Authentication, characterization and contamination detection of cell lines, xenografts and organoids by barcode deep NGS sequencing

Chen, Xiaobo; Qian, Wubin; Song, Zhenzhen; Li, Qi-Xiang; Guo, Sheng

doi:10.1093/nargab/lqaa060

Cited by 16 publications

(22 citation statements)

References 53 publications

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“…The established organoids generally had varying growth kinetics, with culturing time ranging predominantly from 7–14 days before requiring passaging, similar to those described for PDOs by others. In addition, PDXOs could be cryopreserved with nearly 100% recovery rate, which was critical for establishing a living biobank as well as the PDXO identity authenticated by single-nucleotide polymorphism (SNP) as previously reported [ 32 ]. Using bright-field microscopy, the morphology of PDXOs look similar to those typically observed for PDOs [ 23 , 34 , 43 ], inclusive of cystic, compact [ 36 ], grape-like and budding morphologies (representative morphology phenotypes are shown in S1a Fig , with selected models shown in Fig 1b ), supporting the hypothesis that PDXO structure and morphology is generally similar to those seen for PDOs.…”

Section: Resultsmentioning

confidence: 99%

“…PDX establishment, maintenance and biobanking have been previously described [ 7 ], including models being individually quality controlled and tracked (authentication and virus infection status and mycoplasma status etc .) [ 32 ]. Briefly, all PDX were maintained in immunocompromised mice.…”

Section: Methodsmentioning

confidence: 99%

“…Organoid culture medium was refreshed every 3–4 days and organoids passaged every 7–14 days at certain ratios depending on the density of the culture and models and transferred to 24 well plates. The expanded organoids culture were cryopreserved to create a master biobank of early passage organoids [ 31 , 36 ], which were quality controlled and tracked similar to our PDX biobank [ 32 , 40 ].…”

Section: Methodsmentioning

confidence: 99%

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A living biobank of matched pairs of patient-derived xenografts and organoids for cancer pharmacology

Kumari²,

Zhou

et al. 2023

PLoS ONE

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Patient-derived tumor xenograft (PDX)/organoid (PDO), driven by cancer stem cells (CSC), are considered the most predictive models for translational oncology. Large PDX collections reflective of patient populations have been created and used extensively to test various investigational therapies, including population-trials as surrogate subjects in vivo. PDOs are recognized as in vitro surrogates for patients amenable for high-throughput screening (HTS). We have built a biobank of carcinoma PDX-derived organoids (PDXOs) by converting an existing PDX library and confirmed high degree of similarities between PDXOs and parental PDXs in genomics, histopathology and pharmacology, suggesting “biological equivalence or interchangeability” between the two. Here we demonstrate the applications of PDXO biobank for HTS “matrix” screening for both lead compounds and indications, immune cell co-cultures for immune-therapies and engineering enables in vitro/in vivo imaging. This large biobank of >550 matched pairs of PDXs/PDXOs across different cancers could become powerful tools for the future cancer drug discovery.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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A living biobank of matched pairs of patient-derived xenografts and organoids for cancer pharmacology

Kumari²,

Zhou

et al. 2023

PLoS ONE

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“…Short‐tandem repeat (STR) and single‐nucleotide polymorphisms (SNPs) assays are commonly employed to authenticate biosamples. A SNP‐NGS‐based and DNA barcoding–based method has been described for authentication and detection of contamination, such as mouse content, mycoplasma, and pathogens (Chen, Qian, Song, Li, & Guo, 2020).…”

Section: Establishing a Biobank Of Matched Organoid And Pdx Modelsmentioning

confidence: 99%

Translational and Clinical Relevance of PDX‐Derived Organoid Models in Oncology Drug Discovery and Development

