Immunohistochemistry of Pulmonary Biomarkers: A Perspective From Members of the Pulmonary Pathology Society

The use of immunohistochemistry for the determination of pulmonary carcinoma biomarkers is a well-established and powerful technique. Immunohistochemisty is readily available in pathology laboratories, is relatively easy to perform and assess, can provide clinically meaningful results very quickly, and is relatively inexpensive. Pulmonary predictive biomarkers provide results essential for timely and accurate therapeutic decision making; for patients with metastatic non-small cell lung cancer, predictive immunohistochemistry includes ALK and programmed death ligand-1 (PD-L1) (ROS1, EGFR in Europe) testing. Handling along proper methodologic lines is needed to ensure patients receive the most accurate and representative test outcomes.

Use of Oncogenic Driver Mutations in Staging of Multiple Primary Lung Carcinomas: A Single-Center Experience

OBJECTIVE

The staging of multiple pulmonary adenocarcinomas requires the distinction of intrapulmonary metastasis (IPM) from multiple primary lung cancers (MPLCs). This can be challenging in some patients, and the addition of data from oncogenic driver mutations in these tumors may be helpful in this determination.

METHODS

As a proof of principle, molecular driver results from primary tumors and their metastases in 45 patients were compared (cohort 1). Then, 69 patients with a total of 154 synchronous or metachronous lung carcinomas were identified, and the pathologic findings were compared with oncogenic driver mutation. Each patient was assigned a highest potential T or M category on the basis of clinical, histopathologic, and molecular findings (cohort 2).

RESULTS

The concordance rate of EGFR, KRAS, BRAF, and ALK receptor tyrosine kinase gene (ALK) mutations was 96% in cohort 1. In cohort 2, 36% of multiple same-lobe nodules were MPLCs, 40% were IPM, and 24% were noninformative by molecular findings. Of nodules with multiple lobe involvement, 81.5% were MPLCs and 7.4% were IPM, with 11% noninformative. Of metachronous tumors, 52.9% were MPLCs. Overall survival was 100% at 2 years, 95% at 3 years, and 80% at 4 years in patients with available follow-up.

CONCLUSIONS

Oncogenic driver mutations are concordant between primary tumors and metastasis. The largest proportion of MPLCs was seen in tumors of multiple lobes, but with a substantial proportion of MPLCs among single-lobe nodules and with metachronous tumors. Overall survival was higher than expected for the respective highest T or M category, which is in support of the high frequency of MPLC.

Genome-wide association study of subclinical interstitial lung disease in MESA

Background

We conducted a genome-wide association study (GWAS) of subclinical interstitial lung disease (ILD), defined as high attenuation areas (HAA) on CT, in the population-based Multi-Ethnic Study of Atherosclerosis Study.

Methods

We measured the percentage of high attenuation areas (HAA) in the lung fields on cardiac CT scan defined as voxels with CT attenuation values between -600 and -250 HU. Genetic analyses were performed in MESA combined across race/ethnic groups: non-Hispanic White (n = 2,434), African American (n = 2,470), Hispanic (n = 2,065) and Chinese (n = 702), as well as stratified by race/ethnicity.

Results

Among 7,671 participants, regions at genome-wide significance were identified for basilar peel-core ratio of HAA in FLJ35282 downstream of ANRIL (rs7852363, P = 2.1x10⁻⁹) and within introns of SNAI3-AS1 (rs140142658, P = 9.6x10⁻⁹) and D21S2088E (rs3079677, P = 2.3x10⁻⁸). Within race/ethnic groups, 18 additional loci were identified at genome-wide significance, including genes related to development (FOXP4), cell adhesion (ALCAM) and glycosylation (GNPDA2, GYPC, GFPT1 and FUT10). Among these loci, SNP rs6844387 near GNPDA2 demonstrated nominal evidence of replication in analysis of n = 1,959 participants from the Framingham Heart Study (P = 0.029). FOXP4 region SNP rs2894439 demonstrated evidence of validation in analysis of n = 228 White ILD cases from the Columbia ILD Study compared to race/ethnicity-matched controls from MESA (one-sided P = 0.007). In lung tissue from 15 adults with idiopathic pulmonary fibrosis compared to 15 adults without lung disease. ANRIL (P = 0.001), ALCAM (P = 0.03) and FOXP4 (P = 0.046) were differentially expressed.

