The Evolution of complexity in self-maintaining cellular information processing networks

We examine the role of self-maintenance (collective autocatalysis) in the evolution of computational biochemical networks. In primitive proto-cells (lacking separate genetic machinery) self-maintenance is a necessary condition for the direct reproduction and inheritance of what we here term Cellular Information Processing Networks (CIPNs). Indeed, partially reproduced or defective CIPNs may generally lead to malfunctioning or premature death of affected cells. We explore the interaction of this self-maintenance property with the evolution and adaptation of CIPNs capable of distinct information processing abilities. We present an evolutionary simulation platform capable of evolving artificial CIPNs from a bottom-up perspective. This system is an agent-based multi-level selectional Artificial Chemistry (AC) which employs a term rewriting system called the Molecular Classifier System (MCS). The latter is derived from the Holland broadcast language formalism. Using this system, we successfully evolve an artificial CIPN to improve performance on a simple pre-specified information processing task whilst subject to the constraint of continuous self-maintenance. We also describe the evolution of self-maintaining, crosstalking and multitasking, CIPNs exhibiting a higher level of topological and functional complexity. This proof of concept aims at contributing to the understanding of the open-ended evolutionary growth of complexity in artificial systems

Autocatalytic closure and the evolution of cellular information processing networks

Cellular Information Processing Networks (CIPNs) are chemical networks of interacting molecules occurring in living cells. Through complex molecular interactions, CIPNs are able to coordinate critical cellular activities in response to internal and external stimuli. We hypothesise that CIPNs may be abstractly regarded as subsets of collectively autocatalytic (i.e., organisationally closed) reaction networks. These closure properties would subsequently interact with the evolution and adaptation of CIPNs capable of distinct information processing abilities. This hypothesis is motivated by the fact that CIPNs may require a mechanism enabling the self-maintenance of core components of the network when subjected to internal and external perturbations and during cellular divisions. Indeed, partially replicated or defective CIPNs may lead to the malfunctioning and premature death of the cell. In this thesis, we evaluate different existing computational approaches to model and evolve chemical reaction networks in silico. Following this literature review, we propose an evolutionary simulation platform capable of evolving artificial CIPNs from a bottom-up perspective. This system is a novel agent-based Artificial Chemistry (AC) which employs a term rewriting system called the Molecular Classifier System (MCS.bl). The latter is derived from the Holland broadcast language formalism. Our first series of experiments focuses on the emergence and evolution of selfmaintaining molecular organisations in the MCS.bl. Such experiments naturally relate to similar studies conducted in ACs such as Tierra, Alchemy and α-universes. Our results demonstrate some counter-intuitive outcomes, not indicated in previous literature. We examine each of these “unexpected” evolutionary dynamics (including an elongation catastrophe phenomenon) which presented various degenerate evolutionary trajectories. To address these robustness and evolvability issues, we evaluate several model variants of the MCS.bl. This investigation illuminates the key properties required to allow the self-maintenance and stable evolution of closed reaction networks in ACs. We demonstrate how the elongation catastrophe phenomenon can be prevented using a multi-level selectional model of the MCS.bl (which acts both at the molecular and cellular level). Using this multi-level selectional MCS.bl which was implemented as a parallel system, we successfully evolve an artificial CIPN to perform a simple pre-specified information processing task. We also demonstrate how signalling crosstalk may enable the cooperation of distinct closed CIPNs when mixed together in the same reaction space. We finally present the evolution of closed crosstalking and multitasking CIPNs exhibiting a higher level of complexity

Intrinsic synergistic-topological mechanism versus synergistic-topological matrix in microtubule self-organization

