The thyroid cancer proteome

Thyroid cancer is fairly common. The annual incidence is between 0.5-10 per 100,000 in various populations and 2-4 times more frequent in women compared to men. The most common form of thyroid cancer is papillary carcinoma (70-80%), followed by follicular carcinoma (10-20%), medullary carcinoma (5-10%) and anaplastic carcinoma (2-10%). The classification of thyroid cancer is dependent on histological features according to WHO. Thyroid tumors can also be classified according to aggressiveness into low-grade malignant, intermediate-grade malignant and high-grade malignant.

The prognosis for thyroid cancer is good, with a 10-year relative survival rate of approximately 98% for papillary carcinomas. Apart from age, where young patients have a considerably better prognosis, the size of the primary tumor and the tumor stage are the most significant prognostic factors.

For most thyroid tumors, diagnosis can be established by microscopic examination alone, although immunohistochemistry plays an important role in tumors exhibiting unusual morphological features.

Here, we explore the thyroid cancer proteome using TCGA transcriptomics data and antibody-based protein data. 346 genes are suggested as prognostic based on transcriptomics data from 501 patients; 185 genes are associated with unfavorable prognosis and 161 genes are associated with favorable prognosis.

TCGA data analysis

In this metadata study we used data from TCGA where transcriptomics data was available from 501 patients with thyroid carcinoma. The total dataset included 366 female and 135 males. Most of the patients (485 patients) were still alive at the time of data collection. The stage distribution was stage i) 281 patients, stage ii) 52 patients, stage iii) 111 patients, stage iv) 55 patients and 2 patients with missing stage information.

Unfavorable prognostic genes in thyroid cancer

For unfavorable genes, higher relative expression levels at diagnosis give significantly lower overall survival for the patients. There are 185 genes associated with an unfavorable prognosis in thyroid cancer. In Table 1, the top 20 most significant genes related to an unfavorable prognosis are listed.

LARS is a gene associated with an unfavorable prognosis in thyroid cancer. The best separation is achieved by an expression cutoff at 12.8 fpkm which divides the patients into two groups with 79% 5-year survival for patients with high expression versus 98% for patients with low expression, p-value: 2.98e-4. Immunohistochemical staining using an antibody targeting LARS1 (HPA036424) shows a differential expression pattern in thyroid cancer samples.

p<0.001
LARS1 - survival analysis
LARS1 - high expression
LARS1 - low expression

Table 1. The 20 genes with highest significance associated with an unfavorable prognosis in thyroid cancer.

Gene	Description	Predicted location	mRNA (cancer)	p-value
ROR2	receptor tyrosine kinase like orphan receptor 2	Membrane	1.9	4.28e-8
PRKAB2	protein kinase AMP-activated non-catalytic subunit beta 2	Intracellular	2.3	6.78e-7
SNAI1	snail family transcriptional repressor 1	Intracellular	4.1	8.82e-7
FIBIN	fin bud initiation factor homolog	Intracellular	2.8	1.85e-6
PDLIM3	PDZ and LIM domain 3	Intracellular	1.6	2.13e-6
COPZ2	COPI coat complex subunit zeta 2	Intracellular	8.0	2.89e-6
FAM171A1	family with sequence similarity 171 member A1	Intracellular,Membrane	4.3	4.90e-6
SYNDIG1	synapse differentiation inducing 1	Membrane	1.6	6.16e-6
MAP1A	microtubule associated protein 1A	Intracellular	1.4	1.09e-5
GAS1	growth arrest specific 1	Intracellular	1.6	1.13e-5
ALDH1B1	aldehyde dehydrogenase 1 family member B1	Intracellular	7.9	1.17e-5
ANTXR1	ANTXR cell adhesion molecule 1	Intracellular,Membrane	11.5	1.22e-5
WDR37	WD repeat domain 37	Intracellular	4.5	1.34e-5
GUF1	GUF1 homolog, GTPase	Intracellular	4.9	1.65e-5
TSHZ1	teashirt zinc finger homeobox 1	Intracellular	3.6	1.71e-5
CILP	cartilage intermediate layer protein	Secreted	1.5	2.24e-5
RINT1	RAD50 interactor 1	Intracellular	3.6	2.39e-5
SENP6	SUMO specific peptidase 6	Intracellular	8.2	2.83e-5
PAPSS2	3'-phosphoadenosine 5'-phosphosulfate synthase 2	Intracellular	2.9	3.21e-5
BCKDHA	branched chain keto acid dehydrogenase E1 subunit alpha	Intracellular	2.3	3.27e-5
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Favorable prognostic genes in thyroid cancer

For favorable genes, higher relative expression levels at diagnosis give significantly higher overall survival for the patients. There are 161 genes associated with a favorable prognosis in thyroid cancer. In Table 2, the top 20 most significant genes related to a favorable prognosis are listed.

