Holistic Systems Biology Approaches to Molecular Mechanisms of Human Helper T Cell Differentiation to Functionally Distinct Subsets

Current knowledge of helper T cell differentiation largely relies on data generated from mouse studies. To develop therapeutical strategies combating human diseases, understanding the molecular mechanisms how human naïve T cells differentiate to functionally distinct T helper (Th) subsets as well as studies on human differentiated Th cell subsets is particularly valuable. Systems biology approaches provide a holistic view of the processes of T helper differentiation, enable discovery of new factors and pathways involved and generation of new hypotheses to be tested to improve our understanding of human Th cell differentiation and immune‐mediated diseases. Here, we summarize studies where high‐throughput systems biology approaches have been exploited to human primary T cells. These studies reveal new factors and signalling pathways influencing T cell differentiation towards distinct subsets, important for immune regulation. Such information provides new insights into T cell biology and into targeting immune system for therapeutic interventions.     

Immunobiology of chimeric antigen receptor T cells and novel designs

Advances in the development of immunotherapies have offered exciting new options for the treatment of malignant diseases that are refractory to conventional cytotoxic chemotherapies. The adoptive transfer of T cells expressing chimeric antigen receptors (CARs) has demonstrated dramatic results in clinical trials and highlights the promise of novel immune‐based approaches to the treatment of cancer. As experience with CAR T cells has expanded with longer follow‐up and to a broader range of diseases, new obstacles have been identified which limit the potential lifelong benefits of CAR T cell therapy. These obstacles highlight not only the gaps in knowledge of the optimal clinical application of this “living drug”, but also gaps in our understanding of the fundamental biology of CAR T cells themselves. In this review, we discuss the obstacles facing CAR T cell therapy, how these relate to our current understanding of CAR T cell biology and approaches to enhance the clinical efficacy of this therapy.     

Trained innate immunity

The innate immune system acts rapidly in an identical and nonspecific way every time the body is exposed to pathogens. As such, it cannot build and maintain immunological memory to help prevent reinfection. Researchers contend that trained immunity is influenced by intracellular metabolic pathways and epigenetic remodeling. The purpose of this review was to explore the topic of trained innate immunity based on the results of relevant previous studies. This systematic review entailed identifying articles related to trained innate immunity. The sources were obtained from PubMed using different search terms that included “trained innate immunity,” “trained immunity,” “trained,” “innate,” “immunity,” and “immune system.” Boolean operators were used to combine terms and phrases. A review of previous study results revealed that little is currently known about the molecular and cellular processes that mediate or induce a trained immune response in animals. However, it is believed that alterations in the phenotypes of cell populations and the numbers of specific cells may play a critical role in mediating the trained immune response. Increasing evidence shows that the protective processes and actions that occur during a secondary infection are not entirely linked to the adaptive immune system. Instead, these events also involve heightened activation of innate immune cells. While trained innate immune cells may have a shorter memory, they assist in the fight against pathogens and provide cross-protection. Identification of the mechanisms and molecules that underlie trained innate immunity has highlighted important features of the human immune response. Such advances continue to open doors for future research on how the body responds to disease-causing pathogens.

     

Plasticity of Mesangial Cells: A Basis for Understanding Pathological Alterations

In the last two decades, the ability of mesangial cells to respond to various stimuli or injurious agents by altering their phenotype and function has become recognized. The plasticity of these mesangial cells has been linked to the morphological and functional alterations responsible for the pathologic findings. Many of the glomerular disorders target the mesangium as the primary and/or initial site of injury. Understanding how mesangial cells are altered in the various conditions provides a platform for conceptualizing pathologic mechanisms and defining key steps amenable to therapeutic intervention. The present paper reviews the normal and altered mesangium with an emphasis on mechanisms involved in alterations of mesangial homeostasis. Mesangial cells and matrix are very important in maintaining normal glomerular structure, and function and the plasticity of these cells is responsible for pathological manifestations, repair, and scarring. Our more sophisticated understanding of mesangial cell behavior and matrix biology provides very useful information to help design new therapeutic approaches to the treatment of renal diseases. The potential for bone marrow-derived cells to differentiate into mesangial cells and repopulate damaged mesangium, thus “healing” what is today considered to be irreversible damage represents an exciting new area of research.     

