Single cell sequencing technology and its application in liver metastasis of colorectal cancer_CHINESE JOURNAL OF BASES AND CLINICS IN GENERAL SURGERY

Authors：

CHEN Jingli ¹ ,  WANG Guorong ²

1. Xi’an Medical College, Xi’an 710021, P. R. China;
2. Department of General Surgery, Shaanxi Provincial People’s Hospital, Xi’an 710068, P. R. China;

Corresponding author：

WANG Guorong, Email: 13227701303@qq.com

Keywords：

single cell sequencing; colorectal cancer; liver metastasis

DOI：

10.7507/1007-9424.202301046

Video：

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Objective To explore the research progress in molecular mechanisms, clinical diagnosis and treatment of single cell sequencing (SCS) techniques in the progression of colorectal cancer liver metastasis (CRLM). Method The literatures on SCS in CRLM at home and abroad in recent years were reviewed. Results SCS technology could perform high-throughput sequencing on the genetic information of different cell subsets at the single-cell level, which was helpful to explore the molecular mechanism of action in the occurrence, development, metastasis, immune escape and drug resistance of colorectal cancer liver metastasis. Thus making the clinical diagnosis, treatment, and prognosis of colorectal cancer more accurate. Conclusion SCS technology, as an emerging sequencing technology, can provide us with updated ideas and more perspectives to explore the occurrence and development of tumors and the prevention and treatment of tumors.

Citation： CHEN Jingli, WANG Guorong. Single cell sequencing technology and its application in liver metastasis of colorectal cancer. CHINESE JOURNAL OF BASES AND CLINICS IN GENERAL SURGERY, 2023, 30(6): 745-750. doi: 10.7507/1007-9424.202301046 Copy

