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, 韋燁, 任黎, 等. 中山醫院結直腸癌MDT討論治療策略分析. 中華結直腸疾病電子雜志, 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.	鄭小翠. 單細胞測序技術在實體瘤研究中的應用進展. 中國癌癥雜志, 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.	魏穎. 單細胞轉錄組測序在哮喘研究中應用的研究進展. 復旦學報(醫學版), 2021, 48(3): 404-409.
13.	王莉, 李曉輝. 單細胞測序技術在動脈粥樣硬化研究中的研究進展. 醫學研究生學報, 2021, 34(9): 969-973.
14.	操利超, 巴穎, 張核子. 單細胞測序方法研究進展. 生物信息學, 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.	王權, 王鑄, 張振, 等. 單細胞測序的技術概述. 中國醫藥導刊, 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. 單細胞多組學技術新進展及其在發育生物學研究中的應用. 中國科學:生命科學, 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.	王智鋒. 單細胞全外顯子組測序在轉移性結直腸癌克隆進化中的初步應用. 華南理工大學, 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在結直腸炎-癌轉變中的作用機制研究進展. 細胞與分子免疫學雜志, 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.	中國醫師協會外科醫師分會, 中華醫學會外科學分會胃腸外科學組, 中華醫學會外科學分會結直腸外科學組, 等. 中國結直腸癌肝轉移診斷和綜合治療指南(2020版). 中國實用外科雜志, 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, 鐘華戈, 嚴林海, 等. 基于生物信息學分析結直腸癌STIM1高頻突變介導的免疫抵抗模式及其分子機制. 中國癌癥防治雜志, 2020, 12(5): 566-571.
47.	付衛, 黃坤蓉, 付敏, 等. CD73在結直腸癌組織中的表達及其與臨床病理參數的關系. 現代腫瘤醫學, 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.	馬燕如, 季林華, 童天潁, 等. 基于單細胞RNA測序的結直腸癌預后預測模型的建立和驗證. 上海交通大學學報(醫學版), 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, 韋燁, 任黎, 等. 中山醫院結直腸癌MDT討論治療策略分析. 中華結直腸疾病電子雜志, 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. 鄭小翠. 單細胞測序技術在實體瘤研究中的應用進展. 中國癌癥雜志, 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. 魏穎. 單細胞轉錄組測序在哮喘研究中應用的研究進展. 復旦學報(醫學版), 2021, 48(3): 404-409.
13. 王莉, 李曉輝. 單細胞測序技術在動脈粥樣硬化研究中的研究進展. 醫學研究生學報, 2021, 34(9): 969-973.
14. 操利超, 巴穎, 張核子. 單細胞測序方法研究進展. 生物信息學, 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. 王權, 王鑄, 張振, 等. 單細胞測序的技術概述. 中國醫藥導刊, 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. 單細胞多組學技術新進展及其在發育生物學研究中的應用. 中國科學:生命科學, 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. 王智鋒. 單細胞全外顯子組測序在轉移性結直腸癌克隆進化中的初步應用. 華南理工大學, 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在結直腸炎-癌轉變中的作用機制研究進展. 細胞與分子免疫學雜志, 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. 中國醫師協會外科醫師分會, 中華醫學會外科學分會胃腸外科學組, 中華醫學會外科學分會結直腸外科學組, 等. 中國結直腸癌肝轉移診斷和綜合治療指南(2020版). 中國實用外科雜志, 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, 鐘華戈, 嚴林海, 等. 基于生物信息學分析結直腸癌STIM1高頻突變介導的免疫抵抗模式及其分子機制. 中國癌癥防治雜志, 2020, 12(5): 566-571.
47. 付衛, 黃坤蓉, 付敏, 等. CD73在結直腸癌組織中的表達及其與臨床病理參數的關系. 現代腫瘤醫學, 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. 馬燕如, 季林華, 童天潁, 等. 基于單細胞RNA測序的結直腸癌預后預測模型的建立和驗證. 上海交通大學學報(醫學版), 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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