In defense of the somatic mutation theory of cancer

Initiation of Cancer: The Journey From Mutations in Somatic Cells to Epigenetic Changes in Tissue-resident VSELs

Multiple theories exist to explain cancer initiation, although a consensus on this is crucial for developing effective therapies. 'Somatic mutation theory' suggests that mutations in somatic cells during DNA repair initiates cancer but this concept has several attached paradoxes. Research efforts to identify quiescent cancer stem cells (CSCs) that survive therapy and result in metastasis and recurrence have remained futile. In solid cancers, CSCs are suggested to appear during epithelial-mesenchymal transition by the dedifferentiation and reprogramming of epithelial cells. Pluripotent and quiescent very small embryonic-like stem cells (VSELs) exist in multiple tissues but remain elusive owing to their small size and scarce nature. VSELs are developmentally connected to primordial germ cells, undergo rare, asymmetrical cell divisions and are responsible for the regular turnover of cells to maintain tissue homeostasis throughout life. VSELs are directly vulnerable to extrinsic endocrine insults because they express gonadal and gonadotropin hormone receptors. VSELs undergo epigenetic changes due to endocrine insults and transform into CSCs. CSCs exhibit genomic instability and develop mutations due to errors during DNA replication while undergoing excessive proliferation and clonal expansion to form spheroids. Thus tissue-resident VSELs offer a connection between extrinsic insults and variations in cancer incidence reported in various body tissues. To conclude, cancer is indeed a stem cell disease with mutations occurring as a consequence. In addition to immunotherapy, targeting mutations, and Lgr5 + organoids for developing new therapeutics, targeting CSCs (epigenetically altered VSELs) by improving their niche and epigenetic status could serve as a promising strategy to treat cancer.

Stem cell mutations, associated cancer risk, and consequences for regenerative medicine

Mutation accumulation in stem cells has been associated with cancer risk. However, the presence of numerous mutant clones in healthy tissues has raised the question of what limits cancer initiation. Here, we review recent developments in characterizing mutation accumulation in healthy tissues and compare mutation rates in stem cells during development and adult life with corresponding cancer risk. A certain level of mutagenesis within the stem cell pool might be beneficial to limit the size of malignant clones through competition. This knowledge impacts our understanding of carcinogenesis with potential consequences for the use of stem cells in regenerative medicine.

The essential molecular requirements for the transformation of normal cells into established cancer cells, with implications for a novel anti-cancer agent

BACKGROUND

Normal adult mammalian cells can respond to oncogenic somatic mutations by committing suicide through a well-described, energy dependent process termed apoptosis. Cancer cells avoid oncogene promoted apoptosis. Oncogenic somatic mutations are widely acknowledged to be the cause of the relentless unconstrained cell proliferation which characterises cancer. But how does the normal cell with the very first oncogenic mutation survive to proliferate without undergoing apoptosis?

NEW FINDINGS

The phenomena of malignant transformation by somatic mutation, apoptosis, aneuploidy, aerobic glycolysis and Cdk4 upregulation in carcinogenesis have each been extensively discussed separately in the literature but an overview explaining how they may be linked at the initiation of the cancer process has not previously proposed.

CONCLUSION

A hypothesis is presented to explain how in addition to the initial oncogenic mutation, the expression of certain key normal genes is, counter-intuitively, also required for successful malignant transformation from a normal cell to a cancer cell. The hypothesis provides an explanation for how the cyclic amphiphilic peptide HILR-056, derived from peptides with homology to a hexapeptide in the C-terminal region of Cdk4, kill cancer cells but not normal cell by necrosis rather than apoptosis.

The scientific basis for the use of the linear no-threshold (LNT) model at low doses and dose rates in radiological protection

The linear no-threshold (LNT) model was introduced into the radiological protection system about 60 years ago, but this model and its use in radiation protection are still debated today. This article presents an overview of results on effects of exposure to low linear-energy-transfer radiation in radiobiology and epidemiology accumulated over the last decade and discusses their impact on the use of the LNT model in the assessment of radiation-related cancer risks at low doses. The knowledge acquired over the past 10 years, both in radiobiology and epidemiology, has reinforced scientific knowledge about cancer risks at low doses. In radiobiology, although certain mechanisms do not support linearity, the early stages of carcinogenesis comprised of mutational events, which are assumed to play a key role in carcinogenesis, show linear responses to doses from as low as 10 mGy. The impact of non-mutational mechanisms on the risk of radiation-related cancer at low doses is currently difficult to assess. In epidemiology, the results show excess cancer risks at dose levels of 100 mGy or less. While some recent results indicate non-linear dose relationships for some cancers, overall, the LNT model does not substantially overestimate the risks at low doses. Recent results, in radiobiology or in epidemiology, suggest that a dose threshold, if any, could not be greater than a few tens of mGy. The scientific knowledge currently available does not contradict the use of the LNT model for the assessment of radiation-related cancer risks within the radiological protection system, and no other dose-risk relationship seems more appropriate for radiological protection purposes.

