Category Archives: Research

Ambitious £4 million project to develop clinical platform for blood cancer prevention

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4th Feb 2024 – Edward Pinches

Professor George Vassiliou from the Wellcome-MRC Cambridge Stem Cell Institute (CSCI), University of Cambridge will spearhead the project, which focuses on myeloid blood cancers, a group of blood cancers that accounts for more than 11,000 deaths each year in the UK.

The blood cancers, which affect both the bone marrow and blood, include acute myeloid leukaemia (AML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN) and rarer cancers like chronic myelomonocytic leukaemia (CMML).

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Truong on the Rationale for Investigating ERK2 Substrate Binding Modalities in MPNs

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Billy Truong, PhD candidate, Fox Chase Cancer Center, discusses the rationale for investigating the functions of ERK2 substrate binding modalities in myeloproliferative neoplasms (MPNs).

Truong and colleagues are conducting research investigating cell signaling programs that are altered in MPNs. Specifically, treatment resistance often arises from the activation of the MAPK pathway, Truong says. Approximately 85% of cancers have genetic modifications in proteins, especially in the RAS protein, which ultimately drive uncontrolled tumor cell proliferation, Truong explains.

Downstream of the MAPK pathway is the ERK2 protein, which is a common target of cancer therapies, Truong notes. However, drugs that target the kinase function of ERK2 are traditionally designed to be nonspecific and are therefore toxic to healthy cells expressing ERK2, Truong emphasizes. Accordingly, drug specificity remains an unmet need for patients with MPNs.

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Hobbs Highlights Key Research in Hematologic Malignancies at the 2023 ASH Annual Meeting

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Courtney Flaherty

Ruxolitinib (Jakafi)-based combinations continue to demonstrate promising ability to address splenomegaly and a signal toward improvement of tumor-related symptoms in myelofibrosis. As novel targets for development are unearthed and considered for evaluation in combination with standard JAK inhibition, the assessment of other meaningful end points is necessary to confirm the true benefit of such agents alone or in combination across myeloproliferative neoplasms (MPNs), according to Gabriela Hobbs, MD.

Results from the phase 3 TRANSFORM-1 study (NCT04472598)were presented at the 2023 ASH Annual Meeting and demonstrated that up-front navitoclax and ruxolitinib (Jakafi) significantly reduced spleen volume by 35% or more at week 24 vs ruxolitinib plus placebo in patients with myelofibrosis.1 Despite this, no significant difference in total symptom score (TSS) was observed between the arms.

Additionally, data from the phase 3 MANIFEST-2 trial (NCT04603495) showed that pelabresib (CPI-0610) plus ruxolitinib reduced spleen volume by 35% or more in 65.9% of patients with JAK inhibitor–naive myelofibrosis vs 35.2% in those who received placebo/ruxolitinib (95% CI, 21.6-39.3; P < .001). The agent also trended toward improving TSS reduction by 50% (TSS50) at 24 weeks.2

“One of the things we must answer as a field is: What is the benefit of using combination therapy for this disease?” Hobbs, who is clinical director of the Leukemia Service at Massachusetts General Cancer Center, and an assistant in medicine at Massachusetts General Hospital in Boston, Massachusetts, stressed in an interview with OncLive®News Network: On Location during the 2023 ASH Annual Meeting. “We need to have end points that are meaningful, [as well as] therapies that are well tolerated and affordable for patients.”

In the interview, Hobbs discussed the significance of key data from the TRANSFORM-1 and MANIFEST-2 trials for patients with myelofibrosis, expanded on the ongoing or future development of novel targets and potential combination regimens across MPNs, and spotlighted the phase 1/2 SAVE study (NCT05360160) and other key research efforts being made in leukemia.

OncLive: What key data on novel ruxolitinib-based combination regimens were reported at the 2023 ASH Annual Meeting?

Hobbs: I primarily treat MPN, and this is probably the first ASH Meeting where 2 different phase 3 studies [in this space] were presented at the same time. The navitoclax data are impressive, specifically when it comes to the improvement that we see with the combination of navitoclax and ruxolitinib for improving spleen volume response [SVR]. That can be very meaningful for patients—especially those with myelofibrosis who have very large spleens. We saw a very similar SVR with the combination of pelabresib and ruxolitinib as up-front therapy in patients who had not received a JAK inhibitor before.

How do you distinguish between these 2 agents in clinical practice?

In addition to showing an impressive improvement in SVR, neither study showed a dramatic improvement in symptoms [with the combinations] compared with ruxolitinib alone. That’s something that we need to consider. Pelabresib probably did a better job at improving symptoms than navitoclax. However, we need to start thinking about whether there are more meaningful end points other than expecting agents to improve SVR and symptoms. For example, could they potentially delay progression to leukemia, improve overall survival, or improve treatment outcomes in general or after transplant? Those are difficult end points to demonstrate, so they weren’t the primary objectives of the studies.

