Medical Oncology

, 35:145 | Cite as

Genetic variations using whole-exome sequencing might predict response for neoadjuvant chemoradiotherapy in locally advanced rectal cancer

  • In Hee Lee
  • Keunsoo Kang
  • Byung Woog Kang
  • Soo jung Lee
  • Woo Kyun Bae
  • Jun Eul Hwang
  • Hye Jin Kim
  • Su Yeon Park
  • Jun Seok Park
  • Gyu Seog Choi
  • Jong Gwang KimEmail author
Original Paper


A good pathologic response to neoadjuvant chemoradiotherapy (CRT) in locally advanced rectal cancer (LARC) is associated with a better prognosis. However, there is no effective method to predict CRT response in LARC patients. Therefore, this study used whole-exome sequencing (WES) to identify novel biomarker predicting CRT benefit in LARC. Two independent tumor tissue sets were used to evaluate the genetic differences between the good CRT response group (15 patients achieved a pathologic complete response (pCR)) and the poor CRT response group (15 patients with pathologic stage III). After applying WES to the discovery set of 30 patients, additional samples (n = 67) were genotyped for candidate variants using TaqMan or Sanger sequencing for validation. Overall, this study included a total of 97 LARC patients. In the discovery and validation set, there was no known genetic mutation to predict response between two groups, while five candidate variants (BCL2L10 rs2231292, DLC1 rs3816748, DNAH14 rs3105571, ITIH5 rs3824658, and RAET1L rs912565) were found to be significantly associated with pCR. In the dominant model, the GC/CC genotype of DLC1 rs3816748 (p = 0.032), AC/CC genotype of DNAH14 rs3105571 (p = 0.009), and TT genotype of RAET1 rs912565 (p < 0.0001) were associated with a higher pCR rate. In the recessive model, BCL2L10 rs2231292 (p = 0.036) and ITIH5 rs3824658 (p = 0.003) were significantly associated with pCR. In the co-dominant model, 4 candidate variants (DLC1 rs3816748, DNAH14 rs3105571, ITIH5 rs3824658, and RAET1L rs912565) were significantly correlated with pCR. However, none of the candidate variants was associated with relapse-free or overall survival. The present results suggest that genetic variations of the BCL2L10 rs2231292, DLC1 rs3816748, DNAH14 rs3105571, ITIH5 rs3824658, and RAET1L rs912565 genes can be used as biomarkers predicting the CRT response for patients with LARC.


Next-generation sequencing Whole-exome sequencing Pathologic complete response Neoadjuvant chemoradiotherapy Locally advanced rectal cancer 



This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (2014R1A5A2009242) and Korean Cancer Foundation (K20170519).

Compliance with ethical standards

Conflict of interest

The authors declared no conflicts of interest.

Ethics approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the Kyungpook National University Hospital Institutional Review Board (IRB).

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

12032_2018_1202_MOESM1_ESM.docx (51 kb)
Supplementary material 1 (DOCX 51 KB)


