The head and neck squamous cell carcinoma proteome TCGA data analysis Unfavorable prognostic genes in head and neck squamous cell carcinoma Favorable prognostic genes in head and neck squamous cell carcinoma CPTAC relative protein expression data The head and neck squamous cell carcinoma transcriptome Additional information Relevant links and publications

The head and neck squamous cell carcinoma 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 non-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 squamous cell carcinoma proteome using TCGA transcriptomics data and antibody-based protein data. 872 genes are suggested as prognostic based on transcriptomics data from 492 patients; 396 genes are associated with unfavorable prognosis and 476 genes are associated with favorable prognosis.

TCGA data analysis

In this metadata study, we used data from TCGA where transcriptomics data was available from 492 patients with head and neck squamous cell carcinoma. The total dataset included 131 females and 361 males. Around 57% of the patients (279 patients) were still alive at the time of data collection. The stage distribution was stage i) 24 patients, stage ii) 69 patients, stage iii) 76 patients, stage iv) 256 patients and 67 patients with missing stage information.

Unfavorable prognostic genes in head and neck squamous cell carcinoma

For unfavorable genes, higher relative expression levels at diagnosis give significantly lower overall survival for the patients. There are 396 genes associated with an unfavorable prognosis in head and neck squamous cell carcinoma. 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 squamous cell carcinoma. The best separation is achieved by an expression cutoff at 91 TPM which divides the patients into two groups with 39% 5-year survival for patients with high expression versus 54% for patients with low expression, p-value: 4.86e-5. Immunohistochemical staining using an antibody targeting LIMA1 (HPA052645) shows a differential expression pattern in head and neck squamous cell carcinoma 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 squamous cell carcinoma.

Gene	Description	Predicted location	mRNA (cancer)	p-value	Prognostic
DKK1	Dickkopf WNT signaling pathway inhibitor 1	Secreted	14.0	3.17e-8	potential
SEC61G	SEC61 translocon subunit gamma	Membrane	547.2	4.81e-7	potential
MRPS5	Mitochondrial ribosomal protein S5	Intracellular	6.5	5.49e-7	potential
CAMK2N1	Calcium/calmodulin dependent protein kinase II inhibitor 1	Intracellular	15.2	5.68e-7	potential
AUP1	AUP1 lipid droplet regulating VLDL assembly factor	Membrane	135.6	6.37e-6	potential
DDIT4	DNA damage inducible transcript 4	Intracellular	254.6	1.08e-5	potential
EIF3B	Eukaryotic translation initiation factor 3 subunit B	Intracellular	149.5	1.14e-5	potential
OST4	Oligosaccharyltransferase complex subunit 4, non-catalytic	Membrane	493.1	2.28e-5	potential
PCMT1	Protein-L-isoaspartate (D-aspartate) O-methyltransferase	Membrane, Intracellular	61.5	2.96e-5	potential
NIFK	Nucleolar protein interacting with the FHA domain of MKI67	Intracellular	57.6	6.33e-5	potential
LRRC59	Leucine rich repeat containing 59	Membrane, Intracellular	107.5	8.10e-5	potential
TLL1	Tolloid like 1	Secreted, Intracellular	1.5	1.02e-4	potential
CCT8	Chaperonin containing TCP1 subunit 8	Intracellular	139.9	1.33e-4	potential
JPT1	Jupiter microtubule associated homolog 1	Intracellular	418.8	1.40e-4	potential
RSL24D1	Ribosomal L24 domain containing 1	Intracellular	73.9	1.51e-4	potential
PNPLA4	Patatin like phospholipase domain containing 4	Intracellular	22.1	1.80e-4	potential
POLD2	DNA polymerase delta 2, accessory subunit	Intracellular	135.8	1.90e-4	potential
IGF2BP2	Insulin like growth factor 2 mRNA binding protein 2	Intracellular	33.7	1.93e-4	potential
TOMM34	Translocase of outer mitochondrial membrane 34	Intracellular	32.7	2.19e-4	potential
YKT6	YKT6 v-SNARE homolog	Intracellular	92.2	2.92e-4	potential
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Favorable prognostic genes in head and neck squamous cell carcinoma

For favorable genes, higher relative expression levels at diagnosis give significantly higher overall survival for the patients. There are 476 genes associated with a favorable prognosis in head and neck squamous cell carcinoma. 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 squamous cell carcinoma. The best separation is achieved by an expression cutoff at 63 TPM which divides the patients into two groups with 53% 5-year survival for patients with high expression versus 36% for patients with low expression, p-value: 4.24e-5. Immunohistochemical staining using an antibody targeting CALML5 (HPA040725) shows a differential expression pattern in head and neck squamous cell carcinoma 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 squamous cell carcinoma.

