Validation of Novel Molecular Imaging Targets Identified by Functional Genomic mRNA Profiling to Detect Dysplasia in Barrett’s Esophagus

X. Zhao; R. Y. Gabriëls; W. T. R. Hooghiemstra; M. Koller; G. J. Meersma; M. Buist-Homan; L. Visser; D. J. Robinson; A. Tenditnaya; D. Gorpas; V. Ntziachristos; A. Karrenbeld; G. Kats-Ugurlu; R. S. N. Fehrmann; W. B. Nagengast

doi:10.3390/cancers14102462

Validation of Novel Molecular Imaging Targets Identified by Functional Genomic mRNA Profiling to Detect Dysplasia in Barrett’s Esophagus

X. Zhao, R. Y. Gabriëls, W. T. R. Hooghiemstra, M. Koller, G. J. Meersma, M. Buist-Homan, L. Visser, D. J. Robinson, A. Tenditnaya, D. Gorpas, V. Ntziachristos, A. Karrenbeld, G. Kats-Ugurlu, R. S. N. Fehrmann, W. B. Nagengast^*

^*Corresponding author for this work

Otorhinolaryngology and Head and Neck Surgery

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

2 Citations (Scopus)

Abstract

Barrett’s esophagus (BE) is the precursor of esophageal adenocarcinoma (EAC). Dysplastic BE (DBE) has a higher progression risk to EAC compared to non-dysplastic BE (NDBE). However, the miss rates for the endoscopic detection of DBE remain high. Fluorescence molecular endoscopy (FME) can detect DBE and mucosal EAC by highlighting the tumor-specific expression of proteins. This study aimed to identify target proteins suitable for FME. Publicly available RNA expression profiles of EAC and NDBE were corrected by functional genomic mRNA (FGmRNA) profiling. Following a class comparison between FGmRNA profiles of EAC and NDBE, predicted, significantly upregulated genes in EAC were prioritized by a literature search. Protein expression of prioritized genes was validated by immunohistochemistry (IHC) on DBE and NDBE tissues. Near-infrared fluorescent tracers targeting the proteins were developed and evaluated ex vivo on fresh human specimens. In total, 1976 overexpressed genes were identified in EAC (n = 64) compared to NDBE (n = 66) at RNA level. Prioritization and IHC validation revealed SPARC, SULF1, PKCι, and DDR1 (all p < 0.0001) as the most attractive imaging protein targets for DBE detection. Newly developed tracers SULF1-800CW and SPARC-800CW both showed higher fluorescence intensity in DBE tissue compared to paired non-dysplastic tissue. This study identified SPARC, SULF1, PKCι, and DDR1 as promising targets for FME to differentiate DBE from NDBE tissue, for which SULF1-800CW and SPARC-800CW were successfully ex vivo evaluated. Clinical studies should further validate these findings.

Original language	English
Article number	2462
Journal	Cancers
Volume	14
Issue number	10
DOIs	https://doi.org/10.3390/cancers14102462
Publication status	Published - 1 May 2022

Bibliographical note

Funding Information:
Funding: The research position of Ruben Y. Gabriëls is supported by the Dutch Cancer Society, Amsterdam, the Netherlands, TRANSCAN-2 (project TRANSCAN-147, ESCEND). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 801347 (SENSISTIVE).

Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.

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https://www.scopus.com/inward/record.uri?eid=2-s2.0-85130767816&doi=10.3390%2fcancers14102462&partnerID=40&md5=f90d3f8e0bcba674801bcd412385132a

Cite this

Zhao, X., Gabriëls, R. Y., Hooghiemstra, W. T. R., Koller, M., Meersma, G. J., Buist-Homan, M., Visser, L., Robinson, D. J., Tenditnaya, A., Gorpas, D., Ntziachristos, V., Karrenbeld, A., Kats-Ugurlu, G., Fehrmann, R. S. N., & Nagengast, W. B. (2022). Validation of Novel Molecular Imaging Targets Identified by Functional Genomic mRNA Profiling to Detect Dysplasia in Barrett’s Esophagus. Cancers, 14(10), [2462]. https://doi.org/10.3390/cancers14102462