A critical appraisal of the relative contribution of tissue architecture, genetics, epigenetics and cell metabolism to carcinogenesis

Here we contrast several carcinogenesis models. The somatic-mutation-theory posits mutations as main causes of malignancy. However, inconsistencies led to alternative explanations. For example, the tissue-organization-field-theory considers disrupted tissue-architecture as main cause. Both models can be reconciled using systems-biology-approaches, according to which tumors hover in states of self-organized criticality between order and chaos, are emergent results of multiple deviations and are subject to general laws of nature: inevitable variation(mutation) explainable by increased entropy(second-law-of-thermodynamics) or indeterminate decoherence upon measurement of superposed quantum systems(quantum mechanics), followed by Darwinian-selection. Genomic expression is regulated by epigenetics. Both systems cooperate. So cancer is neither just a mutational nor an epigenetic problem. Rather, epigenetics links environmental cues to endogenous genetics engendering a regulatory machinery that encompasses specific cancer-metabolic-networks. Interestingly, mutations occur at all levels of this machinery (oncogenes/tumor-suppressors, epigenetic-modifiers, structure-genes, metabolic-genes). Therefore, in most cases, DNA mutations may be the initial and crucial cancer-promoting triggers.

Biology of cancer; from cellular and molecular mechanisms to developmental processes and adaptation

Cancer research has been largely focused on the cellular and molecular levels of investigation. Recent data show that not only the cell but also the extracellular matrix plays a major role in the progression of malignancy. In this way, the cells and the extracellular matrix create a specific local microenvironment that supports malignant development. At the same time, cancer implies a systemic evolution which is closely related to developmental processes and adaptation. Consequently, there is currently a real gap between the local investigation of cancer at the microenvironmental level, and the pathophysiological approach to cancer as a systemic disease. In fact, the cells and the matrix are not only complementary structures but also interdependent components that act synergistically. Such relationships lead to cell-matrix integration, a supracellular form of biological organization that supports tissue development. The emergence of this supracellular level of organization, as a structure, leads to the emergence of the supracellular control of proliferation, as a supracellular function. In humans, proliferation is generally involved in developmental processes and adaptation. These processes suppose a specific configuration at the systemic level, which generates high-order guidance for local supracellular control of proliferation. In conclusion, the supracellular control of proliferation act as an interface between the downstream level of cell division and differentiation, and upstream level of developmental processes and adaptation. Understanding these processes and their disorders is useful not only to complete the big picture of malignancy as a systemic disease, but also to open new treatment perspectives in the form of etiopathogenic (supracellular or informational) therapies.

Glioblastoma CD105+ cells define a SOX2- cancer stem cell-like subpopulation in the pre-invasive niche

Glioblastoma (GBM) is the most common and most aggressive primary brain tumor in adults. Glioma stem like cells (GSC) represent the highest cellular hierarchy in GBM and have a determining role in tumor growth, recurrence and patient prognosis. However, a better definition of GSC subpopulations, especially at the surgical resection margin, is warranted for improved oncological treatment options. The present study interrogated cells expressing CD105 (CD105⁺) specifically within the tumor front and the pre-invasive niche as a potential GSC subpopulation. GBM primary cell lines were generated from patients (n = 18) and CD105⁺ cells were isolated and assessed for stem-like characteristics. In vitro, CD105⁺ cells proliferated and enriched in serum-containing medium but not in serum-free conditions. CD105⁺ cells were characterized by Nestin⁺, Vimentin⁺ and SOX2^-, clearly distinguishing them from SOX2⁺ GCS. GBM CD105⁺ cells differentiated into osteocytes and adipocytes but not chondrocytes. Exome sequencing revealed that GBM CD105⁺ cells matched 83% of somatic mutations in the Cancer cell line encyclopedia, indicating a malignant phenotype and in vivo xenotransplantation assays verified their tumorigenic potential. Cytokine assays showed that immunosuppressive and protumorigenic cytokines such as IL6, IL8, CCL2, CXCL-1 were produced by CD105⁺ cells. Finally, screening for 88 clinical drugs revealed that GBM CD105⁺ cells are resistant to most chemotherapeutics except Doxorubicin, Idarubicin, Fludarabine and ABT-751. Our study provides a rationale for targeting tumoral CD105⁺ cells in order to reshape the tumor microenvironment and block GBM progression.

Scales of Cancer Evolution: Selfish Genome or Cooperating Cells?

Simple Summary

Cancer continuously evolves its ability to survive in time-varying microenvironment, which results, regarding the therapeutic context, in its therapeutic resistance. As it is accepted that the development of resistance is the direct consequence of intratumour heterogeneity, its evolutionary etiology is intensively studied. Models of carinogenesis are often assessed accordingly to how well they fit into the evolutionary scenario. In the paper, the relevant observations and concepts in cancer research, such as intratumour heterogeneity, cell plasticity, and Markov cell state dynamics, are reviewed and integrated into an evolutionary model. The possibility that the interaction between cancer cells can be interpreted as cooperation is proposed.

Abstract

The exploitation of the evolutionary modus operandi of cancer to steer its progression towards drug sensitive cancer cells is a challenging research topic. Integrating evolutionary principles into cancer therapy requires properly identified selection level, the relevant timescale, and the respective fitness of the principal selection unit on that timescale. Interpretation of some features of cancer progression, such as increased heterogeneity of isogenic cancer cells, is difficult from the most straightforward evolutionary view with the cancer cell as the principal selection unit. In the paper, the relation between the two levels of intratumour heterogeneity, genetic, due to genetic instability, and non-genetic, due to phenotypic plasticity, is reviewed and the evolutionary role of the latter is outlined. In analogy to the evolutionary optimization in a changing environment, the cell state dynamics in cancer clones are interpreted as the risk diversifying strategy bet hedging, optimizing the balance between the exploitation and exploration of the cell state space.

Why Do We Care More About Disease than Health?

