Tracing and targeting cancer stem cells: New venture for personalized molecular cancer therapy

Tumors consist of a mixture of heterogeneous cell types. Cancer stem cells(CSCs) are a minor sub-population within the bulk cancer fraction which has been foundto reconstitute and propagate the disease and to be frequently resistant to chemotherapy, irradiation, cytotoxic drugs and probably also against immune attack. CSCs are considered as the seeds of tumor recurrence, driving force of tumorigenesis and metastases. This underlines the urgent need for innovative methods to identify and target CSCs. However, the role and existence of CSCs in therapy resistance and cancer recurrence remains a topic of intense debate. The underlying biological properties of the tumor stem cells are extremely dependent on numerous signals, and the targeted inhibition of these stem cell signaling pathways is one of the promising approaches of the new antitumor therapy approaches. This perspective review article summarizes the novel methods of tracing CSCs and discusses the hallmarks of CSC identification influenced by the microenvironment or by having imperfect detection markers. In addition, explains the known molecular mechanisms of therapy resistance in CSCs as reliable and clinically predictive markers that could enable the use of new targeted antitumor therapy in the sense of personalized medicine.     

Analytical metabolomics: nutritional opportunities for personalized health

Nutrition is the cornerstone of health; survival depends on acquiring essential nutrients, and dietary components can both prevent and promote disease. Metabolomics, the study of all small molecule metabolic products in a system, has been shown to provide a detailed snapshot of the body's processes at any particular point in time, opening up the possibility of monitoring health and disease, prevention and treatment. Metabolomics has the potential to fundamentally change clinical chemistry and, by extension, the fields of nutrition, toxicology and medicine. Technological advances, combined with new knowledge of the human genome and gut microbiome, have made and will continue to make possible earlier, more accurate, less invasive diagnoses, all while enhancing our understanding of the root causes of disease and leading to a generation of dietary recommendations that enable optimal health. This article reviews the recent contributions of metabolomics to the fields of nutrition, toxicology and medicine. It is expected that these fields will eventually blend together through development of new technologies in metabolomics and genomics into a new area of clinical chemistry: personalized medicine.     

Gut microorganisms, mammalian metabolism and personalized health care

The mammalian gut microbiota interact extensively with the host through metabolic exchange and co-metabolism of substrates. Such metabolome-metabolome interactions are poorly understood, but might be implicated in the aetiology of many human diseases. In this paper, we assess the importance of the gut microbiota in influencing the disposition, fate and toxicity of drugs in the host, and conclude that appropriate consideration of individual human gut microbial activities will be a necessary part of future personalized health-care paradigms.     

The implications of electronic health record for personalized medicine

The emerging concept of an electronic health record (EHR) targeted at a patient centric, cross-institutional and longitudinal information entity (possibly spanning the individuals lifetime) has great promise for personalized medicine. In fact, it is probably the only vehicle through which we may truly realize the personalization of medicine beyond population-based genetic profiles that are expected to become part of medication and treatment indications in the near future. The new EHR standards include mechanisms that integrate clinical data with genomic testing results obtained through applying research-type procedures, such as full DNA sequencing, to an individual patient. Although the most optimal process for the utilization of integrated clinical-genomic data in the EHR framework is still unclear, the new Health Level Seven (HL7) Clinical Genomics Draft Standard for Trial Use suggests using the 'encapsulate & bubble-up' approach, which includes two main phases: the encapsulation of raw genomic data and bubbling-up the most clinically significant portions of that data, while associating it with clinical phenotypes residing in the individual's EHR.     

Tracing dynamic biological processes during phase transition

Background

Phase transition widely exists in the biological world, such as transformation of cell cycle phases, cell differentiation stages, disease development, and so on. Such a nonlinear phenomenon is considered as the conversion of a biological system from one phenotype/state to another. Studies on the molecular mechanisms of biological phase transition have attracted much attention, in particular, on different genotypes (or expression variations) in a specific phase, but with less of focus on cascade changes of genes' functions (or system state) during the phase shift or transition process. However, it is a fundamental but important mission to trace the temporal characteristics of a biological system during a specific phase transition process, which can offer clues for understanding dynamic behaviors of living organisms.

Results

By overcoming the hurdles of traditional time segmentation and temporal biclustering methods, a causal process model (CPM) in the present work is proposed to study the biological phase transition in a systematic manner, i.e. first, we make gene-specific segmentation on time-course expression data by developing a new boundary gene estimation scheme, and then infer functional cascade dynamics by constructing a temporal block network. After the computational validation on synthetic data, CPM was used to analyze the well-known Yeast cell cycle data. It was found that the dynamics of the boundary genes are periodic and consistent with the phases of the cell cycle, and the temporal block network indeed demonstrates a meaningful cascade structure of the enriched biological functions. In addition, we further studied protein modules based on the temporal block network, which reflect temporal features in different cycles.

