Absolute lung cancer risk increases among individuals with >15 quit-years: Analyses to inform the update of the American Cancer Society lung cancer screening guidelines.

BACKGROUND: This report quantifies counteracting effects of quit-years and concomitant aging on lung cancer risk, especially on exceeding 15 quit-years, when the US Preventive Services Task Force (USPSTF) recommends curtailing lung-cancer screening. METHODS: Cox models were fitted to estimate absolute lung cancer risk among Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO) and National Lung Screening Trial (NLST) participants who ever smoked. Absolute lung cancer risk and gainable years of life from screening for individuals aged 50 to 80 in the US-representative National Health Interview Survey (NHIS) 2015-2018 who ever smoked were projected. Relaxing USPSTF recommendations to 20/25/30 quit-years versus augmenting USPSTF criteria with individuals whose estimated gain in life expectancy from screening exceeded 16.2 days according to the Life Years From Screening-CT (LYFS-CT) prediction model was compared. RESULTS: Absolute lung cancer risk increased by 8.7%/year (95% CI, 7.7%-9.7%; p < .001) as individuals aged beyond 15 quit-years in the PLCO, with similar results in NHIS and NLST. For example, mean 5-year lung cancer risk for those aged 65 years with 15 quit-years = 1.47% (95% CI, 1.35%-1.59%) versus 1.76% (95% CI, 1.62%-1.90%) for those aged 70 years with 20 quit-years in the PLCO. Removing the quit-year criterion would make 4.9 million more people eligible and increase the proportion of preventable lung cancer deaths prevented (sensitivity) from 63.7% to 74.2%. Alternatively, augmentation using LYFS-CT would make 1.7 million more people eligible while increasing the lung cancer death sensitivity to 74.0%. CONCLUSIONS: Because of aging, absolute lung cancer risk increases beyond 15 quit-years, which does not support exemption from screening or curtailing screening once it has been initiated. Compared with relaxing the USPSTF quit-year criterion, augmentation using LYFS-CT could prevent most of the deaths at substantially superior efficiency, while also preventing deaths among individuals who currently smoke with low intensity or long duration.

Methods for Using Race and Ethnicity in Prediction Models for Lung Cancer Screening Eligibility.

Importance: Using race and ethnicity in clinical prediction models can reduce or inadvertently increase racial and ethnic disparities in medical decisions. Objective: To compare eligibility for lung cancer screening in a contemporary representative US population by refitting the life-years gained from screening-computed tomography (LYFS-CT) model to exclude race and ethnicity vs a counterfactual eligibility approach that recalculates life expectancy for racial and ethnic minority individuals using the same covariates but substitutes White race and uses the higher predicted life expectancy, ensuring that historically underserved groups are not penalized. Design, Setting, and Participants: The 2 submodels composing LYFS-CT NoRace were refit and externally validated without race and ethnicity: the lung cancer death submodel in participants of a large clinical trial (recruited 1993-2001; followed up until December 31, 2009) who ever smoked (n = 39 180) and the all-cause mortality submodel in the National Health Interview Survey (NHIS) 1997-2001 participants aged 40 to 80 years who ever smoked (n = 74 842, followed up until December 31, 2006). Screening eligibility was examined in NHIS 2015-2018 participants aged 50 to 80 years who ever smoked. Data were analyzed from June 2021 to September 2022. Exposure: Including and removing race and ethnicity (African American, Asian American, Hispanic American, White) in each LYFS-CT submodel. Main Outcomes and Measures: By race and ethnicity: calibration of the LYFS-CT NoRace model and the counterfactual approach (ratio of expected to observed [E/O] outcomes), US individuals eligible for screening, predicted days of life gained from screening by LYFS-CT. Results: The NHIS 2015-2018 included 25 601 individuals aged 50 to 80 years who ever smoked (2769 African American, 649 Asian American, 1855 Hispanic American, and 20 328 White individuals). Removing race and ethnicity from the submodels underestimated lung cancer death risk (expected/observed [E/O], 0.72; 95% CI, 0.52-1.00) and all-cause mortality (E/O, 0.90; 95% CI, 0.86-0.94) in African American individuals. It also overestimated mortality in Hispanic American (E/O, 1.08, 95% CI, 1.00-1.16) and Asian American individuals (E/O, 1.14, 95% CI, 1.01-1.30). Consequently, the LYFS-CT NoRace model increased Hispanic American and Asian American eligibility by 108% and 73%, respectively, while reducing African American eligibility by 39%. Using LYFS-CT with the counterfactual all-cause mortality model better maintained calibration across groups and increased African American eligibility by 13% without reducing eligibility for Hispanic American and Asian American individuals. Conclusions and Relevance: In this study, removing race and ethnicity miscalibrated LYFS-CT submodels and substantially reduced African American eligibility for lung cancer screening. Under counterfactual eligibility, no one became ineligible, and African American eligibility increased, demonstrating the potential for maintaining model accuracy while reducing disparities.

Identification of Gene Co-Expression Networks Associated with Consensus Molecular Subtype-1 of Colorectal Cancer.

