The molecular diagnosis of rejection in liver transplant biopsies: First results of the INTERLIVER study

Abstract

Molecular diagnosis of rejection is emerging in kidney, heart, and lung transplant biopsies and could offer insights for liver transplant biopsies. We measured gene expression by microarrays in 235 liver transplant biopsies from 10 centers. Unsupervised archetypal analysis based on expression of previously annotated rejection-related transcripts identified 4 groups: normal "R1 normal " (N = 129), T cell-mediated rejection (TCMR) "R2 TCMR " (N = 37), early injury "R3 injury " (N = 61), and fibrosis "R4 late " (N = 8). Groups differed in median time posttransplant, for example, R3 injury 99 days vs R4 late 3117 days. R2 TCMR biopsies expressed typical TCMR-related transcripts, for example, intense IFNG-induced effects. R3 injury displayed increased expression of parenchymal injury transcripts (eg, hypoxia-inducible factor EGLN1). R4 late biopsies showed immunoglobulin transcripts and injury-related transcripts. R2 TCMR correlated with histologic rejection although with many discrepancies, and R4 late with fibrosis. R2 TCMR , R3 injury , and R4 late correlated with liver function abnormalities. Supervised classifiers trained on histologic rejection showed less agreement with histology than unsupervised R2 TCMR scores. No confirmed cases of clinical antibody-mediated rejection (ABMR) were present in the population, and strategies that previously revealed ABMR in kidney and heart transplants failed to reveal a liver ABMR phenotype. In conclusion, | 2157 MADILL-THOMSEN ET AL. 1 | INTRODUC TI ON Diagnosis of rejection in liver transplantation remains an important issue in clinical management. 1-4 The current standard-of-care (SOC) for liver biopsy diagnoses is histology, generally following Banff guidelines. 5 Histology is based on pattern recognition by experts, and assessments differ between observers. 6-11 Reported kappa values for pathology related to T cell-mediated rejection (TCMR) are low to moderate (0.15-0.62 12) especially when comorbidities are present, 7 leaving an unmet need for improvement in precision. Moreover, the diagnosis and prevalence of antibody-mediated rejection (ABMR) in liver transplants remain controversial. 5,13-15 Liver transplants present unique challenges because of their tolerogenic properties, inviting clinicians to consider reducing immunosuppression. 16-20 However, this practice requires a precise and accurate system for diagnosing rejection. 21-25 Liver function test abnormalities are associated with rejection but cannot distinguish TCMR from other diseases such as steatohepatitis. 26,27 Molecular measurement of gene expression using microarrays coupled with machine learning has the potential to improve the assessment of transplant biopsies by overcoming the limitations of conventional diagnostics. 28 We previously developed the Molecular Microscope ® Diagnostic System (MMDx) for kidney, 29-32 heart, 33,34 and lung transplants. 35-37 A number of factors argue that MMDx testing is more accurate than histology 29 : for example, use of continuous quantitative measurements, 29 low samplin...

Non-invasive alloimmune risk stratification of long-term liver transplant recipients

“…The molecular pathogenesis of subclinical liver allograft damage is known to be driven by an interferon gamma-orchestrated cellular immune response 8,9 closely resembling what is observed in clinically-apparent 'classical' TCMR 14,25,26 . Our results indicate that both reduced IS exposure and increased number of HLA epitope mismatches between donor and recipient are implicated in this response.…”

Antibody-mediated rejection of the liver allograft: An update and a clinico-pathological perspective

“…88 A recent study utilising molecular analysis of gene expression in biopsies of LT recipients was able to correlate rejection-associated gene transcripts with histologic TCMR, although its utility in liver AMR remains unknown. 89 It is possible that progressive fibrosis after LT in paediatric recipients may reflect ongoing silent AMR. 90 Normal liver tests in the setting of progressive inflammation and fibrosis may indicate the need for protocol liver biopsies combined with routine DSA and C4d analysis, especially in patients with medication non-adherence, persistently low levels of immunosuppression, or in candidates for immunosuppression withdrawal.…”

The Molecular Microscope (MMDXR) interpretation of thoracic and abdominal allograft biopsies: Putting things in perspective for the clinician

“…The INTERLIVER study 35 has recently developed a classifier of TCMR by a text‐based analysis of biopsy reports. Biopsies with non‐zero inflammation scores were all interpreted to be varying degrees of rejection, even though rejection had not been diagnosed by the pathologist or validated by the treating physician.…”