Background In this body of work we investigate the synergistic-topological relationship during self-organization of the microtubule fiber in vitro, which is composed of straight, axially shifted and non-shifted, acentrosomal microtubules under crowded conditions. Methods We used electron microscopy to observe morphological details of ordered straight microtubules. This included the observation of the differences in length distribution between microtubules in ordered and non-ordered phases followed by the observation of the formation of interface gaps between axially shifted and ordered microtubules. We performed calculations to confirm that the principle of summation of pairwise electrostatic forces act between neighboring microtubules all their entire length. Results We have shown that the self-organization of a microtubule fiber imposes a variety of topological restrictions onto its constituting components: (a) tips of axially shifted neighboring microtubules are not in direct contact but rather create an ‘interface gap’; (b) fibers are always composed of a restricted number of microtubules at given solution conditions; (c) the average length of microtubules that constitute a fiber is always shorter than that of microtubules outside a fiber; (d) the length distribution of microtubules that constitute a fiber is narrower than that of microtubules outside a fiber and this effect is more pronounced at higher GTP-tubulin concentrations; (e) a cooperative motion of fiber microtubules due to actualization of the summation principle of pairwise electrostatic forces; (f) appearance of local GTP-tubulin depletion immediately in front of the tips of fiber microtubules. Conclusion Overall our data indicate that under crowded conditions in vitro, the self-organization of a microtubule fiber is governed by an intrinsic synergistic-topological mechanism, which in conjunction with the topological changes, GTP-tubulin depletion, and cooperative motion of fiber constituting microtubules, may generate and maintain a ‘synergistic-topological matrix’. Failure of the mechanism to form biologically feasible microtubule synergistic-topological matrix may, per se, precondition tumorigenesis. © 2014 BioMed Central Lt

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Anchor or Accelerate – A Study on Cancer Cell Adhesion and Motility

Cell migration and adhesion to the extracellular matrix (ECM) are crucial in many biological and pathological processes such as morphogenesis, tissue repair, inflammatory responses, survival, and cancer. Cell-matrix adhesion is mediated by the integrin family of transmembrane receptors, which not only anchor cells to their surroundings, but also transmit bidirectional signalling at the cell surface and couple the ECM to the cytoskeleton. Another group of adhesion receptors are the syndecan proteoglycans, which engage the ECM and possess signalling activity in response to a variety of ligands. Cell migration is a complex process that requires spatial and temporal coordination of adhesion, cell contractility, intracellular traffic of integrins, and matrix turnover by matrix metalloproteinases (MMPs). Thus, integrins and syndecans, as well as MMPs, play essential roles in cancer cell migration and invasion. The understanding of the cooperation of syndecans and integrins was broadened in this thesis study. The results reveal that syndecan-1 functions in concert with 21 integrin in cell adhesion to collagen, whereas syndecan-4 is essential in 21 integrin-mediated matrix contraction. Finally, oncogenic K-Ras was shown to regulate 21 integrin, membrane-type 1 MMP, and syndecan-1 and -4 expression and their cooperation in cell invasion. Epithelial-mesenchymal transition (EMT) is fundamental during embryogenesis and organ development. Activation of EMT processes, including the upregulation of mesenchymal intermediate filament protein vimentin, has also been implicated in the acquisition of a malignant phenotype by epithelial cancer cells. Members of the protein kinase C (PKC) superfamily are involved in cell migration and various integrindependent cellular functions. One aim of this work was to shed light on the role of vimentin in the regulation of integrin traffic and cell motility. In addition, the mechanism by which vimentin participates in EMT was investigated. The results show that integrin recycling and motility are dependent on the PKC–mediated phosphorylation of vimentin. In addition, vimentin was found to be a positive regulator of EMT and regulate the expression of several migratory genes. Specifically, vimentin governs the expression of receptor tyrosine kinase Axl, which is implicated in tumour growth and metastasis. Taken together, the findings described in this thesis reveal novel aspects of the complex interplay between distinct cellular components: integrins, syndecans, and the vimentin cytoskeleton, which all contribute to the regulation of human cancer cell adhesion, migration, and invasion.Siirretty Doriast

