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Principal Investigator: OLGA ANCZUKOW-CAMARDA
Organization: JACKSON LABORATORY
Fiscal Year: 2024
Award: $527,984
Funding agency: National Cancer Institute
SUMMARY
Alternative RNA splicing is a key step in gene expression regulation and contributes to transcriptional diversity
by selecting which transcript isoforms are produced in a specific cell at a specific time point. Aberrantly spliced
isoforms can impact every one of the hallmarks of cancer, including increased cell proliferation, migration, or
resistance to apoptosis. Regulatory splicing factors (SFs) have recently emerged as a new class of oncoproteins
and tumor suppressors. In particular, the tumorigenic capacity of the oncogenic transcription factor MYC, which
is dysregulated in >50% of human tumors, has been shown to be dependent on the splicing machinery and on
at least 3 SFs directly regulated by MYC. However, we currently do not have a comprehensive understanding of
which component(s) of the splicing machinery are regulated by MYC, or of the functions of MYC-induced spliced
isoforms. The goal of this proposal is to systematically characterize the mechanisms by which MYC-regulated
SFs and spliced isoforms drive tumor growth and maintenance. To begin to address this gap in knowledge, in
our preliminary studies we used a mammary cell line harboring an inducible form of MYC to greatly expand the
number of known SFs regulated by MYC. We uncovered that MYC activation promotes alternative splicing of
>4,000 isoforms and expression of 125 SFs. These SFs are also upregulated in MYC-active breast tumors and
can be grouped, based on co-expression, into groups or modules. Six SF-modules highly correlate with MYC
activity in breast tumors and cell lines, and are enriched in triple negative breast cancer (TNBC). Which of these
SFs play a role in MYC-driven transformation, and whether co-expression of multiple MYC-induced SFs has a
stronger tumorigenic effect than individual SFs, is not known. Further, co-expression analysis in 33 TCGA tumors
of different tissue origin identified an SF-module shared across all MYC-active tumors, suggesting a pan-cancer
vulnerability. We hypothesize that MYC regulates a network of SFs which cooperate in tumor pathogenesis and
that disrupting this network could provide a novel strategy to slow growth of MYC-driven tumors. Here, we will
leverage our expertise in RNA splicing and cancer biology and apply a functional genomics approach to gain
novel insights into MYC's oncogenicity. Aim 1 will characterize the function of 6 MYC-induced SF modules and
their splicing targets in TNBC tumor growth in vitro and in vivo. Since it is unknown whether MYC regulates a
shared set of isoforms in distinct tissues, Aim 2 will identify pan-cancer splicing signatures predictive of MYC
activity and clinical outcomes, which may serve as clinical biomarkers, and will deliver putative neo-antigens
generated from MYC-induced isoforms. Finally, Aim 3 will implement genomic approaches to determine which
MYC-induced isoforms are essential for the growth of MYC-driven cancer cells and patient-derived organoids.
This project will reveal fundamental mechanisms by which oncogenic SFs and their target spliced isoforms drive
tumorigenesis downstream of MYC. These results could help inform development of therapeutic strategies for
tumors driven by MYC, which remains an undruggable target.
