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Beatriz Bellosillo
Moderator of
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ES12 - Lung Cancer Pathology in the Age of Genomics (ID 15)
- Event: WCLC 2019
- Type: Educational Session
- Track: Pathology
- Presentations: 5
- Now Available
- Moderators:Masayuki Noguchi, Beatriz Bellosillo
- Coordinates: 9/08/2019, 15:15 - 16:45, Toronto (1985)
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ES12.01 - Multiple Lung Nodules (Now Available) (ID 3218)
15:15 - 16:45 | Presenting Author(s): Sanja Dacic
- Abstract
- Presentation
Abstract
Advanced imaging techniques resulted in increased detection of multiple tumors of the lung. Distinguishing synchronous primary lung cancers from intrapulmonary metastases (separate nodules) is important because treatments are very different. In addition, patients with independent primary tumors are expected to have better prognosis. Staging of such tumors as independent primary tumors or intrapulmonary metastases is often challenging, particularly in squamous cell carcinomas. Martini and Melamed modified criteria were used as the main approach for many decades with the idea that morphology of metastases should match the primary tumor, while different morphology supports classification of tumors as unrelated separate primaries. The 8th edition of the AJCC staging of the lung cancer pretty much has replaced this classification by establishing a multidisciplinary approach to these tumors as a standard of care and by promoting the tools such as comprehensive histologic assessment, imaging studies and molecular characterization either by CGH or biomarker testing. Comprehensive histologic assessment is based on the 2015 WHO classification of lung cancers and includes determination of the main histologic tumor type, quantitative subtyping particularly of lung adenocarcinomas, and assessment of cytologic and stromal characteristics. This approach can be relatively easily applied in lung adenocarcinomas, while squamous cell carcinoma remains a great challenge. A recent study conducted by the IASLC Pathology committee showed a good agreement (κ score 0.60) among thoracic pathologists in the histologic assessment of independent primary tumors from intrapulmonary metastasis. Despite a good agreement, there were cases with split opinions supporting a need for ancillary studies.
Over the past decade many studies reported different molecular approaches to analysis of multiple lung tumor nodules including DNA microsatellite analysis, CGH/aCHG and most recently next generation sequencing. The data from published reports indicate a highly variable percentage of multifocal tumors identified as clonally related (up to 70%). Discrepancy between clinical and molecular classification of originally presumed cases of multiple primary lung cancers ranged in different series from 18% to 30%. Recent recommendations for routine molecular profiling of lung adenocarcinoma resulted in a widespread use of targeted mutational profiling for oncogenic mutations (i.e. EGFR, KRAS, BRAF etc) and gene rearrangements (i.e.ALK, ROS1) which results can be used in staging of multiple lung cancers. A different mutation profile in oncogenic mutations strongly indicates two separate primary tumors. However, the presence of a common driver mutation does not necessarily indicate tumors of similar origin. Therefore, limited molecular panels may not be sufficient in some cases. The detection of shared identical breakpoints by whole genome sequencing has been recently proposed as potentially more accurate and specific for lineage determination than the analysis of driver mutations alone. Also whole exome and whole genome sequencing approaches have been reported, but these assays may be technically challenging and turnaround time may not be suitable for routine clinical use.
References:
Girard N, Deshpande C, Lau C, Finley D, Rusch V, Pao W, et al. Comprehensive histologic assessment helps to differentiate multiple lung primary nonsmall cell carcinomas from metastases. Am J Surg Pathol. 2009;33(12):1752-64.
Detterbeck FC, Franklin WA, Nicholson AG, Girard N, Arenberg DA, Travis WD, 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):651-65
Nicholson AG, Torkko K, Viola P, Duhig E, Geisinger K, Borczuk AC, et al. Interobserver Variation among Pathologists ts and Refinement of Criteria in Distinguishing Separate Primary Tumors from Intrapulmonary Metastases in Lung. J Thorac Oncol. 2018;13(2):205-17.
Murphy SJ, Aubry MC, Harris FR, Halling GC, Johnson SH, Terra S, et al. Identification of independent primary tumors and intrapulmonary metastases using DNA rearrangements in non-small-cell lung cancer. J Clin Oncol. 2014;32(36):4050-8.