Modern Western biomedical research and clinical practice are primarily focused on disease. This disease-centric approach has yielded an impressive amount of knowledge around what goes wrong in illness. However, in comparison, researchers and physicians know little about health. What is health? How do we quantify it? And how do we improve it? We currently do not have good answers to these questions. Our lack of fundamental knowledge about health is partly driven by three main factors: (i) a lack of understanding of the dynamic processes that cause variations in health/disease states over time, (ii) an excessive focus on genes, and (iii) a pervasive psychological bias towards additive solutions. Here I briefly discuss potential reasons why scientists and funders have generally adopted a gene- and disease-centric framework, how medicine has ended up practicing "diseasecare" rather than healthcare, and present cursory evidence that points towards an alternative energetic view of health. Understanding the basis of human health with a similar degree of precision that has been deployed towards mapping disease processes could bring us to a point where we can actively support and promote human health across the lifespan, before disease shows up on a scan or in bloodwork.

Bioelectric Dysregulation in Cancer Initiation, Promotion, and Progression

Cancer is primarily a disease of dysregulation – both at the genetic level and at the tissue organization level. One way that tissue organization is dysregulated is by changes in the bioelectric regulation of cell signaling pathways. At the basis of bioelectricity lies the cellular membrane potential or V_mem, an intrinsic property associated with any cell. The bioelectric state of cancer cells is different from that of healthy cells, causing a disruption in the cellular signaling pathways. This disruption or dysregulation affects all three processes of carcinogenesis – initiation, promotion, and progression. Another mechanism that facilitates the homeostasis of cell signaling pathways is the production of extracellular vesicles (EVs) by cells. EVs also play a role in carcinogenesis by mediating cellular communication within the tumor microenvironment (TME). Furthermore, the production and release of EVs is altered in cancer. To this end, the change in cell electrical state and in EV production are responsible for the bioelectric dysregulation which occurs during cancer. This paper reviews the bioelectric dysregulation associated with carcinogenesis, including the TME and metastasis. We also look at the major ion channels associated with cancer and current technologies and tools used to detect and manipulate bioelectric properties of cells.

Towards the characterization of neutron carcinogenesis through direct action simulations of clustered DNA damage

Neutron exposure poses a unique radiation protection concern because neutrons have a large, energy-dependent relative biological effectiveness (RBE) for stochastic effects. Recent computational studies on the microdosimetric properties of neutron dose deposition have implicated clustered DNA damage as a likely contributor to this marked energy dependence. So far, publications have focused solely on neutron RBE for inducing clusters of DNA damage containing two or more DNA double strand breaks (DSBs). In this study, we have conducted a novel assessment of neutron RBE for inducing all types of clustered DNA damage that contain two or more lesions, stratified by whether the clusters contain DSBs (complex DSB clusters) or not (non-DSB clusters). This assessment was conducted for eighteen initial neutron energies between 1 eV and 10 MeV as well as a reference radiation of 250 keV x-rays. We also examined the energy dependence of cluster length and cluster complexity because these factors are believed to impact the DNA repair process. To carry out our investigation, we developed a user-friendly TOPAS-nBio application that includes a custom nuclear DNA model and a novel algorithm for recording clustered DNA damage. We found that neutron RBE for inducing complex DSB clusters exhibited similar energy dependence to the canonical neutron RBE for stochastic radiobiological effects, at multiple depths in human tissue. Qualitatively similar results were obtained for non-DSB clusters, although the quantitative agreement was lower. Additionally we identified a significant neutron energy dependence in the average length and complexity of clustered lesions. These results support the idea that many types of clustered DNA damage contribute to the energy dependence of neutron RBE for stochastic radiobiological effects and imply that the size and constituent lesions of individual clusters should be taken into account when modeling DNA repair. Our results were qualitatively consistent for (i) multiple radiation doses (including a low-dose 0.1 Gy irradiation), (ii) variations in the maximal lesion separation distance used to define a cluster, and (iii) two distinct collections of physics models used to govern particle transport. Our complete TOPAS-nBio application has been released under an open-source license to enable others to independently validate our work and to expand upon it.

A bioelectric model of carcinogenesis, including propagation of cell membrane depolarization and reversal therapies

As the main theory of carcinogenesis, the Somatic Mutation Theory, increasingly presents difficulties to explain some experimental observations, different theories are being proposed. A major alternative approach is the Tissue Organization Field Theory, which explains cancer origin as a tissue regulation disease instead of having a mainly cellular origin. This work fits in the latter hypothesis, proposing the bioelectric field, in particular the cell membrane polarization state, and ionic exchange through ion channels and gap junctions, as an important mechanism of cell communication and tissue organization and regulation. Taking into account recent experimental results and proposed bioelectric models, a computational model of cancer initiation was developed, including the propagation of a cell depolarization wave in the tissue under consideration. Cell depolarization leads to a change in its state, with the activation and deactivation of several regulation pathways, increasing cell proliferation and motility, changing its epigenetic state to a more stem cell-like behavior without the requirement of genomic mutation. The intercellular communication via gap junctions leads, in certain circumstances, to a bioelectric state propagation to neighbor cells, in a chain-like reaction, till an electric discontinuity is reached. However, this is a reversible process, and it was shown experimentally that, by implementing a therapy targeted on cell ion exchange channels, it is possible to reverse the state and repolarize cells. This mechanism can be an important alternative way in cancer prevention, diagnosis and therapy, and new experiments are proposed to test the presented hypothesis.

