Production and use of antigen tetramers to study antigen-specific B cells

B cells generate antibodies that provide protection from infection, but also cause pathology in autoimmune and allergic conditions. Antigen-specific B cells can be detected by binding their surface antibody receptors with native antigens conjugated to fluorescent probes, a technique that has revealed substantial insight into B cell activation and function. This protocol describes the process of generating fluorescent antigen tetramer probes and delineates a process of enriching large samples based on antigen-specificity for high-resolution analyses of the antigen-specific B cell repertoire. Enrichment of tetramer-binding cells allows for detection of antigen-specific B cells as rare as 1 in 100 million cells, providing sufficient resolution to study naive B cells and IgE-expressing cells by flow cytometry. The generation of antigen tetramers involves antigen biotinylation, assessment of biotin:antigen ratio for optimal tetramer loading and polymerization around a streptavidin-fluorophore backbone. We also describe the construction of a control tetramer to exclude B cells binding to the tetramer backbone. We provide a framework to validate whether tetramer probes are detecting true antigen-specific B cells and discuss considerations for experimental design. This protocol can be performed by researchers trained in basic biomedical/immunological research techniques, using instrumentation commonly found in most laboratories. Constructing the antigen and control tetramers takes 9 h, though their specificity should be assessed before experimentation and may take weeks to months depending on the method of validation. Sample enrichment requires ~2 h but is generally time and cost neutral as fewer cells are run through the flow cytometer.

Ultrasensitive chimerism enhances measurable residual disease testing after allogeneic hematopoietic cell transplantation

Increasing mixed chimerism (reemerging recipient cells) after allogeneic hematopoietic cell transplant (allo-HCT) can indicate relapse, the leading factor determining mortality in blood malignancies. Most clinical chimerism tests have limited sensitivity and are primarily designed to monitor engraftment. We developed a panel of quantitative polymerase chain reaction assays using TaqMan chemistry capable of quantifying chimerism in the order of 1 in a million. At such analytic sensitivity, we hypothesized that it could inform on relapse risk. As a proof-of-concept, we applied our panel to a retrospective cohort of patients with acute leukemia who underwent allo-HCT with known outcomes. Recipient cells in bone marrow aspirates (BMAs) remained detectable in 97.8% of tested samples. Absolute recipient chimerism proportions and rates at which these proportions increased in BMAs in the first 540 days after allo-HCT were associated with relapse. Detectable measurable residual disease (MRD) via flow cytometry in BMAs after allo-HCT showed limited correlation with relapse. This correlation noticeably strengthened when combined with increased recipient chimerism in BMAs, demonstrating the ability of our ultrasensitive chimerism assay to augment MRD data. Our technology reveals an underappreciated usefulness of clinical chimerism. Used side by side with MRD assays, it promises to improve identification of patients with the highest risk of disease reoccurrence for a chance of early intervention.

NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy

Mitophagy, the elimination of mitochondria via the autophagy-lysosome pathway, is essential for the maintenance of cellular homeostasis. The best characterised mitophagy pathway is mediated by stabilisation of the protein kinase PINK1 and recruitment of the ubiquitin ligase Parkin to damaged mitochondria. Ubiquitinated mitochondrial surface proteins are recognised by autophagy receptors including NDP52 which initiate the formation of an autophagic vesicle around the mitochondria. Damaged mitochondria also generate reactive oxygen species (ROS) which have been proposed to act as a signal for mitophagy, however the mechanism of ROS sensing is unknown. Here we found that oxidation of NDP52 is essential for the efficient PINK1/Parkin-dependent mitophagy. We identified redox-sensitive cysteine residues involved in disulphide bond formation and oligomerisation of NDP52 on damaged mitochondria. Oligomerisation of NDP52 facilitates the recruitment of autophagy machinery for rapid mitochondrial degradation. We propose that redox sensing by NDP52 allows mitophagy to function as a mechanism of oxidative stress response.

