DNA barcode to trace the development and differentiation of cord blood stem cells (Review)
- Authors:
- Mo-Yu Wang
- Yang Zhou
- Guang-Shun Lai
- Qi Huang
- Wen-Qi Cai
- Zi-Wen Han
- Yingying Wang
- Zhaowu Ma
- Xian-Wang Wang
- Ying Xiang
- Shu-Xian Fang
- Xiao-Chun Peng
- Hong-Wu Xin
-
Affiliations: Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China, Department of Digestive Medicine, People's Hospital of Lianjiang, Lianjiang, Guangdong 524400, P.R. China, State Key Laboratory of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China - Published online on: October 12, 2021 https://doi.org/10.3892/mmr.2021.12489
- Article Number: 849
-
Copyright: © Wang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
This article is mentioned in:
Abstract
Broxmeyer HE, Douglas GW, Hangoc G, Cooper S, Bard J, English D, Arny M, Thomas L and Boyse EA: Human umbilical cord blood as a potential source of transplantable hematopoietic stem/progenitor cells. Proc Natl Acad Sci USA. 86:3828–3832. 1989. View Article : Google Scholar | |
Buzańska L, Jurga M and Domańska-Janik K: Neuronal differentiation of human umbilical cord blood neural stem-like cell line. Neurodegener Dis. 3:19–26. 2006. View Article : Google Scholar | |
Zhang J, Huang X, Guo B, Cooper S, Capitano ML, Johnson TC, Siegel DR and Broxmeyer HE: Effects of eupalinilide E and UM171, alone and in combination on cytokine stimulated ex-vivo expansion of human cord blood hematopoietic stem cells. Blood Cells Mol Dis. 84:1024572020. View Article : Google Scholar | |
Sunitha MM, Srikanth L, Kumar PS, Chandrasekhar C and Sarma P: Down-regulation of PAX2 promotes in vitro differentiation of podocytes from human CD34+ cells. Cell Tissue Res. 370:477–488. 2017. View Article : Google Scholar | |
Alatyyat SM, Alasmari HM, Aleid OA, Abdel-Maksoud MS and Elsherbiny N: Umbilical cord stem cells: Background, processing and applications. Tissue Cell. 65:1013512020. View Article : Google Scholar | |
Francese R and Fiorina P: Immunological and regenerative properties of cord blood stem cells. Clin Immunol. 136:309–322. 2010. View Article : Google Scholar | |
Fatrai S, Schepers H, Tadema H, Vellenga E, Daenen SM and Schuringa JJ: Mucin1 expression is enriched in the human stem cell fraction of cord blood and is upregulated in majority of the AML cases. Exp Hematol. 36:1254–1265. 2008. View Article : Google Scholar | |
Castillo-Melendez M, Yawno T, Jenkin G and Miller SL: Stem cell therapy to protect and repair the developing brain: A review of mechanisms of action of cord blood and amnion epithelial derived cells. Front Neurosci. 7:1942013. View Article : Google Scholar | |
Cairo MS and Wagner JE: Placental and/or umbilical cord blood: An alternative source of hematopoietic stem cells for transplantation. Blood. 90:4665–4678. 1997. View Article : Google Scholar | |
Mayani H and Lansdorp PM: Biology of human umbilical cord blood-derived hematopoietic stem/progenitor cells. Stem Cells. 16:153–165. 1998. View Article : Google Scholar | |
Liu G, Ye X, Zhu Y, Li Y, Sun J, Cui L and Cao Y: Osteogenic differentiation of GFP-labeled human umbilical cord blood derived mesenchymal stem cells after cryopreservation. Cryobiology. 63:125–128. 2011. View Article : Google Scholar | |
Zheng JH, Zhang JK, Kong DS, Song YB, Zhao SD, Qi WB, Li YN, Zhang ML and Huang XH: Quantification of the CM-Dil-labeled human umbilical cord mesenchymal stem cells migrated to the dual injured uterus in SD rat. Stem Cell Res Ther. 11:2802020. View Article : Google Scholar | |
Kebschull JM and Zador AM: Cellular barcoding: Lineage tracing, screening and beyond. Nat Methods. 15:871–879. 2018. View Article : Google Scholar | |
Wagner DE and Klein AM: Lineage tracing meets single-cell omics: Opportunities and challenges. Nat Rev Genet. 21:410–427. 2020. View Article : Google Scholar | |