Conclusions

Our results suggest novel roles for protein glycosylation and cell cycle disinhibition by long non-coding RNA in the pathogenesis of ILD.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-017-0581-2) contains supplementary material, which is available to authorized users.

Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth

Targeted cancer therapies, which act on specific cancer-associated molecular targets, are predominantly inhibitors of oncogenic kinases. While these drugs have achieved some clinical success, the inactivation of kinase signaling via stimulation of endogenous phosphatases has received minimal attention as an alternative targeted approach. Here, we have demonstrated that activation of the tumor suppressor protein phosphatase 2A (PP2A), a negative regulator of multiple oncogenic signaling proteins, is a promising therapeutic approach for the treatment of cancers. Our group previously developed a series of orally bioavailable small molecule activators of PP2A, termed SMAPs. We now report that SMAP treatment inhibited the growth of KRAS-mutant lung cancers in mouse xenografts and transgenic models. Mechanistically, we found that SMAPs act by binding to the PP2A Aα scaffold subunit to drive conformational changes in PP2A. These results show that PP2A can be activated in cancer cells to inhibit proliferation. Our strategy of reactivating endogenous PP2A may be applicable to the treatment of other diseases and represents an advancement toward the development of small molecule activators of tumor suppressor proteins.

Prognostic considerations of the new World Health Organization classification of lung adenocarcinoma

The 2015 World Health Organization (WHO) lung adenocarcinoma classification divides tumours into categories of indolent pre-invasive, minimally invasive and predominantly lepidic and, by examining predominant patterns of invasion, allows for further stratification into intermediate and high-grade tumours. The impact of the 2015 classification on prognosis was reviewed by a PubMed search for search terms "adenocarcinoma", "lung pathology" and "prognosis" and relevant publications reviewed. These were sorted for data on stage and survival as impacted by histological classification, and survival studies were separated into all stage versus stage 1 studies. Predictive aspects of histological classification were also examined, but molecular correlates were not. The separation of adenocarcinoma in situ and minimally invasive adenocarcinoma from invasive subtypes as distinct prognostic entities and the prognostic significance, for disease specific and overall survival for low- and high-grade categories, are discussed. The impact on stage at presentation including risk of node metastasis by histology is examined, as well as histology in relation to recurrence after surgery. Early data with regard to the value of predominant histology in the prediction of chemotherapy response will also be explored.

The Use of Immunohistochemistry Improves the Diagnosis of Small Cell Lung Cancer and Its Differential Diagnosis. An International Reproducibility Study in a Demanding Set of Cases

INTRODUCTION

The current WHO classification of lung cancer states that a diagnosis of SCLC can be reliably made on routine histological and cytological grounds but immunohistochemistry (IHC) may be required, particularly (1) in cases in which histologic features are equivocal and (2) in cases in which the pathologist wants to increase confidence in diagnosis. However, reproducibility studies based on hematoxylin and eosin-stained slides alone for SCLC versus large cell neuroendocrine carcinoma (LCNEC) have shown pairwise κ scores ranging from 0.35 to 0.81. This study examines whether judicious use of IHC improves diagnostic reproducibility for SCLC.

METHODS

Nineteen lung pathologists studied interactive digital images of 79 tumors, predominantly neuroendocrine lung tumors. Images of resection and biopsy specimens were used to make diagnoses solely on the basis of morphologic features (level 1), morphologic features along with requested IHC staining results (level 2), and all available IHC staining results (level 3).

RESULTS

For the 19 pathologists reading all 79 cases, the rate of agreement for level 1 was 64.7%, and it increased to 73.2% and 77.5% in levels 2 and 3, respectively. With IHC, κ scores for four tumor categories (SCLC, LCNEC, carcinoid tumors, and other) increased in resection samples from 0.43 to 0.60 and in biopsy specimens from 0.43 to 0.64.

