Advancing Lung Cancer Staging: Integrating IASLC Recommendations and Bioinformatics to Delineate Tumor Origins.

<div>AbstractPurpose:<p>In patients with >1 non–small cell lung carcinoma (NSCLC), the distinction between separate primary lung carcinomas (SPLCs) and intrapulmonary metastases (IPMs) is a common diagnostic dilemma with critical staging implications. Here, we compared the performance of comprehensive next-generation sequencing (NGS) with standard histopathologic approaches for distinguishing NSCLC clonal relationships in clinical practice.</p>Experimental Design:<p>We queried 4,119 NSCLCs analyzed by 341–468 gene MSK-IMPACT NGS assay for patients with >1 surgically resected tumor profiled by NGS. Tumor relatedness predicted by prospective histopathologic assessment was contrasted with comparative genomic profiling by subsequent NGS.</p>Results:<p>Sixty patients with NGS performed on >1 NSCLCs were identified, yielding 76 tumor pairs. NGS classified tumor pairs into 51 definite SPLCs (median, 14; up to 72 unique somatic mutations per pair), and 25 IPMs (24 definite, one high probability; median, 5; up to 16 shared somatic mutations per pair). Prospective histologic prediction was discordant with NGS in 17 cases (22%), particularly in the prediction of IPMs (44% discordant). Retrospective review highlighted several histologic challenges, including morphologic progression in some IPMs. We subsampled MSK-IMPACT data to model the performance of less comprehensive assays, and identified several clinicopathologic differences between NGS-defined tumor pairs, including increased risk of subsequent recurrence for IPMs.</p>Conclusions:<p>Comprehensive NGS allows unambiguous delineation of clonal relationship among NSCLCs. In comparison, standard histopathologic approach is adequate in most cases, but has notable limitations in the recognition of IPMs. Our results support the adoption of broad panel NGS to supplement histology for robust discrimination of NSCLC clonal relationships in clinical practice.</p></div>

In patients with >1 non-small cell lung carcinoma (NSCLC), the distinction between separate primary lung carcinomas (SPLCs) and intrapulmonary metastases (IPMs) is a common diagnostic dilemma with critical staging implications. Here, we compared the performance of comprehensive next-generation sequencing (NGS) with standard histopathologic approaches for distinguishing NSCLC clonal relationships in clinical practice. We queried 4,119 NSCLCs analyzed by 341-468 gene MSK-IMPACT NGS assay for patients with >1 surgically resected tumor profiled by NGS. Tumor relatedness predicted by prospective histopathologic assessment was contrasted with comparative genomic profiling by subsequent NGS. Sixty patients with NGS performed on >1 NSCLCs were identified, yielding 76 tumor pairs. NGS classified tumor pairs into 51 definite SPLCs (median, 14; up to 72 unique somatic mutations per pair), and 25 IPMs (24 definite, one high probability; median, 5; up to 16 shared somatic mutations per pair). Prospective histologic prediction was discordant with NGS in 17 cases (22%), particularly in the prediction of IPMs (44% discordant). Retrospective review highlighted several histologic challenges, including morphologic progression in some IPMs. We subsampled MSK-IMPACT data to model the performance of less comprehensive assays, and identified several clinicopathologic differences between NGS-defined tumor pairs, including increased risk of subsequent recurrence for IPMs. Comprehensive NGS allows unambiguous delineation of clonal relationship among NSCLCs. In comparison, standard histopathologic approach is adequate in most cases, but has notable limitations in the recognition of IPMs. Our results support the adoption of broad panel NGS to supplement histology for robust discrimination of NSCLC clonal relationships in clinical practice.