Liu Y, Zhang J, Li L et al. Genomic heterogeneity of multiple synchronous lung cancer. Nat Commun 2016 Oct 21;7:13200.
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ES12.02 - Invasive Mucinous Adenocarcinoma (Now Available) (ID 3219)
15:15 - 16:45 | Presenting Author(s): Yasushi YATABE
- Abstract
- Presentation
Abstract
Invasive mucinous adenocarcinoma (IMA) is a variant of adenocarcinoma defined by the current WHO classification of lung tumors.1 Although IMA used to be categorized into mucinous bronchioloalveolar carcinoma in most cases with the previous classification scheme,2 separation of this variant was based on unique clinical, radiological, pathological, and genetic characteristics as shown in the following table. Morphologically, IMAs consist of goblet and/or columnar tumor cells, which resemble normal intestinal and/or primitive gut epithelium. This subtype adenocarcinoma develops not only in the lung but also in every organ system, such as the ovary, pancreas, colorectum, and stomach, which are associated with the primitive gut tube in development. Interesting, all mucinous carcinomas have frequent KRAS mutations and quite similar immunohistochemical phenotype, including expression of CK20, CDX2, HNF4a, and villin. The strong correlation between KRAS mutations and heavy smokers is known, but IMA is not such a case. Indeed, TP53 mutations, which is also associated more with smokers, are quite rare in IMAs. IMA commonly develops in the peripheral lung parenchyma, but there are no normal counterpart cells. Recently, inactivating mutations of TTF1/NKX2.1 have been reported in IMA.3, 4 This alteration can repress TTF1 function, resulting in gastrointestinal differentiation. TTF1-depletion using KRASG12D-transgenic mice induced mucinous tumors, which shared a morphological and phenotypical resemblance to IMA, including columnar tumor cells with goblet cell features and HNF4a expression.5, 6 Because the other mechanisms of TTF1 impairment, the molecular pathway of IMA could be summarized in figure 1. However, it remains unclear why KRAS is selectively mutated in this subtype, and what induce TTF1 mutations.
References
1. Travis WD, Brambilla E, Burke A, et al. WHO Classification of Tumours of the Lung, Pleura, Thymus and Heart. Lyon: International Agency for Research on Cancer; 2015.
2. Travis WD, Brambilla E, Noguchi M, et al. International Association for the study of lung cancer/American thoracic society/European respiratory society international multidisciplinary classification of lung adenocarcinoma. J Thorac Oncol 2011;6:244-285.
3. Matsubara D, Soda M, Yoshimoto T, et al. Inactivating mutations and hypermethylation of the NKX2-1/TTF-1 gene in non-terminal respiratory unit-type lung adenocarcinomas. Cancer science 2017;108:1888-1896.
4. Hwang DH, Sholl LM, Rojas-Rudilla V, et al. KRAS and NKX2-1 Mutations in Invasive Mucinous Adenocarcinoma of the Lung. J Thorac Oncol 2016;11:496-503.
5. Maeda Y, Tsuchiya T, Hao H, et al. Kras(G12D) and Nkx2-1 haploinsufficiency induce mucinous adenocarcinoma of the lung. J Clin Invest 2012;122:4388-4400.
