The head and neck cancer proteome

Head and neck cancer arises in the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx (voice box). Head and neck cancers are common in several regions of the world where tobacco usage and alcohol consumption is high. Head and neck cancers comprise approximately 10% of all newly diagnosed cancers in the western world, but one-third in India. The variation in incidence between regions is mostly related to the relative distribution of major risk factors such as tobacco and alcohol consumption. Head and neck cancer has a 5-year survival rate of approximately 60%, depending on locations on primary tumor and grade.

There is increasing evidence that viruses might contribute to the cause of head and neck cancer. DNA from human papillomavirus (HPV) has been detected in cancerous tissue from the head and neck and infection with Epstein-Barr virus is associated with nasopharyngeal cancer. Surprisingly, patients with advanced forms of cancer in the upper portion of the throat have a better outcome if the tumor is positive for HPV. The occurrence of head and neck cancer in young adults and , that falls tonon-users of tobacco and alcohol suggests that genetic predisposition may be a possible etiological factor.

Most head and neck cancers arise from squamous epithelium and are squamous cell carcinomas of different histologic grades. The tumor cells in well-differentiated cancers closely resemble normal squamous epithelium, whereas poorly differentiated cancers are difficult to classify as being of squamous epithelial origin. Salivary gland tumors (mainly adenocarcinomas) comprise a minority of head and neck tumors.

Here, we explore the head and neck cancer proteome using TCGA transcriptomics data and antibody-based protein data. 897 genes are suggested as prognostic based on transcriptomics data from 499 patients; 340 genes are associated with unfavorable prognosis and 557 genes are associated with favorable prognosis.

TCGA data analysis

In this metadata study, we used data from TCGA where transcriptomics data was available from 499 patients with head and neck cancer. The total dataset included 133 females and 366 males. Around 56% of the patients (281 patients) were still alive at the time of data collection. The stage distribution was stage i) 25 patients, stage ii) 69 patients, stage iii) 78 patients, stage iv) 259 patients and 68 patients with missing stage information.

Unfavorable prognostic genes in head and neck cancer

For unfavorable genes, higher relative expression levels at diagnosis give significantly lower overall survival for the patients. There are 340 genes associated with an unfavorable prognosis in head and neck cancer. In Table 1, the top 20 most significant genes related to an unfavorable prognosis are listed.

LIMA1 is a gene associated with an unfavorable prognosis in head and neck cancer. The best separation is achieved by an expression cutoff at 38.2 fpkm which divides the patients into two groups with 36% 5-year survival for patients with high expression versus 54% for patients with low expression, p-value: 1.76e-6. Immunohistochemical staining using an antibody targeting LIMA1 (HPA052645) shows a differential expression pattern in head and neck cancer samples.

p<0.001
LIMA1 - survival analysis
LIMA1 - high expression
LIMA1 - low expression

Table 1. The 20 genes with highest significance associated with an unfavorable prognosis in head and neck cancer.

Gene	Description	Predicted location	mRNA (cancer)	p-value
DKK1	dickkopf WNT signaling pathway inhibitor 1	Secreted	8.6	4.35e-8
CAMK2N1	calcium/calmodulin dependent protein kinase II inhibitor 1	Intracellular	9.5	1.37e-7
NDFIP1	Nedd4 family interacting protein 1	Membrane	13.5	2.33e-7
AIG1	androgen induced 1	Membrane, Intracellular	5.3	3.25e-7
SEC61G	SEC61 translocon subunit gamma	Membrane	56.4	4.64e-7
TMCO1	transmembrane and coiled-coil domains 1	Membrane	15.3	5.17e-7
STC2	stanniocalcin 2	Secreted, Intracellular	4.8	1.76e-6
LIMA1	LIM domain and actin binding 1	Intracellular	39.7	1.76e-6
CTTN	cortactin	Intracellular	81.7	2.19e-6
PGK1	phosphoglycerate kinase 1	Intracellular	128.7	2.65e-6
EFNB2	ephrin B2	Membrane	19.5	3.11e-6
TMED2	transmembrane p24 trafficking protein 2	Membrane, Intracellular	69.3	3.36e-6
HK1	hexokinase 1	Intracellular	41.4	3.39e-6
PCTP	phosphatidylcholine transfer protein	Intracellular	2.3	3.43e-6
ZDHHC4	zinc finger DHHC-type palmitoyltransferase 4	Membrane	8.3	3.95e-6
SEC14L2	SEC14 like lipid binding 2	Intracellular	5.4	7.63e-6
TCEAL8	transcription elongation factor A like 8	Intracellular	21.5	8.53e-6
KARS1	lysyl-tRNA synthetase 1	Intracellular	45.2	8.84e-6
MANF	mesencephalic astrocyte derived neurotrophic factor	Secreted	29.3	9.58e-6
LRRC59	leucine rich repeat containing 59	Membrane, Intracellular	45.1	1.00e-5
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Favorable prognostic genes in head and neck cancer

For favorable genes, higher relative expression levels at diagnosis give significantly higher overall survival for the patients. There are 557 genes associated with a favorable prognosis in head and neck cancer. In Table 2, the top 20 most significant genes related to a favorable prognosis are listed.

