Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism

Physiological states of bacterial cells exhibit a wide spectrum of timescale. Under nutrient-rich conditions, most of the cells in an isogenic bacterial population grow at certain rates, while a small subpopulation sometimes stays in a dormant state where the growth rates slow down by orders of magnitude. For revealing the origins of such heterogeneity of timescales, we studied the kinetic model of Escherichia coli central carbon metabolism including the dynamics of the energy currency molecules. We found that the model robustly exhibits both the growing- and the dormant state. In order to unveil the mechanism of distinct behaviours, we developed a recursive method to simplify the model without changing the qualitative feature of the dynamics. Analytical and numerical studies of the 2-variable minimal model revealed the necessary conditions for the distinct behaviour, namely, the depletion of energy due to the futile cycle and its non-uniform impact on the kinetics because of the coexistence of the energy currency-coupled and uncoupled reactions as well as branching of the network. The result is consistent with the experimental reports that the dormant cells commonly exhibit low ATP levels, and provides a possible explanation for the appearance of dormant cells that causes antibiotic persistence.

Microenvironment-mediated cancer dormancy: Insights from metastability theory

Dormancy is an evolutionarily conserved protective mechanism widely observed in nature. A pathological example is found during cancer metastasis, where cancer cells disseminate from the primary tumor, home to secondary organs, and enter a growth-arrested state, which could last for decades. Recent studies have pointed toward the microenvironment being heavily involved in inducing, preserving, or ceasing this dormant state, with a strong focus on identifying specific molecular mechanisms and signaling pathways. Increasing evidence now suggests the existence of an interplay between intracellular as well as extracellular biochemical and mechanical cues in guiding such processes. Despite the inherent complexities associated with dormancy, proliferation, and growth of cancer cells and tumor tissues, viewing these phenomena from a physical perspective allows for a more global description, independent from many details of the systems. Building on the analogies between tissues and fluids and thermodynamic phase separation concepts, we classify a number of proposed mechanisms in terms of a thermodynamic metastability of the tumor with respect to growth. This can be governed by interaction with the microenvironment in the form of adherence (wetting) to a substrate or by mechanical confinement of the surrounding extracellular matrix. By drawing parallels with clinical and experimental data, we advance the notion that the local energy minima, or metastable states, emerging in the tissue droplet growth kinetics can be associated with a dormant state. Despite its simplicity, the provided framework captures several aspects associated with cancer dormancy and tumor growth.

MacroH2A impedes metastatic growth by enforcing a discrete dormancy program in disseminated cancer cells

MacroH2A variants have been associated with tumor suppression through inhibition of proliferation and metastasis, as well as their role in cellular senescence. However, their role in regulating the dormant state of disseminated cancer cells (DCCs) remains unclear. Here we reveal that solitary dormant DCCs display increased levels of macroH2A variants in head and neck squamous cell carcinoma PDX models and patient samples compared to proliferating primary or metastatic lesions. We further demonstrate that microenvironmental and stress adaptive signals such as TGFβ2 and p38α/β, which induce DCC dormancy, upregulate macroH2A expression. Functionally, we find that overexpression of macroH2A variants is sufficient to induce tumor cells into dormancy and notably, inducible expression of the macroH2A2 variant suppresses the growth of DCCs into overt metastasis. However, this dormant state does not require well-characterized dormancy factors such as DEC2 and NR2F1, suggesting alternate pathways. Our transcriptomic analyses reveal that macroH2A2 overexpression inhibits E2F, RAS and MYC signaling programs, while upregulating inflammatory cytokines commonly secreted by senescent cells. Taken together, our results demonstrate that macroH2A2 enforces a stable dormant phenotype in DCCs by activating a select subset of dormancy and senescence genes that limit metastasis initiation.