6. Snyder EL, Watanabe H, Magendantz M, et al. Nkx2-1 represses a latent gastric differentiation program in lung adenocarcinoma. Mol Cell 2013;50:185-199.Table 1 Difference between IMA and AIS/MIA/LPA1
Table 1 Difference between IMA and AIS/MIA/LPA Invasive Mucinous ADC
AIS/MIA/LPA
Female
~60%
~70%
Smoker
~45%
~46%
Clinical symptoms
Mucinous sputa
Mostly no symptom
Radiographic appearance
Majority consolidation; Air-bronchogram
Majority ground-glass attenuation
Frequent multifocal & multi-lobar presentation
Cell type
Mucin-filled, columnar and/or goblet
Type II pneumocyte &/or Clara cell
Phenotype
CK7
Mostly positive (90%)
Positive (~95%)
CK20
Positive (~54%)
Negative (<5%)
TTF1
Mostly negative (<10%)
Positive (~65%)
CDX2
Possible to be positive
Negative
Genotype
KRAS
Frequent (~75%)
Some (~15%)
EGFR
Almost none (<5%)
Frequent (~45%)
AIS, adenocarcinoma in situ; MIA, minimally invasive adenocarcinoma; LPA, lepidic predominant adenocarcinoma
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ES12.03 - Tumor Heterogeneity (Now Available) (ID 3220)
15:15 - 16:45 | Presenting Author(s): Wendy Cooper
- Abstract
- Presentation
Abstract
While intertumoral heterogeneity is well recognised in many solid tumours including NSCLC, intratumoral heterogeneity has only recently gained attention. Heterogeneity of tumor morphology, protein expression, gene expression, epigenetic or genetic alterations has the potential to impact optimal biopsy strategies, diagnostic assessment, treatment decisions and clinical outcome.
Sequencing of NSCLC from multiple sites of disease shows frequent evidence of intratumoral heterogeneity in terms of genetic mutations, translocations and copy number alterations, although not to the same extent as seen in other tumor types, such as clear cell renal cell carcinoma. NSCLC studies have demonstrated a common pattern of intratumoral heterogeneity with main clonal driver mutations and branched evolutionary acquired mutations. Of clinical relevance, mutations in known lung cancer driver oncogenes (such as EGFR, BRAF and MET) are generally present in all tumor regions in keeping with early evolutionary events. This finding is consistent with the high response rates to tyrosine kinase inhibitors that target these genetic alterations, across multiple sites of disease.
Later subclonal driver mutations are found commonly in NSCLC and include alterations in genes such as PIK3CA and NF1. Metastatic sites can exhibit mutational profiles closely related to specific spatial regions of the primary tumor demonstrating that subclones can determine the course of systemic disease resulting in subclonal diversification. Clonal evolution is driven by multiple factors including selective pressure from targeted therapies and adaptive mechanisms due to interaction with immune cells and the microenvironment. Treatment resistance can occur due to acquisition and/or selection of clones and contributes to temporal heterogeneity. The hierarchy of genetic alterations can be used to trace clonal intratumoral heterogeneity although adequate sequencing depth is required to accurately assess for subclonal mutations.
Reassuringly, sequencing of a single region of a tumor should be sufficient to identify known targetable driver mutations as they generally occur early in the evolutionary course of the disease. The exact clinical significance of various subclonal mutations is less well understood. Intratumoral heterogeneity can potentially lead to sampling errors when single sites of disease are sampled for mutational events that may only exist in another metastatic site. For this reason, testing for genetic markers of treatment resistance may be more appropriately performed on circulating tumour DNA as the ctDNA may derive from multiple metastatic deposits, although lower sensitivity limits the effectiveness of this approach. Liquid biopsy approaches also have the advantage of providing a contemporaneous sample, more likely to reflect impact of most recent therapy.
Further investigation of spatial and temporal tumoral heterogeneity by comprehensive deep sequencing of multiple spatially discrete sites of disease at different time points may assist in understanding the complexity of intratumoral heterogeneity and could potentially impact optimal biopsy and treatment strategies, particularly when assessing for drug resistance.
