Advances in Organoid Culture Research

Abstract

Organoids are powerful systems to facilitate the study of individuals' disorders and personalized treatments because they mimic the structural and functional characteristics of organs. However, the full potential of organoids in research has remained unrealized and the clinical applications have been limited. One of the reasons is organoids are most efficient grown in reconstituted extracellular matrix hydrogels from mouse-derived, whose poorly defined, batch-to-batch variability and immunogenicity. Another reason is that organoids lack host conditions. As a component of the tumor microenvironment, microbiota and metabolites can regulate the development and treatment in several human malignancies. Here, we introduce several engineering matrix materials and review recent advances in the coculture of organoids with microbiota and their metabolites. Finally, we discuss current trends and future possibilities to build more complex cocultures.

Keywords

Organoid / material / microbiota / microbial metabolites

References

[1] Kim J, Koo BK, Knoblich JA.Human organoids: model systems for human biology and medicine. Nat Rev Mol Cell Biol 2020; 21(10): 571-584

[2] Drost J, Clevers H.Organoids in cancer research. Nat Rev Cancer 2018; 18(07): 407-418

[3] Jin K, Teng L, Shen Y, He K, Xu Z, Li G.Patient-derived human tumour tissue xenografts in immunodeficient mice: a systematic review. Clin Transl Oncol 2010; 12(07): 473-480

[4] McCauley HA, Wells JM. Pluripotent stem cell-derived organoids: using principles of developmental biology to grow human tissues in a dish. Development 2017; 144(06): 958-962

[5] Nejman D, Livyatan I, Fuks G.et al.The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science 2020; 368(6494): 973-980

[6] Sato T, Vries RG, Snippert HJ.et al.Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 2009; 459(7244): 262-265

[7] Lancaster MA, Knoblich JA.Organogenesis in a dish: modeling development and disease using organoid technologies. Science 2014; 345(6194): 1247125

[8] Huch M, Dorrell C, Boj SF.et al.In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration. Nature 2013; 494(7436): 247-250

[9] Barker N, Huch M, Kujala P.et al.Lgr5(+ve) stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro. Cell Stem Cell 2010; 6(01): 25-36

[10] Lancaster MA, Renner M, Martin CA.et al.Cerebral organoids model human brain development and microcephaly. Nature 2013; 501(7467): 373-379

[11] Xia Y, Nivet E, Sancho-Martinez I.et al.Directed differentiation of human pluripotent cells to ureteric bud kidney progenitor-like cells. Nat Cell Biol 2013; 15(12): 1507-1515

[12] Li M, Izpisua Belmonte JC.Organoids - preclinical models of human disease. N Engl J Med 2019; 380(06): 569-579

[13] Kopper O, de Witte CJ, Lõhmussaar K.et al. An organoid platform for ovarian cancer captures intra- and interpatient heterogeneity. Nat Med 2019; 25(05): 838-849

[14] Vlachogiannis G, Hedayat S, Vatsiou A.et al.Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science 2018; 359(6378): 920-926

[15] Sachs N, de Ligt J, Kopper O.et al. A living biobank of breast cancer organoids captures disease heterogeneity. Cell2018; 172 (1-2): 373-386.e10

[16] Matano M, Date S, Shimokawa M.et al.Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids. Nat Med 2015; 21(03): 256-262

[17] Drost J, van Jaarsveld RH, Ponsioen B.et al. Sequential cancer mutations in cultured human intestinal stem cells. Nature 2015; 521(7550): 43-47

[18] Miura A, Yamada D, Nakamura M.et al.Oncogenic potential of human pluripotent stem cell-derived lung organoids with HER2 overexpression. Int J Cancer 2021; 149(08): 1593-1604

[19] Fumagalli A, Drost J, Suijkerbuijk SJE.et al.Genetic dissection of colorectal cancer progression by orthotopic transplantation of engineered cancer organoids. Proc Natl Acad Sci U S A 2017; 114(12): E2357-E2364

[20] Yin X, Mead BE, Safaee H, Langer R, Karp JM, Levy O.Engineering stem cell organoids. Cell Stem Cell 2016; 18(01): 25-38

[21] Kleinman HK, Martin GR.Matrigel: basement membrane matrix with biological activity. Semin Cancer Biol 2005; 15(05): 378-386

[22] Jabaji Z, Brinkley GJ, Khalil HA.et al.Type I collagen as an extracellular matrix for the in vitro growth of human small intestinal epithelium. PLoS One 2014; 9(09): e107814