What other emerging agents of interest were discussed during the meeting?

There were lots of interesting novel agents presented at the meeting. There is a single-agent study [examining] a selective PIM kinase inhibitor and [we saw] some updated results in approximately 30 patients who have received the agent. [The agent appears to be] incredibly well tolerated, with very little impact on blood counts in a group of heavily pretreated patients. We’re also seeing a variety of other agents that are being developed. We’re seeing results from [the phase 2 VALENTINE-PTCL01 (NCT04703192)] study with the LSD1 inhibitor valemetostat tosylate [DS-3201b], an agent that also helps to prevent the development of fibrosis.

Are any of these agents viable options for further investigation as part of combination regimens?

That is the question to answer in [the] MPN [field]. Many studies have focused on combining a novel agent with a JAK inhibitor, primarily with ruxolitinib since it’s the one that has been around for the longest. I wouldn’t be surprised if the future of myelofibrosis [will be] to utilize combinations. [However,] we must remember that there’s a difference between treating patients in clinical trials vs treating patients in real life.

At this year’s meeting, findings from the phase 1/2 SAVE study of revumenib (SNDX-5613) plus decitabine/cedazuridine, (ASTX727) and venetoclax (Venclexta) were also presented. How did the results live up to expectations surrounding the use of menin inhibitors, and what are the next steps for the regimen?

That was an exciting study [done in] a group of patients with heavily pretreated AML. Some of these patients had undergone allogeneic stem cell transplantation and had received several lines of [prior] therapy. Patients who have refractory AML must go to clinic very frequently. Being able to offer them a regimen that’s all oral is very meaningful because [they do not] have to come to clinic as frequently to receive an IV hypomethylating agent. Most patients had at least some response [to the combination], and many had impressive responses. [Notably,] many patients had been previously treated with venetoclax. Menin inhibitors have been practice-changing in AML, and we’ve seen some responses [with this approach] in patients who have previously not responded to anything else. I look forward to seeing [more about] this combination, and hopefully [we can] bring it into earlier lines of therapy.

What were the biggest updates in chronic myeloid leukemia (CML) according to data presented at the meeting?

CML is very interesting. We all think that CML is a disease that we’ve conquered. We [see] great outcomes and almost normal life expectancy in most patients who are responding to therapy. [However], there is still a lot of development in the field. Several studies are investigating asciminib [Scemblix] in several different ways. The first study that we see is the [phase 3] ASCEMBL study [NCT03106779] comparing asciminib with bosutinib [Bosulif]. Updated [data presented at this year’s meeting] showed that asciminib is still outperforming bosutinib in terms of molecular remissions. [Investigators are] also studying asciminib in different, more creative ways in CML. They’re combining asciminib with other TKIs either in the up-front setting or in a later-line setting because of its slightly different mechanism of action. We’re also seeing the development of other TKIs that are either similar to asciminib or similar to ponatinib [Iclusig] in their mechanisms of action. There is still a lot of drug development in a disease where we thankfully have [achieved] a lot of great outcomes.

[It will be interesting to see how this next generation of agents impact current practice,] especially if they improve tolerability. For a disease where [a patient has] to be on life-long therapy, it’s important to have agents that are well tolerated.

Editor’s note: This interview was conducted prior to the conclusion of the 2023 ASCO Annual Meeting.

References

  1. Pemmaraju N, Mead AJ, Somervaille T, et al. Transform-1: a randomized, double-blind, placebo-controlled, multicenter, international phase 3 study of navitoclax in combination with ruxolitinib versus ruxolitinib plus placebo in patients with untreated myelofibrosis. Blood. 2023;142(suppl 1):620. doi:10.1182/blood-2023-173509
  2. Rampal R, Grosicki S, Chraniuk D, et al. Pelabresib in combination with ruxolitinib for Janus Kinase Inhibitor treatment-naïve patients with myelofibrosis: results of the MANIFEST-2 randomized, double-blind, phase 3 study. Blood. 2023;142(suppl 1):628. doi:10.1182/blood-2023-179141

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Exploring the Molecular Aspects of Myeloproliferative Neoplasms Associated with Unusual Site Vein Thrombosis: Review of the Literature and Latest Insights

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by Erika Morsia1,2,*, Elena Torre1, Francesco Martini 2,3, Sonia Morè 1,2, Antonella Poloni 1,2, Attilio Olivieri 1,2 and Serena Rupoli 1