@article{5c615f98a6844199a73538a3f641c192,

title = "Validation of Novel Molecular Imaging Targets Identified by Functional Genomic mRNA Profiling to Detect Dysplasia in Barrett{\textquoteright}s Esophagus",

abstract = "Barrett{\textquoteright}s esophagus (BE) is the precursor of esophageal adenocarcinoma (EAC). Dysplastic BE (DBE) has a higher progression risk to EAC compared to non-dysplastic BE (NDBE). However, the miss rates for the endoscopic detection of DBE remain high. Fluorescence molecular endoscopy (FME) can detect DBE and mucosal EAC by highlighting the tumor-specific expression of proteins. This study aimed to identify target proteins suitable for FME. Publicly available RNA expression profiles of EAC and NDBE were corrected by functional genomic mRNA (FGmRNA) profiling. Following a class comparison between FGmRNA profiles of EAC and NDBE, predicted, significantly upregulated genes in EAC were prioritized by a literature search. Protein expression of prioritized genes was validated by immunohistochemistry (IHC) on DBE and NDBE tissues. Near-infrared fluorescent tracers targeting the proteins were developed and evaluated ex vivo on fresh human specimens. In total, 1976 overexpressed genes were identified in EAC (n = 64) compared to NDBE (n = 66) at RNA level. Prioritization and IHC validation revealed SPARC, SULF1, PKCι, and DDR1 (all p < 0.0001) as the most attractive imaging protein targets for DBE detection. Newly developed tracers SULF1-800CW and SPARC-800CW both showed higher fluorescence intensity in DBE tissue compared to paired non-dysplastic tissue. This study identified SPARC, SULF1, PKCι, and DDR1 as promising targets for FME to differentiate DBE from NDBE tissue, for which SULF1-800CW and SPARC-800CW were successfully ex vivo evaluated. Clinical studies should further validate these findings.",

author = "X. Zhao and Gabri{\"e}ls, {R. Y.} and Hooghiemstra, {W. T. R.} and M. Koller and Meersma, {G. J.} and M. Buist-Homan and L. Visser and Robinson, {D. J.} and A. Tenditnaya and D. Gorpas and V. Ntziachristos and A. Karrenbeld and G. Kats-Ugurlu and Fehrmann, {R. S. N.} and Nagengast, {W. B.}",

note = "Funding Information: Funding: The research position of Ruben Y. Gabri{\"e}ls is supported by the Dutch Cancer Society, Amsterdam, the Netherlands, TRANSCAN-2 (project TRANSCAN-147, ESCEND). This project has received funding from the European Union{\textquoteright}s Horizon 2020 research and innovation program under grant agreement No. 801347 (SENSISTIVE). Publisher Copyright: {\textcopyright} 2022 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2022",

month = may,

day = "1",

doi = "10.3390/cancers14102462",

language = "English",

volume = "14",

number = "10",

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Zhao, X, Gabriëls, RY, Hooghiemstra, WTR, Koller, M, Meersma, GJ, Buist-Homan, M, Visser, L, Robinson, DJ, Tenditnaya, A, Gorpas, D, Ntziachristos, V, Karrenbeld, A, Kats-Ugurlu, G, Fehrmann, RSN & Nagengast, WB 2022, 'Validation of Novel Molecular Imaging Targets Identified by Functional Genomic mRNA Profiling to Detect Dysplasia in Barrett’s Esophagus', Cancers, vol. 14, no. 10, 2462. https://doi.org/10.3390/cancers14102462

TY - JOUR

T1 - Validation of Novel Molecular Imaging Targets Identified by Functional Genomic mRNA Profiling to Detect Dysplasia in Barrett’s Esophagus

AU - Zhao, X.

AU - Gabriëls, R. Y.

AU - Hooghiemstra, W. T. R.

AU - Koller, M.

AU - Meersma, G. J.

AU - Buist-Homan, M.

AU - Visser, L.

AU - Robinson, D. J.

AU - Tenditnaya, A.

AU - Gorpas, D.

