Clinical and Genetic Implications of Mutation Burden in Squamous Cell Carcinoma of the Lung

Tumor Location Is an Independent Prognostic Factor in Completely Resected Pathological Stage I Non-Small Cell Lung Cancer: A Multicenter Retrospective Study

Previous studies suggested that the location of the primary tumor in non-small cell lung cancer (NSCLC) is associated with clinical features and prognosis, but results are conflicting. The purpose of this study was to explore tumor location as an independent risk factor of survival for patients with completely resected pathological stage I NSCLC. This was a multicenter retrospective study conducted in Taiwan. Included patients were diagnosed with stage I NSCLC and had undergone primary tumor resection. Variables including tumor location, pathological stage, histological differentiation, and International Association for the Study of Lung Cancer (IASLC) grade were evaluated for predictive ability for disease-free survival (DFS) and overall survival (OS). A total of 208 patients were included, with 123 (59.1%) patients having a primary tumor in the upper and middle lobes. The median duration of follow-up for survivors was 60.5 months. Compared to patients with IASLC Grade 3 disease, patients with Grade 1 disease had significantly longer DFS. Tumor location and IASLC grade were independent predictors for OS in multivariate analysis. Specifically, patients with NSCLC in the lower lobe and patients who are histologically classified as IASLC Grade 3 may have poorer prognosis and require greater attention to improve outcomes.

A Novel High-Dimensional Kernel Joint Non-Negative Matrix Factorization With Multimodal Information for Lung Cancer Study

Judging and identifying biological activities and biomarkers inside tissues from imaging features of diseases is challenging, so correlating pathological image data with genes inside organisms is of great significance for clinical diagnosis. This paper proposes a high-dimensional kernel non-negative matrix factorization (NMF) method based on muti-modal information fusion. This algorithm can project RNA gene expression data and pathological images (WSI) into a common feature space, where the heterogeneous variables with the largest coefficient in the same projection direction form a co-module. In addition, the miRNA-mRNA and miRNA-lncRNA interaction networks in the ceRNA network are added to the algorithm as a priori information to explore the relationship between the images and the internal activities of the gene. Furthermore, the radial basis kernel function is used to calculate the feature proportion between different kinds of genes mapped in the high-dimensional feature space and projected into the common feature space to explore the gene interaction in the high-dimensional situation. The original feature matrix is regularized to improve biological correlation, and the feature factors are sparse by orthogonal constraints to reduce redundancy. Experimental results show that the proposed NMF method is better than the traditional NMF method in stability, decomposition accuracy, and robustness. Through data analysis applied to lung cancer, genes related to tissue morphology are found, such as COL7A1, CENPF and BIRC5. In addition, gene pairs with a correlation degree exceeding 0.8 are found, and potential biomarkers of significant correlation with survival are obtained such as CAPN8. It has potential application value for the clinical diagnosis of lung cancer.

Copy number loss of KDM5D may be a predictive biomarker for ATR inhibitor treatment in male patients with pulmonary squamous cell carcinoma

A limited number of patients with lung squamous cell carcinoma (SCC) benefit clinically from molecular targeted drugs because of a lack of targetable driver alterations. We aimed to understand the prevalence and clinical significance of lysine-specific demethylase 5D (KDM5D) copy number loss in SCC and explore its potential as a predictive biomarker for ataxia-telangiectasia and Rad3-related (ATR) inhibitor treatment. We evaluated KDM5D copy number loss in 173 surgically resected SCCs from male patients using fluorescence in situ hybridization. KDM5D copy number loss was detected in 75 of the 173 patients (43%). Genome-wide expression profiles of the transcription start sites (TSSs) were obtained from 17 SCCs, for which the cap analysis of gene expression assay was performed, revealing that upregulated genes in tumors with the KDM5D copy number loss are associated with 'cell cycle', whereas downregulated genes in tumors with KDM5D copy number loss were associated with 'immune response'. Clinicopathologically, SCCs with KDM5D copy number loss were associated with late pathological stage (p = 0.0085) and high stromal content (p = 0.0254). Multiplexed fluorescent immunohistochemistry showed that the number of tumor-infiltrating CD8+ /T-bet+ T cells was lower in SCCs with KDM5D copy number loss than in wild-type tumors. In conclusion, approximately 40% of the male patients with SCC exhibited KDM5D copy number loss. Tumors in patients who show this distinct phenotype can be 'cold tumors', which are characterized by the paucity of tumor T-cell infiltration and usually do not respond to immunotherapy. Thus, they may be candidates for trials with ATR inhibitors.

