Tissue-based research in kidney cancer: current challenges and future directions

PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

PURPOSE

Programmed death-ligand 1 (PD-L1) status by IHC is prognostic in metastatic renal cell carcinoma (mRCC), and its role as a potential predictive biomarker is under investigation. Using tumor tissue from the METEOR (NCT01865747) and CABOSUN (NCT01835158) clinical trials, we explored whether PD-L1 expression and the extent of the immune cell infiltrate can serve as prognostic and/or predictive biomarkers for cabozantinib and other targeted agents.

EXPERIMENTAL DESIGN

IHC double staining for PD-L1 and CD45/CD163 (immune cell markers) was performed on tumor tissue from METEOR (n = 306) and CABOSUN (n = 110) clinical trials. Immune cell density and MET expression levels were also analyzed. Our primary aim was to correlate progression-free survival (PFS) by independent central review with PD-L1 status in patients treated with cabozantinib, everolimus (METEOR), or sunitinib (CABOSUN). Overall survival (OS) was also interrogated.

RESULTS

Tumor cell (TC) PD-L1 expression (≥1% cutoff) was detected in 29% and 23% of tumors from patients in the METEOR and CABOSUN trials, respectively. On univariate analysis, patients with PD-L1-positive TC had poorer PFS and OS than patients with PD-L1-negative TC on both trials, independent of therapy. On multivariable analysis and when combining the two trials, the association between TC PD-L1 expression and OS was statistically significant for all patients (P = 0.034) and for patients treated with cabozantinib only (P = 0.038). Cabozantinib was associated with improved PFS (HR < 0.70) and OS (HR < 0.85) compared with everolimus and sunitinib irrespective of PD-L1 expression.

CONCLUSIONS

Higher PD-L1 expression results in worse clinical outcomes in mRCC treated with targeted therapy. Furthermore, PD-L1 expression is not predictive of response to cabozantinib therapy.

Molecular markers to predict response to therapy

Currently approved treatments for metastatic renal cell carcinoma (RCC) include vascular endothelial growth factor (VEGF)-blocking agents, mammalian target of rapamycin (mTOR) inhibitors, and cytokine therapy. In the near future, we are likely to add immune checkpoint blocking agents to this list. As we develop treatment platforms around each therapeutic class, determining which drug is best for a particular patient becomes increasingly important. At this point, we do not have validated predictive biomarkers for patients with RCC. Here, we discuss the logistical challenges surrounding biomarker development, summarize the current crop of biomarker candidates, and explore potential avenues for the development of more effective predictive tools for patients with advanced RCC.

The role of aberrant VHL/HIF pathway elements in predicting clinical outcome to pazopanib therapy in patients with metastatic clear-cell renal cell carcinoma

PURPOSE

Inactivation of von Hippel-Lindau (VHL) gene in clear-cell renal cell carcinoma (RCC) leads to increased levels of hypoxia-inducible factors (HIF) and overexpression of HIF target genes, such as VEGF and others. VEGF-targeted agents are standard in advanced clear-cell RCC but biomarkers of activity are lacking.

EXPERIMENTAL DESIGN

We analyzed tumor tissue samples from metastatic clear-cell RCC patients who received pazopanib as part of clinical trial VEG102616. We evaluated several components of the VHL/HIF pathway: VHL gene inactivation (mutation and/or methylation), HIF-1α and HIF-2α immunohistochemistry staining, and HIF-1α transcriptional signature. We evaluated the association of these biomarkers with best overall response rate (ORR) and progression-free survival (PFS) to pazopanib, a standard first-line VEGF-targeted agent.

RESULTS

The VEG102616 trial enrolled 225 patients, from whom 78 samples were available for tumor DNA extraction. Of these, 70 patients had VHL mutation or methylation. VHL gene status did not correlate with ORR or PFS. Similarly, HIF-1α (65 samples) and HIF-2α (66 samples) protein levels (high vs. low) did not correlate with ORR or PFS to pazopanib. The HIF-1α transcriptional signature (46 samples) was enriched in tumors expressing high HIF-1α levels. However, the HIF-1α gene expression signature was not associated with clinical outcome to pazopanib.

CONCLUSIONS

In patients with advanced clear-cell RCC, several potential biomarkers along the VHL/HIF-1α/HIF-2α axis were not found to be predictive for pazopanib activity. Additional efforts must continue to identify biomarkers associated with clinical outcome to VEGF-targeted agents in metastatic RCC.

Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue.