Abstract

Myeloproliferative neoplasms (MPNs) are the leading causes of unusual site thrombosis, affecting nearly 40% of individuals with conditions like Budd–Chiari syndrome or portal vein thrombosis. Diagnosing MPNs in these cases is challenging because common indicators, such as spleen enlargement and elevated blood cell counts, can be obscured by portal hypertension or bleeding issues. Recent advancements in diagnostic tools have enhanced the accuracy of MPN diagnosis and classification. While bone marrow biopsies remain significant diagnostic criteria, molecular markers now play a pivotal role in both diagnosis and prognosis assessment. Hence, it is essential to initiate the diagnostic process for splanchnic vein thrombosis with a JAK2 V617F mutation screening, but a comprehensive approach is necessary. A multidisciplinary strategy is vital to accurately determine the specific subtype of MPNs, recommend additional tests, and propose the most effective treatment plan. Establishing specialized care pathways for patients with splanchnic vein thrombosis and underlying MPNs is crucial to tailor management approaches that reduce the risk of hematological outcomes and hepatic complications.

Red Blood Cell Contribution to Thrombosis in Polycythemia Vera and Essential Thrombocythemia

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Julien Grenier, Wassim El Nemer, and Maria De Grandis

Abstract

Polycythemia vera (PV) and essential thrombocythemia (ET) are myeloproliferative neoplasms (MPN) characterized by clonal erythrocytosis and thrombocytosis, respectively. The main goal of therapy in PV and ET is to prevent thrombohemorrhagic complications. Despite a debated notion that red blood cells (RBCs) play a passive and minor role in thrombosis, there has been increasing evidence over the past decades that RBCs may play a biological and clinical role in PV and ET pathophysiology. This review summarizes the main mechanisms that suggest the involvement of PV and ET RBCs in thrombosis, including quantitative and qualitative RBC abnormalities reported in these pathologies. Among these abnormalities, we discuss increased RBC counts and hematocrit, that modulate blood rheology by increasing viscosity, as well as qualitative changes, such as deformability, aggregation, expression of adhesion proteins and phosphatidylserine and release of extracellular microvesicles. While the direct relationship between a high red cell count and thrombosis is well-known, the intrinsic defects of RBCs from PV and ET patients are new contributors that need to be investigated in depth in order to elucidate their role and pave the way for new therapeutical strategies.

Prediction models for essential thrombocythemia from two longitudinal studies involving 2000 patients

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January 23, 2024

Tiziano Barbui and Alessandra Carobbio

Over the past two decades, significant progress has been made in several areas of Philadelphia chromosome-negative myeloproliferative neoplasms (Ph-neg MPNs), namely polycythemia vera (PV), essential thrombocythemia (ET), and myelofibrosis (MF). The driver mutations in the JAK2-V617, MPL, calreticulin opened new diagnostic and prognostic possibilities and provided new targets for therapy [1].

ET is currently diagnosed according to the World Health Organization (WHO) [2] and International Consensus Criteria (ICC) [3] criteria, involving a comprehensive evaluation of clinical, laboratory and molecular features, and is defined by clonal thrombocytosis with characteristic bone marrow megakaryocyte morphology, which allows a differentiation from PV and prefibrotic myelofibrosis (pre-PMF); the latter is a distinct entity with a clinical picture often characterized by isolated thrombocytosis mimicking ET. In a multicenter series of 1104 patients previously classified as having ET, the diagnosis was re-evaluated following strict application of the 2008 WHO classification, which includes well-defined histopathological criteria. The diagnosis of ET was confirmed in 891 patients (81%) and revised to pre-PMF in 180 (16%) [4]. A subset of ET patients has a triple-negative (TN) genotype due to the absence of detectable mutations in driver genes and is observed in ~10% of ET cases [1].

Current information on risk factors of the major critical events (thrombosis, evolution to MF, blast phase (BP), and survival) derives from registry and multicenter observational studies while single-center reports conducted at tertiary referral institutions are very limited [5]. Each study design has its strengths and limitations. Observational multicenter studies and registries can capture a large number of cases but may face challenges related to data quality and consistency. Ensuring the accuracy and uniformity of data across multiple centers becomes a critical consideration.

Studies conducted in tertiary centers, exemplified by those presented in this Blood Cancer Journal issue from Florence [6] and Mayo Clinic [7] hospitals, are more robust in nature as they can provide a solid description of natural history of this myeloproliferative neoplasm. These are conducted by specialized teams comprising clinician hematologists, pathologists, geneticists, and other experts with proficiency in MPNs and are equipped with up-to-date technologies including molecular analyses, which are essential in the case of ET where genetic mutations play a significant role in diagnosis and prognosis. Nevertheless, despite providing comprehensive insights into a well-defined cohort of patients, these centers may have a patient referral bias and limited generalizability to the broader population. This may suggest that description of disease presentation and results on prognostic factors may not be universally reproducible, and caution should be exercised when extrapolating the results to consecutive patient groups.

