The cancer puzzle: Welcome to organicism

Persistent and novel changes in plasma microRNA profiles in patients with non-small cell lung cancer following tumour resection

Background

Non-small cell lung cancer (NSCLC) accounts for 80% of lung cancers, the leading cause of cancer mortality. microRNAs (miRNA, miR) have emerged as important components of carcinogenesis and promising biomarkers. We aimed to analyse global plasma miRs in NSCLC patients before and at least one year after tumour resection.

Methods

Plasma was collected from the peripheral blood of 24 donors without cancer and of NSCLC patients before surgery (n=36) and at least 1 year after surgery (n=12). Next-generation sequencing (NGS)-based miR profiling was performed. Patients were followed-up for 4 to 12 years after surgery to assess disease recurrence.

Results

Untreated NSCLC patients exhibited significant changes in plasma miR levels compared to cancer-free donors (48 up- and 17 down-regulated miRs). miR profiles in patients with adenocarcinoma (ADC) (n=18) and squamous cell carcinoma (SCC) significantly differed (16 and 86 miRs up-, and 15 and 16 miRs down-regulated, respectively). A subset of pre-surgery deregulated miRs was found to be associated with recurrence (49 miRs). Six miRs were shown to have independent prognostic value. After tumour resection, some pre-surgery miR alterations returned to control levels (18 miRs), some others persisted (27 miRs), while also novel plasma miR changes emerged (75 miRs) in patients with no clinical evidence of recurrence.

Conclusions

Untreated NSCLC patients present deregulated plasma miRs, some of which may have a potential of prognostic markers. After tumour excision plasma miR profiles change, some miR levels normalise, some changes persist and novel miR changes are observed despite no clinical symptoms of recurrence. Plasma miR profiles in NSCLC patients may suggest systemic abnormalities predisposing to lung cancer and/or reflect a systemic response to pre-cancer/dormant cancer cells.

Transcending the hegemony of the molecular machine through an organic renewal of biology and biomedicine

The dominant approach to the study of living systems in the 20th century into today has been that of a reductionist approach focused on genetics and biochemistry. The hunt for genes and the elucidation of their biochemical outputs has organized funding in research, educational curricula, academic promotion, and the distribution of prestige through awards. Such reductionism has gone hand in hand with an ontology of the machine. We will discuss how viewing life as if it emanated from a set of molecular machines is the main bottleneck in addressing key questions in biology. We will discuss how moving beyond it is not contingent on new technologies but rather a refreshed perspective of life that can be termed "organic". Furthermore, we suggest that the study of how form arises, morphogenesis, is the key to an organic renewal of biology and biomedicine. Although morphogenesis is currently seen as a subsidiary branch of developmental biology as well as the consequence of molecular patterning processes at the subcellular scale, we will argue that morphology and its self-organizing capacity at the supracellular scale is the fundamental nexus in embryonic development as well as disease. We see the inability to appreciate form through an organic supracellular perspective as the principal bottleneck for making inroads into health issues such as cancer and the chronic disease epidemic.

The end of the genetic paradigm of cancer

Genome sequencing of cancer and normal tissues, alongside single-cell transcriptomics, continues to produce findings that challenge the idea that cancer is a 'genetic disease', as posited by the somatic mutation theory (SMT). In this prevailing paradigm, tumorigenesis is caused by cancer-driving somatic mutations and clonal expansion. However, results from tumor sequencing, motivated by the genetic paradigm itself, create apparent 'paradoxes' that are not conducive to a pure SMT. But beyond genetic causation, the new results lend credence to old ideas from organismal biology. To resolve inconsistencies between the genetic paradigm of cancer and biological reality, we must complement deep sequencing with deep thinking: embrace formal theory and historicity of biological entities, and (re)consider non-genetic plasticity of cells and tissues. In this Essay, we discuss the concepts of cell state dynamics and tissue fields that emerge from the collective action of genes and of cells in their morphogenetic context, respectively, and how they help explain inconsistencies in the data in the context of SMT.

Is Cancer Metabolism an Atavism?

The atavistic theory of cancer posits that cancer emerges and progresses through the reversion of cellular phenotypes to more ancestral types with genomic and epigenetic changes deactivating recently evolved genetic modules and activating ancient survival mechanisms. This theory aims at explaining the known cancer hallmarks and the paradox of cancer's predictable progression despite the randomness of genetic mutations. Lineweaver and colleagues recently proposed the Serial Atavism Model (SAM), an enhanced version of the atavistic theory, which suggests that cancer progression involves multiple atavistic reversions where cells regress through evolutionary stages, losing recently evolved traits first and reactivating primitive ones later. The Warburg effect, where cancer cells upregulate glycolysis and lactate production in the presence of oxygen instead of using oxidative phosphorylation, is one of the key feature of the SAM. It is associated with the metabolism of ancient cells living on Earth before the oxygenation of the atmosphere. This review addresses the question of whether cancer metabolism can be considered as an atavistic reversion. By analyzing several known characteristics of cancer metabolism, we reach the conclusion that this version of the atavistic theory does not provide an adequate conceptual frame for cancer research. Cancer metabolism spans a whole spectrum of metabolic states which cannot be fully explained by a sequential reversion to an ancient state. Moreover, we interrogate the nature of cancer metabolism and discuss its characteristics within the framework of the SAM.

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.

Is Cancer Reversible? Rethinking Carcinogenesis Models-A New Epistemological Tool

A growing number of studies shows that it is possible to induce a phenotypic transformation of cancer cells from malignant to benign. This process is currently known as "tumor reversion". However, the concept of reversibility hardly fits the current cancer models, according to which gene mutations are considered the primary cause of cancer. Indeed, if gene mutations are causative carcinogenic factors, and if gene mutations are irreversible, how long should cancer be considered as an irreversible process? In fact, there is some evidence that intrinsic plasticity of cancerous cells may be therapeutically exploited to promote a phenotypic reprogramming, both in vitro and in vivo. Not only are studies on tumor reversion highlighting a new, exciting research approach, but they are also pushing science to look for new epistemological tools capable of better modeling cancer.

From developmental to atavistic bet-hedging: How cancer cells pervert the exploitation of random single-cell phenotypic fluctuations

Stochastic gene expression plays a leading developmental role through its contribution to cell differentiation. It is also proposed to promote phenotypic diversification in malignant cells. However, it remains unclear if these two forms of cellular bet-hedging are identical or rather display distinct features. Here we argue that bet-hedging phenomena in cancer cells are more similar to those occurring in unicellular organisms than to those of normal metazoan cells. We further propose that the atavistic bet-hedging strategies in cancer originate from a hijacking of the normal developmental bet-hedging of metazoans. Finally, we discuss the constraints that may shape the atavistic bet-hedging strategies of cancer cells.

Roadmap on plasticity and epigenetics in cancer

The role of plasticity and epigenetics in shaping cancer evolution and response to therapy has taken center stage with recent technological advances including single cell sequencing. This roadmap article is focused on state-of-the-art mathematical and experimental approaches to interrogate plasticity in cancer, and addresses the following themes and questions: is there a formal overarching framework that encompasses both non-genetic plasticity and mutation-driven somatic evolution? How do we measure and model the role of the microenvironment in influencing/controlling non-genetic plasticity? How can we experimentally study non-genetic plasticity? Which mathematical techniques are required or best suited? What are the clinical and practical applications and implications of these concepts?