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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Oncol.</journal-id>
<journal-title>Frontiers in Oncology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Oncol.</abbrev-journal-title>
<issn pub-type="epub">2234-943X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fonc.2021.732081</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Oncology</subject>
<subj-group>
<subject>Hypothesis and Theory</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Bridging Tumorigenesis and Therapy Resistance With a Non-Darwinian and Non-Lamarckian Mechanism of Adaptive Evolution</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Catania</surname>
<given-names>Francesco</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/355680"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ujvari</surname>
<given-names>Beata</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1134390"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Roche</surname>
<given-names>Benjamin</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/416044"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Capp</surname>
<given-names>Jean-Pascal</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/564011"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Thomas</surname>
<given-names>Fr&#xe9;d&#xe9;ric</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>Institute for Evolution and Biodiversity, University of M&#xfc;nster</institution>, <addr-line>M&#xfc;nster</addr-line>, <country>Germany</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University</institution>, <addr-line>Deakin, VIC</addr-line>, <country>Australia</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>CREEC/CANECEV, MIVEGEC (CREES), Centre de Recherches Ecologiques et Evolutives sur le Cancer, University of Montpellier, CNRS</institution>, <addr-line>IRD, Montpellier</addr-line>, <country>France</country>
</aff>
<aff id="aff4">
<sup>4</sup>
<institution>Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS</institution>, <addr-line>INRAE, Toulouse</addr-line>, <country>France</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Chang Zou, Jinan University, China</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Lorenza Putignani, Bambino Ges&#xf9; Children Hospital (IRCCS), Italy; Irina Kareva, EMD Serono, United States</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Francesco Catania, <email xlink:href="mailto:francesco.catania@uni-muenster.de">francesco.catania@uni-muenster.de</email> </p>
</fn>
<fn fn-type="other" id="fn002">
<p>This article was submitted to Molecular and Cellular Oncology, a section of the journal Frontiers in Oncology</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>10</day>
<month>09</month>
<year>2021</year>
</pub-date>
<pub-date pub-type="collection">
<year>2021</year>
</pub-date>
<volume>11</volume>
<elocation-id>732081</elocation-id>
<history>
<date date-type="received">
<day>28</day>
<month>06</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>25</day>
<month>08</month>
<year>2021</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2021 Catania, Ujvari, Roche, Capp and Thomas</copyright-statement>
<copyright-year>2021</copyright-year>
<copyright-holder>Catania, Ujvari, Roche, Capp and Thomas</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>Although neo-Darwinian (and less often Lamarckian) dynamics are regularly invoked to interpret cancer&#x2019;s multifarious molecular profiles, they shine little light on how tumorigenesis unfolds and often fail to fully capture the frequency and breadth of resistance mechanisms. This uncertainty frames one of the most problematic gaps between science and practice in modern times. Here, we offer a theory of adaptive cancer evolution, which builds on a molecular mechanism that lies outside neo-Darwinian and Lamarckian schemes. This mechanism coherently integrates non-genetic and genetic changes, ecological and evolutionary time scales, and shifts the spotlight away from positive selection towards purifying selection, genetic drift, and the creative-disruptive power of environmental change. The surprisingly simple <italic>use-it</italic> or <italic>lose-it</italic> rationale of the proposed theory can help predict molecular dynamics during tumorigenesis. It also provides simple rules of thumb that should help improve therapeutic approaches in cancer.</p>
</abstract>
<kwd-group>
<kwd>tumor evolution</kwd>
<kwd>adaptation</kwd>
<kwd>cell growth</kwd>
<kwd>stress response</kwd>
<kwd>natural selection</kwd>
<kwd>environment</kwd>
<kwd>cancer therapy</kwd>
</kwd-group>
<counts>
<fig-count count="1"/>
<table-count count="1"/>
<equation-count count="0"/>
<ref-count count="235"/>
<page-count count="15"/>
<word-count count="6948"/>
</counts>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>
<p>Cancer cells are often thought of as a pile of aberrant genetic variants, hence the prevailing view of cancer as a genetic disease (<xref ref-type="bibr" rid="B1">1</xref>). However, cancer is also &#x2014; and first of all &#x2014; an adaptation to its microenvironment with a strong non-genetic component (<xref ref-type="bibr" rid="B2">2</xref>&#x2013;<xref ref-type="bibr" rid="B10">10</xref>). Transcriptional plasticity and epigenetic heterogeneity are increasingly recognized as major players in the ability of cancer cells to evade therapies (<xref ref-type="bibr" rid="B11">11</xref>&#x2013;<xref ref-type="bibr" rid="B19">19</xref>). This growing body of evidence revises the view of mutations as sole or principal drivers of drug resistance (<xref ref-type="bibr" rid="B20">20</xref>&#x2013;<xref ref-type="bibr" rid="B26">26</xref>), and offers more than an additional perspective on an old problem. It implies that interpreting therapeutic resistance as an unambiguous indicator of selection of random beneficial mutations may be inaccurate. This potential inaccuracy may have direct and serious consequences for cancer patients. Moreover, as it is possible that the adaptive dynamics that foster therapeutic resistance also unfold during tumorigenesis, it calls for a more cautious interpretation of previous findings related to cancer initiation and progression.</p>
</sec>
<sec id="s2">
<title>The Problem</title>
<p>Although non-genetic resistance to chemotherapy/target-selective drugs appears to be pervasive in cancer cells, the molecular mechanisms that drive this resistance are yet incompletely understood (<xref ref-type="bibr" rid="B12">12</xref>, <xref ref-type="bibr" rid="B27">27</xref>). Non-genetic resistance can be acquired by environmental induction, <italic>i.e.</italic>, drug-induced epigenetic reconfigurations can enhance cells&#x2019; survival to the very therapeutic environment (<xref ref-type="bibr" rid="B28">28</xref>, <xref ref-type="bibr" rid="B29">29</xref>). Alternatively, epigenetic configurations that are advantageous in the therapeutic environment may be pre-existing and undergo positive selection (<xref ref-type="bibr" rid="B30">30</xref>, <xref ref-type="bibr" rid="B31">31</xref>). Moreover, while resistance can be coupled with purely epigenetic or purely genetic changes, it is also possible that initially non-genetic changes become genetically hardwired/assimilated over time, <italic>i.e.</italic>, an environmentally induced phenotype is made constitutive (<xref ref-type="bibr" rid="B12">12</xref>, <xref ref-type="bibr" rid="B32">32</xref>, <xref ref-type="bibr" rid="B33">33</xref>). In sum, cancer populations can achieve drug resistance through genetic and/or non-genetic means and <italic>via</italic> a mix of neo-Darwinian and <italic>quasi</italic>-Lamarckian mechanisms of adaptive evolution (a fully Lamarckian scheme of adaptation would entail, <italic>inter alia</italic>, that environmental factors cause directed adaptive changes).</p>
