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Thrombotic events are very frequent and represent the main cause of morbidity and mortality in patients with Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs), mainly polycythemia vera and essential thrombocythemia. Pathogenesis of blood clotting activation in these diseases is multifactorial, and it involves various abnormalities of platelets, erythrocytes, and leukocytes, as well as dysfunctions of endothelial cells. These include not only elevations in the counts of circulating blood cells, arising from the clonal proliferation of hematopoietic progenitor cells, but also modifications of several physiological/molecular properties. Patients with MPN can be stratified in “high-risk” or “low-risk” thrombotic categories according to the age and history of thrombosis. The most commonly used front-line drugs for the treatment of high-risk patients include hydroxyurea and interferon alpha, whereas in low-risk patients, primary antithrombotic prophylaxis with aspirin is used. Future research should be focused on the evaluation of the role of biomarkers in identifying MPN patients at higher risk of thrombosis, who may benefit from primary thromboprophylaxis. Finally, a better understanding of the molecular events leading to the progress of the hypercoagulable state in MPN patients may provide appropriate tools for the development of targeted therapies based on reversal of coagulopathy.