CONCLUSIONS

Diagnosis using hematoxylin and eosin staining alone showeds moderate agreement among pathologists in tumors with neuroendocrine morphology, but agreement improved to good in most cases with the judicious use of IHC, especially in the diagnosis of SCLC. An approach for IHC in the differential diagnosis of SCLC is provided.

Challenges of Frozen Section in Thoracic Pathology: Lepidic Lesions, Limited Resections, and Margins

CONTEXT

- The use of frozen section in thoracic pathology includes assessment of peripheral lung lesions with lepidic pattern, with greater emphasis on evaluating lung-sparing resections and margin assessment.

OBJECTIVE

- To review pitfalls of frozen section in thoracic pathology; in this setting, reduction of false-positive and false-negative diagnosis in lesion identification and margin assessment is critical.

DATA SOURCES

- PubMed search of frozen section lung pathology yielded specific references related to the use of frozen section in the identification of lepidic lesions and the clinical recommendation for margin distance.

CONCLUSIONS

- Frozen section diagnosis is overall accurate in assessment of lepidic lesions. Pitfalls include rare benign mimickers and more common reactive lesions. Standard approaches to gross assessment and margin measurement require further research with increasing use of lung-sparing resections.

An analysis of the relationship between metastases and cachexia in lung cancer patients

Weight loss and hematogenous metastases are poor prognosis factors in lung cancer patients that can but do not necessarily co‐occur. We retrospectively investigated the clinical association between cachexia, tumor characteristics (such as metastatic burden and mutational status), and treatment in lung cancer patients. The medical records of 394 lung cancer patients from two institutions (Columbia University, USA and Tohoku University, Japan) were reviewed. Information collected included the presence of cachexia, histologic subtype, tumor stage, number of metastases, mutation status, treatment, and survival. Descriptive statistics were performed. Only stage IV patients exhibited >5% weight loss (0.8%, 2.2%, 3.6%, and 5.1%, for stages I to IV; P = 0.0001). Patients with metastases developed cachexia more often than patients without metastases independent of treatment (6.0% and 7.1% weight loss in patients with metastases vs. 2.5% and 2.0% in patients without metastases, before [P = 0.0001] and after [P < 0.0001] treatment, respectively). The change in number of metastatic sites over time correlated with increasing weight loss (5.2%, 10.6%, 13.4%, and 13.4%, for an increase of 0, 1, 2, and ≥3 metastatic sites, from initial diagnosis to the endpoint; P < 0.0001). Patients with cachexia had worse survival than patients without cachexia (hazard ratio, 2.94; 95% confidence interval, 2.08–4.16; P < 0.0001). Tumors with mutated KRAS were associated with an increased risk of weight loss (11.4% weight loss in patients with mutated KRAS vs. 6.0% in patients with wild‐type KRAS; P = 0.0011). Our findings suggest that the capabilities of lung cancer to metastasize and cause cachexia might be linked intrinsically and are independent of treatments administered. KRAS‐mutated tumors were more commonly associated with cachexia.

Dataset for Reporting of Malignant Mesothelioma of the Pleura or Peritoneum: Recommendations From the International Collaboration on Cancer Reporting (ICCR)

CONTEXT

-The International Collaboration on Cancer Reporting is a not-for-profit organization formed by the Royal Colleges of Pathologists of Australasia and the United Kingdom; the College of American Pathologists; the Canadian Association of Pathologists-Association Canadienne des Pathologists, in association with the Canadian Partnership Against Cancer; and the European Society of Pathology. Its goal is to produce common, internationally agreed upon, evidence-based datasets for use throughout the world.

OBJECTIVE

-To describe a dataset developed by the Expert Panel of the International Collaboration on Cancer Reporting for reporting malignant mesothelioma of both the pleura and peritoneum. The dataset is composed of "required" (mandatory) and "recommended" (nonmandatory) elements.

DESIGN

-Based on a review of the most recent evidence and supported by explanatory commentary.

RESULTS

-Eight required elements and 7 recommended elements were agreed upon by the Expert Panel to represent the essential information for reporting malignant mesothelioma of the pleura and peritoneum.