Mitchell KE, Weiss ML, Mitchell BM, Martin P, Davis D, Morales L, Helwig B, Beerenstrauch M, Abou-Easa K, Hildreth T, et al: Matrix cells from Wharton's jelly form neurons and glia. Stem Cells. 21:50–60. 2003. View Article : Google Scholar | |
Fu YS, Shih YT, Cheng YC and Min MY: Transformation of human umbilical mesenchymal cells into neurons in vitro. J Biomed Sci. 11:652–660. 2004. View Article : Google Scholar | |
Rodrigues LP, Iglesias D, Nicola FC, Steffens D, Valentim L, Witczak A, Zanatta G, Achaval M, Pranke P and Netto CA: Transplantation of mononuclear cells from human umbilical cord blood promotes functional recovery after traumatic spinal cord injury in Wistar rats. Braz J Med Biol Res. 45:49–57. 2012. View Article : Google Scholar | |
Wang HS, Hung SC, Peng ST, Huang CC, Wei HM, Guo YJ, Fu YS, Lai MC and Chen CC: Mesenchymal stem cells in the Wharton's jelly of the human umbilical cord. Stem Cells. 22:1330–1337. 2004. View Article : Google Scholar | |
Kakinuma S, Tanaka Y, Chinzei R, Watanabe M, Shimizu-Saito K, Hara Y, Teramoto K, Arii S, Sato C, Takase K, et al: Human umbilical cord blood as a source of transplantable hepatic progenitor cells. Stem Cells. 21:217–227. 2003. View Article : Google Scholar | |
Tang XP, Zhang M, Yang X, Chen LM and Zeng Y: Differentiation of human umbilical cord blood stem cells into hepatocytes in vivo and in vitro. World J Gastroenterol. 12:4014–4019. 2006. View Article : Google Scholar | |
Mayani H, Wagner JE and Broxmeyer HE: Cord blood research, banking, and transplantation: Achievements, challenges, and perspectives. Bone Marrow Transplant. 55:48–61. 2020. View Article : Google Scholar | |
Shetty P, Cooper K and Viswanathan C: Comparison of proliferative and multilineage differentiation potentials of cord matrix, cord blood, and bone marrow mesenchymal stem cells. Asian J Transfus Sci. 4:14–24. 2010. View Article : Google Scholar | |
Han JY, Goh RY, Seo SY, Hwang TH, Kwon HC, Kim SH, Kim JS, Kim HJ and Lee YH: Cotransplantation of cord blood hematopoietic stem cells and culture-expanded and GM-CSF-/SCF-transfected mesenchymal stem cells in SCID mice. J Korean Med Sci. 22:242–247. 2007. View Article : Google Scholar | |
Hutton JF, D'Andrea RJ and Lewis ID: Potential for clinical ex vivo expansion of cord blood haemopoietic stem cells using non-haemopoietic factor supplements. Curr Stem Cell Res Ther. 2:229–237. 2007. View Article : Google Scholar | |
Demerdash Z, El-Baz HG, Maher K, Hassan S, Salah F, Hassan M, Elzallat M, El-Shafei M and Taha T: Effect of repeated passaging and cell density on proliferation and differentiation potential of cord blood unrestricted somatic stem cells. New Horiz Transl Med. 2:672015. | |
Esmaeili M, Niazi V, Pourfathollah AA, Hosseini MKM, Nakhlestani M, Golzadeh K, Taheri M, Ghafouri-Fard S and Atarodi K: The impact of parathyroid hormone treated mesenchymal stem cells on ex-vivo expansion of cord blood hematopoietic stem cells. Gene Rep. 17:1004902019. View Article : Google Scholar | |
Mokhtari S, Baptista PM, Vyas DA, Freeman CJ, Moran E, Brovold M, Llamazares GA, Lamar Z, Porada CD, Soker S and Almeida-Porada G: Evaluating interaction of cord blood hematopoietic stem/progenitor cells with functionally integrated three-dimensional microenvironments. Stem Cells Transl Med. 7:271–282. 2018. View Article : Google Scholar | |
Chaurasia P, Gajzer DC, Schaniel C, D'Souza S and Hoffman R: Epigenetic reprogramming induces the expansion of cord blood stem cells. J Clin Invest. 124:2378–2395. 2014. View Article : Google Scholar | |
Li Q, Zhao D, Chen Q, Luo M, Huang J, Yang C, Wang F, Li W and Liu T: Wharton's jelly mesenchymal stem cell-based or umbilical vein endothelial cell-based serum-free coculture with cytokines supports the ex vivo expansion/maintenance of cord blood hematopoietic stem/progenitor cells. Stem Cell Res Ther. 10:3762019. View Article : Google Scholar | |
Zhang B, Wu X, Zhang X, Sun Y, Yan Y, Shi H, Zhu Y, Wu L, Pan Z, Zhu W, et al: Human umbilical cord mesenchymal stem cell exosomes enhance angiogenesis through the Wnt4/β-catenin pathway. Stem Cells Transl Med. 4:513–522. 2015. View Article : Google Scholar | |