1.	Siegel RL, Miller KD, Fuchs HE, et al. Cancer statistics, 2022. CA Cancer J Clin, 2022, 72(1): 7-33.
2.	Zhang Y, Song J, Zhao Z, et al. Single-cell transcriptome analysis reveals tumor immune microenvironment heterogenicity and granulocytes enrichment in colorectal cancer liver metastases. Cancer Lett, 2020, 470: 84-94.
3.	朱德祥, 韦烨, 任黎, 等. 中山医院结直肠癌MDT讨论治疗策略分析. 中华结直肠疾病电子杂志, 2020, 9(3): 236-239.
4.	Liu L, Liu C, Quintero A, et al. Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nat Commun, 2019, 10(1): 470.
5.	Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A, 1977, 74(12): 5463-5467.
6.	Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A, 1977, 74(2): 560-564.
7.	Mccombie WR, Mcpherson JD, Mardis ER. Next-generation sequencing technologies. Cold Spring Harb Perspect Med, 2019, 9(11):doi: 10.1101/cshperspect.a036798.
8.	van Dijk EL, Jaszczyszyn Y, Naquin D, et al. The third revolution in sequencing technology. Trends Genet, 2018, 34(9): 666-681.
9.	Mannarapu M, Dariya B, Bandapalli OR. Application of single-cell sequencing technologies in pancreatic cancer. Mol Cell Biochem, 2021, 476(6): 2429-2437.
10.	郑小翠. 单细胞测序技术在实体瘤研究中的应用进展. 中国癌症杂志, 2019, 29(7): 535-539.
11.	Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet, 2016, 17(3): 175-188.
12.	魏颖. 单细胞转录组测序在哮喘研究中应用的研究进展. 复旦学报(医学版), 2021, 48(3): 404-409.
13.	王莉, 李晓辉. 单细胞测序技术在动脉粥样硬化研究中的研究进展. 医学研究生学报, 2021, 34(9): 969-973.
14.	操利超, 巴颖, 张核子. 单细胞测序方法研究进展. 生物信息学, 2022, 20(2): 91-99.
15.	Song Y, Xu X, Wang W, et al. Single cell transcriptomics: moving towards multi-omics. Analyst, 2019, 144(10): 3172-3189.
16.	Evrony GD, Hinch AG, Luo C. Applications of single-cell DNA sequencing. Annu Rev Genomics Hum Genet, 2021, 22: 171-197.
17.	Feng Y, Zhang Y, Ying C, et al. Nanopore-based fourth-generation DNA sequencing technology. Genomics Proteomics Bioinformatics, 2015, 13(1): 4-16.
18.	Olsen TK, Baryawno N. Introduction to Single-Cell RNA Sequencing. Curr Protoc Mol Biol, 2018, 122(1): e57. doi: 10.1002/cpmb.57.
19.	Yasen A, Aini A, Wang H, et al. Progress and applications of single-cell sequencing techniques. Infect Genet Evol, 2020, 80: 104198. doi: 10.1016/j.meegid.2020.104198.
20.	王权, 王铸, 张振, 等. 单细胞测序的技术概述. 中国医药导刊, 2020, 22(7): 433-439.
21.	Harada A, Kimura H, Ohkawa Y. Recent advances in single-cell epigenomics. Curr Opin Struct Biol, 2021, 71: 116-122.
22.	程馨, 燕蕊, 郭帆. 单细胞多组学技术新进展及其在发育生物学研究中的应用. 中国科学:生命科学, 2021, 51(5): 496-506.
23.	Macaulay IC, Haerty W, Kumar P, et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods, 2015, 12(6): 519-522.
24.	Li H, Courtois ET, Sengupta D, et al. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat Genet, 2017, 49(5): 708-718.
25.	Tang F, Barbacioru C, Wang Y, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods, 2009, 6(5): 377-382.
26.	Bass AJ, Lawrence MS, Brace LE, et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet, 2011, 43(10): 964-968.
27.	Yu C, Yu J, Yao X, et al. Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing. Cell Res, 2014, 24(6): 701-712.
28.	Zhao J, Chen Y. Systematic identification of cancer-associated-fibroblast-derived genes in patients with colorectal cancer based on single-cell sequencing and transcriptomics. Front Immunol, 2022, 13: 988246. doi: 10.3389/fimmu.2022.988246.