Positron emission tomography in renal cell carcinoma: an imaging biomarker in development

Positron emission tomography (PET) has revolutionized cancer imaging. The current workhorse of molecular imaging, fluorodeoxyglucose (FDG) PET is used in the majority of malignant tumors with a few exceptions. Renal cell carcinoma (RCC) is one of those exceptions because of its variable uptake of FDG, although this variable uptake may actually be an asset in predicting response to some targeted agents, as will be discussed later. Beyond FDG, there is only scattered information in the literature on the use of PET in RCC. The purpose of this review is to summarize the current status of PET usage in RCC and point out its potentials and future directions. We will start with a brief overview of the demographics, molecular pathogenesis, and evolving treatment strategies in RCC because this information is essential for better understanding of uptake of various PET radiotracers in this cancer and their indications. This will be followed by discussing the role of PET in characterization of indeterminate renal masses, in staging and restaging of RCC, and, finally, in predicting and monitoring therapy response. Each of these 3 areas of PET usage will include the relevant radiotracers currently in use or in development.

Current and future systemic treatments for renal cell carcinoma

Systemic treatment of renal cell carcinoma has changed dramatically since 2007, with the development and approval of six new agents, which target complex molecular pathways regulating tumour angiogenesis and cell proliferation and survival. These treatments have significantly improved survival times in metastatic renal cell carcinoma, but remain palliative. A number of newer agents are in clinical development, which offer theoretical advantages over existing treatments, and research methodologies are adapting with the aim of defining an individualised approach to therapy which exploits the underlying tumour biology. This review will provide an overview of current and emerging systemic treatments and how they might be integrated with surgical therapy, with a particular focus on advanced, clear cell metastatic renal cell carcinoma.

Bridging the gap: moving predictive and prognostic assays from research to clinical use

The development of clinically useful molecular diagnostics requires validation of clinical assay performance and achievement of clinical qualification in clinical trials. As discussed elsewhere in this Focus section on molecular diagnostics, validation of assay performance must be rigorous, especially when the assay will be used to guide treatment decisions. Here we review some of the problems associated with assay development, especially for academic investigators. These include lack of expertise and resources for analytical validation, lack of experience in designing projects for a specific clinical use, lack of specimens from appropriate patient groups, and lack of access to Clinical Laboratory Improvement Amendments-certified laboratories. In addition, financial support for assay validation has lagged behind financial support for marker discovery or drug development, even though the molecular diagnostic may be considered necessary for the successful use of the companion therapeutic. The National Cancer Institute supports a large number of clinical trials and a significant effort in drug development. In order to address some of these barriers for predictive and prognostic assays that will be used in clinical trials to select patients for a particular treatment, stratify patients into molecularly defined subgroups, or choose between treatments for molecularly defined tumors, the National Cancer Institute has begun a pilot program designed to lessen barriers to the development of validated prognostic and predictive assays.

Electronic biorepository application system: web-based software to manage receipt, peer review, and approval of researcher applications to a biobank

The importance of suitably characterized and preserved biospecimens for research is acknowledged, yet providing information about the availability of biospecimens and associated data, responding to enquiries from researchers, processing applications for material, and seeking independent scientific review of proposed projects are complex and time-consuming processes. Most biorepositories operate as not-for-profit entities; therefore, cost containment is a major consideration. We identified that online systematizing and automation of all of the tasks associated with application management could reduce the administrative workload and therefore reduce costs and improve the efficiency of a biobank. Accordingly, we have developed a Web-based electronic Biorepository Application System (eBAS) that allows researchers to search for suitable material from the biobank database, submit an online expression of interest, and complete all the information required for a full application. Peer review is also managed through eBAS. Implementation of eBAS has streamlined application management and external peer review of researcher applications, and has facilitated automated record storage and management. This approach has potential to reduce the costs and complexities of administering researcher applications. We have also linked eBAS to an open-source clinical research and specimen management database, Caisis.

Delivering preventive, predictive and personalised cancer medicine for renal cell carcinoma: the challenge of tumour heterogeneity

Recent years have seen major advances in the management of metastatic renal cell carcinoma (mRCC). The tyrosine kinase and mammalian target of rapamycin inhibitors have resulted in disease control and improved survival for many patients with mRCC, but they have not led to preventive, predictive or personalised medicine (PPPM). Failure to achieve this rests ultimately with inadequate knowledge of tissue and molecular heterogeneity; discovery of these drugs was based upon identification of pathogenic molecular pathways in RCC, but research into molecular factors which underpin drug response, resistance and selection of therapy for individual patients has lagged well behind clinical trials of drug development. This review will provide an overview of the development of targeted drug therapies for mRCC, will discuss the challenges which currently impede the delivery of PPPM, including identification of biomarkers, drug resistance and molecular heterogeneity, and will propose research methodologies and technologies required to overcome these obstacles.

