Decoding the antibody repertoire : high throughput sequencing of multiple transcripts from single B cells

Next-generation (high throughput) DNA sequencing of immunoglobulin variable region and T-cell receptor gene repertoires is providing critical information for understanding adaptive immune responses and for diagnostic and therapeutic applications¹⁻⁴. However, existing immune repertoire sequencing technologies yield data on only one of the two chains of immune receptors and thus cannot provide information on the identity of immune receptor pairs encoded by individual B or T lymphocytes⁵⁻⁷. This work directly addressed these limitations by developing two new technologies for sequencing the complementary DNA (cDNA) of multiple mRNA transcripts from isolated single cells with very high throughput. In these methods, cells are sequestered into individual compartments and lysed in situ to capture single-cell mRNA onto magnetic beads, then the magnetic beads are used as template for RT-PCR reactions inside emulsion droplets that physically link cDNA of multiple transcripts for subsequent analysis by high-throughput DNA sequencing. Experimental throughput of over 2x10⁶ cells in a single day with antibody heavy and light chain pairing accuracy greater than 97% was demonstrated with in vitro expanded human B cells. These new single-cell sequencing technologies were also applied for rapid discovery of new human antibodies and for analysis of the human immune response to vaccination. Finally we applied the techniques developed here to gain new insights regarding development of the antibody repertoire through high-throughput and high-resolution examination of naïve and memory B-cell compartments in healthy human donors.Chemical Engineerin

Human antibody immune responses are personalized by selective removal of MHC-II peptide epitopes [preprint]

Human antibody responses are established by the generation of combinatorial sequence diversity in antibody variable domains, followed by iterative rounds of mutation and selection via T cell recognition of antigen peptides presented on MHC-II. Here, we report that MHC-II peptide epitope deletion from B cell receptors (BCRs) correlates with antibody development in vivo. Large-scale antibody sequence analysis and experimental validation of peptide binding revealed that MHC-II epitope removal from BCRs is linked to genetic signatures of T cell help, and donor-specific antibody repertoire modeling demonstrated that somatic hypermutation selectively targets the personalized MHC-II epitopes in antibody variable regions. Mining of class-switched sequences and serum proteomic data revealed that MHC-II epitope deletion is associated with antibody class switching and long-term secretion into serum. These data suggest that the MHC-II peptide epitope content of a BCR is an important determinant of antibody maturation that shapes the composition and durability of humoral immunity

Automatic memory processes in normal ageing and Alzheimer’s disease

This study examined the contribution of automatic and controlled uses of memory to stem completion in young, middle-aged and older adults, and compared these data with a study involving patients with Alzheimer’s disease (AD) who performed the same task (Hudson and Robertson, 2007). In an inclusion task participants aimed to complete three-letter word stems with a previously studied word, in an exclusion task the aim was to avoid using studied words to complete stems. Performances under inclusion and exclusion conditions were contrasted to obtain estimates of controlled and automatic memory processes using process-dissociation calculations (Jacoby, 1991). An age-related decline, evident from middle age was observed for the estimate of controlled processing, whereas the estimate of automatic processing remained invariant across the age groups. This pattern stands in contrast to what is observed in AD, where both controlled and automatic processes have been shown to be impaired. Therefore, the impairment in memory processing on stem completion that is found in AD is qualitatively different from that observed in normal ageing

BACE1 activity impairs neuronal glucose oxidation:rescue by beta-hydroxybutyrate and lipoic acid

Glucose hypometabolism and impaired mitochondrial function in neurons have been suggested to play early and perhaps causative roles in Alzheimer's disease (AD) pathogenesis. Activity of the aspartic acid protease, beta-site amyloid precursor protein (APP) cleaving enzyme 1 (BACE1), responsible for beta amyloid peptide generation, has recently been demonstrated to modify glucose metabolism. We therefore examined, using a human neuroblastoma (SH-SY5Y) cell line, whether increased BACE1 activity is responsible for a reduction in cellular glucose metabolism. Overexpression of active BACE1, but not a protease-dead mutant BACE1, protein in SH-SY5Y cells reduced glucose oxidation and the basal oxygen consumption rate, which was associated with a compensatory increase in glycolysis. Increased BACE1 activity had no effect on the mitochondrial electron transfer process but was found to diminish substrate delivery to the mitochondria by inhibition of key mitochondrial decarboxylation reaction enzymes. This BACE1 activity-dependent deficit in glucose oxidation was alleviated by the presence of beta hydroxybutyrate or α-lipoic acid. Consequently our data indicate that raised cellular BACE1 activity drives reduced glucose oxidation in a human neuronal cell line through impairments in the activity of specific tricarboxylic acid cycle enzymes. Because this bioenergetic deficit is recoverable by neutraceutical compounds we suggest that such agents, perhaps in conjunction with BACE1 inhibitors, may be an effective therapeutic strategy in the early-stage management or treatment of AD

Apoptotic interactions of cytochrome c: Redox flirting with anionic phospholipids within and outside of mitochondria