Rim YA, Nam Y and Ju JH: Application of cord blood and cord blood-derived induced pluripotent stem cells for cartilage regeneration. Cell Transplant. 28:529–537. 2019. View Article : Google Scholar | |
Zheng YL, Sun YP, Zhang H, Liu WJ, Jiang R, Li WY, Zheng YH and Zhang ZG: Mesenchymal stem cells obtained from synovial fluid mesenchymal stem cell-derived induced pluripotent stem cells on a matrigel coating exhibited enhanced proliferation and differentiation potential. PLoS One. 10:e01442262015. View Article : Google Scholar | |
Zhou RQ, Wu JH, Gong YP, Guo Y and Xing HY: Transcription factor SCL/TAL1 mediates the phosphorylation of MEK/ERK pathway in umbilical cord blood CD34+ stem cells during hematopoietic differentiation. Blood Cells Mol Dis. 53:39–46. 2014. View Article : Google Scholar | |
Ajami M, Soleimani M, Abroun S and Atashi A: Comparison of cord blood CD34 + stem cell expansion in coculture with mesenchymal stem cells overexpressing SDF-1 and soluble/membrane isoforms of SCF. J Cell Biochem. 120:15297–15309. 2019. View Article : Google Scholar | |
Naka K, Muraguchi T, Hoshii T and Hirao A: Regulation of reactive oxygen species and genomic stability in hematopoietic stem cells. Antioxid Redox Signal. 10:1883–1894. 2008. View Article : Google Scholar | |
Bonifazi F, Dan E, Labopin M, Sessa M, Guadagnuolo V, Ferioli M, Rizzi S, De Carolis S, Sinigaglia B, Motta MR, et al: Intrabone transplant provides full stemness of cord blood stem cells with fast hematopoietic recovery and low GVHD rate: Results from a prospective study. Bone Marrow Transplant. 54:717–725. 2019. View Article : Google Scholar | |
Lee YH: Clinical utilization of cord blood over human health: Experience of stem cell transplantation and cell therapy using cord blood in Korea. Korean J Pediatr. 57:110–116. 2014. View Article : Google Scholar | |
Li X, Ma X, Chen Y, Peng D, Wang H, Chen S, Xiao Y, Li L, Zhou H, Cheng F, et al: Coinhibition of activated p38 MAPKα and mTORC1 potentiates stemness maintenance of HSCs from SR1-expanded human cord blood CD34+ cells via inhibition of senescence. Stem Cells Transl Med. 9:1604–1616. 2020. View Article : Google Scholar | |
Fares I, Chagraoui J, Gareau Y, Gingras S, Ruel R, Mayotte N, Csaszar E, Knapp DJ, Miller P, Ngom M, et al: Cord blood expansion. Pyrimidoindole derivatives are agonists of human hematopoietic stem cell self-renewal. Science. 345:1509–1512. 2014. View Article : Google Scholar | |
Seghatoleslam M, Jalali M, Alamdari DH, Nikravesh MR, Hosseini SM and Fazel AR: Effect of incubation time on the in vitro labeling of umbilical cord blood hematopoietic stem cells with bromodeoxyuridine (BrdU). Clin Biochem. 44 (Suppl):S1532011. View Article : Google Scholar | |
Walsh C and Cepko CL: Widespread dispersion of neuronal clones across functional regions of the cerebral cortex. Science. 255:434–440. 1992. View Article : Google Scholar | |
Gerrits A, Dykstra B, Kalmykowa OJ, Klauke K, Verovskaya E, Broekhuis MJ, de Haan G and Bystrykh LV: Cellular barcoding tool for clonal analysis in the hematopoietic system. Blood. 115:2610–2618. 2010. View Article : Google Scholar | |
Zorita E, Cuscó P and Filion GJ: Starcode: Sequence clustering based on all-pairs search. Bioinformatics. 31:1913–1919. 2015. View Article : Google Scholar | |
Schepers K, Swart E, van Heijst JW, Gerlach C, Castrucci M, Sie D, Heimerikx M, Velds A, Kerkhoven RM, Arens R and Schumacher TN: Dissecting T cell lineage relationships by cellular barcoding. J Exp Med. 205:2309–2318. 2008. View Article : Google Scholar | |
Kristiansen TA, Jaensson Gyllenbäck E, Zriwil A, Björklund T, Daniel JA, Sitnicka E, Soneji S, Bryder D and Yuan J: Cellular barcoding links B-1a B cell potential to a fetal hematopoietic stem cell state at the single-cell level. Immunity. 45:346–357. 2016. View Article : Google Scholar | |
