The impact of the lung EDRN-CVC on Phase 1, 2, & 3 biomarker validation studies

1.1The Mission of the EDRN and the role of the CVC

The Early Detection Research Network’s (EDRN) purpose is to discover, develop and validate biomarkers and imaging methods to detect early-stage cancers or at-risk individuals. Furthermore, the EDRN seeks to translate these biomarkers and imaging methods into diagnostic tests. A consortium of more than 300 investigators that include teams from academic institutions, private sector and the National Cancer Institute work collaboratively to bring biomarkers and imaging methods to clinical use.

The EDRN is composed of sites that fall into four categories: Biomarker Developmental Laboratories, Biomarker Reference Laboratories, Clinical Validation Centers (CVC) and Data Management and Coordinating Centers. Each component has a crucial role to play within the mission of the EDRN. The primary role of the CVCs is to support biomarker developers through validation trials on promising biomarkers discovered by both EDRN and non-EDRN investigators. CVCs also provide high-quality, well-annotated biospecimens to the biomarker developers for biomarker discovery, assay development and pre-validation studies. The EDRN supports CVCs to create biorepositories utilizing rigorous standard operating procedures for recruitment and specimen handling which, in turn, helps minimize false discoveries arising from poor specimen quality.

Within the EDRN, the Lung Group CVC has three main missions: (1) To conduct innovative research on the validation of candidate biomarkers for early cancer detection and risk assessment of lung cancer in an observational study; (2) To compare biomarker performance, whether biological or imaging based, for eventual clinical utility trial; and (3) To serve as a resource center for collaborative research within the Network by partnering with established EDRN biomarker developers, reference laboratories, new laboratories and industry partners. This report outlines the impact of the Vanderbilt University Medical Center (VUMC) EDRN Lung CVC and describes the role in promoting and validating biological and imaging biomarkers.

1.2Clinical foundation of the VUMC EDRN lung CVC

Hospital and clinical infrastructure: Central to a strong clinical validation center is a quaternary interdisciplinary hospital system where excellent care is offered across a variety of disciplines. To this end, VUMC provides an ideal foundation for the EDRN Lung CVC and study participant recruitment. The adult hospital contains the region’s only Level I Trauma Center along with one of the largest transplant programs by volume in the United States. The free-standing Monroe Carell Jr. Children’s Hospital at Vanderbilt is the most comprehensive children’s hospital in the state and provides the highest level of neonatal intensive care in the state. The Vanderbilt Clinic comprises more than 95 outpatient specialty practices in several campus locations which collectively see about 1,000,000 patients per year. The Vanderbilt-Ingram Cancer Center (VICC) cares for about 4,500 new cancer patients and conducts more than 65,000 outpatient visits annually. According to the most recent figures available from the Tennessee Department of Health, Vanderbilt is the largest uncompensated care provider in the Nashville area, providing a safety network for the underserved.

Medical center catchment area and lung cancer prevalence: The medical center’s primary catchment area of Middle Tennessee, Northern Mississippi and Alabama and South-Central Kentucky has some of the highest lung cancer mortality rates in the United States. Overall, Tennessee had the 5th highest lung cancer mortality (51.3 compared to the national average of 38.5 per 100,000) and incidence (74.5 compared to the national average of 58.3 per 100,000) based upon the latest data 2014–2018 [1]. Similarly, Tennessee has the 5th highest current smoking prevalence, 20.7%, among adults in the United States [2]. The CVC draws its study participants from this population of high risk individuals and seeks to apply the discoveries from its efforts to them.

Pulmonary nodule clinic, interventional pulmonary and thoracic surgery support: The Interventional Pulmonology Program and Pulmonary Nodule Clinic at Vanderbilt offer the full spectrum of diagnostic, therapeutic and palliative airway procedures. Currently the Vanderbilt Pulmonary Nodule Clinic evaluates over 750 patients annually with suspicious nodules. In patients with lung cancer, this extends from early detection and endoscopic treatment to palliative airway procedures for rapid symptom relief in patients with advanced lung cancer. The Interventional Pulmonary Program at Vanderbilt is staffed by three pulmonologists and an advanced practice nurse and manages a plethora of complex airway problems. The Department of Thoracic Surgery is staffed by five surgeons and over 800 thoracic operations are performed and over 400 patients with known or suspected lung cancer are evaluated annually.