29.	Dai W, Zhou F, Tang D, et al. Single-cell transcriptional profiling reveals the heterogenicity in colorectal cancer. Medicine (Baltimore), 2019, 98(34): e16916. doi: 10.1097/MD.0000000000016916.
30.	Zhou Y, Bian S, Zhou X, et al. Single-Cell multiomics sequencing reveals prevalent genomic alterations in tumor stromal cells of human colorectal cancer. Cancer Cell, 2020, 38(6): 818-828.
31.	Li C, Sun YD, Yu GY, et al. Integrated omics of metastatic colorectal cancer. Cancer Cell, 2020, 38(5): 734-747.
32.	Tsilimigras DI, Brodt P, Clavien PA, et al. Liver metastases. Nat Rev Dis Primers, 2021, 7(1): 27. doi: 10.1038/s41572-021-00261-6.
33.	Heitzer E, Auer M, Gasch C, et al. Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res, 2013, 73(10): 2965-2975.
34.	Kim TM, Jung SH, An CH, et al. Subclonal genomic architectures of primary and metastatic colorectal cancer based on intratumoral genetic heterogeneity. Clin Cancer Res, 2015, 21(19): 4461-4472.
35.	Leung ML, Davis A, Gao R, et al. Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer. Genome Res, 2017, 27(8): 1287-1299.
36.	Bian S, Hou Y, Zhou X, et al. Single-cell multiomics sequencing and analyses of human colorectal cancer. Science, 2018, 362(6418): 1060-1063.
37.	王智锋. 单细胞全外显子组测序在转移性结直肠癌克隆进化中的初步应用. 华南理工大学, 2019.
38.	Miyaki M, Iijima T, Konishi M, et al. Higher frequency of Smad4 gene mutation in human colorectal cancer with distant metastasis. Oncogene, 1999, 18(20): 3098-3103.
39.	李承君, 和水祥. IL-17在结直肠炎-癌转变中的作用机制研究进展. 细胞与分子免疫学杂志, 2022, 38(2): 177-182.
40.	Wu Y, Yang S, Ma J, et al. Spatiotemporal immune landscape of colorectal cancer liver metastasis at single-cell level. Cancer Discov, 2022, 12(1): 134-153.
41.	Tang J, Tu K, Lu K, et al. Single-cell exome sequencing reveals multiple subclones in metastatic colorectal carcinoma. Genome Med, 2021, 13(1): 148. doi: 10.1186/s13073-021-00962-3.
42.	中国医师协会外科医师分会, 中华医学会外科学分会胃肠外科学组, 中华医学会外科学分会结直肠外科学组, 等. 中国结直肠癌肝转移诊断和综合治疗指南(2020版). 中国实用外科杂志, 2021, 41(1): 1-11.
43.	Tauriello DV, Calon A, Lonardo E, et al. Determinants of metastatic competency in colorectal cancer. Mol Oncol, 2017, 11(1): 97-119.
44.	Kreso A, O'Brien CA, van Galen P, et al. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science, 2013, 339(6119): 543-548.
45.	Jabbari N, Kenerson HL, Lausted C, et al. Modulation of immune checkpoints by chemotherapy in human colorectal liver metastases. Cell Rep Med, 2020, 1(9): 100160. doi: 10.1016/j.xcrm.2020.100160.
46.	袁浩, 钟华戈, 严林海, 等. 基于生物信息学分析结直肠癌STIM1高频突变介导的免疫抵抗模式及其分子机制. 中国癌症防治杂志, 2020, 12(5): 566-571.
47.	付卫, 黄坤蓉, 付敏, 等. CD73在结直肠癌组织中的表达及其与临床病理参数的关系. 现代肿瘤医学, 2019, 27(10): 1753-1757.
48.	Künzli BM, Bernlochner MI, Rath S, et al. Impact of CD39 and purinergic signalling on the growth and metastasis of colorectal cancer. Purinergic Signal, 2011, 7(2): 231-241.
49.	Kim M, Min YK, Jang J, et al. Single-cell RNA sequencing reveals distinct cellular factors for response to immunotherapy targeting CD73 and PD-1 in colorectal cancer. J Immunother Cancer, 2021, 9(7): e002503. doi: 10.1136/jitc-2021-002503.
50.	Lin C, Yang H, Zhao W, et al. CTSB⁺ macrophage repress memory immune hub in the liver metastasis site of colorectal cancer patient revealed by multi-omics analysis. Biochem Biophys Res Commun, 2022, 626: 8-14.
51.	马燕如, 季林华, 童天颍, 等. 基于单细胞RNA测序的结直肠癌预后预测模型的建立和验证. 上海交通大学学报(医学版), 2021, 41(2): 159-165.