Lu R, Neff NF, Quake SR and Weissman IL: Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nat Biotechnol. 29:928–933. 2011. View Article : Google Scholar | |
Naik SH, Perié L, Swart E, Gerlach C, van Rooij N, de Boer RJ and Schumacher TN: Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature. 496:229–232. 2013. View Article : Google Scholar | |
Verovskaya E, Broekhuis MJ, Zwart E, Ritsema M, van Os R, de Haan G and Bystrykh LV: Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding. Blood. 122:523–532. 2013. View Article : Google Scholar | |
Keller G, Paige C, Gilboa E and Wagner EF: Expression of a foreign gene in myeloid and lymphoid cells derived from multipotent haematopoietic precursors. Nature. 318:149–154. 1985. View Article : Google Scholar | |
Lemischka IR, Raulet DH and Mulligan RC: Developmental potential and dynamic behavior of hematopoietic stem cells. Cell. 45:917–927. 1986. View Article : Google Scholar | |
Ludwig LS, Lareau CA, Ulirsch JC, Christian E, Muus C, Li LH, Pelka K, Ge W, Oren Y, Brack A, et al: Lineage tracing in humans enabled by mitochondrial mutations and single-cell genomics. Cell. 176:1325–1339.e22. 2019. View Article : Google Scholar | |
Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG and Klein AM: Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science. 360:981–987. 2018. View Article : Google Scholar | |
Guo C, Kong W, Kamimoto K, Rivera-Gonzalez GC, Yang X, Kirita Y and Morris SA: CellTag Indexing: Genetic barcode-based sample multiplexing for single-cell genomics. Genome Biol. 20:902019. View Article : Google Scholar | |
Bramlett C, Jiang D, Nogalska A, Eerdeng J, Contreras J and Lu R: Clonal tracking using embedded viral barcoding and high-throughput sequencing. Nat Protoc. 15:1436–1458. 2020. View Article : Google Scholar | |
Pei W, Feyerabend TB, Rössler J, Wang X, Postrach D, Busch K, Rode I, Klapproth K, Dietlein N, Quedenau C, et al: Polylox barcoding reveals haematopoietic stem cell fates realized in vivo. Nature. 548:456–460. 2017. View Article : Google Scholar | |
Pei W, Wang X, Rössler J, Feyerabend TB, Hofer T and Rodewald HR: Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice. Nat Protoc. 14:1820–1840. 2019. View Article : Google Scholar | |
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA and Zhang F: Multiplex genome engineering using CRISPR/Cas systems. Science. 339:819–823. 2013. View Article : Google Scholar | |
McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF and Shendure J: Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science. 353:aaf79072016. View Article : Google Scholar | |
Frieda KL, Linton JM, Hormoz S, Choi J, Chow KK, Singer ZS, Budde MW, Elowitz MB and Cai L: Synthetic recording and in situ readout of lineage information in single cells. Nature. 541:107–111. 2017. View Article : Google Scholar | |
Perli SD, Cui CH and Lu TK: Continuous genetic recording with self-targeting CRISPR-Cas in human cells. Science. 353:aag05112016. View Article : Google Scholar | |
Kalhor R, Mali P and Church GM: Rapidly evolving homing CRISPR barcodes. Nat Methods. 14:195–200. 2017. View Article : Google Scholar | |
Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P and Church GM: Developmental barcoding of whole mouse via homing CRISPR. Science. 361:eaat98042018. View Article : Google Scholar | |
Loveless TB, Grotts JH, Schechter MW, Forouzmand E, Carlson CK, Agahi BS, Liang G, Ficht M, Liu B, Xie X and Liu CC: DNA writing at a single genomic site enables lineage tracing and analog recording in mammalian cells. bioRxiv. 6391202019. | |
Bowling S, Sritharan D, Osorio FG, Nguyen M, Cheung P, Rodriguez-Fraticelli A, Patel S, Yuan WC, Fujiwara Y, Li BE, et al: An engineered CRISPR-Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells. Cell. 181:1410–1422.e27. 2020. View Article : Google Scholar | |
