Multiplexed Nucleic Acid programmable protein arrays

Xiaobo Yu, Lusheng Song, Brianne Petritis, Xiaofang Bian, Haoyu Wang, Jennifer Viloria, Jin Park, Hoang Bui, Han Li, Jie Wang, Lei Liu, Liuhui Yang, Hu Duan, David N. McMurray, Jacqueline M. Achkar, Dewey Magee, Ji Qiu, Joshua LaBaer

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Rationale: Cell-free protein microarrays display naturally-folded proteins based on just-in-time in situ synthesis, and have made important contributions to basic and translational research. However, the risk of spot-to-spot cross-talk from protein diffusion during expression has limited the feature density of these arrays. Methods: In this work, we developed the Multiplexed Nucleic Acid Programmable Protein Array (M-NAPPA), which significantly increases the number of displayed proteins by multiplexing as many as five different gene plasmids within a printed spot. Results: Even when proteins of different sizes were displayed within the same feature, they were readily detected using protein-specific antibodies. Protein-protein interactions and serological antibody assays using human viral proteome microarrays demonstrated that comparable hits were detected by M-NAPPA and non-multiplexed NAPPA arrays. An ultra-high density proteome microarray displaying > 16k proteins on a single microscope slide was produced by combining M-NAPPA with a photolithography-based silicon nano-well platform. Finally, four new tuberculosis-related antigens in guinea pigs vaccinated with Bacillus Calmette-Guerin (BCG) were identified with M-NAPPA and validated with ELISA. Conclusion: All data demonstrate that multiplexing features on a protein microarray offer a cost-effective fabrication approach and have the potential to facilitate high throughput translational research.

Original languageEnglish (US)
Article number20151
JournalTheranostics
Volume7
Issue number16
DOIs
StatePublished - 2017

Fingerprint

Protein Array Analysis
Nucleic Acids
Proteins
Translational Medical Research
Proteome
Antibodies
Silicon
Mycobacterium bovis
Guinea Pigs
Tuberculosis
Plasmids
Enzyme-Linked Immunosorbent Assay
Antigens
Costs and Cost Analysis

Keywords

  • Antibody
  • Biomarker
  • Cell-free protein microarray
  • Protein-protein interaction
  • Proteomics

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Pharmacology, Toxicology and Pharmaceutics (miscellaneous)

Cite this

Yu, X., Song, L., Petritis, B., Bian, X., Wang, H., Viloria, J., ... LaBaer, J. (2017). Multiplexed Nucleic Acid programmable protein arrays. Theranostics, 7(16), [20151]. https://doi.org/10.7150/thno.20151

Multiplexed Nucleic Acid programmable protein arrays. / Yu, Xiaobo; Song, Lusheng; Petritis, Brianne; Bian, Xiaofang; Wang, Haoyu; Viloria, Jennifer; Park, Jin; Bui, Hoang; Li, Han; Wang, Jie; Liu, Lei; Yang, Liuhui; Duan, Hu; McMurray, David N.; Achkar, Jacqueline M.; Magee, Dewey; Qiu, Ji; LaBaer, Joshua.

In: Theranostics, Vol. 7, No. 16, 20151, 2017.

Research output: Contribution to journalArticle

Yu, X, Song, L, Petritis, B, Bian, X, Wang, H, Viloria, J, Park, J, Bui, H, Li, H, Wang, J, Liu, L, Yang, L, Duan, H, McMurray, DN, Achkar, JM, Magee, D, Qiu, J & LaBaer, J 2017, 'Multiplexed Nucleic Acid programmable protein arrays', Theranostics, vol. 7, no. 16, 20151. https://doi.org/10.7150/thno.20151
Yu X, Song L, Petritis B, Bian X, Wang H, Viloria J et al. Multiplexed Nucleic Acid programmable protein arrays. Theranostics. 2017;7(16). 20151. https://doi.org/10.7150/thno.20151
Yu, Xiaobo ; Song, Lusheng ; Petritis, Brianne ; Bian, Xiaofang ; Wang, Haoyu ; Viloria, Jennifer ; Park, Jin ; Bui, Hoang ; Li, Han ; Wang, Jie ; Liu, Lei ; Yang, Liuhui ; Duan, Hu ; McMurray, David N. ; Achkar, Jacqueline M. ; Magee, Dewey ; Qiu, Ji ; LaBaer, Joshua. / Multiplexed Nucleic Acid programmable protein arrays. In: Theranostics. 2017 ; Vol. 7, No. 16.
@article{43854a7396964b918b5645ac23efe9f3,
title = "Multiplexed Nucleic Acid programmable protein arrays",
abstract = "Rationale: Cell-free protein microarrays display naturally-folded proteins based on just-in-time in situ synthesis, and have made important contributions to basic and translational research. However, the risk of spot-to-spot cross-talk from protein diffusion during expression has limited the feature density of these arrays. Methods: In this work, we developed the Multiplexed Nucleic Acid Programmable Protein Array (M-NAPPA), which significantly increases the number of displayed proteins by multiplexing as many as five different gene plasmids within a printed spot. Results: Even when proteins of different sizes were displayed within the same feature, they were readily detected using protein-specific antibodies. Protein-protein interactions and serological antibody assays using human viral proteome microarrays demonstrated that comparable hits were detected by M-NAPPA and non-multiplexed NAPPA arrays. An ultra-high density proteome microarray displaying > 16k proteins on a single microscope slide was produced by combining M-NAPPA with a photolithography-based silicon nano-well platform. Finally, four new tuberculosis-related antigens in guinea pigs vaccinated with Bacillus Calmette-Guerin (BCG) were identified with M-NAPPA and validated with ELISA. Conclusion: All data demonstrate that multiplexing features on a protein microarray offer a cost-effective fabrication approach and have the potential to facilitate high throughput translational research.",
keywords = "Antibody, Biomarker, Cell-free protein microarray, Protein-protein interaction, Proteomics",
author = "Xiaobo Yu and Lusheng Song and Brianne Petritis and Xiaofang Bian and Haoyu Wang and Jennifer Viloria and Jin Park and Hoang Bui and Han Li and Jie Wang and Lei Liu and Liuhui Yang and Hu Duan and McMurray, {David N.} and Achkar, {Jacqueline M.} and Dewey Magee and Ji Qiu and Joshua LaBaer",
year = "2017",
doi = "10.7150/thno.20151",
language = "English (US)",
volume = "7",
journal = "Theranostics",
issn = "1838-7640",
publisher = "Ivyspring International Publisher",
number = "16",