PATHOMORPHOLOGY OF EXPERIMENTAL INFECTION CAUSED BY DORMANT YERSINIA PSEUDOTUBERCULOSIS STRAINS

In the 2000s, with the development of scientific research on the uncultivated (dormant) state of pathogenic bacteria, the ideas about persistent, chronically recurrent infections, difficult to respond to antibiotic therapy have begun to shape. However, regarding human pseudotuberculosis (Far Eastern scarlet-like fever, FESLF), this question remains open. While analyzing the pathology of pseudotuberculosis, its clinical and epidemic manifestation as FESLF, we identified the etiopathogenetic prerequisites for the disease recurrence and development of persistent infection [3]. In this study, it was found that the strains of Yersinia pseudotuberculosis, which were in a dormant state, caused the development of a peculiar granulomatous inflammation in target organs with pronounced delayed-type hypersensitivity reactions in vivo. To reproduce the experimental infection, sexually mature white mice were inoculated with the strain 512 Y. pseudotuberculosis, serotype I sored for 10 years at the Museum of the Research Somov Institute of Epidemiology and Microbiology and transformed into a dormant state. For comparative studies, a dormant form from vegetative bacteria of the strain 512 Y. pseudotuberculosis was obtained by exposure to a large dose of kanamycin (the minimum antibiotic dose was exceeded 25 times). The infecting dose of both forms of bacteria was 108 µ/mouse. Samples of target organs (lung, liver, spleen) were collected for histological examination on days 3, 7, 10, 14, 21 and 32 after infection. Histological sections with 3-5 µm thickness were stained with hematoxylin and eosin according to standard techniques. It was established that strains of Y. pseudotuberculosis in dormant state caused in vivo development of a peculiar granulomatous inflammation due to delayed-type hypersensitivity reactions (DHR), which characterizes the protective reaction in infected host and reflects formation of local, tissue immunity in target organs. The peculiarities of granulomatous inflammation were revealed, in comparison with that of found during infection with vegetative ("wild") Y. pseudotuberculosis bacteria, namely: the granulomas were predominantly small in size, clearly delimited from the surrounding tissue, without destruction of central zone cells and formation of the so-called "granulomas with central karyorrhexis" (terminology proposed by A.P. Avtsyn) [4]; perivascular infiltrates and vasculitis consisted mainly of lymphocytes and often had a follicle-like appearance, resembling the follicles in lymphoid organs; in the lungs, a well-marked reaction of the bronchial-associated lymphoid tissue was observed, and in the spleen, a follicular hyperplasia, indicating a T-cell defense reaction, was observed. Thus, the causative agent of Y.pseudotuberculosis infection / FESLF, being in a dormant state, initiates the development of immunomorphological changes of a protective nature such as productive granulomatous inflammation with reactions of local tissue immunity in target organs and can contribute to the formation of persistent infection.

The mTOR Pathway in Pluripotent Stem Cells: Lessons for Understanding Cancer Cell Dormancy

Currently, the success of targeted anticancer therapies largely depends on the correct understanding of the dormant state of cancer cells, since it is increasingly regarded to fuel tumor recurrence. The concept of cancer cell dormancy is often considered as an adaptive response of cancer cells to stress, and, therefore, is limited. It is possible that the cancer dormant state is not a privilege of cancer cells but the same reproductive survival strategy as diapause used by embryonic stem cells (ESCs). Recent advances reveal that high autophagy and mTOR pathway reduction are key mechanisms contributing to dormancy and diapause. ESCs, sharing their main features with cancer stem cells, have a delicate balance between the mTOR pathway and autophagy activity permissive for diapause induction. In this review, we discuss the functioning of the mTOR signaling and autophagy in ESCs in detail that allows us to deepen our understanding of the biology of cancer cell dormancy.

Propylene Polymerization and Deactivation Processes with Isoselective {Cp/Flu} Zirconocene Catalysts

Industrially relevant single-site precatalysts used to produce isotactic polypropylene (iPP) include C2-symmetric {SBI} and C1-symmetric {Cp/Flu} complexes of group 4 metals. While the latter can produce iPPs with a higher degree of isotacticity, they also suffer from poor productivity compared to their {SBI} counterparts. Several causes for this trend have been suggested—2,1-Regioinsertions are frequently pointed out, as they are suspected to drive the catalyst into a dormant state. While this event does not seem to significantly impact the productivity of {SBI} systems, the influence of these regioerror is poorly documented for isoselective {Cp/Flu} precatalysts. To address this issue, new Ph2X(Cp)(Flu) (Ph2X = Ph2C, FluC, Ph2Si) proligands (2a–k) and some of the corresponding dichlorozirconocenes (3a–h,k) were synthesized. These new compounds were characterized and tested in homogeneous propylene polymerization at 60 °C and the amounts of regioerrors in the resulting polymers were examined by 13C NMR spectroscopy. A possible correlation between poor productivity and a high number of regioerrors was investigated and is discussed. Furthermore, a C-H activation process in the bulky nBu3C substituent upon activation of 4c (the dimethylated analog of 3c) by B(C6F5)3 has been evidenced by NMR; DFT calculations support this C-H activation as a deactivation mechanism.