Cancer progression as a sequence of atavistic reversions

It has long been recognized that cancer onset and progression represent a type of reversion to an ancestral quasi-unicellular phenotype. This general concept has been refined into the atavistic model of cancer that attempts to provide a quantitative analysis and testable predictions based on genomic data. Over the past decade, support for the multicellular-to-unicellular reversion predicted by the atavism model has come from phylostratigraphy. Here, we propose that cancer onset and progression involve more than a one-off multicellular-to-unicellular reversion, and are better described as a series of reversionary transitions. We make new predictions based on the chronology of the unicellular-eukaryote-to-multicellular-eukaryote transition. We also make new predictions based on three other evolutionary transitions that occurred in our lineage: eukaryogenesis, oxidative phosphorylation and the transition to adaptive immunity. We propose several modifications to current phylostratigraphy to improve age resolution to test these predictions. Also see the video abstract here: https://youtu.be/3unEu5JYJrQ.

Evaluating the Predictability of Cancer Types from 536 Somatic Mutations: A New Dataset

In this paper, we introduce a new dataset for cancer research containing somatic mutation states of 536 genes of the Cancer Gene Census (CGC). We used somatic mutation information from the Cancer Genome Atlas (TCGA) projects to create this dataset. As preliminary investigations, we employed machine learning techniques, including k-Nearest Neighbors, Decision Tree, Random Forest, and Artificial Neural Networks (ANNs) to evaluate the potential of these somatic mutations for classification of cancer types. We compared our models on accuracy, precision, recall, and F1-score. We observed that ANNs outperformed the other models with F1-score of 0.36 and overall classification accuracy of 40%, and precision ranging from 12% to 92% for different cancer types. The 40% accuracy is significantly higher than random guessing which would have resulted in 3% overall classification accuracy. Although the model has relatively low overall accuracy, it has an average classification specificity of 98%. The ANN achieved high precision scores (> 0.7) for 5 of the 33 cancer types. The introduced dataset can be used for research on TCGA data, such as survival analysis, histopathology image analysis and content-based image retrieval. The dataset is available online for download: https://kimialab.uwaterloo.ca/kimia/.

The Biophysics of Regenerative Repair Suggests New Perspectives on Biological Causation

Evolution exploits the physics of non-neural bioelectricity to implement anatomical homeostasis: a process in which embryonic patterning, remodeling, and regeneration achieve invariant anatomical outcomes despite external interventions. Linear "developmental pathways" are often inadequate explanations for dynamic large-scale pattern regulation, even when they accurately capture relationships between molecular components. Biophysical and computational aspects of collective cell activity toward a target morphology reveal interesting aspects of causation in biology. This is critical not only for unraveling evolutionary and developmental events, but also for the design of effective strategies for biomedical intervention. Bioelectrical controls of growth and form, including stochastic behavior in such circuits, highlight the need for the formulation of nuanced views of pathways, drivers of system-level outcomes, and modularity, borrowing from concepts in related disciplines such as cybernetics, control theory, computational neuroscience, and information theory. This approach has numerous practical implications for basic research and for applications in regenerative medicine and synthetic bioengineering.

Cell Reversal From a Differentiated to a Stem-Like State at Cancer Initiation

Even if the Somatic Mutation Theory of carcinogenesis explains many of the relevant experimental results in tumor origin and development, there are frequent events that are not justified, or are even contradictory to this widely accepted theory. A Cell Reversal Theory is presented, putting forward the hypothesis that cancer is originated by reversal of a differentiated cell into a non-differentiated stem-like state, by a change of its intrinsic epigenetic state, following a perturbation on the cell and/or its microenvironment. In the current proposal a cluster of cancer stem cells can be established, without the strict control mechanisms of a normal stem cell niche, and initiate a tumor. It is proposed that a reversal to a pluripotent state is at tumor origin and not tumor progress that prompts cell dedifferentiation. The uncontrolled proliferation of cancer stem cells causes a microenvironment disorganization, resulting in stressful conditions, like hypoxia and nutrient deprivation, which induces the genetic instability characteristic of a tumor; thus, in most cases, mutations are a consequence and not the direct cause of a tumor. It is also proposed that metastases result from dedifferentiation signaling dispersion instead of cell migration. However, conceivably, once the microenvironment is normalized, the stem cell-like state can differentiate back to a mature cell state and loose its oncogenic capacity. Therefore, this can be a reversible condition, suggesting important therapeutic opportunities.

Conversion of Stem Cells to Cancer Stem Cells: Undercurrent of Cancer Initiation

Cancer stem cells (CSCs) also known as cancer-initiating cells (CIC), are responsible for the sustained and uncontrolled growth of malignant tumors and are proposed to play significant roles in metastasis and recurrence. Several hypotheses have proposed that the events in either stem and/or differentiated cells, such as genomic instability, inflammatory microenvironment, cell fusion, and lateral gene transfer, should be considered as the possible origin of CSCs. However, until now, the exact origin of CSC has been obscure. The development of induced pluripotent stem cells (iPSCs) in 2007, by Yamanaka's group, has been met with much fervency and hailed as a breakthrough discovery by the scientific and research communities, especially in regeneration therapy. The studies on the development of CSC from iPSCs should also open a new page of cancer research, which will help in designing new therapies applicable to CSCs. Currently most reviews have focused on CSCs and CSC niches. However, the insight into the niche before the CSC niche should also be of keen interest. This review introduces the novel concept of cancer initiation introducing the conversion of iPSCs to CSCs and proposes a relationship between the inflammatory microenvironment and cancer initiation as the key concept of the cancer-inducing niche responsible for the development of CSC.

