MPL W515L/K Mutations in Chronic Myeloproliferative Neoplasms

Assessment of intestinal status in MPLW515L mutant myeloproliferative neoplasms mice model

The MPLW515L mutation is a prevalent genetic mutation in patients with myeloproliferative neoplasms (MPN), and utilizing this mutation in mice model can provide important insights into the disease. However, the relationship between intestinal homeostasis and MPN mice model remains elusive. In this study, we utilized a retroviral vector to transfect hematopoietic stem cells with the MPLW515L mutation, creating mutated MPN mice model to investigate their intestinal status. Our results revealed that the MPLW515L in MPN mice model aggravated inflammation in the intestines, decreased the levels of tight junction proteins and receptors for bacteria metabolites. Additionally, there was increased activation of the caspase1/IL-1β signaling pathway and a significant reduction in phos-p38 levels in the intestinal tissue in MPN mice. The MPLW515L mutation also led to up-expression of anti-microbial genes in the intestinal tract. Though the mutation had no impact on the alpha diversity and dominant bacterial taxa, it did influence the rare bacterial taxa/sub-communities and consequently impacted intestinal homeostasis. Our findings demonstrate the significance of MPLW515L mice model for studying MPN disease and highlight the mutation's influence on intestinal homeostasis, including inflammation, activation of the IL-1β signaling pathway, and the composition of gut microbial communities.

Molecular Genetics of Thrombotic Myeloproliferative Neoplasms: Implications in Precision Oncology

Classical BCR-ABL-negative myeloproliferative neoplasms (MPN) include polycythaemia vera, essential thrombocythaemia, and primary myelofibrosis. Unlike monogenic disorders, a more complicated series of genetic mutations are believed to be responsible for MPN with various degrees of thromboembolic and bleeding complications. Thrombosis is one of the early manifestations in patients with MPN. To date, the driver genes responsible for MPN include JAK2, CALR, MPL, TET2, ASXL1, and MTHFR. Affords have been done to elucidate these mutations and the incidence of thromboembolic events. Several lines of evidence indicate that mutations in JAK2, MPL, TET2 and ASXL1 gene and polymorphisms in several clotting factors (GPIa, GPIIa, and GPIIIa) are associated with the occurrence and prevalence of thrombosis in MPN patients. Some polymorphisms within XRCC1, FBG, F2, F5, F7, F12, MMP9, HPA5, MTHFR, SDF-1, FAS, FASL, TERT, ACE, and TLR4 genes may also play a role in MPN manifestation. This review aims to provide an insightful overview on the genetic perspective of thrombotic complications in patients with MPN.

Extramedullary Hematopoiesis of the Liver and Spleen

Hematopoiesis is the formation of blood cellular components and, consequently, immune cells. In a more complete definition, this process refers to the formation, growth, maturation, and specialization of blood cells, from the hematopoietic stem cell, through the hematopoietic progenitor cells, to the s pecialized blood cells. This process is tightly regulated by several elements of the bone marrow microenvironment, such as growth factors, transcription factors, and cytokines. During embryonic and fetal development, hematopoiesis takes place in different organs: the yolk sac, the aorta–gonad mesonephros region, the lymph nodes, and not lastly, the fetal liver and the spleen. In the current review, we describe extramedullary hematopoiesis of the spleen and liver, with an emphasis on myeloproliferative conditions.

Clinical and Laboratory Features of JAK2 V617F, CALR, and MPL Mutations in Malaysian Patients with Classical Myeloproliferative Neoplasm (MPN)

Mutations of JAK2V617F, CALR, and MPL genes confirm the diagnosis of myeloproliferative neoplasm (MPN). This study aims to determine the genetic profile of JAK2V617F, CALR exon 9 Type 1 (52 bp deletion) and Type 2 (5 bp insertion), and MPL W515 L/K genes among Malaysian patients and correlate these mutations with clinical and hematologic parameters in MPN. Mutations of JAK2V617F, CALR, and MPL were analyzed in 159 Malaysian patients using allele-specific polymerase chain reaction, including 76 polycythemia vera (PV), 41 essential thrombocythemia (ET), and 42 primary myelofibrosis (PMF) mutations, and the demographics of the patients were retrieved. The result showed that 73.6% JAK2V617F, 5.66% CALR, and 27.7% were triple-negative mutations. No MPL W515L/K mutation was detected. In ET and PMF, the predominance type was the CALR Type 1 mutation. In JAK2V617F mutant patients, serum LDH was significantly higher in PMF compared to PV and ET. PV has a higher risk of evolving to post PV myelofibrosis compared to ET. A thrombotic event at initial diagnosis of 40.9% was high compared to global incidence. Only one PMF patient had a CALR mutation that transformed to acute myeloid leukemia. JAK2V617F and CALR mutations play an important role in diagnostics. Hence, every patient suspected of having a myeloproliferative neoplasm should be screened for these mutations.

