Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers

The Changing Role of Renal Mass Biopsy

The incidence and prevalence of small renal masses (SRMs) continues to rise and with increased detection comes increases in surgical management, although the probability of an SRM being benign is upward of 30%. An extirpative treatment first diagnose-later strategy persists and clinical tools for risk stratification such as renal mass biopsy remain severely underutilized. The overtreatment of SRMs has multiple detrimental effects including surgical complications, psychosocial stress, financial loss, and reduced renal function leading to downstream effects such as the need for dialysis and cardiovascular disease.

Urine Molecular Biomarkers for Detection and Follow-Up of Small Renal Masses

Active surveillance (AS) is the best strategy for small renal masses (SRMs) management; however, reliable methods for early detection and disease aggressiveness prediction are urgently needed. The aim of the present study was to validate DNA methylation biomarkers for non-invasive SRM detection and prognosis. The levels of methylated genes TFAP2B, TAC1, PCDH8, ZNF677, FLRT2, and FBN2 were evaluated in 165 serial urine samples prospectively collected from 39 patients diagnosed with SRM, specifically renal cell carcinoma (RCC), before and during the AS via quantitative methylation-specific polymerase chain reaction. Voided urine samples from 92 asymptomatic volunteers were used as the control. Significantly higher methylated TFAP2B, TAC1, PCDH8, ZNF677, and FLRT2 levels and/or frequencies were detected in SRM patients' urine samples as compared to the control. The highest diagnostic power (AUC = 0.74) was observed for the four biomarkers panel with 92% sensitivity and 52% specificity. Methylated PCDH8 level positively correlated with SRM size at diagnosis, while TFAP2B had the opposite effect and was related to SRM progression. To sum up, SRMs contribute significantly to the amount of methylated DNA detectable in urine, which might be used for very early RCC detection. Moreover, PCDH8 and TFAP2B methylation have the potential to be prognostic biomarkers for SRMs.

Accurate detection of benign and malignant renal tumor subtypes with MethylBoostER: An epigenetic marker-driven learning framework

Current gold standard diagnostic strategies are unable to accurately differentiate malignant from benign small renal masses preoperatively; consequently, 20% of patients undergo unnecessary surgery. Devising a more confident presurgical diagnosis is key to improving treatment decision-making. We therefore developed MethylBoostER, a machine learning model leveraging DNA methylation data from 1228 tissue samples, to classify pathological subtypes of renal tumors (benign oncocytoma, clear cell, papillary, and chromophobe RCC) and normal kidney. The prediction accuracy in the testing set was 0.960, with class-wise ROC AUCs >0.988 for all classes. External validation was performed on >500 samples from four independent datasets, achieving AUCs >0.89 for all classes and average accuracies of 0.824, 0.703, 0.875, and 0.894 for the four datasets. Furthermore, consistent classification of multiregion samples (N = 185) from the same patient demonstrates that methylation heterogeneity does not limit model applicability. Following further clinical studies, MethylBoostER could facilitate a more confident presurgical diagnosis to guide treatment decision-making in the future.

Methylation of PCDH17 and NEFH as prognostic biomarker for nonmetastatic RCC: A cohort study

