Circulating Cell-Free DNA in Renal Cell Carcinoma

Circulating Cell-Free DNA in Renal Cell Carcinoma: History

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Subjects: Oncology

Contributor: Edoardo Francini ,

Giuseppe Nicolò Fanelli

, Filippo Pederzoli ,

Sandor Spisak

, Erika Minonne ,

Massimiliano Raffo

Hubert Pakula

Viktoria Tisza

, Cristian Scatena , Antonio Giuseppe Naccarato , Massimo Loda , Pier Vitale Nuzzo

Tumor biopsy is still the gold standard for diagnosing and prognosis renal cell carcinoma (RCC). However, its invasiveness, costs, and inability to accurately picture tumor heterogeneity represent major limitations to this procedure. Analysis of circulating cell-free DNA (cfDNA) is a non-invasive cost-effective technique that has the potential to ease cancer detection and prognosis. In particular, cfDNA could be a complementary tool to identify and prognosticate RCC while providing contemporary mutational profiling of the tumor.

kidney cancer
liquid biopsy
cell-free methylated DNA
genetic

1. Introduction

Kidney cancer is the third most frequent urologic cancer in adults and accounts for approximately 2–3% of all annually diagnosed malignancies in the United States [1]. Renal cell carcinoma (RCC) accounts for the vast majority of kidney cancers. RCC early diagnosis is challenging and typically incidental, primarily relying on radiological procedures executed for other indications [2]. Radical or partial nephrectomy offers curative responses in patients with localized RCC and selected patients with advanced RCC [3]. However, the disease recurs in about one-third of patients after resection of the primary tumor [4]. Existing prognostic classification systems based on clinical-pathological features, such as TNM stage and Fuhrman grading, showed limited potential to predict recurrence [5]. Currently, several therapeutic modalities comprising tyrosine kinase inhibitors, mammalian target rapamycin inhibitors, and immunotherapeutic agents are used for the treatment of metastatic RCC (mRCC) [6,7,8]. However, no established biomarker predictive of response to any of these treatments has been established yet, and there is uncertainty regarding their optimal choice and sequence of use in clinical practice. Therefore, identifying simple, accurate, and easily accessible biomarkers to boost the diagnostic specificity, effectively evaluate the risk of relapse following nephrectomy and predict the response to the therapeutic regimens currently offered for metastatic disease is an unmet clinical need.

Circulating tumor DNA (ctDNA), DNA released from cancer cells into the bloodstream or other body fluids, has been increasingly investigated as a “liquid biopsy” and proved to enable comprehensive genomic profiling of several tumors at various time points [22,23,24,25,26,27,28,29]. Further, the analysis of cfDNA was shown to be a viable, inexpensive, and less-invasive method to diagnose and monitor cancer hence circumventing the well-known shortcomings of invasive tissue biopsies [26,30]. In the recent past, as the concordance of genetic alterations between cfDNA and matched tumor biopsy was validated, there has been growing enthusiasm for the use of cfDNA as a potential blood cancer biomarker. In addition, epigenetic features of cfDNA, such as methylation of cfDNA (cfMeDNA), have been increasingly investigated in recent years [31,32]. Methylation of the pyrimidine ring of cytosine was shown to inhibit transcription when found in CpG islands and stabilize the genome when found in non-coding DNA regions [32,33]. The stability and specificity of CpG island methylation patterns demonstrated high sensitivity for detecting and classifying several tumor types, and thus, the analysis of DNA methylome is a promising cancer biomarker [34,35,36].

2. Applications of cfDNA Analysis in RCC

2.1. Diagnostic Role

RCC is typically detected by an abdominal ultrasound examination [2]. However, owing to its precision and accuracy limitations, suspicious findings must be validated by CT or MRI scans [55]. While the analysis of cfDNA could aid the detection of early signs of the disease and the distinction between benign and malignant renal lesions, there are no clear recommendations yet regarding the use of cfDNA for these aims. A major hurdle to RCC diagnosis by means of cfDNA analysis is that of all extracranial tumors studied, RCC sheds the least amount of ctDNA in the bloodstream, and its detection is challenging [56,57,58]. In addition, the relevant discrepancies of cfDNA isolation and detection techniques among the studies investigating cfDNA in RCC make comparisons of findings quite challenging. Standardization of these methods within large prospective trials is warranted to validate cfDNA as a screening biomarker for RCC.