1. Siegel RL, Miller KD, Fuchs HE, et al. Cancer statistics, 2022. CA Cancer J Clin, 2022, 72(1): 7-33.
2. Zhang Y, Song J, Zhao Z, et al. Single-cell transcriptome analysis reveals tumor immune microenvironment heterogenicity and granulocytes enrichment in colorectal cancer liver metastases. Cancer Lett, 2020, 470: 84-94.
3. 朱德祥, 韦烨, 任黎, 等. 中山医院结直肠癌MDT讨论治疗策略分析. 中华结直肠疾病电子杂志, 2020, 9(3): 236-239.
4. Liu L, Liu C, Quintero A, et al. Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nat Commun, 2019, 10(1): 470.
5. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A, 1977, 74(12): 5463-5467.
6. Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A, 1977, 74(2): 560-564.
7. Mccombie WR, Mcpherson JD, Mardis ER. Next-generation sequencing technologies. Cold Spring Harb Perspect Med, 2019, 9(11):doi: 10.1101/cshperspect.a036798.
8. van Dijk EL, Jaszczyszyn Y, Naquin D, et al. The third revolution in sequencing technology. Trends Genet, 2018, 34(9): 666-681.
9. Mannarapu M, Dariya B, Bandapalli OR. Application of single-cell sequencing technologies in pancreatic cancer. Mol Cell Biochem, 2021, 476(6): 2429-2437.
10. 郑小翠. 单细胞测序技术在实体瘤研究中的应用进展. 中国癌症杂志, 2019, 29(7): 535-539.
11. Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet, 2016, 17(3): 175-188.
12. 魏颖. 单细胞转录组测序在哮喘研究中应用的研究进展. 复旦学报(医学版), 2021, 48(3): 404-409.
13. 王莉, 李晓辉. 单细胞测序技术在动脉粥样硬化研究中的研究进展. 医学研究生学报, 2021, 34(9): 969-973.
14. 操利超, 巴颖, 张核子. 单细胞测序方法研究进展. 生物信息学, 2022, 20(2): 91-99.
15. Song Y, Xu X, Wang W, et al. Single cell transcriptomics: moving towards multi-omics. Analyst, 2019, 144(10): 3172-3189.
16. Evrony GD, Hinch AG, Luo C. Applications of single-cell DNA sequencing. Annu Rev Genomics Hum Genet, 2021, 22: 171-197.
17. Feng Y, Zhang Y, Ying C, et al. Nanopore-based fourth-generation DNA sequencing technology. Genomics Proteomics Bioinformatics, 2015, 13(1): 4-16.
18. Olsen TK, Baryawno N. Introduction to Single-Cell RNA Sequencing. Curr Protoc Mol Biol, 2018, 122(1): e57. doi: 10.1002/cpmb.57.
19. Yasen A, Aini A, Wang H, et al. Progress and applications of single-cell sequencing techniques. Infect Genet Evol, 2020, 80: 104198. doi: 10.1016/j.meegid.2020.104198.
20. 王权, 王铸, 张振, 等. 单细胞测序的技术概述. 中国医药导刊, 2020, 22(7): 433-439.
21. Harada A, Kimura H, Ohkawa Y. Recent advances in single-cell epigenomics. Curr Opin Struct Biol, 2021, 71: 116-122.
22. 程馨, 燕蕊, 郭帆. 单细胞多组学技术新进展及其在发育生物学研究中的应用. 中国科学:生命科学, 2021, 51(5): 496-506.
23. Macaulay IC, Haerty W, Kumar P, et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods, 2015, 12(6): 519-522.
24. Li H, Courtois ET, Sengupta D, et al. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat Genet, 2017, 49(5): 708-718.
25. Tang F, Barbacioru C, Wang Y, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods, 2009, 6(5): 377-382.
26. Bass AJ, Lawrence MS, Brace LE, et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet, 2011, 43(10): 964-968.
27. Yu C, Yu J, Yao X, et al. Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing. Cell Res, 2014, 24(6): 701-712.
28. Zhao J, Chen Y. Systematic identification of cancer-associated-fibroblast-derived genes in patients with colorectal cancer based on single-cell sequencing and transcriptomics. Front Immunol, 2022, 13: 988246. doi: 10.3389/fimmu.2022.988246.
29. Dai W, Zhou F, Tang D, et al. Single-cell transcriptional profiling reveals the heterogenicity in colorectal cancer. Medicine (Baltimore), 2019, 98(34): e16916. doi: 10.1097/MD.0000000000016916.