<p>This wealth of possible paths to resistance is confusing and consequently not good news for the design of effective cancer therapies. On the positive side, several observations (<xref ref-type="bibr" rid="B27">27</xref>, <xref ref-type="bibr" rid="B34">34</xref>, <xref ref-type="bibr" rid="B35">35</xref>) indicate that mechanisms similar to those that drive therapeutic resistance in cancer cells may also drive adaptive phases during the poorly understood process of tumorigenesis. Thus, the insights gained in the context of therapeutic resistance may shine light on tumorigenesis and help reveal some general principles and/or deterministic dynamics (<xref ref-type="bibr" rid="B36">36</xref>), which can in turn contribute to the development of more effective cancer prevention. Here, we explore this possibility. More specifically, we ask two questions: Are there distinct intracellular mechanisms and simple evolutionary dynamics (not necessarily neo-Darwinian or Lamarckian), which can help explain the progression of events during oncogenic transformation? And if so, can these mechanisms/dynamics have clinical utility and general implications for cancer evolution and therapy? An empirically supported positive answer to these questions can be given when the dominant and deep-rooted neo-Darwinian (ND) model of adaptive evolution is bypassed.</p>
</sec>
<sec id="s3">
<title>A Short Overview of the Neo-Darwinian Model</title>
<p>The ND model is nearly universally invoked to explain how living beings adapt to their surroundings. In this model, which integrates Darwinian dynamics and Mendelian genetics, natural selection acts on spontaneous genetic mutations, favoring the spread of heritable variants that are advantageous in the prevailing conditions (<xref ref-type="bibr" rid="B37">37</xref>). Selectable genetic changes predate adaptation and chance plays a central role in the occurrence of genetic changes. The ND model is powerful: its implications are entrenched in modern thinking and far-reaching.</p>
<p>Against this background, it may come as no surprise that the ND model is also widely leveraged for explaining the genesis and the evolution of adaptive traits in cancer (<xref ref-type="bibr" rid="B21">21</xref>, <xref ref-type="bibr" rid="B38">38</xref>&#x2013;<xref ref-type="bibr" rid="B44">44</xref>). For example, positive selection is widely thought to promote recurring inactivating mutations in <italic>TP53</italic>, the most mutated gene across human cancer types (<xref ref-type="bibr" rid="B45">45</xref>). More generally, it is most often undisputed, let alone plausible, that accidental genomic variants that are advantageous in prevailing conditions drive adaptations of cancer cells to the tumor microenvironment and therapy resistance. The ND model serves as an evolutionary framework for cancer genomics studies to reconstruct clonal evolution: mutation and selection of new mutations that happen to be beneficial in the tumor microenvironment drive the expansion of subclones (<xref ref-type="bibr" rid="B46">46</xref>).</p>
<p>In the ND model, the speed of adaptation partly relies on the rate at which beneficial mutations appear, survive, and spread (<xref ref-type="bibr" rid="B47">47</xref>). As plausible as the fixation of beneficial mutations is, the chance of it happening may be miniscule (<xref ref-type="bibr" rid="B48">48</xref>). Beneficial (driver) mutations in cancer cells emerge and/or segregate in a context where most co-occurring (passenger) mutations are deleterious (<xref ref-type="bibr" rid="B44">44</xref>). Ubiquitous purifying selection is expected to most often purge these cells alongside possible beneficial mutations that frequently confer only a minimal selective advantage (<xref ref-type="bibr" rid="B49">49</xref>). Even when purifying selection is relaxed, the mere interaction of accruing deleterious mutations may facilitate adaptation (<xref ref-type="bibr" rid="B50">50</xref>, <xref ref-type="bibr" rid="B51">51</xref>). Finally, random genetic drift can lead to the fixation of deleterious mutations by sheer chance (<xref ref-type="bibr" rid="B52">52</xref>&#x2013;<xref ref-type="bibr" rid="B56">56</xref>), and this drift also limits the ability of selection to refine a phenotype (<xref ref-type="bibr" rid="B57">57</xref>). In short, it is certainly not a given that beneficial mutations, if present, spread and reach fixation. Consistent with this, no beneficial mutations followed by selective sweeps and clonal expansion were detected in recent cancer genomic studies (<xref ref-type="bibr" rid="B58">58</xref>, <xref ref-type="bibr" rid="B59">59</xref>). Besides, when driver genes are reported [<italic>e.g.,</italic> (<xref ref-type="bibr" rid="B60">60</xref>)], the evidence that these typically highly mutated genes are positively selected for (often inactivating) tumorigenesis-driving mutations does not rule out alternative explanations (see below and <xref ref-type="boxed-text" rid="box1">
<bold>Box 1</bold>
</xref>). More generally, although selection of beneficial mutations has for long time provided the primary mechanistic account for the origin of adaptive phenotypic traits (<xref ref-type="bibr" rid="B61">61</xref>, <xref ref-type="bibr" rid="B62">62</xref>), unambiguous cases of evolved adaptation driven by positive selection of both new rare beneficial mutations and standing genetic variation appear to be relatively rare (<xref ref-type="bibr" rid="B63">63</xref>) or unsubstantiated (<xref ref-type="bibr" rid="B64">64</xref>). In the majority of cases they rely largely or entirely on the statistical analysis of sequence data without a biological mechanism that underlay the presumed selection (<xref ref-type="bibr" rid="B65">65</xref>).</p>
<boxed-text id="box1" position="float">
<label>Box 1</label>
<title>Is dN/dS &gt; 1 irrefutable evidence for positive selection?</title>
<p>The <italic>use-it</italic> or <italic>lose-it</italic> model does not exclude that positive selection may play a role in evolutionary adaptation. At the same time, it offers a null hypothesis against which the explanatory power of the neo-Darwinian framework can be measured. Genes with cancer-associated mutations in healthy tissues are a valuable test bed for assessing the explanatory power of the <italic>use-it</italic> or <italic>lose-it</italic> model <italic>vs</italic>. the commonly assumed neo-Darwinian dynamics.</p>
<p>In healthy somatic tissues, genes that operate as cancer drivers have been reported to preferentially accrue mutations and to be under positive selection (dN/dS &gt; 1) (<xref ref-type="bibr" rid="B66">66</xref>). If dN/dS &gt; 1 is irrefutable evidence for positive selection, then this finding is in contradiction with the <italic>use-it</italic> or <italic>lose-it</italic> model, so we decided to reexamine it. In the <italic>use-it</italic> or <italic>lose-it</italic> model, the mutational enrichment of cancer driver genes in healthy somatic tissues suggests that healthy cells and cancer cells can experience similar microenvironmental conditions, as expected given that cancer cells originate from healthy cells. It also implies that cancer-inducing microenvironmental conditions can occur throughout the human body without necessarily giving rise to cancer but presumably increasing the risk of developing it (<xref ref-type="bibr" rid="B67">67</xref>). Finally, in the <italic>use-it</italic> or <italic>lose-it</italic> model the preferential accumulation of cancer mutations in healthy tissues flags relaxed purifying selection (rather than positive selection) in the presence of a cancer-inducing environment. It predicts that the somatic genes under focus should accumulate inactivating mutations and exhibit dN/dS values &#x2248; 1.</p>
