Mayo <i>CALR</i> mutation type classification guide using alpha helix propensity
Authors: Terra L. Lasho, Christy M. Finke, Alexander Tischer, Animesh Pardanani, Ayalew Tefferi
Journal: American Journal of Hematology (2018)

Myeloproliferative neoplasms (MPN) constitute one of the major categories of myeloid neoplasms, according to the World Health Organization (WHO) classification system.1 Included under the 2016 WHO MPN category are polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). These three clinicopathologic entities are distinguished from other MPNs, not only by their morphologic features, but also by their close association with the driver mutations JAK2 (Janus kinase 2; 9p24), CALR (calreticulin; 19p13.2), and MPL (myeloproliferative leukemia virus oncogene; 1p34).2 Mutational frequencies are approximately 97%, 55%, and 65% for JAK2; 0%, 25%, and 20% for CALR; and 0%, 3%, and 8% for MPL, in PV, ET, and PMF, respectively.2 The discovery of CALR mutations in JAK2/MPL mutation-negative ET and PMF, in 2013, was accompanied by the realization of their distinct phenotypic and prognostic attributes.2 More than 80% of CALR mutations seen in MPN are classified as either "type 1" or "type 2"; type 1 denotes a 52-bp deletion (p.L367fs*46) and type 2 a 5-bp TTGTC insertion (p.K385fs*47). In one study of 368 CALR-mutated patients with MPN,3 206 (56%) harbored type 1, 119 (32%) type 2, and 43 (12%) other CALR variants; the corresponding incidences in PMF were 70%, 13%, and 17% and in ET 51%, 39%, and 10%.3 In 2014, we reported a higher platelet count in ET patients with type 2 CALR mutations, compared to those with the type 1 variant.4 The same year, we discovered that the survival advantage of CALR mutations in PMF was restricted to patients with the type 1 variant.5 Having established the remarkable prognostic distinction between type 1 and type 2 CALR mutations in PMF,5 and in view of the multiple functions of native CALR, which includes handling of protein folding and transport, we considered the possibility that differences in secondary structure of mutant CALR variants might underlie the differences in their corresponding clinical phenotypes. One of the major determinants of protein secondary structure is helical content. Accordingly, we used a statistical approximation algorithm (AGADIR) to calculate helix propensity for 31 unique amino acid sequences that were altered by CALR mutations, in order to sub-classify CALR mutations that were neither type 1 nor type 2, into type 1-like and type 2-like variants.6 We were subsequently able to show similarities in survival between type 1 and type 1-like and between type 2 and type 2-like CALR variants.6 A number of other studies have since validated our methods and the prognostic distinction between type 1/type 1-like and type 2/type 2-like CALR variants in PMF7, 8; this distinction is now formally incorporated in the recently unveiled mutation-enhanced international prognostic scoring systems for transplant-age patients with PMF (MIPSS70 and MIPSS70-plus).9 In the current communication, we provide a list of CALR variants, seen at our institution (n = 363) or cited in major published studies (n = 62) and their corresponding AGADIR-predicted helical content, in order to facilitate accurate classification by the practicing physician and clinical pathologist (Figure 1; Supporting Information Figure 1). The AGADIR-derived predicted helix propensity score, using the most recently updated online tool (agadir.crg.es), was 33.62 for wild-type CALR (which is close to what is expected for α-helix content for an average globular protein), 17.5 for type 1, and 40.02 for type 2 CALR variants. Accordingly, and consistent with our previously employed methodology, non-type 1 or 2 CALR variants with helix propensity scale close to or above that of wild-type CALR were classified as type 2-like (range 30.95-44.89) and those with values close to or below the value for type 1 were classified as type 1-like (range 4.97-25.12) (Figure 1; Supporting Information Figure 1). Mayo CALR mutation type classification guide using alpha helix propensity. If the mutation of interest is missing from the list, we recommend consultation with the molecular pathologist submitting the report in order to determine the amino acid sequence resulting from the specific mutation. This information can then be entered into the online available AGADIR protocol, in order to determine the helix propensity score. In this regard, the cutoffs we used to clinically demonstrate survival impact were an AGADIR scale of 26% or less for type 1-like and 30% or more for type 2-like CALR variants (Figure 1). Occasionally, one encounters CALR variants with an AGADIR scale in the range of 27%-29%; we prefer the term "indeterminate" in such circumstances and recommend, instead, reliance on other prognostic markers, such as karyotype and other mutations, instead of forcing assignment to a specific category. None Additional Supporting Information may be found online in the supporting information tab for this article. Supporting Information Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.