Immuno-isolation in cancer gene therapy

The implantation of genetically-modified non-autologous cells in immuno-protected microcapsules is an alternative to ex vivo gene therapy. Such cells delivering a recombinant therapeutic product are isolated from the host's immune system by being encapsulated within permselective microcapsules. This approach has been successful in pre-clinical animal studies involving delivery of hormone or enzymes to treat dwarfism, lysosomal storage disease, or hemophilia B. Recently, this platform technology has shown promise in the treatment for more complex diseases such as cancer. One of the earliest strategy was to augment the chemotherapeutic effect of a prodrug by implanting encapsulated cells that can metabolise prodrugs into cytotoxic products in close proximity to the cancer cells. More recent approaches include enhancing tumor cell death through immunotherapy, or suppressing tumor cell proliferation through anti-angiogenesis. These can be achieved by delivering single molecules of cytokines or angiostatin, respectively, by implanting microencapsulated cells engineered to secrete these recombinant products. Recent refinements of these approaches include genetic fusion of cytokines or angiostatin to additional functional groups with tumor targeting or tumor cell killing properties, thus enhancing the potency of the recombinant products. Furthermore, a COMBO strategy of implanting microencapsulated cells to deliver multiple products targeted to diverse pathways in tumor suppression also showed much promise. This review will summarise the application of microencapsulation of genetically-modified cells to cancer treatment in animal models, the efficacy of such approaches, and how these studies have led to better understanding of the biology of cancer treatment. The flexibility of this modular system involving molecular engineering, cellular genetic modification, and polymer chemistry provides potentially a huge range of application modalities, and a tremendous multi-disciplinary challenge for the future.     

New frontiers in modeling tuberous sclerosis with human stem cell-derived neurons and brain organoids

Recent advances in human stem cell and genome engineering have enabled the generation of genetically defined human cellular models for brain disorders. These models can be established from a patient's own cells and can be genetically engineered to generate isogenic, controlled systems for mechanistic studies. Given the challenges of obtaining and working with primary human brain tissue, these models fill a critical gap in our understanding of normal and abnormal human brain development and provide an important complement to animal models. Recently, there has been major progress in modeling the neuropathophysiology of the canonical “mTORopathy” tuberous sclerosis complex (TSC) with such approaches. Studies using two- and three-dimensional cultures of human neurons and glia have provided new insights into how mutations in the TSC1 and TSC2 genes impact human neural development and function. Here we discuss recent progress in human stem cell-based modeling of TSC and highlight challenges and opportunities for further efforts in this area.     

Creating Living Cellular Machines

Development of increasingly complex integrated cellular systems will be a major challenge for the next decade and beyond, as we apply the knowledge gained from the sub-disciplines of regenerative medicine, synthetic biology, micro-fabrication and nanotechnology, systems biology, and developmental biology. In this prospective, we describe the current state-of-the-art in the assembly of source cells, derived from pluripotent cells, into populations of a single cell type to produce the components or building blocks of higher order systems and finally, combining multiple cell types, possibly in combination with scaffolds possessing specific physical or chemical properties, to produce higher level functionality. We also introduce the issue, questions and ample research opportunities to be explored by others in the field. As these “living machines” increase in capabilities, exhibit emergent behavior and potentially reveal the ability for self-assembly, self-repair, and even self-replication, questions arise regarding the ethical implications of this work. Future prospects as well as ways of addressing these complex ethical questions will be discussed.     