<p>Interestingly, genes with cancer-associated mutations in healthy tissues do exhibit dN/dS values &#x2248; 1 when missense mutations are examined. dN/dS values &gt; 1 are only detected when inactivating mutations are considered (<xref ref-type="bibr" rid="B66">66</xref>). Thus, the putative signature of positive selection reported for cancer driver genes in healthy somatic tissues rests only on the preferential accrual of inactivating mutations, which is in line with the <italic>use-it</italic> or <italic>lose-it</italic> model. How about the dN/dS ratio &gt;1, which is interpreted as indicating the presence of beneficial mutations? According to the <italic>use-it</italic> or <italic>lose-it</italic> model, this interpretation may be inaccurate. In addition to previously reported problems with using the dN/dS metric as an unambiguous indicator of evolutionary adaptation (<xref ref-type="bibr" rid="B68">68</xref>&#x2013;<xref ref-type="bibr" rid="B70">70</xref>), a couple of remarks support this possibility. First, a focus on nonsense mutations can lead to an increased dN/dS ratio because termination codons are A + T rich, and in the human genome (as well as others) a mutational bias toward A + T has been found (<xref ref-type="bibr" rid="B71">71</xref>). Second, it is not clear how healthy cells, which lack a &#x201c;self-defined&#x201d; fitness (<xref ref-type="bibr" rid="B72">72</xref>), may benefit from selectively advantageous mutations. Back to the <italic>use-it</italic> or <italic>lose-it</italic> model, the inactivating mutations that accrue in cancer driver genes in healthy tissues are predicted to be effectively neutral because they <italic>follow</italic> the environmentally induced and epigenetically controlled manifestation of the adaptive (alternative) phenotype in the pre-tumor environment.</p>
</boxed-text>
<p>This raises a question that deserves careful consideration: does the ND model offer the only possible account for the evolution of adaptive traits? Shifting our focus on cancer, are there other equally viable mechanisms of adaptation, which could help explain how tumors emerge or therapy resistance is acquired (see also <xref ref-type="boxed-text" rid="box1">
<bold>Box 1</bold>
</xref>)? In a time where cancer is among the leading causes of death globally, an alternative or additional mechanism of adaptive evolution could offer new perspectives on how to interpret cancer genomic data and address cancer as a health problem. An additional and equally viable mechanism of adaptive evolution would also provide a null hypothesis against which the explanatory power of the ND model can be measured [reminiscent of the neutral theory of molecular evolution (<xref ref-type="bibr" rid="B73">73</xref>) and the mutational hazard hypothesis (<xref ref-type="bibr" rid="B74">74</xref>, <xref ref-type="bibr" rid="B75">75</xref>)].</p>
</sec>
<sec id="s4">
<title>A Mechanism of Adaptive Evolution Without Positive Selection</title>
<p>Like the ND model, a non-Darwinian model that describes how evolved adaptations may arise during tumorigenesis or in response to therapy should help explain and interpret a wide range of observations. Ideally, it should have several properties. For example, it should help integrate ubiquitous and well-established phenomena such as pleiotropy, plasticity, and trade-offs (<xref ref-type="bibr" rid="B76">76</xref>). Also, it should be explicit about the relative contribution of evolutionary forces in the onset of adaptations as well as the interaction between these forces and the environment [<italic>e.g.</italic>, surrounding tumor cells (<xref ref-type="bibr" rid="B77">77</xref>)]. Further, it should be able to integrate genetics and epigenetics, both of which play a central role in the emergence of cancer and cancer drug resistance [<italic>e.g.,</italic> (<xref ref-type="bibr" rid="B13">13</xref>)]. It should also generate testable hypotheses. Last, it should help make predictions.</p>
<p>An elegant non-Darwinian and non-Lamarckian mechanism that exhibits all of the foregoing properties has been previously proposed (<xref ref-type="bibr" rid="B78">78</xref>), and largely overlooked. Dubbed plasticity-relaxation-mutation, this mechanism builds on the idea that environmentally-induced traits may become genetically determined (or assimilated) (<xref ref-type="bibr" rid="B79">79</xref>&#x2013;<xref ref-type="bibr" rid="B83">83</xref>), and that phenotypic plasticity precedes the origin of evolutionary adaptations (<xref ref-type="bibr" rid="B84">84</xref>, <xref ref-type="bibr" rid="B85">85</xref>). The rationale of this mechanism is simple (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>). Let us imagine two alternative phenotypes (P<sub>A</sub> and P<sub>B</sub>), each of which is expressed in one of two different environments (E<sub>A</sub> and E<sub>B</sub>, respectively). An environmentally regulated genetic switch controls the expression of P<sub>A</sub> or P<sub>B</sub>. Lastly, P<sub>A</sub>-expressing organisms/cells in E<sub>A</sub> are assumed to exhibit a higher reproductive success relative to those expressing P<sub>B</sub> in E<sub>A</sub> (conversely, P<sub>B</sub> in E<sub>B</sub> has a higher fitness than P<sub>A</sub> in E<sub>B</sub>). In these circumstances, the expression of the phenotype P<sub>A</sub> in the environment E<sub>A</sub> shelters the molecular determinants of the alternative phenotype P<sub>B</sub> from purifying selection. Given a sufficiently long exposure to E<sub>A</sub>, the DNA sequences that underlay the unused phenotype P<sub>B</sub> may accrue silencing mutations, which can spread by random genetic drift. Thus, habitual exposure to an environment can promote the permanent expression of one phenotype while favoring the loss of the alternative phenotype alongside the inactivation of its molecular basis.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Graphic representation of the plasticity-relaxation-mutation model (Hughes, 2012) and its expanded version (this study). <bold>(A)</bold> A genetic switch controls the expression of two alternate pathways (a, b) leading, respectively, to two alternate phenotypes (a, b) in response to two different environments (a, b). When environment A is no longer encountered by the organism/cell, there is no longer purifying selection against mutations that eliminate pathway a (modified after Hughes, 2012). <bold>(B)</bold> If phenotype A and phenotype B are antagonistically regulated, then the negative molecular regulators of the disfavored phenotype A are redundant and preferentially accumulate mutations. The positive regulators of the adaptive phenotype B are highly expressed, and their copy number may increase as a result of intracellular processes.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fonc-11-732081-g001.tif"/>
</fig>
<p>The explanatory power of the plasticity-relaxation-mutation mechanism ( (<xref ref-type="bibr" rid="B78">78</xref>) and below) may be further expanded when the genetic switch is explicitly treated as non-binary (<italic>i.e.</italic>, a continuum of states) and the regulation of the phenotypes is unpacked (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>). In an environment (E<sub>A</sub>) where P<sub>A</sub> is favored and the alternative P<sub>B</sub> is disfavored/unused (with P<sub>A</sub> and P<sub>B</sub> being antagonistically regulated), the positive regulators of P<sub>B</sub> are downregulated. In these circumstances, the persistent nonuse of P<sub>B</sub> in E<sub>A</sub> renders P<sub>B</sub>&#x2019;s negative regulators redundant and hence vulnerable to inactivating mutations. Thus, the negative regulators of a phenotype that is disfavored/unused in a habitual environment are likely to be the first molecular components to be taken out of action by silencing mutations. On the other hand, the persistent up-regulation of P<sub>A</sub>&#x2019;s positive regulators in the environment E<sub>A</sub> may favor their sequence amplification <italic>via</italic> physiological intracellular mechanisms (see below). Hence, the positive regulators of a phenotype that is favored in a habitual environment are the most likely to accrue copy number variants. Finally, the molecular inactivation of a disfavored/unused phenotype could have surprisingly wide phenotypic effects. Besides being viewed as individual traits, the alternative phenotypes, P<sub>A</sub> and P<sub>B</sub>, may each be viewed also as a collection of traits, which were molecularly linked over evolutionary time because of the selective advantage conferred by their functional integration. If so, mutations that inactivate even one or a few components of the molecular basis of, say, P<sub>B</sub> in E<sub>A</sub> can at once impact the expression of multiple linked traits.</p>