<div>AbstractPurpose:<p>In patients with >1 non–small cell lung carcinoma (NSCLC), the distinction between separate primary lung carcinomas (SPLCs) and intrapulmonary metastases (IPMs) is a common diagnostic dilemma with critical staging implications. Here, we compared the performance of comprehensive next-generation sequencing (NGS) with standard histopathologic approaches for distinguishing NSCLC clonal relationships in clinical practice.</p>Experimental Design:<p>We queried 4,119 NSCLCs analyzed by 341–468 gene MSK-IMPACT NGS assay for patients with >1 surgically resected tumor profiled by NGS. Tumor relatedness predicted by prospective histopathologic assessment was contrasted with comparative genomic profiling by subsequent NGS.</p>Results:<p>Sixty patients with NGS performed on >1 NSCLCs were identified, yielding 76 tumor pairs. NGS classified tumor pairs into 51 definite SPLCs (median, 14; up to 72 unique somatic mutations per pair), and 25 IPMs (24 definite, one high probability; median, 5; up to 16 shared somatic mutations per pair). Prospective histologic prediction was discordant with NGS in 17 cases (22%), particularly in the prediction of IPMs (44% discordant). Retrospective review highlighted several histologic challenges, including morphologic progression in some IPMs. We subsampled MSK-IMPACT data to model the performance of less comprehensive assays, and identified several clinicopathologic differences between NGS-defined tumor pairs, including increased risk of subsequent recurrence for IPMs.</p>Conclusions:<p>Comprehensive NGS allows unambiguous delineation of clonal relationship among NSCLCs. In comparison, standard histopathologic approach is adequate in most cases, but has notable limitations in the recognition of IPMs. Our results support the adoption of broad panel NGS to supplement histology for robust discrimination of NSCLC clonal relationships in clinical practice.</p></div>

Genomic Profiling With Large-Scale Next-Generation Sequencing Panels Distinguishes Separate Primary Lung Adenocarcinomas From Intrapulmonary Metastases

Expression of Bone Morphogenetic Proteins in Human Lung Carcinomas

Radiomics has shown potential in disease diagnosis, but its feasibility for non-small cell lung carcinoma (NSCLC) subtype classification is unclear. This study aims to explore the diagnosis value of texture and colour features from positron emission tomography computed tomography (PET-CT) images in differentiation of NSCLC subtypes: adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). Two patient cohorts were retrospectively collected into a dataset of 341 18F-labeled 2-deoxy-2fluoro-d-glucose ([18F] FDG) PET-CT images of NSCLC tumours (125 ADC, 174 SqCC, and 42 cases with unknown subtype). Quantification of texture and colour features was performed using freehand regions of interest. The relation between extracted features and commonly used parameters such as age, gender, tumour size, and standard uptake value (SUVmax) was explored. To classify NSCLC subtypes, support vector machine algorithm was applied on these features and the classification performance was evaluated by receiver operating characteristic curve analysis. There was a significant difference between ADC and SqCC subtypes in texture and colour features (P < 0.05); this showed that imaging features were significantly correlated to both SUVmax and tumour diameter (P < 0.05). When evaluating classification performance, features combining texture and colour showed an AUC of 0.89 (95% CI, 0.78–1.00), colour features showed an AUC of 0.85 (95% CI, 0.71–0.99), and texture features showed an AUC of 0.68 (95% CI, 0.48–0.88). DeLong’s test showed that AUC was higher for features combining texture and colour than that for texture features only (P = 0.010), but not significantly different from that for colour features only (P = 0.328). HSV colour features showed a similar performance to RGB colour features (P = 0.473). The colour features are promising in the refinement of NSCLC subtype differentiation, and features combining texture and colour of PET-CT images could result in better classification performance.

Background:Cytomegalovirus (CMV) is a virus with high seroprevalence in general population. Recent evidence shows that CMV is linked to various types of cancer, including lung cancer. This study aims to determine the relationship between CMV and non-small cell lung carcinoma (NSCLC). Data from this study will be useful for further research in elucidating the link between CMV and lung cancer. Method:This research was an observational study using a cross-sectional method to determine the proportion of CMV DNA in NSCLC tissue samples. Formalin-fixed paraffin-embedded (FFPE) tissue samples were taken from archival at Persahabatan Hospital on 2017-2023. The detection of CMV was carried out using polymerase chain reaction (PCR) and electrophoresis. Accompanying data was taken from medical records. Results:A total of 87 tissue samples from 87 different subjects were included in this study. Most of the research subjects were male smokers, had a heavy Brinkman index with an average age of 59.1 years. The proportion of CMV DNA detected in FFPE samples was 21%. The proportion of CMV DNA was higher in tissue samples with positive EGFR mutations although not statistically significant. The proportion of CMV DNA was not related to smoking status, Brinkman index, tissue sampling method, and NSCLC subtype. Conclusion:High proportion of cytomegalovirus DNA were detected in NSCLC FFPE samples in Indonesia. The proportion of CMV DNA was higher in NSCLC with EGFR mutations.

