We present an attempt at exome analysis in two ME/CFS patients. Pt. 1 presents a mild form of carboxypeptidase N (CPN1) deficiency (a missense in exon 3) while Pt. 2 revealed two rare intronic variants in the same gene. CPN1 is an enzyme that inactivates kinins and complement proteins split products (such as C4a, a known anaphylatoxin). Therefore, CPN1 deficiency could explain C4a increase after exercise and mast cell abnormalities previously reported in ME/CFS. It could also explain the high prevalence of POTS in ME/CFS since kinins are vasodilators.
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease characterized by cognitive deficits, fatigue, orthostatic intolerance with symptoms exacerbated after exertion (IOM, 2015). This disease has no known cause but several abnormalities have been observed in energy metabolism (Tomas C. and Newton J. 2018), immune system and gut flora (Blomberg J. et al. 2018), brain (Zeineh MM. et al. 2014). In this population of patients, several abnormalities have been found to be triggered by exercise, such as abnormal aerobic performance (Snell C. et al. 2013), enhanced gene expression of specific receptors (White AT. et al. 2012), abnormal gut flora translocation (Shukla SK et al. 2015) and failure in blood clearance of complement protein 4 split product A (C4a) (Sorensen B et al. 2003). An increase in C4a is part of the human physiologic response to physical exercise, but these levels return to baseline within 30 minutes to 2 hours (Dufaux B et al. 1991) while in ME/CFS there is a peak in serum C4a six hours after exertion. A possible explanation for slow C4a inactivation could be a problem in carboxypeptidase N (CPN1), an enzyme involved in the inactivation of C3a, C4a, C5a. CPN1 is required for kinins inactivation too, such as bradykinin, kalladin (Hugli T. 1978), (Plummer TH et Hurwitz MY 1978), that are vasodilators. We report on the case of a ME/CFS patient (Pt. 1) with a missense variant in CPN1 gene that is linked to reduced function of the enzyme and of another ME/CFS patient (Pt. 2) with rare variants in introns 1 and 6 of the same gene with uncertain significance (table 1, figure 1).
Materials and Methods
Whole exome sequencing (WES) has been performed on cells from the saliva of two ME/CFS patients, with an average 100X coverage (Dante Labs). The first search for pathogenic variants and insertions/deletions was performed with the software EVE, provided by Sequencing.com. A further refinement of the search was conducted by manual insertion of these SNPs in VarSome. The search for possible unknown pathogenic variants within the gene for CPN1 has been performed using Integrative Genome Viewer (IGV), an opensource tool for genetic data analysis.
Results from the analysis of the two exomes performed with EVE and refined with VarSome are collected in table 2 (Pt. 1) and table 3 (Pt. 2).
Pt. 2 is carrier of a mitochondrial disease (table 3, first line): a missense in gene for medium-chain acyl-CoA dehydrogenase (MCAD) which leads to mild functional impairment of the enzyme involved in the oxidation of fatty acids (44% residual activity) (Koster KL. et al. 2014).
Pt. 2 is also homozygous for a variation in gene arylsulfatase A (ARSA) that is linked to a residual activity of only 10% of normal (Gomez-Ospina N. 2010). Arylsulfatase A deficiency (also known as metachromatic leukodystrophy or MLD) is a disorder of impaired breakdown of sulfatides (cerebroside sulfate or 3-0-sulfo-galactosylceramide), sulfate-containing lipids that occur throughout the body and are found in greatest abundance in nervous tissue, kidneys, and testes. Sulfatides are critical constituents in the nervous system, where they comprise approximately 5% of the myelin lipids. Sulfatide accumulation in the nervous system eventually leads to myelin breakdown (leukodystrophy) and a progressive neurologic disorder (Von Figura et al 2001). Nevertheless, this genotype does not cause MLD, and this benign condition of reduced ARSA activity is called ARSA pseudodeficiency. There are about 4 homozygotes in 1000 persons among non-Finnish Europeans (VarSome)
Pt. 1 is a carrier of a missense in gene CPN1 (table 2, first line) which leads to a loss of more than 60% of activity, according to a study on a single patient (Mathews KP. et al. 1980), (Cao H. et Hegele RA. 2003). The study of gene CPN1 in both patients (using IGV) has led to the identification of two rare variants (frequency less than 0.002) in intron 1 and 6 of one allele from Pt. 2 (table 1, figure 1). In MCAD no other damaging variations have been identified in these two patients by direct inspection with IGV (data not shown).
