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. 2024 Feb;19(2):273-284.
doi: 10.1016/j.jtho.2023.09.275. Epub 2023 Sep 16.

Genomic Staging of Multifocal Lung Squamous Cell Carcinomas Is Independent of the Comprehensive Morphologic Assessment

Sanja Dacic  1 , Xuanye Cao  2 , Neus Bota-Rabassedas  2 , Beatriz Sanchez-Espiridion  2 , Sabina Berezowska  3 , Yuchen Han  4 , Jin-Haeng Chung  5 , Mary Beth Beasley  6 , Lin Dongmei  7 , David Hwang  8 , Mari Mino-Kenudson  9 , Yuko Minami  10 , Mauro Papotti  11 , Natasha Rekhtman  12 , Anja C Roden  13 , Erik Thunnissen  14 , Ming-Sound Tsao  15 , Yasushi Yatabe  16 , Akihiko Yoshida  16 , Linghua Wang  2 , Douglas J Hartman  17 , Jacob A Jerome  17 , Humam Kadara  2 , Teh-Ying Chou  18 , Ignacio I Wistuba  2 ; IASLC Pathology Committee
Affiliations

Genomic Staging of Multifocal Lung Squamous Cell Carcinomas Is Independent of the Comprehensive Morphologic Assessment

Sanja Dacic et al. J Thorac Oncol. 2024 Feb.

Abstract

Introduction: Morphologic and molecular data for staging of multifocal lung squamous cell carcinomas (LSCCs) are limited. In this study, whole exome sequencing (WES) was used as the gold standard to determine whether multifocal LSCC represented separate primary lung cancers (SPLCs) or intrapulmonary metastases (IPMs). Genomic profiles were compared with the comprehensive morphologic assessment.

Methods: WES was performed on 20 tumor pairs of multifocal LSCC and matched normal lymph nodes using the Illumina NovaSeq6000 S4-Xp (Illumina, San Diego, CA). WES clonal and subclonal analysis data were compared with histologic assessment by 16 thoracic pathologists. In addition, the immune gene profiling of the study cases was characterized by the HTG EdgeSeq Precision Immuno-Oncology Panel.

Results: By WES data, 11 cases were classified as SPLC and seven cases as IPM. Two cases were technically suboptimal. Analysis revealed marked genomic and immunogenic heterogeneity, but immune gene expression profiles highly correlated with mutation profiles. Tumors classified as IPM have a large number of shared mutations (ranging from 33.5% to 80.7%). The agreement between individual morphologic assessments for each case and WES was 58.3%. One case was unanimously interpreted morphologically as IPM and was in agreement with WES. In a further 17 cases, the number of pathologists whose morphologic interpretation was in agreement with WES ranged from two (one case) to 15 pathologists (one case) per case. Pathologists showed a fair interobserver agreement in the morphologic staging of multiple LSCCs, with an overall kappa of 0.232.

Conclusions: Staging of multifocal LSCC based on morphologic assessment is unreliable. Comprehensive genomic analyses should be adopted for the staging of multifocal LSCC.

Keywords: Histologic subtyping; Multifocal lung cancer; Squamous; Staging; WES.

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Conflict of interest statement

The remaining authors declare no conflict of interest.

Figures

Figure 1.
Figure 1.
The mutation landscape of multifocal LSCC. (a) The top mutated genes are shown with TP53 being the most common. Different types of mutations are shown in different colors. (b) The overall mutation frequency of driver genes in this study cohort is comparable to the TCGA data for lung squamous cell carcinoma.
Figure 2.
Figure 2.
Genomic heterogeneity of multifocal LSCC. (a) Public and private clonal and subclonal mutations in each case are shown as indicated. (b) Tumors considered to represent IPM have large numbers of shared mutations, while two cases (#2 and 10) that represent separate primaries have no overlapping mutations. (c) Jaccardi similarity index for all study cases. Eleven cases with JSI 0 represented SPLC, while seven cases with JSI ranging from 0.27– 084 represent IPM.
Figure 3.
Figure 3.
Examples of cases interpreted as intrapulmonary metastases with similar clonality but differences in Jaccard similarity index.(a) Case 6 showed Jaccard similarity index of 0.33. The VAF of the gene mutations CDH10 and TP53 were different between the two tumor nodules (T1 0.2–0.4, while T2 0.1–0.15). Although the mutation proportion of different types of nucleotide substitution was not significant, T1 had another gene mutation NFE2L2, while T2 did not have this mutation. (b) Case 12 had a much higher Jaccard similarity index (0.73). Two tumor nodules shared the same TP53 gene mutation with the same VAF. On the other hand, although the mutation proportion of nucleotide substitution was significantly different, the clonality of two samples were very similar. They also shared the same NFE2L2 and PIK3CA mutations.
Figure 4.
Figure 4.
Diagnostic interpretations of the multifocal LSCC by MPTN Working Group pathologists based on morphology only. The pathologists were blinded to the genomic and clinical data. In one case unanimous opinion that the tumor represents intrapulmonary metastases was reached (case #20). WES clonality interpretations are included for comparison. (SPLC- separate primary lung carcinoma; IPM-intrapulmonary metastasis; NA-not applicable).
Figure 5.
Figure 5.
In addition to the mutation similarities, intrapulmonary metastases showed high similarity in the immune transcriptomic profiles. (a) The PCA plot illustrates that two tumors from case 6 (intrapulmonary metastases) have very similar transcriptomic profiles, while tumors in case 10 (separate primaries) showed different profiles. (b) The immune-stroma-TME plot also validated these findings. (c) MCP-counter generated immune cell composition heatmap demonstrating intrapulmonary metastases with similar immune cell composition
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References

    1. Martini N, Melamed MR. Multiple primary lung cancers. J Thorac Cardiovasc Surg. 1975;70(4):606–612. - PubMed
    1. Girard N, Deshpande C, Lau C, et al. Comprehensive histologic assessment helps to differentiate multiple lung primary nonsmall cell carcinomas from metastases. Am J Surg Pathol. 2009;33(12):1752–1764. - PMC - PubMed
    1. Detterbeck FC, Franklin WA, Nicholson AG, et al. The IASLC Lung Cancer Staging Project: Background Data and Proposed Criteria to Distinguish Separate Primary Lung Cancers from Metastatic Foci in Patients with Two Lung Tumors in the Forthcoming Eighth Edition of the TNM Classification for Lung Cancer. J Thorac Oncol. 2016;11(5):651–665. - PubMed
    1. Travis WD BE, Burke AP, Marx A, Nicholson AG. WHO Classification of tumors of the lung, pleura, thymus and heart. Vol 7. Lyon: IARC Press; 2015. - PubMed
    1. Nicholson AG, Torkko K, Viola P, et al. Interobserver Variation among Pathologists and Refinement of Criteria in Distinguishing Separate Primary Tumors from Intrapulmonary Metastases in Lung. J Thorac Oncol. 2018;13(2):205–217. - PMC - PubMed

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