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Article ; Online: Biophysical Techniques for Target Validation and Drug Discovery in Transcription-Targeted Therapy.

Moustaqil, Mehdi / Gambin, Yann / Sierecki, Emma

International journal of molecular sciences

2020 Volume 21, Issue 7

Abstract: In the post-genome era, pathologies become associated with specific gene expression profiles and defined molecular lesions can be identified. The traditional therapeutic strategy is to block the identified aberrant biochemical activity. However, an ... ...

Abstract	In the post-genome era, pathologies become associated with specific gene expression profiles and defined molecular lesions can be identified. The traditional therapeutic strategy is to block the identified aberrant biochemical activity. However, an attractive alternative could aim at antagonizing key transcriptional events underlying the pathogenesis, thereby blocking the consequences of a disorder, irrespective of the original biochemical nature. This approach, called transcription therapy, is now rendered possible by major advances in biophysical technologies. In the last two decades, techniques have evolved to become key components of drug discovery platforms, within pharmaceutical companies as well as academic laboratories. This review outlines the current biophysical strategies for transcription manipulation and provides examples of successful applications. It also provides insights into the future development of biophysical methods in drug discovery and personalized medicine.
MeSH term(s)	Animals ; Cryoelectron Microscopy/methods ; Drug Discovery/methods ; Humans ; Molecular Targeted Therapy/methods ; Single Molecule Imaging/methods ; Transcription Factors/antagonists & inhibitors
Chemical Substances	Transcription Factors
Language	English
Publishing date	2020-03-26
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21072301
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Article ; Online: Biophysical Techniques for Target Validation and Drug Discovery in Transcription-Targeted Therapy

Mehdi Moustaqil / Yann Gambin / Emma Sierecki

International Journal of Molecular Sciences, Vol 21, Iss 7, p

2020 Volume 2301

Abstract	In the post-genome era, pathologies become associated with specific gene expression profiles and defined molecular lesions can be identified. The traditional therapeutic strategy is to block the identified aberrant biochemical activity. However, an attractive alternative could aim at antagonizing key transcriptional events underlying the pathogenesis, thereby blocking the consequences of a disorder, irrespective of the original biochemical nature. This approach, called transcription therapy, is now rendered possible by major advances in biophysical technologies. In the last two decades, techniques have evolved to become key components of drug discovery platforms, within pharmaceutical companies as well as academic laboratories. This review outlines the current biophysical strategies for transcription manipulation and provides examples of successful applications. It also provides insights into the future development of biophysical methods in drug discovery and personalized medicine.
Keywords	transcription factors ; biophysical techniques ; drug discovery ; therapy ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The blood vasculature instructs lymphatic patterning in a SOX7-dependent manner.

The EMBO journal

2023 Volume 42, Issue 5, Page(s) e109032

Abstract: Despite a growing catalog of secreted factors critical for lymphatic network assembly, little is known about the mechanisms that modulate the expression level of these molecular cues in blood vascular endothelial cells (BECs). Here, we show that a BEC- ... ...

Abstract	Despite a growing catalog of secreted factors critical for lymphatic network assembly, little is known about the mechanisms that modulate the expression level of these molecular cues in blood vascular endothelial cells (BECs). Here, we show that a BEC-specific transcription factor, SOX7, plays a crucial role in a non-cell-autonomous manner by modulating the transcription of angiocrine signals to pattern lymphatic vessels. While SOX7 is not expressed in lymphatic endothelial cells (LECs), the conditional loss of SOX7 function in mouse embryos causes a dysmorphic dermal lymphatic phenotype. We identify novel distant regulatory regions in mice and humans that contribute to directly repressing the transcription of a major lymphangiogenic growth factor (Vegfc) in a SOX7-dependent manner. Further, we show that SOX7 directly binds HEY1, a canonical repressor of the Notch pathway, suggesting that transcriptional repression may also be modulated by the recruitment of this protein partner at Vegfc genomic regulatory regions. Our work unveils a role for SOX7 in modulating downstream signaling events crucial for lymphatic patterning, at least in part via the transcriptional repression of VEGFC levels in the blood vascular endothelium.
MeSH term(s)	Humans ; Mice ; Animals ; Endothelial Cells/metabolism ; Lymphatic Vessels/metabolism ; Gene Expression Regulation ; Endothelium, Vascular ; Transcription Factors/metabolism ; Lymphangiogenesis/genetics ; SOXF Transcription Factors/genetics ; SOXF Transcription Factors/metabolism
Chemical Substances	Transcription Factors ; SOX7 protein, human ; SOXF Transcription Factors ; Sox7 protein, mouse
Language	English
Publishing date	2023-01-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.2021109032
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Article ; Online: Correction: Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice.

