Somatic evolution in cancer


Somatic evolution is the accumulation of mutations and epimutations in somatic cells during a lifetime, and the effects of those mutations and epimutations on the fitness of those cells. This evolutionary process has first been shown by the studies of Bert Vogelstein in colon cancer. Somatic evolution is important in the process of aging as well as the development of some diseases, including cancer.

Natural selection in cancer

Cells in pre-malignant and malignant neoplasms evolve by natural selection. This accounts for how cancer develops from normal tissue and why it has been difficult to cure. There are three necessary and sufficient conditions for natural selection, all of which are met in a neoplasm:
  1. There must be variation in the population. Neoplasms are mosaics of different mutant cells with both genetic and epigenetic changes that distinguish them from normal cells.
  2. The variable traits must be heritable. When a cancer cell divides, both daughter cells inherit the genetic and epigenetic abnormalities of the parent cell, and may also acquire new genetic and epigenetic abnormalities in the process of cellular reproduction.
  3. That variation must affect survival or reproduction. While many of the genetic and epigenetic abnormalities in neoplasms are probably neutral evolution, many have been shown to increase the proliferation of the mutant cells, or decrease their rate of death.
Cells in neoplasms compete for resources, such as oxygen and glucose, as well as space. Thus, a cell that acquires a mutation that increases its fitness will generate more daughter cells than competitor cells that lack that mutation. In this way, a population of mutant cells, called a clone, can expand in the neoplasm. Clonal expansion is the signature of natural selection in cancer.
Cancer therapies act as a form of artificial selection, killing sensitive cancer cells, but leaving behind resistant cells. Often the tumor will regrow from those resistant cells, the patient will relapse, and the therapy that had been previously used will no longer kill the cancer cells. This selection for resistance is similar to the repeatedly spraying crops with a pesticide and selecting for resistant pests until the pesticide is no longer effective.

Evolution in complex biological systems

Modern descriptions of biological evolution will typically elaborate on major contributing factors to evolution such as the formation of local micro-environments, mutational robustness, molecular degeneracy, and cryptic genetic variation. Many of these contributing factors in evolution have been isolated and described for cancer.

Multilevel selection

Cancer is a classic example of what evolutionary biologists call multilevel selection: at the level of the organism, cancer is usually fatal so there is selection for genes and the organization of tissues that suppress cancer. At the level of the cell, there is selection for increased cell proliferation and survival, such that a mutant cell that acquires one of the hallmarks of cancer, will have a competitive advantage over cells that have not acquired the hallmark. Thus, at the level of the cell there is selection for cancer.

History

Pre-Nowell & Cairns

The earliest ideas about neoplastic evolution come from Boveri who proposed that tumors originated in chromosomal abnormalities passed on to daughter cells. In the decades that followed, cancer was recognized as having a clonal origin associated with chromosomal aberrations.
Early mathematical modeling of cancer, by Armitage and Doll, set the stage for the future development of the somatic evolutionary theory of cancer. Armitage and Doll explained the cancer incidence data, as a function of age, as a process of the sequential accumulation of somatic mutations.
Advances in cytogenetics facilitated discovery of chromosome abnormalities in neoplasms, including the Philadelphia chromosome in chronic myelogenous leukemia and translocations in acute myeloblastic leukemia. Sequences of karyotypes replacing one another in a tumor were observed as it progressed. Researchers hypothesized that cancer evolves in a sequence of chromosomal mutations and selection and that therapy may further select clones.

Knudson, Cairns, and Nowell

In 1971, Knudson published the 2-hit hypothesis for mutation and cancer based on statistical analysis of inherited and sporadic cases of retinoblastoma. He postulated that retinoblastoma developed as a consequence of two mutations; one of which could be inherited or somatic followed by a second somatic mutation. Cytogenetic studies localized the region to the long arm of chromosome 13, and molecular genetic studies demonstrated that tumorigenesis was associated with chromosomal mechanisms, such as mitotic recombination or non-disjunction, that could lead to homozygosity of the mutation. The retinoblastoma gene was the first tumor suppressor gene to be cloned in 1986.
Cairns hypothesized a different, but complementary, mechanism of tumor suppression in 1975 based on tissue architecture to protect against selection of variant somatic cells with increased fitness in proliferating epithelial populations, such as the intestine and other epithelial organs. He postulated that this could be accomplished by restricting the number of stem cells for example at the base of intestinal crypts and restraining the opportunities for competition between cells by shedding differentiated intestinal cells into the gut. The essential predictions of this model have been confirmed although mutations in some tumor suppressor genes, including CDKN2A, predispose to clonal expansions that encompass large numbers of crypts in some conditions such as Barrett's esophagus. He also postulated an immortal DNA strand that is discussed at Immortal DNA strand hypothesis.
Nowell synthesized the evolutionary view of cancer in 1976 as a process of genetic instability and natural selection. Most of the alterations that occur are deleterious for the cell, and those clones will tend to go extinct, but occasional selectively advantageous mutations arise that lead to clonal expansions. This theory predicts a unique genetic composition in each neoplasm due to the random process of mutations, genetic polymorphisms in the human population, and differences in the selection pressures of the neoplasm's microenvironment. Interventions are predicted to have varying results in different patients. What is more important, the theory predicts the emergence of resistant clones under the selective pressures of therapy. Since 1976, researchers have identified clonal expansions and genetic heterogeneity
within many different types of neoplasms.

