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Techniques & Tools Mass Spectrometry, Genomics & DNA Analysis, Data Analysis, Clinical

RIME and a Reason

Humans are well adapted to create vitamin D because of its importance of absorbing and retaining calcium and phosphorus to build bone density. But what happens when your body cannot produce enough vitamin D?

A team of researchers applied genomic analysis to prostate cancer cells from patients of African and European descent (1). They used chromatin immunoprecipitation sequencing (ChIP-seq) to identify where the vitamin D receptor (VDR) bound across the genome. This was paired with a similar approach known as rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) to identify the proteins that are associated with the VDR in these different cells. The results showed that African American and European American prostate cells have clear differences in VDR complex composition and transcriptional function, which could explain differences in prostate cancer susceptibility.

To learn more about this study, we spoke with lead author Moray Campbell – a research scientist at Cedars-Sinai Cancer.

How did you come to apply genomics to the question of prostate cancer susceptibility?

In the 1990s and the early 2000s, it became apparent that there were disparities in prostate cancer outcomes in America, with African Americans faring worse than European Americans. It was – and still is – the case that African Americans had worse access to healthcare, which was one potential explanation. But we wanted to find out if there were other factors at play.

Last year, a Veterans Affairs study found that African American men got a more aggressive disease at a younger age with worse outcomes than their European American counterparts (2). And that led us to consider the role of genetics.

And why did you home in on vitamin D?

In the 1980s, people started to realize that you could treat leukemia with retinoic acid compounds, which is derivative from vitamin A. And that led to differentiation therapy – altering the tumor into a quiescent state so a patient can live with it as opposed to killing it. When the retinoids bind to a specific receptor, they control genes that manage differentiation. With this knowledge, we questioned if other receptors in the nuclear receptor family could be used for treatment – including vitamin D.

Researchers started down the rabbit hole to define opportunities for vitamin D signaling in differentiation therapy for cancer – from breast to pancreatic. In prostate cancer research, a clinical trial called ASCENT (3) tested vitamin D and chemotherapy versus using chemotherapy alone in advanced cases. However, this trial was terminated because of unexpected deaths, and there became a multitude of reasons for the trials failing before completion. With this understanding of vitamin D’s history in clinical prostate research, I collaborated with Lara Sucheston-Campbell at Immunovia and Clayton Yates at Johns Hopkins University to understand the role of VDR biology in prostate cancer health disparities. 

What analytical challenges did you face during your research?

In biology and biomedicine, genomic approaches have become increasingly popular for clinical research. Unfortunately, studying genomes requires high computational skills and statistical insights, which is largely absent in biology training programs. What we ideally need are biologists who have computation skills, love looking through microscopes and picking apart the world of cells, and want to dissect disease-driver mechanisms from both angles. 

What was so exciting about our study was the collaboration between the three of us. We were able to design and undertake genomic centered experiments – many of which we couldn’t believe had never been done before! This undoubtedly arose because there weren’t many African American prostate models for comparative genomic experiments. There was also the concern that, even if we designed the experiment, how were we going to do it? And if we get results, how could we suggest that they’re realistic?

What analytical techniques did you use? What were the main findings?

We applied a comprehensive suite of high dimensional data approaches to capture the VDR cistrome (where it bound across the genome), the VDR interactome (the proteins it interacts with), and the VDR transcriptome (the Messenger RNA and the MicroRNA regulated by the VDR) in different cell models derived from prostate cancer in both European and African American men. By comparing African American and European American models, we found significant differences in the composition of the VDR complex and associated proteins where it was genomically bound and what genes were regulated differed depending on genomic ancestry. While we were preparing our article, similar findings on the androgen receptor were reported by colleagues at Baylor College of Medicine (4).

Additionally, we collaborated with other researchers – including Chanita Hughes Halbert at the University of Southern California and Adam Murphy at Northwestern University – who shared clinical and genomic patient data for us to analyze for validating our findings. We were able to show that the identified VDR co-regulators influenced correlations between the VDR and its target genes in African American tumors but not in European American tumors. Though surprising, these results supported the idea that the observed differences had a genetic basis.

How could your findings be applied?

We already know that our vitamin D intake is important for bone health, particularly for the elderly. However, it’s unclear if the same amount of vitamin D is important for other aspects of our health, such as prostate and breast health. Our research indicates that we may need variations in levels depending on our genomic ancestry. 

For example, individuals with European ancestry have adapted to environments with reduced sunlight exposure by having lower melanin content in their skin, which allows for more efficient vitamin D synthesis. However, this adaptation may have resulted in other biological changes beyond skin pigmentation and perhaps more directly relate to the function of the epithelial systems such as the prostate and mammary glands. With further research, we can learn more about how to best control vitamin D levels for individuals with different biological needs.

And your next steps?

Our ongoing research involves looking at protein complexes identified in our recent study and involved in nucleosome remodeling and gene regulation. The focus is on two specific proteins called SMARCA5 and BAZ1A, which are part of ATP-dependent nucleosome remodeling complexes. These proteins are crucial in positioning nucleosomes, which is important for transcription and DNA repair. Downregulation of these proteins in African American prostate cancer suggests that gene regulation and DNA repair processes may be affected. Moving forward, we aim to understand the underlying mechanisms driving this issue and the impact on various biological processes.

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  1. M Campbell et al., Cancer Research Communications (2023). DOI: 10.1158/2767-9764.CRC-22-0389.
  2. K Yamoah et al., JAMA Netw Open (2022). DOI: 10.1001/jamanetworkopen.2021.44027.
  3. TM Beer, ASCENT: the androgen-independent prostate cancer study of calcitriol enhancing taxotere (2005). DOI: 10.1111/j.1464-410X.2005.05675.x.
  4. J E Berchuck et al., The Prostate Cancer Androgen Receptor Cistrome in African American Men Associates with Upregulation of Lipid Metabolism and Immune Response (2022). DOI: 10.1158/0008-5472.CAN-21-3552.
About the Author
Jessica Allerton

Associate Editor, The Analytical Scientist

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