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Timon P. H. Buys, BSc, Sarit Aviel-Ronen, MD, Thomas K

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1 Defining Genomic Alteration Boundaries for a Combined Small Cell and Non-small Cell Lung Carcinoma 
Timon P.H. Buys, BSc, Sarit Aviel-Ronen, MD, Thomas K. Waddell, MD, PhD, FRCSC, Wan L. Lam, PhD, Ming-Sound Tsao, MD, FRCPC  Journal of Thoracic Oncology  Volume 4, Issue 2, Pages (February 2009) DOI: /JTO.0b013e Copyright © 2009 International Association for the Study of Lung Cancer Terms and Conditions

2 FIGURE 1 Microscopic features of a combined carcinoma. A, Bordering area of large cell neuroendocrine carcinoma (LCNEC) and adenocarcinoma components. B, Higher magnification of LCNEC showing focal necrosis. C, CD56+ membranous immunostaining for LCNEC tumor cells. D, Adenocarcinoma component with papillary and acinar features. E–H, Small cell carcinoma component of combined tumor with two areas distinguished by their expression of CD56 and chromogranin-A (Chr). SC1 area showed negative or focal chromogranin-A staining (H) and strong membranous CD56 staining (G), while SC2 was chromogranin-A positive (H) but CD56 negative (G). (Magnifications: (A) and (E), ×25; (B), (C), and (F), ×200; (D), ×100; (A), (B), (C), (D), (F): hematoxylin and eosin; (C), (G), (H): immunohistochemistry). Journal of Thoracic Oncology 2009 4, DOI: ( /JTO.0b013e ) Copyright © 2009 International Association for the Study of Lung Cancer Terms and Conditions

3 FIGURE 2 Comparison of genomic alterations between subcomponents of a combined carcinoma. Each clone on the array comparative genomic hybridization (CGH) platform is represented at its known chromosomal position by a small dark blue line. For each array experiment, the signal intensity ratio at each clone is plotted on a log2 scale along the horizontal axis. Vertical lines show log2 signal intensity ratios from −1.0 (green line) to +1.0 (red line), with unchanged regions falling along the zero line (purple), green shading marking regions of segmental genomic loss, and red shading marking regions of segmental gain. A, Two tumors harbored additional copies of the MYC oncogene: a focal amplification spanning this gene was seen for the large cell neuroendocrine carcinoma (LCNEC) component while a lower level segmental gain was seen for the adenocarcinoma (AC) tumor. B, An example of a chromosomal breakpoint shared by SC1 and SC2. Neither the AC nor LCNEC components exhibited this alteration boundary within 13q C, The alterations status of chromosome 20 was different between SC1 and SC2, suggesting ongoing evolution. The first two karyograms show genome profiles generated by comparison of tumor and reference DNA and are annotated as in parts (A) and (B). The third karyogram (within the gray box) shows the results of a direct competitive hybridization experiment between SC1 and SC2. As above, where clones are positioned along the zero line (purple), equivalent copy number between the two samples is inferred. Where log2 <0, it suggests increased DNA copy number for SC2 relative to SC1 (green shading). Where log2 >0, the reverse may be inferred. D, A putative clonal relationship of genetically distinct tumor types in this combined carcinoma. Tumors could have arisen from different normal airway progenitor cells that might be pleuripotent or lineage-defined. Journal of Thoracic Oncology 2009 4, DOI: ( /JTO.0b013e ) Copyright © 2009 International Association for the Study of Lung Cancer Terms and Conditions

4 Supplementary Figure 1 Tiling-path array comparative genomic hybridization (CGH) karyograms for all combined carcinoma components described in this case report. Karyograms are annotated as in Figure 2. A, Adenocarcinoma component (AC). B, Small cell lung carcinoma (SCLC) component with Chr−/CD56+ staining (SC1). C, SCLC component with Chr+/CD56− staining (SC2). D, Large cell neuroendocrine carcinoma component (LCNEC). E, Normal (noncancerous) tissue. F, Direct competitive hybridization between SC1 and SC2 components (annotated as described for Figure 2C). Journal of Thoracic Oncology 2009 4, DOI: ( /JTO.0b013e ) Copyright © 2009 International Association for the Study of Lung Cancer Terms and Conditions