<p>In sum, the dynamics proposed by the plasticity-relaxation-mutation mechanism support a <italic>use-it</italic> or <italic>lose-it</italic> model where genes/pathways that are persistently not used in an environment culminate in being permanently silenced and possibly physically lost (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>). In contrast, the genes that are activated in a habitual environment and underlie the favored (adaptive) phenotype can experience amplification, which could be seen as a <italic>use-it</italic> and <italic>improve-it</italic> dynamic. In this model, relaxed purifying selection together with random genetic drift and effectively neutral or nearly neutral mutations play a central role in the adaptive reconfiguration of genomes and phenotypic (individual or integrated) traits.</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Putative mechanisms responsible for the origin of evolved adaptations.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">Theory of evolution</th>
<th valign="top" align="center">Mechanism of adaptation</th>
<th valign="top" align="center">Driving factor</th>
<th valign="top" align="center">Predictions (sample)</th>
<th valign="top" align="center">Refs</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">
<bold>
<italic>Neo-Darwinism</italic>
</bold>
</td>
<td valign="top" align="left">Natural selection acts on heritable variability that originates through accidental changes in the genetic material.</td>
<td valign="top" align="left">Positive Selection, Mutation</td>
<td valign="top" align="left">
<list list-type="bullet">
<list-item>
<p>Positive selection is necessary for evolutionary adaptation.</p>
</list-item>
<list-item>
<p>DNA sequence contributes more to adaptive evolution than epigenetic variants.</p>
</list-item>
<list-item>
<p>Mutational trajectories are not influenced by the environment.</p>
</list-item>
<list-item>
<p>Adaptive phenotypes are usually built up by a series of relatively small changes.</p>
</list-item>
<list-item>
<p>The frequency of potentially advantageous genetic mutations is extremely low.</p>
</list-item>
<list-item>
<p>Adaptation is limited by mutations.</p>
</list-item>
</list>
</td>
<td valign="top" align="center"> (<xref ref-type="bibr" rid="B37">37</xref>, <xref ref-type="bibr" rid="B64">64</xref>, <xref ref-type="bibr" rid="B86">86</xref>, <xref ref-type="bibr" rid="B87">87</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>
<italic>Neo-Lamarckism</italic>
</bold>
</td>
<td valign="top" align="left">A new environment directly induces adaptive and heritable phenotypic changes. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process.</td>
<td valign="top" align="left">Environment, Epiallelic change (Mutation)</td>
<td valign="top" align="left">
<list list-type="bullet">
<list-item>
<p>Selection is not involved in the spread of heritable and adaptive changes that a particular environmental treatment tends systematically to induce.</p>
</list-item>
<list-item>
<p>Induced epigenetic changes can be stably transmitted over many generations in the absence of the treatment.</p>
</list-item>
<list-item>
<p>Stable epiallelic variants without associated DNA sequence variants are abundant among spontaneous mutations.</p>
</list-item>
</list>
</td>
<td valign="top" align="center"> (<xref ref-type="bibr" rid="B37">37</xref>, <xref ref-type="bibr" rid="B88">88</xref>, <xref ref-type="bibr" rid="B89">89</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">
<bold>
<italic>Use-it or Lose-it</italic>
</bold>
</td>
<td valign="top" align="left">In an environment where a phenotype is permanently expressed, the molecular basis of alternative phenotypes is relaxed. Mutations that permanently eliminate pathways leading to alternative phenotypes can be fixed by genetic drift. Genes that underlie the favoured phenotype may undergo recombination-mediated amplification.</td>
<td valign="top" align="left">Environment, Phenotypic plasticity, Purifying selection, Mutation, Genetic drift, Recombination</td>
<td valign="top" align="left">
<list list-type="bullet">
<list-item>
<p>Positive selection is not necessary for evolutionary adaptation.</p>
</list-item>
<list-item>
<p>Phenotypic plasticity precedes the fixation of evolved adaptations.</p>
</list-item>
<list-item>
<p>Copy number variants are a frequent contributor to adaptation.</p>
</list-item>
<list-item>
<p>Evolved adaptations originate from pre-existing traits that are co-opted for a new function.</p>
</list-item>
<list-item>
<p>Loss-of-function mutations are associated with the evolution of phenotypic novelties.</p>
</list-item>
<list-item>
<p>Evolutionary adaptation can be achieved even when effective population size is small.</p>
</list-item>
<list-item>
<p>Epigenetic silencing of genes involved in the disfavoured pathway could accelerate evolution because it shelters genes from purifying selection.</p>
</list-item>
</list>
</td>
<td valign="top" align="center"> (<xref ref-type="bibr" rid="B87">87</xref>) This study</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s5">
<title>The <italic>Use-It</italic> or <italic>Lose-It</italic> Model of Adaptive Evolution Has Considerable Explanatory Power and Makes Testable Predictions</title>
<p>The foregoing propositions are compatible with many observations. For example, they are consistent with empirical findings showing that environment-induced plasticity can promote adaptive evolution (<xref ref-type="bibr" rid="B90">90</xref>, <xref ref-type="bibr" rid="B91">91</xref>), that expression variability among environments can affect gene evolution (<xref ref-type="bibr" rid="B92">92</xref>), and that a trait&#x2019;s variance may be controlled by genes that are not directly involved in the trait being considered [the Omnigenic Model (<xref ref-type="bibr" rid="B93">93</xref>)]. They align with the increased rate of tandem duplications frequently associated with up-regulated stress-responsive genes in several organisms (<xref ref-type="bibr" rid="B94">94</xref>&#x2013;<xref ref-type="bibr" rid="B96">96</xref>) and with the predictable and frequent formation of <italic>de novo</italic> copy number variation in independent experimental evolution lines of yeast (<xref ref-type="bibr" rid="B97">97</xref>&#x2013;<xref ref-type="bibr" rid="B99">99</xref>). One fulfilled prediction of the <italic>use-it</italic> or <italic>lose-it</italic> model is that the rate of adaptive molecular evolution scales negatively with the intensity of natural purifying selection (<xref ref-type="bibr" rid="B100">100</xref>). Another fulfilled prediction is that an adaptation to a certain environment may limit evolutionary potential under environmental change (<xref ref-type="bibr" rid="B101">101</xref>) and can be deleterious in other environments (<xref ref-type="bibr" rid="B102">102</xref>&#x2013;<xref ref-type="bibr" rid="B104">104</xref>).</p>
<p>The <italic>use-it</italic> or <italic>lose-it</italic> model accounts for &#x2014; without depending on &#x2014; the role of epigenetic changes in favoring the onset of evolved adaptations (<xref ref-type="bibr" rid="B78">78</xref>). Epigenetic mechanisms, such as DNA methylation or small RNA-mediated epigenetic modifications, can help directly regulate the proposed coordinated antagonistic expression of P<sub>A</sub> and P<sub>B</sub> (<xref ref-type="bibr" rid="B105">105</xref>, <xref ref-type="bibr" rid="B106">106</xref>) (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>) and may be inherited (<xref ref-type="bibr" rid="B107">107</xref>). It can also account for the adaptive contribution of spatial and temporal non-genetic heterogeneity in populations of genetically narrow or uniform cells (<xref ref-type="bibr" rid="B28">28</xref>, <xref ref-type="bibr" rid="B108">108</xref>, <xref ref-type="bibr" rid="B109">109</xref>). For example, prolonged proximity to a new and confined source of stress (<italic>e.g.</italic>, inflammation) is expected to locally promote non-genetic changes that are more stable and thus more likely to reoccur across generations compared to changes that occur further apart from the source of stress. Under these circumstances, the <italic>use-it</italic> or <italic>lose-it</italic> model predicts that mutations that silence the molecular basis of the unused phenotype are most likely to accrue locally around, more than further apart from, a changed environment. More broadly, the model makes the testable prediction that non-genetic heterogeneity, the likelihood of genetic inactivation and the loss of phenotypic plasticity all correlate with the intensity/duration of, and distance from, a localized source of stress.</p>