AbstractSince the (re)discovery of cytochrome c (cyt c) in the early 1920s and subsequent detailed characterization of its structure and function in mitochondrial electron transport, it took over 70 years to realize that cyt c plays a different, not less universal role in programmed cell death, apoptosis, by interacting with several proteins and forming apoptosomes. Recently, two additional essential functions of cyt c in apoptosis have been discovered that are carried out via its interactions with anionic phospholipids: a mitochondria specific phospholipid, cardiolipin (CL), and plasma membrane phosphatidylserine (PS). Execution of apoptotic program in cells is accompanied by substantial and early mitochondrial production of reactive oxygen species (ROS). Because antioxidant enhancements protect cells against apoptosis, ROS production was viewed not as a meaningless side effect of mitochondrial disintegration but rather playing some – as yet unidentified – role in apoptosis. This conundrum has been resolved by establishing that mitochondria contain a pool of cyt c, which interacts with CL and acts as a CL oxygenase. The oxygenase is activated during apoptosis, utilizes generated ROS and causes selective oxidation of CL. The oxidized CL is required for the release of pro-apoptotic factors from mitochondria into the cytosol. This redox mechanism of cyt c is realized earlier than its other well-recognized functions in the formation of apoptosomes and caspase activation. In the cytosol, released cyt c interacts with another anionic phospholipid, PS, and catalyzes its oxidation in a similar oxygenase reaction. Peroxidized PS facilitates its externalization essential for the recognition and clearance of apoptotic cells by macrophages. Redox catalysis of plasma membrane PS oxidation constitutes an important redox-dependent function of cyt c in apoptosis and phagocytosis. Thus, cyt c acts as an anionic phospholipid specific oxygenase activated and required for the execution of essential stages of apoptosis. This review is focused on newly discovered redox mechanisms of complexes of cyt c with anionic phospholipids and their role in apoptotic pathways in health and disease

Proteome-based plasma biomarkers for Alzheimer's disease

Alzheimer's disease is a common and devastating disease for which there is no readily available biomarker to aid diagnosis or to monitor disease progression. Biomarkers have been sought in CSF but no previous study has used two-dimensional gel electrophoresis coupled with mass spectrometry to seek biomarkers in peripheral tissue. We performed a case-control study of plasma using this proteomics approach to identify proteins that differ in the disease state relative to aged controls. For discovery-phase proteomics analysis, 50 people with Alzheimer's dementia were recruited through secondary services and 50 normal elderly controls through primary care. For validation purposes a total of 511 subjects with Alzheimer's disease and other neurodegenerative diseases and normal elderly controls were examined. Image analysis of the protein distribution of the gels alone identifies disease cases with 56% sensitivity and 80% specificity. Mass spectrometric analysis of the changes observed in two-dimensional electrophoresis identified a number of proteins previously implicated in the disease pathology, including complement factor H (CFH) precursor and α-2-macroglobulin (α- 2M). Using semi-quantitative immunoblotting, the elevation of CFH and α- 2M was shown to be specific for Alzheimer's disease and to correlate with disease severity although alternative assays would be necessary to improve sensitivity and specificity. These findings suggest that blood may be a rich source for biomarkers of Alzheimer's disease and that CFH, together with other proteins such as α- 2M may be a specific markers of this illness. © 2006 The Author(s).link_to_subscribed_fulltex

Pathological increases in neuronal hyperactivity in selective cholinergic and noradrenergic pathways may limit the efficacy of Aβ-based interventions in MCI and Alzheimer’s disease

In spite of compelling evidence linking Aβ disturbances to the pathophysiology of Alzheimer’s disease, Aβ based treatments have consistently failed to produce any beneficial effects both in mild cognitive impairment (MCI) and Alzheimer’s disease (AD) even with successful reductions of toxic aggregated and soluble Aβ species. Before abandoning both the hypothesis and approach, there is a need to examine some overlooked factors that may have contributed to the lack of efficacy, such as the potential druginduced increases in neuronal hyperactivity leading to adverse cognitive effects. In particular, we posit that selective cholinergic and noradrenergic pathways will be especially vulnerable to this adverse effect. If confirmed, this idea could help identify a potentially preventable and treatable obstacle for enhancing the efficacy of therapeutic agents in MCI and AD

Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity in order to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic and (iv) machine learning methods applied to dissect, quantify and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology towards coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.Comment: 27 pages, 2 figure

Applications of high-throughput single B-cell sequencing to accelerate rational vaccine design

Understanding the antibody repertoire response to vaccination is critical for the rational design and evaluation of experimental vaccines. Immune receptors comprise two chains encoded by separate mRNA strands and thus conventional NextGen sequencing fails to identify the native pairings encoded by individual lymphocytes. To overcome this limitation, we are applying recent technical advances in high-throughput sequencing of complete antibodies (i.e., paired heavy and light chain sequencing) to generate a quantitative understanding of experimental vaccine performance and to accelerate vaccine design. We apply repertoire-based metrics of vaccine-elicited antibodies to evaluate and select promising candidate immunogens for inducing HIV-1 Envelope-specific VRC01-class antibodies. The VRC01 class of broadly neutralizing antibodies have been observed in multiple individuals and targets the HIV CD4 binding site via a common recognition motif that requires specific features in both heavy and light chains (e.g., VH1-2 heavy chain V-gene and a short, £5 amino acid light chain CDR3). We are using paired heavy and light chain sequencing to quantify the performance of various candidate HIV immunogens for inducing VRC01-class broadly neutralizing HIV antibodies in transgenic mouse models. We are also elucidating the ontogeny of antibodies in vaccinated and naturally infected human subjects and animal models via interrogation of paired heavy and light chain antibody sequences and antibody synthesis/testing of promising clones, including experimental influenza vaccine trials and a Phase I Ebola vaccine trial. These next-generation immunoanalytic approaches are providing detailed molecular feedback regarding experimental vaccine performance to accelerate vaccine design efforts against pathogens of major public health importance