Mayo CALR
 mutation type classification guide using alpha helix propensity

Abstract About 25% of patients with essential thrombocythemia (ET) or primary myelofibrosis (PMF) carry a somatic mutation of CALR, the calreticulin gene [N Engl J Med. 2013;369:2379-90]. So far, more than 50 different indels in CALR exon 9 have been found, but a 52-bp deletion (type 1 mutation) and a 5-bp insertion (type 2) are the most common lesions. All indels generate a novel C-terminus of the mutant protein, in which the endoplasmic reticulum retention signal KDEL is lost and the negatively charged amino acids are replaced by neutral and positively charged amino acids, disrupting the Ca-binding site. This suggests that both cellular dislocation and impaired Ca-binding activity may be involved in the abnormal proliferation of cells expressing a mutant calreticulin. It is still unclear, however, why the same mutant gene is associated with 2 different disease phenotypes (ET and PMF). In particular, little in known about the effect of the mutant protein on megakaryocyte biology and bone marrow collagen deposition. We studied the relationships between CALR mutation type, megakaryocyte biology, and clinical phenotype in patients with myeloproliferative neoplasms. According to the 2008 WHO criteria, 716 out of 892 patients had ET and 176 had PMF. Overall, 578 (65%) patients carried JAK2 (V617F), 230 (26%) had a CALR indel, and 84 (9%) had nonmutated JAK2 and CALR. Patients with MPL mutations were excluded. Twenty-six different types of CALR lesions were identified: 120 (52%) patients had type 1 mutation, 75 (33%) had type 2, and 35 (15%) carried other indels. The frequency of type 1 mutation was significantly higher in PMF than in ET (71% vs 46%, P=.004). All these variants involved 3 different stretches of negatively charged amino acids, with an increase in the isoelectric points (pI) of the mutant protein. As type 1 and type 2 mutations affected stretch I and III, respectively, the 26 indels were categorized into 3 groups on the basis of the stretch they affected: i) type 1-like (61%), affecting stretch I; ii) type 2-like (36%), stretch III; iii) and other types (3%), stretch II. The pI values were significantly different in the 3 groups (P<.001). The frequency of type-1 like mutations was significantly higher in PMF than in ET (82% vs 55%, P=.001). In vitro differentiated megakaryocytes from CALR-mutant patients displayed a significant increase in the extent of both intracellular Ca2+ release from the endoplasmic reticulum and extracellular Ca2+ entry inside the cytoplasm, as compared with healthy controls. Megakaryocytes carrying type 1-like CALR mutations exhibited the highest amplitude of Ca2+ flows regardless of the type of disease. In ET, impaired Ca2+ homeostasis was accompanied by atypical proplatelet architecture (ie, more branches and bifurcations). With respect to clinical phenotype at diagnosis, ET patients with type 2-like CALR mutation showed a trend towards higher PLT count (P=.063) and lower age (P=.053), and significantly lower LDH values (P=.021) than those with type 1-like mutation. In a hierarchical cluster analysis including demographic, clinical and molecular data, CALR mutation type (1 vs 2) identified the 2 clusters with the highest dissimilarity. Considering all patients, those with type 2-like CALR lesions had a better survival than those with JAK2 (V617F) (96.1% vs 84.4% at 10 years, P=.039), while no difference was found between the 2 CALR mutation types. ET patients with type 2-like CALR mutations showed a lower risk of thrombosis than those with JAK2 (V617F) (P=.010). By contrast, ET patients with type 1-like CALR mutations had a higher risk of myelofibrotic transformation that those with type 2-like CALR mutations (P=.029) and especially those with JAK2 (V617F) (P=.011). Finally, PMF patients with type 1-like CALR variants had a better survival than those with JAK2 (V617F) (80.1% vs 48% at 10 years, P=.008). In summary, abnormalities in megakaryocyte calcium metabolism and proplatelet architecture are found in patients with CALR-mutant myeloproliferative neoplasms, and their extent is related to mutation type. Type 2-like CALR mutations are more likely to be associated with isolated thrombocytosis without bone marrow fibrosis, ie, with an ET phenotype. By contrast, type 1-like CALR mutations are generally associated with bone marrow fibrosis, ie, with a PMF phenotype. Thus, in CALR-mutant myeloproliferative neoplasms, the mutation type is a major determinant of the clinical phenotype. Disclosures No relevant conflicts of interest to declare.