The Mayo and Florence reports each included 1000 ET patients; all 2000 cases met ICC 2022 and WHO diagnostic criteria and were fully annotated for driver mutations; diagnosis required hematopathology review to minimize unintended inclusion of patients with masked PV or pre-PMF. This revision is critical for patients diagnosed with ET prior to the WHO recognition of masked PV and pre-PMF, as the incidence of complications such as thrombosis, myelofibrosis, blast phase, and overall survival differs between these entities compared to “true ET”. All patients in the two studies were annotated for driver mutations, which were found in approximately 90% of cases, with similar proportions in the two series for JAK2 V617F, CALR including CALR type 1/1-like and CALR type 2/2-like, MPL and TN. Interestingly, female sex clustered preferentially with TN and JAK2 vs. CALR/MPL mutations (p < 0.01), and extreme thrombocytosis clustered with CALR (type 2 more than type 1), TN, and MPL, whereas leukocytosis clustered with JAK2 mutation (p < 0.001). It is noteworthy that the two patients’ series from Mayo and Florence showed remarkably similar presentations over the extensive recruitment period of more than 40 years.

In these retrospective cohorts, 20% of patients had a history of vascular complications at diagnosis and a similar percentage of driver mutations clustered in a similar manner. Importantly, these findings are consistent with data observed in other real-world routine clinical practice of recent reviews on ET [8, 9]. This convergence of information on disease presentation between Mayo and Florence highlights that the characteristics of these two retrospective cohorts are unlikely to have been influenced by potential reference bias. Thus, the consistency of these patterns across different settings adds value to the findings of these two studies, reinforcing the reliability of the observed trends and minimizing the impact of referral bias.

Therefore, the Mayo and Florence longitudinal studies offer the unique advantage of capturing the dynamic evolution of ET disease in real-world clinical practice over an extended period of median 8.5 years (range, 0.01–52.7) and 8 years (range, 0.03–42.9), respectively, providing robust estimates of disease-specific outcomes, i.e., arterial and venous thrombosis, progression to overt MF, BP, and survival. This makes the results on risk factors for each of these critical events highly reliable and generalizable. In this context, the confirmation of the prognostic role of increased neutrophil granulocytes and decreased lymphocytes as independent risk factors for survival in 1164 ET patients should be highlighted. This new knowledge opens new avenues for future clinical trials on the role of inflammation in MPN and the associated new targets for therapy [10, 11]. In addition, the large number of cases annotated for driver mutations allowed the identification of risk scores for progression to myelofibrosis and blast phase and confirmed the predictive power of the International Prognostic Score of Thrombosis (IPSET-thrombosis) score. We agree with the authors that these results, obtained in a large series of patients with ET, mutually validated, can constitute a reference standard against which other series of cases fully annotated for driver mutations and followed up for a long time can be compared.

Inspired by the extensive ET series of these two Blood Cancer Journal papers, we reviewed our data on 891 WHO-diagnosed ET patients enrolled from multi-center institutions, in whom we investigated the effect of post-diagnosis intermediate events (thrombosis, MF, and BP) on mortality using multistate models [12]. Using these models, which increase the precision of estimation by correcting for competing risk factors, we found that patients with incident thrombosis had a progressively increased risk of death compared with patients without this event. As expected, the highest risk of death was associated with the occurrence of MF and BP (Fig. 1). Notably, in the time-dependent multivariate analysis, arterial but not venous thrombosis occurrence during follow-up was independently associated with death, together with evolution into MF and BP (Table 1). Therefore, in future analysis of longitudinal studies, we suggest that the conventional baseline prognostic evaluation in MPN should be revised by considering the intermediate events that might integrate the risk of the final outcome of interest in the single patient.

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A Rare Coexistence of Smoldering Multiple Myeloma and JAK2-Positive Myeloproliferative Neoplasm: A Case of Dual Synchronous Hematological Malignancy

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January 20, 2024

Abstract

This article explores the rare case of an 82-year-old man diagnosed concurrently with essential thrombocythemia and smoldering multiple myeloma (SMM). The limited existing literature on individuals harboring both myeloproliferative neoplasm (MPN) and monoclonal gammopathy (MG) is of significant interest due to the distinct origins of these malignancies. The etiology of MG in MPN patients remains elusive, leading to speculation about a potential relationship or interplay between the two conditions. This unique case prompts a deeper exploration of the mechanisms underlying the coexistence of JAK2-positive MPN and SMM. It underscores the importance of tailored therapeutic strategies that carefully consider the inherent risks and potential adverse outcomes associated with these specific malignancies, thereby warranting further clinical research.

Introduction

While existing literature acknowledges the coexistence of dual malignancies within the same patient [1], there is relatively limited documentation regarding the simultaneous occurrence of dual hematological malignancies (DHMs) [2,3], encompassing both myeloid and lymphoid hemopathies. A noteworthy aspect is the distinctive origin of these two malignancies from separate lineages within the hematopoietic ancestral tree [4]. DHMs can be classified as synchronous, manifesting within six months of the initial malignancy diagnosis, or asynchronous if they arise later [5].