Lobe-specific analysis of perioperative chemotherapy for non-small cell lung cancer patients

OBJECTIVES

Perioperative cisplatin-based chemotherapy decreases the risk of death over surgery alone and is a standard of care. Here, we examined perioperative chemotherapy indications for stage IB-III non-small cell lung cancer (NSCLC) patients according to lobe-specific analysis.

METHODS

Resectable NSCLC patients with stage IB-III who received perioperative chemotherapy with and without radiotherapy after lung resection were identified from the SEER database. Propensity score matching (PSM) analysis was performed to reduce the inherent bias of retrospective studies. The Kaplan-Meier method and log-rank tests were used to assess the differences in overall survival (OS).

RESULTS

The study enrolled 23,844 patients before PSM. The perioperative chemotherapy group had better OS than the nonperioperative chemotherapy group in stage IB-III NSCLC patients before and after PSM. However, subgroup analysis according to stage demonstrated that perioperative chemotherapy did not markedly benefit patients with stage IB. Furthermore, lobar subgroup analysis did not show survival advantages in primary tumors located in either the right middle lobe in stages II and III NSCLC or the right lower lobe in stage III NSCLC.

CONCLUSIONS

Lobe-specific perioperative chemotherapy is recommended in NSCLC patients. For stage IB NSCLC, right middle lobe NSCLC from stage IB-III and right lower lobe NSCLC from stage III, perioperative chemotherapy might not confer survival benefits.

Primary tumor location in lung cancer: the evaluation and administration

ABSTRACT

Lung cancer continues to be the leading cause of cancer-related death in the world, which is classically subgrouped into two major histological types: Non-small cell lung cancer (NSCLC) (85% of patients) and small-cell lung cancer (SCLC) (15%). Tumor location has been reported to be associated with the prognosis of various solid tumors. Several types of cancer often occur in a specific region and are more prone to spread to predilection locations, including colorectal cancer, prostate cancer, gastric cancer, ovarian cancer, cervical cancer, bladder cancer, lung tumor, and so on. Besides, tumor location is also considered as a risk factor for lung neoplasm with chronic obstructive pulmonary disease/emphysema. Additionally, the primary lung cancer location is associated with specific lymph node metastasis. And the recent analysis has shown that the primary location may affect metastasis pattern in metastatic NSCLC based on a large population. Numerous studies have enrolled the "location" factor in the risk model. Anatomy location and lobe-specific location are both important in prognosis. Therefore, it is important for us to clarify the characteristics about tumor location according to various definitions. However, the inconsistent definitions about tumor location among different articles are controversial. It is also a significant guidance in multimode therapy in the present time. In this review, we mainly aim to provide a new insight about tumor location, including anatomy, clinicopathology, and prognosis in patients with lung neoplasm.

TMED3 promotes the progression and development of lung squamous cell carcinoma by regulating EZR

Lung squamous cell carcinoma (LUSC) has a poor clinical prognosis and lacks effective targeted therapy. The transmembrane emp24 trafficking protein 3 (TMED3) belongs to the TMED family, which is responsible for the transport of intracellular proteins. This study was to explore the clinicopathological significance and biological effects of TMED3 in LUSC. Expression of TMED3 in LUSC was detected by immunohistochemical (IHC). The loss-of-function assays were used to investigate the effects of TMED3 on proliferation, apoptosis, cell cycle, and migration of LUSC cells. The influence of TMED3 knockdown on tumor growth in vivo was evaluated by mice xenograft models. In addition, the downstream target of TMED3 was recognized by RNA sequencing and Ingenuity Pathway Analysis (IPA). Moreover, TMED3 was upregulated in LUSC tissue, which was positively correlated with pathological grade. TMED3 knockdown was involved in the regulation of LUSC cell function, such as inhibition of proliferation, reduction of colony formation, induction of apoptosis, and reduction of migration. TMED3 knockdown induced abnormalities in apoptosis-related proteins in LUSC cells. In addition, the inhibition of cell migration by TMED3 knockdown was achieved by regulating EMT. Mechanically, EZR was considered as a potential target for TMED3 to regulate the progress of LUSC. Inhibition of EZR can inhibit the progression of LUSC, and even reduce the promoting effects of TMED3 overexpression on LUSC. In conclusion, TMED3 promoted the progression and development of LUSC by EZR, which may be a novel therapeutic target for LUSC.

