基于体细胞突变数据库筛选免疫原性结直肠癌高频新抗原的方法

doi:10.16288/j.yczz.20-032

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Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (6): 599-612.doi: 10.16288/j.yczz.20-032

• Technique and Method • Previous Articles

A method of screening highly common neoantigens with immunogenicity in colorectal cancer based on public somatic mutation library

Qin Lili^1,², Li Yijian¹, Liang Zhaorui¹, Dai Lei¹, Li Wenhui¹, Chen Chao^1,^3,⁴, Huang Yaling¹, Zhang Le^1,^3,⁴, Liu Songming^1,^3,⁴, Qiu Si^1,⁴, Ge Yuping¹, Peng Wenting^1,³, Lin Xinxin^1,⁴, Zhang Xiuqing^1,⁴, Dong Xuan¹(), Li Bo^1,⁴()

^1. BGI-Shenzhen, Shenzhen 518083, China
^2. College of Basic Medicine, Dali University, Dali 671000, China
^3. BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
^4. BGI-GenoImmune, BGI-Shenzhen, Wuhan 430079, China

Received:2020-04-10 Revised:2020-05-15 Online:2020-06-20 Published:2020-05-19
Contact: Xuan Dong,Bo Li E-mail:dongxuan@genomics.cn;libo@genomics.cn
Supported by:
Supported by the National Natural Science Foundation of China No(81702826);Science, Technology and Innovation Commission of Shenzhen Municipality Nos(JCYJ20170303151334808);Science, Technology and Innovation Commission of Shenzhen Municipality Nos(JCYJ20170817150015170)

Abstract

Abstract:

Colorectal cancer (CRC) is a malignant cancer with high incidence and mortality in the world. Immunotherapy targeting neoantigens can induce durable tumor regression in cancer patients, but is almost limited to personalized precision therapy, due to the individual differences of unique neoantigens. With the discovery of many common oncogenic mutations, and such mutation-associated neoantigens could cover more patients, and hence are valuable in clinical field. However, whether the common neoantigens can be identified in CRC is unknown. Combining the somatic mutations data from 321 CRC patients with a filter standard and 7 predicted algorithms, we screened and obtained 25 HLA-A*1101-restricted common neoantigens with a high binding affinity (IC₅₀<50 nmol/L) and presentation score (>0.90). Besides the positive epitope KRAS_G12V_8-16, 11 out of 25 common neoantigens specifically induced in vitro pre- stimulated cytotoxic lymphocyte (CTL) to secrete interferon gamma (IFN-γ). Moreover, combining cell-sorting technology and single-cell RNA sequencing, the immune repertoire profiles of C1orf170_S418G_413-421 and KRAS_G12V_8-16-specific CTL were analyzed and validated. Their related T-cell receptor engineered T cell (TCR-T) cells could also recognize the neoantigens and secrete IFN-γ. Hence, we have established a method to screen for common neoantigens with immunogenicity in CRC based on the public somatic mutation library. It can provide essential peptide and TCR information for immunotherapies, such as peptides, dendritic cells (DC) vaccines, TCR-like antibodies, TCR-T, etc., for the CRC and other cancers, which has practical application value in the clinics.

Key words: colorectal cancer, common, neoantigen, presentation

Qin Lili, Li Yijian, Liang Zhaorui, Dai Lei, Li Wenhui, Chen Chao, Huang Yaling, Zhang Le, Liu Songming, Qiu Si, Ge Yuping, Peng Wenting, Lin Xinxin, Zhang Xiuqing, Dong Xuan, Li Bo. A method of screening highly common neoantigens with immunogenicity in colorectal cancer based on public somatic mutation library[J]. Hereditas(Beijing), 2020, 42(6): 599-612.