Host MHC class I gene control of NK-cell specificity in the mouse

Summary: The missing self model predicts chat NK cells adapt somatically to the type as well as levels of MHC class I products expressed by their host, Transgenic and gene knock-out mice have provided conclusive evidence chat MHC class I genes control specificity and tolerance of NK cells. The article describes this control and discusses the POSSIBLE Mechanisms behind it. starting from a genetic model to study how natural resistance to tumors is influenced by MHC class I expression in the host as well as in the target cells. Data on host gene regulation of NK-cell functional specificity as well as Lγ49 receptor expression are reviewed, leading up to the central question: how does the system develop and maintain “useful” NK cells, while avoiding “harmful” and “useless” ones? The available data can be fitted with in each of two mutually non-exclusive models: cellular adaptation and clonal selection. Recent studies supporting cellular adaptation bring the focus on different possibilities within this general mechanism, such as energy, receptor calibration and, most importantly, whether the specificity of each NK cell is permanently fixed or subject to continuous regulation.     

Primer and interviews: Promises and realities of induced pluripotent stem cells

In 2006, Yamanaka's group announced they had discovered the proverbial “fountain of youth” for human cells, forever changing the field of stem cell research. After misexpressing within them a cocktail of four genes, adult somatic cells revert into an embryonic stem cell (ESC)‐like state. These so‐called induced pluripotent stem cells (iPSCs) can differentiate into a wide variety of cell types, seemingly bypassing the need for politically charged ESCs. However, iPSCs differ from ESCs in potentially deleterious ways, precluding their use in regenerative medicine. In this primer and adjoining discussion with iPSC biologists William Lowry, PhD, and Clive Svendsen, PhD, we explore these issues as well how iPSCs promise to contribute to the understanding of developmental biology and the etiology, and treatment, of human diseases. Developmental Dynamics 240:2034–2041, 2011. © 2011 Wiley‐Liss, Inc.     

Measuring human energy expenditure: What have we learned from the flex‐heart rate method?

The measurement of daily energy expenditure is an important aspect of research on human health and nutrition. Over the last 30 years, G.B. Spurr has been a leader in developing and implementing methods for more effectively assessing energy expenditure and physical activity in traditional and modernizing populations. One of his most notable contributions has been the development of the “Flex Heart Rate” (flex‐HR) method. Since its inception in the late 1980s, the flex‐HR method has become a standard tool for measuring daily energy expenditure in free‐living human populations. This article reviews the initial development and validation of the flex‐HR technique, and examines recent refinements of the method and its application to research in biomedicine and human population biology. The review and analyses highlight how the flex‐HR technique has improved on earlier methods of assessing energy expenditure and greatly advanced our understanding of variability in human energy requirements. Am. J. Hum. Biol. 15:479–489, 2003. © 2003 Wiley‐Liss, Inc.     

Metabolic and epigenetic reprogramming in the pathogenesis of glioblastoma: Toward the establishment of “metabolism-based pathology”

Molecular genetic approaches are now mandatory for cancer diagnostics, especially for brain tumors. Genotype-based diagnosis has predominated over the phenotype-based approach, with its prognostic and predictive powers. However, comprehensive genetic testing would be difficult to perform in the clinical setting, and translational research is required to histologically decipher the peculiar biology of cancer. Of interest, recent studies have demonstrated discrete links between oncogenotypes and the resultant metabolic phenotypes, revealing cancer metabolism as a promising histologic surrogate to reveal specific characteristics of each cancer type and indicate the best way to manage cancer patients. Here, we provide an overview of our research progress to work on cancer metabolism, with a particular focus on the genomically well-characterized malignant tumor glioblastoma. With the use of clinically relevant animal models and human tissue, we found that metabolic reprogramming plays a major role in the aggressive cancer biology by conferring therapeutic resistance to cancer cells and rewiring their epigenomic landscapes. We further discuss our future endeavor to establish “metabolism-based pathology” on how the basic knowledge of cancer metabolism could be leveraged to improve the management of patients by linking cancer cell genotype, epigenotype, and phenotype through metabolic reprogramming.     