DNA methylation makes up a main part of the molecular mechanism of cancer evolution and has shown promising results in the prognosis of renal cell cancer (RCC). In this study, we investigated the possible association of promoter methylation of PCDH17, NEFH, RASSF1A, and FHIT, genes with the prognosis of nonmetastatic RCC patients. Cancerous and normal adjacent tissues from surgical specimens of 41 patients with long follow-up were treated for DNA isolation and bisulfite conversion. The gene promoter methylation was determined with quantitative methylation-specific PCR (qMSP). Wilcoxon signed-rank test was used for paired methylation comparisons, while univariate linear regression and Mann-Whitney test were applied for associating methylation status with clinical and disease characteristics. Cox regression proportional hazards models and Kaplan-Meier plots were used for survival analyses in reference to methylation status. Paired comparisons showed tissue-specific hypermethylation for PCDH17 (P < .001), NEFH (P < .001), RASSF1A (P = .032), while a positive association of methylation in normal tissues with age was demonstrated for PCDH17 (P < .001), RASSF1A (P < .001), FHIT (P < .001). PCDH17 was more methylated in cases with clear cell RCC (P = .015) and high-grade tumor (P = .013), while NEFH methylation was higher in locally advanced cases (P = .032). PCDH17 hypermethylation in cancerous and normal tissues was linked to shorter disease-specific survival (DSS, P = .026, P = .004), disease-free survival (DFS, P = .004, P = .019) while NEFH hypermethylation in cancerous tissues was related to shorter DSS (P = .032). Increased methylation difference of NEFH was also associated with shorter DSS (P = .041) and DFS (P = .020), while the corresponding parameter for PCDH17 was associated with poor DFS (P = .014). Kaplan-Meier curves for hypermethylation in cancer tissues demonstrated different clinical courses for PCDH17 (P = .017), NEFH (P = .023) regarding DSS, and PCDH17 (P = .001) regarding DFS. Our study not only highlights the prognostic value of promoter methylation of PCDH17 and NEFH in cancer tissues but also is the first report of the prognostic value of methylation alterations in normal tissues. Our findings are the first report of the prognostic value of methylation alterations in normal tissues, which can contribute to improved assessment of recurrence risk.

Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma

BACKGROUND

Merkel cell carcinoma (MCC) is a rare but aggressive skin cancer with limited treatment possibilities. Merkel cell tumors display with neuroendocrine features and Merkel cell polyomavirus (MCPyV) infection in the majority (80%) of patients. Although loss of histone H3 lysine 27 trimethylation (H3K27me3) has been shown during MCC tumorigenesis, epigenetic dysregulation has largely been overlooked.

METHODS

We conducted global DNA methylation profiling of clinically annotated MCC primary tumors, metastatic skin tumors, metastatic lymph node tumors, paired normal tissues, and two human MCC cell lines using the Illumina Infinium EPIC DNA methylation BeadArray platform.

RESULTS

Significant differential DNA methylation patterns across the genome are revealed between the four tissue types, as well as based on MCPyV status. Furthermore, 964 genes directly regulated by promoter or gene body DNA methylation were identified with high enrichment in neuro-related pathways. Finally, our findings suggest that loss of H3K27me3 occupancy in MCC is attributed to KDM6B and EZHIP overexpression as a consequence of promoter DNA hypomethylation.

CONCLUSIONS

We have demonstrated specific DNA methylation patterns for primary MCC tumors, metastatic MCCs, and adjacent-normal tissues. We have also identified DNA methylation markers that not only show potential diagnostic or prognostic utility in MCC management, but also correlate with MCC tumorigenesis, MCPyV expression, neuroendocrine features, and H3K27me3 status. The identification of DNA methylation alterations in MCC supports the need for further studies to understand the clinical implications of epigenetic dysregulation and potential therapeutic targets in MCC.

Surveillance for low-risk kidney cancer: a narrative review of contemporary worldwide practices