Figures/Tables 7

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References 32

[1]	Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A . Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin, 2018,68(6):394-424. doi: 10.3322/caac.21492 pmid: 30207593
[2]	Magee MS, Kraft CL, Abraham TS, Baybutt TR, Marszalowicz GP, Li P, Waldman SA, Snook AE . GUCY2C-directed CAR-T cells oppose colorectal cancer metastases without autoimmunity. Oncoimmunology, 2016,5(10):e1227897. doi: 10.1080/2162402X.2016.1227897 pmid: 27853651
[3]	Ciardiello D, Vitiello PP, Cardone C, Martini G, Troiani T, Martinelli E, Ciardiello F . Immunotherapy of colorectal cancer: Challenges for therapeutic efficacy. Cancer Treat Rev, 2019,76:22-32. doi: 10.1016/j.ctrv.2019.04.003 pmid: 31079031
[4]	Parkhurst MR, Yang JC, Langan RC, Dudley ME, Nathan DA, Feldman SA, Davis JL, Morgan RA, Merino MJ, Sherry RM, Hughes MS, Kammula US, Phan GQ, Lim RM, Wank SA, Restifo NP, Robbins PF, Laurencot CM, Rosenberg SA . T cells targeting carcinoembryonic antigen can mediate regression of metastatic colorectal cancer but induce severe transient colitis. Mol Ther, 2011,19(3):620-626. doi: 10.1038/mt.2010.272
[5]	Zhang CC, Wang Z, Yang Z, Wang ML, Li SQ, Li YY, Zhang R, Xiong ZX, Wei ZH, Shen JJ, Luo YL, Zhang QZ, Liu LM, Qin H, Liu W, Wu F, Chen W, Pan F, Zhang XQ, Bie P, Liang HJ, Pecher G, Qian C . Phase I escalating- dose trial of CAR-T therapy targeting CEA + metastatic colorectal cancers . Mol Ther, 2017,25(5):1248-1258. doi: 10.1016/j.ymthe.2017.03.010 pmid: 28366766
[6]	Morgan RA, Yang JC, Kitano M, Dudley ME, Laurencot CM, Rosenberg SA . Case report of a serious adverse event following the administration of T cells transduced with a chimeric antigen receptor recognizing ERBB2. Mol Ther, 2010,18(4):843-851. doi: 10.1038/mt.2010.24 pmid: 20179677
[7]	Zhou Z, Lyu XZ, Wu JC, Yang XY, Wu SS, Zhou J, Gu X, Su ZX, Chen SQ . TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection. R Soc Open Sci, 2017,4(4):170050. doi: 10.1098/rsos.170050 pmid: 28484631
[8]	Nonomura C, Otsuka M, Kondou R, Iizuka A, Miyata H, Ashizawa T, Sakura N, Yoshikawa S, Kiyohara Y, Ohshima K, Urakami K, Nagashima T, Ohnami S, Kusuhara M, Mitsuya K, Hayashi N, Nakasu Y, Mochizuki T, Yamaguchi K, Akiyama Y . Identification of a neoantigen epitope in a melanoma patient with good response to anti- PD-1 antibody therapy. Immunol Lett, 2019,208:52-59. doi: 10.1016/j.imlet.2019.02.004 pmid: 30880120
[9]	Tran E, Robbins PF, Lu YC, Prickett TD, Gartner JJ, Jia L, Pasetto A, Zheng Z, Ray S, Groh EM, Kriley IR, Rosenberg SA . T-Cell transfer therapy targeting mutant KRAS in cancer. N Engl J Med, 2016,375(23):2255-2262. doi: 10.1056/NEJMoa1609279 pmid: 27959684
[10]	Wirth TC, Kühnel F . Neoantigen targeting-dawn of a new era in cancer immunotherapy? Front Immunol, 2017,8:1848. doi: 10.3389/fimmu.2017.01848 pmid: 29312332
[11]	Cafri G, Yossef R, Pasetto A, Deniger DC, Lu YC, Parkhurst M, Gartner JJ, Jia L, Ray S, Ngo LT, Jafferji M, Sachs A, Prickett T, Robbins PF, Rosenberg SA . Memory T cells targeting oncogenic mutations detected in peripheral blood of epithelial cancer patients. Nat Commun, 2019,10(1):449. doi: 10.1038/s41467-019-08304-z pmid: 30683863
[12]	Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O . Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci, 2003,12(5):1007-1017. doi: 10.1110/ps.0239403 pmid: 12717023
[13]	Nielsen M, Andreatta M . NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med, 2016,8(1):33. doi: 10.1186/s13073-016-0288-x pmid: 27029192
[14]	Jurtz V, Paul S, Andreatta M, Marcatili P, Peters B, Nielsen M . NetMHCpan-4.0: improved Peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data. J Immunol, 2017,199(9):3360-3368. doi: 10.4049/jimmunol.1700893 pmid: 28978689
[15]	Liu G, Li DL, Li Z, Qiu S, Li WH, Chao CC, Yang NB, Li HD, Cheng Z, Song X, Cheng L, Zhang XQ, Wang J, Yang HM, Ma K, Hou Y, Li B . PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity. Gigascience, 2017,6(5):1-11. doi: 10.1093/gigascience/gix004 pmid: 28327916
[16]	Zhang H, Lund O, Nielsen M . The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. Bioinformatics, 2009,25(10):1293-1299. doi: 10.1093/bioinformatics/btp137 pmid: 19297351
