Genetics, FACS, Immunology, and Redox: A Tale of Two Lives Intertwined

Leveraging Systems Immunology to Optimize Diagnosis and Treatment of Inborn Errors of Immunity

Inborn errors of immunity (IEI) are monogenic disorders that can cause diverse symptoms, including recurrent infections, autoimmunity and malignancy. While many factors have contributed, the increased availability of next-generation sequencing has been central in the remarkable increase in identification of novel monogenic IEI over the past years. Throughout this phase of disease discovery, it has also become evident that a given gene variant does not always yield a consistent phenotype, while variants in seemingly disparate genes can lead to similar clinical presentations. Thus, it is increasingly clear that the clinical phenotype of an IEI patient is not defined by genetics alone, but is also impacted by a myriad of factors. Accordingly, we need methods to amplify our current diagnostic algorithms to better understand mechanisms underlying the variability in our patients and to optimize treatment. In this review, we will explore how systems immunology can contribute to optimizing both diagnosis and treatment of IEI patients by focusing on identifying and quantifying key dysregulated pathways. To improve mechanistic understanding in IEI we must deeply evaluate our rare IEI patients using multimodal strategies, allowing both the quantification of altered immune cell subsets and their functional evaluation. By studying representative controls and patients, we can identify causative pathways underlying immune cell dysfunction and move towards functional diagnosis. Attaining this deeper understanding of IEI will require a stepwise strategy. First, we need to broadly apply these methods to IEI patients to identify patterns of dysfunction. Next, using multimodal data analysis, we can identify key dysregulated pathways. Then, we must develop a core group of simple, effective functional tests that target those pathways to increase efficiency of initial diagnostic investigations, provide evidence for therapeutic selection and contribute to the mechanistic evaluation of genetic results. This core group of simple, effective functional tests, targeting key pathways, can then be equitably provided to our rare patients. Systems biology is thus poised to reframe IEI diagnosis and therapy, fostering research today that will provide streamlined diagnosis and treatment choices for our rare and complex patients in the future, as well as providing a better understanding of basic immunology.

Flow Cytometric-Based Analysis of Defects in Lymphocyte Differentiation and Function Due to Inborn Errors of Immunity

The advent of flow cytometry has revolutionized the way we approach our research and answer specific scientific questions. The flow cytometer has also become a mainstream diagnostic tool in most hospital and pathology laboratories around the world. In particular the application of flow cytometry has been instrumental to the diagnosis of primary immunodeficiencies (PIDs) that result from monogenic mutations in key genes of the hematopoietic, and occasionally non-hematopoietic, systems. The far-reaching applicability of flow cytometry is in part due to the remarkable sensitivity, down to the single-cell level, of flow-based assays and the extremely user-friendly platforms that enable comprehensive analysis, data interpretation, and importantly, robust and rapid methods for diagnosing PIDs. A prime example is the absence of peripheral blood B cells in patients with agammaglobulinemia due to mutations in BTK or related genes in the BCR signaling pathway. Similarly, the development of intracellular staining protocols to detect expression of SAP, XIAP, or DOCK8 expedites the rapid diagnosis of the X-linked lymphoproliferative diseases or an autosomal recessive form of hyper-IgE syndrome (HIES), respectively. It has also become evident that distinct cohorts of PID patients exhibit unique “lymphocyte phenotypic signatures” that are often diagnostic even prior to identifying the genetic lesion. Flow cytometry-based sorting provides a technique for separating specific subsets of immune cells such that they can be studied in isolation. Thus, flow-based assays can be utilized to measure immune cell function in patients with PIDs, such as degranulation by cytotoxic cells, cytokine expression by many immune cells (i.e., CD4⁺ and CD8⁺ T cells, macrophages etc.), B-cell differentiation, and phagocyte respiratory burst in vitro. These assays can also be performed using unfractionated PBMCs, provided the caveat that the composition of lymphocytes between healthy donors and the PID patients under investigation is recognized. These functional deficits can assist not only in the clinical diagnosis of PIDs, but also reveal mechanisms of disease pathogenesis. As we move into the next generation of multiparameter flow cytometers, here we review some of our experiences in the use of flow cytometry in the study, diagnosis, and unraveling the pathophysiology of PIDs.

