Cancer as an ecomolecular disease and a neoplastic consortium

TALKIEN: crossTALK IntEraction Network. A web-based tool for deciphering molecular communication through ligand-receptor interactions

Molecular crosstalk, the dialogue between different cell types, is attracting more attention in cancer research. On the one hand, the communication between tumor and non-tumor cells in the microenvironment or between different tumor clones has influential consequences for the progression and spread of tumors and response to treatment. On the other hand, novel techniques such as single-cell sequencing or spatial transcriptomics provide detailed information that needs to be interpreted. TALKIEN: crossTALK IntEraction Network is a simple and intuitive online R/shiny application to visualize molecular crosstalk information through the construction and analysis of a protein-protein interaction network. Taking two or more lists of genes or proteins as input, which are representative of cell lineages, TALKIEN extracts information about ligand-receptor interactions, builds a network and analyzes it using systems biology techniques such as centrality measures and component analysis, among others. Moreover, it expands the network displaying pathways downstream receptors. The application allows users to select different graphical layouts, performs functional analysis and gives information about drugs targeting receptors. In conclusion, TALKIEN allows users to detect ligand-receptor interactions generating new in silico predictions of cell-cell communication thus providing a translational rationale for future experiments. It is freely available at https://www.odap-ico.org/talkien.

Subverted macrophages in the triple-negative breast cancer ecosystem

Tumor-associated macrophages (TAMs) are the most critical effector cells of innate immunity and the most abundant tumor-infiltrating immune cells. They play a key role in the clearance of apoptotic bodies, regulation of inflammation, and tissue repair to maintain homeostasis in vivo. With the progression of triple-negative breast cancer（TNBC）, TAMs are "subverted" from tumor-promoting immune cells to tumor-promoting immune suppressor cells, which play a significant role in tumor development and are considered potential targets for cancer therapy. Here, we explored how macrophages, as the most important part of the TNBC ecosystem, are "subverted" to drive cancer evolution and the uniqueness of TAMs in TNBC progression and metastasis. Similarly, we discuss the rationale and available evidence for TAMs as potential targets for TNBC therapy.

The paradox of cooperation among selfish cancer cells

It is traditionally assumed that during cancer development, tumor cells abort their initially cooperative behavior (i.e., cheat) in favor of evolutionary strategies designed solely to enhance their own fitness (i.e., a "selfish" life style) at the expense of that of the multicellular organism. However, the growth and progress of solid tumors can also involve cooperation among these presumed selfish cells (which, by definition, should be noncooperative) and with stromal cells. The ultimate and proximate reasons behind this paradox are not fully understood. Here, in the light of current theories on the evolution of cooperation, we discuss the possible evolutionary mechanisms that could explain the apparent cooperative behaviors among selfish malignant cells. In addition to the most classical explanations for cooperation in cancer and in general (by-product mutualism, kin selection, direct reciprocity, indirect reciprocity, network reciprocity, group selection), we propose the idea that "greenbeard" effects are relevant to explaining some cooperative behaviors in cancer. Also, we discuss the possibility that malignant cooperative cells express or co-opt cooperative traits normally expressed by healthy cells. We provide examples where considerations of these processes could help understand tumorigenesis and metastasis and argue that this framework provides novel insights into cancer biology and potential strategies for cancer prevention and treatment.

Inflammasome-Mediated Cytokines: A Key Connection between Obesity-Associated NASH and Liver Cancer Progression

Liver cancer is one of the most lethal malignancies and is commonly diagnosed as hepatocellular carcinoma (HCC), a tumor type that affects about 90% of patients. Non-alcoholic steatohepatitis (NASH) and obesity are both risk factors for this disease. HCC initiation and progression are deeply linked with changes in the hepatic microenvironment, with cytokines playing key roles. The understanding of the pathogenic pathways that connect these disorders to liver cancer remains poor. However, the inflammasome-mediated cytokines associated with both diseases are central actors in liver cancer progression. The release of the pro-inflammatory cytokines IL-1β and IL-18 during inflammasome activation leads to several detrimental effects on the liver microenvironment. Considering the critical crosstalk between obesity, NASH, and HCC, this review will present the connections of IL-1β and IL-18 from obesity-associated NASH with HCC and will discuss approaches to using these cytokines as therapeutic targets against HCC.

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.

Group phenotypic composition in cancer

Although individual cancer cells are generally considered the Darwinian units of selection in malignant populations, they frequently act as members of groups where fitness of the group cannot be reduced to the average fitness of individual group members. A growing body of studies reveals limitations of reductionist approaches to explaining biological and clinical observations. For example, induction of angiogenesis, inhibition of the immune system, and niche engineering through environmental acidification and/or remodeling of extracellular matrix cannot be achieved by single tumor cells and require collective actions of groups of cells. Success or failure of such group activities depends on the phenotypic makeup of the individual group members. Conversely, these group activities affect the fitness of individual members of the group, ultimately affecting the composition of the group. This phenomenon, where phenotypic makeup of individual group members impacts the fitness of both members and groups, has been captured in the term 'group phenotypic composition' (GPC). We provide examples where considerations of GPC could help in understanding the evolution and clinical progression of cancers and argue that use of the GPC framework can facilitate new insights into cancer biology and assist with the development of new therapeutic strategies.