[23] Liu H, Bockhorn J, Dalton R.et al.Removal of lactate dehydrogenase-elevating virus from human-in-mouse breast tumor xenografts by cell-sorting. J Virol Methods 2011; 173(02): 266-270

[24] Peterson NC.From bench to cageside: risk assessment for rodent pathogen contamination of cells and biologics. ILAR J 2008; 49(03): 310-315

[25] Henke E, Nandigama R, Ergün S.Extracellular matrix in the tumor microenvironment and its impact on cancer therapy. Front Mol Biosci 2020; 6: 160

[26] Kaur S, Kaur I, Rawal P, Tripathi DM, Vasudevan A.Non-matrigel scaffolds for organoid cultures. Cancer Lett 2021; 504: 58-66

[27] Kratochvil MJ, Seymour AJ, Li TL, Paşca SP, Kuo CJ, Heilshorn SC.Engineered materials for organoid systems. Nat Rev Mater 2019; 4(09): 606-622

[28] Magno V, Meinhardt A, Werner C.Polymer hydrogels to guide organotypic and organoid cultures. Adv Funct Mater 2020; 30(48): 2000097

[29] Heidarian P, Kaynak A, Paulino M, Zolfagharian A, Varley RJ, Kouzani AZ.Dynamic nanocellulose hydrogels: recent advancements and future outlook. Carbohydr Polym 2021; 270: 118357-118357

[30] Zhu L, Zhang Y-Q.Postoperative anti-adhesion ability of a novel carboxymethyl chitosan from silkworm pupa in a rat cecal abrasion model. Mater Sci Eng C 2016; 61: 387-395

[31] Curvello R, Kerr G, Micati DJ.et al.Engineered plant-based nanocellulose hydrogel for small intestinal organoid growth. Adv Sci (Weinh) 2020; 8(01): 2002135

[32] Prince E, Cruickshank J, Ba-Alawi W.et al.Biomimetic hydrogel supports initiation and growth of patient-derived breast tumor organoids. Nat Commun 2022; 13(01): 1466

[33] Meran L, Baulies A, Li VSW.Intestinal stem cell niche: the extracellular matrix and cellular components. Stem Cells Int 2017; 2017: 7970385-11

[34] Wang H, Cui J, Zheng Z.et al; Assembly of RGD-Modified Hydrogel Micromodules into Permeable Three-Dimensional Hollow Microtissues Mimicking in Vivo Tissue Structures. Assembly of RGD-modified hydrogel micromodules into permeable three-dimensional hollow microtissues mimicking in vivo tissue structures. ACS Appl Mater Interfaces 2017; 9(48): 41669-41679

[35] Curvello R, Alves D, Abud HE, Garnier G.A thermo-responsive collagen-nanocellulose hydrogel for the growth of intestinal organoids. Mater Sci Eng C 2021; 124: 112051-112051

[36] Guimarães CF, Gasperini L, Marques AP, Reis RL.The stiffness of living tissues and its implications for tissue engineering. Nat Rev Mater 2020; 5(05): 351-370

[37] Curvello R, Garnier G.Cationic cross-linked nanocellulose-based matrices for the growth and recovery of intestinal organoids. Biomacromolecules 2021; 22(02): 701-709

[38] Lee KY, Mooney DJ.Alginate: properties and biomedical applications. Prog Polym Sci 2012; 37(01): 106-126

[39] Capeling MM, Czerwinski M, Huang S.et al.Nonadhesive alginate hydrogels support growth of pluripotent stem cell-derived intestinal organoids. Stem Cell Reports 2019; 12(02): 381-394

[40] Dong H, Li Z, Bian S.et al.Culture of patient-derived multicellular clusters in suspended hydrogel capsules for pre-clinical personalized drug screening. Bioact Mater 2022; 18: 164-177

[41] Capeling MM, Huang S, Childs CJ.et al.Suspension culture promotes serosal mesothelial development in human intestinal organoids. Cell Rep 2022; 38(07): 110379-110379

[42] Engler AJ, Sen S, Sweeney HL, Discher DE.Matrix elasticity directs stem cell lineage specification. Cell 2006; 126(04): 677-689

[43] Cassel de Camps C, Aslani S, Stylianesis N.et al. Hydrogel mechanics influence the growth and development of embedded brain organoids. ACS Appl Bio Mater 2022; 5(01): 214-224

[44] Fang G, Lu H, Rodriguez de la Fuente L. et al. Mammary tumor organoid culture in non-adhesive alginate for luminal mechanics and high-throughput drug screening. Adv Sci (Weinh) 2021; 8(21): e2102418

