David Bloxham

Somatic CALR Mutations in Myeloproliferative Neoplasms with Nonmutated JAK2

BACKGROUND Somatic mutations in the Janus kinase 2 gene (JAK2) occur in many myeloproliferative neoplasms, but the molecular pathogenesis of myeloproliferative neoplasms with nonmutated JAK2 is obscure, and the diagnosis of these neoplasms remains a challenge. METHODS We performed exome sequencing of samples obtained from 151 patients with myeloproliferative neoplasms. The mutation status of the gene encoding calreticulin (CALR) was assessed in an additional 1345 hematologic cancers, 1517 other cancers, and 550 controls. We established phylogenetic trees using hematopoietic colonies. We assessed calreticulin subcellular localization using immunofluorescence and flow cytometry. RESULTS Exome sequencing identified 1498 mutations in 151 patients, with medians of 6.5, 6.5, and 13.0 mutations per patient in samples of polycythemia vera, essential thrombocythemia, and myelofibrosis, respectively. Somatic CALR mutations were found in 70 to 84% of samples of myeloproliferative neoplasms with nonmutated JAK2, in 8% of myelodysplasia samples, in occasional samples of other myeloid cancers, and in none of the other cancers. A total of 148 CALR mutations were identified with 19 distinct variants. Mutations were located in exon 9 and generated a +1 base-pair frameshift, which would result in a mutant protein with a novel C-terminal. Mutant calreticulin was observed in the endoplasmic reticulum without increased cell-surface or Golgi accumulation. Patients with myeloproliferative neoplasms carrying CALR mutations presented with higher platelet counts and lower hemoglobin levels than patients with mutated JAK2. Mutation of CALR was detected in hematopoietic stem and progenitor cells. Clonal analyses showed CALR mutations in the earliest phylogenetic node, a finding consistent with its role as an initiating mutation in some patients. CONCLUSIONS Somatic mutations in the endoplasmic reticulum chaperone CALR were found in a majority of patients with myeloproliferative neoplasms with nonmutated JAK2. (Funded by the Kay Kendall Leukaemia Fund and others.).

High resolution melting analysis for detection of BRAF exon 15 mutations in hairy cell leukaemia and other lymphoid malignancies

The BRAF V600E mutation has recently been described in all cases of hairy cell leukaemia (HCL). We have developed and validated a rapid and sensitive high‐resolution melting analysis (HRMA) assay that detects BRAF exon 15 mutations when hairy cells are as low as 5–10% in a sample. All 48 HCL patients were positive for the BRAF V600E mutation, while 114 non‐HCL cases were all V600E negative. Interestingly, we detected a novel BRAF D594N mutation in one patient with multiple myeloma. The HRMA assay offers a useful tool to aid the laboratory diagnosis of HCL.

Rapid response of biallelic BRAF V600E mutated hairy cell leukaemia to low dose vemurafenib

All authors declare that they have participated in writing the paper and have seen and approved the final version of the paper. Caterina Canavese: Designed the research study, drafted the paper, revised and approved the final version of the paper. Piero Stratta: Contributed to the designs of the study, critically revised the paper and approved the final version. Isabella Nava: Performed the research, contributed essential reagents or tools and approved the final version. Lorena Duca: Performed the research, contributed essential reagents or tools and approved the final version. MDomenica Cappellini: Interpretated the results, crtitically revised the paper and approved the final version. Cristina Izzo: Performed the research, analysed the data and approved the final version. Marco Quaglia: Designed the research study, wrote the paper and approved the final version.

Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies

The diagnosis of hematologic malignancies relies on multidisciplinary workflows involving morphology, flow cytometry, cytogenetic, and molecular genetic analyses. Advances in cancer genomics have identified numerous recurrent mutations with clear prognostic and/or therapeutic significance to different cancers. In myeloid malignancies, there is a clinical imperative to test for such mutations in mainstream diagnosis; however, progress toward this has been slow and piecemeal. Here we describe Karyogene, an integrated targeted resequencing/analytical platform that detects nucleotide substitutions, insertions/deletions, chromosomal translocations, copy number abnormalities, and zygosity changes in a single assay. We validate the approach against 62 acute myeloid leukemia, 50 myelodysplastic syndrome, and 40 blood DNA samples from individuals without evidence of clonal blood disorders. We demonstrate robust detection of sequence changes in 49 genes, including difficult-to-detect mutations such as FLT3 internal-tandem and mixed-lineage leukemia (MLL) partial-tandem duplications, and clinically significant chromosomal rearrangements including MLL translocations to known and unknown partners, identifying the novel fusion gene MLL-DIAPH2 in the process. Additionally, we identify most significant chromosomal gains and losses, and several copy neutral loss-of-heterozygosity mutations at a genome-wide level, including previously unreported changes such as homozygosity for DNMT3A R882 mutations. Karyogene represents a dependable genomic diagnosis platform for translational research and for the clinical management of myeloid malignancies, which can be readily adapted for use in other cancers.

Discrepancy between impedance and immunofluorescence platelet counting has implications for clinical decision making in patients with idiopathic thrombocytopenia purpura.