Von Hippel-Lindau (VHL) inactivation in sporadic clear cell renal cancer: associations with germline VHL polymorphisms and etiologic risk factors

Renal tumor heterogeneity studies have utilized the von Hippel-Lindau VHL gene to classify disease into molecularly defined subtypes to examine associations with etiologic risk factors and prognosis. The aim of this study was to provide a comprehensive analysis of VHL inactivation in clear cell renal tumors (ccRCC) and to evaluate relationships between VHL inactivation subgroups with renal cancer risk factors and VHL germline single nucleotide polymorphisms (SNPs). VHL genetic and epigenetic inactivation was examined among 507 sporadic RCC/470 ccRCC cases using endonuclease scanning and using bisulfite treatment and Sanger sequencing across 11 CpG sites within the VHL promoter. Case-only multivariate analyses were conducted to identify associations between alteration subtypes and risk factors. VHL inactivation, either through sequence alterations or promoter methylation in tumor DNA, was observed among 86.6% of ccRCC cases. Germline VHL SNPs and a haplotype were associated with promoter hypermethylation in tumor tissue (OR = 6.10; 95% CI: 2.28-16.35, p = 3.76E-4, p-global = 8E-5). Risk of having genetic VHL inactivation was inversely associated with smoking due to a higher proportion of wild-type ccRCC tumors [former: OR = 0.70 (0.20-1.31) and current: OR = 0.56 (0.32-0.99); P-trend = 0.04]. Alteration prevalence did not differ by histopathologic characteristics or occupational exposure to trichloroethylene. ccRCC cases with particular VHL germline polymorphisms were more likely to have VHL inactivation through promoter hypermethylation than through sequence alterations in tumor DNA, suggesting that the presence of these SNPs may represent an example of facilitated epigenetic variation (an inherited propensity towards epigenetic variation) in renal tissue. A proportion of tumors from current smokers lacked VHL alterations and may represent a biologically distinct clinical entity from inactivated cases.

Building a bioresource for esophageal research: lessons from the early experience of an academic medical center

The establishment of biorepositories, linked to clinical and epidemiologic data, are central to the goals of personalized medicine and individualized cancer therapy. Repositories of DNA, RNA, and serum samples are valuable resources for cancer research, enabling the investigation of the underlying causes of cancer development, progression, and prognosis, as well as providing a resource for the investigation of biomarkers for early detection and prediction of response. With a greater reliance on sample-derived data for molecular-based research and clinical care, improved standards and informatics for sample procurement, storage, and analysis are necessary to maximize the value of tissue collection for research participants, investigators, and academic medical centers. We present herein the experience of an academic medical center in establishing a repository for esophageal research, with discussion of elements to be considered when establishing such a resource, from the quality assurance of samples to the organized collection and storage of associated clinical data. The development of this biorepository required significant planning to identify and consent participants by dedicated clinical and research personnel. Ensuring the quality of any biobank is of utmost importance, and one must understand the sample variability that exists during the acquisition of biospecimens. The time and type of fixative have been optimized in our unit by standard operating protocols. Methods for biomolecule extraction were tested by examining both the quality and the quantity of recovered sample. These procedures were overseen by a designated biobank manager, responsible for the acquisition of the sample from surgery, which limits variability in sample collection. Our unit also has a dedicated database manager for the maintenance of quality clinical data linked to the bioresource. The development and expansion of such repositories, at local and national levels, is required to enable leading academic medical centers and their investigators to provide optimal and molecularly guided care to their patients.

Turning laboratory findings into therapy: a marathon goal that has to be reached

The mission of translational research involves difficult tasks to be accomplished for its ultimate goal, i.e., the introduction of novel, effective therapeutic strategies in the clinic to diminish human suffering and cure life-threatening diseases. Translational research (also referred to as translational medicine) facilitates the translation of investment in biomedical research into successful medical treatment. This includes the transfer of diagnostic and therapeutic advances by proving their efficacy in large evidence-based trials. Through the study of humans novel insights about disease are brought back to the laboratory to identify new, observation-based strategies. This "two-way road" ("bench to bedside and bedside to bench") process includes formulating guidelines for drug development and principles for new therapeutic strategies; initiating clinical investigations that provide the biological basis for new therapies, and related clinical trials; defining therapeutic targets and clinical endpoints. It requires a systematic approach beginning with specimen sampling, patient data collection, laboratory investigations, data analysis, preclinical testing, clinical trials, treatment efficacy monitoring, and finally the evaluation of therapeutic result. The marathon well symbolizes the enormous efforts undertaken by clinicians, scientists, regulators, ethicists, patient advocates, drug developers, and others, coordinately attempting to overcome obstacles along this road toward the final "marathon goal in medicine".

