DOI QR코드

DOI QR Code

Development of bioinformatics and multi-omics analyses in organoids

  • Doyeon Ha (Department of Life Sciences, Pohang University of Science and Technology) ;
  • JungHo Kong (Department of Life Sciences, Pohang University of Science and Technology) ;
  • Donghyo Kim (Department of Life Sciences, Pohang University of Science and Technology) ;
  • Kwanghwan Lee (Department of Life Sciences, Pohang University of Science and Technology) ;
  • Juhun Lee (Department of Life Sciences, Pohang University of Science and Technology) ;
  • Minhyuk Park (Department of Life Sciences, Pohang University of Science and Technology) ;
  • Hyunsoo Ahn (Graduate School of Artificial Intelligence, Pohang University of Science and Technology) ;
  • Youngchul Oh (Department of Life Sciences, Pohang University of Science and Technology) ;
  • Sanguk Kim (Department of Life Sciences, Pohang University of Science and Technology)
  • Received : 2022.05.16
  • Accepted : 2022.10.25
  • Published : 2023.01.31

Abstract

Pre-clinical models are critical in gaining mechanistic and biological insights into disease progression. Recently, patient-derived organoid models have been developed to facilitate our understanding of disease development and to improve the discovery of therapeutic options by faithfully recapitulating in vivo tissues or organs. As technological developments of organoid models are rapidly growing, computational methods are gaining attention in organoid researchers to improve the ability to systematically analyze experimental results. In this review, we summarize the recent advances in organoid models to recapitulate human diseases and computational advancements to analyze experimental results from organoids.

