Qualitative Transcriptional Signature for Predicting Pathological Response of Colorectal Cancer to FOLFOX Therapy

Overview

Journal Cancer Sci

Specialty Oncology

Date 2019 Dec 1

PMID 31785020

Citations 5

Authors

Jun He

Jun Cheng

Qingzhou Guan

Haidan Yan

Yawei Li

Wenyuan Zhao

Zheng Guo

Xianlong Wang

Affiliations

Soon will be listed here.

Abstract

FOLFOX (5-fluorouracil, leucovorin and oxaliplatin) is one of the main chemotherapy regimens for colorectal cancer (CRC), but only half of CRC patients respond to this regimen. Using gene expression profiles of 96 metastatic CRC patients treated with FOLFOX, we first selected gene pairs whose within-sample relative expression orderings (REO) were significantly associated with the response to FOLFOX using the exact binomial test. Then, from these gene pairs, we applied an optimization procedure to obtain a subset that achieved the largest F-score in predicting pathological response of CRC to FOLFOX. The REO-based qualitative transcriptional signature, consisting of five gene pairs, was developed in the training dataset consisting of 96 samples with an F-score of 0.90. In an independent test dataset consisting of 25 samples with the response information, an F-score of 0.82 was obtained. In three other independent survival datasets, the predicted responders showed significantly better progression-free survival than the predicted non-responders. In addition, the signature showed a better predictive performance than two published FOLFOX signatures across different datasets and is more suitable for CRC patients treated with FOLFOX than 5-fluorouracil-based signatures. In conclusion, the REO-based qualitative transcriptional signature can accurately identify metastatic CRC patients who may benefit from the FOLFOX regimen.

Citing Articles

Qualitative Transcriptional Signature for Predicting the Pathological Response of Colorectal Cancer to FOLFIRI Therapy.

He J, Wang M, Wu D, Fu H, Shen X Int J Mol Sci. 2024; 25(23).

PMID: 39684481 PMC: 11641733. DOI: 10.3390/ijms252312771.

Identification of cancer risk assessment signature in patients with chronic obstructive pulmonary disease and exploration of the potential key genes.

Guan Q, Zhao P, Tian Y, Yang L, Zhang Z, Li J Ann Med. 2022; 54(1):2309-2320.

PMID: 35993327 PMC: 9415445. DOI: 10.1080/07853890.2022.2112070.

SPTAN1 Expression Predicts Treatment and Survival Outcomes in Colorectal Cancer.

Schrecker C, Behrens S, Schonherr R, Ackermann A, Pauli D, Plotz G Cancers (Basel). 2021; 13(14).

PMID: 34298848 PMC: 8305611. DOI: 10.3390/cancers13143638.

A tumor microenvironment-specific gene expression signature predicts chemotherapy resistance in colorectal cancer patients.

Zhu X, Tian X, Ji L, Zhang X, Cao Y, Shen C NPJ Precis Oncol. 2021; 5(1):7.

PMID: 33580207 PMC: 7881244. DOI: 10.1038/s41698-021-00142-x.

Qualitative transcriptional signature for predicting pathological response of colorectal cancer to FOLFOX therapy.

He J, Cheng J, Guan Q, Yan H, Li Y, Zhao W Cancer Sci. 2019; 111(1):253-265.

PMID: 31785020 PMC: 6942442. DOI: 10.1111/cas.14263.

References

Klupp F, Giese C, Halama N, Franz C, Lasitschka F, Warth A . E3 ubiquitin ligase Smurf2: a prognostic factor in microsatellite stable colorectal cancer. Cancer Manag Res. 2019; 11:1795-1803. PMC: 6391146. DOI: 10.2147/CMAR.S178111. View

Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C . The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2009; 38(Database issue):D525-31. PMC: 2808934. DOI: 10.1093/nar/gkp878. View

Tong M, Zheng W, Lu X, Ao L, Li X, Guan Q . Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues. Oncotarget. 2015; 6(38):41216-27. PMC: 4747401. DOI: 10.18632/oncotarget.5649. View

Wang Y, Xue J, Kuang H, Zhou X, Liao L, Yin F . microRNA-1297 Inhibits the Growth and Metastasis of Colorectal Cancer by Suppressing Cyclin D2 Expression. DNA Cell Biol. 2017; 36(11):991-999. DOI: 10.1089/dna.2017.3829. View

Mewes H, Ruepp A, Theis F, Rattei T, Walter M, Frishman D . MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res. 2010; 39(Database issue):D220-4. PMC: 3013725. DOI: 10.1093/nar/gkq1157. View

