02:59am Monday 14 October 2019

Researchers Discover Hidden Genetic Influence on Cancer

BOSTON – In findings with major implications for the genetics of cancer and human health, researchers at Beth Israel Deaconess Medical Center (BIDMC) and two other science teams in New York City and Rome have uncovered a potentially powerful new genetic network and showed how it may work to drive cancer and normal development.

Four papers published online Oct. 14 in the journal Cell describe aspects of what may be a fundamentally new dimension of genetic activity that involves a vast posse of RNA molecules interacting and manipulating the molecular endgame behind the scenes. Each paper used a different approach, strengthening the basic discovery of the new RNA network.

In the half-century old central dogma of molecular biology, DNA issues its blueprint to messenger RNA, which relays the orders to the protein-making machinery of the cell. The new studies suggest a significant new role for RNA on top of its traditional middle-management job: The RNA of one gene can control and be controlled by dozens or hundreds of RNAs of other genes.

In the case of a major tumor suppressor gene, PTEN, a shift in the associated RNA network appears to be as malevolent as a mutation in the gene itself in human prostate and colon cancer cells, in glioblastoma cells, and in a mouse model of melanoma, according to three of the papers.

The findings may enlarge the framework for investigating how tumors form and progress, who is at risk for cancer, and how to find and disable the essential misbehaving molecules that drive the growth and spread of cancer.

“For instance, we now know that the PTEN tumor suppressor gene is talking to a vast unrecognized RNA network,” said Pier Paolo Pandolfi MD PhD, director of the Cancer Genetics Program at BIDMC and George C. Reisman Professor of Medicine at Harvard Medical School, and the senior author of two of the papers. “It’s incredibly exciting for therapeutic possibilities. You may be able to rewire the crosstalk between the RNAs for cancer prevention and therapy.”

Scientists typically use genetic studies to probe how changes in the DNA code influences the action of its protein. Targeted new therapies have arisen from efforts to counteract the effect of problematic proteins, yet most of the genetic determinants of cancer remain a vexing puzzle. The newly discovered RNA network could explain much of the elusive genetic variation underlying cancer and other diseases, say authors of the papers.

The new RNA regulatory network also appears to extend into the large non-protein-coding region of the human genome and plays an important role in normal muscle development, suggests another related paper in Cell. Because humans share so many protein-coding genes with other creatures, including worms and yeast, it is the large portion that is transcribed into non-coding RNA that makes the human genome distinctive. Much of the function of that non-coding RNA has been a mystery.

“Almost all of the scientific analysis of cancer genes focuses on the two percent of protein-coding genes,” Pandolfi said, referring to the instructions passed from DNA to RNA to proteins. “We know that nearly half of the genome is transcribed into RNA that doesn’t code for protein. Through this new ‘language’ of RNA, we can functionalize this space.”

How it works

The newly discovered network of RNA molecules converse through tiny targeted molecules called microRNAs, Pandolfi and his colleagues have found. A certain fraction of RNA share a vocabulary composed of specific sequences along their strands called microRNA response elements (MREs). RNAs compete for the matching microRNAs. Once attached, microRNAs disable their host RNA molecules. It works through simple math: An increase in RNA can sponge up more microRNA, allowing other RNA to go about their business unhindered.

Scientists have known for a decade that microRNA can block RNA and prevent it from helping to make a protein. Some research has advanced to harnessing specific small microRNA molecules as therapeutic tools to block individual protein-coding genes. What’s new in the Cell papers is the idea that a large RNA network uses microRNA as a regulatory language.

This August, Pandolfi and his co-authors named this RNA language and network activity “competing endogenous RNA” (ceRNA, pronounced SIR-na) in a Cell essay. The paper synthesized the emerging experimental evidence in a new theory. They proposed that ceRNA activity greatly expanded the functional genetic information in the human genome and played important roles in diseases, including cancer.

The ceRNA hypothesis adds a major new layer to the highly regulated basic players defined by the central dogma of molecular biology – DNA, RNA and proteins. Other more established regulatory networks that keep cells healthy — and break down in disease — include small molecules added to proteins, such as the recycling label called ubiquitin. Another layer called epigenetics acts on the DNA and its packaging to lock or unlock certain genes.

The findings in the papers

Two of the Cell papers use a combination of bioinformatics and experimental evidence to connect the PTEN tumor suppressor gene to a network of several hundred RNA molecules in close communication.

One of the new papers from the Pandolfi lab linked about 150 new genes to the tumor suppressor PTEN based on the crosstalk between their RNA products and PTEN. Postdoctoral fellow Yvonne Tay used a computational approach to predict potential ceRNAs in the PTEN network in human prostate and colon cancer cell lines. Working with With Isidore Rigoutsos, a collaborator at Jefferson Medical College in Philadelphia, Tay and her co-authors scanned the RNA transcripts of protein-coding genes based on their MRE sequences and then tested a few of the results. “Surprisingly, PTEN can be regulated by a lot of other genes through the ceRNA network,” Tay said.

In an independent paper, a team headed by Andrea Califano at Columbia University in New York evaluated glioblastoma RNA and microRNA expression data from The Cancer Genome Atlas, a public database. They found a PTEN RNA regulatory network of more than 500 genes. Of those, 13 are frequently deleted in glioblastoma and seemed to work together through the microRNA language to squelch the tumor suppressor activity as if patients had had mutations or deletions of PTEN itself.

“All these papers address different aspects of this compelling story and reinforce each other,” said Califano, who also found RNA networks that appeared to communicate by other means. “PTEN is just an example. In each cell, different cliques of genes are connected by this microRNA-mediated network, including all the established oncogenes and tumor suppressors. This layer explains a significant amount of genetic variability in cancer. It allows genes that have nothing to do with the typical oncogene or tumor suppressor to gang up and regulate it. The discovery of this network allows us to discover genes never before associated with a tumor type or disease.”

In a second paper from the Pandolfi group, mutations in the PTEN RNA network speeded up the growth of cancer in a mouse model of melanoma. Postdoctoral fellow Florian Karreth and his co-authors discovered possible new PTEN ceRNAs in a mutagenesis screen of a mouse model of melanoma that he had developed as a graduate student. With the help of a bioinformatics team from the University of Turin, they did an in-depth analysis of one ceRNA with a human gene counterpart that goes wrong in cancer and verified its role in accelerating cancer progression. “We’re looking at network effects, rather than linear interactions,” Karreth said.

The final study extends functional evidence of the new RNA network phenomenon to the normal development of human muscle cells and to the large realm of human non-coding RNAs. Irene Bozzoni’s group at the Sapienza University of Rome found that a long non-protein coding RNA works similarly as a decoy for microRNAs in normal muscle development in mice and humans. In Duchenne muscular dystrophy, the decoy RNA is missing at a crucial time, preventing muscle cells from maturing.

“This explains in part why Duchenne cells have trouble, and it gives us another circuitry to attack in order to cure the disease,” said Bozzoni, who heard about Pandolfi’s ceRNA hypothesis at a meeting last year. “We have been working on noncoding RNA and microRNA for quite a long time. This cross-talk of RNAs through microRNAs is a revolutionary idea.”

BIDMC Contact: Bonnie Prescott
Phone: (617) 667-7306
Email: bprescot@bidmc.harvard.edu

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