Artificial intelligence-based multi-omics analysis fuels cancer precision medicine

被引:160
作者
He, Xiujing [1 ,2 ]
Liu, Xiaowei [1 ,2 ]
Zuo, Fengli [1 ,2 ]
Shi, Hubing [1 ,2 ]
Jing, Jing [1 ,2 ,3 ]
机构
[1] Sichuan Univ, West China Hosp, Clin Res Ctr Breast, Lab Integrat Med,State Key Lab Biotherapy, Chengdu, Sichuan, Peoples R China
[2] Collaborat Innovat Ctr, Chengdu, Sichuan, Peoples R China
[3] Sichuan Univ, Chengdu, Peoples R China
基金
中国国家自然科学基金;
关键词
Artificial intelligence; Multi-omics technologies; Integration analysis; Precision medicine; Cancer screening and diagnosis; Response assessment; Prognosis prediction; CURRENT CHALLENGES; COLORECTAL-CANCER; PROSTATE-CANCER; OPEN CHROMATIN; SINGLE; PREDICTION; CLASSIFICATION; PROTEOMICS; MOLECULE; METABOLOMICS;
D O I
10.1016/j.semcancer.2022.12.009
中图分类号
R73 [肿瘤学];
学科分类号
100214 ;
摘要
With biotechnological advancements, innovative omics technologies are constantly emerging that have enabled researchers to access multi-layer information from the genome, epigenome, transcriptome, proteome, metab-olome, and more. A wealth of omics technologies, including bulk and single-cell omics approaches, have empowered to characterize different molecular layers at unprecedented scale and resolution, providing a holistic view of tumor behavior. Multi-omics analysis allows systematic interrogation of various molecular information at each biological layer while posing tricky challenges regarding how to extract valuable insights from the expo-nentially increasing amount of multi-omics data. Therefore, efficient algorithms are needed to reduce the dimensionality of the data while simultaneously dissecting the mysteries behind the complex biological processes of cancer. Artificial intelligence has demonstrated the ability to analyze complementary multi-modal data streams within the oncology realm. The coincident development of multi-omics technologies and artificial in-telligence algorithms has fuelled the development of cancer precision medicine. Here, we present state-of-the-art omics technologies and outline a roadmap of multi-omics integration analysis using an artificial intelligence strategy. The advances made using artificial intelligence-based multi-omics approaches are described, especially concerning early cancer screening, diagnosis, response assessment, and prognosis prediction. Finally, we discuss the challenges faced in multi-omics analysis, along with tentative future trends in this field. With the increasing application of artificial intelligence in multi-omics analysis, we anticipate a shifting paradigm in precision medicine becoming driven by artificial intelligence-based multi-omics technologies.
引用
收藏
页码:187 / 200
页数:14
相关论文
共 218 条
[1]   The US Cancer Moonshot initiative [J].
Aelion, C. Marjorie ;
Airhihenbuwa, Collins O. ;
Alemagno, Sonia ;
Amler, Robert W. ;
Arnett, Donna K. ;
Balas, Andrew ;
Bertozzi, Stefano ;
Blakely, Craig H. ;
Boerwinkle, Eric ;
Brandt-Rauf, Paul ;
Buekens, Pierre M. ;
Chandler, G. Thomas ;
Chang, Rowland W. ;
Clark, Jane E. ;
Cleary, Paul D. ;
Curran, James W. ;
Curry, Susan J. ;
Roux, Ana V. Diez ;
Dittus, Robert ;
Ellerbeck, Edward F. ;
El-Mohandes, Ayman ;
Eriksen, Michael P. ;
Erwin, Paul C. ;
Evans, Gregory ;
Finnegan, John R., Jr. ;
Fried, Linda P. ;
Frumkin, Howard ;
Galea, Sandro ;
Goff, David C., Jr. ;
Goldman, Lynn R. ;
Guilarte, Tomas R. ;
Rivera-Gutierrez, Ralph ;
Halverson, Paul K. ;
Hand, Gregory A. ;
Harris, Cynthia M. ;
Healton, Cheryl G. ;
Hennig, Nils ;
Heymann, Jody ;
Hunter, David ;
Hwang, Wenke ;
Jones, Resa M. ;
Klag, Michael J. ;
Klesges, Lisa M. ;
Lahey, Tim ;
Lawlor, Edward F. ;
Maddock, Jay ;
Martin, William J. ;
Mazzaschi, Anthony J. ;
Michael, Max ;
Mohammed, Shan D. .
