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Review
. 2014 Jun;22(6):715-23.
doi: 10.1038/ejhg.2013.247. Epub 2013 Nov 20.

Making the Genomic Leap in HCT: Application of Second-Generation Sequencing to Clinical Advances in Hematopoietic Cell Transplantation

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Free PMC article
Review

Making the Genomic Leap in HCT: Application of Second-Generation Sequencing to Clinical Advances in Hematopoietic Cell Transplantation

Yun R Li et al. Eur J Hum Genet. .
Free PMC article

Abstract

Recent developments in second-generation sequencing (SGS) technologies provide an avenue for achieving rapid and accurate high-throughput analysis of human and microbial genomic diversity. SGS technologies have the potential to transform existing medical management of complex and life-threatening medical conditions by enabling clinicians to develop disease-targeted clinical care plans for each patient. In this review, we outline how innovative SGS-based approaches can improve the care of recipients of allogeneic hematopoietic cell transplantation (HCT), a life-saving procedure that carries a 1-year mortality risk of over 30%. We specifically evaluate foreseeable applications of SGS-based technology in facilitating rapid, phase-sensitive human leukocyte antigen (HLA) typing, assessment of non-HLA genomic compatibility, identifying patients at high risk for adverse drug reactions, and post-HCT monitoring for engraftment, minimal residual disease and infection. We conclude that innovative SGS approaches have the capacity to revolutionize the HCT recipient risk assessment process, support non-invasive clinical monitoring and improve patient outcomes, thereby setting the stage for a new era of genomically informed patient-centered medicine.

Figures

Figure 1
Figure 1
Clinical applications of second-generation sequencing (SGS) technologies to HCT. (a) Diagram of typical workflow from clinical sample to sequencing. SGS of genomic DNA derived from recipient somatic or tumor-cell DNA can be used to profile genomic risk factors of underlying disease or identify causative driver mutations in hematological malignancies. Although the exact methods are platform specific, typical SGS-based techniques follow a standard workflow, requiring the isolation of genomic DNA, DNA fragmentation and the ligation of paired-end adaptors. Depending on whether the whole genome, all coding or specific coding regions are interrogated, additional sequence-specific adaptors for exonic or user-specified regions are used to capture the prespecified target DNA fragments. Adapter-ligated fragments are next captured either in an oil-emulsion bead (454 pyrosequencing) or on a solid platform (bridge amplification) as shown here. All SGS techniques culminate with massively parallel sequencing technology utilizing an array-like platform. As nucleotide bases are added cyclically, light is produced and sequences are read out based on detected fluorescence intensities and wavelengths. (b) Existing and potential SGS applications to HCT patient care using available SGS technology: As discussed in the main text, SGS-based improvements to existing clinical care of HCT recipients can be broadly classified into three major domains: (1) accurate and rapid HLA typing, (2) pre-transplant assessment of adverse drug response and non-HLA genomic risk factors and (3) post-HCT early and routine monitoring for minimal residual disease, engraftment of donor cells, and life-threatening systemic infections.
Figure 2
Figure 2
The role of gene-expressed mismatch antigens in GVHD or rejection following transplantation. (a) Donor-recipient GEMA mismatch in myeloablative HCT: GVHD can occur in an HCT recipient with normal GEMA expression when he or she is transplanted with cells derived from a donor without normal GEMA protein expression. Since GEMAs are ‘self-expressed' antigens, GEMA-derived peptides can be presented in the context of both class I and class II MHC receptors found on recipient cells following HCT. Allorecognition of host MHC molecules presenting GEMA-derived peptides subsequently triggers donor-derived T cells that are not ‘tolerized' to GEMA-derived peptides to attack host cells, resulting in clinical manifestations of GVHD. In addition, because GEMAs such as UGT2B17 can be cell-surface antigens, their antigenicity is not MHC-restricted like most autosomally encoded minor histocompatibility antigens. Like H-Y antigens, a B-cell mediated response to the ‘foreign' GEMA expression can result in the production of autoantibodies by donor-derived B cells that target the host-cell expressed GEMA proteins on the cell surface. McCarroll et al. first demonstrated the clinical significance of GEMA mismatch in HCT by following up on the results from a large genome-wide association study (GWAS)-based screen for homozygous deletion copy number variations (hdCNVs) that appear to be tolerated and are found frequently in an appreciable percentage of the human population. Based on the hypothesis that hdCNVs overlapping a gene-encoding region would cause gene expression mismatch between HCT donors and recipients, McCarroll screened ∼400 HCT recipients and their HLA-matched siblings for six candidate GEMAs. They identified that D−/R+ status for one particular GEMA UGT2B17 increased the risk of Grade 2+ GVHD, a finding that was later replicated in two independent cohorts, together totaling over 1300 patients (combined OR of 2.5). In addition, McCarroll et al showed that UGT2B17+ HCT recipients, who received hematopoeitic cells from UGT2B17−/− donors were seropositive for anti-UGT2B17 antibodies. Moreover, they were able to isolate MHC-bound UGT2B17-derived peptides from the sera of these UGT2B17 mismatched. Given that the average human genome has at least several thousand CNVs greater than 1 kb (which is likely to be an underestimate due to current limitations in CNV detection platforms) and contains ∼100 loss of function (LoF) mutations (with ∼20 in both copies) , other GEMAs are likely to exist. By coupling large-scale RNA-seq and SGS data, a genome-wide search for other GEMAs may reveal hundreds of other such loci across the genome. (b) Donor-recipient GEMA mismatch in the context of reduced-intensity conditioning/non-myeloablative HCT or solid organ transplantation: rejection of donor cells or tissue occurs due to the absence of GEMA protein expression (eg, UGT2B17) in the recipient. Complementary to the scenario illustrated in (a), recipient tissues do not express GEMA proteins. Thus, potentially GEMA-reactive T- and B-cell clones are not eliminated from the host immune repertoire. Following transplantation, immune competent recipient T cells can attack donor stem cells expressing GEMA and inhibit engraftment or cause acute graft rejection.
Figure 3
Figure 3
The application of genomics approaches to improve HCT outcomes. (Left) panels show existing clinical practice, (Center) panel describes recent scientific/research contributions through genomic technology and (Right) panel proposes clinically feasible applications of genomics technology in the coming years. The four categories correspond to the four areas in which genomics technology will likely make the most direct impact on the clinical management of HCT recipients.

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