The relationship between patient perceptions of diabetes and glycemic control: A study of patients living with prediabetes or type 2 diabetes

ObjectiveThis study aims to identify differences in how patients living with prediabetes (preDM) or type 2 diabetes (T2DM) perceive their illness.MethodsFollowing chart review, a cross-sectional survey was administered to patients diagnosed with preDM or T2DM at two US medical centers.ResultsAmong 757 respondents, multivariate tests demonstrate that patients living with T2DM have an overall different personal model of disease than patients living with preDM. Patients who have been diagnosed with T2DM report a better understanding of their disease and perceive it to be more chronic in nature than patients living with preDM. Findings revealed a potential but less significant difference in perceived seriousness.ConclusionsIn this first application of personal models of disease to prediabetes, results inform implications for clinicians to talk with patients about preDM. Patients living with preDM indicate less understanding of the “disease” and perceive it to be less “chronic,” which may result from unclear clinician communication about preDM.Practice implicationsWhen clinicians talk to patients about prediabetes, they should present the risk factor within the spectrum of glucose tolerance. Although labeled a risk factor, clinicians should emphasize that prediabetes remains a serious concern that will not lessen without intervention.     

Innate and virtual memory T cells in man

A hallmark of the antigen‐specific B and T lymphocytes of the adaptive immune system is their capacity to “remember” pathogens long after they are first encountered, a property that forms the basis for effective vaccine development. However, studies in mice have provided strong evidence that some naive T cells can develop characteristics of memory T cells in the absence of foreign antigen encounters. Such innate memory T cells may develop in response to lymphopenia or the presence of high levels of the cytokine IL‐4, and have also been identified in unmanipulated animals, a phenomenal referred to as “virtual memory.” While the presence of innate memory T cells in mice is now widely accepted, their presence in humans has not yet been fully validated. In this issue of the European Journal of Immunology, Jacomet et al. [Eur. J. Immunol. 2015. 45:1926‐1933] provide the best evidence to date for innate memory T cells in humans. These findings may contribute significantly to our understanding of human immunity to microbial pathogens and tumors.     

Biomechanics: Cell Research and Applications for the Next Decade

With the recent revolution in Molecular Biology and the deciphering of the Human Genome, understanding of the building blocks that comprise living systems has advanced rapidly. We have yet to understand, however, how the physical forces that animate life affect the synthesis, folding, assembly, and function of these molecular building blocks. We are equally uncertain as to how these building blocks interact dynamically to create coupled regulatory networks from which integrative biological behaviors emerge. Here we review recent advances in the field of biomechanics at the cellular and molecular levels, and set forth challenges confronting the field. Living systems work and move as multi-molecular collectives, and in order to understand key aspects of health and disease we must first be able to explain how physical forces and mechanical structures contribute to the active material properties of living cells and tissues, as well as how these forces impact information processing and cellular decision making. Such insights will no doubt inform basic biology and rational engineering of effective new approaches to clinical therapy. This is a white-paper developed by the Cell Mechanics working group of the US National Committee on Biomechanics.     

Single-cell elastography: probing for disease with the atomic force microscope

The atomic force microscope (AFM) is emerging as a powerful tool in cell biology. Originally developed for high-resolution imaging purposes, the AFM also has unique capabilities as a nano-indenter to probe the dynamic viscoelastic material properties of living cells in culture. In particular, AFM elastography combines imaging and indentation modalities to map the spatial distribution of cell mechanical properties, which in turn reflect the structure and function of the underlying cytoskeleton. Such measurements have contributed to our understanding of cell mechanics and cell biology and appear to be sensitive to the presence of disease in individual cells. This chapter provides a background on the principles and practice of AFM elastography and reviews the literature comparing cell mechanics in normal and diseased states, making a case for the use of such measurements as disease markers. Emphasis is placed on the need for more comprehensive and detailed quantification of cell biomechanical properties beyond the current standard methods of analysis. A number of technical and practical hurdles have yet to be overcome before the method can be of clinical use. However, the future holds great promise for AFM elastography of living cells to provide novel biomechanical markers that will enhance the detection, diagnosis, and treatment of disease.     

