Abstract
Although genome-wide association studies (GWASs) have identified over 100 colorectal cancer (CRC) risk loci, an understanding of causal genes or risk variants and their biological functions in these loci remain unclear. Recently, genomic loci 10q26.12 with lead SNP rs1665650 was identified as an essential CRC risk loci of Asian populations. However, the functional mechanism of this region has not been fully clarified. Here, we applied an RNA interfering-based on-chip approach to screen for the genes essential for cell proliferation in the CRC risk loci 10q26.12. Notably, HSPA12A had the most significant effect among the identified genes and functioned as a crucial oncogene facilitating cell proliferation. Moreover, we conducted an integrative fine-mapping analysis to identify putative casual variants and further explored their association with CRC risk in a large-scale Chinese population consisting of 4054 cases and 4054 controls and also independently validated in 5208 cases and 20,832 controls from the UK biobank cohort. We identified a risk SNP rs7093835 in the intron of HSPA12A that was significantly associated with an increased risk of CRC (OR 1.23, 95% CI 1.08–1.41, P = 1.92 × 10–3). Mechanistically, the risk variant could facilitate an enhancer–promoter interaction mediated by the transcriptional factor (TF) GRHL1 and ultimately upregulate HSPA12A expression, which provides functional evidence to support our population findings. Collectively, our study reveals the important role of HSPA12A in CRC development and illustrates a novel enhancer–promoter interaction module between HSPA12A and its regulatory elements rs7093835, providing new insights into the etiology of CRC.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
All accession codes or web links for publicly available datasets are described in the paper. Data are available from corresponding author on reasonable request.
References
Ardlie KG, Deluca DS, Segrè AV et al (2015) Human genomics. The genotype-tissue expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science (new York, NY) 348(6235):648–660. https://doi.org/10.1126/science.1262110
Bycroft C, Freeman C, Petkova D et al (2018) The UK Biobank resource with deep phenotyping and genomic data. Nature 562(7726):203–209. https://doi.org/10.1038/s41586-018-0579-z
Chen W, Zheng R, Baade PD et al (2016) Cancer statistics in China, 2015. CA Cancer J Clin 66(2):115–132. https://doi.org/10.3322/caac.21338
Frisch SM, Farris JC, Pifer PM (2017) Roles of grainyhead-like transcription factors in cancer. Oncogene 36(44):6067–6073. https://doi.org/10.1038/onc.2017.178
Fulco CP, Munschauer M, Anyoha R et al (2016) Systematic mapping of functional enhancer–promoter connections with CRISPR interference. Science (new York, NY) 354(6313):769–773. https://doi.org/10.1126/science.aag2445
Gasperoni JG, Fuller JN, Darido C, Wilanowski T, Dworkin S (2022) Grainyhead-like (Grhl) target genes in development and cancer. Int J Mol Sci 23(5):2735. https://doi.org/10.3390/ijms23052735
Gong J, Tian J, Lou J et al (2016) A functional polymorphism in lnc-LAMC2-1:1 confers risk of colorectal cancer by affecting miRNA binding. Carcinogenesis 37(5):443–451. https://doi.org/10.1093/carcin/bgw024
Gong J, Tian J, Lou J et al (2018) A polymorphic MYC response element in KBTBD11 influences colorectal cancer risk, especially in interaction with an MYC-regulated SNP rs6983267. Ann Oncol 29(3):632–639. https://doi.org/10.1093/annonc/mdx789
He Y, Gan M, Wang Y et al (2021) EGFR-ERK induced activation of GRHL1 promotes cell cycle progression by up-regulating cell cycle related genes in lung cancer. Cell Death Dis 12(5):430. https://doi.org/10.1038/s41419-021-03721-9
Howie BN, Donnelly P, Marchini J (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5(6):e1000529. https://doi.org/10.1371/journal.pgen.1000529
Huyghe JR, Bien SA, Harrison TA et al (2019) Discovery of common and rare genetic risk variants for colorectal cancer. Nat Genet 51(1):76–87. https://doi.org/10.1038/s41588-018-0286-6
Jia WH, Zhang B, Matsuo K et al (2013) Genome-wide association analyses in East Asians identify new susceptibility loci for colorectal cancer. Nat Genet 45(2):191–196. https://doi.org/10.1038/ng.2505
Kopp F, Mendell JT (2018) Functional classification and experimental dissection of long noncoding RNAs. Cell 172(3):393–407. https://doi.org/10.1016/j.cell.2018.01.011
Lu Y, Kweon SS, Tanikawa C et al (2019) Large-scale genome-wide association study of east Asians identifies loci associated with risk for colorectal cancer. Gastroenterology 156(5):1455–1466. https://doi.org/10.1053/j.gastro.2018.11.066
McDonald ER 3rd, de Weck A, Schlabach MR et al (2017) Project DRIVE: a compendium of cancer dependencies and synthetic lethal relationships uncovered by large-scale. Deep RNAi Screen Cell 170(3):577-592.e10. https://doi.org/10.1016/j.cell.2017.07.005