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ES12.04 - Machine Learning and Integrative Multi-Omics Analysis Identify Novel Molecular Groups of Lung Neuroendocrine Tumors (Now Available) (ID 3221)
15:15 - 16:45 | Presenting Author(s): Lynnette Fernandez-Cuesta
- Abstract
- Presentation
Abstract
This work is part of the lungNENomics project, a large multi-omic and multidisciplinary effort, built up on our previous published work (1-4). The lungNENomics project aims at the molecular characterization of rare lung neuroendocrine neoplasms through the integration of whole-genome sequencing, transcriptome sequencing and methylation data, as well as the correlation with epidemiological and clinical information, and taking advantage of unique biorepositories, advanced computational approaches, and state-of-the-art in vitro models. The talk would provide an overview of the global lungNENomics project, as well as presenting the identification of a novel molecular entity.The worldwide incidence of pulmonary carcinoids is increasing, but little is known about their molecular characteristics. Through machine learning and multi-omics factor analysis, we compared and contrasted the genomic profiles of 116 pulmonary carcinoids (including 35 atypical), 75 large-cell neuroendocrine carcinomas (LCNEC), and 66 small-cell lung cancers. Integrative analyses on 257 lung neuroendocrine neoplasms stratified atypical carcinoids into two prognostic groups with a 10-year overall survival of 88% and 27%, respectively. We identified therapeutically relevant molecular groups of pulmonary carcinoids, suggesting DLL3 and the immune system as candidate therapeutic targets; we confirmed the value of OTP expression levels for the prognosis and diagnosis of these diseases, and we unveiled the group of supra-carcinoids. This group comprises samples with carcinoid-like morphology yet the molecular and clinical features of the deadly LCNEC, further supporting the previously proposed molecular link between the low- and high-grade lung neuroendocrine neoplasms.
Funding: U.S. National Institutes of Health (NIH), French National Cancer Institute (INCa), French Ligue Nationale contre le Cancer (LNCC), and the Dutch Cancer Society (DCS)
Website: rarecancersgenomics.com
Twitter: @CancersRare
References
1. Peifer M*, Fernández-Cuesta L*, Sos ML, George J, Seidel D, Kasper LH, Plenker D, et al. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet. 2012 PMID: 22941188
2. Fernandez-Cuesta L, Peifer M, Lu X, Sun R, Ozretić L, Seidal D, Zander T, et al. Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids. Nat Commun. 2014 PMID: 24670920
3. George J*, Walter V, Peifer M, Alexandrov LB, Seidel D, Leenders F, Maas L, Müller C, Dahmen I, Delhomme TM, Ardin M, Leblay N, Byrnes G, Sun R, De Reynies A, McLeer-Florin A, Bosco G, Malchers F, Menon R, Altmüller J, Becker C, Nürnberg P, Achter V, Lang U, Schneider PM, Bogus M, Soloway MG, Wilkerson MD, Cun Y, McKay JD, Moro-Sibilot D, Brambilla CG, Lantuejoul S, Lemaitre N, Soltermann A, Weder W, Tischler V, Brustugun OT, Lund-Iversen M, Helland Å, Solberg S, Ansén S, Wright G, Solomon B, Roz L, Pastorino U, Petersen I, Clement JH, Sänger J, Wolf J, Vingron M, Zander T, Perner S, Travis WD, Haas SA, Olivier M, Foll M, Büttner R, Hayes DN, Brambilla E, Fernandez-Cuesta L*, Thomas RK. Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors. Nat Commun. 2018 PMID: 29535388
4. Derks JL, Leblay N, Lantuejoul S, Dingemans AC, Speel EM, Fernandez-Cuesta L. New Insights into the Molecular Characteristics of Pulmonary Carcinoids and Large Cell Neuroendocrine Carcinomas, and the Impact on Their Clinical Management. J Thorac Oncol. 2018 Review. PMID: 29454048
