927G>A.

The authors found variability and inconsistencies with comparing phenotypes using the Walton score compared to 6MWT and FVC.  The authors did not identify any single variants that were strongly associated with variability Pompe disease phenotype.

Importantly, the authors identified 5 difference genes involved in glycogen synthesis, i.e, UGP2, GYG2, GYS2, GBE1, and GSK3A, as genes that had variants that were more commonly found in individuals who have been diagnosed with late-onset Pompe disease.

The study design is relevant to the current landscape for diagnosis and clinical care for individuals who have Pompe disease. Of particular importance and relevance, is the need to be better able to predict phenotype in geographic areas of the world in which newborn screening programs are being piloted or are established.   The determination of phenotype is of utmost importance when a neonate is identified as having Pompe disease. Even in patients with the most severe phenotype, the infantile phenotype, there is heterogeneity.  Better understanding of the correlation of GAA genotype to phenotype, as well as the understanding of other disease modifying genes that may play a critical role, would be invaluable for guidance of clinical care.

Suggestions/questions for the authors:

It would be helpful for the import of the article if the authors could make brief comments in their article that address the 2 following questions:

Are the authors able to comment briefly on whether they are aware if there is any data evaluating the consistency of the phenotype for individuals who are homozygous for c.-32-13T>G? 

Are the authors able to comment about how studies such as theirs (whether using their findings and/or doing additional studies that may be able to further improve understanding of phenotype modifying genes),  may help improve the usefulness of newborn screening for Pompe disease?

Author Response

Suggestions/questions for the authors:  It would be helpful for the import of the article if the authors could make brief comments in their article that address the 2 following questions:  1) Are the authors able to comment briefly on whether they are aware if there is any data evaluating the consistency of the phenotype for individuals who are homozygous for c.-32-13T>G? 

Suggestion 1: we added a sentence to comment the phenotype for individuals homozygous for c.-32-13T>G in the conclusions, line 270

2) Are the authors able to comment about how studies such as theirs (whether using their findings and/or doing additional studies that may be able to further improve understanding of phenotype modifying genes),  may help improve the usefulness of newborn screening for Pompe disease?

Suggestion 2: we added a sentence to comment this topic at the end of discussion. line 285

Reviewer 2 Report

Summary of the key contribution of the paper:

Distribution of exonic variants in glycogen synthesis and catabolism genes in Late Onset Pompe Disease (LOPD) describes that the current clinical scores used in LOPD do not describe muscle impairment with enough qualitative/quantitative details to correlate it with genes whose even slightly reduced function, due to genetic variants, impacts the phenotype and they report potentially relevant variants in genes related to glycogen synthesis and catabolism, identified by whole exome sequencing in a group of 30 patients with Late Onset Pompe Disease (LOPD).The scope of the manuscript is very interesting, the manuscript can be accepted after addressing the following concerns.

1)    The manuscript explains that the genes encoding proteins involved in glycogen synthesis and catabolism may represent excellent candidates as phenotypic modifiers of PD.

2)    The font used in the all the figures should be maintained uniform.

3)    Pompe disease (PD) is a monogenic autosomal recessive disorder caused by biallelic pathogenic variants of the GAA gene encoding lysosomal alpha-glucosidase; its loss causes glycogen storage in lysosomes, mainly in muscular tissue.

4)    A measure considering both the severity of any (motor/respiratory) clinical score and patients’ disease. duration/actual age, could better reflect the phenotype in “dynamic” terms of disease progression and pattern,at least ideally.

5)    In the long term, improving our knowledge of genetic variability and its relationship to phenotypic variability may be useful for the development of new therapeutic approaches.

Lowlights: There are no Lowlights in this paper

Author Response

The scope of the manuscript is very interesting, the manuscript can be accepted after addressing the following concerns. 

1)    The manuscript explains that the genes encoding proteins involved in glycogen synthesis and catabolism may represent excellent candidates as phenotypic modifiers of PD.

we have chosen these genes for our preliminary work because Pompe is a glycogen storage disease;  we are now continuing to work on different set of genes related to muscular and respiratory  insufficiency as well as for genes related to autophagy. these data will be available in the second half of the year and will be the topic of a different paper.

2)    The font used in the all the figures should be maintained uniform.

we made it uniform

3)    Pompe disease (PD) is a monogenic autosomal recessive disorder caused by biallelic pathogenic variants of the GAA gene encoding lysosomal alpha-glucosidase; its loss causes glycogen storage in lysosomes, mainly in muscular tissue.

we substitued this sentence in the introduction, line 56

4)    A measure considering both the severity of any (motor/respiratory) clinical score and patients’ disease. duration/actual age, could better reflect the phenotype in “dynamic” terms of disease progression and pattern, at least ideally.

sorry, we dont understand the requested change; you suggest to modify or erase the sentence?

5)    In the long term, improving our knowledge of genetic variability and its relationship to phenotypic variability may be useful for the development of new therapeutic approaches.

we understand that this sentence is "wishful trhinking", no problem to erase it, if this is trhe request.