Early T helper cell programming of gene expression in human

Molecular mechanisms guiding naïve T helper cell differentiation into functionally specified effector cells are intensively studied. The rapidly growing knowledge is mainly achieved by using mouse cells or disease models. Comparatively exiguous data is gathered from human primary cells although they provide the “ultimate model” for immunology in man, have been exploited in many original studies paving the way for the field, and can be analyzed more easily than ever with the help of modern technology and methods. As usage of mouse models is unavoidable in translational research, parallel human and mouse studies should be performed to assure the relevancy of the hypothesis created during the basic research. In this review, we give an overview on the status of the studies conducted with human primary cells aiming at elucidating the mechanisms instructing the priming of T helper cell subtypes. The special emphasis is given to the recent high-throughput studies. In addition, by comparing the human and mouse studies we intend to point out the regulatory mechanisms and questions which are lacking examination with human primary cells.     

Patient-specific anatomic models from three dimensional medical image data for clinical applications in surgery and endoscopy

Virtual surgery and endoscopy use computer-generated volume renderings and/or models created from 3D medical image scans (CT or MRI) of individual patients. The patient’s anatomy, including organs and other internal structures of interest, are then traversed in a virtual “fly-through,” giving nearly the same visual impression as if the corresponding real organ was being examined intraoperatively, or as if an actual video or fiberoptic endoscopic procedure was being performed. Such virtual examinations may provide capabilities and information not possible or available in physical examinations. The potential is to provide a noninvasive computer-aided treatment plan or diagnostic screening procedure to augment or replace conventional invasive procedures. With sophisticated image processing and computational analysis, it is possible to perform realistic and useful simulations of surgical and endoscopic procedures, including “virtual dissection and resection” and “virtual biopsy.” Surgical margins can be accurately assessed and differential tissue diagnoses made based upon spectral or other information contained in the patient-specific images and models.     

Murine and Human Model Systems for the Study of Dendritic Cell Immunobiology

Dendritic cells are a population of innate immune cells that possess their own effector functions as well as numerous regulatory properties that shape the activity of other innate and adaptive cells of the immune system. Following their development from either lymphoid or myeloid progenitors, the function of dendritic cells is tightly linked to their maturation and activation status. Differentiation into specialized subsets of dendritic cells also contributes to the diverse immunologic functions of these cells. Because of the key role played by dendritic cells in the regulation of both immune tolerance and activation, significant efforts have been focused on understanding dendritic cell biology. This review highlights the model systems currently available to study dendritic cell immunobiology and emphasizes the advantages and disadvantages to each system in both murine and human settings. In particular, in vitro cell culture systems involving immortalized dendritic cell lines, ex vivo systems for differentiating and expanding dendritic cells from their precursor populations, and systems for expanding, ablating, and manipulating dendritic cells in vivo are discussed. Emphasis is placed on the contribution of these systems to our current understanding of the development, function, and immunotherapeutic applications of dendritic cells, and insights into how these models might be extended in the future to answer remaining questions in the field are discussed.     

The Allogeneic Effect Revisited: Exogenous Help for Endogenous,Tumor-Specific T Cells

The “allogeneic effect” refers to the induction of host B cell antibody synthesis or host T cell cytotoxicity, including tumoricidal activity, by an infusion of allogeneic lymphocytes. We show that treatment of mice with cyclophosphamide (Cy) followed by CD8⁺ T cell-depleted allogeneic donor lymphocyte infusion (Cy + CD8⁻ DLI) induces regression of established tumors with minimal toxicity in models of both hematologic and solid cancers, even though the donor cells are eventually rejected by the host immune system. The optimal antitumor effect of Cy + CD8⁻ DLI required the presence of donor CD4⁺ T cells, host CD8⁺ T cells, and alloantigen expression by normal host but not tumor tissue. The results support a model in which a donor CD4⁺ T cell-mediated graft-versus-host (GVH) reaction effectively awakens antitumor immunity among Cy-resistant host CD8⁺ T cells. These events provide the cellular mechanism of the “allogeneic effect” in antitumor immunity. Cy + CD8⁻ DLI may be an effective and minimally toxic strategy for awakening the host immune response to advanced cancers.