Targeted detection and quantitation of histone modifications from 1,000 cells

Nebiyu A. Abshiru; Jacek W. Sikora; Jeannie M. Camarillo; Juliette A. Morris; Philip D. Compton; Tak Lee; Yaseswini Neelamraju; Samuel Haddox; Caroline Sheridan; Martin Carroll; Larry D. Cripe; Martin S. Tallman; Elisabeth M. Paietta; Ari M. Melnick; Paul M. Thomas; Francine E. Garrett-Bakelman; Neil L. Kelleher

doi:10.1371/journal.pone.0240829

Targeted detection and quantitation of histone modifications from 1,000 cells

Nebiyu A. Abshiru, Jacek W. Sikora, Jeannie M. Camarillo, Juliette A. Morris, Philip D. Compton, Tak Lee, Yaseswini Neelamraju, Samuel Haddox, Caroline Sheridan, Martin Carroll, Larry D. Cripe, Martin S. Tallman, Elisabeth M. Paietta, Ari M. Melnick, Paul M. Thomas, Francine E. Garrett-Bakelman, Neil L. Kelleher

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

Histone post-translational modifications (PTMs) create a powerful regulatory mechanism for maintaining chromosomal integrity in cells. Histone acetylation and methylation, the most widely studied histone PTMs, act in concert with chromatin-associated proteins to control access to genetic information during transcription. Alterations in cellular histone PTMs have been linked to disease states and have crucial biomarker and therapeutic potential. Traditional bottom-up mass spectrometry of histones requires large numbers of cells, typically one million or more. However, for some cell subtype-specific studies, it is difficult or impossible to obtain such large numbers of cells and quantification of rare histone PTMs is often unachievable. An established targeted LC-MS/MS method was used to quantify the abundance of histone PTMs from cell lines and primary human specimens. Sample preparation was modified by omitting nuclear isolation and reducing the rounds of histone derivatization to improve detection of histone peptides down to 1,000 cells. In the current study, we developed and validated a quantitative LC-MS/MS approach tailored for a targeted histone assay of 75 histone peptides with as few as 10,000 cells. Furthermore, we were able to detect and quantify 61 histone peptides from just 1,000 primary human stem cells. Detection of 37 histone peptides was possible from 1,000 acute myeloid leukemia patient cells. We anticipate that this revised method can be used in many applications where achieving large cell numbers is challenging, including rare human cell populations.

Original language	English (US)
Article number	e0240829
Journal	PloS one
Volume	15
Issue number	10 October
DOIs	https://doi.org/10.1371/journal.pone.0240829
State	Published - Oct 2020

Funding

This work was carried out with a financial support from The Paul G. Allen Family Foundation (Award # 11715), NCI CCSG P30CA060553 awarded to the Robert H. Lurie Comprehensive Cancer Center, and the National Resource for Translational and Developmental Proteomics supported by P41GM108569 to NLK. We would also like to acknowledge funding from NCI K08CA169055, UVA Cancer Center through the NCI Cancer Center Support Grant P30CA44579, the University of Virginia and the American Society of Hematology (ASHAMFDP-20121) under the ASHAMFDP partnership with The Robert Wood Johnson Foundation to FEG-B. This study was conducted by the ECOG-ACRIN Cancer Research Group (Peter J. O'Dwyer, MD and Mitchell D. Schnall, MD, PhD, Group Co-Chairs) and supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: CA180827, CA180820, CA233290, CA189859, CA233321, CA233270. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

ASJC Scopus subject areas

General

UN SDGs

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

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10.1371/journal.pone.0240829

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Abshiru, N. A., Sikora, J. W., Camarillo, J. M., Morris, J. A., Compton, P. D., Lee, T., Neelamraju, Y., Haddox, S., Sheridan, C., Carroll, M., Cripe, L. D., Tallman, M. S., Paietta, E. M., Melnick, A. M., Thomas, P. M., Garrett-Bakelman, F. E., & Kelleher, N. L. (2020). Targeted detection and quantitation of histone modifications from 1,000 cells. PloS one, 15(10 October), Article e0240829. https://doi.org/10.1371/journal.pone.0240829