Serotype chimeric and fiber-mutated adenovirus Ad5/19p-HIT for targeting renal cancer and untargeting the liver

Despite some advances, patients with advanced renal cell carcinoma (RCC) cannot usually be cured. Alteration of the natural tropism of adenoviruses may permit more specific gene transfer to target tissues. The aim of this study was to use novel targeting moieties for adenoviral gene therapy of RCC. Previous work in rats suggested that use of Ad5/19p (Ad5 capsid with Ad19p fiber) with kidney vascular targeting moieties HTTHREP (HTT), HITSLLS (HIT), and APASLYN (APA) placed into the fiber knob might be useful for targeting kidney vasculature. Therefore, we sought to investigate the utility of Ad5/19p variants for gene delivery to human RCC cell lines, clinical samples, and orthotopic murine models of metastatic RCC. Six different human RCC cell lines were infected but only Ad5/19p-HIT showed increased transduction, and only in one cell line. Thus, we analyzed human normal and cancerous kidney specimens fresh from patients, which might better mimic the three-dimensional architecture of clinical tumors and found that Ad5/19p-HIT showed transduction levels similar to Ad5. In mice, we found that intraperitoneal and intravenous Ad5/19p-HIT transduced tumors at levels comparable to Ad5, and that intratumoral Ad5/19p-HIT was superior to Ad5. Liver tropism was significantly reduced in comparison with Ad5. Improvements in tumor-to-liver transduction ratios suggested that Ad5/19p-HIT may be promising for systemic gene delivery to kidney tumors.

Patterns of gene expression and copy-number alterations in von-hippel lindau disease-associated and sporadic clear cell carcinoma of the kidney

Recent insights into the role of the von-Hippel Lindau (VHL) tumor suppressor gene in hereditary and sporadic clear-cell renal cell carcinoma (ccRCC) have led to new treatments for patients with metastatic ccRCC, although virtually all patients eventually succumb to the disease. We performed an integrated, genome-wide analysis of copy-number changes and gene expression profiles in 90 tumors, including both sporadic and VHL disease-associated tumors, in hopes of identifying new therapeutic targets in ccRCC. We identified 14 regions of nonrandom copy-number change, including 7 regions of amplification (1q, 2q, 5q, 7q, 8q, 12p, and 20q) and 7 regions of deletion (1p, 3p, 4q, 6q, 8p, 9p, and 14q). An analysis aimed at identifying the relevant genes revealed VHL as one of three genes in the 3p deletion peak, CDKN2A and CDKN2B as the only genes in the 9p deletion peak, and MYC as the only gene in the 8q amplification peak. An integrated analysis to identify genes in amplification peaks that are consistently overexpressed among amplified samples confirmed MYC as a potential target of 8q amplification and identified candidate oncogenes in the other regions. A comparison of genomic profiles revealed that VHL disease-associated tumors are similar to a subgroup of sporadic tumors and thus more homogeneous overall. Sporadic tumors without evidence of biallelic VHL inactivation fell into two groups: one group with genomic profiles highly dissimilar to the majority of ccRCC and a second group with genomic profiles that are much more similar to tumors with biallelic inactivation of VHL.

Tissue biomarkers in renal cell carcinoma: issues and solutions

Renal cell carcinoma (RCC) is an aggressive malignancy that is associated with a high rate of metastasis. Although several promising therapeutic strategies are now available for the treatment of patients with metastatic kidney cancer, the prognosis of these patients remains poor. Research is ongoing to identify RCC-specific biomarkers that can improve early diagnosis, surveillance of tumor progression, and prediction of patient prognosis. The identification of biomarkers that may predict response to specific therapies also will be useful in stratifying patients with RCC for treatment selection. Unfortunately, biomarker detection and measurement in kidney tumor tissues can be biased significantly by the lack of standardization in tissue sample acquisition, storage, and analysis. Consequently, the establishment of standardized operating procedures is necessary to maximize the accuracy of tissue-based biomarker assays. Herein, the authors discuss current issues in tissue-based translational research aimed at identifying clinically useful biomarkers for kidney cancer.