Aging is an adaptation that selects in animals against disruption of homeostasis

During evolution, Muller's ratchet permanently generates deleterious germline mutations that eventually must be defused by selection. It seems widely held that cancer and aging-related diseases (ARDs) cannot contribute to this germline gene selection because they tail reproduction and thus occur too late, at the end of the life cycle. Here we posit however that by lessening the offspring's survival by proxy through diminishing parental care, they can still contribute to the selection. The hypothesis in detail: The widespread occurrence of aging in animals suggests that it is an adaptation. But to what benefit? Aging seems to have only drawbacks. In humans, ARDs cause today almost all mortality; they include heart disease, cerebrovascular disease, Alzheimer's disease, kidney disease and cancer. Compensation seems unthinkable. For cancer, the author proposed in a previous study a benefit to the species: purifying selection against deleterious germline genes that when expressed enhance intracellular energy dissipation. This multicausal energy dissipation, posited as the universal origin of cancer initiation, relates to cellular heat generation, disrupted metabolism, and inflammation. The organism reproduces during cancer's dormancy, and when approaching its end of life, the onset of cancer is accelerated in proportion to the cancer-initiating signal. Through cancer, the organism, now a parent, implements the self-actuated programmed death of Skulachev's phenoptosis. This "first death" enhances by proxy the offspring's chance of "second death" (or "double death") through diminished parental care. Repetition over generations realizes a purifying selection against genes causing energy dissipation. The removal of the deleterious germline gene mutations permanently generated by Muller's ratchet gives a benefit. We generalize, motivated by the parallels between cancer and aging, the purifying selection posited for cancer to aging. An ARD would be initiated in the organ by multicausal disruption of homeostasis, and be followed by dormancy and senescence until its onset near the end of the life cycle. Just as for cancer, the ARD eventually enhances double death, and the realized permanent selection gives a benefit to the species through the selection against germ line genes that disrupt homeostasis. Given their similarities, cancer and aging are combined in the posited Unified Cancer-Aging Adaptation (UCAA) model, which may be confirmed by next-generation sequencing data. Also because of the emerging important role of cellular senescence, the hypothesis may guide the development of therapies against both cancer and aging.

A Postgenomic Perspective on Molecular Cytogenetics

BACKGROUND

The postgenomic era is featured by massive data collection and analyses from various large scale-omics studies. Despite the promising capability of systems biology and bioinformatics to handle large data sets, data interpretation, especially the translation of -omics data into clinical implications, has been challenging.

DISCUSSION

In this perspective, some important conceptual and technological limitations of current systems biology are discussed in the context of the ultimate importance of the genome beyond the collection of all genes. Following a brief summary of the contributions of molecular cytogenetics/cytogenomics in the pre- and post-genomic eras, new challenges for postgenomic research are discussed. Such discussion leads to a call to search for a new conceptual framework and holistic methodologies.

CONCLUSION

Throughout this synthesis, the genome theory of somatic cell evolution is highlighted in contrast to gene theory, which ignores the karyotype-mediated higher level of genetic information. Since "system inheritance" is defined by the genome context (gene content and genomic topology) while "parts inheritance" is defined by genes/epigenes, molecular cytogenetics and cytogenomics (which directly study genome structure, function, alteration and evolution) will play important roles in this postgenomic era.

Cancer etiology: Variation in cancer risk among tissues is poorly explained by the number of gene mutations

Recent evidence indicates that the risk of being diagnosed with cancer in a tissue is strongly correlated (0.80) with the number of stem cell divisions accumulated by the tissue. Since cell division can generate random mutations during DNA replication, this correlation has been used to propose that cancer is largely caused by the accumulation of unavoidable mutations in driver genes. However, no correlation between the number of gene mutations and cancer risk across tissues has been reported. Because many somatic mutations in cancers originate prior to tumor initiation and the number of cell divisions occurring during tumor growth is similar among tissues, I use whole genome sequencing information from 22 086 cancer samples and incidence data from the largest cancer registry in each continent to study the relationship between the number of gene mutations and the risk of cancer across 33 tissue types. Results show a weak positive correlation (mean = 0.14) between these 2 parameters in each of the 5 cancer registries. The correlation became stronger (mean = 0.50) when gender-related cancers were excluded. Results also show that 1003 samples from 29 cancer types have zero mutations in genes. These data suggest that cancer etiology can be better explained by the accumulation of stem cell divisions than by the accumulation of gene mutations. Possible mechanisms by which the accumulation of cell divisions in stem cells increases the risk of cancer are discussed.

Cancer-associated fibroblasts in tumor microenvironment - Accomplices in tumor malignancy

There is much cellular heterogeneity in the tumor microenvironment. The tumor epithelia and stromal cells co-evolve, and this reciprocal relationship dictates almost every step of cancer development and progression. Despite this, many anticancer therapies are designed around druggable features of tumor epithelia, ignoring the supportive role of stromal cells. Cancer-associated fibroblasts (CAFs) are the dominant cell type within the reactive stroma of many tumor types. Numerous previous studies have highlighted a pro-tumorigenic role for CAFs via secretion of various growth factors, cytokines, chemokines, and the degradation of extracellular matrix. Recent works showed that CAFs secrete H₂O₂ to effect stromal-mediated field cancerization, transform primary epithelial cells, and aggravate cancer cell aggressiveness, in addition to inflammatory and mitogenic factors. Molecular characterization of CAFs also underscores the importance of Notch and specific nuclear receptor signaling in the activation of CAFs. This review consolidates recent findings of CAFs and highlights areas for future investigations.