The management trend of low-risk kidney cancer over the last decade has been from treatment with radical nephrectomy, to use of nephron sparing procedures of partial nephrectomy and ablation, as well as the option of active surveillance (AS). This narrative review aims to summarise the available guidelines related to AS and review the published descriptions of regional practices on the management of low-risk kidney cancer worldwide. A search of PubMed, Google Scholar and Cochrane Library databases for studies published 2010 to June 2020 identified 15 studies, performed between 2000 and 2019, which investigated 13 different cohorts of low-risk kidney cancer patients on AS. Although international guidelines show a level of agreement in their recommendation on how AS is conducted, in terms of patient selection, surveillance strategy and triggers for intervention, cohort studies show distinct differences in worldwide practice of AS. Prospective studies showed general agreement in their predefined selection criteria for entry into AS. Retrospective studies showed that patients who were older, with greater comorbidities, worse performance status and smaller tumours were more likely to be managed with AS. The rate of percutaneous renal mass biopsy varied between studies from 2% to 56%. The surveillance protocol was different across all studies in terms of recommended modality and frequency of imaging. Of the 6 studies which had set indications for intervention, these were broadly in agreement. Despite clear criteria for intervention, patient or surgeon preference was still the reason in 11–71% of cases of delayed intervention across 5 studies. This review shows that AS is being applied in a variety of centres worldwide and that key areas of patient selection criteria and surveillance strategy have large similarities. However, the rate of renal mass biopsy and of delayed intervention varies significantly between studies, suggesting the process of diagnosing malignant SRM and decision making whilst on AS are varying in practice. Further research is needed on the diagnosis and characterisation of incidentally found small renal masses (SRM), using imaging and histology, and the natural history of these SRM in order to develop evidence-based active surveillance protocols.

Development of a DNA Methylation-Based Diagnostic Signature to Distinguish Benign Oncocytoma From Renal Cell Carcinoma

PURPOSE

A challenge in the diagnosis of renal cell carcinoma (RCC) is to distinguish chromophobe RCC (chRCC) from benign renal oncocytoma, because these tumor types are histologically and morphologically similar, yet they require different clinical management. Molecular biomarkers could provide a way of distinguishing oncocytoma from chRCC, which could prevent unnecessary treatment of oncocytoma. Such biomarkers could also be applied to preoperative biopsy specimens such as needle core biopsy specimens, to avoid unnecessary surgery of oncocytoma.

METHODS

We profiled DNA methylation in fresh-frozen oncocytoma and chRCC tumors and adjacent normal tissue and used machine learning to identify a signature of differentially methylated cytosine-phosphate-guanine sites (CpGs) that robustly distinguish oncocytoma from chRCC.

RESULTS

Unsupervised clustering of Stanford and preexisting RCC data from The Cancer Genome Atlas (TCGA) revealed that of all RCC subtypes, oncocytoma is most similar to chRCC. Unexpectedly, however, oncocytoma features more extensive, overall abnormal methylation than does chRCC. We identified 79 CpGs with large methylation differences between oncocytoma and chRCC. A diagnostic model trained on 30 CpGs could distinguish oncocytoma from chRCC in 10-fold cross-validation (area under the receiver operating curve [AUC], 0.96 (95% CI, 0.88 to 1.00)) and could distinguish TCGA chRCCs from an independent set of oncocytomas from a previous study (AUC, 0.87). This signature also separated oncocytoma from other RCC subtypes and normal tissue, revealing it as a standalone diagnostic biomarker for oncocytoma.

CONCLUSION

This CpG signature could be developed as a clinical biomarker to support differential diagnosis of oncocytoma and chRCC in surgical samples. With improved biopsy techniques, this signature could be applied to preoperative biopsy specimens.

Diagnostic accuracy of contrast-enhanced ultrasound in the detection of small renal masses: A protocol of systematic review and meta-analysis

BACKGROUND

The small renal masses (SRMs) were defined that the diameter of renal masses measured by enhanced image was ≤4 cm. The diagnostic accuracy of contrast-enhanced ultrasound (CEUS) for SRMs is apparently variable among previous studies. Hence, this study will evaluate the diagnostic accuracy of CEUS in the identification of benign and malignant SRMs.

METHODS

A comprehensive search using the databases of Cochrane Library, Embase, PubMed, WANGFANG, and China National Knowledge Infrastructure will be carried out to identify studies in which patients with SRMs are assessed by CEUS. Two investigators will independently screen the literature and extract the data. Any discrepancies will be resolved via discussion with the senior author. Study quality will be assessed by the Quality Assessment of Diagnostic Accuracy Studies 2 tool, and pooled sensitivity and specificity of various CEUS findings for the diagnosis of SRMs will be determined. Summary receiver operating characteristic curve will be used to assess the overall performance of CEUS.