5. Alcala N*, Leblay N*, Gabriel AAG*, Mangiante L, Hervas D, Giffon T, Sertier AS, Ferrari A, Derks J, Ghantous A, Delhomme TM, Chabrier A, Cuenin C, Abedi-Ardekani B, Boland A, Olaso R, Meyer V, Altmuller J, Le Calvez-Kelm F, Durand G, Voegele C, Boyault S, Moonen L, Lemaitre N, Lorimier P, Toffart AC, Soltermann A, Clement JH, Saenger J, Field JK, Brevet M, Blanc-Fournier C, Galateau-Salle F, Le Stang N, Russell PA, Wright G, Sozzi G, Pastorino U, Lacomme S, Vignaud JM, Hofman V, Hofman P, Brustugun OT, Lund-Iversen M, Thomas de Montpreville V, Muscarella LA, Graziano P, Popper H, Stojsic J, Deleuze JF, Herceg Z, Viari A, Nuernberg P, Pelosi G, Dingemans AMC, Milione M, Roz L, Brcic L, Volante M, Papotti MG, Caux C, Sandoval J, Hernandez-Vargas H, Brambilla E, Speel EJM, Girard N, Lantuejoul S, McKay JD, Foll M#, Fernandez-Cuesta L#. Integrative and comparative genomic analyses identify clinically relevant groups of pulmonary carcinoids and unveil the supra-carcinoids. Nat Commun. In Press
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ES12.05 - Impact of STAS in Lung Cancer Staging (Now Available) (ID 3222)
15:15 - 16:45 | Presenting Author(s): William D. Travis | Author(s): Rania G. Aly, Takashi Eguchi, Natasha Rekhtman, Yukako Yagi, Prasad S Adusumilli
- Abstract
- Presentation
Abstract
Spread through air spaces (STAS) is an established histologic marker of poor prognosis found in 15-60% of lung cancers. The association with poor prognosis is supported by data from over 3500 patients from multiple multidisciplinary investigative groups worldwide. This prognostic significance has been demonstrated in all major types of lung cancer including adenocarcinoma,1 squamous cell carcinoma,2 small cell carcinoma,3 large cell neuroendocrine carcinoma,3, atypical carcinoid3 and pleomorphic carcinoma.4, 5
As this large volume of clinical data has accumulated some important issues that have arisen. 1) Importance of processing, 2) Role in Staging? 3) Limited resection vs lobectomy and 4) Frozen section.
Criteria for STAS
The original definition of STAS by Kadota et al and the 2015 WHO consisted of tumor cells within the first alveolar air spaces in the lung parenchyma beyond the edge of the main tumor. In adenocarcinoma it can occur as one of three morphologic patterns including 1) micropapillary structures within air spaces; 2) solid nests or tumor islands and 3) scattered discohesive single cells.1, 6 In a recent paper we also proposed to require the presence of more than a single STAS cluster.3 The solid nest pattern is characteristic in other lung cancer histologies such as squamous cell carcinoma and neuroendocrine tumors. 3-dimensional studies with serial histologic sectioning and microCT whole block imaging suggest that there may be two mechanisms of spread into the adjacent lung: 1) detachment, migration through air spaces and reattachment with vessel co-option and 2) tumor islands of continuous tumor spread into adjacent air spaces.
An important component of the diagnostic criteria is the distinction from artifacts: 1) mechanically induced tumor floaters that are randomly situated often at the edge of the tissue section or out of the plane of section; 2) jagged edges of tumor cell clusters suggesting fragmentation or edges of a knife cut during specimen processing; 3) isolated tumor clusters at a distance from the tumor rather than spreading in a continuous manner from the tumor edge and 4) linear strips of cells lifted off alveolar walls.
Importance of Processing
To assess for STAS histologic sections need to be taken in such a way to maximize the interface between the tumor and adjacent non-neoplastic lung parenchyma. For example, sections of subpleural tumors that maximize assessment of the visceral pleura or the interface with dense fibrotic scars or post-obstructive organizing are not well suited for assessment of STAS. This applies to both frozen and permanent sections.
Role of STAS in Staging?
Although the prognostic significance of STAS, has led some to suggest it might be included as a factor in staging,7, 8 there is insufficient data at this time to make such a recommendation. Tumor size should continue to be measured according to the gross and/or microscopically recognized edge of lung cancers rather than according to the maximum distance of furthest STAS. Although vascular (V) and lymphatic (L) invasion are recognized in TNM staging, only visceral pleural invasion (VPI) is officially incorporated as a T-factor in the 8th Edition. STAS is regarded as a sign of invasion similar to V, L and VPI, however, more data is needed before introducing this as a T-factor for staging.
