Denise M. Wolf

Control, exploitation and tolerance of intracellular noise

Noise has many roles in biological function, including generation of errors in DNA replication leading to mutation and evolution, noise-driven divergence of cell fates, noise-induced amplification of signals, and maintenance of the quantitative individuality of cells. Yet there is order to the behaviour and development of cells. They operate within strict parameters and in many cases this behaviour seems robust, implying that noise is largely filtered by the system. How can we explain the use, rejection and sensitivity to noise that is found in biological systems? An exploration of the sources and consequences of noise calls for the use of stochastic models.

Motifs, modules and games in bacteria

Global explorations of regulatory network dynamics, organization and evolution have become tractable thanks to high-throughput sequencing and molecular measurement of bacterial physiology. From these, a nascent conceptual framework is developing, that views the principles of regulation in term of motifs, modules and games. Motifs are small, repeated, and conserved biological units ranging from molecular domains to small reaction networks. They are arranged into functional modules, genetically dissectible cellular functions such as the cell cycle, or different stress responses. The dynamical functioning of modules defines the organisms strategy to survive in a game, pitting cell against cell, and cell against environment. Placing pathway structure and dynamics into an evolutionary context begins to allow discrimination between those physical and molecular features that particularize a species to its surroundings, and those that provide core physiological function. This approach promises to generate a higher level understanding of cellular design, pathway evolution and cellular bioengineering.

Subtype and pathway specific responses to anticancer compounds in breast cancer

Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many of the molecular subtypes and pathways found in tumors, suggesting that treatment of cell lines with candidate therapeutic compounds can guide identification of associations between molecular subtypes, pathways, and drug response. In a test of 77 therapeutic compounds, nearly all drugs showed differential responses across these cell lines, and approximately one third showed subtype-, pathway-, and/or genomic aberration-specific responses. These observations suggest mechanisms of response and resistance and may inform efforts to develop molecular assays that predict clinical response.

Complexity in bacterial cell–cell communication: Quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay

A common form of quorum sensing in Gram-positive bacteria is mediated by peptides that act as phosphatase regulators (Phr) of receptor aspartyl phosphatases (Raps). In Bacillus subtilis, several Phr signals are integrated in sporulation phosphorelay signal transduction. We theoretically demonstrate that the phosphorelay can act as a computational machine performing a sensitive division operation of kinase-encoded signals by quorum-modulated Rap signals, indicative of cells computing a “food per cell” estimate to decide whether to enter sporulation. We predict expression from the rapA-phrA operon to bifurcate as relative environmental signals change in a developing population. We experimentally observe that the rapA-phrA operon is heterogeneously induced in sporulating microcolonies. Uninduced cells sporulate rather synchronously early on, whereas the RapA/PhrA subpopulation sporulates less synchronously throughout later stationary phase. Moreover, we show that cells sustain PhrA expression during periods of active growth. Together with the model, these findings suggest that the phosphorelay may normalize environmental signals by the size of the (sub)population actively competing for nutrients (as signaled by PhrA). Generalizing this concept, the various Phrs could facilitate subpopulation communication in dense isogenic communities to control the physiological strategies followed by differentiated subpopulations by interpreting (environmental) signals based on the spatiotemporal community structure.

Memory in microbes: quantifying history-Dependent behavior in a bacterium.

Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These “memory” effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to ‘remember’ 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy.

Modularity of stress response evolution

Responses to extracellular stress directly confer survival fitness by means of complex regulatory networks. Despite their complexity, the networks must be evolvable because of changing ecological and environmental pressures. Although the regulatory networks underlying stress responses are characterized extensively, their mechanism of evolution remains poorly understood. Here, we examine the evolution of three candidate stress response networks (chemotaxis, competence for DNA uptake, and endospore formation) by analyzing their phylogenetic distribution across several hundred diverse bacterial and archaeal lineages. We report that genes in the chemotaxis and sporulation networks group into well defined evolutionary modules with distinct functions, phenotypes, and substitution rates as compared with control sets of randomly chosen genes. The evolutionary modules vary in both number and cohesiveness among the three pathways. Chemotaxis has five coherent modules whose distribution among species shows a clear pattern of interdependence and rewiring. Sporulation, by contrast, is nearly monolithic and seems to be inherited vertically, with three weak modules constituting early and late stages of the pathway. Competence does not seem to exhibit well defined modules either at or below the pathway level. Many of the detected modules are better understood in engineering terms than in protein functional terms, as we demonstrate using a control-based ontology that classifies gene function according to roles such as “sensor,” “regulator,” and “actuator.” Moreover, we show that combinations of the modules predict phenotype, yet surprisingly do not necessarily correlate with phylogenetic inheritance. The architectures of these three pathways are therefore emblematic of different modes and constraints on evolution.