Identification of SLC38A7 as a Prognostic Marker and Potential Therapeutic Target of Lung Squamous Cell Carcinoma

BACKGROUND

No effective molecular targeted therapy has been established for SCC. We conducted a comprehensive study of SCC patients using RNA-sequencing and TCGA dataset to clarify the driver oncogene of SCC.

METHOD

Forty-six samples of 23 patients were totally analyzed with RNA-sequencing. We then searched for candidate-oncogenes of SCC using the TCGA database. To identify candidate oncogenes, we used the following 2 criteria: (1) the genes of interest were overexpressed in tumor tissues of SCC patients in comparison to normal tissues; and (2) using an integrated mRNA expression and DNA copy number profiling analysis using the TCGA dataset, the DNA copy number of the genes was positively correlated with the mRNA expression.

RESULT

We identified 188 candidate-oncogenes. Among those, the high expression of SLC38A7 was a strong prognostic marker that was significantly associated with a poor prognosis in terms of both overall survival (OS) and recurrence-free survival in the TCGA dataset (P < 0.05). Additionally, 202 resected SCC specimens were also subjected to an immunohistochemical analysis. Patients with the high expression of SLC38A7 (alternative name is sodium-coupled amino acid transporters 7) protein showed significantly shorter OS in comparison to those with the low expression of SLC38A7 protein [median OS 3.9 years (95% confidence interval, 2.4-6.4 years) vs 2.2 years (95% confidence interval, 1.9-4.1 years); log rank test: P = 0.0021].

CONCLUSION

SLC38A7, which is the primary lysosomal glutamine transporter required for the extracellular protein-dependent growth of cancer cells, was identified as a candidate therapeutic target of SCC.

A comprehensive pan-cancer analysis of CD274 gene amplification, tumor mutation burden, microsatellite instability, and PD-L1 expression in Chinese cancer patients

Background

Immune checkpoint inhibitors blocking programmed cell death 1 (PD-1) or programmed cell death ligand 1 (PD-L1) have emerged as effective treatment options for cancer. However, immunotherapy is only effective in a subset of patients. Identifying effective biomarkers to predict the treatment response to PD-1/PD-L1 inhibitors remains an unmet clinical need.

Methods

This study retrospectively analyzed clinical information and genetic profiling results of 16,013 samples from Chinese patients with various cancer types in order to investigate the prevalence of CD274 (also known as PD-L1) amplification in various cancer types and its association with existing PD-1/PD-L1 biomarkers, including tumor mutational burden (TMB), microsatellite instability (MSI), and PD-L1 expression.

Results

Amplification of CD274 was identified in 174 samples with an overall prevalence of 1.09% among all cancer types in the cohort. The prevalence of CD274 amplification in different cancer types and histological subtypes of lung cancer was varied, with cervical cancer having the highest prevalence. Distinct distributions of TMB, MSI, and PD-L1 expression between CD274-amplified and wild-type samples were observed in several cancer types as well as among different histological subtypes of lung cancer.

Conclusions

Although CD274 amplification was only observed in a small proportion of patients, it demonstrated an association with TMB, MSI, and PD-L1 expression in several common cancer types. The molecular features of CD274 in different cancer types are heterogeneous. The role of CD274 amplification as a novel biomarker of PD-1/PD-L1 inhibitors remains to be characterized in future prospective clinical studies.

Molecular characterization of lung squamous cell carcinoma tumors reveals therapeutically relevant alterations

INTRODUCTION

Unlike lung adenocarcinoma patients, there is no FDA-approved targeted-therapy likely to benefit lung squamous cell carcinoma patients.