[45] Deshpande SR, Hammink R, Nelissen FHT, Rowan AE, Heus HA.Biomimetic stress sensitive hydrogel controlled by DNA nanoswitches. Biomacromolecules 2017; 18(10): 3310-3317

[46] Zhang Y, Tang C, Span PN.et al.Polyisocyanide hydrogels as a tunable platform for mammary gland organoid formation. Adv Sci (Weinh) 2020; 7(18): 2001797

[47] Ye S, Boeter JWB, Mihajlovic M.et al.A chemically defined hydrogel for human liver organoid culture. Adv Funct Mater 2020; 30(48): 2000893

[48] Sorrentino G, Rezakhani S, Yildiz E.et al.Mechano-modulatory synthetic niches for liver organoid derivation. Nat Commun 2020; 11(01): 3416-3416

[49] Op 't Veld RC, van den Boomen OI, Lundvig DMS.et al. Thermosensitive biomimetic polyisocyanopeptide hydrogels may facilitate wound repair. Biomaterials 2018; 181: 392-401

[50] Zimoch J, Padial JS, Klar AS.et al.Polyisocyanopeptide hydrogels: a novel thermo-responsive hydrogel supporting pre-vascularization and the development of organotypic structures. Acta Biomater 2018; 70: 129-139

[51] Eweida AM, Marei MK.Naturally occurring extracellular matrix scaffolds for dermal regeneration: do they really need cells?. BioMed Res Int 2015; 2015: 839694-839699

[52] Hillebrandt KH, Everwien H, Haep N, Keshi E, Pratschke J, Sauer IM.Strategies based on organ decellularization and recellularization. Transpl Int 2019; 32(06): 571-585

[53] Zhang Q, Johnson JA, Dunne LW.et al.Decellularized skin/adipose tissue flap matrix for engineering vascularized composite soft tissue flaps. Acta Biomater 2016; 35: 166-184

[54] Mase Jr VJ, Hsu JR, Wolf SE.et al.Clinical application of an acellular biologic scaffold for surgical repair of a large, traumatic quadriceps femoris muscle defect. Orthopedics 2010; 33(07): 511-511

[55] Jia L, Hua Y, Zeng J.et al.Bioprinting and regeneration of auricular cartilage using a bioactive bioink based on microporous photocrosslinkable acellular cartilage matrix. Bioact Mater 2022; 16: 66-81

[56] Paduano F, Marrelli M, Alom N.et al.Decellularized bone extracellular matrix and human dental pulp stem cells as a construct for bone regeneration. J Biomater Sci Polym Ed 2017; 28(08): 730-748

[57] Li R, Xu J, Rao Z.et al.Facilitate angiogenesis and neurogenesis by growth factors integrated decellularized matrix hydrogel. Tissue Eng Part A 2021; 27(11-12): 771-787

[58] Balestrini JL, Niklason LE.Extracellular matrix as a driver for lung regeneration. Ann Biomed Eng 2015; 43(03): 568-576

[59] Kajbafzadeh A-M, Javan-Farazmand N, Monajemzadeh M, Baghayee A.Determining the optimal decellularization and sterilization protocol for preparing a tissue scaffold of a human-sized liver tissue. Tissue Eng Part C Methods 2013; 19(08): 642-651

[60] Bonandrini B, Figliuzzi M, Papadimou E.et al.Recellularization of well-preserved acellular kidney scaffold using embryonic stem cells. Tissue Eng Part A 2014; 20(9-10): 1486-1498

[61] Li M, Zhang C, Zhong Y, Zhao J.A novel approach to utilize icariin as icariin-derived ECM on small intestinal submucosa scaffold for bone repair. Ann Biomed Eng 2017; 45(11): 2673-2682

[62] Iorio T, Blumberg D.Short-term results of treating primary and recurrent anal fistulas with a novel extracellular matrix derived from porcine urinary bladder. Am Surg 2015; 81(05): 498-502

[63] Sun W, Yang Y, Wang L.et al.Utilization of an acellular cartilage matrix-based photocrosslinking hydrogel for tracheal cartilage regeneration and circumferential tracheal repair. Adv Funct Mater 2022; 32: 2201257

[64] Kim S, Min S, Choi YS.et al.Tissue extracellular matrix hydrogels as alternatives to Matrigel for culturing gastrointestinal organoids. Nat Commun 2022; 13(01): 1692

[65] Willemse J, van Tienderen G, van Hengel E.et al. Hydrogels derived from decellularized liver tissue support the growth and differentiation of cholangiocyte organoids. Biomaterials 2022; 284: 121473-121473