30. Zhou Y, Bian S, Zhou X, et al. Single-Cell multiomics sequencing reveals prevalent genomic alterations in tumor stromal cells of human colorectal cancer. Cancer Cell, 2020, 38(6): 818-828.
31. Li C, Sun YD, Yu GY, et al. Integrated omics of metastatic colorectal cancer. Cancer Cell, 2020, 38(5): 734-747.
32. Tsilimigras DI, Brodt P, Clavien PA, et al. Liver metastases. Nat Rev Dis Primers, 2021, 7(1): 27. doi: 10.1038/s41572-021-00261-6.
33. Heitzer E, Auer M, Gasch C, et al. Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res, 2013, 73(10): 2965-2975.
34. Kim TM, Jung SH, An CH, et al. Subclonal genomic architectures of primary and metastatic colorectal cancer based on intratumoral genetic heterogeneity. Clin Cancer Res, 2015, 21(19): 4461-4472.
35. Leung ML, Davis A, Gao R, et al. Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer. Genome Res, 2017, 27(8): 1287-1299.
36. Bian S, Hou Y, Zhou X, et al. Single-cell multiomics sequencing and analyses of human colorectal cancer. Science, 2018, 362(6418): 1060-1063.
37. 王智锋. 单细胞全外显子组测序在转移性结直肠癌克隆进化中的初步应用. 华南理工大学, 2019.
38. Miyaki M, Iijima T, Konishi M, et al. Higher frequency of Smad4 gene mutation in human colorectal cancer with distant metastasis. Oncogene, 1999, 18(20): 3098-3103.
39. 李承君, 和水祥. IL-17在结直肠炎-癌转变中的作用机制研究进展. 细胞与分子免疫学杂志, 2022, 38(2): 177-182.
40. Wu Y, Yang S, Ma J, et al. Spatiotemporal immune landscape of colorectal cancer liver metastasis at single-cell level. Cancer Discov, 2022, 12(1): 134-153.
41. Tang J, Tu K, Lu K, et al. Single-cell exome sequencing reveals multiple subclones in metastatic colorectal carcinoma. Genome Med, 2021, 13(1): 148. doi: 10.1186/s13073-021-00962-3.
42. 中国医师协会外科医师分会, 中华医学会外科学分会胃肠外科学组, 中华医学会外科学分会结直肠外科学组, 等. 中国结直肠癌肝转移诊断和综合治疗指南(2020版). 中国实用外科杂志, 2021, 41(1): 1-11.
43. Tauriello DV, Calon A, Lonardo E, et al. Determinants of metastatic competency in colorectal cancer. Mol Oncol, 2017, 11(1): 97-119.
44. Kreso A, O'Brien CA, van Galen P, et al. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science, 2013, 339(6119): 543-548.
45. Jabbari N, Kenerson HL, Lausted C, et al. Modulation of immune checkpoints by chemotherapy in human colorectal liver metastases. Cell Rep Med, 2020, 1(9): 100160. doi: 10.1016/j.xcrm.2020.100160.
46. 袁浩, 钟华戈, 严林海, 等. 基于生物信息学分析结直肠癌STIM1高频突变介导的免疫抵抗模式及其分子机制. 中国癌症防治杂志, 2020, 12(5): 566-571.
47. 付卫, 黄坤蓉, 付敏, 等. CD73在结直肠癌组织中的表达及其与临床病理参数的关系. 现代肿瘤医学, 2019, 27(10): 1753-1757.
48. Künzli BM, Bernlochner MI, Rath S, et al. Impact of CD39 and purinergic signalling on the growth and metastasis of colorectal cancer. Purinergic Signal, 2011, 7(2): 231-241.
49. Kim M, Min YK, Jang J, et al. Single-cell RNA sequencing reveals distinct cellular factors for response to immunotherapy targeting CD73 and PD-1 in colorectal cancer. J Immunother Cancer, 2021, 9(7): e002503. doi: 10.1136/jitc-2021-002503.
50. Lin C, Yang H, Zhao W, et al. CTSB⁺ macrophage repress memory immune hub in the liver metastasis site of colorectal cancer patient revealed by multi-omics analysis. Biochem Biophys Res Commun, 2022, 626: 8-14.
51. 马燕如, 季林华, 童天颍, 等. 基于单细胞RNA测序的结直肠癌预后预测模型的建立和验证. 上海交通大学学报(医学版), 2021, 41(2): 159-165.

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CHINESE JOURNAL OF BASES AND CLINICS IN GENERAL SURGERY

Single cell sequencing technology and its application in liver metastasis of colorectal cancer

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