MATERIALS AND METHODS

We performed survival analyses of lung squamous cell carcinoma patients harboring therapeutically relevant alterations identified by whole exome sequencing and mass spectrometry-based validation across 430 lung squamous tumors.

RESULTS

We report a mean of 11.6 mutations/Mb with a characteristic smoking signature along with mutations in TP53 (65%), CDKN2A (20%), NFE2L2 (20%), FAT1 (15%), KMT2C (15%), LRP1B (15%), FGFR1 (14%), PTEN (10%) and PREX2 (5%) among lung squamous cell carcinoma patients of Indian descent. In addition, therapeutically relevant EGFR mutations occur in 5.8% patients, significantly higher than as reported among Caucasians. In overall, our data suggests 13.5% lung squamous patients harboring druggable mutations have lower median overall survival, and 19% patients with a mutation in at least one gene, known to be associated with cancer, result in significantly shorter median overall survival compared to those without mutations.

CONCLUSIONS

We present the first comprehensive landscape of genetic alterations underlying Indian lung squamous cell carcinoma patients and identify EGFR, PIK3CA, KRAS and FGFR1 as potentially important therapeutic and prognostic target.

Mutational signatures in squamous cell carcinoma of the lung

Background

Tumor mutational burden (TMB) has been identified as one of the predictors for the response to anti-programmed cell death-1 (anti-PD-1) antibody therapy and reported to correlate with smoking history in lung adenocarcinoma. However, in squamous cell carcinoma of the lung, the association between TMB and clinicopathological background factors, such as smoking history, has not been reported, including in our previous study. The mutational signature is a tool to identify the mutagens that are contributing to the mutational spectrum of a tumor by investigating the pattern of DNA changes. Here, we analyzed the mutational signature in lung squamous cell carcinoma to identify mutagens affecting the TMB.

Methods

Seven representative mutational signatures including signature 7 (SI7) [ultraviolet (UV)-related], SI4 (smoking), SI6/15 [mismatch repair (MMR)], SI2/13 [apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC)], and SI5 (clock-like) were analyzed in Japanese patients with lung squamous cell carcinoma (n=67) using data generated by next-generation sequencing consisting of a 415-gene panel. The relationships between signatures and clinico-pathological data including TMB and programmed death-ligand 1 (PD-L1) expression were analyzed.

Results

Although the reconstructed mutational counts were small with targeted sequencing (median: 30.1, range: 13.3–98.7), the distributions of signatures were comparable among samples, with 56 cases containing more than four signatures. The smoking-related SI4 was found in 45 cases and was significantly related with pack-year index (PYI) (P=0.026). The reconstructed mutation counts were highly correlated with SI4 (r=0.51, P<0.0001), whereas the correlation was weak with SI6/15 (MMR-related) and SI2/13 (APOBEC-related). There was no mutational signature related with PD-L1 expression. Some patients exhibited unique signatures; the patient with the highest mutational counts had a MMR signature, and another patient with a prominent UV signature had occupational exposure to UV, as he was employed as a neon sign engineer.

Conclusions

Mutational signatures can predict the cause of lung squamous cell carcinoma. Tobacco smoking is the mutagen most related with TMB.

A novel immunogenomic prognostic signature in lung squamous carcinoma

Lung squamous carcinoma (LUSC) is a common subtype of lung cancer with limited available therapy and is thus associated with poor survival. Immune infiltrating cells and immune-related genes (IRGs) play a key role in the clinical outcomes of LUSC. In the present study, we aimed to develop a potential immunogenomic prognostic signature for patients with LUSC. The transcriptional profiles of 501 LUSC samples from The Cancer Genome Atlas (TCGA) and 2498 IRGs from the ImmPort database were used to develop the signature by Cox regression analysis. Ten differentially expressed and survival-associated IRGs were used to develop the risk signature, which could serve as an independent prognostic and predictive factor for patients with LUSC. Furthermore, this risk signature correlated with overall survival and clinical features, including age, in patients with LUSC. In addition, we identified 25 transcription factors that may regulate 15 survival-associated IRGs, using a regulatory network. Collectively, this immunogenomic signature could be a robust prognostic tool for patients with LUSC and holds great promise as individualized immunotherapy for LUSC.