Association of the IL-1B rs1143623 Polymorphism and Cancer Risk: A Meta-Analysis

Aim: To derive a more precise association between the interleukin-1 beta (IL-1B) gene polymorphism rs1143623 and cancer risk. Methods: Published case-control studies up to November 5, 2019, that met all inclusion criteria were identified using PubMed, Web of Science, and EMBASE. Odds ratios and 95% confidence intervals were calculated to estimate the strength of associations using multiple genetic models. Sensitivity analyses and publication biases were also performed. Results: Nine articles covering 11 case-control studies, with 4801 cases and 6116 controls, were included in this meta-analysis. No significant association between the IL-1B rs1143623 polymorphism and cancer risk was observed under the homozygous, heterozygous, dominant, recessive, or allelic genetic models (all p > 0.05). Subgroup analysis by ethnicity indicated that the IL-1B rs1143623 polymorphism may decrease the risk of cancer in Asians under the heterozygous and dominant genetic models (both p < 0.05). Sensitivity analyses showed that none of the individual studies significantly affected the overall results. No significant publication biases were detected in this meta-analysis. Conclusion: Our results suggest that there is no significant association between the IL-1B rs1143623 polymorphism and cancer risk in the overall human population, but that it may provide a protective affect among Asians.

Clinical implications of intratumor heterogeneity: challenges and opportunities

In this review, we highlight the role of intratumoral heterogeneity, focusing on the clinical and biological ramifications this phenomenon poses. Intratumoral heterogeneity arises through complex genetic, epigenetic, and protein modifications that drive phenotypic selection in response to environmental pressures. Functionally, heterogeneity provides tumors with significant adaptability. This ranges from mutual beneficial cooperation between cells, which nurture features such as growth and metastasis, to the narrow escape and survival of clonal cell populations that have adapted to thrive under specific conditions such as hypoxia or chemotherapy. These dynamic intercellular interplays are guided by a Darwinian selection landscape between clonal tumor cell populations and the tumor microenvironment. Understanding the involved drivers and functional consequences of such tumor heterogeneity is challenging but also promises to provide novel insight needed to confront the problem of therapeutic resistance in tumors.

The role of clonal communication and heterogeneity in breast cancer

Background

Cancer is a rapidly evolving, multifactorial disease that accumulates numerous genetic and epigenetic alterations. This results in molecular and phenotypic heterogeneity within the tumor, the complexity of which is further amplified through specific interactions between cancer cells. We aimed to dissect the molecular mechanisms underlying the cooperation between different clones.

Methods

We produced clonal cell lines derived from the MDA-MB-231 breast cancer cell line, using the UbC-StarTrack system, which allowed tracking of multiple clones by color: GFP C3, mKO E10 and Sapphire D7. Characterization of these clones was performed by growth rate, cell metabolic activity, wound healing, invasion assays and genetic and epigenetic arrays. Tumorigenicity was tested by orthotopic and intravenous injections. Clonal cooperation was evaluated by medium complementation, co-culture and co-injection assays.

Results

Characterization of these clones in vitro revealed clear genetic and epigenetic differences that affected growth rate, cell metabolic activity, morphology and cytokine expression among cell lines. In vivo, all clonal cell lines were able to form tumors; however, injection of an equal mix of the different clones led to tumors with very few mKO E10 cells. Additionally, the mKO E10 clonal cell line showed a significant inability to form lung metastases. These results confirm that even in stable cell lines heterogeneity is present. In vitro, the complementation of growth medium with medium or exosomes from parental or clonal cell lines increased the growth rate of the other clones. Complementation assays, co-growth and co-injection of mKO E10 and GFP C3 clonal cell lines increased the efficiency of invasion and migration.

Conclusions

These findings support a model where interplay between clones confers aggressiveness, and which may allow identification of the factors involved in cellular communication that could play a role in clonal cooperation and thus represent new targets for preventing tumor progression.

Electronic supplementary material

The online version of this article (10.1186/s12885-019-5883-y) contains supplementary material, which is available to authorized users.

Integrating clinical, molecular, proteomic and histopathological data within the tissue context: tissunomics

Malignant tumours show a marked degree of morphological, molecular and proteomic heterogeneity. This variability is closely related to microenvironmental factors and the location of the tumour. The activation of genetic alterations is very tissue‐dependent and only few tumours have distinct genetic alterations. Importantly, the activation state of proteins and signaling factors is heterogeneous in the primary tumour and in metastases and recurrences. The molecular diagnosis based only on genetic alterations can lead to treatments with unpredictable responses, depending on the tumour location, such as the tumour response in melanomas versus colon carcinomas with BRAF mutations. Therefore, we understand that the correct evaluation of tumours requires a system that integrates both morphological, molecular and protein information in a clinical and pathological context, where intratumoral heterogeneity can be assessed. Thus, we propose the term ‘tissunomics’, where the diagnosis will be contextualised in each tumour based on the complementation of the pathological, molecular, protein expression, environmental cells and clinical data.

