Squamous cell lung cancer

A subtype of NSCLC for which few therapy options exist

Intercept Lung Cancer Through Immune, Imaging & Molecular Evaluation-InTIME – Part 2

Lung Cancer Interception Award
Grant title (if any)
LUNGevity Foundation-American Lung Association Lung Cancer Interception Dream Team
This grant was co-funded by Stand Up to Cancer, LUNGevity, and the American Lung Association
Avrum Spira, MD, MSc (Principal Investigator)
Boston University
Boston
MA
Steven Dubinett, MD
UCLA
Los Angeles
CA

Lung cancer is the leading cause of cancer death globally, primarily due to challenges in early detection. With funding from Stand Up to Cancer, LUNGevity Foundation, and the American Lung Association, a multidisciplinary team called the Lung Cancer Interception Dream Team was formed in 2017 to tackle this challenge, uniting expertise from various fields to enhance lung cancer interception and prevention. 

This initiative includes the development of a lung pre-cancer genome atlas (PCGA) aimed at understanding molecular changes linked to the progression of pre-cancerous lesions to lung carcinoma. With continued funding from LUNGevity Foundation and the American Lung Association, the team plans to establish a temporal atlas for premalignant lung adenocarcinoma by utilizing robot-assisted bronchoscopy to collect samples from patients with ground glass opacities (GGOs) suspected of lung cancer. This effort will not only help identify these lesions but also facilitate the targeted delivery of intervention agents. 

By gaining insights into progression-associated molecular alterations and cellular interactions, the team aims to significantly advance lung cancer interception strategies - catching cancer at its earliest stages and treatment it before it grows and spreads. Ultimately, the goal is to provide personalized interception approaches for individuals at risk of developing lung cancer.

Research Summary

Cancer interception is catching cancer at its earliest stages and treatment it before it grows and spreads. Our current lack of effective lung cancer interception methods stems from an incomplete understanding of the early molecular events in lung cancer development, Through the 2017 Stand Up To Cancer – LUNGevity Foundation – American Lung Association grant, a multidisciplinary team called the Lung Cancer Interception Dream Team has established the Lung Pre-Cancer Genome Atlas (PCGA), identifying immune and epithelial changes linked to who normal cells become pre-malignant cancer cells. With a second round of funding from LUNGevity Foundation and the American Lung Association, the team will be building on these foundational findings  and enhance their efforts by developing a temporal atlas of genomic (DNA-level changes), transcriptomic (RNA-level), and epigenetic changes in pre-malignant lung adenocarcinoma lesions through longitudinal sampling. The team hypothesizes that these lesions exhibit specific genomic, transcriptomic, and epigenetic alterations, with some evading immune detection and advancing to invasive cancer. Ultimately, the insights gained will provide valuable resources for the research community and significantly impact early-stage lung cancer interception.

Technical Abstract

We lack effective lung cancer interception approaches due to our incomplete understanding of the earliest molecular events associated with lung carcinogenesis, which leave clinicians with few tools to manage precancerous lesions that may be found on CT screening. Our multidisciplinary Lung Cancer Interception Dream Team has made significant progress in establishing a Lung Pre-Cancer Genome Atlas(PCGA) where we have begun to identify immune and epithelial alterations associated with premalignant disease progression. To extend our findings in order to refine targets for lung cancer interception trials, we are proposing to extend our on-going PCGA efforts with two important aims 1) Develop a temporal atlas of premalignant lung adenocarcinoma via establishment of a cohort of longitudinally-sampled ground glass opacities (GGOs) collected with robot-assisted bronchoscopy, representing premalignant and minimally-invasive lung adenocarcinomas and 2) based on our current findings and feedback from our previous reviewers, we will expand our profiling to include spatial and epigenetic profiling of precancerous lesions and minimally invasive carcinoma in biopsy samples collected from the GGO cohort and our Pre-Cancer Genome Atlas 2.0 cohorts. We hypothesize that premalignant lesions bear specific genomic, transcriptomic and epigenetic aberrations, and a subset of these lesions escape immune surveillance and progress to invasive cancer. Our team, will apply spatial profiling using imaging mass cytometry and spatial transcriptomics will allow us to uncover the tissue architecture of the molecular processes associated with progression which in turn will help delineate the cell-cell interactions underlying these processes. Epigenetic profiling via single cell ATAC and bulk DNA methylation sequencing will allow us to overlay information about transcriptional regulation with the other ‘omic data to better understand the regulation of processes associated with progression. Critical to the success of the proposal is the multidisciplinary expertise of the team, involvement of patient advocates and the extensive preliminary data supporting the feasibility of the proposed approaches. The insights gained from successful completion of this project and the data that will made available to the research community will serve as a foundational resource for other investigators in the field and will result in a significant and sustained impact on the interception of early-stage lung cancers.

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.

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.