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Mut-Detecter: An EGFR activating mutation type classification method with a deep convolutional neural network

2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) ◽

10.1109/bibm49941.2020.9313577 ◽

2020 ◽

Author(s):

Yaojun Wang ◽

Xinyu Hua ◽

Yu Wang ◽

Chunming Zhang ◽

Dongbo Bu ◽

...

Keyword(s):

Neural Network ◽

Convolutional Neural Network ◽

Deep Convolutional Neural Network ◽

Classification Method ◽

Activating Mutation ◽

Type Classification ◽

Mutation Type

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The Prognostic Advantage of Calreticulin Mutations in Myelofibrosis Might be Confined to Type 1 or “type 1-like” Calreticulin Variants

Blood ◽

10.1182/blood.v124.21.3166.3166 ◽

2014 ◽

Vol 124 (21) ◽

pp. 3166-3166

Author(s):

Ayalew Tefferi ◽

Terra L Lasho ◽

Alexander Tischer ◽

Emnet A Wassie ◽

Christy Finke ◽

...

Keyword(s):

Leukocyte Count ◽

Alpha Helix ◽

Wild Type ◽

C Terminus ◽

Helix Propensity ◽

The Difference ◽

Calr Mutations ◽

Propensity Scale

Abstract Background : Approximately 25% of patients with primary myelofibrosis (PMF) harbor calreticulin (CALR) mutations, which have been associated with longer survival (Klampf et al. NEJM 2013). More than 80% of CALR mutated patients harbor one of two mutation variants: type 1, a 52-bp deletion (p.L367fs*46) or type 2, a 5-bp TTGTC insertion (p.K385fs*47). Recent studies have suggested phenotypic and prognostic differences between these two variants (Tefferi et al. Blood 2014, Leukemia 2014 and AJH 2014). Furthermore, data are emerging that suggest functionally-relevant structural differences between type 1 and type 2 CALR variants, including a higher alpha-helix content of the mutant C-terminus in type 2, compared to type 1 (Eder-Azanza et al. Leukemia 2014). Objectives : We used statistical models to calculate helix propensity for thirty-one unique amino acid sequences that were altered by CALR mutations and used the results to subclassify non-type 1/2 CALR mutations into “type 1-like” and “type 2-like” variants. Subsequently, we examined the prognostic relevance of these subgroups. Methods : Calculation of helix propensity, which is the percentage of residues that are predicted to be involved in the formation of an alpha-helix, was performed using AGADIR, which is a statistical approximation algorithm (Munoz et al. Biopolymers 1997). The helix tendency calculations were performed using conditions of pH 7.0, 5 and 25 °C, an ionic strength of 0.1 M and no N- or C-terminal protection. Results : 532 PMF patients were screened for JAK2, CALR and MPL mutations; the respective mutational frequencies were 58%, 24.6% and 7.3%. Among the 131 CALR-mutated cases, 98 (74.8%) harbored type 1, 15 (11.5%) type 2 and 18 (13.7%) other variants. Based on predicted helix propensity scale, the “other” CALR mutations were subclassified as type 1-like (n=12) or type 2-like (n=6) and respectively grouped with type 1 and type 2 variants, for purposes of phenotypic and prognostic comparisons. The AGADIR-derived predicted helix propensity scale was 29.69 for wild-type CALR and 8.6 or 34.17 for type 1 and type 2 mutant CALR, respectively; accordingly, CALR variants with values that are close to or above the value for wild-type CALR were classified as “type 2-like” (range 26.47-36.12) and those with values close to or below the value for type 1 as “type 1-like” (range 2.11-17.3). Comparison of “type 1/type 1-like” (n=110) and “type 2/type 2-like” (n=21) CALR mutations showed the latter to be associated with higher DIPSS-plus score (p=0.01), EZH2 mutations (p<0.01), leukocyte count >25 x 10(9)/L (p<0.01), higher circulating blast percentage (p=0.02) and palpable spleen size >10 cm (p<0.01). Comparison of “type 1/type 1-like” CALR and JAK2 mutations (n=309) showed the former to be associated with younger age, higher platelet count, lower transfusion need, higher hemoglobin level, lower leukocyte count and lower DIPSS-plus score (p<0.01 for all comparisons). None of these associations was evident during comparison of “type 2/type 2-like” CALR with JAK2 mutations. Survival was similar between patients with type 1 and “type 1-like” (p=0.8) and between type 2 and “type 2-like” (p=0.63) CALR mutations. In contrast, survival was significantly shorter in patients with type 2 (HR 2.4, 95% CI 1.2-4.8) and “type 2-like” (HR 3.2, 95% CI 1.0-10.6), when compared to those with type 1 CALR mutations. Survival was also significantly shorter with “type 2/type 2-like” vs “type 1/type 1-like” CALR mutations (p=0.003; HR 2.5, 95% CI 1.4-4.5) and the difference remained significant when analysis was adjusted for age (p=0.047), ASXL1 (p=0.003) or EZH2 (p=0.001) mutations. Similarly, compared to JAK2-mutated cases (n=309), survival was longer in patients with “type 1/type 1-like” (HR 0.4, 95% CI 0.3-0.5) but not in those with “type 2/type 2-like” (HR 0.9, 95% CI 0.5-1.6) CALR mutations; the difference in survival between JAK2 and “type 1/type 1-like” CALR mutated cases remained significant (P<0.01) when analysis was adjusted for age, ASXL1 or EZH2 mutations or DIPSS-plus score. Conclusions : CALR mutations in PMF might be subclassified into type 1-like and type 2-like variants, based on predicted helical propensity of their mutant C-terminus. The favorable impact of CALR mutations in PMF might be restricted to type 1 or “type 1-like” variants. Disclosures No relevant conflicts of interest to declare.