[17]	Peters B, Sette A . Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics, 2005,6:132. doi: 10.1186/1471-2105-6-132 pmid: 15927070
[18]	Creaney J, Ma S, Sneddon SA, Tourigny MR, Dick IM, Leon JS, Khong A, Fisher SA, Lake RA, Lesterhuis WJ, Nowak AK, Leary S, Watson MW, Robinson BW . Strong spontaneous tumor neoantigen responses induced by a natural human carcinogen. Oncoimmunology, 2015,4(7):e1011492. doi: 10.1080/2162402X.2015.1011492 pmid: 26140232
[19]	Hu WP, Li YP, Zhang XQ . MHC-I epitope presentation prediction based on transfer learning.Hereditas(Beijing), 41(11):1041-1049.
	胡伟澎, 李佑平, 张秀清 . 基于迁移学习的MHC-I型抗原表位呈递预测. 遗传, 41(11):1041-1049.
[20]	Hu WP, Qiu S, Li YP, Lin XX, Zhang L, Xiang HT, Han X, Chen L, Li S, Li WH, Ren Z, Hou GX, Lin ZL, Lu JL, Liu G, Li B, Lee LJ . EPIP: MHC-I epitope prediction integrating mass spectrometry derived motifs and tissue- specific expression profile. bioRxiv, 2019,567081.
[21]	Tanyi JL, Bobisse S, Ophir E, Tuyaerts S, Roberti A, Genolet R, Baumgartner P, Stevenson BJ, Iseli C, Dangaj D, Czerniecki B, Semilietof A, Racle J, Michel A, Xenarios I, Chiang C, Monos DS, Torigian DA, Nisenbaum HL, Michielin O, June CH, Levine BL, Powell DJ Jr, Gfeller D, Mick R, Dafni U, Zoete V, Harari A, Coukos G, Kandalaft LE. Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer. Sci Transl Med, 2018, 10(436): eaao5931. doi: 10.1126/scitranslmed.aao3003 pmid: 29643228
[22]	Yamamiya D, Mizukoshi E, Kaji K, Terashima T, Kitahara M, Yamashita T, Arai K, Fushimi K, Honda M, Kaneko S . Immune responses of human T lymphocytes to novel hepatitis B virus-derived peptides. PLoS One, 2018,13(6):e0198264. doi: 10.1371/journal.pone.0198264 pmid: 29856876
[23]	Rodenko B, Toebes M, Hadrup SR, van Esch WJ, Molenaar AM, Schumacher TN, Ovaa H,. Generation of peptide-MHC class I complexes through UV-mediated ligand exchange. Nat Protoc, 2006,1(3):1120-1132. doi: 10.1038/nprot.2006.121 pmid: 17406393
[24]	Kim MS, Ma JS, Yun HY, Cao Y, Kim JY, Chi V, Wang D, Woods A, Sherwood L, Caballero D, Gonzalez J, Schultz PG, Young TS, Kim CH . Redirection of genetically engineered CAR-T cells using bifunctional small molecules. J Am Chem Soc, 2015,137(8):2832-2835. doi: 10.1021/jacs.5b00106 pmid: 25692571
[25]	Ali M, Foldvari Z, Giannakopoulou E, Böschen ML, Strønen E, Yang W, Toebes M, Schubert B, Kohlbacher O, Schumacher TN, Olweus J . Induction of neoantigen- reactive T cells from healthy donors. Nat Protoc, 2019,14(6):1926-1943. doi: 10.1038/s41596-019-0170-6 pmid: 31101906
[26]	Lancaster EM, Jablons D, Kratz JR . Applications of next-generation sequencing in eoantigen prediction and cancer vaccine development. Genet Test Mol Biomarkers, 2019,24(2):59-66. doi: 10.1089/gtmb.2018.0211 pmid: 30907630
[27]	The problem with neoantigen prediction. Nat Biotechnol, 2017,35(2):97. doi: 10.1038/nbt.3800 pmid: 28178261
[28]	Cohen CJ, Gartner JJ, Horovitz-Fried M, Shamalov K, Trebska-McGowan K, Bliskovsky VV, Parkhurst MR, Ankri C, Prickett TD, Crystal JS, Li YF, El-Gamil M, Rosenberg SA, Robbins PF, . Isolation of neoantigen- specific T cells from tumor and peripheral lymphocytes. J Clin Invest, 2015,125(10):3981-3991. doi: 10.1172/JCI82416 pmid: 26389673
[29]	Lin QY, Liu Z, Luo MJ, Zheng H, Qiao S, Han CL, Deng DQ, Fan Z, Lu YF, Zhang ZH, Luo QM . Visualizing DC morphology and T cell motility to characterize DC-T cell encounters in mouse lymph nodes under mTOR inhibition. Sci China Life Sci, 2019,62(9):1168-1177. doi: 10.1007/s11427-018-9470-9 pmid: 31016533
[30]	Simoni Y, Becht E, Fehlings M, Loh CY, Koo SL, Teng KWW, Yeong JPS, Nahar R, Zhang T, Kared H, Duan K, Ang N, Poidinger M, Lee YY, Larbi A, Khng AJ, Tan E, Fu C, Mathew R, Teo M, Lim WT, Toh CK, Ong BH, Koh T, Hillmer AM, Takano A, Lim TKH, Tan EH, Zhai W, Tan DSW, Tan IB, Newell EW . Bystander CD8 + T cells are abundant and phenotypically distinct in human tumour infiltrates . Nature, 2018,557(7706):575-579. doi: 10.1038/s41586-018-0130-2 pmid: 29769722
[31]	Whiteside SK, Snook JP, Williams MA, Weis JJ . Bystander T Cells: a balancing act of friends and foes. Trends Immunol, 2018,39(12):1021-1035. doi: 10.1016/j.it.2018.10.003 pmid: 30413351
[32]	Kim TS, Shin EC . The activation of bystander CD8 + T cells and their roles in viral infection . Exp Mol Med, 2019,51(12):1-9. doi: 10.1038/s12276-019-0351-y pmid: 31811117

