Whole exome sequencing of independent lung adenocarcinoma, lung squamous cell carcinoma, and malignant peritoneal mesothelioma: A case report

Abstract

The presence of multiple primary tumors (MPT) in a single patient has been identified with an increasing frequency. A critical issue is to establish if the second tumor represents an independent primary cancer or a metastasis. Therefore, the assessment of MPT clonal origin might help understand the disease behavior and improve the management/prognosis of the patient.Herein, we report a 73-year-old male smoker who developed 2 primary lung cancers (adenocarcinoma and squamous cell carcinoma) and a malignant peritoneal mesothelioma (PM).Whole exome sequencing (WES) of the 3 tumors and of germline DNA was performed to determine the clonal origin and identify genetic cancer susceptibility.Both lung cancers were characterized by a high mutational rate with distinct mutational profiles and activation of tumor-specific pathways. Conversely, the PM harbored a relative low number of genetic variants and a novel mutation in the WT1 gene that might be involved in the carcinogenesis of nonasbestos-related mesothelioma. Finally, WES of the germinal DNA displayed several single nucleotide polymorphisms in DNA repair genes likely conferring higher cancer susceptibility.Overall, WES did not disclose any somatic genetic variant shared across the 3 tumors, suggesting their clonal independency; however, the carcinogenic effect of smoke combined with a deficiency in DNA repair genes and the patient advanced age might have been responsible for the MPT development. This case highlights the WES importance to define the clonal origin of MPT and susceptibility to cancer.

Figure 1

Timeline of oncologic history of the patient. Dashed line means the time of each diagnostic examination (red box) or surgical intervention (violet); Light green, dark green, and dark/light blue boxes report the ADC, SCC, and PM evolution, respectively. Yellow box describes the pharmacological treatment.

Figure 2

Hematoxylin and eosin stained images of ADC (A), SCC (B), and PM (C) (Original magnification 40x). Immunohistochemistry of PM reported a positive staining for Calretinin (D), CK-7 (E), and CK5&6 (F), whereas a negative staining for TFF-1 (G) and p63 (H) (Original magnification 40x).

Figure 3

Relevant figures from CT-scans collected throughout the patient's clinical history. The arrows indicate lesions of interest. Notably, as the patient could not provide CT-scans performed before April 2009 in a different Institution, pictures of the lung adenocarcinoma located in the left lower lobe are not available. (A) CT-scan picture showing the SCC located in the right upper lobe in September 2010, before being treated with carboplatin-based chemotherapy; (B) CT-scan picture showing the same tumor (SCC) as in November 2011, progressing after carboplatin-based chemotherapy and periodical follow-up; (C) CT-scan picture showing diffuse abdominal lesions of PM.

Figure 4

(A) Specific mutational signature for ADC, SCC, and PM according to the base substitutions.^[8] The substitution types are showed on the horizontal axis, whereas the percentages of base substitutions are displayed on the vertical axis. (B) Mutational profile of somatic (ADC, SCC, and PM) and germline (PB) gene variants divided in single nucleotide variant (SNV), multiple nucleotide variant (MNV), and INDEL. Each type of mutation was subdivided into exon or non-exon (intergenic regions, downstream and upstream regions, 5′UTR/3′UTR regions, splice regions, and intron regions) variants. “Stop gained”: variant causes a stop codon; “Start_Stop lost”: variant causes start codon to be mutated into a nonstart codon or variant causes stop codon to be mutated into a nonstop codon, respectively; “Splice region variant”: variant affective putative (Lariat) branch point from U12 splicing machinery, located in the intron; “Sequence Feature”: unknown/any extent of continuous biological sequence.