The early history of Stanford Immunology

From its 1960 beginnings in a pair of windowless Genetics Department laboratories under the Stanford Medical School Dean's Office to its current broad-based program, which joins faculty members from departments across the Medical School, the Stanford Immunology Program has played a central role in shaping both basic and clinical immunology thinking. In this article, we tell the story of the beginnings of this odyssey in a reminiscence-based format that brings the flavor of the time in the words of people who lived and built the history.

A conversation with Leonard and Leonore Herzenberg

Leonard and Leonore Herzenberg have left an indelible mark on the fields of immunology and cell biology, both in research and clinical aspects. They are perhaps best known for developing the technologies of fluorescence flow cytometry and hybridomas. Over six decades, they made a number of important and fundamental discoveries in lymphocyte biology by applying these technologies. During this era, they immersed themselves in the sociopolitical environment, interjecting scientific rationale into public discourse about McCarthyism, nuclear fallout, war, genetics, and other politically charged topics. Their unique philosophy has shaped their lives, their science, and ultimately the scientific community. In this Conversation, we explore some of these driving forces and the impact on the laboratory.

Analysis of the KIR repertoire in human NK cells by flow cytometry

Human natural killer (NK) cells are regulated by a diverse receptor repertoire. This makes multi-color flow cytometry-based approaches highly attractive for detailed phenotypical evaluation of NK cells. Several functional parameters can also be evaluated using this technology. In the present chapter, we demonstrate the applicability of this technology for the analysis of the human killer cell Ig-like receptor (KIR) repertoire. We present an antibody panel allowing simultaneous assessment of the four major inhibitory KIRs and NKG2A. We further provide guidance on how to apply standard operating procedures to multi-color flow cytometry experiments. Finally, we discuss possibilities as well as limitations with the application of multi-color flow cytometry techniques to future studies of human NK cells.

Stems and standards: social interaction in the search for blood stem cells

This essay examines the role of social interactions in the search for blood stem cells, in a recent episode of biomedical research. Linked to mid-20th century cell biology, genetics and radiation research, the search for blood stem cells coalesced in the 1960s and took a developmental turn in the late 1980s, with significant ramifications for immunology, stem cell and cancer biology. Like much contemporary biomedical research, this line of inquiry exhibits a complex social structure and includes several prominent scientific successes, recognized as such by participating researchers. I use personal interviews and the published record to trace the social interactions crucial for scientific success in this episode. All recognized successes in this episode have two aspects: improved models of blood cell development, and new interfaces with other lines of research. The narrative of the search for blood stem cells thus yields a robust account of scientific success in practice, which generalizes to other scientific episodes and lends itself to expansion to include wider social contexts.

Application of nine-color flow cytometry for detailed studies of the phenotypic complexity and functional heterogeneity of human lymphocyte subsets

Innate and adaptive cellular immunity is initiated, directed and regulated by a vast array of cell surface receptors. Attempts to harness the cellular immune system in translational settings such as immunotherapy and vaccine development require tools to accurately describe and isolate lymphocytes with specific characteristics. One such tool, flow cytometry, is undergoing a revolution in instrumentation and reagents, providing opportunities for high resolution phenotypic and functional analysis of lymphocytes. Here, we demonstrate how nine-color flow cytometry can be adapted, optimized and applied to investigate the phenotypic complexity and functional heterogeneity of human lymphocyte subsets. We provide examples of studies of adaptive T cell responses against viruses, as well as the assessment of CD1d-restricted NKT cells and NK cells. We discuss the importance of this technology for detailed investigations of lymphocyte subsets in studies of infectious diseases and cancer.

THE TORTUOUS JOURNEY OF A BIOCHEMIST TO IMMUNOLAND AND WHAT HE FOUND THERE

After starting out to become a physician, by a series of accidents I found myself at NIH in 1951 during its most productive growth phase. At age 26, I had a fully funded, independent laboratory and did not know what to work on. With advice from colleagues, I initiated a study of how penicillin kills bacteria. Twenty years later, my lab had outlined the structure and biosynthesis of the peptidoglycan of bacterial cell walls and had discovered that penicillin inhibited the terminal step in its biosynthesis catalyzed by transpeptidases. I then switched fields, moving to Harvard in 1968 and beginning the study of human HLA proteins. Twenty-five years later, the last half of which was spent in a stimulating collaboration with the late Don Wiley, our labs had isolated, crystallized, and elucidated the three-dimensional structures of these molecules and shown that their principal function was to present peptides to the immune system in initiating an immune response. More recently, the laboratory has focused on natural killer cells and their roles in peripheral blood and in the pregnant uterine decidua. It has been a wonderful scientific journey.