CONCLUSIONS

-In time, the widespread use of an internationally agreed upon, structured, pathology dataset for mesothelioma will lead not only to improved patient management but also provide valuable data for research and international benchmarks.

Genome-wide analysis of abdominal and pleural malignant mesothelioma with DNA arrays reveals both common and distinct regions of copy number alteration

Malignant mesothelioma (MM) is an aggressive tumor arising from mesothelial linings of the serosal cavities. Pleural space is the most common site, accounting for about 80% of cases, while peritoneum makes up the majority of the remaining 20%. While histologically similar, tumors from these sites are epidemiologically and clinically distinct and their attribution to asbestos exposure differs. We compared DNA array-based findings from 48 epithelioid peritoneal MMs and 41 epithelioid pleural MMs to identify similarities and differences in copy number alterations (CNAs). Losses in 3p (BAP1 gene), 9p (CDKN2A) and 22q (NF2) were seen in tumors from both tumor sites, although CDKN2A and NF2 losses were seen at a higher rate in pleural disease (p<0.01). Overall, regions of copy number gain were more common in peritoneal MM, whereas losses were more common in pleural MM, with regions of loss containing known tumor suppressor genes and regions of gain encompassing genes encoding receptor tyrosine kinase pathway members. Cases with known asbestos causation (n = 32 ) were compared with those linked to radiation exposure (n = 9 ). Deletions in 6q, 14q, 17p and 22q, and gain of 17q were seen in asbestos-associated but not radiation-related cases. As reported in post-radiation sarcoma, gains outnumbered losses in radiation-associated MM. The patterns of genomic imbalances suggest overlapping and distinct molecular pathways in MM of the pleura and peritoneum, and that differences in causation (i.e., asbestos vs. radiation) may account for some of these site-dependent differences.

Programmed Death Ligand-1 Immunohistochemistry— A New Challenge for Pathologists: A Perspective From Members of the Pulmonary Pathology Society

The binding of programmed death ligand-1 and ligand-2 (PD-L1 and PD-L2) to PD-1 blocks T-cell–mediated immune response to tumor. Antibodies that target programmed death receptor-1 (PD-1) will block the ligand-receptor interface, thereby allowing T cells to attack the tumor and increase antitumor immune response. In clinical trials, PD-1 inhibitors have been associated with an approximately 20% overall response rate in unselected patients with non–small cell lung cancer, with sustained tumor response in a subset of patients treated by these immune checkpoint inhibitors. Facing a proliferation of PD-L1 immunohistochemistry clones, staining platforms, and scoring criteria, the pathologist must decide on the feasibility of introducing a newly approved companion diagnostic assay that may require purchase not only of a specific antibody kit but of a particular staining platform. Given the likely reality that clinical practice may, in the near future, demand access to 4 different PD-L1 antibodies coupled with different immunohistochemistry platforms, laboratories will be challenged with deciding among this variety of testing methods, each with its own potential benefits. Another immediate challenge to PD-L1 testing in lung cancer patients is that of access to adequate tumor tissue, given that non–small cell lung cancer samples are often extremely limited in size. With PD-L1 testing it has become clear that the historically used US regulatory approach of one assay–one drug will not be sustainable. One evolving concept is that of complementary diagnostics, a novel regulatory pathway initiated by the US Food and Drug Administration, which is distinct from companion diagnostics in that it may present additional flexibility. Although pathologists need to face the practical reality that oncologists will be asking regularly for the PD-L1 immunohistochemistry status of their patients' tumors, we should also keep in mind that there may be room for improvement of biomarkers for immunotherapy response. The field is rich with opportunities for investigation into biomarkers of immunotherapy response, particularly in the form of collaborative, multidisciplinary studies that incorporate oncologists, pathologists, and basic scientists. Pathologists must take the lead in the rational incorporation of these biomarkers into clinical practice.

PD-L1 and Lung Cancer: The Era of Precision-ish Medicine?