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Conservative substitutions at internal sites in sperm whale myoglobin reveal correlations with alpha helix propensity

Protein Engineering Design and Selection ◽

10.1093/protein/6.supplement.18-b ◽

1993 ◽

Keyword(s):

Alpha Helix ◽

Sperm Whale ◽

Helix Propensity ◽

Sperm Whale Myoglobin

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Alpha helix propensity of amino acids

Science ◽

10.1126/science.8235616 ◽

1993 ◽

Vol 262 (5135) ◽

pp. 917-918 ◽

Cited By ~ 3

Author(s):

D Shortle ◽

N Clarke

Keyword(s):

Amino Acids ◽

Alpha Helix ◽

Helix Propensity

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Structural basis of amino acid alpha helix propensity

Science ◽

10.1126/science.8503008 ◽

1993 ◽

Vol 260 (5114) ◽

pp. 1637-1640 ◽

Cited By ~ 331

Author(s):

M Blaber ◽

X. Zhang ◽

B. Matthews

Keyword(s):

Amino Acid ◽

Alpha Helix ◽

Structural Basis ◽

Helix Propensity

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Driver Mutation Profile By MLPA in Myelofibrosis Patients

Blood ◽

10.1182/blood-2018-99-119776 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 5494-5494

Author(s):

Minuncio Juliana ◽

Alexandre Nonino ◽

Juliana Forte Mazzeu ◽

Cintia do Couto Mascarenhas

Keyword(s):

