Henna Myllymäki

To date, very little is known regarding the earliest cellular and molecular events within the initial preneoplastic cell (PNC) niche that might determine the outcome of PNC development. Here, we combine in vivo live imaging and single cell transcriptomics to investigate the immediate cellular and molecular changes that occur in PNCs and responding innate immune cells within the first 24 hours following tumour initiation. We do so using an inducible transgenic zebrafish model of tumour initiation, in which oncogenic HRAS is conditionally expressed within the zebrafish epidermis. We found that, when expressed within basal keratinocytes, oncogenic HRAS was sufficient to drive several cancer hallmarks in nascent PNCs and their niche. Within 8 hours of oncogenic HRAS induction, basal keratinocytes began to dedifferentiate, followed by a bifurcation in PNC fate towards either a cellular state characterised by partial Epithelial-Mesenchymal-Transition (pEMT) and cancer stem cell features or a more differentiated cell state resembling suprabasal keratinocytes. By directly integrating data from PNCs and human SCC patients we show that both of these PNC states likely persist with established tumours, whilst the pEMT state corresponded with a more aggressive phenotype. Strikingly, markers of the PNC subpopulation that underwent pEMT correlated with poor prognosis in multiple human cancer types in the TCGA database. In addition, the pEMT PNC subpopulation expressed higher levels of cytokines that modulate neutrophil development and function, suggesting a major role for these cells in governing pro-tumour neutrophil responses. Indeed, we found that granulopoiesis was altered within PNC-bearing larvae, with a large proportion of neutrophils switching to an Arginase 2 positive phenotype that functioned to promote PNC proliferation. Similar to tumour associated neutrophils in the mammalian system, the cxcr1/2 – Il8 axis is involved in mediating the PNC-promoting function of neutrophils in our model. Thus, oncogenic RAS, when activated in the permissive cellular environment is sufficient to drive enabling cancer hallmarks, such as cellular plasticity and inflammation from the inception of the preneoplastic stage of cancer development. Furthermore, these same features may persist to drive malignant progression.

The antibiotic-tolerant biofilms present in tuberculous granulomas add an additional layer of complexity when treating mycobacterial infections, including tuberculosis (TB). For a more efficient treatment of TB, the biofilm forms of mycobacteria warrant specific attention. Here, we used Mycobacterium marinum (Mmr) as a biofilm-forming model to identify the abundant proteins covering the biofilm surface. We used biotinylation/streptavidin-based proteomics on the proteins exposed at the Mmr biofilm matrices in vitro to identify 448 proteins and ex vivo proteomics to detect 91 Mmr proteins from the mycobacterial granulomas isolated from adult zebrafish. In vitro and ex vivo proteomics data are available via ProteomeXchange with identifiers PXD033425 and PXD039416 , respectively. Data comparisons pinpointed the molecular chaperone GroEL2 as the most abundant Mmr protein within the in vitro and ex vivo proteomes, while its paralog, GroEL1, with a known role in biofilm formation, was detected with slightly lower intensity values. To validate the surface exposure of these targets, we created in-house synthetic nanobodies (sybodies) against the two chaperones and identified sybodies that bind the mycobacterial biofilms in vitro and those present in ex vivo granulomas. Taken together, the present study reports a proof-of-concept showing that surface proteomics in vitro and ex vivo proteomics combined is a valuable strategy to identify surface-exposed proteins on the mycobacterial biofilm. Biofilm surface–binding nanobodies could be eventually used as homing agents to deliver biofilm-targeting treatments to the sites of persistent biofilm infection. IMPORTANCE: With the currently available antibiotics, the treatment of TB takes months. The slow response to treatment is caused by antibiotic tolerance, which is especially common among bacteria that form biofilms. Such biofilms are composed of bacterial cells surrounded by the extracellular matrix. Both the matrix and the dormant lifestyle of the bacterial cells are thought to hinder the efficacy of antibiotics. To be able to develop faster-acting treatments against TB, the biofilm forms of mycobacteria deserve specific attention. In this work, we characterize the protein composition of Mmr biofilms in bacterial cultures and in mycobacteria extracted from infected adult zebrafish. We identify abundant surface-exposed targets and develop the first sybodies that bind to mycobacterial biofilms. As nanobodies can be linked to other therapeutic compounds, in the future, they can provide means to target therapies to biofilms.

