ENIGMACHEK2gether Project: A Comprehensive Study Identifies Functionally ImpairedCHEK2Germline Missense Variants Associated with Increased Breast Cancer Risk
Authors: Stolarova Lenka , Kleiblova Petra , Zemankova Petra , Stastna Barbora , Janatova Marketa , Soukupova Jana , Achatz Maria Isabel , Ambrosone Christine , Apostolou Paraskevi , Arun Banu K. , Auer Paul , Barnard Mollie , Bertelsen Birgitte ,   Biobank Japan, Matsuda Koichi , Kamatani Yoichiro , Morisaki Takayuki , Nagai Akiko , Muto Kaori , Murakami Yoshinori , Furukawa Yoichi , Yamanashi Yuji , Nakamura Yusuke , Mushiroda Taisei , Momozawa Yukihide , Tanaka Toshihiro , Ohnishi Yozo , Kubo Michiaki , Higashiue Shinichi , Kobayashi Shuzo , Minami Shiro , Yamaguhci Hiroki , Arai Hajime , Yamaji Ken , Okazaki Yasushi , Asai Satoshi , Takahashi Yasuo , Fujioka Tomoaki , Obara Wataru , Mori Seijiro , Murayama Shigeo , Nagayama Satoshi , Miki Yoshio , Masumoto Akihide , Yamada Akira , Nishizawa Yasuko , Higashiyama Masahiko , Kutsumi Hiromu , Koretsune Yukihiro , Yoshiyama Takashi , Blok Marinus J. , Boddicker Nicholas , Brunet Joan , Burnside Elizabeth S. , Calvello Mariarosaria , Campbell Ian , Chan Sock Hoai , Chen Fei , Chiang Jian Bang , Coppa Anna , Cortesi Laura , Crujeiras-González Ana ,   Consortium CZECANCA, Borecka Marianna , Cerna Marta , Hovhannisyan Milena , Jelinkova Sandra , Nehasil Petr , Foretova Lenka , Machackova Eva , Krutilkova Vera , Tavandzis Spiros , Cerna Leona , Chvojka Stepan , Koudova Monika , Puchmajerova Alena , Havranek Ondrej , Novotny Jan , Vesela Kamila , Vocka Michal , Hruskova Lucie , Michalovska Renata , Schwetzova Denisa , Vlckova Zdenka , Cerna Monika , Hejnalova Marketa , Jedlickova Nikol , Subrt Ivan , Zavoral Tomas , Kosarova Marcela , Vacinova Gabriela , Janikova Maria , Kratochvilova Romana , Curtisova Vaclava , Vrtel Radek , Scheinost Ondrej , Duskova Petra , Stranecky Viktor , De Leeneer Kim , De Putter Robin , DePersia Allison , Devereux Lisa , Domchek Susan , Efremidis Anna , Engel Christoph , Ernst Corinna , Evans D. Gareth R. , Feliubadaló Lidia , Fostira Florentia , Fuentes-Ríos Olivia , Gómez-García Encarna B. , González Sara , Haiman Christopher , Hansen Thomas van Overeem , Hauke Jan , Hodge James , Hu Chunling , Huang Hongyan , Ishak Nur Diana Binte , Iwasaki Yusuke , Konstantopoulou Irene , Kraft Peter , Lacey James , Lázaro Conxi , Li Na , Lim Weng Khong , Lindstrom Sara , Lori Adriana , Martinez Elana , Martins Alexandra , Matsuda Koichi , Matullo Giuseppe , McInerny Simone , Michailidou Kyriaki , Montagna Marco , Monteiro Alvaro N.A. , Mori Luigi , Nathanson Katherine , Neuhausen Susan L. , Nevanlinna Heli , Olson Janet E. , Palmer Julie , Pasini Barbara , Patel Alpa , Piane Maria , Poppe Bruce , Radice Paolo , Renieri Alessandra , Resta Nicoletta , Richardson Marcy E. , Rosseel Toon , Ruddy Kathryn J. , Santamariña Marta , Dos Santos Elizabeth Santana , Teras Lauren , Toland Amanda E. , Trentham-Dietz Amy , Vachon Celine M. , Volk Alexander E. , Weber-Lassalle Nana , Weitzel Jeffrey N. , Wiesmuller Lisa , Winham Stacey , Yadav Siddhartha , Yannoukakos Drakoulis , Yao Song , Zampiga Valentina , Zethoven Magnus , Zhang Ze Wen , Zima Tomas , Spurdle Amanda B. , Vega Ana , Rossing Maria , Del Valle Jesús , De Nicolo Arcangela , Hahnen Eric , Claes Kathleen B.M. , Ngeow Joanne , Momozawa Yukihide , James Paul A. , Couch Fergus J. , Macurek Libor , Kleibl Zdenek 
Published: July 2023

Purpose:

Germline pathogenic variants in CHEK2 confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense CHEK2 variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT).

Experimental Design:

We collected 460 CHEK2 missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1–CHEK2-knockout cells. Concordant results in both functional assays were used to categorize CHEK2 VUS from 12 ENIGMA case–control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls.

Results:

A total of 430/460 VUS were successfully analyzed, of which 340 (79.1%) were concordant in both functional assays and categorized as functionally impaired (N = 102), functionally intermediate (N = 12), or functionally wild-type (WT)–like (N = 226). We then examined their association with breast cancer risk in the case–control analysis. The OR and 95% CI (confidence intervals) for carriers of functionally impaired, intermediate, and WT-like variants were 2.83 (95% CI, 2.35–3.41), 1.57 (95% CI, 1.41–1.75), and 1.19 (95% CI, 1.08–1.31), respectively. The meta-analysis of population-specific datasets showed similar results.

Conclusions:

We determined the functional consequences for the majority of CHEK2 missense VUS found in patients with breast cancer (3,660/4,436; 82.5%). Carriers of functionally impaired missense variants accounted for 0.5% of patients with breast cancer and were associated with a moderate risk similar to that of truncating CHEK2 variants. In contrast, 2.2% of all patients with breast cancer carried functionally wild-type/intermediate missense variants with no clinically relevant breast cancer risk in heterozygous carriers.