Optimized ChIP-seq method facilitates transcription factor profiling in human tumors

Abhishek A. Singh, Karianne Schuurman, Ekaterina Nevedomskaya, Suzan Stelloo, Simon Linder, Marjolein Droog, Yongsoo Kim, Joyce Sanders, Henk van der Poel, Andries M. Bergman, Lodewyk F.A. Wessels, Wilbert Zwart (Corresponding author)

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1 Citaat (Scopus)

Uittreksel

Chromatin immunoprecipitation (ChIP)-seq analyses of transcription factors in clinical specimens are challenging due to the technical limitations and low quantities of starting material, often resulting in low enrichments and poor signal-to-noise ratio. Here, we present an optimized protocol for transcription factor ChIP-seq analyses in human tissue, yielding an ~100% success rate for all transcription factors analyzed. As proof of concept and to illustrate general applicability of the approach, human tissue from the breast, prostate, and endometrial cancers were analyzed. In addition to standard formaldehyde fixation, disuccinimidyl glutarate was included in the procedure, greatly increasing data quality. To illustrate the sensitivity of the optimized protocol, we provide high-quality ChIP-seq data for three independent factors (AR, FOXA1, and H3K27ac) from a single core needle prostate cancer biopsy specimen. In summary, double-cross-linking strongly improved transcription factor ChIP-seq quality on human tumor samples, further facilitating and enhancing translational research on limited amounts of tissue.

TaalEngels
Artikelnummere201800115
Aantal pagina's12
TijdschriftLife Science Alliance
Volume2
Nummer van het tijdschrift1
DOI's
StatusGepubliceerd - 1 jan 2019

Vingerafdruk

Chromatin Immunoprecipitation
tumor
Chromatin
chromatin
Tumors
Transcription Factors
transcription factors
neoplasms
cancer
Tissue
Neoplasms
Prostatic Neoplasms
data quality
formaldehyde
signal-to-noise ratio
Translational Medical Research
fixation
Biopsy
Signal-To-Noise Ratio
prostatic neoplasms

Citeer dit

Singh, A. A., Schuurman, K., Nevedomskaya, E., Stelloo, S., Linder, S., Droog, M., ... Zwart, W. (2019). Optimized ChIP-seq method facilitates transcription factor profiling in human tumors. Life Science Alliance, 2(1), [e201800115]. DOI: 10.26508/lsa.201800115
Singh, Abhishek A. ; Schuurman, Karianne ; Nevedomskaya, Ekaterina ; Stelloo, Suzan ; Linder, Simon ; Droog, Marjolein ; Kim, Yongsoo ; Sanders, Joyce ; van der Poel, Henk ; Bergman, Andries M. ; Wessels, Lodewyk F.A. ; Zwart, Wilbert . / Optimized ChIP-seq method facilitates transcription factor profiling in human tumors. In: Life Science Alliance. 2019 ; Vol. 2, Nr. 1.
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abstract = "Chromatin immunoprecipitation (ChIP)-seq analyses of transcription factors in clinical specimens are challenging due to the technical limitations and low quantities of starting material, often resulting in low enrichments and poor signal-to-noise ratio. Here, we present an optimized protocol for transcription factor ChIP-seq analyses in human tissue, yielding an ~100{\%} success rate for all transcription factors analyzed. As proof of concept and to illustrate general applicability of the approach, human tissue from the breast, prostate, and endometrial cancers were analyzed. In addition to standard formaldehyde fixation, disuccinimidyl glutarate was included in the procedure, greatly increasing data quality. To illustrate the sensitivity of the optimized protocol, we provide high-quality ChIP-seq data for three independent factors (AR, FOXA1, and H3K27ac) from a single core needle prostate cancer biopsy specimen. In summary, double-cross-linking strongly improved transcription factor ChIP-seq quality on human tumor samples, further facilitating and enhancing translational research on limited amounts of tissue.",
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Singh, AA, Schuurman, K, Nevedomskaya, E, Stelloo, S, Linder, S, Droog, M, Kim, Y, Sanders, J, van der Poel, H, Bergman, AM, Wessels, LFA & Zwart, W 2019, 'Optimized ChIP-seq method facilitates transcription factor profiling in human tumors' Life Science Alliance, vol. 2, nr. 1, e201800115. DOI: 10.26508/lsa.201800115

Optimized ChIP-seq method facilitates transcription factor profiling in human tumors. / Singh, Abhishek A.; Schuurman, Karianne; Nevedomskaya, Ekaterina; Stelloo, Suzan; Linder, Simon; Droog, Marjolein; Kim, Yongsoo; Sanders, Joyce; van der Poel, Henk; Bergman, Andries M.; Wessels, Lodewyk F.A.; Zwart, Wilbert (Corresponding author).

In: Life Science Alliance, Vol. 2, Nr. 1, e201800115, 01.01.2019.

Onderzoeksoutput: Bijdrage aan tijdschriftTijdschriftartikelAcademicpeer review

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AU - Linder,Simon

AU - Droog,Marjolein

AU - Kim,Yongsoo

AU - Sanders,Joyce

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AU - Bergman,Andries M.

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AU - Zwart,Wilbert

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Singh AA, Schuurman K, Nevedomskaya E, Stelloo S, Linder S, Droog M et al. Optimized ChIP-seq method facilitates transcription factor profiling in human tumors. Life Science Alliance. 2019 jan 1;2(1). e201800115. Beschikbaar vanaf, DOI: 10.26508/lsa.201800115