Predictive values of genomic variation, tumor mutational burden, and PD-L1 expression in advanced lung squamous cell carcinoma treated with immunotherapy

Background

Immune checkpoint inhibitors (ICIs) prolong overall survival (OS) in patients with advanced lung squamous cell carcinoma (LUSC). However, predictive and prognostic factors related to ICIs in LUSC remain elusive. This study aimed to identify predictors that are related to better clinical benefit and outcomes in LUSC patients treated with immunotherapy.

Methods

Capture-based targeted sequencing was performed in 64 patients with advanced LUSC who underwent immunotherapy. Tumor mutational burden (TMB) was defined as the sum of nonsynonymous single nucleotide and indel variants. Programmed cell death ligand-1 (PD-L1) expression was evaluated by immunohistochemical analysis. Clinicopathological characteristics including age, sex, performance status, smoking history, body mass index (BMI), blood fat, brain metastases, liver metastases, previous thoracic radiotherapy, and treatment lines were analyzed.

Results

The most commonly mutated genes included TP53, CDKN2A, KEAP1, CREBBP, KRAS, BIM, AMER1, and APC. Copy number variations most frequently occurred in AR, SOX2, PIK3CA, EGFR, RICTOR, FGFR1, and ZNF703. The median and mean TMB was 9.35 and 10.62 mutations per megabase, respectively. Positive PD-L1 expression was detected in 29.7% patients. Patients with a history of heavy smoking (≥ 40 pack-years) were more likely to have positive PD-L1 expression (35% vs. 16.7%, P=0.04) and higher TMB (11.1 vs. 9.8 mut/Mb, P=0.04). Gene alterations had no impact on PD-L1 expression or TMB level. The median progression-free survival (PFS) was 6.7 months and median OS was 13.7 months. Higher TMB was independently associated with longer PFS (P=0.01) and OS (P=0.02), and this correlation was more pronounced in patients treated with ICIs as a single agent (P=0.0001). Higher TMB was also associated with better disease control rate (DCR) (P=0.02). Compared with wild-type, patients with KRAS mutation and EGFR amplification had higher objective response rates (ORR, P=0.01).

Conclusions

The predictive value of TMB is more significant in LUSC patients receiving ICI as a single agent than as a combination therapy. The combination of Eastern Cooperative Oncology Group performance status (ECOG-PS), smoking status, TMB, PD-L1, and genomic variation might be helpful for personalized immunotherapy decisions in clinical practice for advanced LUSC.

Next-Generation Sequencing at High Sequencing Depth as a Tool to Study the Evolution of Metastasis Driven by Genetic Change Events of Lung Squamous Cell Carcinoma

Background: The aim of this study is to report tumoral genetic mutations observed at high sequencing depth in a lung squamous cell carcinoma (SqCC) sample. We describe the findings and differences in genetic mutations that were studied by deep next-generation sequencing methods on the primary tumor and liver metastasis samples. In this report, we also discuss how these differences may be involved in determining the tumor progression leading to the metastasis stage.

Methods: We followed one lung SqCC patient who underwent FDG-PET scan imaging, before and after three months of treatment. We sequenced 26 well-known cancer-related genes, at an average of ~6,000 × sequencing coverage, in two spatially distinct regions, one from a primary lung tumor metastasis and the other from a distal liver metastasis, which was present before the treatment.

Results: A total of 3,922,196 read pairs were obtained across all two samples' sequenced locations. Merged mapped reads showed several variants, from which we selected 36 with high confidence call. While we found 83% of genetic concordance between the distal metastasis and primary tumor, six variants presented substantial discordance. In the liver metastasis sample, we observed three de novo genetic changes, two on the FGFR3 gene and one on the CDKN2A gene, and the frequency of one variant found on the FGFR2 gene has been increased. Two genetic variants in the HRAS gene, which were present initially in the primary tumor, have been completely lost in the liver tumor. The discordant variants have coding consequences as follows: FGFR3 (c.746C>G, p. Ser249Cys), CDKN2A (c.47_50delTGGC, p. Leu16Profs^*9), and HRAS (c.182A>C, p. Gln61Pro). The pathogenicity prediction scores for the acquired variants, assessed using several databases, reported these variants as pathogenic, with a gain of function for FGFR3 and a loss of function for CDKN2A. The patient follow-up using imaging with 18F-FDG PET/CT before and after four cycles of treatment shows discordant tumor progression in metastatic liver compared to primary lung tumor.