The Neoadjuvant Model is Still the Future for Drug Development in Breast Cancer

The many improvements in breast cancer therapy in recent years have so lowered rates of recurrence that it is now difficult or impossible to conduct adequately powered adjuvant clinical trials. Given the many new drugs and potential synergistic combinations, the neoadjuvant approach has been used to test benefit of drug combinations in clinical trials of primary breast cancer. A recent FDA-led meta-analysis showed that pathologic complete response (pCR) predicts disease-free survival (DFS) within patients who have specific breast cancer subtypes. This meta-analysis motivated the FDAs draft guidance for using pCR as a surrogate endpoint in accelerated drug approval. Using pCR as a registration endpoint was challenged at ASCO 2014 Annual Meeting with the presentation of ALTTO, an adjuvant trial in HER2-positive breast cancer that showed a nonsignificant reduction in DFS hazard rate for adding lapatinib, a HER-family tyrosine kinase inhibitor, to trastuzumab and chemotherapy. This conclusion seemed to be inconsistent with the results of NeoALTTO, a neoadjuvant trial that found a statistical improvement in pCR rate for the identical lapatinib-containing regimen. We address differences in the two trials that may account for discordant conclusions. However, we use the FDA meta-analysis to show that there is no discordance at all between the observed pCR difference in NeoALTTO and the observed HR in ALTTO. This underscores the importance of appropriately modeling the two endpoints when designing clinical trials. The I-SPY 2/3 neoadjuvant trials exemplify this approach. Clin Cancer Res; 21(13); 2911–5. ©2015 AACR.

A gene signature for late distant metastasis in breast cancer identifies a potential mechanism of late recurrences

Breast cancer risk of recurrence is known to span 20 years, yet existing prognostic signatures are best at predicting early recurrences (≤5 years). There is a critical need to identify those patients at risk of late‐relapse (>5 years), in order to select potential candidates for further treatment and to identify molecular targets for such treatment.

Gene Co-Expression Modules as Clinically Relevant Hallmarks of Breast Cancer Diversity

Co-expression modules are groups of genes with highly correlated expression patterns. In cancer, differences in module activity potentially represent the heterogeneity of phenotypes important in carcinogenesis, progression, or treatment response. To find gene expression modules active in breast cancer subpopulations, we assembled 72 breast cancer-related gene expression datasets containing ∼5,700 samples altogether. Per dataset, we identified genes with bimodal expression and used mixture-model clustering to ultimately define 11 modules of genes that are consistently co-regulated across multiple datasets. Functionally, these modules reflected estrogen signaling, development/differentiation, immune signaling, histone modification, ERBB2 signaling, the extracellular matrix (ECM) and stroma, and cell proliferation. The Tcell/Bcell immune modules appeared tumor-extrinsic, with coherent expression in tumors but not cell lines; whereas most other modules, interferon and ECM included, appeared intrinsic. Only four of the eleven modules were represented in the PAM50 intrinsic subtype classifier and other well-established prognostic signatures; although the immune modules were highly correlated to previously published immune signatures. As expected, the proliferation module was highly associated with decreased recurrence-free survival (RFS). Interestingly, the immune modules appeared associated with RFS even after adjustment for receptor subtype and proliferation; and in a multivariate analysis, the combination of Tcell/Bcell immune module down-regulation and proliferation module upregulation strongly associated with decreased RFS. Immune modules are unusual in that their upregulation is associated with a good prognosis without chemotherapy and a good response to chemotherapy, suggesting the paradox of high immune patients who respond to chemotherapy but would do well without it. Other findings concern the ECM/stromal modules, which despite common themes were associated with different sites of metastasis, possibly relating to the “seed and soil” hypothesis of cancer dissemination. Overall, co-expression modules provide a high-level functional view of breast cancer that complements the “cancer hallmarks” and may form the basis for improved predictors and treatments.

Bifurcation of power electronic circuits

Abstract This paper studies various bifurcations of periodic orbits in power electronic circuits: cyclic fold bifurcations, period-doubling bifurcations, and bifurcations due to Poincare map discontinuities. We focus on circuits operating under closed-loop control and/or containing nonlinear reactive components. Section III contains an exploration of cyclic fold bifurcations and the associated resonant jump phenomenon in circuits containing saturable reactors. Section IV gives a comprehensive overview of period-doubling phenomena in closed-loop DC-DC conversion circuits. We study circuits with homeomorphic and unimodal Poincare maps, those that period-double a single time and those that period-double repeatedly in a cascade to chaos. This section ends with a result relating non-genericity of a period-doubling bifurcation to halfwave orbital symmetry. An interesting feature of power electronic circuits is that they may have Poincare maps that are continuous but not everywhere differentiable, or discontinuous. In Section V we study, in detail, bifurcation behavior in a thyristor controlled VAR compensator, understood in terms of Poincare map discontinuities. We show that Poincare map discontinuities are due to jumps in circuit switching times. We show how map discontinuities lead to steady state jump phenomena, and distinguish between transient behavior related to switch time jumps and steady state bifurcations. The paper ends with an Appendix, in which concepts underlying cyclic fold bifurcations for the case of a continuous but not everywhere differentiable map are developed.