5 Supplementary Figure 1 Tiling-path array comparative genomic hybridization (CGH) karyograms for all combined carcinoma components described in this case report. Karyograms are annotated as in Figure 2. A, Adenocarcinoma component (AC). B, Small cell lung carcinoma (SCLC) component with Chr−/CD56+ staining (SC1). C, SCLC component with Chr+/CD56− staining (SC2). D, Large cell neuroendocrine carcinoma component (LCNEC). E, Normal (noncancerous) tissue. F, Direct competitive hybridization between SC1 and SC2 components (annotated as described for Figure 2C). Journal of Thoracic Oncology 2009 4, DOI: ( /JTO.0b013e ) Copyright © 2009 International Association for the Study of Lung Cancer Terms and Conditions

6 Supplementary Figure 1 Tiling-path array comparative genomic hybridization (CGH) karyograms for all combined carcinoma components described in this case report. Karyograms are annotated as in Figure 2. A, Adenocarcinoma component (AC). B, Small cell lung carcinoma (SCLC) component with Chr−/CD56+ staining (SC1). C, SCLC component with Chr+/CD56− staining (SC2). D, Large cell neuroendocrine carcinoma component (LCNEC). E, Normal (noncancerous) tissue. F, Direct competitive hybridization between SC1 and SC2 components (annotated as described for Figure 2C). Journal of Thoracic Oncology 2009 4, DOI: ( /JTO.0b013e ) Copyright © 2009 International Association for the Study of Lung Cancer Terms and Conditions

7 Supplementary Figure 1 Tiling-path array comparative genomic hybridization (CGH) karyograms for all combined carcinoma components described in this case report. Karyograms are annotated as in Figure 2. A, Adenocarcinoma component (AC). B, Small cell lung carcinoma (SCLC) component with Chr−/CD56+ staining (SC1). C, SCLC component with Chr+/CD56− staining (SC2). D, Large cell neuroendocrine carcinoma component (LCNEC). E, Normal (noncancerous) tissue. F, Direct competitive hybridization between SC1 and SC2 components (annotated as described for Figure 2C). Journal of Thoracic Oncology 2009 4, DOI: ( /JTO.0b013e ) Copyright © 2009 International Association for the Study of Lung Cancer Terms and Conditions

8 Supplementary Figure 1 Tiling-path array comparative genomic hybridization (CGH) karyograms for all combined carcinoma components described in this case report. Karyograms are annotated as in Figure 2. A, Adenocarcinoma component (AC). B, Small cell lung carcinoma (SCLC) component with Chr−/CD56+ staining (SC1). C, SCLC component with Chr+/CD56− staining (SC2). D, Large cell neuroendocrine carcinoma component (LCNEC). E, Normal (noncancerous) tissue. F, Direct competitive hybridization between SC1 and SC2 components (annotated as described for Figure 2C). Journal of Thoracic Oncology 2009 4, DOI: ( /JTO.0b013e ) Copyright © 2009 International Association for the Study of Lung Cancer Terms and Conditions

9 Supplementary Figure 1 Tiling-path array comparative genomic hybridization (CGH) karyograms for all combined carcinoma components described in this case report. Karyograms are annotated as in Figure 2. A, Adenocarcinoma component (AC). B, Small cell lung carcinoma (SCLC) component with Chr−/CD56+ staining (SC1). C, SCLC component with Chr+/CD56− staining (SC2). D, Large cell neuroendocrine carcinoma component (LCNEC). E, Normal (noncancerous) tissue. F, Direct competitive hybridization between SC1 and SC2 components (annotated as described for Figure 2C). Journal of Thoracic Oncology 2009 4, DOI: ( /JTO.0b013e ) Copyright © 2009 International Association for the Study of Lung Cancer Terms and Conditions

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