| Osteosarcoma (OS) is the most common pediatric malignant bone tumor. Genetically it is the most
complex cancer, associated with faster metastasis, for which there are no targeted therapies.
Genetic mutations used as biomarkers are muddied by the complex genomic instability existing at
baseline in most osteosarcomas. Moreover, the lack of differentiating between responders and nonresponders to conventional chemotherapies early in the treatment regimen further adds to the
challenges.
To understand the molecular mechanisms of chemoresistance and metastasis, we performed a
transposon-mediated forward genetic screen. We discovered a loss-of-function mutation in
ARID1A to be responsible for more aggressive osteosarcoma. ARID1A is a member of the
SWI/SNF chromatin remodeling protein complex which has been implicated in worse prognosis
in many cancers. We hypothesized that loss of ARID1A in osteosarcoma increases the rate of tumor
progression and metastasis by impacting the chromatin configuration and resulting in a
genomically more unstable phenotype.
In-vitro (CRISPR/Cas9) deletion in human OS cell lines validated that ARID1A loss enhances
cancer cell behavior. For the in-vivo study, we used a Cre-mediated, osteoblast-specific conditional
knockout system. We observed a significant drop in survival in the Arid1a-mutant cohort
compared to the wildtype cohort. Furthermore, Arid1a loss enhanced genomic instability, which
we predict can serve as a biomarker for chemosensitivity. Gene expression and chromatin
accessibility analysis further implicate disruption of DNA repair pathways upon deletion of
Arid1a. Arid1a deletion resulted in a general trend of chromatin compaction, which we posit
results in the negative regulation of important tumor suppressor genes. ClaraT bioinformatics tools
highlighted that, among all the hallmarks of cancer, genomic instability and EMT-related pathways
were enhanced in the Arid1a knockout models. This is consistent with our gross phenotypic
evaluation of mice exhibiting more primary metastatic tumors upon Arid1a deletion. Furthermore,
Nanopore sequencing also provided supporting evidence toward genomic instability is a precursor
to aggressiveness in osteosarcoma.
In conclusion, ARID1A loss results in a more aggressive osteosarcoma phenotype. Efforts to better
understand the intersection between genomic instability and epigenetic dysregulation can lead to
earlier decision-making to pursue alternative and sometimes alternative therapies.
Key Words: Osteosarcoma; Epigenetics; Genomic Instability; Arid1a; SWI/SNF; Nanopore; ONT |