Summary: Otto Warburg first described tumour cells as displaying enhanced aerobic glycolysis whilst maintaining defective oxidative phosphorylation (OXPHOS) for energy production almost 100 years ago ^1,2 . Since then, the ‘Warburg effect’ has been widely accepted as a key feature of rapidly proliferating cancer cells ^3,4 . Targeting cancer metabolism is now being considered as a promising precision oncology therapeutic approach ⁵ . What is not clear is how early “Warburg metabolism” initiates during cancer progression and whether changes in energy metabolism might influence tumour progression ab initio . We set out to investigate energy metabolism in HRAS ^G12V driven preneoplastic cell (PNC) at inception, in a zebrafish skin PNC model; and to test how the impact of manipulating energy metabolism in the whole animal may impact PNC initiation. We find that, within 24 hours of HRAS ^G12V induction, PNCs upregulate “Warburg metabolism”, and that this is required for their expansion. We show that blocking glycolysis reduces PNC proliferation, whilst increasing available glucose both enhances PNC proliferation and also reduces apoptosis. Impaired OXPHOS of PNCs might be exploited therapeutically since a mild complex I inhibitor, metformin, selectively induces apoptosis and suppresses proliferation of PNCs. In addition, we find mitochondrial fragmentation in PNCs occur prior to metabolic alteration and this is important for their survival since exposure to Drp1/Dnml1 inhibitor, mdivi, which blocks mitochondrial fragmentation leads to enhanced PNC apoptosis. Our data indicate that altered energy metabolism is one of the earliest events upon oncogene activation in somatic cells, which provide a targeted and effective tumour prevention therapy. Key findings: Glycolysis is upregulated in HRAS ^G12V expressing preneoplastic cells (PNCs) in zebrafish skin, and is required for PNC proliferation OXPHOS respiration is impaired in PNCs and metformin complex I inhibition specifically eliminates PNCs PNC undergo mitochondrial fragmentation and exhibit reduced membrane potential Mdivi reverses mitochondrial fragmentation in PNCs and triggers apoptosis

Methods for evaluating cell proliferation are important for research in the field of developmental biology, cancer biology and cell biology. Recent years, Click-iT EdU Assays by Invitrogen is gaining popularity due to its fast staining speed, mild tissue treatment condition, reproducibility and specificity. However, the standard kit from Invitrogen is designed for tissue cultured cells, hence the manufactory provided protocol is optimized for cells cultured on coverslips. EdU staining became a popular method to evaluate cell proliferation in vivo in zebrafish embryos. However, the protocols that we have tested in the past often yield inconsistent results due to variable EdU incorporation efficiency. Here we describe an EdU staining protocol that we optimized for zebrafish larvae, which incorporated a crucial EdU injection step. Our protocol was used successfully by many new students in training, without any issues.

The zebrafish is now an important model organism for cancer biology studies and provides unique and complementary opportunities in comparison to the mammalian equivalent. The translucency of zebrafish has allowed in vivo live imaging studies of tumour initiation and progression at the cellular level, providing novel insights into our understanding of cancer. Here we summarise the available transgenic zebrafish tumour models and discuss what we have gleaned from them with respect to cancer inflammation. In particular, we focus on the host inflammatory response towards transformed cells during the pre-neoplastic stage of tumour development. We discuss features of tumour-associated macrophages and neutrophils in mammalian models and present evidence that supports the idea that these inflammatory cells promote early stage tumour development and progression. Direct live imaging of tumour initiation in zebrafish models has shown that the intrinsic inflammation induced by pre-neoplastic cells is tumour promoting. Signals mediating leukocyte recruitment to pre-neoplastic cells in zebrafish correspond to the signals that mediate leukocyte recruitment in mammalian tumours. The activation state of macrophages and neutrophils recruited to pre-neoplastic cells in zebrafish appears to be heterogenous, as seen in mammalian models, which provides an opportunity to study the plasticity of innate immune cells during tumour initiation. Although several potential mechanisms are described that might mediate the trophic function of innate immune cells during tumour initiation in zebrafish, there are several unknowns that are yet to be resolved. Rapid advancement of genetic tools and imaging technologies for zebrafish will facilitate research into the mechanisms that modulate leukocyte function during tumour initiation and identify targets for cancer prevention.

The zebrafish is now an important model organism for cancer biology studies and provides some unique and complementary opportunities in comparison to the mammalian equivalent. The translucency of zebrafish has allowed in vivo live imaging studies of tumour initiation and progression at the cellular level thus providing novel insights into our understanding of cancer. Here we summarise and discuss available transgenic zebrafish tumour models and what we have gleaned from them with respect to cancer inflammation. In particular, we focus on the host inflammatory response toward transformed cells during the pre-neoplastic stage of tumour development. We discuss features of tumour associated macrophages and neutrophils in mammalian models and present evidence which supports the idea that these inflammatory cells promote early stage tumour development and progression. Direct live imaging of tumour initiation in zebrafish models has shown that the intrinsic inflammation induced by pre-neoplastic cells is tumour promoting. Signals mediating leukocyte recruitment to pre-neoplastic cells in zebrafish correspond to signals mediating leukocyte recruitment in mammalian tumours. The activation state of macrophages and neutrophils recruited to pre-neoplastic cells appears to be heterogenous, as seen in mammalian models, which provides an opportunity to study the plasticity of innate immune cells during tumour initiation. Although several potential mechanisms are described that might mediate the trophic function of innate immune cells during tumour initiation in zebrafish, there are several unknowns that are yet to be resolved. Rapid advancement of genetic tools and imaging technologies for zebrafish will facilitate research into the mechanisms that modulate leukocyte function during tumour initiation and identify targets for cancer prevention.