<p>Exposure to a new environment triggers a physiological adaptive response (also known as acclimatization), which in the <italic>use-it</italic> or <italic>lose-it</italic> model shapes evolutionary adaptive trajectories. This means that evolutionary adaptive trajectories could be to some degree predicted <italic>via</italic> ecological studies, <italic>e.g.</italic>, <italic>via</italic> the study of transcriptional variation in response to environmental change, in line with previous suggestions (<xref ref-type="bibr" rid="B110">110</xref>). Finally, the <italic>use-it</italic> or <italic>lose-it</italic> model aligns with the widespread evidence for convergence by parallel evolution (<xref ref-type="bibr" rid="B111">111</xref>&#x2013;<xref ref-type="bibr" rid="B114">114</xref>). It predicts that individuals/cells that are habitually exposed to the same biotic or abiotic environment (<italic>e.g.</italic>, diet, medication, hygiene levels, pollutants, oxygen concentration, population density) accumulate inactivating mutations in the molecular basis of the same alternative phenotype that is disfavored/unused in that environment. This prediction matches the increasingly acknowledged role of gene loss for evolutionary adaptation (<xref ref-type="bibr" rid="B115">115</xref>&#x2013;<xref ref-type="bibr" rid="B122">122</xref>). It also provides a plausible explanation for recurrent mutations in cancer cells (see below), recurring intratumoral phenotypic clusters (<xref ref-type="bibr" rid="B77">77</xref>, <xref ref-type="bibr" rid="B123">123</xref>, <xref ref-type="bibr" rid="B124">124</xref>), and the convergence towards the relatively few hallmarks of cancer (<xref ref-type="bibr" rid="B125">125</xref>). Importantly, most if not all the evidence presented above is commonly interpreted as, and may indeed be, the result of positive selection. However, the <italic>use-it</italic> or <italic>lose-it</italic> model offers an additional and equally viable interpretation for these observations.</p>
</sec>
<sec id="s6">
<title>Physiological Adaptation to the Pre-Tumor Environment</title>
<p>How far can the <italic>use-it</italic> or <italic>lose-it</italic> model take us with regard to improving current understanding of cancer initiation and evolution? Below, we provide a broad-brush overview of events that may unfold during tumorigenesis. This work of synthesis illustrates how the <italic>use-it</italic> or <italic>lose-it</italic> model can be used as a lens to interpret common observations and, more generally, as a valuable guide for gaining insights into cancer adaptive dynamics.</p>
<p>Although the exact timing and order of events that determine tumor initiation is not yet fully elucidated (<xref ref-type="bibr" rid="B126">126</xref>), it seems clear that tumorigenesis is a multi-stage (<xref ref-type="bibr" rid="B127">127</xref>) cumulative (<xref ref-type="bibr" rid="B128">128</xref>) process, and that the onset of cancer depends heavily on the surrounding microenvironment. Indeed, chronic inflammation and other types of long-lasting microenvironmental stresses are strongly associated with an increased risk of cancer (<xref ref-type="bibr" rid="B129">129</xref>&#x2013;<xref ref-type="bibr" rid="B131">131</xref>). In healthy somatic cells, microenvironmental stress is expected to induce a stress response. As a part of this response, human cells physiologically upregulate the expression levels of genes such as those encoding HSP70 and p53. The former is a family of proteins, amongst the most conserved across the tree of life (<xref ref-type="bibr" rid="B132">132</xref>, <xref ref-type="bibr" rid="B133">133</xref>). The latter is a metazoan invention (<xref ref-type="bibr" rid="B134">134</xref>), and its encoding gene is among the most frequently mutated across cancer types in human (<xref ref-type="bibr" rid="B135">135</xref>&#x2013;<xref ref-type="bibr" rid="B137">137</xref>). Stress-related proteins such as HSP70 and p53 can play multiple functions in the cell (pleiotropy). For example, HSP70 is also a positive regulator of mitotic cell division (<xref ref-type="bibr" rid="B138">138</xref>), whereas p53 negatively regulates the cell cycle (<xref ref-type="bibr" rid="B139">139</xref>). Moreover, these functions may be mutually exclusive (antagonistic pleiotropy). In accordance with the above example, stress resistance and cell growth are inversely regulated across the tree of life (<xref ref-type="bibr" rid="B110">110</xref>, <xref ref-type="bibr" rid="B140">140</xref>). Finally, stress resistance and cell growth are not isolated biological processes. Energy stores mobilization and cell motility, for example, are evolutionarily and molecularly linked with the cell stress response (<xref ref-type="bibr" rid="B141">141</xref>, <xref ref-type="bibr" rid="B142">142</xref>). Instead, processes such as microenvironment sensing, adhesion signaling, programmed cell death, and circadian clock are intimately connected to cell cycle progression (<xref ref-type="bibr" rid="B143">143</xref>&#x2013;<xref ref-type="bibr" rid="B145">145</xref>). Given these connections, when the molecular basis of one of these processes is altered, then other interlinked processes may also be affected.</p>
<p>This brief account exemplifies how upon exposure to pre-malignant microenvironmental stress, multipurpose proteins such as HSP70 could take on the role of environmentally controlled genetic switch that is hypothesized in the plasticity-relaxation-mutation mechanism (<xref ref-type="bibr" rid="B78">78</xref>) (see above and <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>). The switch could simply reflect a biased allocation of pleiotropic factors between the competing demands of growth and stress resistance/somatic maintenance <italic>e.g.</italic>, following post-translational modifications (<xref ref-type="bibr" rid="B146">146</xref>, <xref ref-type="bibr" rid="B147">147</xref>). In any case, proteins with critical roles in stress response and cell cycle progression such as HSP70 may fail to accurately mediate cell division in a stressful environment (<xref ref-type="bibr" rid="B148">148</xref>). This is expected to hinder cell growth and may generate ploidy alterations (<xref ref-type="bibr" rid="B149">149</xref>) and copy number variation (<xref ref-type="bibr" rid="B98">98</xref>) in a context, the pre-malignant environment, where stress resistance is the adaptive phenotype. According to the <italic>use-it</italic> or <italic>lose-it</italic> model, the positive regulators of this stress-resistance phenotype are upregulated and may accrue structural changes (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>). Instead, cell growth is the alternative disfavored/unused phenotype, whose expression is antagonistically regulated <italic>via</italic> epigenetic changes, and whose molecular negative regulators preferentially accrue silencing DNA mutations (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>).</p>
<p>The above dynamics align well with observations from long-term experimental evolution studies. In one example, independently evolving yeast populations accumulate adaptive copy number variants in response to stress. These variants predictably emerge across replicates and appear to result from DNA replication-mediated processes (<xref ref-type="bibr" rid="B97">97</xref>). These findings and others (<xref ref-type="bibr" rid="B150">150</xref>&#x2013;<xref ref-type="bibr" rid="B153">153</xref>) align with the suggestion that in a constant environment active transcription can contribute to the formation of copy number variants (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>). In a constant environment, these variants can be repeatedly generated across individuals/cells and hence they can increase frequency in a population even when the power of selection is weaker relative to the power of genetic drift.</p>