Conclusions: Our results report the occurrence of several genetic changes between primary tumor and distant liver metastasis in lung SqCC, among which non-silent mutations may be associated with tumor evolution during metastasis.

Whole exome sequencing of lung adenocarcinoma and lung squamous cell carcinoma in one individual: A case report

Multiple primary lung cancers (MPLCs) refers to two or more primary malignant tumors that occur simultaneously or successively in the lung of the same patient. Distinguishing MPLCs from intrapulmonary metastases is important for treatment strategy and prognosis. MPLCs have been considered as having different origins and clonal evolutionary processes. Whole genome sequencing (WGS) and whole exome sequencing (WES) are regarded as an effective way to identify the relationship and differentiation among MPLC nodules. Here, we report the case of a 63‐year‐old MPLC male patient who smoked for 40 years. Two nodules were found on chest computed tomography (CT) scan, which were further confirmed by pathology to be lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SCC), respectively. WES of the two different nodules was performed, and the results showed that there was a significant genetic difference between the two nodules. Further analysis of the tumor mutation burden (TMB) of the two tumor lesions showed that the TMB of the squamous cell carcinoma was higher than that of the adenocarcinoma, indicating that the squamous cell carcinoma had a higher mutation frequency. According to the pathology and WES sequencing results, MPLCs for this case were regarded as independent of each other, with different origins and clonal evolutionary processes. In this case report, we emphasize that WES should play an important role in determining the origin of MPLC clones, and also make some explorations for the further discovery of new potential driver genes and therapeutic targets.

Optimizing Tissue Use: A Step-wise Approach to Diagnosing Squamous Cell Lung Carcinoma on Small Biopsies

Background:

Histologic subtyping of lung cancer has significant implications for treatment planning. Accurate diagnosis based on cytology/small biopsy specimens is challenging and frequently determined by morphology, as material is often not sufficient for immunohistochemical studies (IHC). We investigated the concordance between the rates of diagnosis from cytology/small biopsies compared with surgical specimens in patients with squamous cell lung cancer (SCC) and the utility of IHC for diagnostic precision in lung cancer subtyping.

Methods:

We conducted a 5-year retrospective analysis identifying cases of SCC diagnosed on cytology/small biopsies ± IHC and compared them with subsequent surgical specimens when available. The number of patients with SCC on surgical biopsy and the concordance between cytology ± IHC was determined.

Results:

Over the 5-year period (2011-2015), 231 cases were identified. Surgery was performed on 66 cases (28.5%), of which 87.9% concurred with cytological diagnosis (95% exact binomial confidence interval [CI] = 77.5%-94.6%). There were 36 cases diagnosed in 2014 and 2015 with IHC data. Of those cytology cases with IHC (n = 12), SCC was confirmed by surgery in 91.7% (95% CI = 61.5%-99.8%). Of those without IHC (n = 24), 95.8% were confirmed SCC by surgery (95% CI = 78.9%-99.9%). These rates were not different (Fisher exact test). All cases with IHC were morphologically squamous.

Conclusions:

Our data demonstrate that diagnostic precision of identifying SCC by cytology/small biopsy is comparable with or without additional IHC studies. We recommend judicious use of IHC on cytology specimens, reserving it for cases where cytomorphology is equivocal. Tissue should be preserved for molecular analysis, which may have therapeutic implications.