Potential of Immunotherapies in Treating Hematological Cancer-Infection Comorbidities—A Mathematical Modelling Approach

The immune system protects the human body against threats such as emerging cancers or infections, e.g., COVID-19. Mutated malignant cells may in many cases be controlled by the immune system to be kept at unnoticed low amount. However, a severe infection may compromise the immune system in controlling such malignant clones leading to escape and fatal cancer progression. A novel mechanism based computational model coupling cancer and infection to the adaptive immune system is presented and analyzed. The model pin-points important physiological mechanisms responsible for cancer progression and explains numerous medical observations. The progression of a cancers and the effects of treatments depend on cancer burden, the level of infection and on the efficiency of the adaptive immune system. The model exhibits bi-stability, i.e., gravitate towards one of two stable steady states: a harmless dormant state or a full-blown cancer-infection disease state. A borderline exists and if infection exceeds this for a sufficiently long period of time the cancer escapes. Early treatment is vital for remission and may control the cancer back into the stable dormant state. CAR T-cell immunotherapy is investigated by help of the model. The therapy significantly improves its efficacy in combination with antibiotics or immunomodulation.

Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism

Physiological states of bacterial cells exhibit a wide spectrum of timescale. Under the nutrient-rich conditions, most of the cells in an isogenic bacterial population grow at certain rates, while a small subpopulation sometimes stays in a dormant state where the growth rates slow down by orders of magnitude. What is the origin of such heterogeneity of timescales? Here we addressed this question by studying the kinetic model of Escherichia coli central carbon metabolism including the dynamics of the energy currency molecules, which have often been ignored. We found that the model robustly exhibits both the growing- and the dormant state. In order to unveil the mechanism of distinct behaviours, we developed a recursive method to simplify the model without changing the qualitative feature of the dynamics. Analytical and numerical studies of the 2-variable minimal model revealed the necessary conditions for the distinct behaviour, namely, the depletion of energy due to the futile cycle and its non-uniform impact to the kinetics because of the coexistence of the energy currency-coupled and uncoupled reactions as well as branching of the network. The result is consistent with the experimental evidences of the appearance of the futile cycle in mutants and provides a possible explanation for the appearance of dormant cells that causes antibiotic persistence.

Salmonella enters a dormant state within human epithelial cells for persistent infection

Salmonella Typhimurium (S. Typhimurium) is an enteric bacterium capable of invading a wide range of hosts, including rodents and humans. It targets different host cell types showing different intracellular lifestyles. S. Typhimurium colonizes different intracellular niches and is able to either actively divide at various rates or remain dormant to persist. A comprehensive tool to determine these distinct S. Typhimurium lifestyles remains lacking. Here we developed a novel fluorescent reporter, Salmonella Intracellular Analyzer (SINA), compatible for fluorescence microscopy and flow cytometry in single-bacterium level quantification. This identified a S. Typhimurium subpopulation in infected epithelial cells that exhibits a unique phenotype in comparison to the previously documented vacuolar or cytosolic S. Typhimurium. This subpopulation entered a dormant state in a vesicular compartment distinct from the conventional Salmonella-containing vacuoles (SCV) as well as the previously reported niche of dormant S. Typhimurium in macrophages. The dormant S. Typhimurium inside enterocytes were viable and expressed Salmonella Pathogenicity Island 2 (SPI-2) virulence factors at later time points. We found that the formation of these dormant S. Typhimurium is not triggered by the loss of SPI-2 effector secretion but it is regulated by (p)ppGpp-mediated stringent response through RelA and SpoT. We predict that intraepithelial dormant S. Typhimurium represents an important pathogen niche and provides an alternative strategy for S. Typhimurium pathogenicity and its persistence.