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预测的新抗原表位	基因	突变位点	突变频率	新抗原突变位置	亲和力 (nmol/L)	EPIP分数	肿瘤中的作用
GLCE_V533I_526-535	GLCE	V533I	6/321	STIDESPIFK	2.7	0.989077	?
C1orf170_S418G_413-421	C1orf170	S418G	5/321	SVAGPGPNK	21.7	0.974471	?
MUC3A_I29T_28-36	MUC3A	I29T	6/321	STSQVPFPR	13.8	0.970609	?
CCRL2_F179Y_174-183	CCRL2	F179Y	5/321	ATLPEYVVYK	4.7	0.968889	?-
KIAA1683_M313T_311-319	KIAA1683	M313T	6/321	STTTTTPPK	7.9	0.964324	?
KLHL40_N345S_341-349	KLHL40	N345S	5/321	ASLSSQVPK	9.4	0.956861	?
MUC3A_S175P_172-181	MUC3A	S175P	6/321	STYPMTTTEK	5.8	0.952998	?
RNF43_I47V_46-54	RNF43	I47V	7/321	AVIRVIPLK	7.8	0.949232	TSG
SYNE2_A2395T_2389-2398	SYNE2	A2395T	5/321	STQESATVEK	28.9	0.946256	?
TLR10_I369L_367-375	TLR10	I369L	5/321	RTLQLPHLK	13.2	0.945037	?
ANKRD36C_N1571S_1571-1579	ANKRD36C	N1571S	5/321	STMEKCIEK	6.6	0.94484	?
IYD_F231I_229-237	IYD	F231I	6/321	QVIGKIILK	21.4	0.940062	?
SSX5_E19Q_12-20	SSX5	E19Q	5/321	RVGSQIPQK	35.7	0.936871	?
MUC3A_S326T_319-327	MUC3A	S326T	7/321	TTLPTTITR	16.1	0.936033	?
ARHGEF11_H1427R_1427-1435	ARHGEF11	H1427R	5/321	RTIEQLTLK	10.8	0.933929	?
CTNNB1_T41A_41-49	CTNNB1	T41A	6/321	ATAPSLSGK	6.9	0.932574	癌基因
LILRB5_L605F_603-611	LILRB5	L605F	5/321	RSFPLTLPR	6.9	0.931333	?
EIF2A_T92S_86-95	EIF2A	T92S	5/321	ATWQPYSTSK	12.9	0.931289	?
TMPRSS15_P732S_732-740	TMPRSS15	P732S	5/321	STDGGPFVK	12	0.930946	?
MUC6_P2049L_2044-2053	MUC6	P2049L	9/321	GTVPPLTTLK	16.5	0.917963	?
TMEM185B_A42G_42-51	TMEM185B	A42G	5/321	GVFAPIWLWK	5.7	0.904248	?
UNC93A_M403T_402-410	UNC93A	M403T	6/321	STFLCVHVK	4.5	0.903415	?
MUC3A_Q31H_28-36	MUC3A	Q31H	5/321	SISHVPFPR	14.1	0.901598	?
FSIP2_R1288Q_1285-1293	FSIP2	R1288Q	5/321	SSLQSQLSK	13.8	0.900572	?
FSIP2_T184NX	FSIP2	T184NX	2/321	TTLPKFNKK	10.2	0.961067	?

