Evolution of living organisms as a multilevel process

Carcino-Evo-Devo, A Theory of the Evolutionary Role of Hereditary Tumors

A theory of the evolutionary role of hereditary tumors, or the carcino-evo-devo theory, is being developed. The main hypothesis of the theory, the hypothesis of evolution by tumor neofunctionalization, posits that hereditary tumors provided additional cell masses during the evolution of multicellular organisms for the expression of evolutionarily novel genes. The carcino-evo-devo theory has formulated several nontrivial predictions that have been confirmed in the laboratory of the author. It also suggests several nontrivial explanations of biological phenomena previously unexplained by the existing theories or incompletely understood. By considering three major types of biological development-individual, evolutionary, and neoplastic development-within one theoretical framework, the carcino-evo-devo theory has the potential to become a unifying biological theory.

The Theory of Carcino-Evo-Devo and Its Non-Trivial Predictions

To explain the sources of additional cell masses in the evolution of multicellular organisms, the theory of carcino-evo-devo, or evolution by tumor neofunctionalization, has been developed. The important demand for a new theory in experimental science is the capability to formulate non-trivial predictions which can be experimentally confirmed. Several non-trivial predictions were formulated using carcino-evo-devo theory, four of which are discussed in the present paper: (1) The number of cellular oncogenes should correspond to the number of cell types in the organism. The evolution of oncogenes, tumor suppressor and differentiation gene classes should proceed concurrently. (2) Evolutionarily new and evolving genes should be specifically expressed in tumors (TSEEN genes). (3) Human orthologs of fish TSEEN genes should acquire progressive functions connected with new cell types, tissues and organs. (4) Selection of tumors for new functions in the organism is possible. Evolutionarily novel organs should recapitulate tumor features in their development. As shown in this paper, these predictions have been confirmed by the laboratory of the author. Thus, we have shown that carcino-evo-devo theory has predictive power, fulfilling a fundamental requirement for a new theory.

Mammalian tumor-like organs. 1. The role of tumor-like normal organs and atypical tumor organs in the evolution of development (carcino-evo-devo)

Background

Earlier I hypothesized that hereditary tumors might participate in the evolution of multicellular organisms. I formulated the hypothesis of evolution by tumor neofunctionalization, which suggested that the evolutionary role of hereditary tumors might consist in supplying evolving multicellular organisms with extra cell masses for the expression of evolutionarily novel genes and the origin of new cell types, tissues, and organs. A new theory—the carcino-evo-devo theory—has been developed based on this hypothesis.

Main text

My lab has confirmed several non-trivial predictions of this theory. Another non-trivial prediction is that evolutionarily new organs if they originated from hereditary tumors or tumor-like structures, should recapitulate some tumor features in their development. This paper reviews the tumor-like features of evolutionarily novel organs. It turns out that evolutionarily new organs such as the eutherian placenta, mammary gland, prostate, the infantile human brain, and hoods of goldfishes indeed have many features of tumors. I suggested calling normal organs, which have many tumor features, the tumor-like organs.

Conclusion

Tumor-like organs might originate from hereditary atypical tumor organs and represent the part of carcino-evo-devo relationships, i.e., coevolution of normal and neoplastic development. During subsequent evolution, tumor-like organs may lose the features of tumors and the high incidence of cancer and become normal organs without (or with almost no) tumor features.

Biological Computation and Compatibility Search in the Possibility Space as the Mechanism of Complexity Increase During Progressive Evolution

The idea of computational processes, which take place in nature, for example, DNA computation, is discussed in the literature. DNA computation that is going on in the immunoglobulin locus of vertebrates shows how the computations in the biological possibility space could operate during evolution. We suggest that the origin of evolutionarily novel genes and genome evolution constitute the original intrinsic computation of the information about new structures in the space of unrealized biological possibilities. Due to DNA computation, the information about future structures is generated and stored in DNA as genetic information. In evolving ontogenies, search algorithms are necessary, which can search for information about evolutionary innovations and morphological novelties. We believe that such algorithms include stochastic gene expression, gene competition, and compatibility search at different levels of structural organization. We formulate the increase in complexity principle in terms of biological computation and hypothesize the possibility of in silico computing of future functions of evolutionarily novel genes.

Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans

Abstract

Earlier we suggested a new hypothesis of the possible evolutionary role of hereditary tumors (Kozlov, Evolution by tumor Neofunctionalization, 2014), and described a new class of genes – tumor specifically expressed, evolutionarily novel (TSEEN) genes - that are predicted by this hypothesis (Kozlov, Infect Agents Cancer 11:34, 2016). In this paper we studied evolutionarily novel genes expressed in fish tumors after regression, as a model of evolving organs. As evolutionarily novel genes may not yet have organismal functions, we studied the acquisition of new gene functions by comparing fish evolutionarily novel genes with their human orthologs. We found that many genes involved in development of progressive traits in humans (lung, mammary gland, placenta, ventricular septum, etc.) originated in fish and are expressed in fish tumors and tumors after regression. These findings support a possible evolutionary role of hereditary tumors, and in particular the hypothesis of evolution by tumor neofunctionalization.

Research highlights

Earlier we described a new class of genes that are tumor-specifically expressed and evolutionarily novel (TSEEN). As the functions of TSEEN genes are often uncertain, we decided to study TSEEN genes of fishes so that we could trace the appearance of their new functions in higher vertebrates. We found that many human genes which are involved in development of progressive traits (placenta development, mammary gland and lung development etc.,) originated in fishes and are expressed in fish tumors.

Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently

Earlier we showed that human genome contains many evolutionarily young or novel genes with tumor-specific or tumor-predominant expression. We suggest calling such genes Tumor Specifically Expressed, Evolutionarily New (TSEEN) genes. In this paper we performed a study of the evolutionary ages of different classes of human genes, using homology searches in genomes of different taxa in human lineage. We discovered that different classes of human genes have different evolutionary ages and confirmed the existence of TSEEN gene classes. On the other hand, we found that oncogenes, tumor-suppressor genes and differentiation genes are among the oldest gene classes in humans and their evolution occurs concurrently. These findings confirm non-trivial predictions made by our hypothesis of the possible evolutionary role of hereditary tumors. The results may be important for better understanding of tumor biology. TSEEN genes may become the best tumor markers.

The Role of Heritable Tumors in Evolution of Development: a New Theory of Carcino-evo-devo

The hypothesis of evolution by tumor neofunctionalization (the "main hypothesis") describes the possible role of hereditary tumors in evolution. The present article examines the relationship of the main hypothesis to other biological theories. As shown in this paper, the main hypothesis does not contradict to the existing biological theories, but fills the lacunas between them and explains some unexplained (or not completely understood) questions. Common features of embryonic development and tumorigenesis are described by several recognized theories. Similarities between normal development and tumorigenesis suggest that tumors could participate in the evolution of ontogenesis and in the origin of new cell types, tissues and organs. A wide spectrum of non-trivial explanations and non-trivial predictions in different fields of biology, suggested by the main hypothesis, is an indication of its fundamental nature and the potential to become a new biological theory, a theory of the role of tumors in evolution of development, or carcino-evo-devo.

