Chimerism monitoring following allogeneic hematopoietic stem cell transplantation

Cell Subset-Specific Chimerism Testing by Short Tandem Repeats Analysis for Engraftment Monitoring After Hematopoietic Stem Cell Transplantation

Chimerism is the unique state when cells from genetically different individuals coexist. Chimerism testing allows measuring the donor and recipient immune cell subsets in recipient blood and bone marrow following stem cell transplantation. Chimerism testing is the standard diagnostic test for monitoring engraftment dynamics and early relapse prediction in the recipient following stem cell transplantation. Chimerism testing is also helpful to detect graft-versus-host disease following liver transplantation. Herein, we describe a step-by-step procedure of an in-house-developed method assessing chimerism levels using fragment length analysis of short tandem repeats.

Immune Cell Lineage-Specific Chimerism Testing by Next-Generation Sequencing for Engraftment Monitoring After Allogeneic Hematopoietic Stem Cell Transplantation

Chimerism is an unusual state in which a person's body comprises cells from genetically different people. Chimerism testing allows monitoring for the relative proportion of recipient and donor-derived cell subsets in recipient blood and bone marrow. In the bone marrow transplant setting, chimerism testing is the standard diagnostic tool for early detection of graft rejection and the risk of malignant disease relapse. Chimerism testing enables the identification of patients with increased risk for recurrence of the underlying disease. Herein, we describe a step-by-step technical procedure of a novel, commercially available, next-generation sequencing-based chimerism testing method for use in the clinical laboratory.

Evaluation of ArmedXpert software tools, MixtureAce and Mixture Interpretation, to analyze MPS-STR data

Massively parallel sequencing (MPS) technologies have revolutionized studies of genomic variations and transformed DNA analysis in multiple fields. Assays based on MPS must be capable of discriminating variations introduced by the method, i.e. artifacts from true polymorphisms. In PCR-MPS methods targeting microsatellite markers, artifacts can arise from PCR mis-incorporation, PCR strand slippage (stutter), and sequencing error. Reliable detection of artifacts in mixed DNA samples is a significant challenge that must be addressed in forensic DNA analysis. The ArmedXpert (NicheVision) software tools, MixtureAce™ and Mixture Interpretation, can analyze MPS data by categorizing sequence reads in alleles, stutter, and non-stutter artifacts and analyzing autosomal STR loci of mixed samples. In this study, we evaluated the ArmedXpert tools for the analysis of STR profiles of single-sourced and mixed samples generated by the ForenSeq™ DNA Signature Prep kit (Verogen). Data from eight experimental runs (240 samples) were analyzed: one benchmark run, two runs testing sensitivity with down to 50 pg DNA input, one run testing artificially degraded samples and DNA derived from bones, blood cards and teeth, as well as four runs with mixed DNA samples of varying ratios, sex, and different number of contributors (two to six). The MixtureAce stutter thresholds were initially set following the recommendations from Verogen, plus a non-stutter artifact threshold was set at 5% of allele read counts. A benchmark run, of 30 samples, plus two controls, containing 2310 total alleles, revealed over 5000 artifacts, above an analytical threshold of 10. A total of 4869 artifacts were correctly classified, while 435 were mis-classified as alleles due to exceedance of initial threshold settings. False positives must be resolved by an analyst, which can be time consuming. Stutter thresholds were adjusted based on the benchmark data and the samples were re-tested, resulting in only 57 false positive allele calls. The revised settings were then used in the analysis of the remaining seven experimental runs. Results show that MixtureAce can accurately classify artifacts and alleles when laboratory-specific threshold settings are used. The Mixture Interpretation tool was applied on two- and three-person mixtures. This tool utilized the analyzed data from MixtureAce to calculate, based on the number of alleles at a locus and their read counts, possible deconvolution outcomes with their respective ratios.

Possible involvement of IL-6-producing tissue-resident macrophages in early-onset pericardial effusion pathogenesis after hematopoietic stem cell transplantation

PURPOSE

Pericardial effusion (PE) is a potentially life-threatening complication following hematopoietic stem cell transplantation (HCT). A higher incidence of early-onset PE, unrelated to graft-versus-host disease, before day 100 after HCT has been reported in pediatric patients, but the pathogenic mechanism is poorly understood. Aiming to determine the pathogenesis of early-onset PE in pediatric patients, we analyzed the cytokine concentration and cell population in the pericardial fluid of four pediatric patients with PE.