Regulation of BAP1 tumor suppressor complex by post-translational modifications

Le régulateur transcriptionnel BAP1 est une déubiquitinase nucléaire (DUB) dont le substrat est l’histone H2A modifiée par monoubiquitination au niveau des residus lysines 118 et 119 (K118/K119). Depuis les dernières années, BAP1 emerge comme un gene suppresseur de tumeur majeur. En effet, BAP1 est inactivé dans un plethore de maladies humaines héréditaires et sporadiques. Cependant, malgré l’accumulation significative des connaissances concernant l’occurrence, la pénétrance et l’impact des défauts de BAP1 sur le développement de cancers, ses mécanismes d’action et de régulation restent très peu compris. Cette étude est dédiée à la caractérisation moléculaire et fonctionnelle du complexe multi-protéique de BAP1 et se présente parmi les premiers travaux décrivant sa régulation par des modifications post-traductionnelles. D’abord, nous avons défini la composition du corps du complexe BAP1 ainsi que ses principaux partenaires d’interaction. Ensuite, nous nous sommes spécifiquement intéressés a investiguer d’avantage deux principaux aspects de la régulation de BAP1. Nous avons d’abord décrit l’inter-régulation entre deux composantes majeures du complexe BAP1, soit HCF-1 et OGT. D’une manière très intéressante, nous avons trouvé que le cofacteur HCF-1 est un important régulateur des niveaux protéiques d’OGT. En retour, OGT est requise pour la maturation protéolytique de HCF-1 en promouvant sa protéolyse par O-GlcNAcylation, un processus de régulation très important pour le bon fonctionnement de HCF-1. D’autre part, nous avons découvert un mécanisme unique de régulation de BAP1 médiée par l’ubiquitine ligase atypique UBE2O. en effet, UBE2O se caractérise par le fait qu’il s’agit aussi bien d’une ubiquitine conjuratrice et d’une ubiquitine ligase. UBE2O, multi-monoubiquitine BAP1 au niveau de son domaine NLS et promeut son exclusion du noyau, le séquestrant ainsi dans le cytoplasme. De façon importante, nos travaux ont permis de mettre de l’emphase sur le rôle de l’activité auto-catalytique de chacune de ces enzymes, soit l’activité d’auto-déubiquitination de BAP1 qui est requise pour la maintenance de sa localisation nucléaire ainsi que l’activité d’auto-ubiquitination d’UBE2O impliquée dans son transport nucléo-cytoplasmique. De manière significative, nous avons trouvé que des défauts au niveau de l’auto-déubiquitination de BAP1 due à des mutations associées à certains cancers indiquent l’importance d’une propre regulation de cette déubiquitinase pour les processus associés à la suppression de tumeurs.BAP1 is a nuclear deubiquitinating enzyme (DUB) that acts as a transcription regulator and a DUB of nucleosomal histone H2AK119. In the recent years, it has become clear that BAP1 is a major tumor suppressor, inactivated in a plethora of hereditary and sporadic human malignancies. Although, we now accumulated a significant body of knowledge in respect to the occurrence, penetrance and impact of BAP1 disruption in cancer, its mechanism of action and regulation remained poorly defined. This work is dedicated to the biochemical and functional characterization of the BAP1 multiprotein complex and presents one of the first cases regarding its regulation by post-translational modifications. First, we defined the initial composition of the BAP1 complex and its main interacting components. Second, we specifically focused on two aspects of BAP1 regulation. We described the cross regulation between the two major components of the complex namely HCF-1 and OGT. We found that HCF-1 is important for the maintenance of the cellular levels of OGT. OGT, in turn, is required for the proper maturation of HCF-1 by promoting O-GlcNAcylation-mediated limited proteolysis of its precursor. Third, we discovered an intricate regulatory mechanism of BAP1 mediated by the atypical ubiquitin ligase UBE2O. UBE2O multi-monoubiquitinates BAP1 on its NLS and promotes its exclusion from the nucleus. Importantly, our work emphasises the role of the autocatalytic activity of both enzymes namely the auto-deubiquitination activity of BAP1, required for the maintenance of nuclear BAP1 and the auto-ubiquitination of UBE2O implicated in its nucleocytoplasmic transport. Significantly, we found that auto-deubiquitination of BAP1 is disrupted by cancer-associated mutations, indicating the involvement of this process in tumor suppression

Cooperation of MT1-MMP and receptor tyrosine kinase signalling in cancer cell invasion