Bone Marrow ◽

High Risk ◽

Acute Leukemia ◽

Triple Negative ◽

Low Risk ◽

Calr Mutations ◽

Mutation Type ◽

Calr Mutation

Abstract Myelofibrosis is the rarest and most severe Ph- myeloproliferative neoplasm and can present de novo or post Polycythemia Vera or Essential Thrombocythemia. It is characterized by bone marrow fibrosis, extramedullary hematopoiesis and abnormal expression of inflammatory cytokines resulting in several atypical events and may progress to Acute Leukemia. The disease arises from clonal expansion of a single hematopoietic stem cell (HSC), driven by a somatic mutation of JAK2, CALR or MPL genes combined with dysregulation of hematopoietic microenvironment, additional mutations and cytogenetic abnormalities.The aims of this study are to assess driver mutations status in primary or secondary myelofibrosis patients and to correlate their mutational profile with clinical outcomes. The search for JAK2V617F, exon 12 JAK2, calreticulin exon 9 c.1092_1143del52 and c.1154_1155insTTGT, MPLW515K and MPLW515L mutations was performed in 31 subjects using MLPA technique, a method of DNA analysis that allows simultaneous appraisal of different mutations in multiple samples. 48.4% of patients present the JAK2V617F mutation,indel CALR mutations in 38.7% of patients (of these, 66.7% with del52 bp, 33.3% harbored insTTGTC),MPL W515L in 3.2% of patients and 9.7% of patients were triple-negative. From the mutational profile information obtained by MLPA,the clinical-molecular risk score was calculated for each of the individuals in the sample, according Rumi et al.. Being at 12,9% (4) as very low risk, 9.7% (3) as low risk,35.4% (11) as intermediary risk, 29.1% (9) and of high risk, and 12.9%(4) as very high risk. Patients with mutated JAK2 were older, with minor degree of anemia and more leukocytosis, whereas those with CALR mutations had less frequency of leukocytosis and thrombocytopenia. Triple-negative subjects displayed the lowest median age at diagnosis (49.3 years), and bone marrow failure phenotype, similar to Myelodysplastic Syndrome. Risk stratification provided by DIPSS was similar to other centers.Individuals with PMF present constitutional symptoms significantly more often than those with post-ET MF(p = 0.0365).Mortality rate was 29%, and mean survival after diagnosis was 68.3 months. CALR mutated individuals presented higher average survival and median survival according to DIPSS was higher than predicted by the prognostic model, possibly due to the higher frequency of CALR mutations reported.Median follow-up time was 32 months (ranging from 10 months to 13 years).Thromboembolic phenomena were recorded in 19.3% of patients, and evolution to AML in 6.4% of patients and it was verified that 75% of the individuals with Myelofibrosis Post-ET presented thrombotic events at some point in the disease. The association between the DIPSS clinical-laboratory parameters and the demand of transfusion at diagnosis, with the occurrence of Acute Leukemia was assessed using Fisher's exact test but have no significant difference in these parameters between patients who evolved or not for Acute Leukemia. The JAK2 V617F mutation is expected to be present in 60 to 65% of individuals with Myelofibrosis, but this mutation has been identified in only 48% of patients. In contrast, the observed frequency of indel of the CALR, of 38%, was higher than the classically described, from 25 to 30%. The rate of mutation type 2 (ins 5-bp) was also higher than expected, 33.6%.Regarding the mutation subtypes of CALR, mutation type 1 (52-bp deletion) is observed in up to 80% of MFP cases, but has a similar frequency as type 2 (5-bp insertion) in patients with ET. The grouping of patients with primary MF and post-ET may have contributed to the higher incidence of type 2 CALR mutation observed in this sample, although much higher than the 13% frequency described in the literature in a mixed population. The type 1 mutation was observed in 66% of our patients with post-ET and mutated CALR, but the small number of individuals in the study does not allow to estimate the impact of this mutation in the evolution of the disease. Our fraction of CALR-mutated patients is much higher than those described in Asian, European, North American and Argentinean populations. The complex genetic landscape involved in initiation and progression of Myelofibrosis, instigates the adoption of integrative prognostic stratification models. In this scenario, MLPA is a powerful tool for molecular study, and a promising ally for MPN molecular characterization. Disclosures No relevant conflicts of interest to declare.

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Physico-Chemical Properties of Recombinant Desulphatohirudin

Thrombosis and Haemostasis ◽

10.1055/s-0038-1645073 ◽

1990 ◽

Vol 63 (03) ◽

pp. 499-504 ◽

Cited By ~ 4

Author(s):

A Electricwala ◽

L Irons ◽

R Wait ◽

R J G Carr ◽

R J Ling ◽

...

Keyword(s):

Molecular Weight ◽

Gel Filtration ◽

Chemical Properties ◽

Alpha Helix ◽

Apparent Molecular Weight ◽

Correlation Spectroscopy ◽

Nmr Studies ◽

Recombinant Hirudin ◽

Physico Chemical ◽

Recombinant Molecule

SummaryPhysico-chemical properties of recombinant desulphatohirudin expressed in yeast (CIBA GEIGY code No. CGP 39393) were reinvestigated. As previously reported for natural hirudin, the recombinant molecule exhibited abnormal behaviour by gel filtration with an apparent molecular weight greater than that based on the primary structure. However, molecular weight estimation by SDS gel electrophoresis, FAB-mass spectrometry and Photon Correlation Spectroscopy were in agreement with the theoretical molecular weight, with little suggestion of dimer or aggregate formation. Circular dichroism studies of the recombinant molecule show similar spectra at different pH values but are markedly different from that reported by Konno et al. (13) for a natural hirudin-variant. Our CD studies indicate the presence of about 60% beta sheet and the absence of alpha helix in the secondary structure of recombinant hirudin, in agreement with the conformation determined by NMR studies (17)

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