Intratumoral heterogeneity and hypoxia gene expression signatures: Is a single biopsy adequate?

Jelena Lukovic; Kathy Han; Melania Pintilie; Naz Chaudary; Richard P Hill; Anthony Fyles; Michael Milosevic

doi:10.1016/j.ctro.2019.09.006

Intratumoral heterogeneity and hypoxia gene expression signatures: Is a single biopsy adequate?

Clin Transl Radiat Oncol. 2019 Oct 3:19:110-115. doi: 10.1016/j.ctro.2019.09.006. eCollection 2019 Nov.

Authors

Jelena Lukovic^{1

2}, Kathy Han^{1

2

3}, Melania Pintilie^{1

4}, Naz Chaudary¹, Richard P Hill^{1

2

5}, Anthony Fyles^{1

2

3}, Michael Milosevic^{1

2

3}

Affiliations

¹ Princess Margaret Cancer Centre, 610 University Ave, Toronto, Ontario M5G 2M9, Canada.
² University of Toronto, Department of Radiation Oncology, 149 College Street, Toronto, Ontario M5T 1P5, Canada.
³ University of Toronto, Institute of Medical Sciences, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
⁴ Princess Margaret Cancer Centre, Department of Biostatistics, 610 University Ave, Toronto, Ontario M5G 2M9, Canada.
⁵ University of Toronto, Department of Medical Biophysics, Toronto, Ontario M5G 2M9, Canada.

Abstract

Background and purpose: Gene expression signatures are often used to identify hypoxic tumors. However, intratumoral heterogeneity raises concern that multiple biopsies may be necessary to assess global hypoxia status. The objective of this study was to compare the impact of heterogeneity on the discriminative capacity of several previously described hypoxia gene signatures and determine if a single biopsy is sufficient to obtain a reliable estimate of hypoxia in cervical cancer.

Materials and methods: Multiple biopsies (33) were obtained from 11 locally advanced (FIGO IB to IVB) cervical cancers prior to treatment. Ten hypoxia gene signatures were analyzed. Variance component analysis was used to determine the ratio of within-tumor variability to total-tumor variability when one to five biopsies are available for analysis (W/T_1-5). The mean standardized error in the signature scores was estimated by comparing the score using one biopsy randomly selected from each tumor to the 'global' score using all available biopsies.

Results: The ten hypoxia signatures were comprised of 6-99 genes each. The W/T₁ ratios for individual genes commonly found in the signatures ranged from 0.17 to 0.73. W/T₁ ratios for the signatures were generally lower (0.21-0.45), implying greater capacity to discriminate among tumors. With additional biopsies, the signature W/T ratios (ie W/T_2-5) decreased further. The mean error in the signature scores varied from 0.27 to 0.40 of one standard deviation, suggesting high capacity to discriminate among tumors with different global hypoxia scores.

Conclusions: Compared with individual probes, hypoxia gene expression signatures are generally more consistent across multiple biopsies from different regions of a tumor and more tolerant of intratumoral heterogeneity.

Keywords: Cervical cancer; Gene signature; Heterogeneity; Hypoxia.