2.1.1. cfDNA Levels in RCC, Healthy Controls and Non-Cancer Disease

Five prospective studies evaluated cfDNA levels in a total of more than 300 RCC patients and 140 control subjects [57,59,60,61,62]. Although an analysis of the aggregate data of these reports is biased by the several heterogeneities among the studies, including cfDNA sources (serum versus plasma), isolation and evaluation techniques, and populations with different disease states, it should be noted that in all five analyses the levels of cfDNA in RCC patients were higher than in healthy controls.

The analysis by Perego et al. of 48 patients with RCC and 41 healthy subjects showed that the mean pre-operative plasma cfDNA concentration in the RCC group was eight times higher than that of the healthy controls (26.4 vs. 3.2 ng/mL, p = 0.003) and decreased after nephrectomy [59]. Of note, the significance with respect to the controls persisted even when patients were stratified by sex, age, histology, tumor size, grading, and pathological TNM stratification [59].

Although, in aggregate, these data seem to suggest a correlation between raised plasma or serum levels of cfDNA and the presence of RCC, the cumulative body of evidence is still not sufficiently solid. Because increased cfDNA may be found in other non-cancer conditions, such as benign lesions, inflammatory or autoimmune diseases, and tissue traumas, the utility of cfDNA quantification to detect the presence of RCC is indeed limited [63,64,65]. Therefore, cfDNA analysis alone should not be considered a valid screening instrument for RCC at present.

2.1.2. cfDNA Integrity as a Tool for Differentiating RCC and Non-Cancer Controls

Using quantitative real-time PCR, Hauser et al. analyzed the serum cfDNA integrity, defined as the ratio of the longer fragment actine-beta gene 384 (ACTB³⁸⁴) derived from necrosis and the shorter fragment actine-beta gene 106 (ACTB¹⁰⁶) derived from apoptosis of 35 RCC patients and 54 healthy controls [66]. The levels of both cfDNA fragments were found to increase in the pre-operative serum of RCC patients compared to the healthy individuals, indicating that cfDNA is fragmented to a higher degree in cancer patients [66].

Although the findings of most studies support the hypothesis that ctDNA is more likely released by necrotic cancer cells and thus it is composed of larger fragments compared to non-tumor-derived cfDNA, likely released by apoptotic cells, the limited number of samples analyzed, the lack of standardization in measuring long vs. short fragments of cfDNA and the modest sensitivity and specificity values for short and long fragment detection prevent us from considering cfDNA size as a reliable diagnostic biomarker. The specific size of tumor-derived DNA fragments, the detailed characterization of tumor-derived alterations, and the potential implications of these biological differences have not been sufficiently explored yet.

2.1.3. cfDNA Genetic Alterations

The identification of genetic alterations (GA), such as microsatellite instability (MSI) or loss of heterozygosity (LOH) in the cfDNA, is another feature of cfDNA which holds potential as a biomarker of early diagnosis of RCC.

Goessl et al. detected GAs in plasma cfDNA of RCC patients by applying only four markers for microsatellite alterations (MSI or LOH) on chromosome 3p [79]. The observed alterations were not correlated with the stage of the tumor and were not found in the healthy controls [79].

A later analysis focused on 20 microsatellite markers located on chromosomes 3p and 5q [80]. Serum cfDNA GAs were detected in 74% of cases using 9 markers, in 87% of cases using 11 markers, and only in 15% of controls using 10 markers, suggesting that cfDNA GAs may be associated with RCC [80]. In this respect, Perego et al. investigated five microsatellite alterations on chromosome 3p in nine of the 54 RCC patients whose pre-operative plasma was available [59]. Five of those nine patients had at least one of the five microsatellite markers, and these variations were also demonstrated in their primary tumor [59]. Although in aggregate, these data would portend a potential association between cfDNA GAs and RCC detection, the sensitivity and specificity of these analyses seem to depend on the number of microsatellites investigated. In this regard, the comprehensive study of microsatellites and GAs currently offered by NGS may be a more efficient and accurate method of analysis.

2.1.4. cfDNA Epigenetic Alterations: A New Promising Method to Detect RCC

Another feature recently increasingly investigated as a potential diagnostic biomarker of RCC is the hyper- or hypo-methylation of cfDNA. Targeted methylation and global methylation analyses seemed to provide high specificity and sensitivity in distinguishing RCC patients from healthy controls compared to genetic analysis. The high tissue and cell type specificity of DNA methylation, as well as its high stability, would make it an ideal biomarker of RCC detection [31,32]. Moreover, methylation of genes occurs frequently in the early stages of RCC [81].