Lung cancer screening program: VUMC participated as one of approximately thirty sites enrolling patients as part of the National Lung Screening Trial [3]. After the trial’s publication, the Vanderbilt Lung Screening Program (VLSP) was established. The program is a certified lung screening center and recognized as a Screening Center of Excellence by the GO2 Foundation. As of July 2020, over 2,500 unique patients have been screened for lung cancer. There have been over 4,000 low-dose computed tomography (CT) scans performed and over 80 cancers diagnosed. Imaging for the lung screening program is performed at three outpatient facilities, which are co-operated by VUMC and Vanderbilt Imaging Services (VIS). Imaging is performed in accordance with all American College of Radiology (ACR) standards and results are reported to the ACR registry. Low-dose CT scans and follow up imaging are interpreted solely by cardiothoracic trained radiologists. Reporting is performed in accordance with the ACR Lung-RADS system. The program is centralized with shared decision making performed by two dedicated lung screening nurse practitioners, both of whom are certified tobacco treatment specialists. A program patient navigator assists with scheduling of baseline and follow up examinations and with necessary referrals including to the Vanderbilt Lung Institute.

1.3Research infrastructure for the VUMC EDRN lung CVC

In addition to the clinical care, a CVC relies upon intimate integration of the research environment with the clinical setting, VUMC is an academically oriented institution that strongly supports basic and clinical research. Much institutional effort has been spent on developing an environment which nurtures such activities and provides high quality general support services through institutional cores and shared resources. These designated cores and shared resources offer cutting edge scientific services, enabling access to high-end equipment, advanced techniques and specialized expertise for all Vanderbilt investigators. Of the 39 core facilities and 15 centers in the VUMC, the most relevant to the EDRN CVC are the Advanced Computing Center for Research and Education (ACCRE), Clinical Trials Shared Resource, Digital Histology Shared Resource, Translational Pathology Shared Resource and Clinical Research Center. The CVC is housed within the Vanderbilt-Ingram Cancer Center (VICC) and the cancer center directly supports the CVC through information technology and computing support, laboratory space and administrative effort.

Other shared resources specific to VICC and utilized by the CVC or EDRN members include: 1) The Clinical Trials Shared Resource (CTSR) assists cancer investigators in developing, initiating and completing scientifically meritorious clinical trials in an efficient, cost-effective and technically sound manner. The CTSR service support includes protocol development, regulatory compliance, study start-up, data management, research nursing, auditing, and patient accrual. 2) Translational Pathology Shared Resource (TPSR) provides access to human tissue samples, histology services and specialized equipment to researchers. Human tissues are collected prospectively from routine surgical resections and autopsies for use by investigators in basic, translational, and clinical research studies. These tissues are available fresh, snap frozen or in a variety of fixatives as requested by the investigator. Normal, neoplastic, and other diseased tissues are available for study. 3) Digital Histology Shared Resource provides large scale digital archiving and quantitative analysis of histological, immunocytochemical and immunofluorescence staining for tissue sections and tissue microarrays. 4) Institute for Medicine and Public Health at Vanderbilt University Medical Center encompasses four centers and one training program — the Center for Health Services Research, the Institute for Community Health, the Center for Improving Patient Safety, the VA Geriatric Research, Education and Clinical Center (GRECC) and the Quality Scholars Program. 5) Vanderbilt Institute for Clinical and Translational Research (VICTR) is an institutional program that fosters development of innovative clinical and translational research opportunities. One major impediment to T1 and T2 translation is the difficulty to expeditiously determine whether a scientific idea is of real merit. The generation of preliminary data and pilot initiatives for clinical and translational studies is fundamental to addressing such an impediment. VICTR provides financial and content expertise (biostatistics, bioinformatics, health services, scientific writing, etc.) of early research through pilot funds which are available to all levels of academic status, undergraduate students through established independent investigators. Supported, in part, by the funding from Vanderbilt’s Clinical Translational Science Award (CTSA), the VICTR pilot funding program funds clinical and translational pilot and feasibility studies for projects that involve human tissue, human information (e.g., medical records) and/or application to human health.

1.4REDCap (research electronic data capture)

Translational research at this scale srequires a robust, easily modifiable, rapidly developed data input, storage, and retrieval system. The primary data repository and retrieval system that facilitates all translation research at VUMC is built upon REDCap. This system, developed and supported by Vanderbilt’s CTSA, provides HIPAA-compliant secure data management with very short development times. The REDCap consortium is an international group promoting the use and development of this open-source research tool. REDCap is in use by more than 1,500 institutions nationally and internationally, and recently received a $1.3M CTSA supplement grant for system enhancements. It is an example of the leveraging of CTSA-supported resources for cancer research. REDCap is the multi-center epidemiological data capture infrastructure used in the Cancer versus Fungus (CanVFun) consortium, the CVC’s clinical data capture and for some supplemental projects that require specific patient or tissue data. The EDRN’s clinical data survey is in REDCap and metadata for local database creation and data collection available to all EDRN members and the public. REDCap was recently implemented as a Veteran’s Affairs-wide data capture solution and is available with user support through the VA Information Resource Center (VIReC).