  1. 1.
    Park IJ, You YN, Agarwal A, Skibber JM, Rodriguez-Bigas MA, Eng C, et al. Neoadjuvant treatment response as an early response indicator for patients with rectal cancer. J Clin Oncol. 2012;30(15):1770–6. Scholar
  2. 2.
    Maas M, Nelemans PJ, Valentini V, Das P, Rodel C, Kuo LJ, et al. Long-term outcome in patients with a pathological complete response after chemoradiation for rectal cancer: a pooled analysis of individual patient data. Lancet Oncol. 2010;11(9):835–44. Scholar
  3. 3.
    Molinari C, Matteucci F, Caroli P, Passardi A. Biomarkers and molecular imaging as predictors of response to neoadjuvant chemoradiotherapy in patients with locally advanced rectal cancer. Clin Colorectal Cancer. 2015;14(4):227–38. Scholar
  4. 4.
    Kim CW, Yu CS, Yang SS, Kim KH, Yoon YS, Yoon SN, et al. Clinical significance of pre- to post-chemoradiotherapy s-CEA reduction ratio in rectal cancer patients treated with preoperative chemoradiotherapy and curative resection. Ann Surg Oncol. 2011;18(12):3271–7. Scholar
  5. 5.
    Kim NK, Hur H. New perspectives on predictive biomarkers of tumor response and their clinical application in preoperative chemoradiation therapy for rectal cancer. Yonsei Med J. 2015;56(6):1461–77. Scholar
  6. 6.
    Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26(10):1135–45. Scholar
  7. 7.
    Lips EH, Michaut M, Hoogstraat M, Mulder L, Besselink NJ, Koudijs MJ, et al. Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response. Breast Cancer Res. 2015;17(1):134. Scholar
  8. 8.
    Park K, Choi MK, Jung HH, Do IG, Lee KH, Ahn T, et al. Molecular characterization of patients with pathologic complete response or early failure after neoadjuvant chemotherapy for locally advanced breast cancer using next generation sequencing and nCounter assay. Oncotarget. 2015;6(27):24499–510. Scholar
  9. 9.
    Crumley SM, Pepper KL, Phan AT, Olsen RJ, Schwartz MR, Portier BP. Next-generation sequencing of matched primary and metastatic rectal adenocarcinomas demonstrates minimal mutation gain and concordance to colonic adenocarcinomas. Arch Pathol Lab Med. 2016;140(6):529–35. Scholar
  10. 10.
    Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754–60. Scholar
  11. 11.
    Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P. Sambamba: fast processing of NGS alignment formats. Bioinformatics. 2015;31(12):2032–4. Scholar
  12. 12.
    Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164. Scholar
  13. 13.
    Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6. Scholar
  14. 14.
    Ha YJ, Tak KH, Kim CW, Roh SA, Choi EK, Cho DH, et al. PSMB8 as a candidate marker of responsiveness to preoperative radiation therapy in rectal cancer patients. Int J Radiat Oncol Biol Phys. 2017;98(5):1164–73. Scholar
  15. 15.
    Carames C, Cristobal I, Moreno V, del Puerto L, Moreno I, Rodriguez M, et al. MicroRNA-21 predicts response to preoperative chemoradiotherapy in locally advanced rectal cancer. Int J Colorectal Dis. 2015;30(7):899–906. Scholar
  16. 16.
    Dayde D, Tanaka I, Jain R, Tai MC, Taguchi A. Predictive and prognostic molecular biomarkers for response to neoadjuvant chemoradiation in rectal cancer. Int J Mol Sci. 2017;18(3). Scholar
  17. 17.
    Kim JC, Ha YJ, Roh SA, Cho DH, Choi EY, Kim TW, et al. Novel single-nucleotide polymorphism markers predictive of pathologic response to preoperative chemoradiation therapy in rectal cancer patients. Int J Radiat Oncol Biol Phys. 2013;86(2):350–7. Scholar
  18. 18.
    Davis BN, Hilyard AC, Lagna G, Hata A. SMAD proteins control DROSHA-mediated microRNA maturation. Nature. 2008;454(7200):56–61. Scholar
  19. 19.
    Dreussi E, Pucciarelli S, De Paoli A, Polesel J, Canzonieri V, Agostini M, et al. Predictive role of microRNA-related genetic polymorphisms in the pathological complete response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer patients. Oncotarget. 2016;7(15):19781–93. Scholar
