Gene Expression Profiling Identifies Potential Biomarkers for Colorectal Cancer Using NanoString nCounter Assay

doi:10.1007/s12204-022-2440-7

Abstract

Abstract: Colorectal cancer (CRC) is one of the most common malignancies worldwide. Development of predictivemolecular markers may help to achieve the best outcome in clinic. The purpose of this study is to identify thedifferentially expressed genes and new potential predictive and prognostic molecular biomarkers for CRC. Inthis study, CRC and matched normal tissues acquired from the same patient were used to extract total RNA.The NanoString nCounter assay was applied to determine the differentially expressed genes. The results werethen validated by using the Cancer Genome Atlas data. Finally, we identified 27 genes that revealed significantcorrelation with CRC in the tumor tissue. Several genes in the pan-cancer panel showed significant differentialexpression, which were more universal than others in the CRC tissue. Since some of them have not been reportedas being directly related to CRC yet, future mechanism studies can be designed based on this study. Our studydemonstrated NanoString nCounter assay could serve as an alternative approach for gene expression analysis andidentified several unreported differently expressed genes in CRC patients, which may provide some importantclues for more in-depth study of CRC and serve as potential predictive molecular biomarkers for clinical diagnosisapplication.

Key words: colorectal cancer, biomarkers, gene expression, NanoString nCounter assay

摘要： 大肠癌（CRC）是世界上最常见的恶性肿瘤之一。预测性分子标记物的开发可能有助于在临床上获得最佳结果。本研究的目的是鉴定CRC的差异表达基因和新的潜在预测和预后分子生物标志物。在这项研究中，使用从同一患者获得的CRC和匹配的正常组织来提取总RNA。应用NanoString nCounter测定法测定差异表达的基因。然后使用癌症基因组图谱数据验证结果。最后，我们在肿瘤组织中鉴定了27个与CRC显著相关的基因。泛癌组中的几个基因显示出显著的差异表达，这在CRC组织中比其他基因更普遍。由于其中一些尚未被报道与CRC直接相关，因此可以根据这项研究设计未来的机制研究。我们的研究表明，NanoString nCounter检测可以作为基因表达分析的替代方法，并在CRC患者中鉴定了几个未报告的不同表达基因，这可能为更深入地研究CRC提供一些重要线索，并作为临床诊断应用的潜在预测分子生物标志物。

关键词: 大肠癌，生物标志物，基因表达，NanoString nCounter assay

CLC Number:

R 735

ZHAO Hui (赵晖)，WEN Baiqing (文柏清)，KANG Yani*(康亚妮). Gene Expression Profiling Identifies Potential Biomarkers for Colorectal Cancer Using NanoString nCounter Assay[J]. J Shanghai Jiaotong Univ Sci, 2023, 28(4): 432-.