Since its inclusion in the classification of monoclonal gammopathy (MG), smoldering multiple myeloma (SMM) has emerged as a significant aspect of MG [6], attracting attention in various clinical investigations.

Currently, no established strategies exist for treating or monitoring patients with myeloproliferative neoplasms (MPNs) and concurrent SMM. Additionally, the precise source of SMM in patients with MPN is not well understood, and there is uncertainty regarding whether an aberrant plasma cell condition arises from the identical hematopoietic clone as the MPN.

Numerous case reports have highlighted the occurrence of monoclonal gammopathy of undetermined significance (MGUS) or multiple myeloma (MM) in patients with MPN, with details from only a limited number of patient cohorts published [7]. Remarkably, to date, there have been no reported instances of the concurrent diagnosis of essential thrombocythemia (ET) and SMM. In this report, we present a case of synchronous concurrent SMM and ET and provide a comprehensive review of the existing literature.

Case Presentation

An 82-year-old man with a history of hypertension and diabetes was referred to our department for the management of thrombocytosis. Physical examination revealed no remarkable findings, and there was no evidence of lymphadenopathy or hepatosplenomegaly. Laboratory results indicated a platelet count of 946 g/L, hemoglobin of 12.5 g/dL, and a white blood cell count of 6.4 g/L. The patient had no systemic symptoms.

Thrombocytosis workup was initiated, initially excluding infections and iron deficiency. The platelet count was notably elevated, suggesting uncommonly high levels for secondary causes of thrombocytosis.

The patient’s chemistry panel results are shown in Table 1. Monoclonal protein was measured at 36.6 g/L. Serum immunofixation electrophoresis revealed IgG lambda gammopathy. Free light chain lambda was elevated, and kappa was normal.

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Dr Vincelette on MYC Expression in Myelofibrosis

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Nicole D. Vincelette, PhD

Nicole D. Vincelette, PhD, postdoctoral fellow, Moffitt Cancer Center, discusses findings from a study investigating the role of MYC expression and S100A9-mediated inflammation in a subgroup of triple-negative myeloproliferative neoplasms (MPNs).

To determine how MYC expression drives MPNs, such as polycythemia vera, essential thrombocythemia, and primary myelofibrosis, Vincelette and colleagues conducted a study in which they generated a mouse model that overexpresses MYC in the stem cell compartment. This analysis demonstrated that MYC overexpression was associated with the mice developing a myelofibrosis-like phenotype, which included anemia, atypical megakaryocytes, splenomegaly, bone marrow fibrosis, liver fibrosis, spleen fibrosis. The mice also experienced adverse clinical outcomes, such as reduced overall survival (OS), compared with wild-type mice, Vincelette says.

Since the MYC-overexpressed mice developed myelofibrosis, the next step of this research was to investigate how MYC drives myelofibrosis, Vincelette explains. Investigators performed single-cell RNA sequencing to compare the bone marrow cells from MYC-overexpressed and wild-type mice. MYC overexpression correlated with upregulation of the S100A9 protein, which contributes to inflammation and innate immunity, according to Vincelette. Therefore, MYC drives the development of myelofibrosis through S100A9-mediated chronic inflammation. To validate the role of S100A9 downstream of MYC in myelofibrosis, investigators created a mouse model with S100A9 knockout in the presence of MYC overexpression, Vincelette notes. The S100A9 knockout protected against the development of myelofibrosis phenotype in that mouse model, Vincelette emphasizes.

By generating a mouse model that overexpresses S100A9, investigators also determined that S100A9 overexpression alone contributes to the development of myelofibrosis phenotypes, Vincelette says. When investigators treated the MYC-overexpressing mice with the S100A9 inhibitor tasquinimod (ABR-215050), the agent only partially abrogated the myelofibrosis phenotype, meaning the mice had reduced atypical megakaryocytes and splenomegaly. Additionally, the mice developed anemia and no OS difference occurred between tasquinimod and vehicle treatment, potentially because of off-target drug effects, Vincelette concludes.

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The role of inherited genetic variants in rare blood cancer

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January 17, 2024

Researchers from the University of Cambridge, Wellcome Sanger Institute, and collaborators have shown how inherited genetic variants can influence the risk of developing a rare blood cancer.

Large-scale genetic analysis has helped researchers uncover the relationship between cancer-driving genetic mutations and inherited genetic variants in a rare type of blood cancer.

The team combined datasets to understand the impact of cancer-driving spontaneous mutations and inherited genetic variation on the risk of developing myeloproliferative neoplasms (MPN).