The success of immune checkpoint inhibitor therapy in lung cancer, both in squamous and nonsquamous non-small cell carcinoma, has led to US Food and Drug Administration approval for 2 medications that have as part of their prescribing information an associated immunohistochemistry-based companion or complementary diagnostic test for programmed death ligand-1 (PD-L1). The intense interest in drug development in this area has resulted in additional agents with associated diagnostics looming on the horizon in 2016. In the era of precision medicine, the paradigm of paired molecular target and molecular test, which serves as a model of oncogenic mutation-driven cancer therapy, is challenged by the proliferation of immunohistochemistry-based tests with different antibodies, instruments, and scoring. The difficulty inherent to targeted therapy aimed at a moving target is discussed, as well as the emerging challenges to pathologists and oncologists who seek to optimize care in this complex therapeutic arena.

Prognostic significance of morphological growth patterns and mitotic index of epithelioid malignant peritoneal mesothelioma

AIMS

The prognostic significance of histological subtyping of epithelioid pleural mesotheliomas has been recently reported, but similar data are lacking for peritoneal mesotheliomas. The aim of this study was to investigate possible relationships between histological growth patterns of epithelioid peritoneal mesotheliomas, clinicopathological features, and patient outcome.

METHODS AND RESULTS

Eighty-four cases of chemotherapy-naive epithelioid peritoneal mesothelioma were classified into tubulopapillary, micropapillary, papillary, tubular, solid and trabecular growth patterns. Pathological features such as depth of invasion, lymphocytic host response, mitotic count, nuclear grade, lymphovascular invasion, lymph node metastasis and stromal desmoplasia were analysed. The most common histological patterns were solid (n = 37, 44%), tubulopapillary (n = 24, 29%), and micropapillary (n = 11, 13%). The overall median survival was 36 months. Patients with solid mesothelioma had shorter overall survival (median, 29 months) than patients with tubulopapillary and micropapillary growth patterns (median, 51 and 53 months, respectively; P = 0.053). A high mitotic index (>5 in 50 high-power fields) was found to be associated with poor survival (P < 0.03). A moderate to severe lymphocytic host response was associated with longer median survival (P = 0.13).

CONCLUSIONS

Our study highlights the prognostic importance of the solid growth pattern among diffuse epithelioid peritoneal mesotheliomas, and reaffirms mitotic index as a predictor of overall survival.

Abstract 696: Comprehensive genomic analysis identifies frequent MET juxtamembrane domain deletions as an actionable genomic alteration in pulmonary sacromatoid carcinoma

Background:

Pulmonary sarcomatoid carcinoma (SC) is a rare and highly aggressive lung tumor, and it is associated with poor prognosis and high rate of resistance to conventional chemotherapy. We performed whole-exome next generation sequencing followed by a careful ranking and validation strategy to understand its unique differentiation pattern and to identify actionable targets.

Methods:

Twenty-nine patients with pulmonary SC diagnosed at our institution between 1998 and 2013 were enrolled and divided into a discovery set (n = 10) and a validation set (n = 19). Whole-exome sequencing was performed on genomic DNA samples extracted from fresh frozen tumor tissue and paired normal tissue in the discovery set. TruSeq Amplicon-Cancer 48 gene panel and bidirectional Sanger sequencing was performed to validate mutations. Validated genes were then screened for mutations using Sanger sequencing on FFPE-DNA of the patients in the validation set. Total RNA and protein were extracted from fresh frozen tumor tissues and paired normal tissues when available. RT-PCR and Western blotting were performed to validate MET juxtamembrane domain deletion. Ablation of MET signaling by siRNA or pharmacological inhibitors was conducted in cell line models harboring MET exon 14 skipping, and cell line models harboring wild-type MET. MTS assay and western blotting were then performed to assess cell proliferation and MET downstream signaling changes.

Results:

Previously reported mutations in TP53 (7/10) KRAS (2/10) and PIK3CA (2/10), as well as novel mutations in RASA1(2/10), CDH4 (2/10), CDH7 (2/10), LAMB4 (3/10), MET (2/10), SCAF1 (2/10), and LMTK2 (2/10), were detected and validated in the discovery set. CDH4, CDH7, SCAF1, LMTK2, and MET were screened in the validation set, and two SCAF1 mutations and five MET mutations were identified. In total, 24% (7/29) of pulmonary SC harbor somatic mutations in the splice sites of MET exon 14, including five D1010H point mutations in the 3p splice acceptor site. RT-PCR and Western blotting confirmed the presence of exon 14 skipped MET variant. Inactivation of MET using the MET inhibitor Crizotinib decreased cell proliferation and inhibited downstream AKT and mitogen-activated protein kinase activation in cell lines harboring MET exon14 skipping (H596 lung adenocarcinoma and Hs746T gastric cancer), whereas effects of MET inhibition on cell proliferation and downstream protein activation were negligible in MET wild-type cell lines. Further functional studies utilizing specific siRNA and MET exon 14 expression constructs are ongoing.

