- 1. Department of Radiology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, P.R. China;
- 2. Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou 510080, P.R. China;
Cancer presents a significant global public health challenge, impacting human health on a broad scale. In recent years, the rapid advancement of big data-based bioinformatics has unveiled crucial potential in precision oncology through various omics research methods. The advent of radiomics has notably expanded the application scope of medical imaging in the field. However, due to the multi-level and multifactorial nature of tumor initiation and progression, a single omics information remains insufficient to meet the demands for advancing precision oncology strategies. Multi-omics research has become an emerging trend. The research paradigm integrating radiomics with other omics offers a novel perspective for personalized decision-making in oncology. Nevertheless, there persists a need to introduce more integrated new technologies and theories to expedite the progress of this field.
Citation: HUANG Yanqi, LIU Zaiyi. Integrating radiomics into multi-omics research: unveiling new perspectives on precision oncology. CHINESE JOURNAL OF BASES AND CLINICS IN GENERAL SURGERY, 2024, 31(3): 257-264. doi: 10.7507/1007-9424.202312050 Copy
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2. | Gillies RJ, Kinahan PE, Hricak H. Radiomics: images are more than pictures, They are data. Radiology, 2016, 278(2): 563-577. |
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- 1. Lambin P, Rios-Velazquez E, Leijenaar R, et al. Radiomics: extracting more information from medical images using advanced feature analysis. Eur J Cancer, 2012, 48(4): 441-446.
- 2. Gillies RJ, Kinahan PE, Hricak H. Radiomics: images are more than pictures, They are data. Radiology, 2016, 278(2): 563-577.
- 3. Huang YQ, Liang CH, He L, et al. Development and validation of a radiomics nomogram for preoperative prediction of lymph node metastasis in colorectal cancer. J Clin Oncol, 2016, 34(18): 2157-2164.
- 4. Lambin P, Leijenaar RTH, Deist TM, et al. Radiomics: the bridge between medical imaging and personalized medicine. Nat Rev Clin Oncol, 2017, 14(12): 749-762.
- 5. Bi WL, Hosny A, Schabath MB, et al. Artificial intelligence in cancer imaging: Clinical challenges and applications. CA Cancer J Clin, 2019, 69(2): 127-157.
- 6. Xu X, Zhang HL, Liu QP, et al. Radiomic analysis of contrast-enhanced CT predicts microvascular invasion and outcome in hepatocellular carcinoma. J Hepatol, 2019, 70(6): 1133-1144.
- 7. Conti A, Duggento A, Indovina I, et al. Radiomics in breast cancer classification and prediction. Semin Cancer Biol, 2021, 72: 238-250.
- 8. Bera K, Braman N, Gupta A, et al. Predicting cancer outcomes with radiomics and artificial intelligence in radiology. Nat Rev Clin Oncol, 2022, 19(2): 132-146.
- 9. Hieter P, Boguski M. Functional genomics: it’s all how you read it. Science, 1997, 278(5338): 601-602.
- 10. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet, 2009, 10(1): 57-63.
- 11. Ding Z, Wang N, Ji N, et al. Proteomics technologies for cancer liquid biopsies. Mol Cancer, 2022, 21(1): 53.
- 12. Jacob M, Lopata AL, Dasouki M, et al. Metabolomics toward personalized medicine. Mass Spectrom Rev, 2019, 38(3): 221-238.
- 13. Akhoundova D, Rubin MA. Clinical application of advanced multi-omics tumor profiling: Shaping precision oncology of the future. Cancer Cell, 2022, 40(9): 920-938.
- 14. Nam AS, Chaligne R, Landau DA. Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics. Nat Rev Genet, 2021, 22(1): 3-18.
- 15. Le Large TYS, Bijlsma MF, Kazemier G, et al. Key biological processes driving metastatic spread of pancreatic cancer as identified by multi-omics studies. Semin Cancer Biol, 2017 Jun: 44: 153-169.
- 16. Jing Y, Yang J, Johnson DB, et al. Harnessing big data to characterize immune-related adverse events. Nat Rev Clin Oncol, 2022, 19(4): 269-280.
- 17. Aldea M, Friboulet L, Apcher S, et al. Precision medicine in the era of multi-omics: can the data tsunami guide rational treatment decision? ESMO Open, 2023, 8(5): 101642. doi: 10.1016/ j. esmoop.2023.101642.