[66] Simsa R, Rothenbücher T, Gürbüz H.et al.Brain organoid formation on decellularized porcine brain ECM hydrogels. PLoS One 2021; 16(01): e0245685-e0245685

[67] Manichanh C, Borruel N, Casellas F, Guarner F.The gut microbiota in IBD. Nat Rev Gastroenterol Hepatol 2012; 9(10): 599-608

[68] Krautkramer KA, Fan J, Bäckhed F.Gut microbial metabolites as multi-kingdom intermediates. Nat Rev Microbiol 2021; 19(02): 77-94

[69] Nicholson JK, Holmes E, Kinross J.et al.Host-gut microbiota metabolic interactions. Science 2012; 336(6086): 1262-1267

[70] Matson V, Fessler J, Bao R.et al.The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science 2018; 359(6371): 104-108

[71] Routy B, Le Chatelier E, Derosa L.et al.Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. In: Science, United States. Vol. 359. American Association for the Advancement of Science; United States: 2018: 91-97

[72] Dejea CM, Fathi P, Craig JM.et al.Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 2018; 359(6375): 592-597

[73] Wong SH, Zhao L, Zhang X.et al. Gavage of fecal samples from patients with colorectal cancer promotes intestinal carcinogenesis in germ-free and conventional mice. Gastroenterology2017; 153 (06): 1621-1633.e6

[74] Viaud S, Saccheri F, Mignot G.et al.The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 2013; 342(6161): 971-976

[75] Roy S, Trinchieri G.Microbiota: a key orchestrator of cancer therapy. Nat Rev Cancer 2017; 17(05): 271-285

[76] Frankel AE, Coughlin LA, Kim J.et al.Metagenomic shotgun sequencing and unbiased metabolomic profiling identify specific human gut microbiota and metabolites associated with immune checkpoint therapy efficacy in melanoma patients. Neoplasia 2017; 19(10): 848-855

[77] Rubert J, Schweiger PJ, Mattivi F, Tuohy K, Jensen KB, Lunardi A.Intestinal organoids: a tool for modelling diet-microbiome-host interactions. Trends Endocrinol Metab 2020; 31(11): 848-858

[78] Duchartre Y, Kim YM, Kahn M.The Wnt signaling pathway in cancer. Crit Rev Oncol Hematol 2016; 99: 141-149

[79] Fruman DA, Chiu H, Hopkins BD, Bagrodia S, Cantley LC, Abraham RT.The PI3K pathway in human disease. Cell 2017; 170(04): 605-635

[80] Li X, Huang J, Yu T.et al.Fusobacterium nucleatum promotes the progression of colorectal cancer through Cdk5-activated Wnt/β-catenin signaling. Front Microbiol 2021; 11: 545251

[81] Long X, Wong CC, Tong L.et al.Peptostreptococcus anaerobius promotes colorectal carcinogenesis and modulates tumour immunity. Nat Microbiol 2019; 4(12): 2319-2330

[82] Ternes D, Tsenkova M, Pozdeev VI.et al.The gut microbial metabolite formate exacerbates colorectal cancer progression. Nat Metab 2022; 4(04): 458-475

[83] Levy M, Kolodziejczyk AA, Thaiss CA, Elinav E.Dysbiosis and the immune system. Nat Rev Immunol 2017; 17(04): 219-232

[84] Round JL, Mazmanian SK.Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A 2010; 107(27): 12204-12209

[85] Jia W, Xie G, Jia W.Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis. Nat Rev Gastroenterol Hepatol 2018; 15(02): 111-128

[86] Wang S, Dong W, Liu L.et al.Interplay between bile acids and the gut microbiota promotes intestinal carcinogenesis. Mol Carcinog 2019; 58(07): 1155-1167

[87] Ma C, Han M, Heinrich B.et al. Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells. Science2018; 360 (6391): eaan5931

[88] Hanfrey CC, Pearson BM, Hazeldine S.et al.Alternative spermidine biosynthetic route is critical for growth of Campylobacter jejuni and is the dominant polyamine pathway in human gut microbiota. J Biol Chem 2011; 286(50): 43301-43312

[89] Di Martino ML, Campilongo R, Casalino M, Micheli G, Colonna B, Prosseda G.Polyamines: emerging players in bacteria-host interactions. Int J Med Microbiol 2013; 303(08): 484-491

[90] Pegg AE.Toxicity of polyamines and their metabolic products. Chem Res Toxicol 2013; 26(12): 1782-1800

