1. Between-tumor and within-tumor heterogeneity in invasive potential
- Author
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Joel S. Bader, Yohannes Tsehay, Kevin J. Cheung, Andrew J. Ewald, and Veena Padmanaban
- Subjects
0301 basic medicine ,Genome-wide association study ,Biochemistry ,Metastasis ,0302 clinical medicine ,Breast Tumors ,Basic Cancer Research ,Medicine and Health Sciences ,Tumor Cells, Cultured ,Organ Cultures ,Neoplasm Metastasis ,Biology (General) ,Ecology ,Invasive Tumors ,Genomics ,Primary tumor ,Phenotype ,3. Good health ,Organoids ,Phenotypes ,Oncology ,Computational Theory and Mathematics ,Modeling and Simulation ,Keratins ,Biomarker (medicine) ,Female ,Biological Cultures ,Research Article ,QH301-705.5 ,Breast Neoplasms ,Computational biology ,Biology ,Research and Analysis Methods ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Breast cancer ,Genome-Wide Association Studies ,Biomarkers, Tumor ,Genetics ,Organoid ,medicine ,Humans ,Neoplasm Invasiveness ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Evolutionary Biology ,Population Biology ,Keratin-14 ,Cancers and Neoplasms ,Biology and Life Sciences ,Proteins ,Computational Biology ,Cancer ,Human Genetics ,Genome Analysis ,medicine.disease ,Cytoskeletal Proteins ,030104 developmental biology ,Population Genetics ,030217 neurology & neurosurgery - Abstract
For women with access to healthcare and early detection, breast cancer deaths are caused primarily by metastasis rather than growth of the primary tumor. Metastasis has been difficult to study because it happens deep in the body, occurs over years, and involves a small fraction of cells from the primary tumor. Furthermore, within-tumor heterogeneity relevant to metastasis can also lead to therapy failures and is obscured by studies of bulk tissue. Here we exploit heterogeneity to identify molecular mechanisms of metastasis. We use “organoids”, groups of hundreds of tumor cells taken from a patient and grown in the lab, to probe tumor heterogeneity, with potentially thousands of organoids generated from a single tumor. We show that organoids have the character of biological replicates: within-tumor and between-tumor variation are of similar magnitude. We develop new methods based on population genetics and variance components models to build between-tumor and within-tumor statistical tests, using organoids analogously to large sibships and vastly amplifying the test power. We show great efficiency for tests based on the organoids with the most extreme phenotypes and potential cost savings from pooled tests of the extreme tails, with organoids generated from hundreds of tumors having power predicted to be similar to bulk tests of hundreds of thousands of tumors. We apply these methods to an association test for molecular correlates of invasion, using a novel quantitative invasion phenotype calculated as the spectral power of the organoid boundary. These new approaches combine to show a strong association between invasion and protein expression of Keratin 14, a known biomarker for poor prognosis, with p = 2 × 10−45 for within-tumor tests of individual organoids and p < 10−6 for pooled tests of extreme tails. Future studies using these methods could lead to discoveries of new classes of cancer targets and development of corresponding therapeutics. All data and methods are available under an open source license at https://github.com/baderzone/invasion_2019., Author summary For women with access to healthcare and early detection, breast cancer deaths are caused primarily by metastasis rather than growth of the primary tumor. Metastasis has been difficult to study because it happens deep in the body, occurs over years, and involves a small fraction of cells from the primary tumor. Furthermore, individual cells within a tumor can behave very differently, leading to failures of therapies. Here we exploit heterogeneity to develop new methods to identify molecular mechanisms of metastasis. We use “organoids”, groups of hundreds tumor cells taken from a patient and grown in the lab. Thousands of organoids can be generated from a single tumor sample to probe different regions and amplify the amount of information provided. Organoids provide information about metastasis because they vary in their ability to invade the growth medium. We introduce a new phenotype for invasion obtained by converting the boundary of an organoid into a frequency spectrum, then summing the power across all frequencies. We analyze this metastasis-related phenotype by adapting methods from population genetics that compare the most extreme siblings in a family. We analogously compare the most invasive vs. least invasive organoids from each tumor. Power calculations suggest that studies of 50–100 individuals, with 100-1000 organoids generated from each, could reveal DNA mutations and aberrant gene expression associated with invasion. We validate this approach by demonstrating strong statistical significance between invasion and protein expression of Keratin 14, a known biomarker for poor prognosis. Future studies using these methods could lead to discoveries of new classes of cancer targets and development of corresponding therapeutics.
- Published
- 2020