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title = "Targeted detection and quantitation of histone modifications from 1,000 cells",

abstract = "Histone post-translational modifications (PTMs) create a powerful regulatory mechanism for maintaining chromosomal integrity in cells. Histone acetylation and methylation, the most widely studied histone PTMs, act in concert with chromatin-associated proteins to control access to genetic information during transcription. Alterations in cellular histone PTMs have been linked to disease states and have crucial biomarker and therapeutic potential. Traditional bottom-up mass spectrometry of histones requires large numbers of cells, typically one million or more. However, for some cell subtype-specific studies, it is difficult or impossible to obtain such large numbers of cells and quantification of rare histone PTMs is often unachievable. An established targeted LC-MS/MS method was used to quantify the abundance of histone PTMs from cell lines and primary human specimens. Sample preparation was modified by omitting nuclear isolation and reducing the rounds of histone derivatization to improve detection of histone peptides down to 1,000 cells. In the current study, we developed and validated a quantitative LC-MS/MS approach tailored for a targeted histone assay of 75 histone peptides with as few as 10,000 cells. Furthermore, we were able to detect and quantify 61 histone peptides from just 1,000 primary human stem cells. Detection of 37 histone peptides was possible from 1,000 acute myeloid leukemia patient cells. We anticipate that this revised method can be used in many applications where achieving large cell numbers is challenging, including rare human cell populations.",

author = "Abshiru, {Nebiyu A.} and Sikora, {Jacek W.} and Camarillo, {Jeannie M.} and Morris, {Juliette A.} and Compton, {Philip D.} and Tak Lee and Yaseswini Neelamraju and Samuel Haddox and Caroline Sheridan and Martin Carroll and Cripe, {Larry D.} and Tallman, {Martin S.} and Paietta, {Elisabeth M.} and Melnick, {Ari M.} and Thomas, {Paul M.} and Garrett-Bakelman, {Francine E.} and Kelleher, {Neil L.}",

note = "Funding Information: This work was carried out with a financial support from The Paul G. Allen Family Foundation (Award # 11715), NCI CCSG P30CA060553 awarded to the Robert H. Lurie Comprehensive Cancer Center, and the National Resource for Translational and Developmental Proteomics supported by P41GM108569 to NLK. We would also like to acknowledge funding from NCI K08CA169055, UVA Cancer Center through the NCI Cancer Center Support Grant P30CA44579, the University of Virginia and the American Society of Hematology (ASHAMFDP-20121) under the ASHAMFDP partnership with The Robert Wood Johnson Foundation to FEG-B. This study was conducted by the ECOG-ACRIN Cancer Research Group (Peter J. O'Dwyer, MD and Mitchell D. Schnall, MD, PhD, Group Co-Chairs) and supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: CA180827, CA180820, CA233290, CA189859, CA233321, CA233270. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: {\textcopyright} 2020 Abshiru et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

year = "2020",

month = oct,

doi = "10.1371/journal.pone.0240829",

language = "English (US)",

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Abshiru, NA, Sikora, JW, Camarillo, JM, Morris, JA, Compton, PD, Lee, T, Neelamraju, Y, Haddox, S, Sheridan, C, Carroll, M, Cripe, LD, Tallman, MS, Paietta, EM, Melnick, AM, Thomas, PM, Garrett-Bakelman, FE & Kelleher, NL 2020, 'Targeted detection and quantitation of histone modifications from 1,000 cells', PloS one, vol. 15, no. 10 October, e0240829. https://doi.org/10.1371/journal.pone.0240829

TY - JOUR

T1 - Targeted detection and quantitation of histone modifications from 1,000 cells

AU - Abshiru, Nebiyu A.

AU - Sikora, Jacek W.

AU - Camarillo, Jeannie M.

AU - Morris, Juliette A.

AU - Compton, Philip D.

AU - Lee, Tak

AU - Neelamraju, Yaseswini

AU - Haddox, Samuel

AU - Sheridan, Caroline

AU - Carroll, Martin

AU - Cripe, Larry D.

AU - Tallman, Martin S.

AU - Paietta, Elisabeth M.