References

[1] ZHU J, TAN Z, HOLLIS-HANSEN K, et al. Epidemiological trends in colorectal cancer in China: An ecological study [J]. Digestive Diseases and Sciences, 2017,62(1): 235-243.
[2] ANSA B, COUGHLIN S, ALEMA-MENSAH E, etal. Evaluation of colorectal cancer incidence trends inthe United States (2000–2014) [J]. Journal of ClinicalMedicine, 2018, 7(2): 22.
[3] CUNNINGHAM D, ATKIN W, LENZ H, et al. Colorectal cancer [J]. Lancet, 2010, 375(9719): 1030-1047.
[4] GEISS G K, BUMGARNER R E, BIRDITT B, etal. Direct multiplexed measurement of gene expressionwith color-coded probe pairs [J]. Nature Biotechnology,2008, 26(3): 317-325.
[5] OZSOLAK F, MILOS P M. RNA sequencing: Advances, challenges and opportunities [J]. Nature Reviews Genetics, 2011, 12(2): 87-98.
[6] SHETH J, ARNOLDO A, ZHONG Y, et al. Sarcomasubgrouping by detection of fusion transcripts usingNanoString nCounter technology [J]. Pediatric and Developmental Pathology, 2019, 22(3): 205-213.
[7] HYEON J, CHO S Y, HONG M E, et al. NanoStringnCounter? approach in breast cancer: A comparativeanalysis with quantitative real-time polymerase chainreaction, in situ hybridization, and immunohistochemistry [J]. Journal of Breast Cancer, 2017, 20(3): 286-296.
[8] TSANG H F, XUE V W, KOH S P, et al. NanoString, anovel digital color-coded barcode technology: Currentand future applications in molecular diagnostics [J].Expert Review of Molecular Diagnostics, 2017, 17(1):95-103.
[9] TANG Z, LI C, KANG B, et al. GEPIA: A web serverfor cancer and normal gene expression profiling andinteractive analyses [J]. Nucleic Acids Research, 2017,45(W1): W98-W102.
[10] LU J, KSENDZOVSKY A, YANG C, et al. CNTFreceptor subunit α as a marker for glioma tumorinitiating cells and tumor grade: Laboratory investigation [J]. Journal of Neurosurgery, 2012, 117(6): 1022-1031.
[11] MA D, JING X, SHEN B, et al. Leukemia inhibitoryfactor receptor negatively regulates the metastasis ofpancreatic cancer cells in vitro and in vivo [J]. Oncology Reports, 2016, 36(2): 827-836.
[12] LUO Q, WANG C, JIN G, et al. LIFR functions as ametastasis suppressor in hepatocellular carcinoma bynegatively regulating phosphoinositide 3-kinase/AKTpathway [J]. Carcinogenesis, 2015, 36(10): 1201-1212.
[13] GREGORY K J, MORIN S M, SCHNEIDER S S.Regulation of early growth response 2 expression bysecreted frizzled related protein 1 [J]. BMC Cancer,2017, 17(1): 473.
[14] BOLDRUP L, GU X, COATES P J, et al. Gene expression changes in tumor free tongue tissue adjacent totongue squamous cell carcinoma [J]. Oncotarget, 2017,8(12): 19389-19402.
[15] FISCHER H, STENLING R, RUBIO C, et al. Colorectal carcinogenesis is associated with stromal expressionof COL11A1 and COL5A2 [J]. Carcinogenesis, 2001,22(6): 875-878.
[16] GALV′AN J A, GARC′IA-MART′INEZ J, V′AZQUEZVILLA F, et al. Validation of COL11A1/procollagen11A1 expression in TGF-β 1-activated immortalisedhuman mesenchymal cells and in stromal cells of human colon adenocarcinoma [J]. BMC Cancer, 2014, 14:867.
[17] CHEN L, LU D, SUN K, et al. Identification ofbiomarkers associated with diagnosis and prognosis ofcolorectal cancer patients based on integrated bioinformatics analysis [J]. Gene, 2019, 692: 119-125.
[18] JIANG H, GE F, HU B, et al. rs35301225 polymorphism in miR-34a promotes development of humancolon cancer by deregulation of 3’UTR in E2F1 in Chinese population [J]. Cancer Cell International, 2017,17: 39.
[19] SHANTHA KUMARA H M C, GAITA D J, MIYAGAKI H, et al. Minimally invasive colorectal resectionis associated with significantly elevated levels of plasmamatrix metalloproteinase 3 (MMP-3 ) during the firstmonth after surgery which may promote the growth ofresidual metastases [J]. Surgical Endoscopy and OtherInterventional Techniques, 2014, 28(12): 3322-3328.
[20] JUNG Y, JUN S, LEE S H, et al. Wnt2 complementsWnt/β-catenin signaling in colorectal cancer [J]. Oncotarget, 2015, 6(35): 37257-37268.
[21] KRAMER N, SCHMOELLERL J, UNGER C, et al.Autocrine WNT2 signaling in fibroblasts promotes colorectal cancer progression [J]. Oncogene, 2017, 36(39):5460-5472.
[22] HUANG R, MO D, WU J, et al. CD133 expression correlates with clinicopathologic features and poorprognosis of colorectal cancer patients: An updatedmeta-analysis of 37 studies [J]. Medicine, 2018, 97(23):e10446.
[23] MESCI A, TAEB S, HUANG X, et al. Pea3 expression promotes the invasive and metastatic potential ofcolorectal carcinoma [J]. World Journal of Gastroenterology, 2014, 20(46): 17376-17387.
[24] HUANG H. Matrix metalloproteinase-9 (MMP-9 ) asa cancer biomarker and MMP-9 biosensors: Recentadvances [J]. Sensors, 2018, 18(10): 3249.
[25] LIANG S, CHANG L. Serum matrixmetalloproteinase-9 level as a biomarker for colorectal cancer: A diagnostic meta-analysis [J].Biomarkers in Medicine, 2018, 12(4): 393-402.
[26] POLI V, FAGNOCCHI L, FASCIANI A, et al. MYC -driven epigenetic reprogramming favors the onset oftumorigenesis by inducing a stem cell-like state [J]. Nature Communications, 2018, 9: 1024.
[27] SCHICK M, HABRINGER S, NILSSON J A, et al.Pathogenesis and therapeutic targeting of aberrantMYC expression in haematological cancers [J]. BritishJournal of Haematology, 2017, 179(5): 724-738.
[28] YU T, WANG L, LI W, et al. Downregulation of miR-491-5p promotes gastric cancer metastasis by regulating SNAIL and FGFR4 [J]. Cancer Science, 2018,109(5): 1393-1403.
[29] ARABPOUR M, RASOLMALI R, TALEI A, et al.Granzyme B production by activated B cells derivedfrom breast cancer-draining lymph nodes [J]. Molecular Immunology, 2019, 114: 172-178.
[30] SUMTER T F, XIAN L, HUSO T, et al. The highmobility group A1 (HMGA1) transcriptome in cancer and development [J]. Current Molecular Medicine,2016, 16(4): 353-393.
[31] GAO Y, NAN X, SHI X, et al. SREBP1 promotes theinvasion of colorectal cancer accompanied upregulationof MMP7 expression and NF-κB pathway activation[J]. BMC Cancer, 2019, 19(1): 685.
[32] YANG L, SONG X, ZHU J, et al. Tumor suppressor microRNA-34a inhibits cell migration and invasionby targeting MMP-2/MMP-9/FNDC3B in esophagealsquamous cell carcinoma [J]. International Journal ofOncology, 2017, 51(1): 378-388.
[33] FENG D, ZHAO T, YAN K, et al. Gonadotropins promote human ovarian cancer cell migration and invasionvia a cyclooxygenase 2-dependent pathway [J]. Oncology Reports, 2017, 38(2): 1091-1098.