DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD

Christian Klingler; Jon Ashley; Ke Shi; Adeline Stiefvater; Michael Kyba; Michael Sinnreich; Hideki Aihara; Jochen Kinter

doi:10.1096/fj.201902696

DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD

Christian Klingler, Jon Ashley, Ke Shi, Adeline Stiefvater, Michael Kyba, Michael Sinnreich, Hideki Aihara, Jochen Kinter

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

18 Scopus citations

Abstract

Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio-scapulo-humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases. By applying Systematic Evolution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specific secondary structural elements conveying high affinity to DUX4 as assessed by fluorescence resonance energy transfer and fluorescence polarization techniques. Sequences analysis of these aptamers revealed the presence of two consensus DUX4 motifs in a reverse complementary fashion forming hairpins interspersed with bulge loops at distinct positions that enlarged the binding surface with the DUX4 protein, as determined by crystal structure analysis. We demonstrate that insertion of specific structural elements into transcription factor binding oligonucleotides can enhance specificity and affinity.

Original language	English (US)
Pages (from-to)	4573-4590
Number of pages	18
Journal	FASEB Journal
Volume	34
Issue number	3
DOIs	https://doi.org/10.1096/fj.201902696
State	Published - Mar 1 2020

Bibliographical note

Funding Information:
We thank Tracy Dinh, Nicholas Moeller, and Kayo Orellana for help with protein purification and crystallization, and the staff of the NE-CAT beamline for assistance with x-ray data collection. This research used resources of the Advanced Photon Source (APS), a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science under Contract No. DE-AC02-06CH11357. The Northeastern Collaborative Access Team (NE-CAT) beamlines are funded by the National Institutes of Health (NIH) (P30 GM124165). The Eiger 16M detector on 24-ID-E beam line is funded by a NIH grant (S10OD021527). This work was supported by NIH grant GM118047 (to H. A.). We thank CSL Behring AG for an unrestricted research grant.

Funding Information:
We thank Tracy Dinh, Nicholas Moeller, and Kayo Orellana for help with protein purification and crystallization, and the staff of the NE‐CAT beamline for assistance with x‐ray data collection. This research used resources of the Advanced Photon Source (APS), a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science under Contract No. DE‐AC02‐06CH11357. The Northeastern Collaborative Access Team (NE‐CAT) beamlines are funded by the National Institutes of Health (NIH) (P30 GM124165). The Eiger 16M detector on 24‐ID‐E beam line is funded by a NIH grant (S10OD021527). This work was supported by NIH grant GM118047 (to H. A.). We thank CSL Behring AG for an unrestricted research grant.

Publisher Copyright:
© 2020 The Authors. The FASEB Journal published by Wiley Periodicals, Inc. on behalf of Federation of American Societies for Experimental Biology

Keywords

PAX7
PROP1
bulge loop
decoy
transcription factor

UN SDGs

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

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title = "DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD",

abstract = "Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio-scapulo-humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases. By applying Systematic Evolution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specific secondary structural elements conveying high affinity to DUX4 as assessed by fluorescence resonance energy transfer and fluorescence polarization techniques. Sequences analysis of these aptamers revealed the presence of two consensus DUX4 motifs in a reverse complementary fashion forming hairpins interspersed with bulge loops at distinct positions that enlarged the binding surface with the DUX4 protein, as determined by crystal structure analysis. We demonstrate that insertion of specific structural elements into transcription factor binding oligonucleotides can enhance specificity and affinity.",

keywords = "PAX7, PROP1, bulge loop, decoy, transcription factor",

author = "Christian Klingler and Jon Ashley and Ke Shi and Adeline Stiefvater and Michael Kyba and Michael Sinnreich and Hideki Aihara and Jochen Kinter",

note = "Funding Information: We thank Tracy Dinh, Nicholas Moeller, and Kayo Orellana for help with protein purification and crystallization, and the staff of the NE-CAT beamline for assistance with x-ray data collection. This research used resources of the Advanced Photon Source (APS), a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science under Contract No. DE-AC02-06CH11357. The Northeastern Collaborative Access Team (NE-CAT) beamlines are funded by the National Institutes of Health (NIH) (P30 GM124165). The Eiger 16M detector on 24-ID-E beam line is funded by a NIH grant (S10OD021527). This work was supported by NIH grant GM118047 (to H. A.). We thank CSL Behring AG for an unrestricted research grant. Funding Information: We thank Tracy Dinh, Nicholas Moeller, and Kayo Orellana for help with protein purification and crystallization, and the staff of the NE‐CAT beamline for assistance with x‐ray data collection. This research used resources of the Advanced Photon Source (APS), a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science under Contract No. DE‐AC02‐06CH11357. The Northeastern Collaborative Access Team (NE‐CAT) beamlines are funded by the National Institutes of Health (NIH) (P30 GM124165). The Eiger 16M detector on 24‐ID‐E beam line is funded by a NIH grant (S10OD021527). This work was supported by NIH grant GM118047 (to H. A.). We thank CSL Behring AG for an unrestricted research grant. Publisher Copyright: {\textcopyright} 2020 The Authors. The FASEB Journal published by Wiley Periodicals, Inc. on behalf of Federation of American Societies for Experimental Biology",

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AU - Sinnreich, Michael

AU - Aihara, Hideki

AU - Kinter, Jochen

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N2 - Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio-scapulo-humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases. By applying Systematic Evolution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specific secondary structural elements conveying high affinity to DUX4 as assessed by fluorescence resonance energy transfer and fluorescence polarization techniques. Sequences analysis of these aptamers revealed the presence of two consensus DUX4 motifs in a reverse complementary fashion forming hairpins interspersed with bulge loops at distinct positions that enlarged the binding surface with the DUX4 protein, as determined by crystal structure analysis. We demonstrate that insertion of specific structural elements into transcription factor binding oligonucleotides can enhance specificity and affinity.

AB - Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio-scapulo-humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases. By applying Systematic Evolution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specific secondary structural elements conveying high affinity to DUX4 as assessed by fluorescence resonance energy transfer and fluorescence polarization techniques. Sequences analysis of these aptamers revealed the presence of two consensus DUX4 motifs in a reverse complementary fashion forming hairpins interspersed with bulge loops at distinct positions that enlarged the binding surface with the DUX4 protein, as determined by crystal structure analysis. We demonstrate that insertion of specific structural elements into transcription factor binding oligonucleotides can enhance specificity and affinity.

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DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD

Abstract

Bibliographical note

Keywords

UN SDGs

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