The possible evolutionary role of tumors in the origin of new cell types

The ability of tumor cells to differentiate in combination with their ability to express genes that are not expressed in normal tissues, may result in the emergence of new cell types in evolution. Tumors may play an evolutionary role by providing conditions (space and resources) for the expression of newly evolving genes. Genetically or epigenetically predetermined tumors at the early stages of progression, benign tumors, and some tumor-like processes in invertebrates and plants, all of which are modes of excess cell growth which provide evolving multicellular organisms with extra cell masses, are considered as potentially evolutionarily meaningful. Malignant tumors at the late stages of progression, however, are not. The preexisting cell types of multicellular organisms had restricted potential for the expression of newly evolving genes. Because of regulation and gene competition, some of the newly evolving genes may stay silent. Multicellular organisms would need excess cell masses for the expression of newly evolving genes. The preexisting cell types cannot provide such excess cell masses because of limitations imposed on the number of possible cell divisions. Tumors could provide the evolving multicellular organisms with the excess cell masses for the expression of newly evolving genes. We suggest that tumors could be a sort of proving ground (or reservoir) for the expression of newly evolving genes that originate in the course of genome evolution in the DNA of germ cells (i.e., not in tumor cells themselves). The case in which the expression of a newly evolving gene in tumors results in the origin of a new function would be associated with the origin of new feedback and regulatory circuits, as in root nodules in legumes and macromelanophores in Xiphophorus fishes. Tumor cells would differentiate, resulting in a new cell type for the given multicellular species. This cell type would be inherited because of epigenomic mechanisms similar to those in preexisting cell types. Populations of tumor-bearing organisms with genetically or epigenetically programmed tumors could represent the transition between established species of organisms at different stages of progressive evolution. Experimental confirmation of the prediction of the hypothesis of evolution by tumor cells differentiation concerning the expression of evolutionarily new genes and/or silent (neutrally evolving) sequences in tumor cells is presented.

Evolutionarily new sequences expressed in tumors

Background

Earlier we suggested the concept of the positive evolutionary role of tumors. According to this concept, tumors provide conditions for the expression of evolutionarily new and/or sleeping genes in their cells. Thus, tumors are considered as evolutionary proving ground or reservoir of expression. To support this concept we have previously characterized in silico and experimentally a new class of human tumor-related transcribed sequences.

Results

In this article we describe results of further studies of previously described tumor-related sequences. The results of molecular phylogeny studies, Southern hybridization experiments and computational comparison with genomes of other species are presented.

Conclusion

These results suggest that these previously described tumor-related human transcripts are also relatively evolutionarily new.

Experimental Study of Human Expressed Sequences Newly Identified in Silico as Tumor Specific

In our previous studies, we used global computational differential display of ESTs that belong to UNIGENE clusters and identified human sequences differentially expressed in human tumors, as well as a considerable amount of transcripts represented only in tumor-derived cDNA libraries. Most of the tumor-specific EST clusters are derived from the plurality of the tumor types originated in tissues of both ectodermal and mesodermal origin. We found that many of such tumor-specific ESTs do not contain long open reading frames and cannot be classified as protein-encoding genes. To experimentally assess patterns of expression of these EST clusters, we studied four of them in PCR experiments on Clontech MTC panels. The experimental data confirm the results obtained by in silico screening, i.e. tumor specificity of their expression. We suggest that a significant increase in the expression of non-coding RNA is a fundamental feature of cancer cells, and that such transcripts could serve as markers for the diagnosis or monitoring of human malignancies.

Gene competition and the possible evolutionary role of tumours

The evolutionary role of tumours might consist of providing the conditions for the expression of evolutionary new genes and thus in providing the material for the origin of new cell types. To approach this concept the principle of gene competition is essential. With an increase in gene number in the genomes of the evolving multicellular organisms the enforcement of gene competition should take place. Therefore, the pre-existing cell types possess limited possibilities for the expression of evolutionary new genes. Like evolutionary new genes originated from extra copies (duplicates) of old genes, evolutionary new cell types had to originate from extra cells which were not functionally necessary to the organism. Tumours could have supplied the evolving multicellular organisms with extra cells for the expression of originating evolutionary new genes. Of course, on the basis of this proposal only tumours at the earlier stages of progression are considered to be meaningful, or some kind of tumour-like processes, but not malignant tumours at late stages of progression. The evolutionary new genes originate in the DNA of germ line cells but not in DNA of tumour cells. Until the moment of their expression in the tumour cells these genes could stay silent. After the expression of these genes tumour cells should acquire the function in the organism, differentiate and lose their previous autonomy. The organisms with a new cell type should then be selected against their fitness and competitive abilities.