Subtyping of Undifferentiated Non-small Cell Carcinomas in Bronchial Biopsy Specimens

Histopathological associations, molecular findings and clinical outcomes of patients with non-small cell lung carcinoma with MET alterations: a 3-year retrospective Australian case series.

Non-small cell lung carcinoma (NSCLC) is the most common lung cancer worldwide. Secreted frizzled-related proteins (SFRPs) are important tumour suppressors and antagonists of the Wnt signalling pathway, which is linked with cancer development. The aim of this study was to evaluate the concentrations of SFRP1, SFRP2, and SFRP5 proteins in tumour and non-tumour (NT) samples obtained from 65 patients with primary NSCLC. An enzyme-linked immunosorbent assay (ELISA) was used to measure the concentrations of SFRPs in the tissue homogenates. A significantly lower SFRP2 protein concentration was found in the total NSCLC tumour samples and the following NSCLC subtypes: squamous cell carcinoma (SCC) and adenocarcinoma (AC) (p > 0.05, p = 0.028 and p = 0.001, respectively). AC tumour samples had a higher SFRP1 level than NT samples (p = 0.022), while the highest SFRP1 concentration was found in NSCLC samples from patients with clinical stage T4 cancer. Increased concentrations of SFRP1 and SFRP5 were present in stage III NSCLC samples, while the tumour samples with high pleural invasion (PL2) had an increased level of SFRP2. The results from this study suggest that the tumour suppressor or oncogenic roles of SFRPs could be connected with the NSCLC subtype. The levels of SFRPs varied according to the clinicopathological parameters of NSCLC.

Alternative splicing of pre-mRNA, a key post-transcriptional mechanism allowing for the production of distinct proteins from a single gene, affects over 90% of human genes. Splicing plays a major role in gene regulation in normal tissues as well as in disease. In cancer, alternative splicing permits the generation of protein isoforms having different biological activities. Thus, splicing alterations participate in the diversity and phenotypic plasticity of tumor cells. The identification of such molecular changes represent promising avenues for cancer diagnosis and therapy.Lung cancer is the leading cause of cancer mortality. Over 80% of lung cancers are non-small cell lung carcinomas (NSCLC). Adenocarcinoamas (AC) and Squamous Cell Carcinomas (SCC) are the two most common subtypes of NSCLC and account for more than 60% of lung cancer cases. Despite being categorized together in NSCLC due to similar microscopic appearance of their tumour cells and similar treatment options in the clinic, AC and SCC are heterogeneous in many clinical aspects, these include distinct oncogenic mutations and divergent therapeutic responses, thus heightening the emphasis on accurate NSCLC subtyping.Here, we describe two approaches to seek transcriptome changes that discriminate between SCC and AC subtypes. To do so, we profiled SCC and AC biopsies together with their adjacent normal tissues on Exonhit's Genome Wide SpliceArray™, a new generation of microarray that extends transcriptomic profiling to the monitoring of alternative splicing, thereby increasing the discriminatory power of the analyses. Through this discovery platform, disease status, progression, and drug response can be monitored. First, we developed transcriptomic signatures using combinations of exon body, exon-intron junction, evidenced and discovery probes and performed principal component analyses at various q values and fold change thresholds. Using a t-test on the first principal component, we compared their respective efficacy to discriminate between SCC and AC subtypes. The data that will be discussed highlight the importance of discovery and junction probes in the signatures. Second, an epitope identification approach was conducted. We focused on splicing events that generate potential novel amino acid sequences. Events up-regulated were selected based on combination of statistical analysis of probe sets deregulations, protein knowledge and pathway analyses. The events were used to identify novel cell surface epitopes which may be suitable for antibody development. These findings should be validated with larger sample numbers but indicate that alternative RNA splicing offers a currently underexploited source of biological information for cancer research. Platforms dedicated to splicing can be useful to allow identification of biomarkers and novel targets, as well as guidance in the selection and follow-up of patients for therapy. Citation Format: Laurent Désiré, Anne-Sophie Casagrande, Florence Mahé, Emeline Throo, Matthew P. Pando. An alternative splicing study approach to discriminate between NSCLC subtypes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4147. doi:10.1158/1538-7445.AM2013-4147