1.5Development of the VUMC EDRN CVC

The Vanderbilt-Ingram Cancer Center has a well-established Thoracic specimen biorepository dedicated to the support of lung cancer research. This biorepository was started by Dr. David Carbone in 2001 with the acquisition of a Lung SPORE grant that lasted until 2012. The biorepository follows the National Cancer Institute Best Practices for Biospecimen Resources (revised in 2011). Any specimens distributed are de-identified per HIPAA standards, as required by the Institutional Review Board (IRB). All specimens are collected and processed following a detailed standard operating procedure including low dose chest CT imaging data acquisition. Since 2009, protocols followed the EDRN tissue collection specifications as defined on the EDRN’s web portal (https://edrn.nci.nih.gov/archive/standard-operating-procedures/standard-operating-procedures). The development of the VUMC EDRN CVC can be understood as three main stages.

1.5.1Stage 1 – Infrastructure development

Biospecimen quality: Superlative biospecimen quality control is essential to the success of any research program. To this end, standard operating procedures (SOPs) for all tissue collection need to be developed and tested, and following implementation, adherence to these protocols must be regularly validated. Stage I of the EDRN CVC development process (2009 to 2015 at VUMC) was focused on defining the goals and procedures, implementing the workflows and ensuring compliance. Additionally, Stage I focused on integrating sample collection with a custom-built REDCap database that linked samples and de-identified clinical information and streamlining processes for requesting access to samples from outside institutions and internal collaborators while tracking sample disbursement.

To facilitate sample acquisition, Stage I focused on technical infrastructure development and procuring the requisite hardware to enable efficient and reproducible processing of all samples. This includes storage space, freezers, centrifuges, mass balances and barcoding systems. During this development stage, unique patient accrual averaged approximately 330 per year (Fig. 1). This enrollment volume does not represent the total number of longitudinal study encounters or specimen collections, as most patients were seen multiple times over the course of their evaluation and disease treatment, with multiple biospecimen and imaging collections (Table 1). Many patients who maintain VUMC as their primary clinic undergo continuing research and biorepository participation.

Figure 1.

(A) Patients consented for research over time in the VUMC Thoracic Biorepository. (B) Samples collected through the Nashville Lung Cancer Screening program.

Following several iterations of sample collection and testing, several core sample processing SOPs were developed. Key SOPs are included in the supplementary material. All tissue acquisition is performed or supervised by a trained pathologist or certified pathologist assistant. Tumors with > 80% tumor necrosis are considered inadequate. We routinely create formalin-fixed paraffin embedded QC blocks during tissue processing. Cases with insufficient tumor for QC blocks undergo review of frozen sections when distributed to individual investigators. Plasma and serum samples are monitored for degree of hemolysis. All specimens collected are carefully annotated. Each specimen is assigned a unique barcode under a unique patient ID number. Data entry into the password-protected database includes patient ID, name, age, gender, race/ethnicity, and associated specimen information including type (tumor, normal, bronchus, etc.), anatomic site including laterality, storage method (fresh, snap frozen, etc.), size, weight, volume, numbers of aliquots and time to freeze.

2.1VUMC institutionally supported biospecimen acquisition

VUMC has developed its own internal processes for biospecimen collections across a wide range of tissues that supplement these phase I/II/III studies across multiple lung cancer histological subtypes, which have benefitted the EDRN. Core to these studies are the protocols for obtaining biospecimens of the following types: fresh tissue, frozen tissues, paraffin block tissue, research pathology, linked tumor/normal tissue micro array, bronchioalveolar lavage, nasal rinse, sputum, serum, plasma, whole blood, buffy coat and urine. While the end goal of the EDRN is focused on easily accessible samples for non-invasive early detection, such as blood or urine, the availability of these other biospecimen types allows more complex studies such as the relation between the biology internal to the tumor and the circulating biomarkers. Matched tissue/tumor/blood sample sets are vital to this effort.