Kumari¹,

Li³

2022

Current Protocols

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Patient‐derived cancer disease models conserve many key features of the original human cancers, potentially allowing higher predictive power than traditional cell line models. Accordingly, in vivo patient‐derived xenografts (PDX) are frequently utilized in preclinical and translational oncology studies as patient surrogates for population‐based screens (“mouse clinical trials”), for which large PDX biobanks have been generated over the last decade from various cancer types. In vitro patient‐derived organoids (PDO) have recently emerged as a disruptive technology, enabling early “patient in a dish” clinical trials. Like PDX, PDOs retain the histology/genomics of the original tumor and are highly predictive of the clinical response. Organoids derived from adult stem cells (ASC) in patient tissue can function as mini‐organs. They have greater advantages over other 3D in vitro systems, making them highly predictive, reliable, and consistent in vitro models. Large biobanks enable the adoption of organoids in early drug screening and patient selection. PDX biobanks, as a source of human material, have been used to create 3D in vitro screens, but with limitations. However, creating organoids from the ASCs residing in PDXs has been successfully used as a rapid and cost‐effective way to enable higher throughput in vitro screens and generate matched in vitro/in vivo model pairs that retain genomic, histopathological, and pharmacology profiles. This overview summarizes the generation of matched in vitro/in vivo models from patient material, the advantages over other systems, and the applications to drug discovery. © 2022 Wiley Periodicals LLC.

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“…Существует ряд доступных методов, которые предоставляют информацию о качестве клеточных линий: кариотипирование, профилирование коротких тандемных повторов (short tandem repeat, STR) [9][10][11], профилирование однонуклеотидных полиморфизмов (SNP) [12,13], использование видоспецифичных праймеров, штрих-кодирование дезоксирибонуклеиновой кислоты (ДНК), высокопроизводительное секвенирование [14][15][16], СО1 бар-кодирование 5 . Метод STR-профилирования зарекомендовал себя в качестве надежного и воспроизводимого варианта [17][18][19] и занял ведущие позиции, в связи с чем Американским национальным институтом стандартов (The American National Standards Institute, ANSI) и Американской коллекцией типовых культур (American Type Culture Collection, ATCC) был разработан стандарт аутентификации клеточных линий человека ASN-0002 (Authentication of Human Cell Lines: Standardization of STR Profiling).…”

Section: Introductionunclassified

Using short tandem repeat profiling to validate cell lines in biobanks

Кособокова¹,

Malchenkova²,

Kalinina³

et al. 2022

Cardiovasc Ther Prev

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Aim. To approve the COrDIS kit (Gordiz, Russia) for the authenticity of cell lines from the Bioresource Collection of the N.N. Blokhin National Medical Research Center of Oncology by the short tandem repeat (STR) profiling.Material and methods. The chosen method proved to be a reliable and reproducible option. With this approach, a number of polymorphic STR loci are amplified using commercially available primer sets. Polymerase chain reaction (PCR) products are analyzed simultaneously with size standards using automated fluorescent detection methods. The results are presented as a simple number code corresponding to the lengths of the PCR products amplified at each locus. By applying this method to cell lines, the laboratory can both authenticate commercial cell lines and build a database of their lines. In the work, we used the COrDIS EXPERT 26 kit (Gordiz, Russia), validated for molecular genetic identification of personality based on multiplex PCR analysis of 26 highly polymorphic loci of human genomic deoxyribonucleic acid. PCR results were analyzed by capillary electrophoresis using an automatic genetic analyzer with laser-induced fluorescence detection (Applied Biosystems 3500xL).Results. When testing the method, profiling of 37 cell lines was carried out, of which 18 were announced in international databases and 19 were unique, obtained at the N. N. Blokhin National Medical Research Center of Oncology, as well as a cell line mixture in order to determine the limits of contamination detection. The obtained results showed the correspondence of commercial cell lines with the data in international databases. Within the framework of this work, profiles of unique lines were obtained and the foundation of own genetic database was laid. Studies to identify the limit of contamination detection by another line have shown that even 4% of the contaminant culture in the total pool can be used to identify its individual alleles.Conclusion. The results obtained indicate the possibility of using the method to identify samples of the collection and detect intraspecific contamination.

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Authentication, characterization and contamination detection of cell lines, xenografts and organoids by barcode deep NGS sequencing

Cited by 16 publications

References 53 publications

A living biobank of matched pairs of patient-derived xenografts and organoids for cancer pharmacology

A living biobank of matched pairs of patient-derived xenografts and organoids for cancer pharmacology

Translational and Clinical Relevance of PDX‐Derived Organoid Models in Oncology Drug Discovery and Development

Using short tandem repeat profiling to validate cell lines in biobanks

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