Sequence Neighborhoods Enable Reliable Prediction of Pathogenic Mutations in Cancer Genomes

Simple Summary

Cancer is caused by the accumulation of somatic mutations, some of which are responsible for the disease’s progression (drivers) while others are functionally neutral (passengers). Although several methods have been developed to distinguish between the two classes of mutations, very few have concentrated on using the neighborhood nucleotide sequences as potential discrimination features. In this study, we show that driver mutations’ neighborhood is significantly different from that of passengers. We further develop a novel machine learning tool, NBDriver, which is highly efficient at identifying pathogenic variants from multiple independent test datasets. Efficient and accurate identification of novel pathogenic variants from sequenced cancer genomes would help facilitate more effective therapies tailored to patients’ mutational profiles.

Abstract

Identifying cancer-causing mutations from sequenced cancer genomes hold much promise for targeted therapy and precision medicine. “Driver” mutations are primarily responsible for cancer progression, while “passengers” are functionally neutral. Although several computational approaches have been developed for distinguishing between driver and passenger mutations, very few have concentrated on using the raw nucleotide sequences surrounding a particular mutation as potential features for building predictive models. Using experimentally validated cancer mutation data in this study, we explored various string-based feature representation techniques to incorporate information on the neighborhood bases immediately 5′ and 3′ from each mutated position. Density estimation methods showed significant distributional differences between the neighborhood bases surrounding driver and passenger mutations. Binary classification models derived using repeated cross-validation experiments provided comparable performances across all window sizes. Integrating sequence features derived from raw nucleotide sequences with other genomic, structural, and evolutionary features resulted in the development of a pan-cancer mutation effect prediction tool, NBDriver, which was highly efficient in identifying pathogenic variants from five independent validation datasets. An ensemble predictor obtained by combining the predictions from NBDriver with three other commonly used driver prediction tools (FATHMM (cancer), CONDEL, and MutationTaster) significantly outperformed existing pan-cancer models in prioritizing a literature-curated list of driver and passenger mutations. Using the list of true positive mutation predictions derived from NBDriver, we identified a list of 138 known driver genes with functional evidence from various sources. Overall, our study underscores the efficacy of using raw nucleotide sequences as features to distinguish between driver and passenger mutations from sequenced cancer genomes.

Retrospective analysis of the clinical features of 172 patients with BCR-ABL1-negative chronic myeloproliferative neoplasms

Background

To explore the clinical features of the patients with BCR-ABL1-negative chronic myeloproliferative neoplasms (MPNs) in our hospital and to reveal the unique features of BCR-ABL1-negative MPNs patients in our center.

Methods

Retrospective analysis of routine karyotype analysis results, driver gene mutations and other related clinical parameters of 172 patients with newly diagnosed BCR-ABL1-negative MPNs who were admitted to our hospital between October 2013 and June 2018.

Results

(1) The rate of karyotypic abnormalities were 25, 6.3 and 2.9% in primary myelofibrosis (PMF), polycythemia vera (PV) and essential thrombocythemia (ET) patients, respectively. (2) The mutation rate of JAK2-V617F was 62.5%, and that of the CALR, MPL and EZH2 genes was 4.2% in PMF. The mutation rates of JAK2-V617F and JAK2-12exon were 91.3 and 1.3% in PV, respectively. The mutation rates of JAK2-V617F and CALR were 69.1 and 11.8% in ET, respectively. (3) Patients with JAK2-V617F mutation than with the wild-type gene were more often female in PMF (P = 0.027); had higher peripheral blood white blood cell (WBC) counts (P = 0.006), platelet (PLT) count (P = 0.001) and splenomegaly (P < 0.05) in PV; and had higher WBC (P = 0.001), hemoglobin concentrations (P = 0.001), lower PLT (P = 0.037), splenomegaly and endogenous coagulopathy (P < 0.05) in ET. (4) Among the PV and ET patients, those with thrombus were older than those in the nonthrombotic group.

Conclusion

PMF patients have more chromosomal abnormalities than PV and ET patients, and the effect of driver mutations on the clinical features of patients with MPNs differs among the three subtypes.