2.2EDRN nashville lung cancer screening cohort

The primary patient accrual instrument for the EDRN is an ongoing prospective longitudinal cohort of individuals at high-risk of developing lung cancer that was established to build a biorepository of carefully annotated biological specimens and low dose computed tomography (LDCT) chest images for derivation and validation of candidate biomarkers for early detection of lung cancer. The goal of this study is to characterize individuals with high risk for lung cancer, accumulating valuable biospecimens and LDCT chest scan longitudinally over five years. Participants 55–80 years of age and with a 6-year estimated risk of developing lung cancer greater than 1.5%, according to the PLCO model, were recruited and enrolled from clinics at Vanderbilt University Medical Center, the Veteran Affairs Medical Center, and Meharry Medical Center. Individual demographic characteristics were assessed via questionnaire at baseline. Participants underwent a LDCT scan, spirometry, sputum cytology and research bronchoscopy at the time of enrollment. Participants will be followed yearly for five years. Positive LDCT scans are followed up according to standard of care. The clinical, imaging and biospecimen data are collected prospectively and stored in the biorepository. Participants are offered smoking cessation counseling at each study visit. A total of 480 participants were enrolled at study baseline and consented to sharing of their data and biospecimens for research. Participants are followed with yearly clinic visits to collect imaging data and biospecimens. To date, a total of 19 lung cancers (13 adenocarcinomas, 4 squamous cell carcinoma, 1 large cell neuroendocrine and 1 small cell lung cancer) have been identified. We established a unique prospective cohort of individuals at high-risk for lung cancer, enrolled at three institutions for which full clinical data, well-annotated LDCT and biospecimens are being collected longitudinally. This repository will allow for the derivation of independent validation of clinical, imaging and molecular biomarkers of risk or diagnosis of lung cancer [4] (Table 1).

2.3Lung cancer screening in underrepresented populations

Developing a study population from an academic center runs the risk of under-representing certain populations, including those that may be at highest risk of disease and would most benefit from early detection. For this reason, VUMC has leveraged its CVC infrastructure to partner with Meharry Medical College through the Meharry-Vanderbilt Alliance and its affiliation with Nashville General Hospital, the city’s safety net hospital, to develop a cohort focused on underserved and underinsured persons. Study enrollment began at Meharry Medical College in September 2019. We have recruited and completed a baseline study visit for a total of 104 participants for our underserved (under-insured) protocol. Our population recruited from Meharry Medical College (n= 22) had a mean age of 61 years, is 41% African American, 59% female and comprised mostly of participants who smoke (91%). Participants recruited from all other referral sources (n= 45) were 11% African American, 31% female and 76% who currently smoke. The first two years of accrual focused on developing the infrastructure, and future years will focus on increasing the levels of diversity in patient accrual through existing infrastructure and additional, directed marketing and recruitment.

2.4Geographically diverse specimen collection (CanVFun consortium)

Another crucial role in the purview of the CVC is to identify collaborative centers that would improve population and sample diversity while benefitting from the infrastructure already in place at the CVC. In this approach, the CVC helps to collect biospecimens and clinical data for other institutions while organizing these extramural biospecimens into a cohesive, representative cohort. In this instance, VUMC serves as the hub for a firmly established 4 site consortium, the Cancer Versus Fungus (CanVFun) Consortium, with Washington University in St. Louis, the University of Kentucky, the University of Cincinnati and VUMC. This consortium is working to develop a diverse patient cohort representative of the indeterminate pulmonary nodule population within the central US to develop and validate both malignant and benign lung disease specific imaging and liquid biomarkers. Without the existing CVC infrastructure at VUMC for biospecimen collection and storage, image deidentification and storage and clinical data capture through REDCap using EDRN defined data dictionaries, it would be much more difficult for these external sites to develop study populations of their own. To date, CanVFun has prospectively consented 65 participants and collected biospecimens and clinical data based upon the EDRN’s standardized initial patient survey data collection form that was transcribed into a secure multi-site REDCap database. A separate set of 51 retrospectively acquired patients were contributed from Cincinnati with complete imaging and clinical information history. The goal for enrollment is 120 patients by July 2022. Specimen totals are included in Table 2.

2.5Non-EDRN collections facilitated by EDRN-developed infrastructure

Outside of the context of the EDRN specifically, several ongoing patient accrual studies at VUMC provide supplementary biospecimens that have been leveraged for both internal EDRN collaborative studies and external studies within the field of lung cancer. The EDRN-funded infrastructure has augmented and bolstered these accrual abilities and these specimens are available to EDRN investigators. For example, we have enrolled 98 patients into DECAMP studies [5].