Roughly one third of the human population carries a latent Mycobacterium tuberculosis infection, with a 5-10% lifetime risk of reactivation to active tuberculosis and further spreading the disease. The mechanisms leading to the reactivation of a latent Mycobacterium tuberculosis infection are insufficiently understood. Here, we used a natural fish pathogen, Mycobacterium marinum, to model the reactivation of a mycobacterial infection in the adult zebrafish (Danio rerio). A low-dose intraperitoneal injection (∼40 colony-forming units) led to a latent infection, with mycobacteria found in well-organized granulomas surrounded by a thick layer of fibrous tissue. A latent infection could be reactivated by oral dexamethasone treatment, which led to disruption of the granuloma structures and dissemination of bacteria. This was associated with the depletion of lymphocytes, especially CD4⁺ T cells. Using this model, we verified that ethambutol is effective against an active disease but not a latent infection. In addition, we screened 15 mycobacterial antigens as postexposure DNA vaccines, of which RpfB and MMAR_4207 reduced bacterial burdens upon reactivation, as did the Ag85-ESAT-6 combination. In conclusion, the adult zebrafish-M. marinum infection model provides a feasible tool for examining the mechanisms of reactivation in mycobacterial infections, and for screening vaccine and drug candidates. This article has an associated First Person interview with the first author of the paper.

Tuberculosis (TB) remains a major global health challenge and the development of a better vaccine takes center stage in fighting the disease. For this purpose, animal models that are capable of replicating the course of the disease and are suitable for the early-stage screening of vaccine candidates are needed. A Mycobacterium marinum infection in adult zebrafish resembles human TB. Here, we present a pre-clinical screen for a DNA-based tuberculosis vaccine in the adult zebrafish using an M. marinum infection model. We tested 15 antigens representing different types of mycobacterial proteins, including the Resuscitation Promoting factors (Rpf), PE/PPE protein family members, other membrane proteins and metabolic enzymes. The antigens were expressed as GFP fusion proteins, facilitating the validation of their expression in vivo. The efficiency of the antigens was tested against a low-dose intraperitoneal M. marinum infection (≈ 40 colony forming units), which mimics a primary M. tuberculosis infection. While none of the antigens was able to completely prevent a mycobacterial infection, four of them, namely RpfE, PE5_1, PE31 and cdh, led to significantly reduced bacterial burdens at four weeks post infection. Immunization with RpfE also improved the survival of the fish against a high-dose intraperitoneal injection with M. marinum (≈ 10.000 colony forming units), resembling the disseminated form of the disease. This study shows that the M. marinum infection model in adult zebrafish is suitable for the pre-clinical screening of tuberculosis vaccines and presents RpfE as a potential antigen candidate for further studies.

Tuberculosis (TB) is a global health emergency. Up to one third of the world’s population is infected with Mycobacterium tuberculosis, and the pathogen continues to kill almost two million people annually. Currently, the means for preventing, diagnosing, and treating TB are unsatisfactory. One of the main reasons for the poor progress in TB research has been a lack of good animal models to study the latency, dormancy and reactivation of the disease. Although sophisticated in vitro and in silico methods suitable for TB research are constantly being developed, they cannot reproduce the complete vertebrate immune system and its interplay with pathogens and vaccines. However, the zebrafish has recently emerged as a useful alternative to more traditional models, such as mice, rabbits, guinea pigs, and non-human primates, for studying the complex pathophysiology of a mycobacterial infection. The model is based on the similarity between Mycobacterium marinum – a natural fish pathogen – and Mycobacterium tuberculosis. In both zebrafish larvae and adult fish, an infection with M. marinum leads to the formation of macrophage aggregates and granulomas, which resemble the M. tuberculosis infections in humans. In this review we will summarize the current status of the zebrafish model in TB research and highlight the advantages of using zebrafish to dissect mycobacterial virulence strategies as well as the host immune responses elicited against them. In addition, we will discuss the possibilities of using the adult zebrafish model for studying latency, dormancy, and reactivation in a mycobacterial infection.