Keywords

References

  1. Li X, Nadauld L, Ootani A et al (2014) Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture. Nat Med 20, 769-777 https://doi.org/10.1038/nm.3585
  2. Artegiani B, van Voorthuijsen L, Lindeboom RGH et al (2019) Probing the tumor suppressor function of BAP1 in CRISPR-engineered human liver organoids. Cell Stem Cell 24, 927-943 e6
  3. Ringel T, Frey N, Ringnalda F et al (2020) Genome-scale CRISPR screening in human intestinal organoids identifies drivers of TGF-β resistance. Cell Stem Cell 26, 431-440 e8
  4. Michels BE, Mosa MH, Streibl BI et al (2020) Pooled in vitro and in vivo CRISPR-Cas9 screening identifies tumor suppressors in human colon organoids. Cell Stem Cell 26, 782-792 e7
  5. Takeda H, Kataoka S, Nakayama M et al (2019) CRISPR-Cas9-mediated gene knockout in intestinal tumor organoids provides functional validation for colorectal cancer driver genes. Proc Natl Acad Sci U S A 116, 15635-15644 https://doi.org/10.1073/pnas.1904714116
  6. Ungricht R, Guibbal L, Lasbennes MC et al (2022) Genome-wide screening in human kidney organoids identifies developmental and disease-related aspects of nephrogenesis. Cell Stem Cell 29, 160-175 e7
  7. Beumer J, Geurts MH, Lamers MM et al (2021) A CRISPR/ Cas9 genetically engineered organoid biobank reveals essential host factors for coronaviruses. Nat Commun 12, 5498
  8. Schwank G, Koo BK, Sasselli V et al (2013) Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell 13, 653-658 https://doi.org/10.1016/j.stem.2013.11.002
  9. Khurana E, Fu Y, Colonna V et al (2013) Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 342, 1235587
  10. Ng PC and Henikoff S (2001) Predicting deleterious amino acid substitutions. Genome Res 11, 863-874 https://doi.org/10.1101/gr.176601
  11. Kim D, Han SK, Lee K, Kim I, Kong JH and Kim S (2019) Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites. Nucleic Acids Res 47, e94
  12. Adzhubei IA, Schmidt S, Peshkin L et al (2010) A method and server for predicting damaging missense mutations. Nat Methods 7, 248-249 https://doi.org/10.1038/nmeth0410-248
  13. Desmet FO, Hamroun D, Lalande M, Collod-Beroud G, Claustres M and Beroud C (2009) Human splicing finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 37, e67
  14. Arnold F, Gout J, Wiese H et al (2021) RINT1 regulates SUMOylation and the DNA damage response to preserve cellular homeostasis in pancreatic cancer. Cancer Res 81, 1758-1774 https://doi.org/10.1158/0008-5472.CAN-20-2633
  15. Schadt EE, Lamb J, Yang X et al (2005) An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 37, 710-717 https://doi.org/10.1038/ng1589
  16. Chen Y, Zhu J, Lum PY et al (2008) Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429-435 https://doi.org/10.1038/nature06757
  17. Cowan CS, Renner M, de Gennaro M et al (2020) Cell types of the human retina and its organoids at single-cell resolution. Cell 182, 1623-1640 e34
  18. Kanton S, Boyle MJ, He Z et al (2019) Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature 574, 418-422 https://doi.org/10.1038/s41586-019-1654-9
  19. Kathuria A, Lopez-Lengowski K, Vater M, McPhie D, Cohen BM and Karmacharya R (2020) Transcriptome analysis and functional characterization of cerebral organoids in bipolar disorder. Genome Med 12, 34
  20. Liu K, Newbury PA, Glicksberg BS et al (2019) Evaluating cell lines as models for metastatic breast cancer through integrative analysis of genomic data. Nat Commun 10, 2138
  21. Krieger TG, le Blanc S, Jabs J et al (2021) Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy. Nat Commun 12, 5826
  22. Norkin M, Ordonez-Moran P and Huelsken J (2021) Highcontent, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer. Cell Rep 35, 109026
  23. Raspe E, Decraene C and Berx G (2012) Gene expression profiling to dissect the complexity of cancer biology: Pitfalls and promise. Semin Cancer Biol 22, 250-260 https://doi.org/10.1016/j.semcancer.2012.02.011
  24. Menche J, Sharma A, Kitsak M et al (2015) Uncovering disease-disease relationships through the incomplete interactome. Science 347, 1257601
  25. Hofree M, Shen JP, Carter H, Gross A and Ideker T (2013) Network-based stratification of tumor mutations. Nat Methods 10, 1108-1115 https://doi.org/10.1038/nmeth.2651
  26. Kong JH, Lee H, Kim D et al (2020) Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients. Nat Commun 11, 5485
  27. Amiri A, Coppola G, Scuderi S et al (2018) Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science 362, eaat6720
  28. Gordon A, Yoon SJ, Tran SS et al (2021) Long-term maturation of human cortical organoids matches key early postnatal transitions. Nat Neurosci 24, 331-342 https://doi.org/10.1038/s41593-021-00802-y
