The lung squamous cell carcinoma proteome

Lung cancer is the most prevalent cancer in the world and the leading cause of cancer-related deaths. Smoking is accepted as the major risk factor, responsible for 70-90% of all lung cancer cases, although the etiology of lung cancer appears multifactorial with both environmental and genetic factors playing a role. Lung cancer patients have a poor outcome with a 5-year survival rate of 13.6% among men and 19.4% among women across all stages. The poor prognosis is partly explained by late diagnosis, but also by lack of effective treatments.

Based on histology, lung cancer is primarily divided into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). SCLC originates from neuroendocrine cells and accounts for approximately 15% of all primary lung cancers. This extremely rapidly proliferating cancer is generally treated with chemotherapy with an initial good response which unfortunately in most cases is followed by resistance to treatment and poor survival outcome.

NSCLC is suggested to originate from bronchogenic or alveolar cells. It is the most common form of primary lung cancer and represents approximately 80-85% of all lung cancer cases. Based on histology, NSCLC can further be divided into different subtypes, with adenocarcinoma and squamous cell carcinoma being most common. Treatment for NSCLC is mainly based on the tumor extent. In principle, limited stage tumors are surgically treated, sometimes with the addition of chemotherapy and radiotherapy whereas tumors with advanced stages are palliatively treated with a combination of cytotoxic drugs and recently developed targeted drugs. Unfortunately, the treatment effect is limited and the majority of patients experience only modest survival prolongation.

Here, we explore the lung squamous cell carcinoma proteome using TCGA transcriptomics data and antibody-based protein data. 508 genes are suggested as prognostic based on transcriptomics data from 489 patients; 284 genes are associated with unfavorable prognosis and 224 genes are associated with favorable prognosis.

TCGA data analysis

In this metadata study we used data from TCGA where transcriptomics data was available from 489 patients with lung squamous cell carcinoma. The total dataset included 127 female and 362 males. A majority of the patients (279 patients) were still alive at the time of data collection. The stage distribution was stage i) 239 patients, stage ii) 156 patients, stage iii) 83 patients, stage iv) 7 patients and 4 patients with missing stage information.

Unfavorable prognostic genes in lung squamous cell carcinoma

For unfavorable genes, higher relative expression levels at diagnosis give significantly lower overall survival for the patients. There are 284 genes associated with an unfavorable prognosis in lung squamous cell carcinoma, among these potential prognostic genes there are 7 genes that were validated in a separate study. In Table 1, the top 20 most significant genes related to an unfavorable prognosis are listed.

CD151 is a gene associated with an unfavorable prognosis in lung squamous cell carcinoma. The best separation is achieved by an expression cutoff at 112 TPM which divides the patients into two groups with 38% 5-year survival for patients with high expression versus 64% for patients with low expression, p-value: 5.10e-5. Immunohistochemical staining using an antibody targeting CD151 (CAB002428) shows a differential expression pattern in lung squamous cell carcinoma samples.

p<0.001
CD151 - survival analysis
CD151 - high expression
CD151 - low expression

GAB2 is another gene associated with an unfavorable prognosis in lung squamous cell carcinoma. The best separation is achieved by an expression cutoff at 5.7 TPM which divides the patients into two groups with 29% 5-year survival for patients with high expression versus 53% for patients with low expression, p-value: 8.11e-5. Immunohistochemical staining using an antibody targeting GAB2 (CAB022159) shows a differential expression pattern in lung squamous cell carcinoma samples.

p<0.001
GAB2 - survival analysis
GAB2 - high expression
GAB2 - low expression

Table 1. The 20 genes with highest significance associated with an unfavorable prognosis in lung squamous cell carcinoma.

Favorable prognostic genes in lung squamous cell carcinoma

For favorable genes, higher relative expression levels at diagnosis give significantly higher overall survival for the patients. There are 224 genes associated with a favorable prognosis in lung squamous cell carcinoma, among these potential prognostic genes there are 1 gene that was validated in a separate study. In Table 2, the top 20 most significant genes related to a favorable prognosis are listed.