AU - Ntziachristos, V.

AU - Karrenbeld, A.

AU - Kats-Ugurlu, G.

AU - Fehrmann, R. S. N.

AU - Nagengast, W. B.

N1 - Funding Information: Funding: The research position of Ruben Y. Gabriëls is supported by the Dutch Cancer Society, Amsterdam, the Netherlands, TRANSCAN-2 (project TRANSCAN-147, ESCEND). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 801347 (SENSISTIVE). Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2022/5/1

Y1 - 2022/5/1

N2 - Barrett’s esophagus (BE) is the precursor of esophageal adenocarcinoma (EAC). Dysplastic BE (DBE) has a higher progression risk to EAC compared to non-dysplastic BE (NDBE). However, the miss rates for the endoscopic detection of DBE remain high. Fluorescence molecular endoscopy (FME) can detect DBE and mucosal EAC by highlighting the tumor-specific expression of proteins. This study aimed to identify target proteins suitable for FME. Publicly available RNA expression profiles of EAC and NDBE were corrected by functional genomic mRNA (FGmRNA) profiling. Following a class comparison between FGmRNA profiles of EAC and NDBE, predicted, significantly upregulated genes in EAC were prioritized by a literature search. Protein expression of prioritized genes was validated by immunohistochemistry (IHC) on DBE and NDBE tissues. Near-infrared fluorescent tracers targeting the proteins were developed and evaluated ex vivo on fresh human specimens. In total, 1976 overexpressed genes were identified in EAC (n = 64) compared to NDBE (n = 66) at RNA level. Prioritization and IHC validation revealed SPARC, SULF1, PKCι, and DDR1 (all p < 0.0001) as the most attractive imaging protein targets for DBE detection. Newly developed tracers SULF1-800CW and SPARC-800CW both showed higher fluorescence intensity in DBE tissue compared to paired non-dysplastic tissue. This study identified SPARC, SULF1, PKCι, and DDR1 as promising targets for FME to differentiate DBE from NDBE tissue, for which SULF1-800CW and SPARC-800CW were successfully ex vivo evaluated. Clinical studies should further validate these findings.

AB - Barrett’s esophagus (BE) is the precursor of esophageal adenocarcinoma (EAC). Dysplastic BE (DBE) has a higher progression risk to EAC compared to non-dysplastic BE (NDBE). However, the miss rates for the endoscopic detection of DBE remain high. Fluorescence molecular endoscopy (FME) can detect DBE and mucosal EAC by highlighting the tumor-specific expression of proteins. This study aimed to identify target proteins suitable for FME. Publicly available RNA expression profiles of EAC and NDBE were corrected by functional genomic mRNA (FGmRNA) profiling. Following a class comparison between FGmRNA profiles of EAC and NDBE, predicted, significantly upregulated genes in EAC were prioritized by a literature search. Protein expression of prioritized genes was validated by immunohistochemistry (IHC) on DBE and NDBE tissues. Near-infrared fluorescent tracers targeting the proteins were developed and evaluated ex vivo on fresh human specimens. In total, 1976 overexpressed genes were identified in EAC (n = 64) compared to NDBE (n = 66) at RNA level. Prioritization and IHC validation revealed SPARC, SULF1, PKCι, and DDR1 (all p < 0.0001) as the most attractive imaging protein targets for DBE detection. Newly developed tracers SULF1-800CW and SPARC-800CW both showed higher fluorescence intensity in DBE tissue compared to paired non-dysplastic tissue. This study identified SPARC, SULF1, PKCι, and DDR1 as promising targets for FME to differentiate DBE from NDBE tissue, for which SULF1-800CW and SPARC-800CW were successfully ex vivo evaluated. Clinical studies should further validate these findings.

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U2 - 10.3390/cancers14102462

DO - 10.3390/cancers14102462

M3 - Article

VL - 14

IS - 10

M1 - 2462

ER -

Validation of Novel Molecular Imaging Targets Identified by Functional Genomic mRNA Profiling to Detect Dysplasia in Barrett’s Esophagus

Abstract

Bibliographical note

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