Clinical implication of genetic intratumor heterogeneity for targeted therapy in head and neck cancer

Figures & data

Figure 1. Illustration of the pathological sectioning. This figure illustrates the pathological sectioning of the tumor specimen. The red lines indicate the locations of biopsies taken from block 1 (central), block 2 (semi-peripheral), and block 3 (peripheral). The top panels depict the specimen, with the black contour delineating the tumor tissue and the area where biopsies for genetic analyses were performed. Distances between the biopsies are indicated for reference.

Table 1. Patient characteristics.

Patient characteristics	Value
Age
Median	63
Range	50–80
Sex
Male	16
Female	12
Tumor subsite
Oral cavity	16
Oropharynx	4
Hypopharynx/larynx	3
Maxillary sinus	2
Lymph node	3 (+5)^a
p16
Negative	26
Positive	2^b
Recurrence
Yes	10
No	18
Smoking
Never	3
Former	15
Current	10

^a Five patients had both a primary tumor and a lymph node metastasis.

^b One of the patients with a tumor in the oropharynx was p16 positive, and one of the three patients with only a lymph node metastasis was p16 positive.

Figure 2. Illustration of SCNAs detected in 45 preselected genes in biopsies from the 33 tumors. The Y-axis depicts the 45 preselected genes and the X-axis depicts the biopsies grouped and ordered by patient number. At the bottom, sample numbers are visible. The three entries for each tumor correspond to the three biopsy positions: the central biopsy is labeled as 1, the semi-peripheral biopsy as 2, and the peripheral biopsy as 3. Primary tumors and lymph node metastases are indicated with P and L respectively. The color bar to the right displays the actual aberration in the specific gene. Abbreviations. A: amplification; D: deletion; LOH: loss of heterozygosity; NO: none observed. The genes above the dashed horizontal line correspond to Table 2 and the results marked with a circle indicate clinically relevant heterogeneity in genes in Table 2 as well.

Figure 3. Sinaplots and boxplots illustrate differences in numbers of SCNAs. The Y-axis depicts the number of SCNAs and the X-axis depicts the biopsy location (left panel) or the primary versus recurrent disease (right panel). Each dot in both panels represents one of the biopsies. The left panel depicts the number of SCNA in a biopsy, grouped by the biopsy location in the tumor (central, semi-peripheral, and peripheral). The right panel depicts the number of SCNA in a biopsy, grouped by new primary and recurrent disease.

Figure 4. Illustration of the type of change in SCNAs between the three biopsies. The Y-axis depicts the 45 preselected genes and the X-axis depicts biopsies from primary tumors grouped by biopsy location (central and semi-peripheral; central and peripheral; semi-peripheral and peripheral). At the bottom, sample numbers are visible. Left: the differences between central and semi-peripheral biopsies amount to 6 changed aberrations, 36 lost aberrations, and 27 new aberrations. Middle: the differences between central and peripheral biopsies: 11 changed, 68 lost, and 23 new aberrations. Right: the differences between semi-peripheral and peripheral biopsies: 12 changed, 62 lost, and 26 new aberrations. The color bar to the right depicts the type of aberration. Abbreviations. A: amplification; D: deletion; LOH: loss of heterozygosity; NO: none observed.

Table 2. ESCAT score of assessable SCNAs and hotspot mutations with relevant findings in the current population.

	Genomic alteration	ESCAT score	Drug	Heterogeneity # tumor	Reference
PIK3CA	Amplification^a	IIIB	PIK3i	None	[24]
FBXW7	Deletion/LOH	IVB	GAKi	20 (L)	[40]
				5
				7
				27
EGFR	Amplification	IIA	EGFRi	2	[41]
FGFR1	Amplification	IIIA	FGFRi	13 (P)	[42]
CD274	Amplification^b	IIIB	Immune checkpoint inhibitor	5	[43]
(PD-L1)	Deletion/LOH			20 (L)
				24
PTEN	Deletion/LOH Inactivation hotspot mutation	IIIA	Resistance to EGFR mAB	1	[44]
				20 (L)
				21
				3(hotspot mutation R159S)
TP53	Y220 C hotspot mutation	IIB	PC14586	2 (hotspot mutation Y220C)	[45]

^aIntertumor heterogeneity between primary tumor (P) and lymph node metastasis (L) in tumor 20.

^bIntertumor heterogeneity between primary tumor (P) and lymph node metastasis (L) in tumor 11.

Abbreviations. LOH: loss of heterozygosity; P: primary tumor; L: lymph node metastasis.

Table 3. The 10 tumors with heterogeneity in SCNAs and hotspot mutations with potential clinical relevance and the implications for therapy.

Tumor #	Gene with heterogeneity	Potential therapeutic relevance
1	PTEN deletion	Resistance to EGFR mAB
2	EGFR amplification	Efficacy of EGFR targeted therapy
	TP53 Y220C	Efficacy of TP53 Y220Ci
3	Inactivating PTEN mutation (R159S)	Resistance to EGFR mAB
5	FBXW7 LOH	Efficacy of GAKi
	PD-L1 amplification and LOH	Efficacy or lack of efficacy, respectively, of immune checkpoint inhibitor
7	FBXW7 deletion + LOH	Efficacy of GAKi
13(P)	FGFR1 amplification	Efficacy of FGFR1i
20(L)	FBXW7 deletion	Efficacy of GAKi
	PD-L1 deletion	Lack of efficacy of immune checkpoint inhibitor
	PTEN LOH	Resistance to EGFR mAB
21	PTEN deletion + LOH	Resistance to EGFR mAB
24	PD-L1 deletion + LOH	Lack of efficacy of immune checkpoint inhibitor
27	FBXW7 LOH	Efficacy of GAKi

Abbreviations. LOH: loss of heterozygosity; P: primary tumor; L: lymph node metastasis.

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Data availability statement

The data set used and analyzed during the study is available from the corresponding author upon reasonable request.