[91] Holbert CE, Cullen MT, Casero Jr RA, Stewart TM.Polyamines in cancer: integrating organismal metabolism and antitumour immunity. Nat Rev Cancer 2022; 22(08): 467-480

[92] Ghanavati R, Akbari A, Mohammadi F.et al.Lactobacillus species inhibitory effect on colorectal cancer progression through modulating the Wnt/β-catenin signaling pathway. Mol Cell Biochem 2020; 470(1-2): 1-13

[93] Nadeem A, Aung KM, Ray T.et al.Suppression of β-catenin signaling in colon carcinoma cells by a bacterial protein. Int J Cancer 2021; 149(02): 442-459

[94] Zununi Vahed S, Barzegari A, Rahbar Saadat Y, Goreyshi A, Omidi Y.Leuconostoc mesenteroides-derived anticancer pharmaceuticals hinder inflammation and cell survival in colon cancer cells by modulating NF-κB/AKT/PTEN/MAPK pathways. Biomed Pharmacother 2017; 94: 1094-1100

[95] Watschinger C, Moschen AR.Lactobacillus reuteri-an old acquaintance takes on a new task in colorectal tumor surveillance. Cancer Cell 2022; 40(02): 125-127

[96] Cervantes-Barragan L, Chai JN, Tianero MD.et al.Lactobacillus reuteri induces gut intraepithelial CD4+CD8αα+ T cells. Science 2017; 357(6353): 806-810

[97] Dodd D, Spitzer MH, Van Treuren W.et al.A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 2017; 551(7682): 648-652

[98] Pardoll D.Cancer and the immune system: basic concepts and targets for intervention. Semin Oncol 2015; 42(04): 523-538

[99] Chen DS, Mellman I.Oncology meets immunology: the cancer-immunity cycle. Immunity 2013; 39(01): 1-10

[100] Wang Y, Ma R, Liu F, Lee SA, Zhang L.Modulation of gut microbiota: a novel paradigm of enhancing the efficacy of programmed death-1 and programmed death ligand-1 blockade therapy. Front Immunol 2018; 9(MAR): 374-374

[101] Elkrief A, Derosa L, Zitvogel L, Kroemer G, Routy B.The intimate relationship between gut microbiota and cancer immunotherapy. Gut Microbes 2019; 10(03): 424-428

[102] Helmink BA, Khan MAW, Hermann A, Gopalakrishnan V, Wargo JA.The microbiome, cancer, and cancer therapy. Nat Med 2019; 25(03): 377-388

[103] Vétizou M, Pitt JM, Daillère R.et al.Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 2015; 350(6264): 1079-1084

[104] Sivan A, Corrales L, Hubert N.et al.Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 2015; 350(6264): 1084-1089

[105] Mager LF, Burkhard R, Pett N.et al.Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy. Science 2020; 369(6510): 1481-1489

[106] Griffin ME, Espinosa J, Becker JL.et al.Enterococcus peptidoglycan remodeling promotes checkpoint inhibitor cancer immunotherapy. Science 2021; 373(6558): 1040-1046

[107] Chen LC, Chen YY.Bacteria recycle tumour waste to fuel immune cells. Nature 2021; 598(7882): 570-571

[108] Canale FP, Basso C, Antonini G.et al.Metabolic modulation of tumours with engineered bacteria for immunotherapy. Nature 2021; 598(7882): 662-666

[109] Arrieta MC, Walter J, Finlay BB.Human microbiota-associated mice: a model with challenges. Cell Host Microbe 2016; 19(05): 575-578

[110] Engevik MA, Ruan W, Esparza M.et al.Immunomodulation of dendritic cells by Lactobacillus reuteri surface components and metabolites. Physiol Rep 2021; 9(02): e14719

[111] Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A.et al; Genomics England Research Consortium. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli. Nature 2020; 580(7802): 269-273

[112] Fu A, Yao B, Dong T.et al. Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer. Cell2022; 185 (08): 1356-1372.e26

[113] Puschhof J, Pleguezuelos-Manzano C, Martinez-Silgado A.et al.Intestinal organoid cocultures with microbes. Nat Protoc 2021; 16(10): 4633-4649

[114] Bartfeld S, Bayram T, van de Wetering M.et al. In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection. Gastroenterology2015; 148 (01): 126-136.e6

[115] Puschhof J, Pleguezuelos-Manzano C, Clevers H.Organoids and organs-on-chips: insights into human gut-microbe interactions. Cell Host Microbe 2021; 29(06): 867-878

[116] Jalili-Firoozinezhad S, Gazzaniga FS, Calamari EL.et al.A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat Biomed Eng 2019; 3(07): 520-531

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