RESULTS

This study will evaluate the diagnostic accuracy of CEUS for the diagnosis of SRMs through sensitivity, specificity, positive and negative likelihood ratio, and diagnostic odds ratio.

CONCLUSION

This study will summarize the most recent evidence that focusing on the diagnosis of CEUS for SRMs.

STUDY REGISTRATION

INPLASY202060040.

Clinical utility of contrast-enhanced ultrasonography in the diagnosis of benign and malignant small renal masses among Asian population

We assessed the clinical utility of contrast-enhanced ultrasonography (CEUS) in the diagnosis of benign and malignant small renal masses using a meta-analysis of diagnostic test. We performed a comprehensive online search in the following database including PubMed, Embase, Web of Science, Wanfang, and Chinese National Knowledge Infrastructure from the inception to August 25, 2019. the following index were calculated for assessing the diagnostic ability, including sensitivity, specificity, diagnostic odds ratio (DOR), negative likelihood ratio (NLR), positive likelihood ratio (PLR), area under the curve (AUC) with 95% confidence intervals (CIs). Seventeen studies were included in the qualitative and quantitative analyses. The overall sensitivity was 0.93 with 95% CI of 0.88-0.95. The specificity was 0.71 and the 95% CI was 0.60-0.80. The pooled AUC was 0.91 (95% CI: 0.88-0.93). The diagnostic odds ratio was 31 (95% CI: 21-45). The NLR and PLR were 0.10 (95% CI: 0.07-0.15) and 3.2(95% CI: 2.3-4.4), respectively. There is a slight heterogeneity within studies. The subgroup analysis was also performed. For retrospective and perspective, the sensitivity and specificity were 0.93, 0.92 and 0.71, 0.73; For different diameter lesions, the sensitivity and specificity were 0.93, 0.94 and 0.64, 0.74; For sample size (≤median vs. >median), the sensitivity and specificity were 0.94, 0.93 and 0.67, 0.77. The Deek's funnel plot asymmetry test in indicated no publication bias. The CEUS have a high diagnostic ability in differentiating benign and malignant small renal masses among Asian population.

Needle Biopsy Adequacy in the Era of Precision Medicine and Value-Based Health Care

CONTEXT.—

Needle biopsy of diseased tissue is an essential diagnostic tool that is becoming even more important as precision medicine develops. However, the capability of this modality to efficiently provide samples adequate for diagnostic and prognostic analysis remains quite limited relative to current diagnostic needs. For physicians and patients, inadequate biopsy frequently leads to diagnostic delay, procedure duplication, or insufficient information about tumor biology leading to delay in treatment; for health systems, this results in substantial incremental costs and inefficient use of scarce specialized diagnostic resources.

OBJECTIVE.—

To review current needle biopsy technology, devices, and practice with a perspective to identify current limitations and opportunities for improvement in the context of advancing precision medicine.

DATA SOURCES.—

PubMed searches of fine-needle aspiration and core needle biopsy devices and similar technologies were made generally, by tissue site, and by adequacy as well as by health economics of these technologies.

CONCLUSIONS.—

Needle biopsy adequacy can be improved by recognizing the importance of this diagnostic tool by promoting common criteria for needle biopsy adequacy; by optimizing needle biopsy procedural technique, technologies, clinical practice, professional education, and quality assurance; and by bundling biopsy procedure costs with downstream diagnostic modalities to provide better accountability and incentives to improve the diagnostic process.

Classification tree for the prediction of malignant disease and the prediction of non-diagnostic biopsies in patients with small renal masses

INTRODUCTION

Preoperative prediction of benign vs. malignant small renal masses (SRMs) remains a challenge. This study: 1) validates our previously published classification tree (CT) with an external cohort; 2) creates a new CT with the combined cohort; and 3) evaluates the RENAL and PADUA scoring systems for prediction of malignancy.