5.1Infrastructure available to industry

The EDRN Lung CVC has participated in industry-led and industry-supported biomarker development efforts across the range of biomarker development phases. Since the inception of the CVC, the VUMC CVC has collaborated with 13 biospecimen-focused industry partners and three imaging-focused partners. These collaborations are mutually beneficial, as industry support can offset some of the costs in maintaining sample and enrollee volumes while the specimens and independent validation offered to the industry collaborators ensure quality biomarker discovery and validation.

In contrast to pay-for-sample biobanks, the VUMC biospecimen repository offers well adjudicated quality sample sets that are de-identified, but the link to the patient’s medical record remains intact which allows further data acquisition if new endpoints or clinical data elements are desired which were not originally collected. Additionally, the biostatistics, clinical implementation infrastructure and epidemiological expertise at the CVC allows for true independent validation and replication of any industry-sponsored biomarkers. This independent analysis and validation is beneficial to the field overall, as any biomarkers that succeed in transition to commercial platforms are of the highest quality, but also beneficial to the industry partners as the data validation can then aide in submission for government regulatory approval. Lastly, the clinical trial infrastructure at the VUMC EDRN CVC enables easy transition from Phase I/II/III studies into interventional trials. This infrastructure, which is beneficial to the institution, the industry partners and the field as whole, would be unsustainable without the EDRN CVC foundation.

5.2Industry partnerships using biospecimens

These collaborations have facilitated biomarker development from Phase I through to commercially available products. For example, blood specimens from VUMC were included in the initial development and validation of an autoantibody panel that is now commercially available from Biodesix (Boulder, CA) in the US as the EarlyCDT test and from Oncimmune (Nottingham, UK) in Europe [14]. In addition to biospecimens, VUMC scientists contributed to the development effort, providing clinical, scientific and biostatistics expertise. Similarly, the multi-reaction-monitoring proteomic signature (MRM) that VUMC contributed specimens, clinical experience, scientific expertise and biostatistics validation for is also now available commercially from Biodesix as the NodifyXL2 test [25]. The magnetic nanosensor based biomarker detection platform for which VUMC provided a validation sample set and expertise is now commercially available from MagArray (Malpitas, CA) [18, 19, 50].

A collaboration between the EDRN CVC, Abbott Diagnostics, Lahey Medical Center and OneFlorida Clinical Research Consortium created a test case to assess “the economic feasibility, clinical utility, and medical validity of a blood-based in vitro diagnostic device (IVD) biomarker test panel (Class II/Class III) for risk stratification of suspicious lung nodules using Real-World Data (RWD)”. The test case was developed and overseen by the National Evaluation System for health Technology Coordinating Center (NESTcc), an FDA supported effort to generate real world evidence applicable to medical device development and surveillance. This project generated methods to define, collect and measure clinical utility data for the diagnosis of indeterminate pulmonary nodules (IPN). Clinical utility was defined as time to diagnosis and number of invasive or non-invasive diagnostic tests performed to achieve a diagnosis. This data collection methodology will be published and subsequently made available to the EDRN. Our approach allows for the retrospective evaluation of clinical utility among those with biological and imaging data in the CVC as their specimen and epidemiological survey data (see “Nodule Evaluation” in the supplementary material) are linked to their clinical data through the Research Derivative (Fig. 2, Section 4 above). Therefore, moving forward all future validation studies using EDRN CVC, CanVFun or other VUMC recruited participants will have the capability of measuring how the biomarker or combination of biomarkers might impact time to diagnosis and the healthcare effort necessary to achieve that diagnosis.

5.3Imaging industry partnerships

The VUMC imaging repository has collaborated with industry to develop and validate radiomic platforms that are in clinical use to improve the early detection of lung cancer. A cohort of patients undergoing CT scans at VUMC was used to validate the deep learning-based Lung Cancer Prediction-Convolutional Neural Network (LCP-CNN) which is now approved for use through the FDA and was developed and marketed by Optellum (Oxford, UK). In addition to the images, VUMC based

scientists, biostatisticians and radiologists collaborated in the development process to ensure proper implementation of the LCP-CNN for IPN management. Similar studies were performed for Phase I, II and III studies with Dr. Gillies that resulted in the HealthMyne radiomic platform [51, 52]. A Phase 4 study (R01CA252964 Grogan/Baron) using the HealthMyne radiomics combined with hsCYFRA 21.1 is now funded as a randomized clinical utility trial.

5.4Grants secured

The impact on lung cancer research at VUMC has been substantial. Multiple additional grants have been secured, in part due to efforts related to this EDRN CVC grant (Table 4). These include only grants obtained or pending at this institution. Most if not every collaborator has active funding applications related to this work and has benefited from our CVC infrastructure, but are not listed.