Limited resection vs lobectomy
Evidence is accumulating that indicates an increased risk of recurrence and worse survival associated with STAS positive tumors treated by limited resection compared to lobectomy.5, 9
Role of Frozen Sections in Assessing STAS
There is limited data evaluating pathologist’s ability to recognize STAS in frozen section. Eguchi et al found the sensitivity and specificity of frozen section for prediction of STAS were 71% and 92%. respectively and interrater reliability across 5 pathologists was 0.67.9
Walts AE et al studied frozen section for evaluation of STAS and recommended that current evidence did not warrant frozen section evaluation for STAS.10 However, frozen section sensitivity to detect STAS positivity was 50%, with a 100% positive predictive value and an 8% negative predictive value. These studies suggest if a pathologist sees STAS on a frozen section there is a 92-100% likelihood it will be present on permanent sections. Both studies were retrospective so attention was not always given to including the tumor edge and adjacent lung. More studies are needed to evaluate the potential role of frozen section in detecting STAS and guiding intraoperative decisions by surgeons.
REFERENCES
1. Kadota K, et al. Tumor Spread through Air Spaces is an Important Pattern of Invasion and Impacts the Frequency and Location of Recurrences after Limited Resection for Small Stage I Lung Adenocarcinomas. J Thorac Oncol 2015;10:806-14.
2. Lu S, et al. Spread through Air Spaces (STAS) Is an Independent Predictor of Recurrence and Lung Cancer-Specific Death in Squamous Cell Carcinoma. J Thorac Oncol 2017;12:223-34.
3. Aly RG, et al. Spread Through Air Spaces (STAS) Is Prognostic in Atypical Carcinoid, Large Cell Neuroendocrine Carcinoma, and Small Cell Carcinoma of the Lung. J Thorac Oncol 2019.
4. Yokoyama S, et al. Tumor Spread Through Air Spaces Identifies a Distinct Subgroup With Poor Prognosis in Surgically Resected Lung Pleomorphic Carcinoma. Chest 2018;154:838-47.
5. Liu H, et al. Prognostic Impact of Tumor Spread Through Air Spaces in Non-small Cell Lung Cancers: a Meta-Analysis Including 3564 Patients. Pathol Oncol Res 2019.
6. Travis WD, et al. WHO Classification of Tumours of the Lung, Pleura, Thymus and Heart. 4th ed. Lyon: International Agency for Research on Cancer; 2015.
7. Uruga H, et al. Will spread through air spaces be a staging parameter in lung cancer? Journal of thoracic disease 2018;10:593-6.
8. Dai C, et al. Tumor Spread through Air Spaces Affects the Recurrence and Overall Survival in Patients with Lung Adenocarcinoma >2 to 3 cm. J Thorac Oncol 2017;12:1052-60.
9. Eguchi T, et al. Lobectomy Is Associated with Better Outcomes than Sublobar Resection in Spread through Air Spaces (STAS)-Positive T1 Lung Adenocarcinoma: A Propensity Score-Matched Analysis. J Thorac Oncol 2019;14:87-98.
10. Walts AE, et al. Current Evidence Does Not Warrant Frozen Section Evaluation for the Presence of Tumor Spread Through Alveolar Spaces. Arch Pathol Lab Med 2018;142:59-63.
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Author of
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P1.09 - Pathology (ID 173)
- Event: WCLC 2019
- Type: Poster Viewing in the Exhibit Hall
- Track: Pathology
- Presentations: 1
- Moderators:
- Coordinates: 9/08/2019, 09:45 - 18:00, Exhibit Hall
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P1.09-32 - Concurrent Genomic Alterations in ALK-Rearranged Non-Small Cell Lung Cancer Patients (ID 2463)
09:45 - 18:00 | Author(s): Beatriz Bellosillo
- Abstract
Background
Recent progress in genomic analysis using next-generation sequencing (NGS) has enabled the comprehensive detection of targetable alterations in non-small cell lung cancer (NSCLC) patients. As the detection of ALK gene fusions is being established by NGS, identification of concurrent alterations will lead to better characterization of the molecular landscape of ALK-rearranged patients.
Method
Thirty-one NSCLC samples with known ALK status (18 positive and 13 negative) tested in our Institution using FISH, IHC, and NGS (Oncomine Focus Assay, ThermoFisher Scientific) were further evaluated by an expanded NGS gene panel (PGDx elio™ tissue complete assay (under developement), Personal Genome Diagnostics). This NGS panel comprises 500+ genes and screens for clinically relevant genomic alterations (single base substitutions/insertion and deletions, fusion genes and copy number variations), and provides TMB scores (expressed as mutations per megabase, exome equivalent). Statistical associations were assessed using Pearson’s χ2 and Mann-Whitney U test.