METHODS

This study includes a total of 818 patients with renal masses; 395 underwent surgical resection and 423 underwent biopsy. A CT to predict benign disease was developed using patient and tumour characteristics from the 709 eligible participants. Our CT is based on four parameters: tumour volume, symptoms, gender, and symptomatology. CART modelling was also used to determine if RENAL and PADUA scoring could predict malignancy.

RESULTS

When externally validated with the surgical cohort, the predictive accuracy of the old CT dropped. However, by combining the cohorts and creating a new CT, the predictive accuracy increased from 74% to 87% (95% confidence interval 0.84-0.89). RENAL and PADUA score alone were not predictive of malignancy. One limitation was the lack of available histological data from the biopsy series.

CONCLUSIONS

The validated old CT and new combined-cohort CT have a predictive value greater than currently published nomograms and single-biopsy cohorts. Overall, RENAL and PADUA scores were not able to predict malignancy.

The Role of DNA Methylation in Renal Cell Carcinoma

Renal cell carcinoma (RCC) is the most common kidney cancer and includes several molecular and histological subtypes with different clinical characteristics. While survival rates are high if RCC is diagnosed when still confined to the kidney and treated definitively, there are no specific diagnostic screening tests available and symptoms are rare in early stages of the disease. Management of advanced RCC has changed significantly with the advent of targeted therapies, yet survival is usually increased by months due to acquired resistance to these therapies. DNA methylation, the covalent addition of a methyl group to a cytosine, is essential for normal development and transcriptional regulation, but becomes altered commonly in cancer. These alterations result in broad transcriptional changes, including in tumor suppressor genes. Because DNA methylation is one of the earliest molecular changes in cancer and is both widespread and stable, its role in cancer biology, including RCC, has been extensively studied. In this review, we examine the role of DNA methylation in RCC disease etiology and progression, the preclinical use of DNA methylation alterations as diagnostic, prognostic and predictive biomarkers, and the potential for DNA methylation-directed therapies.

Identification of clear cell renal cell carcinoma and oncocytoma using a three-gene promoter methylation panel

BACKGROUND

Promoter methylation has emerged as a promising class of epigenetic biomarkers for diagnosis and prognosis of renal cell tumors (RCTs). Although differential gene promoter methylation patterns have been reported for the major subtypes (clear cell, papillary and chromophobe renal cell carcinoma, and oncocytoma), validation of diagnostic performance in independent series have been seldom performed. Herein, we aimed at assessing the diagnostic performance of genes previously shown to be hypermethylated in RCTs in different clinical settings.

METHODS

Promoter methylation levels of HOXA9 and OXR1 were assessed by quantitative methylation specific PCR. ROC curves were generated for OXR1, OXR1 combined with MST1R and HOXA9. Sensitivity, specificity, positive predictive value, negative predictive value and accuracy were computed, maximizing specificity. Methylation levels were also correlated with clinical and pathological relevant parameters.

RESULTS

HOXA9 and OXR1 promoter methylation was disclosed in 73 and 87% of RCTs, respectively. A two-gene methylation panel comprising OXR1 and MST1R identified malignancy with 98% sensitivity and 100% specificity, and clear cell renal cell carcinoma with 90% sensitivity and 98% specificity. HOXA9 promoter methylation allowed for discrimination between oncocytoma and both papillary and chromophobe renal cell carcinoma but only with 77% sensitivity and 73% specificity. Significantly higher OXR1 promoter methylation levels (p = 0.005) were associated with high nuclear grade in ccRCC.

CONCLUSIONS

A panel including OXR1 and MST1R promoter methylation allows specific and sensitive identification of renal cell tumors, and, especially, of clear cell renal cell carcinoma. Moreover, higher OXR1 promoter methylation levels associate with clear cell renal cell carcinoma nuclear grade, a surrogate for tumor aggressiveness. Thus, gene promoter methylation analysis might a useful ancillary tool in diagnostic management of renal masses.