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Posts Tagged ‘intratumor variability’


Tumor Progression

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

GEN News Highlights Nov 10, 2015   Darwinian Selection Does Not Influence Tumor Progression
http://www.genengnews.com/gen-news-highlights/darwinian-selection-does-not-influence-tumor-progression/81251958/

http://www.genengnews.com/Media/images/GENHighlight/85273_large1068523712.jpg

 

New answers may have just emerged in a long-standing debate in the field of oncology and molecular evolution. The neutral theory of molecular evolution states that changes occurring at the molecular level are not caused by natural selection, but rather by the random genetic drift of mutant alleles. In contrast, Darwinian selection adheres to the idea that a molecular mutation holds some selective advantage over the wild-type, allowing it to thrive.

When viewing these two theories through the lens of carcinogenesis, it is not difficult to envision the applicability of either theory. However now, new evidence from scientists at the University of Chicago and the Beijing Institute of Genomics may tip the scales in favor of neutral theory. This collaborative scientific effort assembled data from one of the most rigorous genetic sequencing ever carried out on a single tumor—revealing a much greater level of genetic diversity than expected.

The investigators excised a tumor roughly 3.5 centimeters in diameter (slightly smaller than a ping-pong ball), from a hepatocellular carcinoma tumor of the liver. The research team estimated that the tumor contained more than 100 million distinct mutations within genetic coding regions, which is thousands of times more than they anticipated. The impact of this finding is that even microscopic tumors are likely to contain extremely high genetic diversity and with so much variation there are likely many cells contained within able to resist standard post-surgical cancer treatment such as chemotherapy and radiation.

“With 100 million mutations, each capable of altering a protein in some way, there is a high probability that a significant minority of tumor cells will survive, even after aggressive treatment,” explained study director Chung-I Wu, Ph.D., professor of ecology and evolution at the University of Chicago. “In a setting with so much diversity, those cells could multiply to form new tumors, which would be resistant to standard treatments.”

The findings from this study were published recently in PNAS through an article entitled “Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.”

 

Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution

Shaoping Linga,1Zheng Hua,1Zuyu Yanga,1Fang Yanga,1Yawei LiaPei LinbKe ChenaLili DongaLihua CaoaYong Taoa , et al.
PNAS Nov 11, 2015,              http://dx.doi.org:/10.1073/pnas.1519556112

Significance

A tumor comprising many cells can be compared to a natural population with many individuals. The amount of genetic diversity reflects how it has evolved and can influence its future evolution. We evaluated a single tumor by sequencing or genotyping nearly 300 regions from the tumor. When the data were analyzed by modern population genetic theory, we estimated more than 100 million coding region mutations in this unexceptional tumor. The extreme genetic diversity implies evolution under the non-Darwinian mode. In contrast, under the prevailing view of Darwinian selection, the genetic diversity would be orders of magnitude lower. Because genetic diversity accrues rapidly, a high probability of drug resistance should be heeded, even in the treatment of microscopic tumors.

 

The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 “polymorphic” SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model,MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors.

intratumor heterogeneity  genetic diversity  neutral evolution  cancer evolution  natural selection

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1519556112/-/DCSupplemental.

 

Scientists at the Beijing Institute of Genomics sampled nearly 300 regions from one slice of the hepatocellular tumor and sequenced or genotyped each one searching for genetic changes. Once they analyzed their data and applied a modern population genetic theory, their results lead them to the 100 million coding-region mutation estimate for the whole tumor.

This extensive level of heterogeneity within a single tumor, which is way beyond what a Darwinian process would permit, makes the selectionism vs. neutralism debate of the 1980s “suddenly medically relevant,” Dr. Wu remarked. Since previous to the current study, no one had ever genetically dissected a tumor as thoroughly, the commonly held theory was that tumors had from a few hundred up to 20,000 genetic alterations that were not present in the patient’s healthy cells.

“Our study is the non-Darwinian process writ small, down to the cellular level,” Dr. Wu noted. “In the Darwinian struggle, there are—from the tumor’s point of view—few beneficial mutations, meaning changes that give tumor cells a growth advantage. When there are no such limits on genetic variation, however, mutations can emerge and apparently thrive.”

“This could potentially change how we think about tumor growth and spread, but the direct clinical implications of this study may not be obvious on the surface,” added co-author Daniel Catenacci, M.D., assistant professor and medical oncologist at the University of Chicago.

While the bulk of the mutations were at very low frequencies, drug intervention could provide some of the genetic mutations with a progression path forward.

“The presence of so many random mutations could present a problem to specifically targeted therapies,” Dr. Catenacci stated. “It almost guarantees that some cells will be resistant. But it also suggests that aggressive treatment could push tumor cells into a more Darwinian mode.”

Since the current study only focused on a single tumor type, it remains to be seen how comparable this data will be for other types of cancerous tumors. However, regardless of narrow focus, the results from this analysis raises important question about tumor evolution and heterogeneity.

 

 

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