MPL W515 L/K mutations in myeloproliferative neoplasms

Background

Myeloproliferative neoplasms (MPNs) describe a group of diseases involving the bone marrow (BM). Classical MPNs are classified into chronic myelogenous leukemia (CML), polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). This classification is based on the presence of Philadelphia (Ph) chromosome (BCR/ABL1). CML is BCR/ABL1-positive while PV, ET, and PMF are negative. JAK2 p. Val617Phe pathological variant is the most associated mutation in BCR/ABL1-negative MPNs. The frequency of JAK2 p. Val617Phe is 90–95% in PV patients, 50–60% in ET, and 40–50% in patients with PMF. Studies on MPL gene led to the revelation of a gain of function pathological variants in JAK2 p. Val617Phe-negative myeloproliferative neoplasms (MPNs). MPL p. W515 L/K pathological variants are the most common across all mutations in MPL gene. The prevalence of these pathological variants over the Egyptian population is not clear enough. In the present study, we aimed to investigate the prevalence of MPL p. W515 L/K pathological variants in the Philadelphia (Ph)-negative MPNs over the Egyptian population.

Results

We have tested 60 patients with Ph-negative MPNs for MPL p. W515 L/K pathological variants. Median age was 51 (22–73) years. No MPL p. W515 L/K pathological variants were detected among our patients. JAK2 p. Val617Phe in PV and PMF patients showed significantly lower frequency than other studies. Splenomegaly was significantly higher in ET patients compared to other studies.

Conclusion

MPL p. W515 L/K pathological variants are rare across the Egyptian Ph-negative MPNs, and further studies on a large number are recommended. MPN patients in Egypt are younger compared to different ethnic groups.

Somatic Mutations in Philadelphia Chromosome-Negative Myeloproliferative Neoplasms

Myeloproliferative neoplasms (MPN) include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). MPN are characterized by clonal proliferation of myeloid progenitors leading to erythrocytosis, thrombocytosis, or leukocytosis, and risk of hemorrhagic and thrombotic events, as well as myelofibrosis and blast transformation. The discovery of somatic mutations in MPN, namely JAK2 V617F, JAK2 exon 12, MPL, and CALR mutations, has permitted a more specific approach to diagnosis and treatment. The prevalence of JAK2 V617F mutations is higher than 95% in PV, 50%-75% in ET and 40%-75% in PMF. JAK2 exon 12 mutations are specific of PV. A 20%-30% of patients with ET and PMF present a CALR mutation. The screening of mutations strengthens the diagnosis of MPN since 97% of MPN have at least 1 somatic mutation. Interestingly, different mutations grant different phenotype and prognosis. Of particular importance, CALR mutations grant a favorable prognosis in ET and PMF, while ASXL1 mutations confer a poorer outcome. In fact, the use of CALR/ASXL1 status for the prognostication of patients has increased clinical value and is now suggested for guidance of therapy in PMF. The increasing importance of mutations in the management of MPN warrants a more frequent revision of current diagnostic criteria and prognostic models and a better understanding of the mechanisms leading to MPN subset differentiation.

Prevalence of MPL (W515K/L) Mutations in Patients with Negative-JAK2 (V617F) Myeloproliferative Neoplasm in North-East of Iran

BACKGROUND AND OBJECTIVE

Janus kinase 2 (JAK2) and Myeloproliferative Leukemia (MPL) mutations are confirmatory indicators for Myeloproliferative Neoplasm (MPN). The current study was performed to determine the frequency of MPL mutation in MPN patients without JAK2 mutation, in order to assign MPL mutation frequency in North-East of Iran.

METHODS

Total of 105 negative JAK2 cases including 5 Myeloproliferative Disorders (MPD), 15 Polycytemia Vera (PV) and 15 Essential Thrombocytosis (ET) who referred to Qaem Medical Center were assigned to this study. ARMS-PCR was carried out for measuring MPL mutations.

RESULTS

A significant difference was observed between MPL mutant and non-mutant groups from overview of MPL mutation (P=0.00001). From the total studied population, 14.28% were ET cases and 4.71% of them had splenomegaly. About 66.66% had thrombocytosis and 33.33% of all the individuals had leukocytosis according to WHO criteria, and 4.76% of non-MPL mutant individuals had splenomegaly (P=1).This mutation was reported in 4-6% of ET and PMF individuals. In this research, 4.76 % of studied individuals had MPL (W515L/K) mutation, which were diagnosed with ET.

CONCLUSION

Generally, the presence of JAK2 and MPL mutations are the most important criteria for MPN diagnosis. The obtained frequency of MPL mutation was similar to previous studies. Despite the high frequency of JAK2 and Philadelphia abnormality, MPL mutation was rare in myeloprolifrative disorders. Further studies are suggested to investigate its prognostic effects for these diseases.