Cancer metastasis is a stepwise process of cancer cell dissemination from a primary tumour into adjacent and distant tissues and causes around 90 % of cancer-associated mortality. Metastatic cancer dissemination is initiated and promoted by intracellular and intercellular signalling within tumour microenvironment. Extracellular matrix (ECM) degradation also promotes cancer cell invasion and metastasis in many types of cancer. Membrane type-1 matrix metalloproteinase (MT1-MMP) degrades variety of ECM components and cell surface proteins as well as modulates numerous intracellular signalling pathways to regulate cancer invasion. The molecular mechanisms of pro-invasive MT1-MMP activities are getting more attention to reveal cancer-associated cooperative signalling, which will aid in planning more efficient and effective therapeutic interventions for patients with cancer. In the current studies, we performed a genome-wide gain-of-function human kinome screen to identify cancer-associated upstream and co-operating signalling for MT1-MMP activities. We identified both known and novel positive regulators of MT1-MMP. Among the novel MT1-MMP regulators we focused on the functions of two receptor tyrosine kinases, namely fibroblast growth factor receptor 4 (FGFR4) and Eph receptor type A2 (EphA2) in cancer cell invasion. Overexpression and aberrant signalling of these kinases are linked to aggressive cancer progression and anti-cancer drug resistance. A single nucleotide polymorphism (SNP) of FGFR4 (G388R) associated with poor cancer prognosis was identified as a positive regulator of MT1-MMP activity. We revealed that the complexes of MT1-MMP and FGFR4-R388 risk variant stabilised and activated both MT1-MMP and FGFR4 proteins, resulting in enhancing FGF signalling and pericellular proteolytic activities of MT1-MMP. The FGFR4-R388-MT1-MMP axis induced epithelial-to-mesenchymal transition, promoting prostate carcinoma cell invasion and invasive growth within collagen matrix and in mouse xenograft models. In contrast, the FGFR4-G388 variant and MT1-MMP down-regulated each other. EphA2 was co-expressed with MT1-MMP in invasive breast carcinoma cells, where EphA2 signalling increased MT1-MMP transcription. MT1-MMP in turn cleaved EphA2 in protein complexes on the same cell-surface. This cleavage coupled with EphA2-dependent Src activation triggered intracellular EphA2 translocation and an increase in RhoA activity, leading to actomyosine contraction, cell-cell repulsion, and cell junction disassembly. These signalling events ultimately induced cell invasion phenotype transition from collective to single-cell within three-dimensional collagen matrix and in vivo. Taken together, these studies identified the FGFR4-R388 variant and EphA2 as novel co-operators for pro-invasive MT1-MMP activities in cancer invasion. FGFR4 genetic background affects the activity of an FGFR4-MT1-MMP complex in cancer progression, and an EphA2-MT1-MMP axis regulates cancer invasion plasticity. These findings provide novel insights into the cooperative molecular basis of pro-invasive capabilities of MT1-MMP and FGF and EphA2 signalling in cancer cell invasion.Syövän metastasointi on portaittainen prosessi syöpäsolun leviämisestä primäärikasvaimesta viereisiin ja etäisempiin kudoksiin ja se aiheuttaa 90% syöpiin liittyvästä kuolleisuudesta. Metastaattinen syövän leviäminen saa alkunsa ja se edistyy kasvaimen mikroympäristön solunsisäisen ja solujenvälisen signaloinnin kautta. Soluväliaineen hajoaminen myös edistää syöpäsolujen invaasiota ja ja metastasointia monissa syöpätyypeissä. Solukalvoon kiinnittynyt tyypin 1 matriksin metalloproteinaasi (MT1-MMP) hajottaa erilaisia soluväliaineen komponentteja ja solukalvon proteiineja sekä moduloi useita solunsisäisiä signalointiketjuja säädelläkseen syövän invaasiota. MT1-MMP:n invasiivisuutta edistävän toiminnan molekulaaristen mekanismien osakseen saama lisääntyvä huomio valottaa syöpään liittyvää kooperatiivista signalointia, mikä tulee auttamaan tehokkaampien hoitojen suunnittelussa syöpäpotilaille. Tutkimuksissamme suoritimme genomin laajuisen gain-of-function kinomiseulonnan tunnistaaksemme syövän kanssa assosioituvaa ja MT1-MMP:n aktiivisuuteen liittyvää yläjuoksun ja kooperatiivista signalointia. Tunnistimme sekä ennestään löydettyjä että uusia positiivisia MT1-MMP:n säätelijöitä. Uusista MT1-MMP:n säätelijöistä keskityimme kahden reseptorityrosiinikinaasin, fibroblastikasvutekijän reseptori 4:n (FGFR4) ja Eph-reseptori tyyppi A2:n (EphA2), toimintaan syöpäsolujen leviämisessä. Näiden kinaasien yli-ilmentyminen ja poikkeava signalointi liittyvät aggressiiviseen syövän etenemiseen ja vastustuskykyyn syöpälääkkeitä kohtaan. Huonoon syöpäennusteeseen assosioituva FGFR4:n yhden nukleotidin polymorfismi (SNP) G388R tunnistettiin MT1-MMP:n toiminnan positiiviseksi säätelijäksi. Paljastimme MT1-MMP:n ja FGFR4-R388 riskivariantin kompleksien stabiloivan ja aktivoivan sekä MT1-MMP- että FGFR4-proteiineja johtaen FGF-signaloinnin tehostumiseen ja MT1-MMP:n solunläheiseen proteolyyttiseen aktiivisuuteen. FGFR4-R388-MT1-MMP-akseli indusoi epiteliaali-mesenkymaalitransition (EMT) edistäen eturauhaskarsinoomasolujen invaasiota ja invasiivista kasvua kollageenimatriksissa ja hiiren ksenograftimallissa. Sitä vastoin FGFR4-G388-variantti ja MT1-MMP vaimennussäätelivät toisiaan. EphA2 ilmentyi yhdessä MT1-MMP:n kanssa invasiivissa rintakarsinoomasoluissa, missä EphA2-signalointi lisäsi MT1-MMP:n transkriptiota. MT1-MMP puolestaan pilkkoi EphA2:ta proteiinikomplekseissa samalla solukalvolla. Tämä pilkkominen yhdessä EphA2-riippuvaisen Src-aktivaation kanssa sai aikaan solunsisäisen EphA2:n translokaation ja RhoA-aktiivisuuden lisääntymisen johtaen aktomyosiinin supistumiseen, solujenväliseen repulsioon ja soluliitoksen hajoamiseen. Nämä signalointitapahtumat lopulta indusoivat invaasiofenotyypin muutoksen kollektiivisesta yksittäissoluiseen kolmiulotteisessa kollageenimatriksissa ja in vivo. Yhdessä nämä tutkimukset tunnistivat FGFR4-R388-variantin ja EphA2:n uusina kooperaattoreina invaasiota edistävässä MT1-MMP-aktiivisuudessa syövän invaasiossa. FGFR4:n geneettinen tausta vaikuttaa FGFR4-MT1-MMP-kompleksin aktiivisuuteen syövän etenemisessä ja EphA2-MT1-MMP-akseli säätelee syöpäinvaasion plastisuutta. Nämä löydökset tarjoavat uusia näkemyksiä MT1-MMP-, FGF- ja EphA2-signaloinnin invaasiota edistävien kykyjen kooperatiiviseen molekulaariseen perustaan syöpäsolun invaasiossa

