Harnessing hotspot specific differences among SF3B1 mutations to define novel mechanisms of tumorigenicity and targetability in solid malignancies

PROJECT SUMMARY
SF3B1 is the most commonly mutated splicing factor in cancer, occurring in thousands of cancer patients
annually. Mutations in SF3B1 result in a neomorphic protein that causes aberrant splicing of hundreds of
transcripts, including known cancer associated genes. While the mechanisms by which these alterations promote
tumorigenesis are incompletely understood, our lab has previously shown SF3B1 mutations are attractive
therapeutic targets. SF3B1 mutations are prevalent in many cancers (breast, melanoma, bladder, pancreatic,
leukemias), so improving our ability to target these mutations could have major public health implications. To do
this, there is a fundamental need to better understand how SF3B1 mutations drive tumorigenesis. Recent work
in acute myeloid leukemia shows differences in missplicing, oncogenic effects and prognosis among various
SF3B1 hotspot mutations, yet there are no studies to date investigating these in solid malignancies. To determine
potential therapeutic strategies, novel model systems are required. An innovative genome editing approach will
allow us to study the mutations at the most common hotspots from breast cancer and melanoma, K700 and
R625, respectively in several representative cell line models. Changes in the transcriptome and phenotypic
differences in proliferation, migration, and invasion will determine whether there are specific alterations in
SF3B1 that lead to distinct oncogenic phenotypes. Additionally, preliminary systematic analysis of online
cancer databases shows SF3B1 mutations and TP53 alterations are mutually exclusive in cancer. This often
suggests either synthetic lethality or a lack of selection for co-occurrence due to shared roles in tumorigenesis.
Successful generation of dual SF3B1 mutant and TP53 mutant or TP53 knock out cell lines demonstrates that
the mutations are unlikely to be synthetic lethal. Instead, this relationship likely demonstrates a shared role
and will allow us to determine novel mechanisms of SF3B1-mediated tumorigenesis. Previous findings in
SF3B1 mutants demonstrate dysfunctional cellular respiration due to missplicing and degradation of a UQCC1,
a component of mitochondrial complex III. There is a resultant increase in glucose, similar to p53’s well known
role in promoting the Warburg effect. Further studying the relationship between mutant SF3B1 and TP53 may
identify therapeutic vulnerabilities that can be additionally leveraged against the large subset of cancers with
TP53 mutations. The sponsor’s robust history of utilizing genome editing strategies to study individual mutations
in breast cancer in conjunction with the abundant resources and core facilities at Vanderbilt University make
these Aims achievable. Completion of these aims provide an excellent foundation in cancer molecular genetics.
This will allow the PI to acquire the technical skills to build toward an independent investigational career in
oncology, specifically studying novel pathologic features of cancers that lead to uniquely targetable
vulnerabilities.

Grant Number: 5F30CA268325-03
NIH Institute/Center: NIH
Principal Investigator: Riley Bergman