Myeloproliferative neoplasms: Current molecular biology and genetics

Myeloproliferative neoplasms (MPNs) are clonal disorders characterized by increased production of mature blood cells. Philadelphia chromosome-negative MPNs (Ph-MPNs) consist of polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). A number of stem cell derived mutations have been identified in the past 10 years. These findings showed that JAK2V617F, as a diagnostic marker involving JAK2 exon 14 with a high frequency, is the best molecular characterization of Ph-MPNs. Somatic mutations in an endoplasmic reticulum chaperone, named calreticulin (CALR), is the second most common mutation in patients with ET and PMF after JAK2 V617F mutation. Discovery of CALR mutations led to the increased molecular diagnostic of ET and PMF up to 90%. It has been shown that JAK2V617F is not the unique event in disease pathogenesis. Some other genes' location such as TET oncogene family member 2 (TET2), additional sex combs-like 1 (ASXL1), casitas B-lineage lymphoma proto-oncogene (CBL), isocitrate dehydrogenase 1/2 (IDH1/IDH2), IKAROS family zinc finger 1 (IKZF1), DNA methyltransferase 3A (DNMT3A), suppressor of cytokine signaling (SOCS), enhancer of zeste homolog 2 (EZH2), tumor protein p53 (TP53), runt-related transcription factor 1 (RUNX1) and high mobility group AT-hook 2 (HMGA2) have also identified to be involved in MPNs phenotypes. Here, current molecular biology and genetic mechanisms involved in MNPs with a focus on the aforementioned factors is presented.

Essential thrombocythemia with Mpl W515 K mutation in a child presenting with Budd-Chiari syndrome

Essential thrombocythemia (ET) is an extremely rare childhood disorder characterised by clonal expansion of megakaryocytic lineage in bone marrow, leading to a persistent increase in the number of circulating thrombocytes and thus increased risk for thrombotic and haemorrhagic events. The molecular mechanisms of ET are not fully understood. Most children with ET have the JAK2 V617F somatic mutation; however, another mutation, involving a W to L or K substitution at Mpl codon 515, was reported in a small proportion of adult ET patients that is extremely rare in children. Herein, we describe a Mpl W515K somatic mutation in a paediatric case of ET who presented with Budd-Chiari syndrome. No paediatric patient harbouring a Mpl W515K mutation has been previously reported.

The mutation profile of JAK2, MPL and CALR in Mexican patients with Philadelphia chromosome-negative myeloproliferative neoplasms

CONTEXT AND OBJECTIVE

By using molecular markers, it is possible to gain information on both the classification and etiopathogenesis of chronic myeloproliferative neoplasias (MPN).

METHODS

In a group of 27 Mexican mestizo patients with MPNs, we studied seven molecular markers: the BCR/ABL1 fusion gene, the JAK2 V617F mutation, the JAK2 exon 12 mutations, the MPL W515L mutation, the MPL W515K mutation, and the calreticulin (CALR) exon 9 deletion or insertion. Patients with the BCR/ABL1 fusion gene were excluded. We studied 14 patients with essential thrombocythemia (ET), eight with polycythemia vera (PV), four with primary myelofibrosis (MF), and one with undifferentiated MPN.

RESULTS

We found twelve individuals with the JAK2 V617F mutation; five of them had been clinically classified as PV, five as ET, and one as MF. One patient with the MPL W515L was identified with a clinical picture of ET. Five patients with the CALR mutation were identified, four ET and one MF. No individuals with either the MPL W515K mutation or the JAK2 exon 12 mutations were identified. The most consistent relationship was that between PV and the JAK2 V617F mutation (p=.01).

CONCLUSIONS

Despite its small size, the study shows much less prevalence of JAK2 mutation in PV, ET and MF, which does not match international data.

Low frequency of c-MPL gene mutations in Iranian patients with Philadelphia-negative myeloproliferative disorders

BACKGROUND

Myeloproliferative disorders are a group of diseases characterized by increased proliferation of myeloid lineage. In addition to JAK2V617F mutation, several mutations in the c-MPL gene have been reported in patients with philadelphia-negative chronic myeloproliferative disorders that could be important in the pathogenesis of diseases. The aim of the present study was to investigate the frequency of c-MPL and JAK2V617F mutations in Iranian patients with Philadelphia-negativemyeloproliferative disorders.

MATERIAL AND METHODS

Peripheral blood samples were collected from 60 patients with Philadelphia-negative MPD) Subgroups ET and PMF) and 25 healthy subjects as control group. The mutation status of c-MPL and Jak2V617F were investigated by using Amplification-refractory mutation system (ARMS) and Allele-Specific PCR (AS-PCR), respectively. The results were confirmed by sequencing.

RESULTS

Among 60 patients, 34 (56.6%) and 1(1.7%) had Jak2V617F and c-MPL mutation, respectively. Patients with Jak2V617F mutation had higher WBC counts and hemoglobin concentration than those without the mutation (p= 0.005, p=0.003). In addition, for all healthy subjects in control group, mutations were negative.

CONCLUSIONS

The present study revealed that the c-MPL mutations unlike the Jak2V617F mutations are rare in Iranian patients with Ph-negative MPNs and the low mutation rate should be considered in the design of screening strategies of MPD patients.