抗原肽	TCR克隆	CDR3 序列	TRV 基因	J 基因	比例(%)
C1orf170_S418G_413-421	Clonotype1	TRA: CAASGGAQKLVF	TRAV29DV5	TRAJ54	53.2
		TRA: CAGLLYNSGNTPLVF	TRAV35	TRAJ29
		TRB: CASSRDRGSNQPQHF	TRBV27	TRBJ1-5
	Clonotype2	TRA: CAASGGAQKLVF	TRAV29DV5	TRAJ54	31.6
	Clonotype2	TRB: CASSRDRGSNQPQHF	TRBV27	TRBJ1-5	31.6
KRAS_G12V_8-16	Clonotype1	TRA: CASNDYKLSF	TRAV8-3	TRAJ20	80.5
	Clonotype1	TRB: CASSLDGVSYEQYF	TRBV11-2	TRBJ2-7	80.5
	Clonotype2	TRA: ?	?	?	14.3
	Clonotype2	TRB: CASSLDGVSYEQYF	TRBV11-2	TRBJ2-7	14.3

A method of screening highly common neoantigens with immunogenicity in colorectal cancer based on public somatic mutation library

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[3]	Yuling Yang, Lan Luo, Yuan Qian, Fang Yang. Cultivation of undergraduates’ self-regulated learning ability in Medical Genetics based on PAD class [J]. Hereditas(Beijing), 2020, 42(11): 1133-1139.
[4]	Huanzi Lu,Dikan Wang,Zhi Wang. Correlation analysis of the prognosis of HPV positive oropharyngeal cancer patients with T cell infiltration and neoantigen load [J]. Hereditas(Beijing), 2019, 41(8): 725-735.
[5]	Weipeng Hu, Youping Li, Xiuqing Zhang. MHC-I epitope presentation prediction based on transfer learning [J]. Hereditas(Beijing), 2019, 41(11): 1041-1049.
[6]	Yuan Gu, Lei Zhang, Faxing Yu. Functions and regulations of the Hippo signaling pathway in intestinal homeostasis, regeneration and tumorigenesis [J]. Hereditas(Beijing), 2017, 39(7): 588-596.
[7]	Zongchang Xu,Yingzhen Kong. Genome-wide identification, subcellular localization and gene expression analysis of the members of CESA gene family in common tobacco (Nicotiana tabacum L.) [J]. Hereditas(Beijing), 2017, 39(6): 512-524.
[8]	Youwang Lu,Kunhua Wang. Research progress on genetic heterogeneity between primary and paired metastatic colorectal cancer [J]. Hereditas(Beijing), 2017, 39(6): 482-490.
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