Ultrasensitive Quantitation of Genomic Chimerism by Single-Molecule Molecular Inversion Probe Capture and High-Throughput Sequencing of Copy Number Deletion Polymorphisms

Genomic chimerism represents co-existing cells with different genotypes and has diagnostic significance in transplant engraftment monitoring, residual cancer detection, and other contexts. We previously described an approach to chimerism detection by interrogating variably present or absent genomic loci using single-molecule molecular inversion probes (smMIPs) and next-generation sequencing, which provided ultrasensitive limits of detection (<1 in 10,000 cells) but was not reliably quantitative. Herein, smMIP testing was modified to accurately quantitate chimeric cells by incorporating copy number neutral control loci for data normalization and computationally modeling cell mixtures from individual-specific genotypes. Data demonstrate precision and accuracy over three orders of magnitude (0.01% to 50% chimerism). Seventy hematopoietic stem cell transplant specimens from single (n = 42) or double (n = 28) donors were evaluated, benchmarking smMIP against conventional variable number tandem repeat (VNTR) analysis and an unrelated, ultrasensitive polymorphism-specific quantitative PCR (PS-qPCR) assay. Quantitative concordance of all three assays was high (P < 0.0005, Pearson correlation coefficient), although smMIP correlated better with VNTR testing than PS-qPCR. smMIP and PS-qPCR collectively identified low-level chimerism in all specimens testing negative by VNTR (n = 41 and n = 45 of 48 specimens, respectively). This work demonstrates the feasibility of smMIP-based chimerism testing for quantitative and ultrasensitive measurement of genomic chimerism at practical levels approaching one in one million cells, and cross-validates the approach.

Active Moderate-to-Severe Graves' Orbitopathy in a Patient With Type 2 Diabetes Mellitus and Vascular Complications

Background: Graves' orbitopathy (GO) is the main extrathyroidal manifestation of Graves' disease (GD). Diabetes mellitus (DM) has been reported to be a risk factor in patients with GO. Moreover, GO can be more frequent and severe in type 2 diabetes patients. High doses of intravenous glucocorticoids represent the first line treatment of moderate-to-severe and active GO according to the international guidelines. However, this therapy is contraindicated in uncontrolled diabetes and in patients with increased cardiovascular risk. Some anti-diabetic drugs can exacerbate GO. We reported the clinical case of an active and moderate-to-severe GO in a patient with uncontrolled type 2 DM and vascular complications. Case Report: A 61-years-old patient came to our ambulatory for a recurrence of GD and a moderate-to-severe bilateral GO. The patient had uncontrolled type 2 DM during insulin therapy and a history of micro and macrovascular complications. At the physical examination, the clinical activity score was 5 and the severity of GO was moderate-to-severe. A blood sample showed overt hyperthyroidism and the persistence of anti-TSH receptor antibodies (TRAb) during treatment with methimazole. A computed tomography scan showed a moderate-to-severe bilateral exophthalmos. We discuss the benefit/risk of treatment of GO in our patient. Conclusion: The available guidelines do not focus on the treatment of diabetic patients with uncontrolled diabetes and severe vascular complications, therefore our patient represents a difficult therapeutic challenge. The screening of thyroid function and the evaluation of GO could be useful in diabetic patients with autoimmune thyroid disease to perform a correct treatment of these disorders.

Is the Isthmus Location an Additional Risk Factor for Indeterminate Thyroid Nodules? Case Report and Review of the Literature

Background: The management of indeterminate thyroid lesions is controversial. The American Thyroid Association (ATA) guidelines suggest a conservative approach for low risk indeterminate thyroid lesions (TIR3A). Case Report: We report a clinical case of a young girl who had TIR3A in a thyroid nodule located in the isthmus. After considering clinical and ultrasound (US) risk factors, we assessed literature data and guidelines to plan the extension of surgery. We found several studies supporting that the isthmus malignant lesions were associated with a higher rate of multifocality, capsular invasion, extrathyroidal extension, and central lymph node (LN) metastases. These data could predict a more aggressive behavior and a poor prognosis of the isthmus thyroid cancer compared to differentiated thyroid cancer, originating in the thyroid lobes. On the basis of these literature data and considering the familial risk for thyroid cancer of our patient, we decided to perform a total thyroidectomy. The histological examination revealed a follicular variant of papillary carcinoma located in the isthmus with capsular invasion. Conclusion: The isthmus location could be an additional risk factor to consider for a correct surgical approach in indeterminate thyroid lesions and thyroid cancer at fine-needle aspiration (FNA). We suggest that a careful ultrasonography should be carried out in patients with isthmus nodules. Total thyroidectomy should be performed in aggressive nodular disease. Prospective studies are needed to establish the best treatment for these lesions.