Predictive and prognostic impact of primary tumor-bearing lobe in nonsmall cell lung cancer patients treated with anti-PD-1 therapy

Immunotherapy targeting programmed cell death-1 (PD-1) has become a standard pharmacological therapy. Although tumor mutation burden level was reported to depend on the tumor location in nonsmall cell lung cancer (NSCLC), predictive impact of the tumor location on the response to anti-PD-1 therapy is unknown. Two hundred and seventeen advanced or recurrent NSCLC patients treated with anti-PD-1 therapy at Kyushu University Hospital and National Hospital Organization Kyushu Cancer Center were analyzed. To minimize the bias arising from the patients' background, adjusted Kaplan-Meier survival curves and Cox proportional hazards regression analyses using inverse probability of treatment weights (IPTW) were performed. Of the 217 patients, 132, 27, and 58 had primary NSCLC in upper, middle, and lower lobes, respectively. Patients with NSCLC in upper lobe were significantly associated with younger age (P = .0070) and smoker (P = .0003). The epidermal growth factor receptor-wild type and tumor location in upper lobe were independent predictors of disease control (P = .0175 and P = .0425, respectively). The IPTW-adjusted Kaplan-Meier curves showed that patients with NSCLC in the upper lobes had significantly longer progression-free survival (PFS) and overall survival (OS) than those in middle/lower lobes (P = .0026 and P = .0015, respectively). On IPTW adjusted Cox analysis, NSCLC in the upper lobe was an independent predictor of PFS and OS (P = .0078 and P = .0034, respectively). Patients with primary NSCLC in the upper lobes may be good candidates for anti-PD-1 therapy. These findings should be validated prospectively.

Genomic landscape and its correlations with tumor mutational burden, PD-L1 expression, and immune cells infiltration in Chinese lung squamous cell carcinoma

INTRODUCTION

To depict the genomic landscape of Chinese early-stage lung squamous cell carcinoma (LUSC) and investigate its correlation with tumor mutation burden (TMB), PD-L1 expression, and immune infiltrates.

METHODS

Whole-exome sequencing was performed on 189 surgically resected LUSC. TMB was defined as the sum of nonsynonymous single nucleotide and indel variants. CD8⁺ tumor-infiltrating lymphocyte (TIL) density and PD-L1 expression were evaluated by immunohistochemistry. Six immune infiltrates were estimated using an online database.

RESULTS

The median TMB was 9.43 mutations per megabase. Positive PD-L1 expression and CD8⁺ TILs density were identified in 24.3% and 78.8%. PIK3CA amplification was associated with significantly higher TMB (P = 0.036). Frequent genetic alterations had no impact on PD-L1 expression but PIK3CA amplification and KEAP1 mutation were independently associated with significantly lower CD8⁺ TIL density (P < 0.001, P = 0.005, respectively). Low TMB and high CD8⁺ TIL density were independently associated with longer disease-free survival (DFS) while none of them could individually predict the overall survival (OS). Combination of TMB and PD-L1 expression or TMB and CD8⁺ TIL density could stratify total populations into two groups with distinct prognosis. Classifying tumor-immune microenvironment based on PD-L1 expression and CD8⁺ TIL density showed discrepant genomic alterations but similar TMB, clinical features, and OS. Notably, patients with different smoking status had distinct prognostic factors.

CONCLUSION

The combination of TMB, PD-L1 expression, immune infiltrates, and smoking status showed the feasibility to subgroup stratification in Chinese patients with early-stage LUSC, which might be helpful for future design of personalized immunotherapy trials in LUSC.

Amyloid precursor protein and its phosphorylated form in non-small cell lung carcinoma

Amyloid precursor protein (APP) is a well-known to be involved in the development of Alzheimer's disease and harbors several phosphorylation sites in its cytoplasmic domain. APP has been also proposed as one of the molecules involved in cell proliferation and invasion in several human malignancies. However, the roles of APP including its phosphorylated form (p-APP) have remained largely unexplored in non-small cell lung carcinoma (NSCLC). Therefore, in this study, we first examined both APP and p-APP expressions and then explored the association between p-APP/APP status and clicopathological parameters in NSCLC. The number of APP-positive cases was 24/91 (26%) in adenocarcinomas (Ad) and 16/35 (46%) in squamous cell carcinomas (Sq), respectively. p-APP-positive cases in Ad and Sq were 28 (31%) and 17 (49%), respectively. In Ad cases, both APP and p-APP were significantly associated with clinical stages (APP and p-APP), pathologic T (p-APP), and pathologic N (APP and p-APP) of the cases examined. In Sq cases, there were no significant associations between APP status and any of the clinicopathological parameters examined with an exception of the significant correlation of p-APP with lymphatic invasion. APP status was not significantly associated with overall survival (OS) of Ad patients but a significant association was detected between p-APP-positive cases and OS of these patients (p < 0.0001). In Sq cases, both APP- (p = 0.01) and p-APP-positive (p = 0.04) groups were also significantly associated with adverse clinical outcome. These results did firstly demonstrate that APP, in particular, p-APP, is considered a potent prognostic factor for both Ad and Sq lung carcinoma patients. However, APP signaling including its phosphorylation signal are considered different between these two types of NSCC cells and further investigations are required for clarification.

