Tumor DNA-methylome derived epigenetic fingerprint identifies HPV-negative head and neck patients at risk for locoregional recurrence after postoperative radiochemotherapy

Bouchra Tawk; Ute Wirkner; Christian Schwager; Katrin Rein; Karim Zaoui; Philippe A Federspil; Sebastian Adeberg; Annett Linge; Ute Ganswindt; Julia Hess; Kristian Unger; Ingeborg Tinhofer; Volker Budach; Fabian Lohaus; Mechthild Krause; Maja Guberina; Martin Stuschke; Panagiotis Balermpas; Claus Rödel; Anca L Grosu; Henning Schäfer; Daniel Zips; Stephanie E Combs; Steffi Pigorsch; Horst Zitzelsberger; Philipp Baumeister; Thomas Kirchner; Melanie Bewerunge-Hudler; Wilko Weichert; Jochen Hess; Esther Herpel; Claus Belka; Michael Baumann; Jürgen Debus; Amir Abdollahi; DKTK-ROG

doi:10.1002/ijc.33842

Tumor DNA-methylome derived epigenetic fingerprint identifies HPV-negative head and neck patients at risk for locoregional recurrence after postoperative radiochemotherapy

Int J Cancer. 2022 Feb 15;150(4):603-616. doi: 10.1002/ijc.33842. Epub 2021 Nov 8.