  29. Trevino AE, Sinnott-Armstrong N, Andersen J et al (2020) Chromatin accessibility dynamics in a model of human forebrain development. Science 367, eaay1645
  30. Broutier L, Mastrogiovanni G, Verstegen MMA et al (2017) Human primary liver cancer-derived organoid cultures for disease modeling and drug screening. Nat Med 23, 1424- 1435 https://doi.org/10.1038/nm.4438
  31. Gao D, Vela I, Sboner A et al (2014) Organoid cultures derived from patients with advanced prostate cancer. Cell 159, 176-187 https://doi.org/10.1016/j.cell.2014.08.016
  32. Boj SF, Hwang CI, Baker LA et al (2015) Organoid models of human and mouse ductal pancreatic cancer. Cell 160, 324-338 https://doi.org/10.1016/j.cell.2014.12.021
  33. Codrich M, Dalla E, Mio C et al (2021) Integrated multiomics analyses on patient-derived CRC organoids highlight altered molecular pathways in colorectal cancer progression involving PTEN. J Exp Clin Cancer Res 40, 198
  34. Toshimitsu K, Takano A, Fujii M et al (2022) Organoid screening reveals epigenetic vulnerabilities in human colorectal cancer. Nat Chem Biol 18, 605-614 https://doi.org/10.1038/s41589-022-00984-x
  35. Chen J, Zhao L, Peng H et al (2021) An organoid-based drug screening identified a menin-MLL inhibitor for endometrial cancer through regulating the HIF pathway. Cancer Gene Ther 28, 112-125 https://doi.org/10.1038/s41417-020-0190-y
  36. Yan HHN, Siu HC, Law S et al (2018) A comprehensive human gastric cancer organoid biobank captures tumor subtype heterogeneity and enables therapeutic screening. Cell Stem Cell 23, 882-897 e11
  37. Schutte M, Risch T, Abdavi-Azar N et al (2017) Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors. Nat Commun 8, 14262
  38. Schumacher D, Andrieux G, Boehnke K et al (2019) Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures. PLoS Genet 15, e1008076
  39. Mills RJ, Parker BL, Quaife-Ryan GA et al (2019) Drug screening in human PSC-cardiac organoids identifies proproliferative compounds acting via the mevalonate pathway. Cell Stem Cell 24, 895-907 e6
  40. Webber JT, Kaushik S and Bandyopadhyay S (2018) Integration of tumor genomic data with cell lines using multi-dimensional network modules improves cancer pharmacogenomics. Cell Syst 7, 526-536 e6
  41. Han SK, Kong J, Kim S, Lee JH and Han DH (2019) Exomic and transcriptomic alterations of hereditary gingival fibromatosis. Oral Dis 25, 1374-1383 https://doi.org/10.1111/odi.13093
  42. Sharifi-Noghabi H, Zolotareva O, Collins CC and Ester M (2019) MOLI: multi-omics late integration with deep neural networks for drug response prediction. Bioinformatics 35, i501-i509 https://doi.org/10.1093/bioinformatics/btz318
  43. Boutros M, Heigwer F and Laufer C (2015) Microscopybased high-content screening. Cell 163, 1314-1325 https://doi.org/10.1016/j.cell.2015.11.007
  44. Dekkers JF, Alieva M, Wellens LM et al (2019) High-resolution 3D imaging of fixed and cleared organoids. Nat Protoc 14, 1756-1771 https://doi.org/10.1038/s41596-019-0160-8
  45. Lukonin I, Serra D, Challet Meylan L et al (2020) Phenotypic landscape of intestinal organoid regeneration. Nature 586, 275-280 https://doi.org/10.1038/s41586-020-2776-9
  46. Renner H, Grabos M, Becker KJ et al (2020) A fully automated high-throughput workflow for 3d-based chemical screening in human midbrain organoids. Elife 9, e52904
  47. Renner H, Scholer HR and Bruder JM (2021) Combining automated organoid workflows with artificial intelligencebased analyses: opportunities to build a new generation of interdisciplinary high-throughput screens for Parkinson's disease and beyond. Mov Disord 36, 2745-2762 https://doi.org/10.1002/mds.28775
  48. Gritti N, le Lim J, Anlas K et al (2021) Morgana: accessible quantitative analysis of organoids with machine learning. Development 148, dev199611
  49. Kassis T, Hernandez-Gordillo V, Langer R and Griffith LG (2019) OrgaQuant: human intestinal organoid localization and quantification using deep convolutional neural networks. Sci Rep 9, 12479
  50. Kok RNU, Hebert L, Huelsz-Prince G et al (2020) OrganoidTracker: efficient cell tracking using machine learning and manual error correction. PLoS One 15, e0240802
  51. Kim E, Choi S, Kang B et al (2020) Creation of bladder assembloids mimicking tissue regeneration and cancer. Nature 588, 664-669 https://doi.org/10.1038/s41586-020-3034-x
  52. Neal JT, Li X, Zhu J et al (2018) Organoid modeling of the tumor immune microenvironment. Cell 175, 1972-1988e16
  53. Han SK, Kim D, Lee H, Kim I and Kim S (2018) Divergence of noncoding regulatory elements explains genephenotype differences between human and mouse orthologous genes. Mol Biol Evol 35, 1653-1667 https://doi.org/10.1093/molbev/msy056
  54. Ha D, Kim D, Kim I et al (2022) Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes. Nucleic Acids Res 50, 1849-1863 https://doi.org/10.1093/nar/gkac050