Somatic evolution in progression

Genetic heterogeneity in neoplasms

There are multiple levels of genetic heterogeneity associated with cancer, including single nucleotide polymorphism, sequence mutations, Microsatellite shifts and instability, loss of heterozygosity, Copy number variation and karyotypic variations including chromosome structural aberrations and aneuploidy. Studies of this issue have focused mainly at the gene mutation level, as copy number variation, LOH and specific chromosomal translocations are explained in the context of gene mutation. It is thus necessary to integrate multiple levels of genetic variation in the context of complex system and multilevel selection.
System instability is a major contributing factor to genetic heterogeneity. For the majority of cancers, genome instability is reflected in a large frequency of mutations in the whole genome DNA sequence. In whole genome sequencing of different types of cancers, large numbers of mutations were found in two breast cancers, 25 melanomas and a lung cancer. Genome instability is also referred to as an enabling characteristic for achieving endpoints of cancer evolution.

Many of the somatic evolutionary studies have traditionally been focused on clonal expansion, as recurrent types of changes can be traced to illustrate the evolutionary path based on available methods. Recent studies from both direct DNA sequencing and karyotype analysis illustrate the importance of the high level of heterogeneity in somatic evolution. For the formation of solid tumors, there is an involvement of multiple cycles of clonal and non-clonal expansion. Even at the typical clonal expansion phase, there are significant levels of heterogeneity within the cell population, however, most are under-detected when mixed populations of cells are used for molecular analysis. In solid tumors, a majority of gene mutations are not recurrent types, and neither are the karyotypes. These analyses offer an explanation for the findings that there are no common mutations shared by most cancers.

Somatic evolution by epigenetics

The state of a cell may be changed epigenetically, in addition to genetic alterations. The best-understood epigenetic alterations in tumors are the silencing or expression of genes by changes in the methylation of CG pairs of nucleotides in the promoter regions of the genes. These methylation patterns are copied to the new chromosomes when cells replicate their genomes and so methylation alterations are heritable and subject to natural selection. Methylation changes are thought to occur more frequently than mutations in the DNA, and so may account for many of the changes during neoplastic progression, in particular in the early stages. For instance, when loss of expression of the DNA repair protein MGMT occurs in a colon cancer, it is caused by a mutation only about 4% of the time, while in most cases the loss is due to methylation of its promoter region. Similarly, when loss of expression of the DNA repair protein PMS2 occurs in colon cancer, it is caused by a mutation about 5% of the time, while in most cases loss of expression is due to methylation of the promoter of its pairing partner MLH1. Epigenetic changes in progression interact with genetic changes. For example, epigenetic silencing of genes responsible for the repair of mispairs or damages in the DNA results in an increase of genetic mutations.
Deficiency of DNA repair proteins PMS2, MLH1, MSH2, MSH3, MSH6 or BRCA2 can cause up to 100-fold increases in mutation frequency Epigenetic deficiencies in DNA repair gene protein expression have been found in many cancers, though not all deficiencies have been evaluated in all cancers. Epigeneticically deficient DNA repair proteins include BRCA1, WRN, MGMT, MLH1, MSH2, ERCC1, PMS2, XPF, P53, PCNA and OGG1, and these are found to be deficient at frequencies of 13% to 100% in different cancers.
In addition to well studied epigenetic promoter methylation, more recently there have been substantial findings of epigenetic alterations in cancer due to changes in histone and chromatin architecture and alterations in the expression of microRNAs For instance, hypomethylation of the promoter for microRNA miR-155 increases expression of miR-155, and this increased miR-155 targets DNA repair genes MLH1, MSH2 and MSH6, causing each of them to have reduced expression.
In cancers, loss of expression of genes occurs about 10 times more frequently by transcription silencing than by mutations. As Vogelstein et al. point out, in a colorectal cancer there are usually about 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. In contrast, in colon tumors compared to adjacent normal-appearing colonic mucosa, there are about 600 to 800 somatically heritable heavily methylated CpG islands in promoters of genes in the tumors while these CpG islands are not methylated in the adjacent mucosa.
Methylation of the cytosine of CpG dinucleotides is a somatically heritable and conserved regulatory mark that is generally associated with transcriptional repression. CpG islands keep their overall un-methylated state extremely stably through multiple cell generations.