LANCET ONCOLOGY, 2016, 17 (05) :E178-E180
[2]   Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence [J].
Alexandrov, Theodore .
ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE, VOL 3, 2020, 2020, 3 :61-87
[3]   Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing [J].
Alfares, Ahmed ;
Aloraini, Taghrid ;
Al Subaie, Lamia ;
Alissa, Abdulelah ;
Al Qudsi, Ahmed ;
Alahmad, Ahmed ;
Al Mutairi, Fuad ;
Alswaid, Abdulrahman ;
Alothaim, Ali ;
Eyaid, Wafaa ;
Albalwi, Mohammed ;
Alturki, Saeed ;
Alfadhel, Majid .
GENETICS IN MEDICINE, 2018, 20 (11) :1328-1333
[4]   Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach [J].
Ali, Mehreen ;
Khan, Suleiman A. ;
Wennerberg, Krister ;
Aittokallio, Tero .
BIOINFORMATICS, 2018, 34 (08) :1353-1362
[5]   Predicting the mutations generated by repair of Cas9-induced double-strand breaks [J].
Allen, Felicity ;
Crepaldi, Luca ;
Alsinet, Clara ;
Strong, Alexander J. ;
Kleshchevnikov, Vitalii ;
De Angeli, Pietro ;
Palenikova, Petra ;
Khodak, Anton ;
Kiselev, Vladimir ;
Kosicki, Michael ;
Bassett, Andrew R. ;
Harding, Heather ;
Galanty, Yaron ;
Munoz-Martinez, Francisco ;
Metzakopian, Emmanouil ;
Jackson, Stephen P. ;
Parts, Leopold .
NATURE BIOTECHNOLOGY, 2019, 37 (01) :64-+
[6]   Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices [J].
Alseekh, Saleh ;
Aharoni, Asaph ;
Brotman, Yariv ;
Contrepois, Kevin ;
D'Auria, John ;
Ewald, Jan ;
Ewald, Jennifer C. ;
Fraser, Paul D. ;
Giavalisco, Patrick ;
Hall, Robert D. ;
Heinemann, Matthias ;
Link, Hannes ;
Luo, Jie ;
Neumann, Steffen ;
Nielsen, Jens ;
de Souza, Leonardo Perez ;
Saito, Kazuki ;
Sauer, Uwe ;
Schroeder, Frank C. ;
Schuster, Stefan ;
Siuzdak, Gary ;
Skirycz, Aleksandra ;
Sumner, Lloyd W. ;
Snyder, Michael P. ;
Tang, Huiru ;
Tohge, Takayuki ;
Wang, Yulan ;
Wen, Weiwei ;
Wu, Si ;
Xu, Guowang ;
Zamboni, Nicola ;
Fernie, Alisdair R. .
NATURE METHODS, 2021, 18 (07) :747-756
[7]   Spatial transcriptomics [J].
Anderson, Ana C. ;
Yanai, Itai ;
Yates, Lucy R. ;
Wang, Linghua ;
Swarbrick, Alexander ;
Sorger, Peter ;
Santagata, Sandro ;
Fridman, Wolf H. ;
Gao, Qiang ;
Jerby, Livnat ;
Izar, Benjamin ;
Shang, Lulu ;
Zhou, Xiang .
CANCER CELL, 2022, 40 (09) :895-900
[8]   Method of the Year 2019: Single-cell multimodal omics [J].
不详 .
NATURE METHODS, 2020, 17 (01) :1-1
[9]   Deep Learning to Estimate RECIST in Patients with NSCLC Treated with PD-1 Blockade [J].
Arbour, Kathryn C. ;
Luu, Anh Tuan ;
Luo, Jia ;
Rizvi, Hira ;
Plodkowski, Andrew J. ;
Sakhi, Mustafa ;
Huang, Kevin B. ;
Digumarthy, Subba R. ;
Ginsberg, Michelle S. ;
Girshman, Jeffrey ;
Kris, Mark G. ;
Riely, Gregory J. ;
Yala, Adam ;
Gainor, Justin F. ;
Barzilay, Regina ;
Hellmann, Matthew D. .
CANCER DISCOVERY, 2021, 11 (01) :59-67
[10]   Artificial intelligence for precision oncology: beyond patient stratification [J].
Azuaje, Francisco .
NPJ PRECISION ONCOLOGY, 2019, 3 (1)