I've Gut A Feeling: Microbiota Impacting the Conceptual and Experimental Perspectives of Personalized Medicine

In recent years, the human microbiota has gained increasing relevance both in research and clinical fields. Increasing studies seem to suggest the centrality of the microbiota and its composition both in the development and maintenance of what we call "health" and in generating and/or favoring (those cases in which the microbiota's complex relational architecture is dysregulated) the onset of pathological conditions. The complex relationships between the microbiota and human beings, which invest core notions of biomedicine such as "health" and "individual," do concern not only problems of an empirical nature but seem to require the need to adopt new concepts and new perspectives in order to be properly analysed and utilized, especially for their therapeutic implementation. In this contribution we report and discuss some of the theoretical proposals and innovations (from the ecological component to the notion of polygenomic organism) aimed at producing this change of perspective. In conclusion, we summarily analyze what impact and what new challenges these new approaches might have on personalized/person centred/precision medicine.

Connexins and Pannexins: Important Players in Tumorigenesis, Metastasis and Potential Therapeutics

Since their characterization more than five decades ago, gap junctions and their structural proteins-the connexins-have been associated with cancer cell growth. During that period, the accumulation of data and molecular knowledge about this association revealed an apparent contradictory relationship between them and cancer. It appeared that if gap junctions or connexins can down regulate cancer cell growth they can be also implied in the migration, invasion and metastatic dissemination of cancer cells. Interestingly, in all these situations, connexins seem to be involved through various mechanisms in which they can act either as gap-junctional intercellular communication mediators, modulators of signalling pathways through their interactome, or as hemichannels, which mediate autocrine/paracrine communication. This complex involvement of connexins in cancer progression is even more complicated by the fact that their hemichannel function may overlap with other gap junction-related proteins, the pannexins. Despite this complexity, the possible involvements of connexins and pannexins in cancer progression and the elucidation of the mechanisms they control may lead to use them as new targets to control cancer progression. In this review, the involvements of connexins and pannexins in these different topics (cancer cell growth, invasion/metastasis process, possible cancer therapeutic targets) are discussed.

Multiclonal tumor origin: Evidence and implications

An accurate understanding of the clonal origins of tumors is critical for designing effective strategies to treat or prevent cancer and for guiding the field of cancer risk assessment. The intent of this review is to summarize evidence of multiclonal tumor origin and, thereby, contest the commonly held assumption of monoclonal tumor origin. This review describes relevant studies of X chromosome inactivation, analyses of tumor heterogeneity using other markers, single cell sequencing, and lineage tracing studies in aggregation chimeras and engineered rodent models. Methods for investigating tumor clonality have an inherent bias against detecting multiclonality. Despite this, multiclonality has been observed within all tumor stages and within 53 different types of tumors. For myeloid tumors, monoclonal tumor origin may be the predominant path to cancer and a monoclonal tumor origin cannot be ruled out for a fraction of other cancer types. Nevertheless, a large body of evidence supports the conclusion that most cancers are multiclonal in origin. Cooperation between different cell types and between clones of cells carrying different genetic and/or epigenetic lesions is discussed, along with how polyclonal tumor origin can be integrated with current perspectives on the genesis of tumors. In order to develop biologically sound and useful approaches to cancer risk assessment and precision medicine, mathematical models of carcinogenesis are needed, which incorporate multiclonal tumor origin and the contributions of spontaneous mutations in conjunction with the selective advantages conferred by particular mutations and combinations of mutations. Adherence to the idea that a growth must develop from a single progenitor cell to be considered neoplastic has outlived its usefulness. Moving forward, explicit examination of tumor clonality, using advanced tools, like lineage tracing models, will provide a strong foundation for future advances in clinical oncology and better training for the next generation of oncologists and pathologists.

Beyond molecular tumor heterogeneity: protein synthesis takes control

One of the daunting challenges facing modern medicine lies in the understanding and treatment of tumor heterogeneity. Most tumors show intra-tumor heterogeneity at both genomic and proteomic levels, with marked impacts on the responses of therapeutic targets. Therapeutic target-related gene expression pathways are affected by hypoxia and cellular stress. However, the finding that targets such as eukaryotic initiation factor (eIF) 4E (and its phosphorylated form, p-eIF4E) are generally homogenously expressed throughout tumors, regardless of the presence of hypoxia or other cellular stress conditions, opens the exciting possibility that malignancies could be treated with therapies that combine targeting of eIF4E phosphorylation with immune checkpoint inhibitors or chemotherapy.