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Principal Investigator: Amy Strom
Organization: PRINCETON UNIVERSITY
Fiscal Year: 2024
Award: $120,534
Funding agency: National Cancer Institute
Project Summary
Despite advances in sequencing, imaging and screening technologies, morphological changes in nuclear
structure are still utilized as a common and reliable diagnosis of cancer. Healthy cells invariably have ellipsoid,
smooth nuclear shape and distinctive chromatin distribution, while cancerous cells are characterized by irregular,
jagged nuclear shape and disrupted chromatin distribution. Relatedly, one of the most commonly mutated
proteins in human cancers is a component of the chromatin remodeler BAF complex known as ARID1A. These
mutations lose nucleosome sliding activity, leading to altered transcriptome and cancer progression. As a
structural scaffold of the BAF complex, many of the mutations in ARID1A that cause cancer result in early
truncation and lead to loss of BAF complex assembly. However, driver mutations also exist in the relatively
uncharacterized intrinsically disordered regions of ARID1A whose molecular mechanism is unknown.
Investigations into nuclear organization have identified the importance of intrinsically disordered regions
and phase separation in dictating overall nuclear structure and organization, as well as forming nuclear bodies
like the nucleolus, and chromatin compartments like heterochromatin, but until recently we have not been able
to control this organization, or link it conclusively to chromatin compartment function. The Brangwynne lab has
developed optogenetic tools that allow for control of in vivo biophysical behavior of condensates.
As a Life Science Research Fellow through the Mark Foundation for Cancer Research, I have determined
the role of chromatin-chromatin crosslinking protein HP1a in determining nuclear shape and mechanics, as well
as discovered rules for chromatin inclusion, exclusion, and compaction dictated by phase separated
compartments. In this proposal I will expand my research to understand the biophysical changes that occur in
these nuclear compartments upon ARID1A mutations that drive cancer, and how this is connected to their
disease phenotype. In Aim 1, I will interrogate interactions that dictate how condensates interact with chromatin,
and utilize light-triggered phase separation to modulate chromatin compaction and transcription in living cells. In
Aim 2, I will determine how the chromatin polymer directs phase separation, and how nuclear stiffness influences
nuclear body volume and functional output. In Aim 3, under the guidance of my co-mentor Dr. Cigall Kadoch, I
will utilize knowledge gained in Aims 1 and 2 to build a molecular mechanism of BAF complex proteins ARID1A
and ARID1B in oncogenesis, including the roles of their IDRs in targeting BAF complex activity and effects of
cancer-associated mutations on condensation behavior, sequence targeting and transcriptional output.
With the support of my mentors and the greater research environment at both Princeton University and
the Dana Farber Cancer Institute, I will have access to unique tools, and will receive training in cancer biology
methods, biophysical theory, and next-generation sequencing assays. Together, these aims will provide a new
perspective on nuclear organization in cancer that may lead to novel venues of therapeutics.
Terms: <30 nm Chromatin Fiber><30 nm Fiber><ARID1A><ARID1A gene><AT- rich interactive domain-containing protein 1A><AT-rich interactive domain 1A gene><Affect><Agreement><Amino Acid Sequence><Area><Assay><Behavior><Binding><Binding Proteins><Binding Sites><Bioassay><Biologic Sciences><Biological Assay><Biological Sciences><Biology><Biophysical Process><Biophysics><Bioscience><Bromodomain><Cancer Biology><Cancer Cause><Cancer Etiology><Cancerous><Cancers><Cell Body><Cell Nucleolus><Cell Nucleus><Cells><Cellular Expansion><Cellular Growth><Chromatin><Chromatin Fiber><Chromosomal Rearrangement><Combining Site><Common Neoplasm><Common Tumor><Complex><DF/HCC><DNA Binding Domain><DNA Sequence><DNA-Binding Protein Motifs><Dana-Farber Cancer Institute><Defect><Disease><Disorder><Dysfunction><Environment><Epigenetic><Epigenetic Change><Epigenetic Mechanism><Epigenetic Process><Exclusion><Expression Signature><Foundations><Functional disorder><Gene Arrangement><Gene Expression Profile><Gene Order><Gene Position><Gene Transcription><Genetic><Genetic Alteration><Genetic Change><Genetic Transcription><Genetic defect><Genome><Genomic Segment><Genomics><Heterochromatin><Human><Image><Investigation><Knowledge><Life Sciences><Ligand Binding Protein><Ligand Binding Protein Gene><Light><Link><Malignant Neoplasms><Malignant Tumor><Mechanics><Mediating><Mentors><Methods><Modeling><Modern Man><Modification><Molecular><Molecular Interaction><Morphology><Mutate><Mutation><NGS Method><NGS system><Non-Polyadenylated RNA><Nuclear><Nuclear Lamina><Nuclear Structure><Nucleosomes><Nucleus><Oncogenesis><Oncogenic><Outcome><Output><Pattern><Phase><Phase Transition><Phenotype><Photoradiation><Physical condensation><Physiopathology><Plasmosome><Polymers><Primary Protein Structure><Process><Protein Binding><Protein Region><Proteins><RNA><RNA Expression><RNA Gene Products><Reactive Site><Research><Ribonucleic Acid><Role><Sampling><Shapes><Site><Slide><Specificity><Structure><Structure-Activity Relationship><System><Technology><Therapeutic><Training><Transcription><Transcription Activation><Transcriptional Activation><Universities><Work><anti-cancer research><biophysical characteristics><biophysical characterization><biophysical foundation><biophysical measurement><biophysical mechanism><biophysical parameters><biophysical principles><biophysical properties><biophysical sciences><body volume><bound protein><cancer diagnosis><cancer progression><cancer research><cell growth><chemical structure function><condensation><density><disease phenotype><driver lesion><driver mutation><epigenetically><gene expression pattern><gene expression signature><genome mutation><genome segment><genomic region><global gene expression><global transcription profile><imaging><in vivo><malignancy><mechanic><mechanical><neoplasm progression><neoplasm/cancer><neoplastic progression><next gen sequencing><next generation sequencing><nextgen sequencing><novel><nucleolus><optogenetics><pathophysiology><polymer><polymeric><protein complex><protein crosslink><protein sequence><scaffold><scaffolding><screening><screenings><social role><structure function relationship><theories><tool><transcriptional profile><transcriptional signature><transcriptome><tumor progression><tumorigenesis><viscoelasticity>