<p>In a second example, independently evolved yeast clones frequently undergo adaptive self-diploidization in response to a chronically stressful environment (<italic>i.e.</italic>, limiting glucose) (<xref ref-type="bibr" rid="B154">154</xref>). Self-diploidization is strongly associated with enhanced stress resistance (<xref ref-type="bibr" rid="B155">155</xref>) and produces similar phenotypic effects as those observed when cell cycle progression-related genes are repressed (<xref ref-type="bibr" rid="B156">156</xref>). These obervations hint at the expected link between stress response and cell growth in yeast. Furthermore, independently evolved yeast clones with no self-diploidization were reported to accumulate a large number of large-effect adaptive mutations in a few genes that affect cell growth (<xref ref-type="bibr" rid="B154">154</xref>). Not only do these recurrent mutations inactivate preferentially negative regulators of the nutrient-responsive Ras/PKA pathway, but mutations that decrease the activity of Ras/PKA genes are known to have strong pleiotropic effects and enhance yeast&#x2019;s response to stress (<xref ref-type="bibr" rid="B157">157</xref>&#x2013;<xref ref-type="bibr" rid="B160">160</xref>). These dynamics align with those described in <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>. Under the ND model, the discussed mutations accrue as a result of positive selection. Under the <italic>use-it</italic> or <italic>lose-it</italic> model, relaxed negative selection favors the accrual of these growth-inhibiting mutations, which in a stressful environment stabilize the enhanced stress response.</p>
<p>In a third and last example, a constant environment with predictable nutrient supply is reproducibly associated with perturbed/disrupted environment-sensitive and growth rate-governing signaling pathways in the single-celled ciliate <italic>Paramecium</italic> (<xref ref-type="bibr" rid="B161">161</xref>) and yeast (<xref ref-type="bibr" rid="B162">162</xref>). In the yeast study, clones adapted to the constant environment show also reduced viability in a fluctuating environment where nutrient abundance varies (<xref ref-type="bibr" rid="B162">162</xref>). These findings align with the <italic>use-it</italic> or <italic>lose-it</italic> model: habitual exposure to a constant environment is expected to wear down the ability to respond to environmental changes. This latter aspect may play a crucial role in oncogenic transformation (see below).</p>
</sec>
<sec id="s7">
<title>Mechanisms Underlying Oncogenic Transformation</title>
<p>But how can the foregoing physiological adaptive dynamics lead to an oncogenic transformation? The <italic>use-it</italic> or <italic>lose-it</italic> model generates a specific prediction based on a few previous observations. First, it is widely known that the growth-inhibitory activity of p53 is elevated in the presence of stress but drops during tumorigenesis (<xref ref-type="bibr" rid="B163">163</xref>). Second and last, across multiple cancer types the p53-encoding gene <italic>TP53</italic> preferentially accrues inactivating mutations, many at the early phases of tumorigenesis (<xref ref-type="bibr" rid="B137">137</xref>, <xref ref-type="bibr" rid="B164">164</xref>). Based on this and the above-presented work of synthesis, the <italic>use-it</italic> or <italic>lose-it</italic> model predicts that the emergence of tumors is coupled with &#x2014; or even prompted by &#x2014; a &#x201c;<italic>stress resistance-cell growth axis</italic>&#x201d; that tilts in favor of cell growth. Because stress resistance is no longer the favored/used phenotype in the newly formed tumor microenvironment (more details below), its molecular basis becomes the preferential target of inactivating mutations (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>).</p>
<p>But what would prompt the putative tilt in the stress resistance-cell growth axis? Although only targeted experiments can reveal the precise causes, the <italic>use-it</italic> or <italic>lose-it</italic> model offers a simple explanation, which can guide future investigations. Under this model, sustained repression of cell growth in the stressful pre-tumor microenvironment favors the accumulation of cancer-associated inactivating mutations in genes that encode cell-growth negative regulators such as p53 (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>). The duration of exposure to the pre-tumor microenvironment is crucial for inactivating mutations to accrue. Thus, the <italic>use-it</italic> or <italic>lose-it</italic> model predicts that tumors irreversibly emerge when the level of environmental stress remains elevated for a sufficiently long time &#x2014; a time span that might even extend for years (<xref ref-type="bibr" rid="B137">137</xref>). The same rationale can be readily used to explain adaptation at later phases of cancer development, <italic>i.e.</italic>, developed tumors would be most likely to evolve genetically-determined adaptations when their microenvironment remains constant for a sufficiently extended time (<xref ref-type="bibr" rid="B165">165</xref>). This implies that long-term exposure to constant drug therapies may be a shortsighted anti-cancer approach, in line with current views (<xref ref-type="bibr" rid="B166">166</xref>) and emerging therapies (<xref ref-type="bibr" rid="B167">167</xref>).</p>
<p>Why should stress resistance be dampened in the emerging tumor microenvironment? Because there are no indications, to our knowledge, that the pre-tumor environmental stress disappears during tumorigenesis, the hypothesized tilt in the stress resistance-cell growth axis can only indicate that newly emerged tumor cells have evolved a considerable level of <italic>insensitivity</italic> to stress (which would effectively dampen or turns off stress response). This may reflect a dampened sensitivity to extracellular and intracellular information and/or a partial loss of contact with the microenvironment. Several observations are in line with this inference. For example, dysregulated signaling is widely recognized as an oncogenic mechanism (<xref ref-type="bibr" rid="B125">125</xref>), with expected effects on the cell&#x2019;s metabolic and epigenetic circuits (<xref ref-type="bibr" rid="B168">168</xref>). Also, the loss of polyploidy can flag a reduced sensitivity to stress (<italic>e.g.</italic>, DNA damage). Polyploidy enhances a cell&#x2019;s ability to survive in stressful conditions (<xref ref-type="bibr" rid="B169">169</xref>) and is frequently observed in pre-malignant lesions (<xref ref-type="bibr" rid="B170">170</xref>). However, polyploidy is frequently lost during the early steps of tumorigenesis (<xref ref-type="bibr" rid="B171">171</xref>) <italic>via</italic> chromosome missegregation (<xref ref-type="bibr" rid="B172">172</xref>), expecially in cells where the function of p53 is down-regulated or absent (<xref ref-type="bibr" rid="B173">173</xref>). Furthermore, the stress-inducing pre-tumor microenvironment can activate the epithelial-to-mesenchymal transition program [reversible when the inducing stress is removed (<xref ref-type="bibr" rid="B174">174</xref>)] which mediates, <italic>inter alia</italic>, the loss of epithelial characteristics (<italic>e.g.</italic>, cell-cell adhesion) (<xref ref-type="bibr" rid="B35">35</xref>, <xref ref-type="bibr" rid="B175">175</xref>). The hypothesized reduced sensitivity to the microenvironment during oncogenic transformation is further consistent with evidence supporting a model of cancer driven by tissue disruption (<xref ref-type="bibr" rid="B176">176</xref>), as well as with the proposed link between the age-related destabilization of the multicellular organizational architecture and cancer (<xref ref-type="bibr" rid="B177">177</xref>, <xref ref-type="bibr" rid="B178">178</xref>). It is also consistent with the suggestion that the onset of cancer reflects a transition to unicellularity (<xref ref-type="bibr" rid="B179">179</xref>&#x2013;<xref ref-type="bibr" rid="B181">181</xref>). More specifically, it has been suggested that a healthy somatic cell within a tissue is <italic>non-evolving</italic> unless this cell breaks loose and thus acquires a self-defined fitness (<xref ref-type="bibr" rid="B72">72</xref>). The hypothesized reduced cell sensitivity to biological information may favor the acquisition of this self-defined fitness alongside the activation of molecular programs that date back to unicellular ancestors (<xref ref-type="bibr" rid="B182">182</xref>&#x2013;<xref ref-type="bibr" rid="B184">184</xref>).</p>