Conclusions:

Our study finds an unprecedently high frequency of exon 14 skipping MET mutations in pulmonary SC and suggests that MET activation might contribute to the mesenchymal differentiation and aggressive biology and defines MET inhibition as a promising novel therapeutic strategy for MET-mutated pulmonary SC.

Citation Format: Xuewen Liu, Yuxia Jia, Yufeng Shen, Haiying Cheng, Sanjay Koul, Alain C. Borczuk, Balazs Halmos. Comprehensive genomic analysis identifies frequent MET juxtamembrane domain deletions as an actionable genomic alteration in pulmonary sacromatoid carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 696. doi:10.1158/1538-7445.AM2015-696

Abstract 5329: Development of small molecule activators of protein phosphatase 2A for the treatment of lung cancer

KRAS is the most common recurrent oncogenomic mutations driving the growth of NSCLC and accounting for ∼25% of patients with advanced NSCLC. Patients with KRAS mutations respond poorly to current therapies. Thus, novel therapies, are critically needed, to improve the lives of patients suffering from KRAS driven lung cancers. While oncogenic kinases have proven to be successful targets for cancer treatment, the therapeutic targeting of phosphatases, the key negative regulators of these same pathways, has remained largely unexplored. Through reverse engineering of tricyclic neuroleptic drugs, we developed a first-in-class series of small molecule activators of PP2A activators (SMAPs) molecules, as represented by TRC-794 and TRC-1154, that have favorable pharmaceutical properties directly bind and activate the serine/threonine phosphatase 2A (PP2A). PP2A accounts for the majority of cellular serine/threonine phosphatase activity, and its dominant and best-defined targets are oncogenic protein kinases including ERK and AKT. In this study, we sought to determine both the association of PP2A inactivation in lung cancer with specific molecular genotypes and the biological and functional consequences of PP2A reactivation in lung cancer. We determined the PP2A activation status by immunohistochemistry for the Y307 PP2A residue, a well documented inactivating site on the phosphatase, in a large cohort of primary lung tumors and identified that KRAS G12C mutant tumors displayed coordinate overexpression of both pERK and PP2A Y307. Global phosphoproteomic analysis of TRC-794 treated KRAS lung cancer cell lines revealed ERK signaling as the only commonly perturbed pathway in drug treated cell lines which was confirmed by western blotting. Treatment of lung cancer cell lines with TRC resulted in decreased cell viability, decreased colony formation, and an increase in apoptosis. Given the marked dephosphorylation of ERK upon treatment of cell lines with TRC-1154, we overexpressed a constitutively active form of MEK (MEKDD) to blunt SMAP mediated ERK dephosphorylation to determine the relevance of ERK inactivation to the biological effects of SMAPs on cellular apoptosis. Overexpression of MEKDD resulted in blunting the apoptotic response to TRC-1154 treatment. Single agent TRC-794 or TRC-1154 treatment of KRAS GEMM and xenograft mouse models of lung cancer resulted in tumor stasis, induction of tumor cell apoptosis and cell cycle arrest to comparable levels seen with a combination of AKT and MEK inhibitors. Western blotting and immunohistochemical analysis of the tumors demonstrated that SMAP treatment resulted in of ERK, AKT, and PP2A-Y307 dephosphorylation in vivo. Additionally, these compounds demonstrate favorable pharmacokinetics and show no overt toxicity. Taken together, these findings point to therapeutic activation of PP2A as a novel strategy for the treatment of advanced KRAS-mutant NSCLC.