}

TY - JOUR

T1 - Multiplexed Nucleic Acid programmable protein arrays

AU - Yu, Xiaobo

AU - Song, Lusheng

AU - Petritis, Brianne

AU - Bian, Xiaofang

AU - Wang, Haoyu

AU - Viloria, Jennifer

AU - Park, Jin

AU - Bui, Hoang

AU - Li, Han

AU - Wang, Jie

AU - Liu, Lei

AU - Yang, Liuhui

AU - Duan, Hu

AU - McMurray, David N.

AU - Achkar, Jacqueline M.

AU - Magee, Dewey

AU - Qiu, Ji

AU - LaBaer, Joshua

PY - 2017

Y1 - 2017

N2 - Rationale: Cell-free protein microarrays display naturally-folded proteins based on just-in-time in situ synthesis, and have made important contributions to basic and translational research. However, the risk of spot-to-spot cross-talk from protein diffusion during expression has limited the feature density of these arrays. Methods: In this work, we developed the Multiplexed Nucleic Acid Programmable Protein Array (M-NAPPA), which significantly increases the number of displayed proteins by multiplexing as many as five different gene plasmids within a printed spot. Results: Even when proteins of different sizes were displayed within the same feature, they were readily detected using protein-specific antibodies. Protein-protein interactions and serological antibody assays using human viral proteome microarrays demonstrated that comparable hits were detected by M-NAPPA and non-multiplexed NAPPA arrays. An ultra-high density proteome microarray displaying > 16k proteins on a single microscope slide was produced by combining M-NAPPA with a photolithography-based silicon nano-well platform. Finally, four new tuberculosis-related antigens in guinea pigs vaccinated with Bacillus Calmette-Guerin (BCG) were identified with M-NAPPA and validated with ELISA. Conclusion: All data demonstrate that multiplexing features on a protein microarray offer a cost-effective fabrication approach and have the potential to facilitate high throughput translational research.

AB - Rationale: Cell-free protein microarrays display naturally-folded proteins based on just-in-time in situ synthesis, and have made important contributions to basic and translational research. However, the risk of spot-to-spot cross-talk from protein diffusion during expression has limited the feature density of these arrays. Methods: In this work, we developed the Multiplexed Nucleic Acid Programmable Protein Array (M-NAPPA), which significantly increases the number of displayed proteins by multiplexing as many as five different gene plasmids within a printed spot. Results: Even when proteins of different sizes were displayed within the same feature, they were readily detected using protein-specific antibodies. Protein-protein interactions and serological antibody assays using human viral proteome microarrays demonstrated that comparable hits were detected by M-NAPPA and non-multiplexed NAPPA arrays. An ultra-high density proteome microarray displaying > 16k proteins on a single microscope slide was produced by combining M-NAPPA with a photolithography-based silicon nano-well platform. Finally, four new tuberculosis-related antigens in guinea pigs vaccinated with Bacillus Calmette-Guerin (BCG) were identified with M-NAPPA and validated with ELISA. Conclusion: All data demonstrate that multiplexing features on a protein microarray offer a cost-effective fabrication approach and have the potential to facilitate high throughput translational research.

KW - Antibody

KW - Biomarker

KW - Cell-free protein microarray

KW - Protein-protein interaction

KW - Proteomics

UR - http://www.scopus.com/inward/record.url?scp=85030639126&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85030639126&partnerID=8YFLogxK

U2 - 10.7150/thno.20151

DO - 10.7150/thno.20151

M3 - Article

C2 - 29109798

AN - SCOPUS:85030639126

VL - 7

JO - Theranostics

JF - Theranostics

SN - 1838-7640

IS - 16

M1 - 20151

ER -