  20. 20.
    Ullmannova V, Popescu NC. Expression profile of the tumor suppressor genes DLC-1 and DLC-2 in solid tumors. Int J Oncol. 2006;29(5):1127–32.PubMedGoogle Scholar
  21. 21.
    Xie CR, Sun HG, Sun Y, Zhao WX, Zhang S, Wang XM, et al. Significance of genetic variants in DLC1 and their association with hepatocellular carcinoma. Mol Med Rep. 2015;12(3):4203–9. Scholar
  22. 22.
    Peng H, Long F, Wu Z, Chu Y, Li J, Kuai R, et al. Downregulation of DLC-1 gene by promoter methylation during primary colorectal cancer progression. Biomed Res Int. 2013;2013:181384. Scholar
  23. 23.
    Pazour GJ, Agrin N, Walker BL, Witman GB. Identification of predicted human outer dynein arm genes: candidates for primary ciliary dyskinesia genes. J Med Genet. 2006;43(1):62–73. Scholar
  24. 24.
    Chang H, Rha SY, Jeung HC, Jung JJ, Kim TS, Kwon HJ, et al. Identification of genes related to a synergistic effect of taxane and suberoylanilide hydroxamic acid combination treatment in gastric cancer cells. J Cancer Res Clin Oncol. 2010;136(12):1901–13. Scholar
  25. 25.
    Antoun A, Vekaria D, Salama RA, Pratt G, Jobson S, Cook M, et al. The genotype of RAET1L (ULBP6), a ligand for human NKG2D (KLRK1), markedly influences the clinical outcome of allogeneic stem cell transplantation. Br J Haematol. 2012;159(5):589–98. Scholar
  26. 26.
    Eagle RA, Traherne JA, Hair JR, Jafferji I, Trowsdale J. ULBP6/RAET1L is an additional human NKG2D ligand. Eur J Immunol. 2009;39(11):3207–16. Scholar
  27. 27.
    Mikata R, Fukai K, Imazeki F, Arai M, Fujiwara K, Yonemitsu Y, et al. BCL2L10 is frequently silenced by promoter hypermethylation in gastric cancer. Oncol Rep. 2010;23(6):1701–8.PubMedGoogle Scholar
  28. 28.
    Kobayashi H, Gotoh J, Hirashima Y, Fujie M, Sugino D, Terao T. Inhibitory effect of a conjugate between human urokinase and urinary trypsin inhibitor on tumor cell invasion in vitro. J Biol Chem. 1995;270(14):8361–6.CrossRefPubMedGoogle Scholar
  29. 29.
    Rose M, Gaisa NT, Antony P, Fiedler D, Heidenreich A, Otto W, et al. Epigenetic inactivation of ITIH5 promotes bladder cancer progression and predicts early relapse of pT1 high-grade urothelial tumours. Carcinogenesis. 2014;35(3):727–36. Scholar
  30. 30.
    Kloten V, Rose M, Kaspar S, von Stillfried S, Knuchel R, Dahl E. Epigenetic inactivation of the novel candidate tumor suppressor gene ITIH5 in colon cancer predicts unfavorable overall survival in the CpG island methylator phenotype. Epigenetics. 2014;9(9):1290–301. Scholar
  31. 31.
    Veeck J, Chorovicer M, Naami A, Breuer E, Zafrakas M, Bektas N, et al. The extracellular matrix protein ITIH5 is a novel prognostic marker in invasive node-negative breast cancer and its aberrant expression is caused by promoter hypermethylation. Oncogene. 2008;27(6):865–76. Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • In Hee Lee
    • 1
  • Keunsoo Kang
    • 2
  • Byung Woog Kang
    • 1
  • Soo jung Lee
    • 1
  • Woo Kyun Bae
    • 3
  • Jun Eul Hwang
    • 3
  • Hye Jin Kim
    • 4
  • Su Yeon Park
    • 4
  • Jun Seok Park
    • 4
  • Gyu Seog Choi
    • 4
  • Jong Gwang Kim
    • 1
    Email author
  1. 1.Department of Oncology/HematologySchool of Medicine, Kyungpook National University, Kyungpook National University Chilgok HospitalDaeguRepublic of Korea
  2. 2.Department of Microbiology, College of Natural SciencesDankook UniversityCheonanRepublic of Korea
  3. 3.Department of Hematology-OncologyChonnam National University Medical SchoolGwangjuRepublic of Korea
  4. 4.Department of SurgerySchool of Medicine, Kyungpook National University, Kyungpook National University Chilgok HospitalDaeguRepublic of Korea

Personalised recommendations