e21038 Background: Patients with multiple primary lung cancers (MPLC) and intrapulmonary metastasis (IPM) are considered as different clinical stages and require different treatment strategies. At present, the molecular identification criteria employed for distinguishing MPLC and IPM still need to be improved. Therefore, there is an unmet medical need in regards to a diagnostic standard that could effectively distinguish MPLC from IPM. Methods: Between December 2014 and April 2020, a total of 35 patients, with more than two lung lesions, were selected and divided into a training cohort (N = 22) and a validation cohort (N = 13). Imaging, anatomical evidence, pathological results, and histological examinations of the primary tumor, as well as histological subtypes, were used to differentiate MPLC from IPM. Genomic profiles obtained using a targeted sequencing with 450 cancer-related genes panel were analyzed. Modified diagnostic criteria for MPLC and IPM were established based on Martini and Melamed criteria, as well as molecular profiles. Results: We developed interpretation criteria using a flowchart that distinguishes MPLC from IPM, as follows: 1) MPLC can be determined using the following aspects: no common mutations are present; one lesion has no mutations (tumor = 2); two common high frequency driver gene mutations are present, or one driver gene mutation and one rare mutation comprising the p53 mutation are present; and only one common mutation is present. 2) IPM can be determined using the following aspects: one driver gene mutation and one rare mutation comprising the p53 mutation (concordance rare ≥ 50%) are present; two driver gene mutations (concordance rare ≥ 60%) are present; all mutations are common; and more than three common mutations are present. 3) Undetermined results are based on the following aspects: no mutations in one tumor are present (tumor &gt; 2); no mutations are identified in all tumors; or two rare mutations are present. Undetermined patients were identified by combining histological identifications. Subsequently, to verify the criteria, 13 patients were recruited as a validation cohort. Eight MPLC and 5 IPM patients were identified, and the results were 100% consistent with independent imaging and pathological diagnoses. Conclusions: In this work, we proposed more comprehensive and detailed molecular identification criteria for MPLC and IPM, and it suggested that genetic alterations may be an effective method for diagnosing MPLC and IPM. We also determined that NGS may be a useful tool for assisting with differential diagnoses. Key words: Multiple lung cancer, Multiple primary lung cancer, Intrapulmonary metastasis, Next-generation sequencing, molecular classification.

Subtyping of Non-small Cell Lung Carcinoma: A Comparison of Small Biopsy and Cytology Specimens

Due to therapeutic advances, the subclassification of non-small cell lung carcinomas (NSCLC) between the adenocarcinomas and squamous cell carcinomas subtypes is essential for the practice of personalized and targeted medicine. The clinical management for these two NSCLC subtypes is different due to their different molecular properties and histological origins. Immunohistochemistry (IHC) markers such is TTF-1 play a key role in the differentiation of lung adenocarcinomas and squamous cell carcinomas. However, immunohistochemistry is a complex process involving many critical steps and the reliability of results depends on the standardization of the assay as well as the appropriate interpretation. Different laboratories use different reagents and different IHC approaches for the detection of TTF-1 in lung cancer tumors. Here we describe an automated IHC protocol used in our laboratory for the detection of TTF-1 in formalin-fixed, paraffin-embedded (FFPE) tissue sections from lung tumors.

AimVarious approaches have been reported for distinguishing separate primary lung adenocarcinomas from intrapulmonary metastases in patients with two lung nodules. The aim of this study was to determine whether histological...