Mutations, evolution and the central role of a self-defined fitness function in the initiation and progression of cancer

The origin and progression of cancer is widely viewed as "somatic evolution" driven by the accumulation of random genetic changes. This theoretical model, however, neglects fundamental conditions for evolution by natural selection, which include competition for survival and a local environmental context. Recent observations that the mutational burden in different cancers can vary by 2 orders of magnitude and that multiple mutations, some of which are "oncogenic," are observed in normal tissue suggests these neglected Darwinian dynamics may play a critical role in modifying the evolutionary consequences of molecular events. Here we discuss evolutionary principles in normal tissue focusing on the dynamical tension between different evolutionary levels of selection. Normal somatic cells within metazoans do not ordinarily evolve because their survival and proliferation are governed by tissue signals and internal controls (e.g. telomere shortening) that maintain homeostatic function. The fitness of each cell is, thus, identical to the whole organism, which is the evolutionary level of selection. For a cell to evolve, it must acquire a self-defined fitness function so that its survival and proliferation is determined entirely by its own heritable phenotypic properties. Cells can develop independence from normal tissue control through randomly accumulating mutations that disrupt its ability to recognize or respond to all host signals. A self-defined fitness function can also be gained non-genetically when tissue control signals are lost due to injury, inflammation, or infection. Accumulating mutations in cells without a self-defined fitness function will produce no evolution - consistent with reports showing mutations, including some that would ordinarily be oncogenic, are present in cells from normal tissue. Furthermore, once evolution begins, Darwinian forces will promote mutations that increase fitness and eliminate those that do not. Thus, cancer cells will typically have a mutational burden similar to adjacent normal cells and many (perhaps most) mutations observed in cancer cells occurred prior to somatic evolution and may not contribute to the cell's malignant phenotype. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.

Changing mutational and adaptive landscapes and the genesis of cancer

By the time the process of oncogenesis has produced an advanced cancer, tumor cells have undergone extensive evolution. The cellular phenotypes resulting from this evolution have been well studied, and include accelerated growth rates, apoptosis resistance, immortality, invasiveness, and immune evasion. Yet with all of our current knowledge of tumor biology, the details of early oncogenesis have been difficult to observe and understand. Where different oncogenic mutations may work together to enhance the survival of a tumor cell, in isolation they are often pro-apoptotic, pro-differentiative or pro-senescent, and therefore often, somewhat paradoxically, disadvantageous to a cell. It is also becoming clear that somatic mutations, including those in known oncogenic drivers, are common in tissues starting at a young age. These observations raise the question: how do we largely avoid cancer for most of our lives? Here we propose that evolutionary forces can help explain this paradox. As humans and other organisms age or experience external insults such as radiation or smoking, the structure and function of tissues progressively degrade, resulting in altered stem cell niche microenvironments. As tissue integrity declines, it becomes less capable of supporting and maintaining resident stem cells. These stem cells then find themselves in a microenvironment to which they are poorly adapted, providing a competitive advantage to those cells that can restore their functionality and fitness through mutations or epigenetic changes. The resulting oncogenic clonal expansions then increase the odds of further cancer progression. Understanding how the causes of cancer, such as aging or smoking, affect tissue microenvironments to control the impact of mutations on somatic cell fitness can help reconcile the discrepancy between marked mutation accumulation starting early in life and the somatic evolution that leads to cancer at advanced ages or following carcinogenic insults. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.

Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape

The observed intercellular heterogeneity within a clonal cell population can be mapped as dynamical states clustered around an attractor point in gene expression space, owing to a balance between homeostatic forces and stochastic fluctuations. These dynamics have led to the cancer cell attractor conceptual model, with implications for both carcinogenesis and new therapeutic concepts. Immortalized and malignant EBV-carrying B-cell lines were used to explore this model and characterize the detailed structure of cell attractors. Any subpopulation selected from a population of cells repopulated the whole original basin of attraction within days to weeks. Cells at the basin edges were unstable and prone to apoptosis. Cells continuously changed states within their own attractor, thus driving the repopulation, as shown by fluorescent dye tracing. Perturbations of key regulatory genes induced a jump to a nearby attractor. Using the Fokker-Planck equation, this cell population behavior could be described as two virtual, opposing influences on the cells: one attracting toward the center and the other promoting diffusion in state space (noise). Transcriptome analysis suggests that these forces result from high-dimensional dynamics of the gene regulatory network. We propose that they can be generalized to all cancer cell populations and represent intrinsic behaviors of tumors, offering a previously unidentified characteristic for studying cancer.

SMT or TOFT? How the two main theories of carcinogenesis are made (artificially) incompatible

The building of a global model of carcinogenesis is one of modern biology's greatest challenges. The traditional somatic mutation theory (SMT) is now supplemented by a new approach, called the Tissue Organization Field Theory (TOFT). According to TOFT, the original source of cancer is loss of tissue organization rather than genetic mutations. In this paper, we study the argumentative strategy used by the advocates of TOFT to impose their view. In particular, we criticize their claim of incompatibility used to justify the necessity to definitively reject SMT. First, we note that since it is difficult to build a non-ambiguous experimental demonstration of the superiority of TOFT, its partisans add epistemological and metaphysical arguments to the debate. This argumentative strategy allows them to defend the necessity of a paradigm shift, with TOFT superseding SMT. To do so, they introduce a notion of incompatibility, which they actually use as the Kuhnian notion of incommensurability. To justify this so-called incompatibility between the two theories of cancer, they move the debate to a metaphysical ground by assimilating the controversy to a fundamental opposition between reductionism and organicism. We show here that this argumentative strategy is specious, because it does not demonstrate clearly that TOFT is an organicist theory. Since it shares with SMT its vocabulary, its ontology and its methodology, it appears that a claim of incompatibility based on this metaphysical plan is not fully justified in the present state of the debate. We conclude that it is more cogent to argue that the two theories are compatible, both biologically and metaphysically. We propose to consider that TOFT and SMT describe two distinct and compatible causal pathways to carcinogenesis. This view is coherent with the existence of integrative approaches, and suggests that they have a higher epistemic value than the two theories taken separately.