<p>What mediates enhanced cell proliferation in the emerging tumor microenvironment? As stated above, the inactivated or inhibited p53 no longer carries out its anti-proliferative transcriptional program. This is expected to promote cell growth, in addition to influencing a plethora of other cellular processes (<xref ref-type="boxed-text" rid="box2">
<bold>Box 2</bold>
</xref>). Additionally, putative genetic switches such as HSP70, which is typically highly expressed in tumors (<xref ref-type="bibr" rid="B133">133</xref>), may be re-allocated from chiefly enhancing stress response in the pre-tumor environment to primarily promoting mitotic division in the tumor microenvironment. In line with this, HSP70 plays a key role in cancer initiation and progression (<xref ref-type="bibr" rid="B185">185</xref>). Moreover, its loss prevents malignant transformation (<xref ref-type="bibr" rid="B185">185</xref>). More in general, environmentally-controlled reallocations along the stress resistance-cell growth axis are consistent with two highly correlated phenotypes which are detected in cancer and unicellular systems such as the ciliate <italic>Paramecium</italic> (<xref ref-type="bibr" rid="B148">148</xref>): dormancy and elevated stress resistance <italic>vs</italic>. rapid proliferation and reduced stress resistance.</p>
<boxed-text id="box2" position="float">
<label>Box 2</label>
<title>Bridging p53 inactivation, cancer and ontogenesis with the <italic>use-it</italic> or <italic>lose-it</italic> model.</title>
<p>Several observations indicate that the functional inactivation of p53 can rewire cells. For example, p53 inactivation/inhibition disfavors DNA repair and apoptosis (<xref ref-type="bibr" rid="B186">186</xref>), may favor cell migration and invasion (<xref ref-type="bibr" rid="B187">187</xref>, <xref ref-type="bibr" rid="B188">188</xref>), induces the de-repression of transposable elements (<xref ref-type="bibr" rid="B189">189</xref>&#x2013;<xref ref-type="bibr" rid="B191">191</xref>), and facilitates the survival and accumulation of de-polyploidized/aneuploid cells (<xref ref-type="bibr" rid="B172">172</xref>, <xref ref-type="bibr" rid="B173">173</xref>, <xref ref-type="bibr" rid="B192">192</xref>, <xref ref-type="bibr" rid="B193">193</xref>) and immune evasion (<xref ref-type="bibr" rid="B194">194</xref>, <xref ref-type="bibr" rid="B195">195</xref>). This massive cascade of events may reflect genome instability in somatic cells that, because of the inoperative p53, are reprogrammed to generate induced pluripotent stem cells (<xref ref-type="bibr" rid="B196">196</xref>). In a seemingly alternative fashion, these events may also reflect the activation of an evolutionary conserved program of unicellular survival against unfavorable changes (<xref ref-type="bibr" rid="B197">197</xref>).</p>
<p>Can the foregoing distinct views be linked under a unifying perspective? This is probably only possible when the hypothesized program of unicellular survival against unfavorable changes matches the transcriptional program of embryonic stem cells. Indeed, the transcriptional program of tumor cells does overlap with that of embryonic stem cells (<xref ref-type="bibr" rid="B198">198</xref>, <xref ref-type="bibr" rid="B199">199</xref>). Similar to cancer cells, early embryo cells exhibit a reduced expression of p53 and a similar activation of LINE-1 elements (<xref ref-type="bibr" rid="B200">200</xref>). Moreover, placental cells exhibit several cancer-like features, <italic>i.e.</italic>, genome instability (<xref ref-type="bibr" rid="B201">201</xref>), invasiveness and suppression of immune responses (<xref ref-type="bibr" rid="B202">202</xref>, <xref ref-type="bibr" rid="B203">203</xref>), methylome and vascular remodeling (<xref ref-type="bibr" rid="B204">204</xref>, <xref ref-type="bibr" rid="B205">205</xref>). Further, tumor cell reprogramming to pluripotency &#x2014; an event that is observed in different phases of cancer biology &#x2014; most likely enhances cell resistance [<italic>e.g.</italic>, to therapy-induced stress (<xref ref-type="bibr" rid="B206">206</xref>)]. In sum, it is plausible that the functional inactivation of p53 in somatic cells triggers some non-random dynamics that reflect a throwback to the early stage of embryogenesis.</p>
<p>Leveraging these similarities between tumor cells and early embryo/placental cells, the <italic>use-it</italic> or <italic>lose-it</italic> model successfully predicts that early embryo cells are habitually exposed to an environment that closely resembles a tumor microenvironment [<italic>e.g.</italic>, hypoxia (<xref ref-type="bibr" rid="B207">207</xref>, <xref ref-type="bibr" rid="B208">208</xref>)]. Despite the many similarities between tumor cells and early embryo/placental cells, tumorigenesis typically does not take place during fetal/placental development. This suggests that the process of embryonic development unfolds in the presence (absence) of factors that prevent (promote) tumor initiation (<xref ref-type="bibr" rid="B209">209</xref>, <xref ref-type="bibr" rid="B210">210</xref>). Based on the rationale of the <italic>use-it</italic> or <italic>lose-it</italic> model, differences in the properties of the microenvironmental stress during embryogenesis and tumorigenesis (<italic>e.g.</italic>, intensity, persistence) may crucially contribute to either building a multicellular system or promoting cancer (<xref ref-type="bibr" rid="B211">211</xref>). If so, then we anticipate that a better understanding of the mechanisms driving cancer evolution can help gain insights into the mechanisms governing embryo development and vice versa.</p>
</boxed-text>
</sec>
<sec id="s8">
<title>Implications for Translational Application</title>
<p>Understanding whether and when cancers adapt <italic>via</italic> a neo-Darwinian model, or a different model of adaptive evolution can have serious practical consequences for patients. At present, recurring mutations that inactivate specific genes in a patient&#x2019;s cancer cells are assumed to flag positive selection-driven adaptations, say an evolved capacity to escape the immune system. Based on this common assumption, inactivated genes are labeled as tumor suppressors and oncologists may adjust or change altogether the cancer treatment to which the patient is subjected. For example, a patient may be treated with different chemotherapeutical drugs or a cocktail thereof to circumvent the hypothetical evolved capacity to evade immune response.</p>
<p>But what if the underlying assumption rooted in the neo-Darwinian paradigm is contentious or, worst, inaccurate? The following example illustrates this possibility. A recent study found that inactivating mutations in metastatic/relapsed breast cancer cells preferentially target the genes <italic>JAK2</italic> and <italic>STAT3</italic>, and more in general, the JAK-STAT signaling pathway (<xref ref-type="bibr" rid="B212">212</xref>). Following the current <italic>modus operandi</italic>, Yates et al. labeled <italic>JAK2</italic> and <italic>STAT3</italic> as tumor suppressor genes in metastatic/relapsed breast cancer. Further, as the loss of <italic>JAK2</italic> was previously shown to lead to a total loss of functional response to interferon gamma (<xref ref-type="bibr" rid="B213">213</xref>), Yates et al. proposed &#x2014; reasonably, under an underlying neo-Darwinian paradigm &#x2014; that the recurring inactivating mutations in the JAK-STAT signaling pathway contribute to disease progression by allowing cancer cells to adaptively escape host immunity. The <italic>use-it</italic> or <italic>lose-it</italic> model offers a different, yet equally viable interpretation for these same findings. If cells with nonfunctional <italic>JAK2</italic> are unable to respond to interferon gamma as previously suggested (<xref ref-type="bibr" rid="B213">213</xref>), then the preferential inactivation of <italic>JAK2</italic> reported by Yates <italic>et al.</italic> can reflect an interferon gamma-poor environment. In other words, rather than being positively selected to escape the immune system (neo-Darwinian model), the recurrent inactivation of JAK-STAT signaling in metastatic/relapsed breast cancer may flag a weakened immune system and favor survival in the interferon-gamma-poor environment (<italic>use-it</italic> or <italic>lose-it</italic> model).</p>