VAMP8 is a gene associated with a favorable prognosis in thyroid cancer. The best separation is achieved by an expression cutoff at 118.0 fpkm which divides the patients into two groups with 98% 5-year survival for patients with high expression versus 66% for patients with low expression, p-value: 8.07e-9. Immunohistochemical staining using an antibody targeting VAMP8 (HPA006882) shows a differential expression pattern in thyroid cancer samples.

p<0.001
VAMP8 - survival analysis
VAMP8 - high expression
VAMP8 - low expression

Table 2. The 20 genes with highest significance associated with a favorable prognosis in thyroid cancer.

Gene	Description	Predicted location	mRNA (cancer)	p-value
VAMP8	vesicle associated membrane protein 8	Intracellular,Membrane	159.4	8.07e-9
HECTD3	HECT domain E3 ubiquitin protein ligase 3	Intracellular	12.7	1.85e-6
TRIM21	tripartite motif containing 21	Intracellular	11.0	2.26e-6
GLTP	glycolipid transfer protein	Intracellular	31.7	4.17e-6
TUBB4B	tubulin beta 4B class IVb	Intracellular	138.7	6.36e-6
MYL12B	myosin light chain 12B	Intracellular	327.9	6.62e-6
CCND3	cyclin D3	Intracellular	25.5	8.08e-6
RAB34	RAB34, member RAS oncogene family	Intracellular	46.9	1.06e-5
INPP1	inositol polyphosphate-1-phosphatase	Intracellular	7.5	1.12e-5
CRACDL	CRACD like	Intracellular	5.2	1.33e-5
UBE2Q1	ubiquitin conjugating enzyme E2 Q1	Intracellular	20.4	1.86e-5
CALM2	calmodulin 2	Intracellular	86.8	1.94e-5
PLAAT3	phospholipase A and acyltransferase 3	Intracellular,Membrane	32.9	2.54e-5
MCM3	minichromosome maintenance complex component 3	Intracellular	19.7	3.13e-5
ADRA1B	adrenoceptor alpha 1B	Intracellular,Membrane	2.5	3.19e-5
C14orf119	chromosome 14 open reading frame 119	Intracellular	18.4	3.30e-5
ZCCHC12	zinc finger CCHC-type containing 12	Intracellular	256.3	3.42e-5
SLC37A1	solute carrier family 37 member 1	Intracellular,Membrane	5.2	3.43e-5
FGF1	fibroblast growth factor 1	Intracellular,Secreted	2.9	3.45e-5
DERA	deoxyribose-phosphate aldolase	Intracellular	15.6	3.64e-5
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The thyroid cancer transcriptome

The transcriptome analysis shows that 68% (n=13739) of all human genes (n=20090) are expressed in thyroid cancer. All genes were classified according to the thyroid cancer-specific expression into one of five different categories, based on the ratio between mRNA levels in thyroid 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 thyroid cancer as well as in all other cancer tissues.

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

Table 3. The number of genes in the subdivided categories of elevated expression in thyroid cancer.

		Distribution in the 17 cancers
		Detected in single	Detected in some	Detected in many	Detected in all	Total
Specificity	Cancer enriched	17	16	26	4	63
	Group enriched	0	26	37	11	74
	Cancer enhanced	11	28	66	47	152
	Total	28	70	129	62	289

Additional information

Papillary thyroid carcinoma is defined as a malignant epithelial tumor. Microscopically the tumor shows evidence of follicular cell differentiation, typically with papillary and follicular structures as well as characteristic changes in tumor cell nuclei. The key to an accurate diagnosis is nuclear characteristics, including a ground glass appearance, large size, pale staining and irregular outline with deep grooves and pseudoinclusions. Papillary thyroid carcinoma is an indolent cancer, with an excellent long-term prognosis, despite a propensity to invade locally and to spread metastatically to regional lymph nodes. Distant metastases are uncommon.

Follicular carcinoma shows follicular differentiation but lacks the diagnostic features of papillary carcinoma. The incidence of follicular carcinoma is higher in areas of endemic goiter, and iodine deficiency appears to be the main contributing risk factor. In contrast to papillary carcinoma, the main mode of metastatic spread is hematogenous rather than through the lymphatic system. Follicular carcinoma is typically delimited by a fibrous capsule surrounding tightly packed follicles, trabeculae or solid sheets of tumor cells. Tumor cells are often cuboidal with dark or pale staining nuclei with inconspicuous nucleoli. Few follicular carcinomas may display nuclear pleomorphism.

Antibodies used in diagnostics of thyroid tumors include thyroglobulin (TG), calcitonin (CALCA) and thyroid transcription factor (TTF1).

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 - Thyroid cancer