Terms: <3-D><3-Dimensional><3D><Abscission><Address><Alternate Splicing><Alternative RNA Splicing><Alternative Splicing><Apoptosis><Apoptosis Pathway><Assay><Automobile Driving><Avian Myelocytomatosis Viral Oncogene Homolog><Basal Transcription Factor><Basal transcription factor genes><Binding><Binding Sites><Bioassay><Biological Assay><Body Tissues><Breast><Breast Cancer><Breast Cancer Cell><Breast Cancer Model><Breast Cancer cell line><Breast Epithelial Cells><Breast Neoplasms><Breast Tumors><Breast tumor cell line><Breast tumor model><CRISPR><CRISPR/Cas system><Cancer Biology><Cancer Cell Growth><Cancer Patient><Cancer Staging><Cancers><Cell Body><Cell Communication and Signaling><Cell Growth in Number><Cell Line><Cell Multiplication><Cell Proliferation><Cell Signaling><Cell model><CellLine><Cells><Cellular Expansion><Cellular Growth><Cellular Proliferation><Cellular model><Clinical><Clustered Regularly Interspaced Short Palindromic Repeats><Combining Site><DNA><Data><Data Set><Deoxyribonucleic Acid><Development><Diagnostic Neoplasm Staging><Distant Cancer><Distant Metastasis><Dropout><Excision><Exons><Extirpation><FDA approved><Failure><Gene Action Regulation><Gene Expression Regulation><Gene Regulation><Gene Regulation Process><Gene Transcription><General Transcription Factor Gene><General Transcription Factors><Generalized Growth><Genes><Genetic Transcription><Genomic approach><Goals><Growth><H-ras><H-ras Gene><H-ras Oncogene><HRAS><HRAS gene><HRAS1><Harvey Rat Sarcoma Viral Oncogene Homolog><Human><Image><In Vitro><Individual><Intracellular Communication and Signaling><Invaded><Isoforms><Knowledge><MYC Transcription Factor><MYC gene><Maintenance><Malignant Breast Neoplasm><Malignant Cell><Malignant Neoplasms><Malignant Tumor><Mammary Cancer><Mammary Neoplasms><Metastasis><Metastasize><Metastatic Lesion><Metastatic Mass><Metastatic Neoplasm><Metastatic Tumor><Methods><Modern Man><Molecular><Molecular Interaction><Neoplasm Metastasis><Neoplasm Staging><Non-Polyadenylated RNA><Oncogene Products><Oncogene Proteins><Oncogenesis><Oncogenic><Oncoproteins><Organoids><Outcome><Pathogenesis><Patient outcome><Patient-Centered Outcomes><Patient-Focused Outcomes><Primary Neoplasm><Primary Tumor><Process><Programmed Cell Death><Protein Isoforms><Proteins><Proteomics><Proto-Oncogene Products c-myc><Proto-Oncogene Proteins c-myc><RAS genes><RASH1><RNA><RNA Expression><RNA Gene Products><RNA Seq><RNA Splicing><RNA sequencing><RNA-Binding Proteins><RNAseq><Reactive Site><Regulation><Removal><Research><Resistance><Ribonucleic Acid><Secondary Neoplasm><Secondary Tumor><Signal Transduction><Signal Transduction Systems><Signaling><Splicing><Strains Cell Lines><Surgical Removal><TCGA><TM-MKR><TNBC><Testing><The Cancer Genome Atlas><Therapeutic Studies><Therapy Research><Time><Tissue Growth><Tissues><Transcript><Transcription><Transcription Factor Proto-Oncogene><Transcription factor genes><Tumor Markers><Tumor Promotion><Tumor Staging><Tumor Suppressor Proteins><biological signal transduction><breast tumor cell><c-myc Proteins><cancer cell><cancer metastasis><cell growth><chemical standard><clinical biomarkers><clinical diagnosis><clinical relevance><clinically relevant><clinically useful biomarkers><cultured cell line><developmental><driving><functional genomics><genomic effort><genomic strategy><imaging><in vivo><inhibitor><insight><knock-down><knockdown><malignancy><malignant breast tumor><mammary><mammary cancer model><mammary epithelial cells><mammary tumor><mammary tumor model><migration><myc Oncogenes><myc Proto-Oncogene Product p62><myc Proto-Oncogene Proteins><neo-antigen><neo-epitopes><neoantigens><neoepitopes><neoplasm/cancer><new approaches><new marker><new therapeutic approach><new therapeutic intervention><new therapeutic strategies><new therapy approaches><new treatment approach><new treatment strategy><novel><novel approaches><novel biomarker><novel marker><novel strategies><novel strategy><novel therapeutic approach><novel therapeutic intervention><novel therapeutic strategies><novel therapy approach><ontogeny><overexpress><overexpression><patient oriented outcomes><patient prognosis><predictive signature><predictive tools><public data base><public database><publicly accessible data base><publicly accessible database><publicly available data base><publicly available database><resection><resistant><targeted drug therapy><targeted drug treatments><targeted therapeutic><targeted therapeutic agents><targeted therapy><targeted treatment><therapeutic agent development><therapeutic development><therapeutic target><three dimensional><tool><transcription factor><transcriptome sequencing><transcriptomic sequencing><triple-negative breast cancer><triple-negative invasive breast carcinoma><tumor><tumor biomarker><tumor cell metastasis><tumor growth><tumor specific biomarker><tumor suppressor><tumorigenesis><tumorigenic><v-Ha-RAS Harvey Rat Sarcoma Viral Oncogene Homolog>