Proteomics in the World of Induced Pluripotent Stem Cells

Lindoso, Rafael Soares; Kasai-Brunswick, Tais Hanae; Monnerat, Gustavo; Collino, Federica; Carvalho, Adriana Bastos; Carvalho, Antônio Carlos Campos de; Vieyra, Adalberto

doi:10.3390/cells8070703

Cited by 13 publications

(16 citation statements)

References 140 publications

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“…Similar outcomes were described in a study showing an analogous result at the proteome level. In contrast, the differences between ESCs and iPSCs could be depicted only when more biological replicated were added, most likely because this variability was introduced by the inclusion of different donors [100].…”

Section: Similarities and Differences Between Ipscs And Escsmentioning

confidence: 99%

iPSC Preparation and Epigenetic Memory: Does the Tissue Origin Matter?

Scesa

Adami

Bottai

2021

Cells

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The production of induced pluripotent stem cells (iPSCs) represent a breakthrough in regenerative medicine, providing new opportunities for understanding basic molecular mechanisms of human development and molecular aspects of degenerative diseases. In contrast to human embryonic stem cells (ESCs), iPSCs do not raise any ethical concerns regarding the onset of human personhood. Still, they present some technical issues related to immune rejection after transplantation and potential tumorigenicity, indicating that more steps forward must be completed to use iPSCs as a viable tool for in vivo tissue regeneration. On the other hand, cell source origin may be pivotal to iPSC generation since residual epigenetic memory could influence the iPSC phenotype and transplantation outcome. In this paper, we first review the impact of reprogramming methods and the choice of the tissue of origin on the epigenetic memory of the iPSCs or their differentiated cells. Next, we describe the importance of induction methods to determine the reprogramming efficiency and avoid integration in the host genome that could alter gene expression. Finally, we compare the significance of the tissue of origin and the inter-individual genetic variation modification that has been lightly evaluated so far, but which significantly impacts reprogramming.

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Section: Similarities and Differences Between Ipscs And Escsmentioning

confidence: 99%

iPSC Preparation and Epigenetic Memory: Does the Tissue Origin Matter?

Scesa

Adami

Bottai

2021

Cells

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“…7,9 More importantly, stem and cancer cell lines exhibit relatively higher diversity in protein expression. Two groups, Lindoso et al 19 and Signer et al, 20 showed that cells with stem-like characteristics possessed greater protein diversity and a higher synthesis rate because stem cells lose some gene expression after differentiation into various types of somatic cells. 21,22 Cancer cells are expected to have a higher diversity of protein expression because they acquire some genetic features of stem cells after transformation.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Cell lines are considered alternative sources for MP identification because they possess the corresponding tissue characteristics but have a relatively even distribution of protein abundance. , More importantly, stem and cancer cell lines exhibit relatively higher diversity in protein expression. Two groups, Lindoso et al and Signer et al, showed that cells with stem-like characteristics possessed greater protein diversity and a higher synthesis rate because stem cells lose some gene expression after differentiation into various types of somatic cells. , Cancer cells are expected to have a higher diversity of protein expression because they acquire some genetic features of stem cells after transformation. For instance, Sato et al developed mouse xenograft models of brain cancer metastasis by intracardiac injection of human breast cancer cell lines and observed that metastasis-related genes were specifically upregulated in both brain tissue and cancer cells .…”

Section: Introductionmentioning

confidence: 99%

D283 Med, a Cell Line Derived from Peritoneal Metastatic Medulloblastoma: A Good Choice for Missing Protein Discovery

Zhang

et al. 2020

J. Proteome Res.

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Since the Chromosome-Centric Human Proteome Project (C-HPP) was launched in 2010, many techniques have been adopted for the discovery of missing proteins (MPs). Because of these efforts, only 1481 MPs remained as of July 2020; however, by relying only on technique optimization, researchers have reached a bottleneck in MP discovery. Protein expression is tissue- or cell-type-dependent. The tissues of the human testis and brain have been reported to harbor a large number of tissue-specific genes and proteins; however, few studies have been performed on human brain tissue or cells to identify MPs. Herein a metastatic cell line derived from brain cancer, D283 Med, was used to search for MPs. With a traditional and simple shotgun workflow to separate the peptides into 20 fractions, 12 MPs containing at least two unique non-nested peptides (amino acid length ≥9) were identified in this cell line with a protein false discovery rate of <1%. Following the same experimental protocol, only one MP was found in a nonmetastatic brain cancer cell line, U-118 MG. Furthermore, 12 MPs were verified as having two non-nested unique peptides by matching them with corresponding chemically synthesized peptides through parallel reaction monitoring. These results clearly demonstrate that the appropriate selection of experimental materials, either tissues or cell lines, is imperative for MP discovery. The data obtained in this study are available via ProteomeXchange (PXD021482) and PeptideAtlas (PASS01627).

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“…It is an analytical pattern in wide ranges to identify, measure and understand post translational concerning of protein in a tissue or cell or body fluid. 1 Proteomic approaches represented an instrumental in providing information of diseases on molecular basis, clear understanding of pathophysiology, prediction of disorders thereby conferred standardized thrust, aiming at therapeutic solutions. Proteomic tools contribute a new clarity for health risk factors and have been recognized as a novel science instead of collection of tools.…”

Section: Introductionmentioning

confidence: 99%

Current applications of proteomics: a key and novel approach

Sharma

Kumar

2019

Int J Adv Med

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Proteomics represented vital applications of technologies in the identification and quantification of high to moderate proteins (cellular signalling networks) found in biological matrix such as tissues, cells and fluids. Proteomics based technical knowledge is applied and verified in several preclinical research settings such as invention of diagnostic markers for specific disease and have shown to be increased in clinical applications. Extensive studies on proteomics resulted in detection of biomarkers that have been highly advanced in using diseases for cancer, lungs, cardiovascular, renal and neuro-regenerative and Parkinson's disease by introducing human origins for biocompatibility such as urine and serum. Advancement in the proteomic methods is conferring candidate right direction for clinical usage. In this review, recent developments and widely used proteomics approaches such as Mass Spectrometry (MS), Microarray chips are elaborately addressed and also focused merits and demerits of commonly used advanced approaches such as Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and Data Independent Acquisition (DIA) and other used proteomics and that roles, in order to aid clinicians, were also discussed in the light of biomedical applications.

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Proteomics in the World of Induced Pluripotent Stem Cells

Cited by 13 publications

References 140 publications

iPSC Preparation and Epigenetic Memory: Does the Tissue Origin Matter?

iPSC Preparation and Epigenetic Memory: Does the Tissue Origin Matter?

D283 Med, a Cell Line Derived from Peritoneal Metastatic Medulloblastoma: A Good Choice for Missing Protein Discovery

Current applications of proteomics: a key and novel approach

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