Kho P, Wang Z, Zhuang L, Li Y, Chew J, Ng H . p53-regulated transcriptional program associated with genotoxic stress-induced apoptosis. J Biol Chem. 2004; 279(20):21183-92. DOI: 10.1074/jbc.M311912200. View

Liu H, Li Y, He J, Guan Q, Chen R, Yan H . Robust transcriptional signatures for low-input RNA samples based on relative expression orderings. BMC Genomics. 2017; 18(1):913. PMC: 5704640. DOI: 10.1186/s12864-017-4280-7. View

Ma Y, Lu B, Ruan W, Wang H, Lin J, Hu H . Tumor suppressor gene insulin-like growth factor binding protein-related protein 1 (IGFBP-rP1) induces senescence-like growth arrest in colorectal cancer cells. Exp Mol Pathol. 2008; 85(2):141-5. DOI: 10.1016/j.yexmp.2008.04.005. View

Oshima T, Kawasaki T, Ohashi R, Hasegawa G, Jiang S, Umezu H . Downregulated P1 promoter-driven hepatocyte nuclear factor-4alpha expression in human colorectal carcinoma is a new prognostic factor against liver metastasis. Pathol Int. 2007; 57(2):82-90. DOI: 10.1111/j.1440-1827.2006.02061.x. View

10.

Song K, Guo Y, Wang X, Cai H, Zheng W, Li N . Transcriptional signatures for coupled predictions of stage II and III colorectal cancer metastasis and fluorouracil-based adjuvant chemotherapy benefit. FASEB J. 2018; 33(1):151-162. DOI: 10.1096/fj.201800222RRR. View

11.

Eisenhauer E, Therasse P, Bogaerts J, Schwartz L, Sargent D, Ford R . New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1). Eur J Cancer. 2008; 45(2):228-47. DOI: 10.1016/j.ejca.2008.10.026. View

12.

Salwinski L, Miller C, Smith A, Pettit F, Bowie J, Eisenberg D . The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2003; 32(Database issue):D449-51. PMC: 308820. DOI: 10.1093/nar/gkh086. View

13.

Grimaldi S, Terroir M, Caramella C . Advances in oncological treatment: limitations of RECIST 1.1 criteria. Q J Nucl Med Mol Imaging. 2017; 62(2):129-139. DOI: 10.23736/S1824-4785.17.03038-2. View

14.

Mekenkamp L, Koopman M, Teerenstra S, van Krieken J, Mol L, Nagtegaal I . Clinicopathological features and outcome in advanced colorectal cancer patients with synchronous vs metachronous metastases. Br J Cancer. 2010; 103(2):159-64. PMC: 2906733. DOI: 10.1038/sj.bjc.6605737. View

15.

Guan Q, Yan H, Chen Y, Zheng B, Cai H, He J . Quantitative or qualitative transcriptional diagnostic signatures? A case study for colorectal cancer. BMC Genomics. 2018; 19(1):99. PMC: 5789529. DOI: 10.1186/s12864-018-4446-y. View

16.

Benson A, Venook A, Al-Hawary M, Cederquist L, Chen Y, Ciombor K . Rectal Cancer, Version 2.2018, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw. 2018; 16(7):874-901. PMC: 10203817. DOI: 10.6004/jnccn.2018.0061. View

17.

Liu Y, Yang Y, Xu H, Dong X . Increased expression of ubiquitin-specific protease 22 can promote cancer progression and predict therapy failure in human colorectal cancer. J Gastroenterol Hepatol. 2010; 25(11):1800-5. DOI: 10.1111/j.1440-1746.2010.06352.x. View

18.

Sun T, Song Z, Tian Y, Tian W, Zhu C, Ji G . Basolateral amygdala input to the medial prefrontal cortex controls obsessive-compulsive disorder-like checking behavior. Proc Natl Acad Sci U S A. 2019; 116(9):3799-3804. PMC: 6397577. DOI: 10.1073/pnas.1814292116. View

19.

Benson 3rd A, Venook A, Cederquist L, Chan E, Chen Y, Cooper H . Colon Cancer, Version 1.2017, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw. 2017; 15(3):370-398. DOI: 10.6004/jnccn.2017.0036. View

20.

Watanabe H, Okada M, Kaji Y, Satouchi M, Sato Y, Yamabe Y . [New response evaluation criteria in solid tumours-revised RECIST guideline (version 1.1)]. Gan To Kagaku Ryoho. 2009; 36(13):2495-501. View