Citation Format: Jaya Sangodkar, Sudeh Izadmehr, Sahar Mahzar, Divya Hoon, Shen Yao, David Kastrinsky, Daniela Schlatzer, Neelesh Sharma, Alain C. Borczuk, Michael Ohlmeyer, Yiannis Ioannou, Goutham Narla. Development of small molecule activators of protein phosphatase 2A for the treatment of lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5329. doi:10.1158/1538-7445.AM2015-5329

Next-Generation Sequencing of Pulmonary Sarcomatoid Carcinoma Reveals High Frequency of Actionable MET Gene Mutations

PURPOSE

To further understand the molecular pathogenesis of pulmonary sarcomatoid carcinoma (PSC) and develop new therapeutic strategies in this treatment-refractory disease.

MATERIALS AND METHODS

Whole-exome sequencing in a discovery set (n = 10) as well as targeted MET mutation screening in an independent validation set (n = 26) of PSC were performed. Reverse transcriptase polymerase chain reaction and Western blotting were performed to validate MET exon 14 skipping. Functional studies for validation of the oncogenic roles of MET exon 14 skipping were conducted in lung adenosquamous cell line H596 (MET exon 14 skipped and PIK3CA mutated) and gastric adenocarcinoma cell line Hs746T (MET exon 14 skipped). Response to MET inhibitor therapy with crizotinib in a patient with advanced PSC and MET exon 14 skipping was evaluated to assess clinical translatability.

RESULTS

In addition to confirming mutations in known cancer-associated genes (TP53, KRAS, PIK3CA, MET, NOTCH, STK11, and RB1), several novel mutations in additional genes, including RASA1, CDH4, CDH7, LAMB4, SCAF1, and LMTK2, were identified and validated. MET mutations leading to exon 14 skipping were identified in eight (22%) of 36 patient cases; one of these tumors also harbored a concurrent PIK3CA mutation. Short interfering RNA silencing of MET and MET inhibition with crizotinib showed marked effects on cell viability and decrease in downstream AKT and mitogen-activated protein kinase activation in Hs746T and H596 cells. Concurrent PIK3CA mutation required addition of a second agent for successful pathway suppression and cell viability effect. Dramatic response to crizotinib was noted in a patient with advanced chemotherapy-refractory PSC carrying a MET exon 14 skipping mutation.

CONCLUSION

Mutational events of MET leading to exon 14 skipping are frequent and potentially targetable events in PSC.

EIF2AK4 mutations in pulmonary capillary hemangiomatosis

BACKGROUND

Pulmonary capillary hemangiomatosis (PCH) is a rare disease of capillary proliferation of unknown cause and with a high mortality. Families with multiple affected individuals with PCH suggest a heritable cause although the genetic etiology remains unknown.

METHODS

We used exome sequencing to identify a candidate gene for PCH in a family with two affected brothers. We then screened 11 unrelated patients with familial (n = 1) or sporadic (n = 10) PCH for mutations.

RESULTS

Using exome sequencing, we identified compound mutations in eukaryotic translation initiation factor 2 α kinase 4 (EIF2AK4) (formerly known as GCN2) in both affected brothers. Both parents and an unaffected sister were heterozygous carriers. In addition, we identified two EIF2AK4 mutations in each of two of 10 unrelated individuals with sporadic PCH. EIF2AK4 belongs to a family of kinases that regulate angiogenesis in response to cellular stress.

CONCLUSIONS

Mutations in EIF2AK4 are likely to cause autosomal-recessive PCH in familial and some nonfamilial cases.

Genomic alterations in pulmonary adenocarcinoma in situ in an adolescent patient

Lung cancer is a rare event in the pediatric and adolescent population. To date, only a few case reports and small case series have been published, and little is known about the risk factors associated with this entity in children and adolescents. We describe a case of adenocarcinoma in situ in a 15-year-old adolescent girl with previous surgical treatment for malignant melanoma. We provide a detailed genomic characterization of this neoplasm by comparative genomic hybridization, genome-wide single-nucleotide polymorphism array, and fluorescence in situ hybridization analyses. We identify chromosomal regions with copy number changes and correlate the corresponding genes within these regions with the available literature in the area.