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Disrupted molecular pathways are often robustly associated with disease outcome in cancer.sup.1-3. Although biologically informative transcriptional pathways can be revealed by RNA sequencing (RNA-seq) at up to hundreds of folds reduction in conventionally used coverage.sup.4-6, it remains unknown how low-depth sequencing datasets perform in the challenging context of developing transcriptional signatures to predict clinical outcomes. Here we assessed the possibility of cancer prognosis with shallow tumor RNA-seq, which would potentially enable cost-effective assessment of much larger numbers of samples for deeper biological and predictive insights. By statistically modeling the relative risk of an adverse outcome for thousands of subjects in The Cancer Genome Atlas.sup.7-13, we present evidence that subsampled tumor RNA-seq data with a few hundred thousand reads per sample provide sufficient information for outcome prediction in several types of cancer. Analysis of predictive models revealed robust contributions from pathways known to be associated with outcomes. Our findings indicate that predictive models of outcomes in cancer may be developed with dramatically increases in sample numbers at low cost, thus potentially enabling the development of more realistic predictive models that incorporate diverse variables and their interactions. This strategy could also be used, for example, in longitudinal analysis of multiple regions of a tumor alongside treatment for quantitative modeling and prediction of outcome in personalized oncology. Application of machine-learning models on very shallow RNA sequencing data maintains predictive performance across different tumor types., Author(s): Pedro Milanez-Almeida [sup.1] [sup.2] , Andrew J. Martins [sup.3] , Ronald N. Germain [sup.1] , John S. Tsang [sup.2] [sup.3] Author Affiliations: (1) Lymphocyte Biology Section, Laboratory of Immune [...]

Regulatory T (Treg) cells are essential for maintaining self-tolerance and modulating inflammatory immune responses. Treg cells either develop within the thymus or are converted from CD4+ naive T (Tnaive) cells in the periphery. The Treg-cell population size is tightly controlled and Treg-cell development and homeostasis have been intensively studied; however, quantitative information about mechanisms of peripheral Treg-cell homeostasis is lacking. Here we developed the first mathematical model of peripheral Treg-cell homeostasis, incorporating secondary lymphoid organs as separate entities and encompassing factors determining the size of the Treg-cell population, namely thymic output, homeostatic proliferation, peripheral conversion, transorgan migration, apoptosis, and the Tnaive-cell population. Quantitative data were collected by monitoring Tnaive-cell homeostasis and Treg-cell rebound after selective in vivo depletion of Treg cells. Our model predicted the previously unanticipated possibility that Treg cells regulate migration of Tnaive cells between spleen and peripheral lymph nodes (LNs), whereas migration of Treg cells between these organs can largely be neglected. Furthermore, our simulations suggested that peripheral conversion significantly contributed to the maintenance of the Treg-cell population, especially in LNs. Hence, we provide the first estimation of the peripheral Treg-cell conversion rate and propose additional facets of Treg-cell-mediated immune regulation that may previously have escaped attention. [ABSTRACT FROM AUTHOR]

Several mechanisms enable immunological self-tolerance. Regulatory T cells (Tregs) are a specialized T cell subset that prevents autoimmunity and excessive immune responses, but can also mediate detrimental tolerance to tumors and pathogens in a Foxp3-dependent manner. Genetic tools exploiting the foxp3 locus including bacterial artificial chromosome (BAC)-transgenic DEREG mice have provided essential information on Treg biology and the potential therapeutic modulation of tolerance. In DEREG mice, Foxp3+ Tregs selectively express eGFP and diphtheria toxin (DT) receptor, allowing for the specific depletion of Tregs through DT administration. We here provide a detailed overview about important considerations such as DT toxicity, which affects any mouse strain treated with DT, and Treg rebound after depletion. Additionally, we point out the specific advantages of BAC-transgenic DEREG mice including their suitability to study organ-specific autoimmunity such as type I diabetes. Moreover, we discuss recent insights into the role of Tregs in viral infections. In summary, DEREG mice are an important tool to study Treg-mediated tolerance and its therapeutic circumvention. [ABSTRACT FROM AUTHOR]

Regulatory T (Treg) cells are essential for maintaining self-tolerance and modulating inflammatory immune responses. Treg cells either develop within the thymus or are converted from CD4(+) naive T (Tnaive) cells in the periphery. The Treg-cell population size is tightly controlled and Treg-cell development and homeostasis have been intensively studied; however, quantitative information about mechanisms of peripheral Treg-cell homeostasis is lacking. Here we developed the first mathematical model of peripheral Treg-cell homeostasis, incorporating secondary lymphoid organs as separate entities and encompassing factors determining the size of the Treg-cell population, namely thymic output, homeostatic proliferation, peripheral conversion, transorgan migration, apoptosis, and the Tnaive-cell population. Quantitative data were collected by monitoring Tnaive-cell homeostasis and Treg-cell rebound after selective in vivo depletion of Treg cells. Our model predicted the previously unanticipated possibility that Treg cells regulate migration of Tnaive cells between spleen and peripheral lymph nodes (LNs), whereas migration of Treg cells between these organs can largely be neglected. Furthermore, our simulations suggested that peripheral conversion significantly contributed to the maintenance of the Treg-cell population, especially in LNs. Hence, we provide the first estimation of the peripheral Treg-cell conversion rate and propose additional facets of Treg-cell-mediated immune regulation that may previously have escaped attention., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Several mechanisms enable immunological self-tolerance. Regulatory T cells (Tregs) are a specialized T cell subset that prevents autoimmunity and excessive immune responses, but can also mediate detrimental tolerance to tumors and pathogens in a Foxp3-dependent manner. Genetic tools exploiting the foxp3 locus including bacterial artificial chromosome (BAC)-transgenic DEREG mice have provided essential information on Treg biology and the potential therapeutic modulation of tolerance. In DEREG mice, Foxp3(+) Tregs selectively express eGFP and diphtheria toxin (DT) receptor, allowing for the specific depletion of Tregs through DT administration. We here provide a detailed overview about important considerations such as DT toxicity, which affects any mouse strain treated with DT, and Treg rebound after depletion. Additionally, we point out the specific advantages of BAC-transgenic DEREG mice including their suitability to study organ-specific autoimmunity such as type I diabetes. Moreover, we discuss recent insights into the role of Tregs in viral infections. In summary, DEREG mice are an important tool to study Treg-mediated tolerance and its therapeutic circumvention.

Foxp3(+) regulatory T cells (Tregs) hamper efficient immune responses to tumors and chronic infections. Therefore, depletion of Foxp3(+) Tregs has been proposed as therapeutic option to boost immune responses and to improve vaccinations. Although Treg-mediated control of T cell homeostasis is well established, Foxp3(+) Treg interaction with other immune cell subsets is only incompletely understood. Thus, the present study aimed at examining dynamic effects of experimental Foxp3(+) Treg depletion on a broad range of immune cell subsets, including B cells, natural killer cells, and myeloid cells. Striking differences were observed when peripheral lymph nodes (LN) and spleen were compared. B cells, for example, showed a massive and long-lasting accumulation only in LN but not in spleen of transiently Treg-depleted mice. In contrast, monocyte-derived dendritic cells, which are potent inducers of T cell responses, also accumulated selectively, but only transiently in LN, suggesting that this cell population is under very strict control of Foxp3(+) Tregs. In summary, the observations described here provide insights into the dynamics of immune cells after selective depletion of Foxp3(+) Tregs. This will allow a better prediction of the impact of Treg ablation in translational studies that aim at boosting immune responses and vaccinations.