Gene	Description	Predicted location	mRNA (cancer)	p-value	Prognostic
TPSAB1	Tryptase alpha/beta 1	Secreted	32.6	4.17e-5	potential
RORC	RAR related orphan receptor C	Intracellular	1.4	5.45e-5	potential
ESR1	Estrogen receptor 1	Intracellular	1.1	1.23e-4	potential
SEMA5A	Semaphorin 5A	Membrane, Intracellular	3.1	1.71e-4	potential
RASIP1	Ras interacting protein 1	Intracellular	6.8	2.23e-4	potential
SMG6	SMG6 nonsense mediated mRNA decay factor	Intracellular	11.9	2.75e-4	potential
SELP	Selectin P	Membrane, Intracellular	2.1	2.91e-4	potential
RAMP3	Receptor activity modifying protein 3	Membrane	11.7	3.96e-4	potential
KLF2	KLF transcription factor 2	Intracellular	7.6	5.36e-4	potential
HOOK1	Hook microtubule tethering protein 1	Intracellular	7.4	5.38e-4	potential
SESN1	Sestrin 1	Intracellular	7.6	5.49e-4	potential
RASGRP3	RAS guanyl releasing protein 3	Intracellular	2.1	6.07e-4	potential
ZNF799	Zinc finger protein 799	Intracellular	1.5	6.51e-4	potential
PLVAP	Plasmalemma vesicle associated protein	Membrane, Intracellular	56.0	7.04e-4	potential
ARID4A	AT-rich interaction domain 4A	Intracellular	3.8	8.06e-4	potential
ZNF879	Zinc finger protein 879	Intracellular	1.0	3.54e-4	potential
GZMM	Granzyme M	Secreted, Intracellular	2.7	5.19e-8	potential
FGD3	FYVE, RhoGEF and PH domain containing 3	Intracellular	5.0	1.79e-7	potential
S1PR4	Sphingosine-1-phosphate receptor 4	Membrane	3.8	4.92e-7	potential
ZNF557	Zinc finger protein 557	Intracellular	1.7	7.22e-7	potential
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CPTAC relative protein expression data

Proteins that are significantly down- or upregulated in head and neck 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 111 tumor samples and 72 normal samples.

In head and neck squamous cell carcinoma, 1914 and 2117 genes are down- (blue) and upregulated (red) compared to normal tissue, respectively. In Table 3, the top 20 most significant genes are listed.

Figure 1. Proteins highlighted in blue are significantly downregulated in cancer tissue, while those in red are significantly upregulated when compared to normal tissue. Gray points represent non-significant proteins based on the log2 (fold change). Wilcox rank test with adjusted p values.

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

Gene	Description	Predicted location	Log2 fold change	p-value	Regulation
CAB39L	Calcium binding protein 39 like	Intracellular	-0.96	2.85e-27	Downregulated
SPTAN1	Spectrin alpha, non-erythrocytic 1	Intracellular	-0.78	2.95e-27	Downregulated
GFAP	Glial fibrillary acidic protein	Intracellular	-1.47	6.37e-27	Downregulated
CAVIN2	Caveolae associated protein 2	Intracellular	-1.95	6.58e-27	Downregulated
CRNN	Cornulin	Intracellular	-3.44	7.72e-27	Downregulated
CDC27	Cell division cycle 27	Intracellular	0.5	7.97e-27	Upregulated
SH3BGRL2	SH3 domain binding glutamate rich protein like 2	Intracellular	-1.8	8.50e-27	Downregulated
NOP2	NOP2 nucleolar protein	Intracellular	0.71	9.66e-27	Upregulated
MGLL	Monoglyceride lipase	Intracellular	-1.4	2.28e-26	Downregulated
CD34	CD34 molecule	Membrane	-1.61	3.13e-26	Downregulated
ADAR	Adenosine deaminase RNA specific	Intracellular	0.58	3.13e-26	Upregulated
ALDH6A1	Aldehyde dehydrogenase 6 family member A1	Membrane, Intracellular	-1.1	4.15e-26	Downregulated
ABLIM1	Actin binding LIM protein 1	Intracellular	-1.43	4.42e-26	Downregulated
CRTAP	Cartilage associated protein	Secreted	1.18	4.71e-26	Upregulated
MUC21	Mucin 21, cell surface associated	Membrane	-2.45	4.82e-26	Downregulated
RECK	Reversion inducing cysteine rich protein with kazal motifs	Membrane	-1.11	5.02e-26	Downregulated
MINDY1	MINDY lysine 48 deubiquitinase 1	Intracellular	-1.04	5.18e-26	Downregulated
PCCB	Propionyl-CoA carboxylase subunit beta	Intracellular	-1.05	5.87e-26	Downregulated
SUOX	Sulfite oxidase	Intracellular	-1	6.06e-26	Downregulated
OGN	Osteoglycin	Secreted, Intracellular	-2.07	6.25e-26	Downregulated
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The head and neck squamous cell carcinoma transcriptome

The transcriptome analysis shows that 70% (n=14092) of all human genes (n=20162) are expressed in head and neck squamous cell carcinoma. All genes were classified according to the head and neck squamous cell carcinoma-specific expression into one of five different categories, based on the ratio between mRNA levels in head and neck 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 head and neck squamous cell carcinoma as well as in all other cancer tissues.

339 genes show some level of elevated expression in head and neck 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. Number of genes in the subdivided categories of elevated expression in head and neck squamous cell carcinoma.

		Distribution in the 31 cancers
		Detected in single	Detected in some	Detected in many	Detected in all	Total
Specificity	Cancer enriched	15	14	13	0	42
	Group enriched	0	40	62	3	105
	Cancer enhanced	16	46	103	27	192
	Total	31	100	178	30	339

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