Result
ALK positive patients were 50% female with a median age of 59 years old and 54% of them never smokers. For the ALK negative cohort, young patients without any known driver alterations were selected: 69% male with a median age of 54 years old and 92% of them current smokers. Of the 18 ALK-positive cases identified, five were considered non-evaluable for expanded genomic analysis due to insufficient sequencing coverage (yield below minimum suggested DNA input). ALK fusions were detected by all techniques in the 13 ALK-positive cases available for analysis. EML4(13)-ALK(20) was the most prevalent gene fusion detected in seven out of 13 cases (54%). Remarkably, we detected a rare ALK gene fusion that has not been yet described: IRF2BP2(1)-ALK(20). The concurrent alterations identified by expanded genomic analysis are shown in an OncoPrint figure comparing both groups. The most frequent concomitant alteration was TP53 mutation: 62% in ALK-positive and 69% ALK-negative (p> 0.05). Regarding gene amplifications, we identified three ALK-positive cases with copy number alterations of which we highlight MYC in two of these cases. Interestingly, a high TMB was significantly associated with ALK-negative cases with a median of 19.9 mut/Mb compared to 7.0 mut/Mb in ALK-positive (p= 0.001).
Conclusion
We have studied the presence of ALK fusion genes with a novel NGS panel that showed excellent correlation with standard techniques. ALK fusions can be interpreted as early strong drivers to carcinogenesis due to the low frequency of concurrent alterations. It remains to determine the clinical impact of these alterations in larger series.
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P2.09 - Pathology (ID 174)
- Event: WCLC 2019
- Type: Poster Viewing in the Exhibit Hall
- Track: Pathology
- Presentations: 1
- Moderators:
- Coordinates: 9/09/2019, 10:15 - 18:15, Exhibit Hall
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P2.09-34 - Next-Generation Sequencing Implementation in Non-Small Cell Lung Cancer Molecular Diagnosis (ID 2337)
10:15 - 18:15 | Author(s): Beatriz Bellosillo
- Abstract
Background
Currently, all patients with advanced non-small cell lung cancer (NSCLC) require EGFR, ALK, ROS1 and BRAF molecular characterization. Next-generation sequencing (NGS) allows the simultaneous analysis of these biomarkers optimizing both the sample and the economic cost. The purpose of this study was to compare NGS results with those obtained using single gene analysis in a prospective clinical setting.
Method
During 12 months, 50 paraffin-embedded samples from patients with advanced NSCLC (46 adenocarcinomas and four NSCLC-NOS) were prospectively analyzed in our institution. Molecular characterization was carried out using the NGS Oncomine Solid Tumor DNA and Fusion Transcript Kits for hotspot mutations and gene fusions (Thermo Fisher) and results were compared with Therascreen EGFR RGQ PCR Kit (Qiagen), and Vysis ALK and ROS1 Break Apart FISH Probe Kits (Abbott Molecular, ZytoVision).
Result
All samples studied by NGS for hotspot mutations were assessable and we detected pathogenic alterations in 90% (n= 45). Regarding targetable alterations, we identified nine patients harboring EGFR mutations (18%), in agreement with real-time PCR (except for one case which had an exon 20 insertion not interrogated by Therascreen), and one patient with a BRAF mutation (2%). We highlight the presence of TP53 mutations in 27 cases (54%), KRAS in 16 cases (32%) and STK11 in three cases (6%). TP53 mutations were concomitant with other alterations in 70% of the cases (n= 19), without being significantly associated with any of them. Gene fusion analysis by NGS was assessable in 80% of the samples (n= 40): six samples had insufficient RNA quality and four had not enough material. We detected only one case with an ALK rearrangement (2%), confirmed by FISH.
Conclusion
NGS technology for NSCLC molecular diagnosis could be considered as the initial screening test although the success rate in gene fusion assessment is closely related to RNA paraffin-embedded evaluation. NGS also detected other genomic alterations that allowed referral of patients to clinical trials.