The methylation of other genes with a key role in renal carcinogenesis also seems to hold a promising role in detecting RCC. In Hoque’s cohort, 67% of RCC patients had a methylated promoter in at least one of the nine genes analyzed [38]. cfDNA analysis in eight selected methylated genes (APC, GSTP1, p14(ARF), p16, RAR-B, RASSF1A, TIMP3, PTGS2) showed that 86% of the patients harbored at least one methylated gene [82]. Although all genes, except p16 and TIMP3, were significantly methylated in RCC patients compared to healthy individuals, only APC was correlated with the advanced tumor stage [82].

2.2. Post-Operative Recurrence and Prognostic Role

An intriguing analysis of pre-operative serum cfDNA of patients with clinically organ-confined RCC reported that all of those with two or three detectable LOH in the 28 studied loci experienced disease recurrence within 2 years after surgery vs. only 7% with no detectable serum LOH [88]. This finding suggested that microsatellite aberrations may detect post-surgery RCC relapse [88]. In contrast, another study analyzing plasma cfDNA of a smaller cohort of localized RCC patients showed that, although cfDNA concentration drastically decreased in all subjects after radical surgery compared to pre-nephrectomy levels, only 20% of those who showed an increase in cfDNA levels during the follow-up experienced recurrence [59]. Additionally, relapse-free survival was not associated with the presence of LOH in cfDNA [59]. A larger analysis reported the efficacy of plasma cfDNA in monitoring post-nephrectomy recurrence in a group of 92 RCC patients [57]. Patients with higher cfDNA levels had a significantly greater recurrence rate than those with lower levels before and after nephrectomy. Interestingly, two contemporary studies showed that RCC patients with detectable pre-operative cfDNA had shorter PFS compared to those without [74,77], suggesting that evidence of pre-surgery cfDNA levels may be a promising biomarker of recurrence in RCC patients following nephrectomy procedure. Similarly, a prospective study of 200 RCC patients with a median follow-up period of 28 months showed that higher pre-nephrectomy serum cfDNA levels were associated with shorter RCC-specific survival [60].

2.3. Predictive Role

Recently, in the largest assessment to date of ctDNA of patients with mRCC, most subjects were found to have clinically relevant GAs [69]. The analysis of the ctDNA profile in a cohort of 220 mRCC patients and across patients receiving first and later-line therapies showed that, while the most common alterations were TP53, VHL, NF1, EGFR, and ARID1A, regardless of the line of treatment, the genetic profiles differed among patients receiving first-line compared to those receiving second-line treatments [69]. In particular, the authors observed GA rate differences in those who had second or later lines versus first-line therapy only, with higher variations found for TP53 (49% vs. 24%), VHL (29% vs. 18%), NF1 (20% vs. 3%), EGFR (15% vs. 8%), and PIK3CA (17% vs. 8%) [69].In aggregate, analysis of cfDNA in the course of the disease may have a predictive role in the treatment of mRCC, but larger datasets are warranted to confirm this hypothesis.

3. Conclusions

The use of cfDNA as a non-invasive biomarker for routine use in oncology has made great progress in recent years. As cfDNA is a fast, low-cost, and easy way to obtain dynamic information about the tumor, continual efforts from intense multidisciplinary studies have been made to transfer the research tools to routine clinical practice. On the one hand, several reports highlight cfDNA as a potential biomarker in RCC diagnosis, prognosis, and treatment and show how technological breakthroughs have brought new cancer detection methods with higher accuracy and efficiency. On the other hand, there are challenges to the widespread use of this new approach in the routine clinical setting. From a technical point of view, particular efforts have to be focused on the improvement of cfDNA technical assays, high-quality output, library preparation procedures, and sequencing depth for precise methylation analyses. Currently, most liquid biopsies tests are commonly used as a complementary technique to standard tissue biopsies, primarily in research settings, with the final aim of standardization of these techniques allowing their adoption in clinical routine.

Although the FDA has encouragingly approved some liquid biopsy tests, such as FoundationOne^®Liquid CDx (Foundation Medicine, Inc.; Cambridge, MA, USA), in the next few years, the huge amount of data collected from the several ongoing prospective clinical trials based on the cfDNA as an integral biomarker will represent the key for further innovation in this promising field, corroborating the clinical evidence of clear benefits for patients, reducing medical overheads, increasing the early diagnostic options, and improving tailored treatments.

This entry is adapted from the peer-reviewed paper 10.3390/cancers14184359

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