Reasons for cancer metastasis: A holistic perspective

Over several years, scientists investigating cancer have focused their efforts on elucidating the mechanisms underlying cancer metastasis, with the aim of finding a way to inhibit this process. These mechanisms, however, only explain the process of cancer metastasis, but do not explain why cancer would metastasize in the first place. Cancer metastasizes due to several factors, namely attack by the immune system, lack of oxygen and necessary nutrients, large amounts of lactic acid produced by glycolysis and increased cell death. Therefore, the majority of the presently available treatments for cancer also bear the potential to induce metastasis. Thus, it is crucial in medical practice to minimize the risk of cancer metastasis during a time when there are no effective means to inhibit this process.

Cancer as a mitochondrial metabolic disease

Cancer is widely considered a genetic disease involving nuclear mutations in oncogenes and tumor suppressor genes. This view persists despite the numerous inconsistencies associated with the somatic mutation theory. In contrast to the somatic mutation theory, emerging evidence suggests that cancer is a mitochondrial metabolic disease, according to the original theory of Otto Warburg. The findings are reviewed from nuclear cytoplasm transfer experiments that relate to the origin of cancer. The evidence from these experiments is difficult to reconcile with the somatic mutation theory, but is consistent with the notion that cancer is primarily a mitochondrial metabolic disease.

Low-fidelity compensatory backup alternative DNA repair pathways may unify current carcinogenesis theories

The somatic mutation carcinogenesis theory has dominated for decades. The alternative theory, tissue organization field theory, argues that the development of cancer is determined by the surrounding microenvironment. However, neither theory can explain all features of cancer. As cancers share the features of uncontrolled proliferation and genomic instability, they are likely to have the same pathogenesis. It has been found that various DNA repair pathways within a cell crosstalk with one another, forming a DNA repair network. When one DNA repair pathways is defective, the others may work as compensatory backups. The latter pathways are explored for synthetic lethal anticancer therapy. In this article, we extend the concept of compensatory alternative DNA repair to unify the theories. We propose that the microenvironmental stress can activate low-fidelity compensatory alternative DNA repair, causing mutations. If the mutation occurs to a DNA repair gene, this secondarily mutated gene can lead to even more mutated genes, including those related to other DNA repair pathways, eventually destabilizing the genome. Therefore, the low-fidelity compensatory alternative DNA repair may mediate microenvironment-dependent carcinogenesis. The proposal seems consistent with the view of evolution: the environmental stress causes mutations to adapt to the changing environment.

A novel pathogenic classification of cancers

According to contemporary epidemiological and experimental evidence, we propose a novel classification of cancers based on pathogenesis instead of classifications based on histological appearance of cancer. This new scheme first defines cancers as either 1. inborn errors of development or 2. sporadic ones, and then sub-defines the former into 1A. inborn inherited errors of development, being those due to mutations contributed by one or both parents' gametes to the developing conceptus, and 1B. inborn induced errors of development when the malformations and/or cancers are due to environmental carcinogenic exposure during pregnancy. It is anticipated that the origin of an increasing number of so-called sporadic cancers will turn out to be linked to the inborn induced errors of development group.

IGF-IR mediated mammary tumorigenesis is enhanced during pubertal development

Although breast cancer typically develops in women over the age of 40, it remains unclear when breast cancer initiating events occur or whether the mammary gland is particularly susceptible to oncogenic transformation at a particular developmental stage. Using MTB-IGFIR transgenic mice that overexpress type I insulin-like growth factor receptor (IGF-IR) in a doxycycline-inducible manner, mammary tumorigenesis was initiated at different developmental stages. Tumor multiplicity was significantly increased while tumor latency was significantly decreased when the IGF-IR transgene was expressed during pubertal development compared to post-pubertal transgene expression. Moreover, metastatic spread of mammary tumors to the lungs was approximately twice as likely when IGF-IR was overexpressed in pubertal mice compared to post-pubertal mice. In addition, engraftment of pubertal MTB-IGFIR mammary tissue into cleared mammary fat pads of pubertal hosts produced tumors more frequently and faster than engraftment into adult hosts. These experiments show that the mammary microenvironment created during puberty renders mammary epithelial cells particularly susceptible to transformation.

Are GATA1 mutations occurring at random in Down syndrome transient leukemia?