Next Generation Sequencing and Genetic Alterations in Squamous Cell Lung Carcinoma: Where Are We Today?

Lung cancer is the leading cause of cancer-related mortality and will affect ~6% of the population. It is divided into two broad categories, small cell lung cancer and non-small cell lung cancer (NSCLC), the latter representing 85% of all lung cancers. It mainly comprises adenocarcinoma (65%) and squamous cell carcinoma (30%) histologies. In recent years, there have been two major therapeutic advances in NSCLC. The first, immunotherapy, has greatly improved the prognosis of adenocarcinomas and squamous cell carcinomas. The second, the treatment of targetable driver mutations, has so far only benefited adenocarcinomas. Squamous cell carcinoma carries a high rate of mutations and is found mostly among smokers. This raises two important problems: identifying driver mutations and finding those of clinical relevance. Large-scale genomic analyses such as The Cancer Genome Atlas have allowed for the identification of frequent gene alterations, although their role and potential for targeted therapy remain unknown. The emergence of next generation sequencing has changed the landscape of precision medicine, in particular in lung cancer. In this review, we discuss the landscape of genetic alterations found in squamous cell lung cancer, the results of current targeted therapy trials, the difficulties in identifying and treating these alterations and how to integrate modern tools in clinical practice.

Next generation sequencing-based gene panel tests for the management of solid tumors

Next generation sequencing (NGS) has been an invaluable tool to put genomic sequencing into clinical practice. The incorporation of clinically relevant target sequences into NGS-based gene panel tests has generated practical diagnostic tools that enable individualized cancer-patient care. The clinical utility of gene panel testing includes investigation of the genetic basis for an individual's response to therapy, such as signaling pathways associated with a response to specific therapies, microsatellite instability and a hypermutated phenotype, and deficiency in the DNA double-strand break repair pathway. In this review, we describe the concept of precision cancer medicine using target sequences in gene panel tests as well as the importance of the control of sample quality in routine NGS-based genomic testing. We describe geographic and ethnic differences in cancer genomes, and discuss issues that need to be addressed in the future based on our experiences in Japan.

Lung Cancers: Molecular Characterization, Clonal Heterogeneity and Evolution, and Cancer Stem Cells

Lung cancer causes the largest number of cancer-related deaths in the world. Most (85%) of lung cancers are classified as non-small-cell lung cancer (NSCLC) and small-cell lung cancer (15%) (SCLC). The 5-year survival rate for NSCLC patients remains very low (about 16% at 5 years). The two predominant NSCLC histological phenotypes are adenocarcinoma (ADC) and squamous cell carcinoma (LSQCC). ADCs display several recurrent genetic alterations, including: KRAS, BRAF and EGFR mutations; recurrent mutations and amplifications of several oncogenes, including ERBB2, MET, FGFR1 and FGFR2; fusion oncogenes involving ALK, ROS1, Neuregulin1 (NRG1) and RET. In LSQCC recurrent mutations of TP53, FGFR1, FGFR2, FGFR3, DDR2 and genes of the PI3K pathway have been detected, quantitative gene abnormalities of PTEN and CDKN2A. Developments in the characterization of lung cancer molecular abnormalities provided a strong rationale for new therapeutic options and for understanding the mechanisms of drug resistance. However, the complexity of lung cancer genomes is particularly high, as shown by deep-sequencing studies supporting the heterogeneity of lung tumors at cellular level, with sub-clones exhibiting different combinations of mutations. Molecular studies performed on lung tumors during treatment have shown the phenomenon of clonal evolution, thus supporting the occurrence of a temporal tumor heterogeneity.