Nguyen LV, Cox CL, Eirew P, Knapp DJ, Pellacani D, Kannan N, Carles A, Moksa M, Balani S, Shah S, et al: DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts. Nat Commun. 5:58712014. View Article : Google Scholar | |
Naik SH, Schumacher TN and Perie L: Cellular barcoding: A technical appraisal. Exp Hematol. 42:598–608. 2014. View Article : Google Scholar | |
Nguyen LV, Pellacani D, Lefort S, Kannan N, Osako T, Makarem M, Cox CL, Kennedy W, Beer P, Carles A, et al: Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells. Nature. 528:267–271. 2015. View Article : Google Scholar | |
McKenzie JL, Gan OI, Doedens M, Wang JC and Dick JE: Individual stem cells with highly variable proliferation and self-renewal properties comprise the human hematopoietic stem cell compartment. Nat Immunol. 7:1225–1233. 2006. View Article : Google Scholar | |
Gonzalez-Murillo A, Lozano ML, Montini E, Bueren JA and Guenechea G: Unaltered repopulation properties of mouse hematopoietic stem cells transduced with lentiviral vectors. Blood. 112:3138–3147. 2008. View Article : Google Scholar | |
Golden JA, Fields-Berry SC and Cepko CL: Construction and characterization of a highly complex retroviral library for lineage analysis. Proc Natl Acad Sci USA. 92:5704–5708. 1995. View Article : Google Scholar | |
Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, et al: A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell. 167:1867–1882.e21. 2016. View Article : Google Scholar | |
Cheung AM, Nguyen LV, Carles A, Beer P, Miller PH, Knapp DJ, Dhillon K, Hirst M and Eaves CJ: Analysis of the clonal growth and differentiation dynamics of primitive barcoded human cord blood cells in NSG mice. Blood. 122:3129–3137. 2013. View Article : Google Scholar | |
Belderbos ME, Jacobs S, Koster TK, Ausema A, Weersing E, Zwart E, de Haan G and Bystrykh LV: Donor-to-donor heterogeneity in the clonal dynamics of transplanted human cord blood stem cells in murine xenografts. Biol Blood Marrow Transplant. 26:16–25. 2020. View Article : Google Scholar | |
Sun J, Ramos A, Chapman B, Johnnidis JB, Le L, Ho YJ, Klein A, Hofmann O and Camargo FD: Clonal dynamics of native haematopoiesis. Nature. 514:322–327. 2014. View Article : Google Scholar | |
Cai WQ, Zeng LS, Wang LF, Wang YY, Cheng JT, Zhang Y, Han ZW, Zhou Y, Huang SL, Wang XW, et al: The latest battles between EGFR monoclonal antibodies and resistant tumor cells. Front Oncol. 10:12492020. View Article : Google Scholar | |
Han ZW, Lyv ZW, Cui B, Wang YY, Cheng JT, Zhang Y, Cai WQ, Zhou Y, Ma ZW, Wang XW, et al: Correction to: The old CEACAMs find their new role in tumor immunotherapy. Invest New Drugs. 38:1899–1900. 2020. View Article : Google Scholar | |
Wang YY, Lyu YN, Xin HY, Cheng JT, Liu XQ, Wang XW, Peng XC, Xiang Y, Xin VW, Lu CB, et al: Identification of putative UL54 (ICP27) transcription regulatory sequences binding to Oct-1, v-Myb, Pax-6 and hairy in herpes simplex viruses. J Cancer. 10:430–440. 2019. View Article : Google Scholar | |
Jensen P and Dymecki SM: Essentials of recombinase-based genetic fate mapping in mice. Methods Mol Biol. 1092:437–454. 2014. View Article : Google Scholar | |
Herring CA, Chen B, McKinley ET and Lau KS: Single-cell computational strategies for lineage reconstruction in tissue systems. Cell Mol Gastroenterol Hepatol. 5:539–548. 2018. View Article : Google Scholar | |
Liu XQ, Xin HY, Lyu YN, Ma ZW, Peng XC, Xiang Y, Wang YY, Wu ZJ, Cheng JT, Ji JF, et al: Oncolytic herpes simplex virus tumor targeting and neutralization escape by engineering viral envelope glycoproteins. Drug Deliv. 25:1950–1962. 2018. View Article : Google Scholar | |
Woodworth MB, Girskis KM and Walsh CA: Building a lineage from single cells: Genetic techniques for cell lineage tracking. Nat Rev Genet. 18:230–244. 2017. View Article : Google Scholar | |
Xu J, Nuno K, Litzenburger UM, Qi Y, Corces MR, Majeti R and Chang HY: Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA. Elife. 8:e451052019. View Article : Google Scholar |