The somatic mutation theory of cancer proposes that cancer begins with a somatic mutation occurring at random in a single cell that then passes the mutation to its progeny, generating a clone of premalignant cells. This clone leads to a full malignant tumor through additional mutations and selection processes. Strikingly, the best-documented human model of early oncogenesis, i.e., transient myeloproliferative disorder followed by acute megakaryoblastic leukemia (AMKL) in infants with Down syndrome (DS, or trisomy 21), exhibits important discrepancies with the SMT. Somatic mutations in megakaryocytic precursors occur at least 100,000 times more frequently in the GATA1 gene in fetuses with DS compared to the general population. Further, mutations are limited to GATA1 only; the general mutation rate does not significantly differ between individuals with DS and euploid individuals. Importantly, the mutations are also lineage-specific, occurring only in the megakaryocytic lineage, and proliferative anomalies of the megakaryocytic lineage are observed before the occurrence of GATA1 mutations. Thus, GATA1 mutations in fetuses with DS cannot be random events occurring in normal cells. Here, transcription-associated mutagenesis is proposed as the mechanism by which the earliest mutations of AMKL occur in DS. Transcription-associated mutagenesis is observed in non-dividing cells when a gene is over-expressed. The over-expression of GATA1 in the megakaryocytic lineage in DS fetal liver cells is proposed to be the cause of targeted GATA1 somatic mutations. As transcription-associated mutagenesis is a universal process, this mechanism may also apply to early oncogenesis in other situations, including after birth and following exposure to a carcinogenic agent. Thus, this hypothesis represents a new avenue for understanding and exploring oncogenesis in the context of DS and in other disease states.

Competing views on cancer

Despite intense research efforts that have provided enormous insight, cancer continues to be a poorly understood disease. There has been much debate over whether the cancerous state can be said to originate in a single cell or whether it is a reflection of aberrant behaviour on the part of a 'society of cells'. This article presents, in the form of a debate conducted among the authors, three views of how the problem might be addressed. We do not claim that the views exhaust all possibilities. These views are (a) the tissue organization field theory (TOFT) that is based on a breakdown of tissue organization involving many cells from different embryological layers, (b) the cancer stem cell (CSC) hypothesis that focuses on genetic and epigenetic changes that take place within single cells, and (c) the proposition that rewiring of the cell's protein interaction networks mediated by intrinsically disordered proteins (IDPs) drives the tumorigenic process. The views are based on different philosophical approaches. In detail, they differ on some points and agree on others. It is left to the reader to decide whether one approach to understanding cancer appears more promising than the other.

Mammary stroma in development and carcinogenesis

Mammary glands of adult human females are secretory organs comprised of interdependent epithelial and mesenchymal cells. These cells constitute an assemblage of collecting ducts that end in terminal duct lobular units with hollow alveolar ductules that can differentiate to produce and expel milk. Systemic and maternal hormones, autocrine and paracrine growth factors, and cytokines regulate virtually all phases of mammary gland development. During organogenesis, epithelial and mesenchymal cells interact to form precursors of the parenchyma and stroma in the mature gland. Organogenesis precedes five stages of postnatal development: puberty, pregnancy, lactation, involution, and menopause. Each stage requires a specific set of morphogenetic changes in glandular structure and function. Cycles of cell proliferation, differentiation, and involution may recur until menopause. In addition, physiological responses such as inflammation and pathological events such as tumorigenesis are remarkable for their similarities to embryonic morphogenesis. Here we take a succinct look at the ever-improving understanding of stroma-epithelial interactions and mesenchyme function in mammary gland biology.

Does cancer start in the womb? altered mammary gland development and predisposition to breast cancer due to in utero exposure to endocrine disruptors

We are now witnessing a resurgence of theories of development and carcinogenesis in which the environment is again being accepted as a major player in phenotype determination. Perturbations in the fetal environment predispose an individual to disease that only becomes apparent in adulthood. For example, gestational exposure to diethylstilbestrol resulted in clear cell carcinoma of the vagina and breast cancer. In this review the effects of the endocrine disruptor bisphenol-A (BPA) on mammary development and tumorigenesis in rodents is used as a paradigmatic example of how altered prenatal mammary development may lead to breast cancer in humans who are also widely exposed to it through plastic goods, food and drink packaging, and thermal paper receipts. Changes in the stroma and its extracellular matrix led to altered ductal morphogenesis. Additionally, gestational and lactational exposure to BPA increased the sensitivity of rats and mice to mammotropic hormones during puberty and beyond, thus suggesting a plausible explanation for the increased incidence of breast cancer.

Suppression of error prone pathway is responsible for antimutagenic activity of honey

Honey, both unifloral (Syzygiumcumini) and bifloral, demonstrated strong antimutagenicity against physical (UV, γ) and chemical (ethylmethane sulfonate) mutagens as ascertained by rpoB/RifR and Ames tests. The effect of honey was evaluated in radiation (UV or γ) exposed Escherichia coli cells for SOS response, a well known error prone repair pathway known to significantly contribute to mutagenicity by quantifying LexA repressor level, measuring cell filamentation frequency, and prophage induction by SIVET (Selectable--In-Vivo Expression Technology) assay. LexA was almost completely degraded, phenotypically long filamentous cells (∼30 μm) were formed, and SIVET induction frequency was increased in radiation exposed E. coli cultures, however, these changes were significantly inhibited in presence of honey confirming its strong antimutagenic nature. Further, rpoB/RifR mutation frequency upon UV exposure in E. coli recA- cells was found to be negligible, whereas, E. coliumuC- and umuD- knockouts showed comparatively higher mutation frequency. Honey did not show any effect on mutagenesis in these knockouts, indicating the SOS dependence of the observed mutagenesis. Honey was also found to suppress EMS induced mutagenesis but through SOS independent mechanism. Phenolics present in honey were found to be one of the important factors contributing to the antimutagenicity of honey.