This study investigated whether differences occur between the impedance and immunofluorescence methods for platelet quantification in idiopathic thrombocytopenia purpura (ITP). Immunofluorescence gave a platelet count >50% higher than the impedance test in 9/35 (26%) patients, of which 4/35 (11%) were >100% higher. The clinical severity of thrombocytopenia was changed as a result of the immunofluorescence test in 14/35 (40%) patients. Neither mean platelet volume nor platelet distribution width predicted impedance/immunofluorescence method discrepancy. It is suggested that immunofluorescence platelet counts should be performed on all ITP patients when the implementation of a therapeutic or diagnostic intervention is being considered.

Detection of cytoplasmic nucleophosmin expression by imaging flow cytometry

Mutations within the nucleophosmin NPM1 gene occur in approximately one‐third of cases of acute myeloid leukemia (AML). These mutations result in cytoplasmic accumulation of the mutant NPM protein. NPM1 mutations are currently detected by molecular methods. Using samples from 37 AML patients, we investigated whether imaging flow cytometry could be a viable alternative to this current technique. Bone marrow/peripheral blood cells were stained with anti‐NPM antibody and DRAQ5 nuclear stain, and data were acquired on an ImageStream imaging flow cytometer (Amnis Corp., Seattle, USA). Using the similarity feature for data analysis, we demonstrated that this technique could successfully identify cases of AML with a NPM1 mutation based on cytoplasmic NPM protein staining (at similarity threshold of 1.1 sensitivity 88% and specificity 90%). Combining data of mean fluorescence intensity and % dissimilar staining in a 0–2 scoring system further improved the sensitivity (100%). Imaging flow cytometry has the potential to be included as part of a standard flow cytometry antibody panel to identify potential NPM1 mutations as part of diagnosis and minimal residual disease monitoring. Imaging flow cytometry is an exciting technology that has many possible applications in the diagnosis of hematological malignancies, including the potential to integrate modalities.

PML protein analysis using imaging flow cytometry

Acute promyelocytic leukaemia (APML) can be promptly diagnosed by detecting abnormal diffuse staining patterns of PML bodies in abnormal promyelocytes using immunofluorescence microscopy. However, this technique is subjective, with low sensitivity. Using samples from 18 patients with acute myeloid leukaemia (AML) (including four with APML), the authors investigated whether imaging flow cytometry could be a viable alternative to this current technique and improve sensitivity levels. Bone marrow/peripheral blood cells were stained with an antibody to PML, and data were acquired on an ImageStream (Amnis Corporation, Seattle, Washington, USA). Using the modulation feature for data analysis, the authors demonstrated that this technique could successfully identify cases of APML. Imaging flow cytometry, by analysing greater numbers of cells and with the potential to include disease-specific antigens, increases the sensitivity of the current immunofluorescence technique. Imaging flow cytometry is an exciting technology that has many possible applications in the diagnosis of haematological malignancies, including the potential to integrate modalities.

BCR rearrangement in apparent essential thrombocythaemia

Summary. The presence of the Philadelphia chromosome is a major determinant of the prognosis of patients with myeloproliferative disorders. We describe a case of apparent essential thrombocythaemia in whom cytogenetic analysis was normal. However, the presence of basophilia, the absence of abnormal megakaryocytes in a trephine biopsy and the female sex of the patient prompted Southern analysis of peripheral granulocyte DNA. This revealed a BCR rearrangement and the patient has therefore undergone allogeneic bone marrow transplantation. This case emphasizes the importance of both cytogenetic and molecular analysis of patients with apparent essential thrombocythaemia.

Complex chromosomal rearrangements in an unusual variant of hairy cell leukemia.

An unusual case of variant HCL with multiple ribosomal lamellar complexes and complex chromosomal changes is described. The karyotype of the main cell clone is characterized by involvement of chromosome 5 at q13.3 and interstitial deletion of 7q. However, there is no other evidence of myelodysplasia and the abnormal cells are of lymphoid origin with a B-cell immunophenotype. The clonal chromosomal evolution involves rearrangements at sites known to be specifically altered in lymphoid tumors.

Automated immunostaining of cell smears: an alternative to flow cytometry

Aims: To assess the applicability of an automated tissue immunostainer machine for the phenotypic analysis of peripheral blood and bone marrow aspirate smears. Methods: Air-dried smears of peripheral blood and bone marrow from normal individuals and 14 patients with haematological malignancies were stained, following fixation, with a range of antibodies to haemopoietic antigens using both immunoperoxidase and immuno-alkaline phosphatase methods on the Bond-maX (Leica Microsystems) automated immunostaining machine. Results: Automated protocols used for staining formalin-fixed paraffin-embedded tissue could be applied to cell smears, giving high quality staining with excellent cytological detail and antigenic preservation for an extensive antibody panel. Optimal quality (morphological preservation and antigen detection without background staining) was obtained with an alkaline phosphatase method and Fast Red chromogenic substrate. Both cell surface and intracellular (cytoplasmic and nuclear) antigens could be detected and gave the expected reactivity. Conclusions: Automated immunostaining is possible for haematological smears. It generates consistent high quality staining, with the exception of surface immunoglobulin, and is applicable to haematological and, potentially, cytological smears. It provides a practical alternative to flow cytometry and will have particular application when smears are available and there is no suitable sample for flow cytometry.