Whole exome sequencing (WES) is a technique that aims at the sequencing of the fraction of our genome that encodes for proteins: about 30 million base pairs (1% of the all the human DNA) divided into about 20 thousand genes (Ng SB et al. 2009). It has become increasingly clear that the use of WES can positively improve the rate of diagnosis and decrease the time needed for a definitive diagnosis in patients with rare genetic diseases (Sawyer SL et al. 2016). WES also positively impacts the ability to discover new pathogenic variants in known disease genes (Polychronakos C. et Seng KC. 2011) and the discovery of completely new disease genes (Boycott KM 2013). ME/CFS seems to have a genetic component: a US study found clear evidence of familial clustering and elevated risk for the disease among relatives of ME/CFS cases (Albright F et al. 2011) and several SNPs in various genes have been reported as more prevalent in ME/CFS patients versus healthy controls (Wang T et al. 2017). And yet, no studies that analyzed whole exomes of ME/CFS patients have been published, to my knowledge.
In this study, we searched for known genetic diseases in the exomes of two ME/CFS patients who fit the IOM criteria for SEID (IOM, 2015), with postural orthostatic tachycardia syndrome (POTS) identified by positive tilt table test. We detected a missense variant in CPN1 (rs61751507) in Pt. 1 (heterozygosis) that has been associated to a loss of activity of the enzyme of at least 60% in a previous study (Mathews KP. et al. 1980), (Cao H. et Hegele RA. 2003). We then found that, although Pt. 2 was not a carrier of this SNP, she had two rare SNPs in intron 1 (rs188667294) and 6 (rs113386068) of gene CPN1 (both present in less than 1/500 alleles, table 1, figure 1). These intronic variations have not been studied, to our knowledge, so their pathogenicity can’t be excluded at present. Variations in introns can be damaging just as missense and nonsense mutations in exons; suffice to say that the main known pathogenic SNP of gene CPN1 is a substitution in intron 1 (Cao H. et Hegele RA. 2003).
Carboxypeptidase N (CPN1) is an enzyme involved in the inactivation of C3a, C4a, C5a, and of kinins (bradykinin, kalladin) (Hugli T. 1978), (Plummer TH et Hurwitz MY 1978). In ME/CFS the physiologic increase in blood of C4a (the split product of the complement protein C4) after exercise is significantly more pronounced than in healthy controls as if there was a defect in C4a inactivation (Sorensen B et al. 2003). Such a defect could very well be a loss of function in CPN1, as found in Pt 1. Moreover, CPN1 is involved in inactivation of bradykinin, which is known to induce vasodilatation (Siltari A. et al. 2016), therefore CPN1 deficiency could play a role in POTS and in orthostatic intolerance in general. Both patients have a tilt table test positive for POTS. C4a has been recently considered to play a causal role in the cognitive deficit of schizophrenia, because of its role in synapsis pruning (Sekar, A et al, 2016); therefore a failure in its inactivation could be implicated in the incapacitating cognitive defects lamented by ME/CFS patients.
Only two patients with CPN1 deficiency have been reported so far in medical literature (Mathews KP. et al. 1980), (Willemse Jl et al. 2008), and the enzymatic defect has been associated to angioedema that most often involved the face and tongue, urticaria, and hay fever and asthma precipitated by exercise. This clinical presentation could be due, at least in part, to mast cell activation: in fact, C4a is a known anaphylatoxin that induces mast cells degranulation and release of histamine (Erdei A. et al. 2004). That said, we can observe that even if the clinical presentation of the only two known cases of CPN1 deficiency doesn’t fit the clinical picture of ME/CFS, mast cell activation syndrome (MCAS) has some commonalities with ME/CFS (Theoharides, TC et al. 2005), and mast cell abnormalities have been reported among ME/CFS patients (Nguyen T. et al. 2016). So we can’t exclude that activation of mast cells by a failure in C4a inactivation may lead to ME/CFS symptoms. The role of exercise as a trigger for symptoms in CPN1 deficiency is also highly suggestive because this is a pathognomonic feature of ME/CFS.
CPN1 deficiency is present (even if in a mild form) in Pt. 1, while Pt. 2 presents two rare intronic variants whose pathogenic role can’t be excluded. CPN1 deficiency could explain the abnormal increase of C4a after exercise and might be a contributing factor to post-exertional malaise and cognitive symptoms in ME/CFS. A search for pathogenetic SNPs in gene CPN1 among ME/CFS patients would clarify the role (if any) of this gene.
Acknowledgments. I would like to thank Chiara Scarpellini for her careful collection of annotations for each of the 2 hundred or so variants found by EVE within the exomes of Pt. 1 and Pt. 2 (table 2 and table 3).