CALML5 is a gene associated with a favorable prognosis in head and neck cancer. The best separation is achieved by an expression cutoff at 60.6 fpkm which divides the patients into two groups with 52% 5-year survival for patients with high expression versus 37% for patients with low expression, p-value: 2.59e-5. Immunohistochemical staining using an antibody targeting CALML5 (HPA040725) shows a differential expression pattern in head and neck cancer samples.

p<0.001
CALML5 - survival analysis
CALML5 - high expression
CALML5 - low expression

Table 2. The 20 genes with highest significance associated with a favorable prognosis in head and neck cancer.

Gene	Description	Predicted location	mRNA (cancer)	p-value
ZNF846	zinc finger protein 846	Intracellular	1.2	5.25e-8
SZT2	SZT2 subunit of KICSTOR complex	Intracellular	2.1	1.47e-7
GZMM	granzyme M	Secreted, Intracellular	1.7	1.87e-7
FGD3	FYVE, RhoGEF and PH domain containing 3	Intracellular	2.2	2.23e-7
IGLV3-21	immunoglobulin lambda variable 3-21	Secreted	177.9	3.26e-7
IGLV3-27	immunoglobulin lambda variable 3-27	Secreted	15.3	3.60e-7
PPFIA3	PTPRF interacting protein alpha 3	Intracellular	3.9	6.46e-7
CD27	CD27 molecule	Membrane	4.7	6.65e-7
IGHV3-73	immunoglobulin heavy variable 3-73	Secreted	26.8	7.25e-7
JCHAIN	joining chain of multimeric IgA and IgM	Secreted	76.3	7.56e-7
CCR7	C-C motif chemokine receptor 7	Membrane	2.8	7.61e-7
IGKV2D-40	immunoglobulin kappa variable 2D-40	Secreted, Intracellular	5.3	9.78e-7
S1PR4	sphingosine-1-phosphate receptor 4	Membrane	2.5	1.45e-6
IGHV3-7	immunoglobulin heavy variable 3-7	Secreted	2.6	1.47e-6
TNFRSF17	TNF receptor superfamily member 17	Membrane, Intracellular	1.2	1.58e-6
IGHV4-4	immunoglobulin heavy variable 4-4	Secreted	5.2	1.60e-6
IRF4	interferon regulatory factor 4	Intracellular	1.3	1.64e-6
ZNF414	zinc finger protein 414	Intracellular	3.4	1.67e-6
IGHV3-49	immunoglobulin heavy variable 3-49	Secreted	27.3	2.34e-6
SMIM14	small integral membrane protein 14	Membrane, Intracellular	8.5	3.00e-6
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The head and neck cancer transcriptome

The transcriptome analysis shows that 69% (n=13955) of all human genes (n=20162) are expressed in head and neck cancer. All genes were classified according to the head and neck cancer-specific expression into one of five different categories, based on the ratio between mRNA levels in head and neck cancer compared to the mRNA levels in the other 16 analyzed cancer tissues.

Figure 1. The distribution of all genes across the five categories based on transcript abundance in head and neck cancer as well as in all other cancer tissues.

355 genes show some level of elevated expression in head and neck cancer compared to other cancers (Figure 1). The elevated category is further subdivided into three categories as shown in Table 3.

Table 3. Number of genes in the subdivided categories of elevated expression in head and neck cancer.

		Distribution in the 17 cancers
		Detected in single	Detected in some	Detected in many	Detected in all	Total
Specificity	Cancer enriched	14	10	16	0	40
	Group enriched	0	58	76	5	139
	Cancer enhanced	14	44	99	19	176
	Total	28	112	191	24	355

Additional information

Head and neck cancers are classified using the TNM System. It describes the extent of the primary tumor (T stage), the absence or presence of spread to nearby lymph nodes (N stage) and the absence or presence of distant spread, or metastasis (M stage). Once the T, N and M are determined, a stage of I, II, III or IV is assigned. Stage I cancers are small, localized and usually curable, while stage II and III cancers typically are locally advanced and/or have spread to local lymph nodes. Stage IV cancers are usually metastatic (have spread to distant parts of the body) and are generally considered inoperable. Early stage (Stage I and II) cancers yield a 60-95% cure rate, which falls to 25% for Stage IV tumors.

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

Histology dictionary - Head and neck cancer