Early detection

The process of detecting lung cancer before it has progressed into full-blown disease

Epigenetic Alterations in Blood as Markers for Early Lung Cancer Detection

Early Detection Research Award
Grant title (if any)
Rising Tide Foundation for Clinical Cancer Research/LUNGevity Foundation Lung Cancer Early Detection Award
This grant was co-funded by Rising Tide Foundation for Clinical Cancer Research
Abhijit Patel, MD, PhD
Yale University
New Haven
CT
Steven Skates, PhD
Harvard Medical School
Cambridge
MA

The objective of this project is to develop a blood test that can improve upon current limitations in lung cancer screening.  Dr. Patel and his team have developed a method to accurately measure alterations in DNA that are cancer-specific by looking at levels of methylation of circulating tumor DNA (ctDNA) in the bloodstream.  Using this method, Dr. Patel will develop a predictive model to identify patients with lung cancer based on these DNA alterations at a single time point, as well as an algorithm that can track these changes in a patient’s DNA over time.  If successful, this could help detect lung cancer earlier in its development, thereby leading to better outcomes for patients.

Research Summary

Lung cancer is by far the most deadly cancer in the U.S., with total lung cancer deaths exceeding those of the next three major cancers combined. Such dismal statistics are largely attributable to the insidious nature of the disease; by the time symptoms appear, the cancer has often spread to an extent that makes cure unlikely or impossible. In contrast, patients who are diagnosed at earlier stages have much better outcomes, as their tumors can be entirely removed or eradicated prior to distant spread. Thus, annual chest CT scans for lung cancer screening have proven to be effective at reducing lung cancer deaths, and are currently recommended for patients with a heavy smoking history. However, CT-based screening programs have been practically challenging to implement, and uptake has been slow. An alternative screening approach that has been garnering much enthusiasm is based on development of a simple blood test that detects DNA fragments shed from tumor cells into the bloodstream. Several commercial and academic groups have been racing to develop blood tests for cancer screening based on this concept, and the field has made impressive progress. However, detection of early-stage lung cancers has remained particularly challenging, with sensitivities reaching only ~20-40% for Stage I disease. A key limitation for detection of small, early-stage tumors has been the extremely low abundance of DNA fragments bearing cancer-specific features (such as mutations) in the circulation. To overcome this limitation, our group has developed a technology that can accurately measure cancer-specific alterations in DNA which are more highly abundant (known as “hypermethylation”). In the current project, we propose to develop a predictive model to identify patients with lung cancer based on probabilities inferred from measurement of these DNA alterations. We will then further improve the sensitivity for detecting the earliest stages of lung cancer by developing an algorithm that tracks longitudinal changes in a patient’s DNA signal over time rather than relying on just a single time-point.

Technical Abstract

Early detection of cancer has long been one of the grand challenges of medicine. It is widely acknowledged that better methods for detection of small, asymptomatic tumors are likely to translate to substantial improvements in cancer survival rates. This is an especially important priority for lung cancer because of its high incidence, high rate of late-stage diagnosis, and high mortality. Over the past decade, liquid biopsy approaches based on detection of cancer-specific mutations or epigenetic changes in cell-free DNA (cfDNA) have made significant inroads towards this goal. However, detection of early-stage lung cancer has been particularly challenging because of the minute amounts of tumor DNA shed into blood. Methylation of cfDNA has emerged as a biomarker of choice for many early detection efforts, but existing technologies are designed to probe for cancer-specific methylation patterns either at pre-specified target sites or across broad genomic regions. The former approach prioritizes a limited subset of cancer-relevant signals, whereas the latter approach yields sparse cancer signals from extensive sequence data. Our group has developed a liquid biopsy technology that comprehensively profiles hypermethylated promoter sequences in cfDNA arising from anywhere in the genome. Using a high-stringency capture strategy based on methylation density rather than sequence, our method is able to globally profile hypermethylated promoters without pre-specifying targets. Gene silencing via promoter hypermethylation is a fundamental mechanism of carcinogenesis, and this aberrant signal can be detected at very low levels in plasma because background methylation patterns in healthy plasma are remarkably consistent. To optimize sensitivity for detection of early-stage lung cancer, we will develop a scoring scheme based on probabilistic machine learning to predict the likelihood of lung cancer by integrating hypermethylation signals across thousands of cell-free DNA fragments. Unlike most current liquid biopsy-based early detection efforts which are focused on identifying individuals with cancer based on a single time-point measurement, here we propose to develop a longitudinal early detection algorithm based on measurement of serial increases in cancer-specific epigenetic signals over time due to tumor growth and accumulating changes in the epigenome.