Published in Nature Genetics, the study describes how inherited genetic variants can influence whether a spontaneous mutation in a particular gene increases the risk of developing this rare blood cancer.

The analysis will have an impact on current clinical predictions of disease development in individuals.

More research is needed to understand the mechanisms behind how the inherited genetic variants influence the probability of developing rare blood cancer.

In the future, the work could aid drug development interventions that reduce the risk of disease.

Myeloproliferative neoplasms

MPNs are a group of rare and chronic blood cancers, with around 4,000 cases in the UK each year. These occur when the bone marrow overproduces blood cells, resulting in blood clots and bleeding.

MPNs can also progress into other forms of blood cancer.

Genetic risk score

There is a large amount of natural variation between individuals’ blood cells which can affect the amount of blood cells a person has and their traits. This is because different genes can influence blood cell features in an individual.

Researchers take known information about these genes during routine blood tests and analyse the variation to give a genetic risk score. This is how likely that individual is to develop a disease over their lifetime.

MPNs have been linked to random somatic mutations in a gene called JAK2; however, mutated JAK2 is commonly found in the global population. The vast majority of these individuals do not have or go on to develop MPN.

Previous studies identified over a dozen associated inherited genetic variants that increase the risk of MPN. However, these studies do not explain why most individuals do not go on to develop MPN.

Inherited genetic variants can influence risk

The new study combined information on the known somatic driver mutations in MPN inherited genetic variants, and genetic risk scores from individuals with MPN.

They found that the inherited genetic variants that cause natural blood cell variation in the population also impact whether a JAK2 somatic mutation will cause MPN. The team also discovered that individuals with an inherited risk of having a higher blood cell count could display MPN features in the absence of cancer-driving mutations, mimicking disease.

Dr Jing Guo, from the University of Cambridge and the Wellcome Sanger Institute and first author of the study, said: “Our large-scale statistical study has helped fill the knowledge gaps in how variants in DNA, both inherited and somatic, interact to influence complex disease risk.

“By combining these three different types of datasets we were able to get a more complete picture of how these variants combine to cause blood disorders.”

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Inherited polygenic effects on common hematological traits influence clonal selection on JAK2V617F and the development of myeloproliferative neoplasms

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Jing Guo, Klaudia Walter, Pedro M. Quiros, Muxin Gu, E. Joanna Baxter, John Danesh, Emanuele Di Angelantonio, David Roberts, Paola Guglielmelli, Claire N. Harrison, Anna L. Godfrey, Anthony R. Green, George S. Vassiliou, Dragana Vuckovic, Jyoti Nangalia & Nicole Soranzo

Nature Genetics (2024)

Abstract

Myeloproliferative neoplasms (MPNs) are chronic cancers characterized by overproduction of mature blood cells. Their causative somatic mutations, for example, JAK2V617F, are common in the population, yet only a minority of carriers develop MPN. Here we show that the inherited polygenic loci that underlie common hematological traits influence JAK2V617F clonal expansion. We identify polygenic risk scores (PGSs) for monocyte count and plateletcrit as new risk factors for JAK2V617F positivity. PGSs for several hematological traits influenced the risk of different MPN subtypes, with low PGSs for two platelet traits also showing protective effects in JAK2V617F carriers, making them two to three times less likely to have essential thrombocythemia than carriers with high PGSs. We observed that extreme hematological PGSs may contribute to an MPN diagnosis in the absence of somatic driver mutations. Our study showcases how polygenic backgrounds underlying common hematological traits influence both clonal selection on somatic mutations and the subsequent phenotype of cancer.

Main

Myeloproliferative neoplasms (MPNs) are rare chronic hematological cancers characterized by the overproduction of mature blood cells leading to elevated blood cell parameters. They are typically driven by somatically mutated JAK2-mediated, calreticulin (CALR)-mediated or MPL-mediated clonal expansion1. JAK2 mutations are found in both polycythemia vera (PV) and essential thrombocythemia (ET), which are distinct but overlapping MPNs characterized by increased numbers of red blood cells and platelets, respectively. Mutant JAK2 is commonly detectable in 0.1–3% of the healthy population as clonal hematopoiesis (CH)2,3,4,5,6,7, with the vast majority of carriers not meeting or going on to develop disease-defining characteristics of MPN. Little is understood about why only a minority of individuals with mutated JAK2 develop more severe hematological manifestations of MPN and the factors that influence blood count heterogeneity in MPNs.

The 46/1 haplotype near JAK2 is a known germline risk factor for MPNs in the population8. Genome-wide association studies (GWAS) have identified additional disease-associated germline risk loci, estimating the liability-scale heritability of MPNs based on common single-nucleotide polymorphisms (SNPs) to be ~6.5% (refs. 9,10,11). However, these germline risk loci insufficiently explain the phenotypic heterogeneity observed within MPNs and in JAK2-mutated healthy carriers.