- 18. Migliozzi S, Oh YT, Hasanain M, et al. Integrative multi-omics networks identify PKCδ and DNA-PK as master kinases of glioblastoma subtypes and guide targeted cancer therapy. Nat Cancer, 2023, 4(2): 181-202.
- 19. Yang J, Chen Y, Jing Y, et al. Advancing CAR T cell therapy through the use of multidimensional omics data. Nat Rev Clin Oncol, 2023, 20(4): 211-228.
- 20. Gao Q, Zhu H, Dong L, et al. Integrated proteogenomic characterization of HBV-related hepatocellular carcinoma. Cell, 2019, 179(2): 561-577.
- 21. Liu Z, Zhao Y, Kong P, et al. Integrated multi-omics profiling yields a clinically relevant molecular classification for esophageal squamous cell carcinoma. Cancer Cell, 2023, 41(1): 181-195.
- 22. Kang W, Qiu X, Luo Y, et al. Application of radiomics-based multiomics combinations in the tumor microenvironment and cancer prognosis. J Transl Med, 2023, 21(1): 598.
- 23. Karlo CA, Di Paolo PL, Chaim J, et al. Radiogenomics of clear cell renal cell carcinoma: associations between CT imaging features and mutations. Radiology, 2014, 270(2): 464-471.
- 24. Mazurowski MA, Zhang J, Grimm LJ, et al. Radiogenomic analysis of breast cancer: luminal B molecular subtype is associated with enhancement dynamics at MR imaging. Radiology, 2014, 273(2): 365-372.
- 25. Yu Y, He Z, Ouyang J, et al. Magnetic resonance imaging radiomics predicts preoperative axillary lymph node metastasis to support surgical decisions and is associated with tumor microenvironment in invasive breast cancer: A machine learning, multicenter study. EBioMedicine, 2021, 69: 103460.
- 26. Jiang L, You C, Xiao Y, et al. Radiogenomic analysis reveals tumor heterogeneity of triple-negative breast cancer. Cell Rep Med, 2022, 3(7): 100694.
- 27. Guo W, Li H, Zhu Y, et al. Prediction of clinical phenotypes in invasive breast carcinomas from the integration of radiomics and genomics data. J Med Imaging (Bellingham), 2015, 2(4): 041007.
- 28. Li H, Zhu Y, Burnside ES, et al. MR imaging radiomics signatures for predicting the risk of breast cancer recurrence as given by research versions of MammaPrint, Oncotype DX, and PAM50 gene assays. Radiology, 2016, 281(2): 382-391.
- 29. Burt JB, Demirtaş M, Eckner WJ, et al. Hierarchy of transcriptomic specialization across human cortex captured by structural neuroimaging topography. Nat Neurosci, 2018, 21(9): 1251-1259.
- 30. Gryglewski G, Seiger R, James GM, et al. Spatial analysis and high resolution mapping of the human whole-brain transcriptome for integrative analysis in neuroimaging. Neuroimage, 2018 Aug 1: 176: 259-267.
- 31. Ritchie J, Pantazatos SP, French L. Transcriptomic characterization of MRI contrast with focus on the T1-w/T2-w ratio in the cerebral cortex. Neuroimage, 2018, 174: 504-517.
- 32. Katrib A, Hsu W, Bui A, et al. “RADIOTRANSCRIPTOMICS”: A synergy of imaging and transcriptomics in clinical assessment. Quant Biol, 2016, 4(1): 1-12.
- 33. Huang C, Cintra M, Brennan K, et al. Development and validation of radiomic signatures of head and neck squamous cell carcinoma molecular features and subtypes. EBioMedicine, 2019, 45: 70-80.
- 34. Fan L, Cao Q, Ding X, et al. Radiotranscriptomics signature-based predictive nomograms for radiotherapy response in patients with nonsmall cell lung cancer: Combination and association of CT features and serum miRNAs levels. Cancer Med, 2020, 9(14): 5065-5074.
- 35. Le NQK, Hung TNK, Do DT, et al. Radiomics-based machine learning model for efficiently classifying transcriptome subtypes in glioblastoma patients from MRI. Comput Biol Med, 2021, 132: 104320.
- 36. Crombé A, Bertolo F, Fadli D, et al. Distinct patterns of the natural evolution of soft tissue sarcomas on pre-treatment MRIs captured with delta-radiomics correlate with gene expression profiles. Eur Radiol, 2023, 33(2): 1205-1218.