Conclusions

All of these results demonstrate that CPM is effective and efficient comparing to traditional methods, and is able to elucidate essential regulatory mechanism of a biological system even with complicated nonlinear phase transitions.

     

Estimating incidence curves of several infections using symptom surveillance data

We introduce a method for estimating incidence curves of several co-circulating infectious pathogens, where each infection has its own probabilities of particular symptom profiles. Our deconvolution method utilizes weekly surveillance data on symptoms from a defined population as well as additional data on symptoms from a sample of virologically confirmed infectious episodes. We illustrate this method by numerical simulations and by using data from a survey conducted on the University of Michigan campus. Last, we describe the data needs to make such estimates accurate.     

Tracing the skeletal progenitor transition during postnatal bone formation

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Nuclear remodelling during viral infections

Because of their limited coding capacity, viruses are not able to encode all proteins that are required for their replication. Therefore, they depend on a wide variety of cellular functions and structures, such as the host cell nucleus. It has been shown that DNA, as well as RNA viruses, exploit the nucleus because it provides essential machinery for viral replication. On the other hand, the nucleus undergoes significant remodelling during viral usurpation or exploitation. Moreover, it is becoming increasingly clear that some subnuclear structures, such as promyelocytic leukaemia nuclear bodies, act as an antiviral defence mechanism, and several viruses antagonize this intracellular defence by modifying subnuclear structures. This article reviews the main alterations that take place in nucleus during viral infections.     

Maximum expiratory flow-volume curves during short periods of microgravity

To elucidate the effect of normal gravitation on the shape of the maximum expiratory flow-volume (MEFV) curve, we studied nine normal subjects in a National Aeronautics and Space Administration microgravity research aircraft. They performed multiple MEFV maneuvers at 0, 1, and approximately 2 G. The MEFV curves for each subject were filtered, aligned at residual volume, and ensemble averaged to produce an average MEFV curve for each state, allowing differences to be studied. Most subjects showed a decrease in the forced vital capacity at 0 G, which we attribute to an increased intrathoracic blood volume. In most of these subjects, the mean lung volume associated with a given flow was lower at 0 G over about the upper half of the vital capacity. This is similar to the change previously reported during headout immersion and is consistent with the known effect of engorgement of the lung with blood on elastic recoil. There were also consistent but highly individual changes in the position and magnitude of detailed features of the curve, the individual patterns being similar to those previously reported on transition from the erect to the supine position. This supports the idea that the location and motion of choke points that determine the detailed individual configuration of MEFV curves can be significantly influenced by gravitational forces, presumably via the effects of change in longitudinal tension on local airway pressure-diameter behavior and thus wave speed.     

Tracing epithelial stem cells during development, homeostasis, and repair

Epithelia ensure many critical functions of the body, including protection against the external environment, nutrition, respiration, and reproduction. Stem cells (SCs) located in the various epithelia ensure the homeostasis and repair of these tissues throughout the lifetime of the animal. Genetic lineage tracing in mice has allowed the labeling of SCs and their progeny. This technique has been instrumental in characterizing the origin and heterogeneity of epithelial SCs, their tissue location, and their differentiation potential under physiological conditions and during tissue regeneration.     

Orofacial clefts and infections during pregnancy

Orofacial clefts (OFCs) are common congenital malformations of the lip, palate, or both caused by complex genetic and environmental factors. Specific antibodies against viruses influenza, rubella, cytomegalovirus, Epstein-Barr, parotitis and hepatitis B were investigated serologically in children with orofacial clefts and in their mothers. The results were compared with those obtained in control children and their mothers. Evaluation of the results and their statistical processing supports the assumption that infection during pregnancy may have occurred in the series studied induced by viruses of influenza, rubella, cytomegalovirus and possibly also by the Epstein-Barr virus. No association with the viruses of hepatitis B and parotitis was established.     

Alternatively activated macrophages during parasite infections

Depending on the cytokine environment, macrophages can differentiate into distinct subsets that perform specific immunological roles. In this regard, the functions of macrophages activated by interferon gamma, referred to as classically activated macrophages, have been extensively documented, particularly during immune responses to infection. Recently, it was recognized that macrophages exposed to cytokines generated by T helper cell type 2 (Th2) cells exert an alternative activation program. However, the nature and functions of alternatively activated macrophages are ill defined. Evidence for the presence of alternatively activated macrophages and their possible influence in the outcome of several parasite diseases are discussed here.     

Bacteriophage burst size during multiple infections

A significant positive correlation was observed between multiplicity of infection and burst size of mycobacteriophage 13. During multiple infections, the average contribution of each infecting phage to the burst size was inversely correlated with multiplicity of infection even when bacterial resources were not limiting. We conclude that the efficiency of phage-coded functions rather than the extent of bacterial resources determines the burst size.