METHODS

Between January 2009 and December 2015, four patients requiring pericardiocentesis for clinically significant PE were identified in 60 patients. We evaluated the interleukin-6 (IL-6), interferon-γ, IL-1β, and tumor necrosis factor-α levels in PE. Two patients were available for analysis with intracellular cytokine flow cytometry and a chimerism assay.

RESULTS

All patients showed the accumulation of pericardial macrophages and high concentrations of IL-6 in PE. Notably, the accumulated pericardial macrophages were CD163⁺ CD15⁺ CD14⁺ cells of host origin that produced IL-6.

CONCLUSION

These IL-6-producing tissue-resident macrophages may be key players in the pathogenesis of early-onset PE.

Usefulness of Post-Transplant Hematopoietic Chimera Monitoring by Use of the Quantitative Fluorescence Polymerase Chain Reaction Method

BACKGROUND

In the light of an increasing number of hematopoietic stem cell transplantations and more frequent use of reduced-intensity conditioning as preparative regimens for hematopoietic stem cell transplantation, post-transplant cell chimera monitoring is considered a necessity.

METHODS

The quantitative fluorescence polymerase chain reaction method, along with the commercial AmpFSTR SGMPlus kit, was applied in research on hematopoietic chimeras.

RESULTS

The total of 102 patients who had undergone allogenic transplantations were investigated. Chimerism monitoring was commenced on the seventh day after transplantation and lasted up to 12 years in some cases, according to the instituted schedule.

CONCLUSIONS

The kit has been shown to be fully sufficient for determining genetic profiles of recipients and donors and selecting informative markers. The method has been proven effective and satisfactory for assessing quantitative chimeras.

A case series of CAEBV of children and young adults treated with reduced-intensity conditioning and allogeneic bone marrow transplantation: a single-center study

BACKGROUND

Epstein-Barr virus (EBV)-infected T or NK cells cause chronic active EBV infection (CAEBV). Allogeneic hematopoietic stem cell transplantation (HSCT) is curative treatment for CAEBV patients. However, chemotherapy prior to HSCT and optimal conditioning regimen for allogeneic HSCT are still controversial.

PATIENTS AND METHODS

We retrospectively analyzed five patients with CAEBV treated with reduced-intensity conditioning (RIC) consisted of fludarabine, cyclophosphamide, and low-dose total-body irradiation followed by allogeneic bone marrow transplantation in a single institute. Only one of five patients received chemotherapy prior to transplantation. We analyzed EBV-infected cells in a patient whose EBV load increased after HSCT by T-cell repertoire assay, separation of T-cell subpopulations, in situ hybridization and microsatellite analysis.

RESULTS

All five patients achieved engraftment, complete chimera, and eradication of EBV load. All patients have been alive without any serious regimen-related toxicity for more than 16 months following HSCT. However, one patient transplanted from HLA-matched sibling donor developed clonal proliferation of CD4+ Vβ3+ T cells caused by monoclonal EBV infection on day 99 after transplantation. Further analysis revealed that the CD4+ Vβ3+ T cells selectively harbored EBV genome, and these infected cells were derived from donor T cells.

CONCLUSIONS

Allogeneic HSCT with RIC is a safe and effective treatment for better overall survival and less regimen-related toxicity in patients with CAEBV. Our first pediatric case reported in the literature suggests that we should consider the possibility of persistent EBV infection in donor T cells as well as the relapse in recipient cells if EBV load increases after allogeneic HSCT.

Validation of chimerism in pediatric recipients of allogeneic hematopoietic stem cell transplantation (HSCT) a comparison between two methods: real-time PCR (qPCR) vs. variable number tandem repeats PCR (VNTR PCR)

Post-hematopoietic stem cell transplantation (HSCT) chimerism monitoring is important to assess relapse and therapeutic intervention. The purpose of our study is to compare two methods variable number tandem repeats (VNTR) vs. quantitative real- time polymerase chain reaction (qPCR) in terms of determining chimerism. 127 (peripheral blood n=112, bone marrow n=15) samples were simultaneously tested by VNTR using APO-B, D1S80, D1S111, D17S30, gene loci SRY and ZP3 and qPCR using 34 assays (CA001-CA034) that are designed to a bi-allelic insertion/deletion (indel) polymorphism in the human genome. Samples were separated in three subsets: total WBC, T-cell and Myeloid cells. Extraction of DNA was performed then quantified. We analyzed column statistics, paired t-test and regression analysis for both methods. There was complete correlation between the two methods. The simplicity and rapidity of the test results from the qPCR method is more efficient and accurate to assess chimerism.