Spatial-temporal regulation of EGFR phosporylation by protein tyrosine phosphatases

The activity of the epidermal growth factor receptor (EGFR) and its interactions with protein tyrosine phosphatases (PTPs) is what determines growth factor signaling. Due to its intrinsic autocatalytic properties, EGFR can undergo autonomous ligand independent activation. EGFR in this case, cycles between the plasma membrane (PM) and recycling endosomes where PTPs dephosphorylate the receptor to avoid spurious receptor signals. EGF-induced receptor dimerization results in a robust trans-phosphorylation of tyrosine residues that allows stable binding of signaling effectors. The majority of EGFR at the PM is internalized and undergoes degradation in lysosomal compartment. After internalization, the EGFR encounters PTPs at different cellular locations, which thereby regulate the signal duration of the receptor. Moreover, specific dephosphorylation of phosphotyrosines that are required for ubiquitin ligase (Cbl) binding reduces the receptor ubiquitylation and thereby its degradation rate. Due to their dephosphorylation activity, PTPs were thought as negative regulators of RTK signalling, but it has been shown that PTPs also promote receptor phosphorylation by activating cytosolic kinases that in turn phosphorylate RTKs (Julien et al., 2011). To understand the spatial-temporal regulation of EGFR phosphorylation by PTPs, we used CA-FLIM (Grecco et al., 2010). This method allowed us to quantify the phosphorylated fraction of EGFR in cells, upon perturbation of PTP expression by siRNAs or cDNAs. Upon opposing perturbations, we identified several PTPs that have indicated either a negative or positive effect on EGFR phosphorylation. Classification of the temporal phosphorylation profiles of EGFR discovered 5 functional groups of PTPs acting at early and/or late time points after EGF stimulation. PTPs within each group showed differences in their regulatory influence highlighting individual impact in EGF signaling. Predominantly cytosolic PTPs regulated early EGFR phosphorylation, whereas receptor-like PTPs (RPTPs) induced a transient response profile. Analysis of the spatial-temporal phosphorylation profile of EGFR upon PTPRA, PTPN1 or PTPN2 expression showed an almost abolished axial phosphorylation of EGFR that might promote receptor recycling. In contrast, we identified a positive regulatory function of MTM1, DUSP7 and PTPN21 that was further validated using multi-parametric single cell information. These PTPs induced an early amplification of receptor phosphorylation near the PM. Our results strongly suggest that MTM1 and PTPN21 inhibit the degradation pathway and thereby enhancing the phosphorylated fraction of internalized EGFR. In summary, the presented work provides novel insights about when and where PTPs regulate EGFR phosphorylation and how this could affect cellular responses