Posted April 29, 2020

Omar Abdel-Wahab, M.D., Sloan Kettering Institute for Cancer Research
Robert Bradley, Ph.D., Fred Hutchinson Cancer Research Center

Myelodysplastic syndromes (MDS) are a group of cancers that typically occur when the normal production of cells in the bone marrow is interrupted or distorted, leading to abnormal cell growth, which is characterized by reduction of one or more types of blood cells. Treatment options for this condition have not been very successful, in part due to limited understanding of ribonucleic acid (RNA) splicing. During this process, newly made precursor messenger RNA is converted to mature RNA. Mutations that arise during RNA splicing have been shown to be present in most MDS patients. Research aimed at targeting RNA spliceosomes is therefore important, as it could lead to positive scientific discoveries and breakthroughs in this field.

Through a Bone Marrow Failure Research Program Fiscal Year 2015 (FY15) Award, Dr. Abdel-Wahab and Dr. Bradley sought (1) to identify a subset of biologically and therapeutically relevant targets that link spliceosomal mutations to MDS and (2) to identify therapeutic strategies that interfere with the altered function of mutant spliceosomal proteins. They hypothesized that, in addition to the mutations occurring during RNA splicing, the synthesis of downstream genes was also being mis-spliced and that targeting the gene splicing errors could help identify possible treatment approaches for MDS.

Drs. Abdel-Wahab and Bradley’s team aimed to identify unifying molecular abnormalities across spliceosomal mutations using combined genomic and proteomic approaches. They engineered mice with specific mutations of the serine/arginine-rich splicing factor 2 (SRSF2) and splicing factor 3B subunit 1 (SF3B1) in a hemizygous manner, which allowed a single copy of a gene instead of two to be present. The mice were also crossed to generate a combination of different mutations, and these mutation effects were studied. From this, they were able to successfully identify convergent biological consequences of splicing factor mutations. They determined the basis for the mutual exclusivity and heterozygous nature of the mutations, which was not previously well understood. Drs. Abdel-Wahab and Bradley discovered that mutations in RNA splicing factors are not tolerated in a homozygous state.¹ This understanding is crucial to determining possible treatment targets. Next, they focused on identifying additional genes that are required for the survival of cells carrying different spliceosomal mutations with synthetic lethality screens. Fetal liver cells were transduced with a green fluorescent protein-expressing retroviral construct and then transplanted into lethally irradiated recipient mice. Recently discovered anticancer compounds termed sulfonamides that degrade RNA-binding proteins (RBPs), which are vital to RNA splicing were tested. Drs. Abdel-Wahab and Bradley found that splicing factor mutant cells are preferentially sensitive to RNA-binding protein 39 (RBM39) degraders.² The effects of RBM39 loss on splicing further pointed toward a strategy for treatment.

Based on these initial outcomes, Drs. Abdel-Wahab and Bradley worked to identify novel therapeutic strategies specifically targeting spliceosomal protein function. The mouse models were treated with a splicing inhibitor, and the resulting differential response was examined. They detected genetic subsets that were most likely to respond to type I protein arginine methyltransferases (PRMTs) inhibition and a mechanistic basis for therapeutic efficacy of PRMT inhibition in cancer. Combined PRMT inhibition produced a greater synergistic effect on cell killing than singular inhibition.³

In addition to these achievements, Drs. Abdel-Wahab and Bradley studied the transcriptomes of 982 patients with myeloid neoplasms and discovered that RNA splicing and epigenomic alterations act combinatorially to drive myeloid neoplasm development.⁴ They also discovered that SF3B1mutations, which are common in MDS, other hematologic diseases, and also in non-hematologic diseases, converge on aberrant splicing of BRD9 (bromodomain-containing protein 9- a protein that is a key to regulating normal gene expression in cells). Correcting BRD9 aberrant splicing had a therapeutic effect on SF3B1 mutant cells. These results in part describe the pervasive nature of SF3B1 mutations and provide a potential mechanism-based approach for targeted therapy.

Findings from this project have yielded significant clinical impact leading to novel approaches of MDS therapeutic development. Collaborating with H3 Biomedicine, Inc., Dr. Abdel-Wahab was part of a group of researchers that developed a drug known as H3B-8800, (a modified form of a natural substance found in soil bacteria) and evaluated it in a Phase I clinical trial.⁵ Preliminary results demonstrate dose-dependent target engagement, predictable PK profile of H3B-8800, and safety even with prolonged dosing. Second, Drs. Abdel-Wahab and Bradley and a team of other scientists are testing an oral treatment of a PRMT5 inhibitor in patients with myeloid malignancies. Last but not the least, through a separate organizational initiative, Dr. Abdel-Wahab is currently leading an effort with a pharmaceutical company to conduct a phase II clinical trial of an oral sulfonamide drug in patients with myeloid neoplasms whose conditions have relapsed or have not successfully responded to conventional therapies. The three approaches described that have resulted from the original project offer promising pathways for developing effective treatment.

Drs. Abdel-Wahab and Bradley hope that collaborative research efforts continue to gain momentum, focusing on these newly identified mechanistic processes to better understand underlying mechanisms and identify more precise treatment targets. Such efforts will likely pave the way for the discovery of more efficacious therapeutics for not only MDS patients but also patients with a variety of tumor/cancer conditions.

 

References:

1. Lee SC, North K, Kim E, et al. 2018. Synthetic lethal and convergent biological effects of cancer-associated spliceosomal gene mutations. Cancer Cell 34(2):225-241.E8.

2. Wang E, Lu, SX, Pastore A, et al. 2019. Targeting an RNA-Binding protein network in acute myeloid leukemia. Cancer Cell 35(3):369-384.E7.

3. Fong JY, Pinata L, Goy P, et al. 2019. Therapeutic targeting of RNA splicing catalysis through inhibition of protein arginine methylation. Cancer Cell 36(2):194-209.E9.

4. Yoshimi A, Lin KT, Wiseman DH, et al. 2019. Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis. Nature 574:273-277

5. Seiler M, Yoshimi A, Darman R, et al. 2018. H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers. Nat Med 24:497-504.

Links:

Public and Technical Abstracts: Therapeutic Targeting of Spliceosomal-Mutant Acquired Bone Marrow Failure Disorders

Results of a Clinical Trial of H3B-8800, a Splicing Modulator, in Patients with Myelodysplastic Syndromes (MDS), Acute Myeloid Leukemia (AML) or Chronic Myelomonocytic Leukemia (CMML)

Splicing May be an Effective Target in the Fight Against Cancer

How a Common Cancer Mutation Actually Drives Cancer – And How to Correct It

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