A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers

Terry CC Lim Kam Sian; Christie Sun; Jason E Cain; Joel R Steele; Iresha Hanchapola; Stoyan Stoychev; Ralf B Schittenhelm; Pouya Faridi

doi:10.1007/978-1-0716-3858-3_17

A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers

Terry CC Lim Kam Sian, Christie Sun, Jason E Cain, Joel R Steele, Iresha Hanchapola, Stoyan Stoychev, Ralf B Schittenhelm, Pouya Faridi

Research output: Chapter in Book/Report/Conference proceeding › Chapter (Book) › Other › peer-review

1 Citation (Scopus)

Abstract

Genomic profiling has identified therapeutic targets for precision treatment of certain cancers, but many patients lack actionable mutations. Additional omics approaches, like proteomics and phosphoproteomics, are essential for comprehensive mapping of cancer-associated molecular phenotypes. In vivo models, such as cell line and patient-derived xenografts (PDX), offer valuable insights into cancer biology and treatment strategies.This chapter presents a semiautomated high-throughput workflow for integrated proteomics and phosphoproteomics analysis on the Kingfish platform coupled with MagReSyn® Zr-IMAC HP. It enhances protein extraction from in vivo xenograft samples and provides better insights into cancers with poor prognosis. The approach successfully identified over 11,000 unique phosphosites and ~6000 proteins in SJSA-1 pediatric osteosarcoma xenografts, demonstrating its efficacy. This workflow is a valuable tool for studying tumor biology and developing precision oncology strategies.

Original language	English
Title of host publication	Patient-Derived Xenografts
Subtitle of host publication	Methods and Protocols
Editors	Mohamed I. Saad
Place of Publication	New York NY USA
Publisher	Humana Press
Chapter	17
Pages	229-242
Number of pages	14
ISBN (Electronic)	9781071638583
ISBN (Print)	9781071638576
DOIs	https://doi.org/10.1007/978-1-0716-3858-3_17
Publication status	Published - 2024

Publication series

Name	Methods in Molecular Biology
Volume	2806
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords

Automation
High-throughput
Mass spectrometry
Patient-derived xenograft
Phosphoproteomics
Proteomics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1007/978-1-0716-3858-3_17

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Lim Kam Sian, T. CC., Sun, C., Cain, J. E., Steele, J. R., Hanchapola, I., Stoychev, S., Schittenhelm, R. B., & Faridi, P. (2024). A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers. In M. I. Saad (Ed.), Patient-Derived Xenografts: Methods and Protocols (pp. 229-242). (Methods in Molecular Biology; Vol. 2806). Humana Press. https://doi.org/10.1007/978-1-0716-3858-3_17

Lim Kam Sian, Terry CC ; Sun, Christie ; Cain, Jason E et al. / A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers. Patient-Derived Xenografts: Methods and Protocols. editor / Mohamed I. Saad. New York NY USA : Humana Press, 2024. pp. 229-242 (Methods in Molecular Biology).

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abstract = "Genomic profiling has identified therapeutic targets for precision treatment of certain cancers, but many patients lack actionable mutations. Additional omics approaches, like proteomics and phosphoproteomics, are essential for comprehensive mapping of cancer-associated molecular phenotypes. In vivo models, such as cell line and patient-derived xenografts (PDX), offer valuable insights into cancer biology and treatment strategies.This chapter presents a semiautomated high-throughput workflow for integrated proteomics and phosphoproteomics analysis on the Kingfish platform coupled with MagReSyn{\textregistered} Zr-IMAC HP. It enhances protein extraction from in vivo xenograft samples and provides better insights into cancers with poor prognosis. The approach successfully identified over 11,000 unique phosphosites and ~6000 proteins in SJSA-1 pediatric osteosarcoma xenografts, demonstrating its efficacy. This workflow is a valuable tool for studying tumor biology and developing precision oncology strategies.",

keywords = "Automation, High-throughput, Mass spectrometry, Patient-derived xenograft, Phosphoproteomics, Proteomics",