<p>This alternative interpretation fits well with the negative impact of cancer and chemotherapy on the immune system (<xref ref-type="bibr" rid="B214">214</xref>). It also cautiously suggests an approach to counter this adaptive cancer phenotype. Treating the patient with interferon gamma could encourage metastatic breast cancer cells to re-activate a silenced or dampened JAK-STAT signaling, while at the same time mitigating the overexpression of the alternative (adaptive) phenotype (<xref ref-type="bibr" rid="B215">215</xref>, <xref ref-type="bibr" rid="B216">216</xref>). It is worth noting that the antitumor effects of an increased interferon gamma approach have been already verified. Treating breast (and other) cancer patients with interferon gamma can help sensitize cancer cells to apoptosis, facilitating their elimination with additional drugs (<xref ref-type="bibr" rid="B217">217</xref>&#x2013;<xref ref-type="bibr" rid="B221">221</xref>). Moreover, the molecular basis of the alternative (adaptive) phenotype may encompass the PI3K/AKT/mTOR signaling pathway. The latter inference is drawn from some observations: the increased activity of the PI3K/AKT/mTOR signaling pathway is frequently observed in breast cancer patients (<xref ref-type="bibr" rid="B222">222</xref>), it increases tumor resistance to multiple drugs (<xref ref-type="bibr" rid="B223">223</xref>, <xref ref-type="bibr" rid="B224">224</xref>), and PI3K/mTOR inhibitors activate the JAK/STAT signaling pathway (<xref ref-type="bibr" rid="B225">225</xref>).</p>
</sec>
<sec id="s9" sec-type="conclusions">
<title>Conclusions</title>
<p>Cancer is an evolutionary adaptation of malignant cells to their microenvironment. Thus, an adequate understanding of the mechanisms that mediate adaptive biological responses is indispensable to make effective progress against cancer. Inspired by a wealth of empirical and theoretical cancer and evolutionary studies, here we build on a non-Darwinian and non-Lamarckian model of adaptive evolution (<xref ref-type="bibr" rid="B78">78</xref>) to gain insights into therapeutic resistance and other steps of cancer biology.</p>
<p>In the neo-Darwinian model, ecology and evolution are treated separately (<xref ref-type="bibr" rid="B226">226</xref>), chance plays a central role in the emergence of mutations, and environmental adaptation is achieved <italic>via</italic> positive selection of spontaneous mutations (<xref ref-type="bibr" rid="B37">37</xref>). In the revived plasticity-relaxation-mutation model (<xref ref-type="bibr" rid="B78">78</xref>) &#x2014; here expanded and renamed with a more intuitive <italic>use-it</italic> or <italic>lose-it</italic> &#x2014; physiological and evolutionary changes are integrated, mutations preferentially accrue in those genomic loci that upon environmental change experience a change of selective regime (<italic>i.e.</italic>, relaxed purifying selection), and adaptation is achieved by losing the phenotype that is unused in a habitual environment.</p>
<p>The <italic>use-it</italic> or <italic>lose-it</italic> model has a considerable explanatory power. Its theoretical propositions align, <italic>inter alia</italic>, with the idea that that enduring environmental conditions can affect simultaneously health and evolutionary trajectories (<xref ref-type="bibr" rid="B227">227</xref>). They can explain the parallel evolution of similar traits in response to the same environment [<italic>e.g.</italic>, recurrent losses in response to the same anti-cancer therapy (<xref ref-type="bibr" rid="B228">228</xref>)], are compatible with the observation that non-genetic heterogeneity can promote transient and rapid adaptation to environmental changes (<xref ref-type="bibr" rid="B229">229</xref>, <xref ref-type="bibr" rid="B230">230</xref>), and with evolution-based therapeutic strategies such as the &#x201c;ersatzdroge&#x201d; strategy to counter drug-resistant phenotypes (<xref ref-type="bibr" rid="B231">231</xref>). In this latter strategy, cells with an evolved adaptation to a certain environment (<italic>e.g.</italic>, resistance to a toxic drug) are outcompeted by the sensitive cells when exposed to a non-toxic version of the same drug (a new environment). The <italic>use-it</italic> or <italic>lose-it</italic> model can help generate a conceivable and coherent mechanistic account of tumorigenesis, and when compared to the neo-Darwinian model it can produce different interpretations of the same empirical observations, thereby encouraging different clinical interventions. These differences deserve special attention given the increasingly widespread use of personalized oncology/medicine and its role in informing clinical treatment.</p>
<p>Finally, the <italic>use-it</italic> or <italic>lose-it</italic> model suggests that the conversion of a healthy cell into a cancerous cell is neither abrupt nor accidental. Rather, it is the result of an environmentally induced process that is for one traceable and for another reversible. If this model is correct, then tracing epimutations induced by a habitual exposure to microenvironmental stress should represent a powerful strategy to anticipate the emergence of cancer. Additionally, in a world where obesity is the first cause of cancer (<xref ref-type="bibr" rid="B232">232</xref>, <xref ref-type="bibr" rid="B233">233</xref>), changes of inflammation-promoting lifestyle and dietary regimes would help reverse and reduce the induction of cancer-related mutational and adaptive events (<xref ref-type="bibr" rid="B234">234</xref>). Twenty-five years ago Lucien Israel wrote: &#x201c;<italic>Killing the last cancer cell without killing the host is an objective that has not yet been reached</italic>&#x201d; (<xref ref-type="bibr" rid="B197">197</xref>). In large part, this is still true today (<xref ref-type="bibr" rid="B235">235</xref>). Considering the foregoing propositions, we urge a profound reconceptualization of anti-cancer therapies. Instead of aiming to kill cancer cells, we suggest that anti-cancer therapies should aim to prevent or alter the (micro)environmental conditions that spawn and/or help preserve cancer cells. In this context, the characterization of genetic and non-genetic cancer variation would no longer serve to design toxic drugs or debilitating treatments tailored to specific molecular targets. Rather, it would help infer the key properties and the vulnerabilities of the tumor-supporting environment, which non-toxic means could help modify.</p>
</sec>
<sec id="s10" sec-type="data-availability">
<title>Data Availability Statement</title>
<p>The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.</p>
</sec>
<sec id="s11" sec-type="author-contributions">
<title>Author Contributions</title>
<p>FC conceived of the presented idea and developed the theory. All authors contributed to the article and approved the submitted version.</p>
</sec>
<sec id="s12" sec-type="funding-information">
<title>Funding</title>
<p>FT is supported by the MAVA Foundation and an ANR TRANSCAN (ANR-18-CE35-0009).</p>
</sec>
<sec id="s13" sec-type="COI-statement">
<title>Conflict of Interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s14" sec-type="disclaimer">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
</body>
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