Early detection and prognosis of lung cancer using bioengineered implants

Pierre Massion Young Investigator Award for Early Detection Research
Ramon Ocadiz Ruiz, PhD
University of Michigan
Ann Arbor
MI

Dr. Ocadiz Ruiz proposes to develop a bioengineered scaffolding and test it in mouse models.  If successful, this research could progress to a phase 1 clinical trial and lay the groundwork for a new technology to be used in individuals with increased risk of lung cancer. This technology has to potential to make biopsies and consequently, early detection, easier.

Comparative Effectiveness of Lung Cancer Screening Strategies

Pierre Massion Young Investigator Award for Early Detection Research
Lawrence Benjamin, MD
University of California Los Angeles
Los Angeles
CA

Dr. Benjamin’s research focuses on improving the rates of lung cancer screening. Currently, there is interest in “centralizing” lung cancer screening into self-contained programs or one-stop shops, with dedicated support staff and clinical personnel to coordinate shared decision-making, scheduling imaging, and arranging appropriate follow-up care. However, it is poorly understood how these centralized programs compare to “decentralized” screening that is coordinated by primary care physicians directly with their patients. Dr. Benjamin seeks to utilize nationwide longitudinal data from multiple lung cancer screening programs from the Veterans Affairs Healthcare System to evaluate and compare the performance of centralized versus decentralized screening programs, with particular focus on highlighting their effectiveness within various racial and income groups.

Integration of Liquid Biopsy Assays for the Early Detection of Lung Cancer

Early Detection Research Award
Maximilian Diehn, MD, PhD
Stanford University
Stanford
CA

Lung cancer is the number one cause of cancer-related deaths in the US because it is often found only after it has spread to other organs in the body, decreasing the likelihood of surviving at least 5 years after diagnosis.  Only 21% of patients are diagnosed then their lung cancer is early stage, when it is most treatable.  The goal of this project is to create a new way to screen for lung cancer using a blood sample that can find early stage disease when patients can still be treated and/or cured.  In preliminary work, Dr. Diehn has developed a blood test that can identify tiny amounts of DNA from lung cancer cells and in this study he will improve this test and apply it to patients and healthy controls.  If successful, Dr. Diehn’s work has the potential to significantly improve early detection of lung cancer and improve outcomes for patients.

VA-CEDAR Tool for Equity in Lung Cancer Screening

Veterans Affairs Research Scholar Award
Neelima Navuluri, MD, MPH
Durham VA Medical Center
Durham
NC

The veteran population is disproportionately affected by lung cancer and relatively few patients that are eligible participate in lung cancer screening. This low participation is due to barriers such as provider bias, structural racism, patient mistrust, and fear of diagnosis. In this project, Dr. Navuluri proposes to develop and test an electronic shared decision-making aid and referral tool to improve equity in lung cancer screening (LCS).  She will pilot test the aid to assess its feasibility and usability among patients and providers within the Durham VA system.

The Germline-Somatic Interaction in Young-Onset Lung Cancer

Career Development Award
This grant was funded in part by Lung Cancer Initiative
Jaclyn LoPiccolo, MD, PhD
Dana-Farber Cancer Institute
Boston
MA

Although the average age at diagnosis is 70, thousands of new patients under 45 are diagnosed with lung cancer every year, most of whom have never smoked.  Dr. LoPiccolo hypothesizes that these patients may share inherited genetic changes that predispose them to developing lung cancer at a younger age.  In a preliminary analysis of young-onset lung cancer patients, Dr. LoPiccolo has found that approximately 30% of these patients carry rare mutations in known cancer-associated genes.  In this study, Dr. LoPiccolo will investigate whether these mutations affect response to targeted or immune-based therapies.  This insight is likely to identify risk factors among young lung cancer patients, which could lead to improved screening and treatment options for this population.

Promoting lung cancer screening in Latinx patients with previous HNSCC

Health Equity and Inclusiveness Junior Investigator Award
Coral Olazagasti, MD
University of Miami
Miami
FL

In addition to tobacco use, having a previous malignancy is a risk factor for developing lung cancer. Head and neck cancer (HNC) survivors with a history of smoking have up to a 13% risk of developing lung cancer. Dr. Olazagasti’s study will assess the awareness and eligibility of lung cancer screening in Hispanic/LatinX HNC survivors via a survey questionnaire and understand the barriers to screening via qualitative interviews. The goal of her research is to create the first lung cancer screening program tailored for and focused exclusively on Hispanic/LatinX HNC survivors.

Investigating incidental pulmonary nodules in underserved communities

Health Equity and Inclusiveness Junior Investigator Award
Neel Chudgar, MD
Montefiore Medical Center
Bronx
NY

Improving lung cancer screening adherence among underserved populations

Health Equity and Inclusiveness Research Fellow Award
Eduardo Nunez, MD
Boston University School of Medicine
Boston
MA

Measuring provider engagement in lung cancer screening

Veterans Affairs Research Scholar Award
Jennifer Lewis, MD, MS, MPH
Vanderbilt University Medical Center/VA-Tennessee Valley Healthcare System
Nashville
TN