CLCA2 is a gene associated with a favorable prognosis in lung squamous cell carcinoma. The best separation is achieved by an expression cutoff at 22 TPM which divides the patients into two groups with 54% 5-year survival for patients with high expression versus 33% for patients with low expression, p-value: 4.40e-4. Immunohistochemical staining using an antibody targeting CLCA2 (HPA047192) shows a differential expression pattern in lung squamous cell carcinoma samples.

p<0.001
CLCA2 - survival analysis
CLCA2 - high expression
CLCA2 - low expression

CHEK2 is another gene associated with a favorable prognosis in lung squamous cell carcinoma. The best separation is achieved by an expression cutoff at 11 TPM which divides the patients into two groups with 53% 5-year survival for patients with high expression versus 29% for patients with low expression, p-value: 6.82e-6. Immunohistochemical staining using an antibody targeting CHEK2 (HPA001878) shows a differential expression pattern in lung squamous cell carcinoma samples.

p<0.001
CHEK2 - survival analysis
CHEK2 - high expression
CHEK2 - low expression

Table 2. The 20 genes with highest significance associated with a favorable prognosis in lung squamous cell carcinoma.

CPTAC relative protein expression data

Proteins that are significantly down- or upregulated in lung squamous cell carcinoma compared to normal tissue is illustrated in a vulcano plot using tandem mass tag (TMT) mass spectrometry data from the CPTAC dataset based on the analysis of 110 tumor samples and 102 normal samples.

In lung squamous cell carcinoma, 3313 and 3670 genes are down- (blue) and upregulated (red) compared to normal tissue, respectively. In Table 3, the top 20 most significant genes are listed.

Table 3. The 20 genes with the highest significance associated with a downregulated or upregulated protein expression in lung squamous cell carcinoma compared to normal tissue.

The lung squamous cell carcinoma transcriptome

The transcriptome analysis shows that 69% (n=13887) of all human genes (n=20162) are expressed in lung squamous cell carcinoma. All genes were classified according to the lung squamous cell carcinoma-specific expression into one of five different categories, based on the ratio between mRNA levels in lung squamous cell carcinoma compared to the mRNA levels in the other 16 analyzed cancer tissues.

Figure 2. The distribution of all genes across the five categories based on transcript abundance in lung squamous cell carcinoma as well as in all other cancer tissues.

151 genes show some level of elevated expression in lung squamous cell carcinoma compared to other cancers (Figure 1). The elevated category is further subdivided into three categories as shown in Table 3.

Table 4. The number of genes in the subdivided categories of elevated expression in lung squamous cell carcinoma.

Additional information

The histological classification of NSCLC is important for treatment options. The most common subtype of NSCLC is adenocarcinoma, comprising around 40% of all lung cancers. Adenocarcinoma is characterized by glandular formation, production of mucin and expression of thyroid transcription factor-1. It is the predominant histological type among younger men, women of all ages and in former and never smokers.

Squamous cell carcinoma, the second most common subtype of NSCLC, is suggested to originate from metaplastic squamous epithelia in the bronchial tree. It is defined by a variable degree of squamous differentiation, such as keratinization or intercellular bridging. This subtype is strongly associated with cigarette smoking. Large cell carcinoma accounts for 5-10% of all lung cancers and is a heterogenous group with no evidence of squamous or adenocarcinoma differentiation.

In addition to these three main subtypes of NSCLC, other less common e.g adenosquamous carcinoma and sarcomatoid carcinoma comprise the remaining NSCLC cases.

Relevant links and publications

Uhlen M et al., A pathology atlas of the human cancer transcriptome. Science. (2017)
PubMed: 28818916 DOI: 10.1126/science.aan2507

Cancer Genome Atlas Research Network et al., The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. (2013)
PubMed: 24071849 DOI: 10.1038/ng.2764

Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Lindskog C et al., The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling. FASEB J. (2014)
PubMed: 25169055 DOI: 10.1096/fj.14-254862

Histology dictionary - Lung cancer