Colorectal cancer (CRC) is driven in part by dysregulated Wnt, Ras-Raf-MAPK, TGF-ß, and PI3K-Akt signaling. The progression of CRC is also promoted by molecular alterations and heterogeneous-yet interconnected-gene mutations, chromosomal instability, transcriptomic subtypes, and immune signatures. Genomic alterations of CRC progression lead to changes in RNA expression, which support CRC metastasis. An RNA-based classification system used for CRC, known as consensus molecular subtyping (CMS), has four classes. CMS1 has the lowest survival after relapse of the four CRC CMS phenotypes. Here, we identify gene signatures and associated coding mRNAs that are co-expressed during CMS1 CRC progression. Using RNA-seq data from CRC primary tumor samples, acquired from The Cancer Genome Atlas (TCGA), we identified co-expression gene networks significantly correlated with CMS1 CRC progression. CXCL13, CXCR5, IL10, PIK3R5, PIK3AP1, CCL19, and other co-expressed genes were identified to be positively correlated with CMS1. The co-expressed eigengene networks for CMS1 were significantly and positively correlated with the TNF, WNT, and ERK1 and ERK2 signaling pathways, which together promote cell proliferation and survival. This network was also aligned with biological characteristics of CMS1 CRC, being positively correlated to right-sided tumors, microsatellite instability, chemokine-mediated signaling pathways, and immune responses. CMS1 also differentially expressed genes involved in PI3K-Akt signaling. Our findings reveal CRC gene networks related to oncogenic signaling cascades, cell activation, and positive regulation of immune responses distinguishing CMS1 from other CRC subtypes.

Multivariate transcriptome analysis identifies networks and key drivers of chronic lymphocytic leukemia relapse risk and patient survival.

BACKGROUND: Chronic lymphocytic leukemia (CLL) is an indolent heme malignancy characterized by the accumulation of CD5+ CD19+ B cells and episodes of relapse. The biological signaling that influence episodes of relapse in CLL are not fully described. Here, we identify gene networks associated with CLL relapse and survival risk. METHODS: Networks were investigated by using a novel weighted gene network co-expression analysis method and examining overrepresentation of upstream regulators and signaling pathways within co-expressed transcriptome modules across clinically annotated transcriptomes from CLL patients (N = 203). Gene Ontology analysis was used to identify biological functions overrepresented in each module. Differential Expression of modules and individual genes was assessed using an ANOVA (Binet Stage A and B relapsed patients) or T-test (SF3B1 mutations). The clinical relevance of biomarker candidates was evaluated using log-rank Kaplan Meier (survival and relapse interval) and ROC tests. RESULTS: Eight distinct modules (M2, M3, M4, M7, M9, M10, M11, M13) were significantly correlated with relapse and differentially expressed between relapsed and non-relapsed Binet Stage A CLL patients. The biological functions of modules positively correlated with relapse were carbohydrate and mRNA metabolism, whereas negatively correlated modules to relapse were protein translation associated. Additionally, M1, M3, M7, and M13 modules negatively correlated with overall survival. CLL biomarkers BTK, BCL2, and TP53 were co-expressed, while unmutated IGHV biomarker ZAP70 and cell survival-associated NOTCH1 were co-expressed in modules positively correlated with relapse and negatively correlated with survival days. CONCLUSIONS: This study provides novel insights into CLL relapse biology and pathways associated with known and novel biomarkers for relapse and overall survival. The modules associated with relapse and overall survival represented both known and novel pathways associated with CLL pathogenesis and can be a resource for the CLL research community. The hub genes of these modules, e.g., ARHGAP27P2, C1S, CASC2, CLEC3B, CRY1, CXCR5, FUT5, MID1IP1, and URAHP, can be studied further as new therapeutic targets or clinical markers to predict CLL patient outcomes.

Using Prediction Models to Reduce Persistent Racial and Ethnic Disparities in the Draft 2020 USPSTF Lung Cancer Screening Guidelines.

We examined whether draft 2020 United States Preventive Services Task Force (USPSTF) lung cancer screening recommendations "partially ameliorate racial disparities in screening eligibility" compared with the 2013 guidelines, as claimed. Using data from the 2015 National Health Interview Survey, USPSTF-2020 increased eligibility by similar proportions for minorities (97.1%) and Whites (78.3%). Contrary to the intent of USPSTF-2020, the relative disparity (differences in percentages of model-estimated gainable life-years from National Lung Screening Trial-like screening by eligible Whites vs minorities) actually increased from USPSTF-2013 to USPSTF-2020 (African Americans: 48.3%-33.4% = 15.0% to 64.5%-48.5% = 16.0%; Asian Americans: 48.3%-35.6% = 12.7% to 64.5%-45.2% = 19.3%; Hispanic Americans: 48.3%-24.8% = 23.5% to 64.5%-37.0% = 27.5%). However, augmenting USPSTF-2020 with high-benefit individuals selected by the Life-Years From Screening with Computed Tomography (LYFS-CT) model nearly eliminated disparities for African Americans (76.8%-75.5% = 1.2%) and improved screening efficiency for Asian and Hispanic Americans, although disparities were reduced only slightly (Hispanic Americans) or unchanged (Asian Americans). The draft USPSTF-2020 guidelines increased the number of eligible minorities vs USPSTF-2013 but may inadvertently increase racial and ethnic disparities. LYFS-CT could reduce disparities in screening eligibility by identifying ineligible people with high predicted benefit regardless of race and ethnicity.