Authors

Bouchra Tawk^{1

2

3

4

5}, Ute Wirkner^{1

2

3

4

5}, Christian Schwager^{1

2

3

4

5}, Katrin Rein^{1

2

3

4

5}, Karim Zaoui⁶, Philippe A Federspil⁶, Sebastian Adeberg^{1

2

7

8}, Annett Linge^{3

9

10

11

12

13

14}, Ute Ganswindt^{15

16}, Julia Hess^{17

18

19}, Kristian Unger^{17

18

19}, Ingeborg Tinhofer^{20

21}, Volker Budach^{20

21}, Fabian Lohaus^{3

9

10

11

12

13

14}, Mechthild Krause^{3

9

10

11

12

13

14}, Maja Guberina^{22

23}, Martin Stuschke^{10

23}, Panagiotis Balermpas^{24

25}, Claus Rödel^{24

26}, Anca L Grosu^{27

28

29}, Henning Schäfer^{27

28}, Daniel Zips^{30

31}, Stephanie E Combs^{15

32}, Steffi Pigorsch^{15

32}, Horst Zitzelsberger^{17

18

19}, Philipp Baumeister^{18

33}, Thomas Kirchner^{15

34}, Melanie Bewerunge-Hudler³⁵, Wilko Weichert^{15

36}, Jochen Hess^{6

37}, Esther Herpel^{1

2

38

39}, Claus Belka^{15

17

18}, Michael Baumann^{1

2

9

10

11}, Jürgen Debus^{1

2

3

4

5}, Amir Abdollahi^{1

2

3

4

5}; DKTK-ROG

Affiliations

¹ German Cancer Research Center (DKFZ), Heidelberg, Germany.
² German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.
³ Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.
⁴ Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany.
⁵ Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University, Heidelberg, Germany.
⁶ Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany.
⁷ Department of Radiation Oncology, University Hospital Heidelberg, Heidelberg, Germany.
⁸ Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg, Germany.
⁹ German Cancer Consortium (DKTK), Partner Site Dresden, Dresden, Germany.
¹⁰ Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
¹¹ OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
¹² National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.
¹³ Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
¹⁴ Helmholtz Association/Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany.
¹⁵ German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.
¹⁶ Department of Radiation Oncology, Medical University of Innsbruck, Innsbruck, Austria.
¹⁷ Department of Radiation Oncology, University Hospital Ludwig-Maximilians-University of Munich, Munich, Germany.
¹⁸ Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.
¹⁹ Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.
²⁰ German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
²¹ Department of Radiooncology and Radiotherapy, Charité University Hospital, Berlin, Germany.
²² German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany.
²³ Department of Radiotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany.
²⁴ German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany.
²⁵ Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland.
²⁶ Department of Radiotherapy and Oncology, Goethe-University Frankfurt, Frankfurt, Germany.
²⁷ German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany.
²⁸ Department of Radiation Oncology, Clinical Study Section, University of Freiburg, Freiburg, Germany.
²⁹ Department of Radiation Oncology, University of Freiburg, Freiburg, Germany.
³⁰ German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.
³¹ Department of Radiation Oncology, Faculty of Medicine and University Hospital Tübingen, Eberhard Karls Universität Tübingen, Tübingen, Germany.
³² Department of Radiation Oncology, Technische Universität München, Munich, Germany.
³³ Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany.
³⁴ Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Munich, Germany.
³⁵ Genomics and Proteomics Core Facility, German Cancer Research Center, Heidelberg, Germany.
³⁶ Institute of Pathology, Technische Universität München, Munich, Germany.
³⁷ Department of Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center, Heidelberg, Germany.
³⁸ Tissue Bank, National Center for Tumor Diseases (NCT), Heidelberg, Germany.
³⁹ Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

PMID: 34648658
DOI: 10.1002/ijc.33842

Abstract

Biomarkers with relevance for loco-regional therapy are needed in human papillomavirus negative aka HPV(-) head and neck squamous cell carcinoma (HNSCC). Based on the premise that DNA methylation pattern is highly conserved, we sought to develop a reliable and robust methylome-based classifier identifying HPV(-) HNSCC patients at risk for loco-regional recurrence (LR) and all-event progression after postoperative radiochemotherapy (PORT-C). The training cohort consisted of HPV-DNA negative HNSCC patients (n = 128) homogeneously treated with PORT-C in frame of the German Cancer Consortium-Radiation Oncology Group (DKTK-ROG) multicenter biomarker trial. DNA Methylation analysis was performed using Illumina 450 K and 850 K-EPIC microarray technology. The performance of the classifier was integrated with a series of biomarkers studied in the training set namely hypoxia-, 5-microRNA (5-miR), stem-cell gene-expression signatures and immunohistochemistry (IHC)-based immunological characterization of tumors (CD3/CD8/PD-L1/PD1). Validation occurred in an independent cohort of HPV(-) HNSCC patients, pooled from two German centers (n = 125). We identified a 38-methylation probe-based HPV(-) Independent Classifier of disease Recurrence (HICR) with high prognostic value for LR, distant metastasis and overall survival (P < 10^-9 ). HICR remained significant after multivariate analysis adjusting for anatomical site, lymph node extracapsular extension (ECE) and size (T-stage). HICR high-risk tumors were enriched for younger patients with hypoxic tumors (15-gene signature) and elevated 5-miR score. After adjustment for hypoxia and 5-miR covariates, HICR maintained predicting all endpoints. HICR provides a novel mean for assessing the risk of LR in HPV(-) HNSCC patients treated with PORT-C and opens a new opportunity for biomarker-assisted stratification and therapy adaptation in these patients.

Keywords: DNA methylation; disease recurrence; head and neck cancers; radiotherapy; stratification.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chemoradiotherapy*
Combined Modality Therapy
DNA Methylation*
DNA, Neoplasm / metabolism*
Female
Head and Neck Neoplasms / genetics*
Head and Neck Neoplasms / immunology
Head and Neck Neoplasms / therapy
Head and Neck Neoplasms / virology
Humans
Male
MicroRNAs / analysis
Middle Aged
Neoplasm Recurrence, Local / etiology*
Papillomaviridae / isolation & purification
Squamous Cell Carcinoma of Head and Neck / genetics*
Squamous Cell Carcinoma of Head and Neck / immunology
Squamous Cell Carcinoma of Head and Neck / therapy
Squamous Cell Carcinoma of Head and Neck / virology

Substances

DNA, Neoplasm
MicroRNAs