Blood cell traits vary widely in the healthy population. The genetic architecture underlying these traits is highly polygenic, with more than 11,000 independently associated genetic variants discovered so far12,13,14. These genome-wide associated variants, when combined in polygenic scores (PGSs), explain a large proportion of phenotypic variance among healthy individuals (from 2.5% for basophil count to 27.3% for mean platelet volume) and are associated with multiple common diseases and rare hematological disorders14. We hypothesized that a genetic burden of germline variants associated with extreme hematological traits could influence phenotypic heterogeneity in association with mutated JAK2, by influencing the clonal dynamics of mutant JAK2 and/or modifying its downstream consequences. In this study, we integrate information on somatic driver mutations, germline genetic variants associated with MPNs, and CH and hematological trait PGSs to study how inherited polygenic variation underlying blood cell traits influences clonal selection on mutated JAK2 and MPN disease phenotypes (Supplementary Fig. 1).

Results

Inherited polygenic contribution to JAK2 V617F positivity

One in 30 healthy individuals reportedly harbors JAK2V617F in their blood, as determined using sensitive assays6. The majority of such individuals have low levels of JAK2V617F and do not meet clinical criteria for MPN due to the absence of elevated blood cell parameters. We wished to understand whether inherited polygenic loci that underlie blood cell traits influence the strength of clonal selection on JAK2V617F.

We studied the germline characteristics of individuals in UK Biobank (UKBB) with and without JAK2V617F. From 162,534 genetically unrelated individuals of European ancestry within the UKBB whole-exome sequencing cohort (‘200k UKBB-WES cohort’; Methods), we identified 540 individuals with one or more mutant reads for JAK2V617F (0.3%, median variant allele frequency (VAF) = 0.056, range = 0.019–1; Supplementary Fig. 2; ‘UKBB-JAK2V617F cohort’). The lower rate of JAK2V617F in the UKBB-WES cohort compared to other population studies6,7 could be explained by its low sequencing coverage (21.5× depth), as also reported previously15 (Supplementary Fig. 3). As expected, there was some overlap among individuals with JAK2V617F and those with a diagnosis of MPN. Of the 423 individuals labeled with a diagnosis of MPN (156 with ET, 161 with PV and 106 with myelofibrosis (MF)), 72 were positive for JAK2V617F (Supplementary Table 1).

We built PGSs for 29 blood cell traits covering a wide range of hematopoietic parameters (Supplementary Table 2). Blood cell trait-specific PGSs were then weighted (by effect size) by the sum of all common (minor allele frequency (MAF) > 0.01) variants that were independently associated with a blood cell trait at genome-wide significance (P < 5 × 10−8) in UKBB (Methods)14. To assess the association between hematological PGSs and small (VAF < 0.1, n = 397) or large (VAF ≥ 0.1, n = 143) JAK2V617F clones, we used multinomial logistic regression including PGSs for each hematological trait (units of s.d.), together with previously reported germline sites associated with MPN9 and CH16 (PGSMPN and PGSCH) as covariates. To account for the recognized predisposition risk for MPN driven by the JAK2 46/1 haplotype8, we computed two PGSMPN scores, separating rs1327494 (tagging the JAK2 46/1 haplotype; PGSMPN–46/1) from nontagging JAK2 variants (PGSMPN-other). We found a negative association between the PGSs for both mean reticulocyte volume (PGSMRV) and immature reticulocyte fraction (PGSIRF) and small JAK2V617F clones (P = 6.2 × 10−4 and 0.0018, false discovery rate (FDR) < 0.05; Supplementary Table 3). We also found significant positive associations with small JAK2V617F clones for the PGSs of plateletcrit (PGSPCT) and monocyte count (PGSMONO) (P = 9.5 × 10−4 and 0.0036, FDR < 0.05). Germline predisposition to high MONO and PCT values was also positively associated with large JAK2V617F clones at modest significance (P = 0.033 and 0.0022, FDR-adjusted P = 0.31 and 0.064; Fig. 1a). Repeating the analysis above excluding MPN cases still demonstrated a significant association between PGSPCT or PGSMONO and small JAK2V617F clones (P < 0.013, Bonferroni corrected; Supplementary Table 4), suggesting that the inherited effects on JAK2V617F were not driven by the subset of MPN cases. These associations were independent of the known germline risk loci associated with MPN and CH (Supplementary Table 3). Validating these associations in the full UKBB-WES dataset (n = 799 and 326 for small and large clones, respectively, and n = 338,919 for controls), we again replicated the associations between PGSPCT and small JAK2V617F clones and between PGSMONO and large JAK2V617F clones at FDR < 0.05 (PCT: odds ratio (OR) = 1.15 (change in odds per increase of 1 s.d. in PGS), 95% confidence interval (CI) = 1.07–1.24, P = 1.4 × 10−4; MONO: OR = 1.20, 95% CI = 1.07–1.34, P = 0.0014; Supplementary Table 5).