AU - Melnick, Ari M.

AU - Thomas, Paul M.

AU - Garrett-Bakelman, Francine E.

AU - Kelleher, Neil L.

N1 - Funding Information: This work was carried out with a financial support from The Paul G. Allen Family Foundation (Award # 11715), NCI CCSG P30CA060553 awarded to the Robert H. Lurie Comprehensive Cancer Center, and the National Resource for Translational and Developmental Proteomics supported by P41GM108569 to NLK. We would also like to acknowledge funding from NCI K08CA169055, UVA Cancer Center through the NCI Cancer Center Support Grant P30CA44579, the University of Virginia and the American Society of Hematology (ASHAMFDP-20121) under the ASHAMFDP partnership with The Robert Wood Johnson Foundation to FEG-B. This study was conducted by the ECOG-ACRIN Cancer Research Group (Peter J. O'Dwyer, MD and Mitchell D. Schnall, MD, PhD, Group Co-Chairs) and supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: CA180827, CA180820, CA233290, CA189859, CA233321, CA233270. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2020 Abshiru et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2020/10

Y1 - 2020/10

N2 - Histone post-translational modifications (PTMs) create a powerful regulatory mechanism for maintaining chromosomal integrity in cells. Histone acetylation and methylation, the most widely studied histone PTMs, act in concert with chromatin-associated proteins to control access to genetic information during transcription. Alterations in cellular histone PTMs have been linked to disease states and have crucial biomarker and therapeutic potential. Traditional bottom-up mass spectrometry of histones requires large numbers of cells, typically one million or more. However, for some cell subtype-specific studies, it is difficult or impossible to obtain such large numbers of cells and quantification of rare histone PTMs is often unachievable. An established targeted LC-MS/MS method was used to quantify the abundance of histone PTMs from cell lines and primary human specimens. Sample preparation was modified by omitting nuclear isolation and reducing the rounds of histone derivatization to improve detection of histone peptides down to 1,000 cells. In the current study, we developed and validated a quantitative LC-MS/MS approach tailored for a targeted histone assay of 75 histone peptides with as few as 10,000 cells. Furthermore, we were able to detect and quantify 61 histone peptides from just 1,000 primary human stem cells. Detection of 37 histone peptides was possible from 1,000 acute myeloid leukemia patient cells. We anticipate that this revised method can be used in many applications where achieving large cell numbers is challenging, including rare human cell populations.

AB - Histone post-translational modifications (PTMs) create a powerful regulatory mechanism for maintaining chromosomal integrity in cells. Histone acetylation and methylation, the most widely studied histone PTMs, act in concert with chromatin-associated proteins to control access to genetic information during transcription. Alterations in cellular histone PTMs have been linked to disease states and have crucial biomarker and therapeutic potential. Traditional bottom-up mass spectrometry of histones requires large numbers of cells, typically one million or more. However, for some cell subtype-specific studies, it is difficult or impossible to obtain such large numbers of cells and quantification of rare histone PTMs is often unachievable. An established targeted LC-MS/MS method was used to quantify the abundance of histone PTMs from cell lines and primary human specimens. Sample preparation was modified by omitting nuclear isolation and reducing the rounds of histone derivatization to improve detection of histone peptides down to 1,000 cells. In the current study, we developed and validated a quantitative LC-MS/MS approach tailored for a targeted histone assay of 75 histone peptides with as few as 10,000 cells. Furthermore, we were able to detect and quantify 61 histone peptides from just 1,000 primary human stem cells. Detection of 37 histone peptides was possible from 1,000 acute myeloid leukemia patient cells. We anticipate that this revised method can be used in many applications where achieving large cell numbers is challenging, including rare human cell populations.

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U2 - 10.1371/journal.pone.0240829

DO - 10.1371/journal.pone.0240829

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AN - SCOPUS:85094840800

SN - 1932-6203

VL - 15

JO - PloS one

JF - PloS one

IS - 10 October

M1 - e0240829

ER -

Targeted detection and quantitation of histone modifications from 1,000 cells

Abstract

Funding

ASJC Scopus subject areas

UN SDGs

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