Molecular Alterations Governing Predisposition to Myelodysplastic Syndromes: Insights from Shwachman-Diamond Syndrome

Abstract

Identifying germline mutations responsible for genetic predisposition to myeloid malignancies would be useful in creating opportunities for early intervention. Recent studies in Shwachman-Diamond syndrome (SDS) have deciphered a role for heterozygous mutations in EIF6 and TP53 in alleviating germline genetic stress and a role for biallelic TP53 mutations in malignant progression. This review has summarized evidence for a mechanistic framework underlying SDS that can potentially be applied to the study of other germline myelodysplastic syndromes (MDS) predisposition disorders.

Introduction

The myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic stem cell disorders that have an increased propensity for development of acute myeloid leukemia (AML) [1]. Typically, MDS affect older adults (median age, 76 years) but also occur in children and young adults [2, 3]. Over the years, studies have indicated a germline genetic predisposition to MDS in both children and older individuals which can arise as part of a syndrome, or multisystem disorder, or as a seemingly sporadic disease [4]. While physical stigmata and family history can provide important signs for an underlying genetic MDS predisposition, clinically silent phenotypes with cryptic presentations have also been described [5]. Moreover, genomic studies have demonstrated the presence of unrecognized bone marrow failure and genetic MDS syndromes among a subset of pediatric and young adult patients presenting with MDS [3, 6, 7]. Altogether, as a group, these patients are estimated to account for approximately 4% to 15% of patients with MDS, thereby leading to being classified as a new category (myeloid neoplasms with germline predisposition) in the updated World Health Organization classification of myeloid neoplasms [1]. Indeed, the early diagnosis of an underlying genetic predisposition among patients, can have profound implications for treatment, transplantation considerations, long-term surveillance, and family counseling [5]. For instance, prompt surveillance of genetically predisposed patients could enable detection of early signs of disease progression. This could lead to timely hematopoietic stem cell transplantation (HSCT) before progression to leukemia and thus, possibly, improve prognostic outcomes for these patients. Additionally, genetic signatures that predispose patients to MDS can inform patient management by identifying comorbidities, modified conditioning regimens, or aid in donor selection for HSCT. Furthermore, an earlier diagnosis of genetic predisposition to MDS could ensure adequate family counseling and genetic testing of potential family member donors for HSCT [5]. Understanding the molecular underpinnings for genetic predisposition to MDS, would hence be of immense benefit. This paper will provide an overview of the germline predisposition of MDS and examine functional insights regarding recurrent somatic mutations in Shwachman-Diamond syndrome (SDS).

Diagnosis of Genetic Predisposition to MDS

Generally, characteristics such as physical anomaly, poor growth, history of recurrent or unusual infections, the presence of medical comorbidities, and a suspicious family history could be indicative of predisposition to MDS. In addition, antecedent cytopenias, macrocytosis, bone marrow failure, multiple malignancies, and excessive toxicity with chemotherapy or radiation should raise the suspicion for underlying predisposition to MDS [8]. Examples of genes harboring germline mutations associated with predisposition to MDS include RUNX1, GATA2, ETV6, CEBPA, DDX41, BRCA1/2, BRAF, TP53, MPL, JAK2, CSF3R, SAMD9/SAMD9L and Ras pathway genes [5, 9]. While most mutations are usually detected on somatic mutation panels and can be shared between germline and somatic contexts, somatic versus germline panels should not be considered equivalent. Moreover, variant allele frequency is not a reliable measure to distinguish between germline versus somatic mutations and in certain situations, sequencing non-hematopoietic tissues such as skin, and testing family members can be done, to determine whether the mutation is germline. Indeed, testing for presence of known germline mutations represents a valuable opportunity for early recognition and intervention before the development of leukemia. Although identifying germline mutations would be especially useful in MDS that have an abysmal prognosis for leukemic transformation, there remains a paucity of data to inform surveillance and treatment. To this end, monitoring of blood counts among patients with SDS, is an insensitive prognostic marker for risk stratification prior to the development of malignancy. Similarly, tests like bone marrow morphology, cytogenetics, fluorescence in-situ hybridization (FISH), and flow cytometry are late markers for impending leukemogenesis [10]. Thus, there continues to be an unmet need for reliable risk stratification determinants for MDS/AML predisposition.

Somatic Mutations in SDS

Studies have therefore turned towards somatic mutation analysis, among patients with rare genetic syndromes at high risk of leukemia, such as SDS, in an effort to elucidate risk factors for MDS/AML [11]. While SDS is caused by autosomal recessive mutations in the eponymous SBDS gene, the multistep processes that ultimately lead to MDS/AML are currently unclear.

Previously, a study focused on early monitoring of the preleukemic phase in patients with SDS showed the presence of TP53 mutations without development of malignancy, thereby suggesting that clonal hematopoiesis is common in germline genetic predisposition disorders [3]. In order to delve deeper into the mechanisms of the initial faulty but benign hematopoiesis in SDS, Kennedy et al. characterized the presence and dynamics of somatic mutations in serial, clinically annotated samples collected prospectively from patients enrolled in the North American SDS Registry [12]. There was a high frequency of mutations not only in TP53 but also in the EIF6 gene. Additionally, individual SDS patients with SBDS mutations, harbored frequent EIF6 and TP53 mutations and tended to have multiple mutations in those genes. Interestingly 91% of SDS patients with TP53-mutated clonal hematopoiesis had concurrent EIF6 mutations but these aberrations were shown to arise in independent parallel clones. Functional analysis demonstrated that the recurrent mutations in EIF6 and TP53 circumvent the SBDS deficiency in SDS by improving hematopoiesis and reducing checkpoint activation independently [12]. However, the presence, number, persistence, and allele abundance of somatic TP53 mutations did not predict leukemia risk in SDS patients with clonal hematopoiesis. Loss of heterozygosity or an allelic imbalance of TP53 was associated with malignancy among seven patients with SDS. Single cell sequencing from patient samples over six years of surveillance was performed to understand the clonal evolution towards the development of malignancy [12]. The data indicate that over four years prior to the development of the malignancy, there was acquisition of a homozygous TP53 mutation. These data indicate that EIF6 and monoallelic TP53 mutations mediate somatic compensation to address ribosome stress in SDS. On the other hand, acquisition of biallelic TP53 alterations precipitates persistent germline genetic stress, thereby resulting in an increased risk of oncogenic progression in SDS [12]. Overall, functional consequences of somatic aberrations could shed light on mechanisms of leukemogenesis of germline MDS predisposition disorders.

Conclusions

Recognition of germline genetic predisposition to myeloid malignancy will be useful in informing medical management, treatment, and surveillance. While the exact molecular determinants remain to be elucidated, recent evidence in SDS, has provided a mechanistic framework whereby a germline mutation can set up a fitness constraint driving parallel selection of somatic clones along specific pathways with distinct biological and clinical outcomes. When adaptive clonal hematopoiesis alleviates the germline genetic stress, the anti-oncogenic checkpoints remain intact; however, when clonal hematopoiesis removes the checkpoint controls and the germline genetic stress persists, there is an increased propensity to progress to malignancy. Ongoing studies will determine the applicability of these results in other germline MDS predisposition disorders.