- 37. Lin P, Lin YQ, Gao RZ, et al. Integrative radiomics and transcriptomics analyses reveal subtype characterization of non-small cell lung cancer. Eur Radiol, 2023, 33(9): 6414-6425.
- 38. Alvarez-Jimenez C, Sandino AA, Prasanna P, et al. Identifying cross-scale associations between radiomic and pathomic signatures of non-small cell lung cancer subtypes: Preliminary results. Cancers (Basel), 2020, 12(12): 3663.
- 39. Brancato V, Cavaliere C, Garbino N, et al. The relationship between radiomics and pathomics in Glioblastoma patients: Preliminary results from a cross-scale association study. Front Oncol, 2022, 12: 1005805.
- 40. Feng L, Liu Z, Li C, et al. Development and validation of a radiopathomics model to predict pathological complete response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer: a multicentre observational study. Lancet Digit Health, 2022, 4(1): e8-e17.
- 41. Wan L, Sun Z, Peng W, et al. Selecting Candidates for Organ-Preserving Strategies After Neoadjuvant Chemoradiotherapy for Rectal Cancer: Development and Validation of a Model Integrating MRI Radiomics and Pathomics. J Magn Reson Imaging, 2022, 56(4): 1130-1142.
- 42. Wang R, Dai W, Gong J, et al. Development of a novel combined nomogram model integrating deep learning-pathomics, radiomics and immunoscore to predict postoperative outcome of colorectal cancer lung metastasis patients. J Hematol Oncol, 2022, 15(1): 11.
- 43. Steyaert S, Pizurica M, Nagaraj D, et al. Multimodal data fusion for cancer biomarker discovery with deep learning. Nat Mach Intell, 2023, 5(4): 351-362.
- 44. Vaidya P, Bera K, Gupta A, et al. CT derived radiomic score for predicting the added benefit of adjuvant chemotherapy following surgery in StageⅠ, Ⅱ resectable non-small cell lung cancer: a retrospective multi-cohort study for outcome prediction. Lancet Digit Health, 2020, 2(3): e116-e128.
- 45. Wang X, Xie T, Luo J, et al. Radiomics predicts the prognosis of patients with locally advanced breast cancer by reflecting the heterogeneity of tumor cells and the tumor microenvironment. Breast Cancer Res, 2022, 24(1): 20.
- 46. Su GH, Xiao Y, You C, et al. Radiogenomic-based multiomic analysis reveals imaging intratumor heterogeneity phenotypes and therapeutic targets. Sci Adv, 2023, 9(40): eadf0837.
- 47. Boehm KM, Aherne EA, Ellenson L, et al. Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer. Nat Cancer, 2022, 3(6): 723-733.
- 48. Vanguri RS, Luo J, Aukerman AT, et al. Multimodal integration of radiology, pathology and genomics for prediction of response to PD-(L)1 blockade in patients with non-small cell lung cancer. Nat Cancer, 2022, 3(10): 1151-1164.
- 49. Luo Y. Evaluating the state of the art in missing data imputation for clinical data. Brief Bioinform, 2022, 23(1): bbab489.
- 50. Yoon J, Zame WR, van der Schaar M. Estimating missing data in temporal data streams using multi- directional recurrent neural networks. IEEE Trans Biomed Eng, 2019, 66(5): 1477-1490.
- 51. Li J, Yan XS, Chaudhary D, et al. Imputation of missing values for electronic health record laboratory data. NPJ Digit Med, 2021, 4(1): 147.
- 52. Cheerla A, Gevaert O. Deep learning with multimodal representation for pancancer prognosis prediction. Bioinformatics, 2019, 35(14): i446-i454.
- 53. Ning Z, Du D, Tu C, et al. Relation-aware shared representation learning for cancer prognosis analysis with auxiliary clinical variables and incomplete multi-modality data. IEEE Trans Med Imaging, 2022, 41(1): 186-198.
- 54. Zhou T, Liu M, Thung KH, et al. Latent representation learning for Alzheimer’s disease diagnosis with incomplete multi-modality neuroimaging and genetic data. IEEE Trans Med Imaging, 2019, 38(10): 2411-2422.
- 55. Hutter C, Zenklusen JC. The cancer genome atlas: creating lasting value beyond its data. Cell, 2018, 173(2): 283-285.
- 56. Grossman RL, Heath AP, Ferretti V, et al. Toward a shared vision for cancer genomic data. N Engl J Med, 2016, 375(12): 1109-1112.
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