Development of an algorithm of satellite markers for monitoring chimerism status in post-allogeneic haematopoietic stem cell transplantation patients

INTRODUCTION

Analysis of variable number tandem repeats (VNTRs) by polymerase chain reaction (PCR) is a common method used to predict engraftment status in post-allogeneic haematopoeitic stem cell transplantation (HSCT) patients. Different populations have different copies of repeated DNA sequence and hence, different percentage of informativeness between patient and donor.

METHODS

PCR amplification of four highly polymorphic VNTR markers (YNZ-22, D1S80, D1S111 and ApoB) was conducted on 60 patient-donor pairs. The informativeness of the markers was analysed using 3% agarose gel electrophoresis.

RESULTS

We developed an algorithm for identification of informative VNTR markers in 60 post-allogeneic HSCT patients. YNZ-22 was the most informative (72%), followed by D1S80 (63%) and D1S111 (60%), while the least informative was ApoB (47%). The degree of informativeness achieved was 95%, which could discriminate 57 patient-donor pairs, when all four markers were combined.

CONCLUSION

Since population genetic studies on VNTR loci are not well established in Southeast Asia, the present study is useful to determine reliable markers during the initial screening step of chimerism analysis. By following this algorithm, we are able to reduce time and cost of finding a suitable VNTR marker in our cohort.

Recent advances in quantitative chimerism analysis

Quantitative chimerism analysis is a diagnostic tool used to monitor engraftment kinetics after allogeneic stem cell transplantation. It reflects the proportion of recipient and donor genotypes and is based on the identification of genetic markers characteristic to a given transplant pair. Currently, PCR amplification of short tandem repeats and single-nucleotide polymorphism-specific quantitative real-time PCR are the most widely used techniques for this purpose. In this review, we will address advances as well as technology-specific imperfections, of both techniques that have emerged over the recent years. We will discuss new principles that may simplify assay design, and improve its robustness and reliability. A better chimerism assay could then guide clinical interventions and may, eventually, improve the outcome of allogeneic stem cell transplantation.

Prevalence of chimerism after non-myeloablative hematopoietic stem cell transplantation

CONTEXT AND OBJECTIVE

Non-myeloablative hematopoietic stem cell transplantation (NMA-HSCT) is performed in onco-hematological patients who cannot tolerate ablative conditioning because of older age or comorbidities. This approach does not completely eliminate host cells and initially results in mixed chimerism. Long-term persistence of mixed chimerism results in graft rejection and relapse. Involvement of graft-versus-host disease is concomitant with complete chimerism and graft-versus-tumor effect. The aim of this study was to evaluate the prevalence of chimerism in onco-hematological patients who underwent NMA-HSCT.

DESIGN AND SETTING

Observational clinical study on chimerism status after human leukocyte antigen-identical NMA-HSCT at the Discipline of Hematology and Hemotherapy of Universidade Federal de São Paulo.

METHODS

We sequentially analyzed the amplification of APO-B, D1S80, DxS52, FVW, 33.6, YNZ-2 and H-ras primers using variable number of tandem repeats (VNTR) on 17 pairs and fluorescent in situ hybridization (FISH) with the XY probe and SRY primer on 13 sex-unmatched pairs.

RESULTS

The informativeness of the primers using VNTR was 60% for APO-B, 75% D1S80, 36% DxS52, 14% FVW, 40% YNZ-22 and 16% H-ras. The SRY primer was informative in female receptors with male donors. The XY-FISH method was informative in 100% of the sex-unmatched pairs.

CONCLUSION

These methods were sensitive and informative. In VNTR, the association of APO-B with D1S80 showed 88% informativeness. The quantitative FISH method was more sensitive, but had the disadvantage of only being used for sex-unmatched pairs.