Tumor draining lymph node immunomodulation to decrease recurrence in NSCLC

Health Equity and Inclusiveness Junior Investigator Award
Jonathan Villena-Vargas, MD
Weill Medical College of Cornell University
New York
NY

Lymph nodes are small structures that work as filters for foreign substances, such as cancer cells and infections. These nodes contain infection-fighting immune cells that are carried in through the lymph fluid. This project will study the lymph node draining basin, which is involved in the spread of a tumor from the original location site to distant sites, and whether activating cancer-fighting T-cells can decrease recurrence in NSCLC.  Dr. Villena-Vargas will use animal models to investigate whether immune checkpoint inhibitors enhance lymph node T-cells memory, which increases their ability to recognize cancer cells in the bod and can prevent metastatic recurrence.

Lung cancer Equity Through Social needs Screening (LETS SCREEN)

Health Equity and Inclusiveness Junior Investigator Award
Ana Velazquez Manana, MD
University of California, San Francisco
San Francisco
CA

Dr. Velasquez Manana will conduct an observational study in a multiethnic group of patients with unresectable lung cancer to determine the association between social needs, care utilization, and quality of life.  The goal of this study is to fill a key knowledge gap in the care of patients with NSCLC and inform interventions to support patients at risk of social adversity during treatment to end disparities in lung cancer care.

Young lung cancer: psychosocial needs assessment

Health Equity and Inclusiveness Junior Investigator Award
Narjust Florez, MD
Dana-Farber Cancer Institute
Boston
MA

Dr. Florez will study the psychosocial and financial impact of lung cancer in young patients (< 50 years of age).  This patient population has seen an increase in incidence in recent years, but little is known about their specific needs.  The study will include administration of a survey and focus groups to understand unmet needs of this group of patients.  The information gathered from this study will be used to identify challenges unique to this population and develop the first clinical and research program of its kind for young lung cancer patients.

Predicting clinical benefit of immunotherapy in veterans

Veterans Affairs Research Scholar Award
Alex Bryant, MD
University of Michigan/VA Ann Arbor Healthcare System
Ann Arbor
MI

This study will use data from the Veterans Affairs system to develop statistical models to predict response to immunotherapy in patients with lung cancer. While immunotherapy has improved outcomes for many patients, it is still not well understood why some respond well and others do not.  If successful, this work will produce a comprehensive prediction model of immunotherapy benefit in lung cancer that could be used to counsel patients, inform patient-physician decision making, and identify patients who need more- or less-aggressive treatment.

Molecular Characterization of Lineage Plasticity

Partner Awards
Grant title (if any)
EGFR Resisters/LUNGevity Lung Cancer Research Award
Helena Yu, MD
Memorial Sloan Kettering Cancer Center
New York
NY

As a mechanism of resistance to EGFR inhibitors, cancers can change histology from adenocarcinoma to small cell or squamous cell lung cancer. Once this happens, EGFR inhibitors are no longer effective treatment; there are no strategies currently available to prevent or reverse transformation after it has occurred. Dr. Yu will use advanced molecular techniques to identify genetic changes that contribute to transformation. Understanding these genetic changes will identify biomarkers that can be utilized to develop treatments to prevent and reverse transformation.

Intercept Lung Cancer Through Immune, Imaging & Molecular Evaluation-InTIME

Lung Cancer Interception Award
Grant title (if any)
SU2C-LUNGevity Foundation-American Lung Association Lung Cancer Interception Dream Team
This grant was co-funded by Stand Up to Cancer, LUNGevity, and the American Lung Association
Avrum Spira, MD, MSc
Boston University
Boston
MA
Steven Dubinett, MD
UCLA
Los Angeles
CA
Julie Brahmer, MD
Johns Hopkins Kimmel Cancer Center
Baltimore
MD
Sam Gambhir, MD, PhD
Stanford University
Palo Alto
CA
Matthew Meyerson, MD, PhD
Harvard/Dana-Farber Cancer Institute
Boston
MA
Charles Swanton, PhD
Francis Crick Institute
London, England

The SU2C-LUNGevity Foundation-American Lung Association Lung Cancer Interception Dream Team, led by LUNGevity SAB member Dr. Avrum Spira, is developing a combination of diagnostic tools, such as non-invasive nasal swabs, blood tests, and radiological imaging, to confirm whether lung abnormalities found on chest imaging are benign lung disease or lung cancer.

Integrated Blood-Based and Radiographic Interception of Lung Cancer

Lung Cancer Interception Award
Grant title (if any)
SU2C-LUNGevity Foundation-American Lung Association Lung Cancer Interception Translational Research Team
This grant was co-funded by Stand Up to Cancer, LUNGevity, and the American Lung Association
Lecia Sequist, MD
Massachusetts General Hospital
Boston
MA
Max Diehn, MD
Stanford University
Palo Alto
CA
Tilak Sundaresan, MD
Kaiser Permanente San Francisco
San Francisco
CA
Gad Getz, PhD
Broad Institute
Cambridge
MA

The SU2C-LUNGevity Foundation-American Lung Association Lung Cancer Interception Translational Research Team, headed by LUNGevity Scientific Advisory Board (SAB) member Dr. Lecia Sequist, is developing a lung cancer interception assay (LCIA) that can be used in conjunction with low-dose CT scans. This assay will be based on an integration of several blood-based assays that examine circulating tumor cells and circulating tumor DNA.