author = "{Lim Kam Sian}, {Terry CC} and Christie Sun and Cain, {Jason E} and Steele, {Joel R} and Iresha Hanchapola and Stoyan Stoychev and Schittenhelm, {Ralf B} and Pouya Faridi",

note = "Publisher Copyright: {\textcopyright} 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",

year = "2024",

doi = "10.1007/978-1-0716-3858-3_17",

language = "English",

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Lim Kam Sian, TCC, Sun, C, Cain, JE , Steele, JR, Hanchapola, I, Stoychev, S, Schittenhelm, RB & Faridi, P 2024, A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers. in MI Saad (ed.), Patient-Derived Xenografts: Methods and Protocols. Methods in Molecular Biology, vol. 2806, Humana Press, New York NY USA, pp. 229-242. https://doi.org/10.1007/978-1-0716-3858-3_17

A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers. / Lim Kam Sian, Terry CC; Sun, Christie; Cain, Jason E et al.
Patient-Derived Xenografts: Methods and Protocols. ed. / Mohamed I. Saad. New York NY USA: Humana Press, 2024. p. 229-242 (Methods in Molecular Biology; Vol. 2806).

Research output: Chapter in Book/Report/Conference proceeding › Chapter (Book) › Other › peer-review

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T1 - A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers

AU - Lim Kam Sian, Terry CC

AU - Sun, Christie

AU - Cain, Jason E

AU - Steele, Joel R

AU - Hanchapola, Iresha

AU - Stoychev, Stoyan

AU - Schittenhelm, Ralf B

AU - Faridi, Pouya

PY - 2024

Y1 - 2024

N2 - Genomic profiling has identified therapeutic targets for precision treatment of certain cancers, but many patients lack actionable mutations. Additional omics approaches, like proteomics and phosphoproteomics, are essential for comprehensive mapping of cancer-associated molecular phenotypes. In vivo models, such as cell line and patient-derived xenografts (PDX), offer valuable insights into cancer biology and treatment strategies.This chapter presents a semiautomated high-throughput workflow for integrated proteomics and phosphoproteomics analysis on the Kingfish platform coupled with MagReSyn® Zr-IMAC HP. It enhances protein extraction from in vivo xenograft samples and provides better insights into cancers with poor prognosis. The approach successfully identified over 11,000 unique phosphosites and ~6000 proteins in SJSA-1 pediatric osteosarcoma xenografts, demonstrating its efficacy. This workflow is a valuable tool for studying tumor biology and developing precision oncology strategies.

AB - Genomic profiling has identified therapeutic targets for precision treatment of certain cancers, but many patients lack actionable mutations. Additional omics approaches, like proteomics and phosphoproteomics, are essential for comprehensive mapping of cancer-associated molecular phenotypes. In vivo models, such as cell line and patient-derived xenografts (PDX), offer valuable insights into cancer biology and treatment strategies.This chapter presents a semiautomated high-throughput workflow for integrated proteomics and phosphoproteomics analysis on the Kingfish platform coupled with MagReSyn® Zr-IMAC HP. It enhances protein extraction from in vivo xenograft samples and provides better insights into cancers with poor prognosis. The approach successfully identified over 11,000 unique phosphosites and ~6000 proteins in SJSA-1 pediatric osteosarcoma xenografts, demonstrating its efficacy. This workflow is a valuable tool for studying tumor biology and developing precision oncology strategies.

KW - Automation

KW - High-throughput

KW - Mass spectrometry

KW - Patient-derived xenograft

KW - Phosphoproteomics

KW - Proteomics

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C2 - 38676807

AN - SCOPUS:85191622851

SN - 9781071638576

T3 - Methods in Molecular Biology

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BT - Patient-Derived Xenografts

A2 - Saad, Mohamed I.

PB - Humana Press

CY - New York NY USA

ER -

Lim Kam Sian TCC, Sun C, Cain JE , Steele JR, Hanchapola I, Stoychev S et al. A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers. In Saad MI, editor, Patient-Derived Xenografts: Methods and Protocols. New York NY USA: Humana Press. 2024. p. 229-242. (Methods in Molecular Biology). doi: 10.1007/978-1-0716-3858-3_17

A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers

Abstract

Publication series

Keywords

UN SDGs

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