Meyers RM, Bryan JG, McFarland JM et al (2017) Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet 49(12):1779–1784. https://doi.org/10.1038/ng.3984
Pan YJ, Huo FC, Kang MJ, Liu BW, Wu MD, Pei DS (2022) Alternative splicing of HSPA12A pre-RNA by SRSF11 contributes to metastasis potential of colorectal cancer. Clin Transl Med 12(11):e1113. https://doi.org/10.1002/ctm2.1113
Song M, Garrett WS, Chan AT (2015) Nutrients, foods and colorectal cancer prevention. Gastroenterology 148(6):1244–60.e16. https://doi.org/10.1053/j.gastro.2014.12.035
Sung H, Ferlay J, Siegel RL et al (2021) Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 71(3):209–249. https://doi.org/10.3322/caac.21660
Tian J, Chang J, Gong J et al (2019a) Systematic functional interrogation of genes in GWAS loci identified ATF1 as a key driver in colorectal cancer modulated by a promoter-enhancer interaction. Am J Hum Genet 105(1):29–47. https://doi.org/10.1016/j.ajhg.2019.05.004
Tian J, Wang Z, Mei S et al (2019b) CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer. Nucleic Acids Res 47(D1):D909-d916. https://doi.org/10.1093/nar/gky954
Tian J, Lou J, Cai Y et al (2020) Risk SNP-mediated enhancer–promoter interaction drives colorectal cancer through both FADS2 and AP002754.2. Cancer Res 80(9):1804–1818. https://doi.org/10.1158/0008-5472.CAN-19-2389
Wang H, Haiman CA, Burnett T et al (2013) Fine-mapping of genome-wide association study-identified risk loci for colorectal cancer in African Americans. Hum Mol Genet 22(24):5048–5055. https://doi.org/10.1093/hmg/ddt337
Wang M, Gu D, Du M et al (2016) Common genetic variation in ETV6 is associated with colorectal cancer susceptibility. Nat Commun 7:11478. https://doi.org/10.1038/ncomms11478
Weintraub AS, Li CH, Zamudio AV et al (2017) YY1 is a structural regulator of enhancer–promoter loops. Cell 171(7):1573-1588.e28. https://doi.org/10.1016/j.cell.2017.11.008
Wu J, Liu T, Rios Z, Mei Q, Lin X, Cao S (2017) Heat shock proteins and cancer. Trends Pharmacol Sci 38(3):226–256. https://doi.org/10.1016/j.tips.2016.11.009
Zeng C, Matsuda K, Jia WH et al (2016) Identification of susceptibility loci and genes for colorectal cancer risk. Gastroenterology 150(7):1633–1645. https://doi.org/10.1053/j.gastro.2016.02.076
Zhang Y, Wong CH, Birnbaum RY et al (2013) Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 504(7479):306–310. https://doi.org/10.1038/nature12716
Zhang B, Jia WH, Matsuda K et al (2014) Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk. Nat Genet 46(6):533–542. https://doi.org/10.1038/ng.2985
Zhao Y, Wei L, Shao M et al (2017) BRCA1-associated protein increases invasiveness of esophageal squamous cell carcinoma. Gastroenterology 153(5):1304-1319.e5. https://doi.org/10.1053/j.gastro.2017.07.042
Acknowledgements
We are grateful to every patient, their families, and referring physicians that have participated in these studies, and the numerous members of our laboratories for their valuable contributions over many years.
Funding
This work was supported by the Program of National Science Fund for Distinguished Young Scholars of China (NSFC-81925032), Key Program of National Natural Science Foundation of China (NSFC-82130098), and Natural Science Foundation of Hubei Province (2019CFA009) for Xiaoping Miao; National Natural Science Foundation of China (NSFC-82103929, NSFC-82273713), Fundamental Research Funds for the Central Universities (WHU:2042022kf1205), Knowledge Innovation Program of Wuhan (whkxjsj011), and Translational Medicine and Interdisciplinary Research Joint Fund of Zhongnan Hospital of Wuhan University (ZNJC202207) for Jianbo Tian; Youth Program of National Natural Science Foundation of China (NSFC-82003547) and Fundamental Research Funds for the Central Universities (WHU: 2042022kf1031) for Ying Zhu.
Author information
Authors and Affiliations
Contributions
JT, BL, and XM were the overall principal investigators in this study who conceived the study and obtained financial support, YZ, HL, JT, BL, and XM were responsible for the study design and supervised the entire study. BL, ZL, and FZ performed statistical analyses, interpreted the results, and drafted the initial manuscript. BL, LF, YC, CC, GL, MZ, JH, CN, YL, WW, HG, YL, SC, HL, SY, HZ, and WT performed laboratory experiments, TY, JL, CH, XY, BX, YZ, RZ, HL, JT, BL, and XM were responsible for patient recruitment and sample preparation. All authors approved the final report for publication.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that they have no competing interests.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Lu, Z., Fan, L., Zhang, F. et al. HSPA12A was identified as a key driver in colorectal cancer GWAS loci 10q26.12 and modulated by an enhancer–promoter interaction. Arch Toxicol 97, 2015–2028 (2023). https://doi.org/10.1007/s00204-023-03494-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00204-023-03494-4