Data are presented as ORs (solid dots) with 95% CIs (error bars). a, PGSs with significant associations with small clone size of JAK2V617F (FDR < 0.05) compared to the CH and MPN PGSs (Supplementary Table 3). OR was defined as the change in odds per increase of 1 s.d. in PGS. b, Causal effects estimated by four MR methods for the exposure traits whose PGSs were found to have significant predisposition risk for JAK2V617F positivity (Supplementary Table 7). OR was defined as the change in odds per increase of 1 s.d. in exposure. The MR results shown were based on GWAS summary statistics for JAK2V617F positivity in the full UKBB (Supplementary Fig. 4). Results based on the main discovery set (200k UKBB-WES cohort) are shown in Supplementary Table 6. The MR result for MRV was not available due to a lack of corresponding GWAS summary data in INTERVAL.

To understand the causal relationship among these associations, we undertook Mendelian randomization (MR) analyses with GWAS estimates for the exposure (blood traits) and the outcome (JAK2V617F positivity; Supplementary Fig. 4) obtained from two independent sources. We used genetic instruments for hematological traits identified from UKBB, with effect size estimates from INTERVAL17 (n = 30,305), an external independent cohort. MRV was excluded due to a lack of data in INTERVAL. Both PCT and MONO showed significant causality on the presence of a JAK2V617F clone based on inverse variance-weighted (IVW)18 MR and demonstrated consistent effect estimates using two other MR methods (simple median and weighted median), suggesting that higher MONO and higher PCT values cause a detectable JAK2V617F clone (Supplementary Table 6).

Extending this analysis to the full UKBB-WES cohort (JAK2V617F, n = 1,125; controls, n = 338,919) validated these causal associations with greater estimation accuracy (PCT: ORIVW = 1.52, 95% CI = 1.29–1.78, P = 3.0 × 10−7; MONO: ORIVW = 1.3, 95% CI = 1.15–1.49, P = 4.6 × 10−5; Fig. 1b and Supplementary Table 7). The IVW method of MR (Methods) assumes that the germline loci that drive MONO and PCT have no direct causal effect on driving a JAK2V617F clone (that is, there are no direct causal effects of the genetic instruments on the outcome). We found no evidence of pleiotropy using the MR-Egger19 test; the estimated intercept was not significantly different from zero with P = 0.84 and P = 0.90 for PCT and MONO, respectively. The causal relationship was also significant for PCT and MONO (P < 0.05; Supplementary Table 7 and Supplementary Fig. 5). Additionally, the estimates were not biased by any potential pleiotropic outlier variants and were highly consistent with outlier-corrected causal estimates (Supplementary Table 7 and Methods). Lastly, to ensure the results were not confounded by the possibility that the genetic loci used as instruments for MR directly promoted the outcome (that is, JAK2V617F positivity), we repeated the analysis excluding genetic instruments associated with JAK2V617F positivity (Passociation < 10−6), as well as those that correlated with JAK2V617F variants (that is, those variants and JAK2V617F variants are in linkage disequilibrium (LD) r2 > 0.01) or were in proximity to JAK2V617F variants (in the 10-Mb region centered on each variant), and found no major changes (Supplementary Table 8). Importantly, any reverse causal effect we detected for MONO and PCT was subtle and with pleiotropic effects (PEgger > 0.05 and PEgger-intercept < 0.05; Supplementary Table 9 and Supplementary Fig. 6).

Overall, the association results combined with MR suggest that higher PCT and MONO are causal for the presence of a JAK2V617F clone. This would also explain why individuals with germline predisposition to high PCT and MONO are also more likely to harbor a JAK2V617F clone. Given that acquisition of somatic mutations in blood is largely stochastic in healthy populations20, our data suggest that genetically predicted PCT and MONO influence clonal selection on nascent JAK2V617F cells to promote mutation acquisition.

Germline contribution to blood cell count variation in MPNs

Having shown that polygenic germline loci can predispose to JAK2 clone positivity through their influence on blood cell trait levels, we next studied the contribution of these inherited sites to clinical phenotypes of MPN. We first considered the four blood cell traits that are used to define MPN subcategories clinically21 as follows: hemoglobin concentration (HGB) (g dl–1 divided by 10), hematocrit (HCT) (%), platelet count (PLT) (×109 divided by 1,000) and white blood cell count (WBC) (×109 divided by 100). We used SNP arrays to measure genome-wide polymorphism in an MPN cohort of 761 patients (PV, n = 112; ET, n = 581; MF, n = 68), in whom diagnostic blood cell counts were available and mutation status for a panel of cancer-associated genes (Fig. 2a) had previously been characterized22.

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