Overman, Jeroen / Fontaine, Frank / Moustaqil, Mehdi / Mittal, Deepak / Sierecki, Emma / Sacilotto, Natalia / Zuegg, Johannes / Robertson, Avril A B / Holmes, Kelly / Salim, Angela A / Mamidyala, Sreeman / Butler, Mark S / Robinson, Ashley S / Lesieur, Emmanuelle / Johnston, Wayne / Alexandrov, Kirill / Black, Brian L / Hogan, Benjamin M / De Val, Sarah /

Capon, Robert J / Carroll, Jason S / Bailey, Timothy L / Koopman, Peter / Jauch, Ralf / Cooper, Matthew A / Gambin, Yann / Francois, Mathias

eLife

2023 Volume 12

Language	English
Publishing date	2023-08-08
Publishing country	England
Document type	Published Erratum
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.90408
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Article ; Online: A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity.

McCann, Alex J / Lou, Jieqiong / Moustaqil, Mehdi / Graus, Matthew S / Blum, Ailisa / Fontaine, Frank / Liu, Hui / Luu, Winnie / Rudolffi-Soto, Paulina / Koopman, Peter / Sierecki, Emma / Gambin, Yann / Meunier, Frédéric A / Liu, Zhe / Hinde, Elizabeth / Francois, Mathias

Nucleic acids research

2021 Volume 49, Issue 19, Page(s) 10931–10955

Abstract: Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly ... ...

Abstract	Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18RaOp disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.
MeSH term(s)	Animals ; COS Cells ; Chlorocebus aethiops ; Disease Models, Animal ; Gene Expression Regulation ; Gene Regulatory Networks ; Genes, Reporter ; Glomerulonephritis/genetics ; Glomerulonephritis/metabolism ; Glomerulonephritis/pathology ; HeLa Cells ; Human Umbilical Vein Endothelial Cells ; Humans ; Hypotrichosis/genetics ; Hypotrichosis/metabolism ; Hypotrichosis/pathology ; Luciferases/genetics ; Luciferases/metabolism ; Lymphedema/genetics ; Lymphedema/metabolism ; Lymphedema/pathology ; MEF2 Transcription Factors/genetics ; MEF2 Transcription Factors/metabolism ; Mice ; Mutation ; SOXF Transcription Factors/genetics ; SOXF Transcription Factors/metabolism ; Single Molecule Imaging ; Telangiectasis/genetics ; Telangiectasis/metabolism ; Telangiectasis/pathology ; Transcription, Genetic
Chemical Substances	MEF2 Transcription Factors ; MEF2C protein, human ; SOX18 protein, human ; SOX7 protein, human ; SOXF Transcription Factors ; Luciferases (EC 1.13.12.-)
Language	English
Publishing date	2021-09-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab820
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bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
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Article ; Online: SARS-CoV-2 proteases PLpro and 3CLpro cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species.

Moustaqil, Mehdi / Ollivier, Emma / Chiu, Hsin-Ping / Van Tol, Sarah / Rudolffi-Soto, Paulina / Stevens, Christian / Bhumkar, Akshay / Hunter, Dominic J B / Freiberg, Alexander N / Jacques, David / Lee, Benhur / Sierecki, Emma / Gambin, Yann

Emerging microbes & infections

2020 Volume 10, Issue 1, Page(s) 178–195

Abstract: The genome of SARS-CoV-2 encodes two viral proteases (NSP3/papain-like protease and NSP5/3C-like protease) that are responsible for cleaving viral polyproteins during replication. Here, we discovered new functions of the NSP3 and NSP5 proteases of SARS- ... ...

Abstract	The genome of SARS-CoV-2 encodes two viral proteases (NSP3/papain-like protease and NSP5/3C-like protease) that are responsible for cleaving viral polyproteins during replication. Here, we discovered new functions of the NSP3 and NSP5 proteases of SARS-CoV-2, demonstrating that they could directly cleave proteins involved in the host innate immune response. We identified 3 proteins that were specifically and selectively cleaved by NSP3 or NSP5: IRF-3, and NLRP12 and TAB1, respectively. Direct cleavage of IRF3 by NSP3 could explain the blunted Type-I IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of cytokines and inflammatory responThe genome of SARS-CoV-2 encodes two viral proteases (NSP3/papain-like protease and NSP5/3C-like protease) that are responsible for cleaving viral polyproteins during replication. Here, we discovered new functions of the NSP3 and NSP5 proteases of SARS-CoV-2, demonstrating that they could directly cleave proteins involved in the host innate immune response. We identified 3 proteins that were specifically and selectively cleaved by NSP3 or NSP5: IRF-3, and NLRP12 and TAB1, respectively. Direct cleavage of IRF3 by NSP3 could explain the blunted Type-I IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of cytokines and inflammatory response observed in COVID-19 patients. We demonstrate that in the mouse NLRP12 protein, one of the recognition site is not cleaved in our
MeSH term(s)	Adaptor Proteins, Signal Transducing/metabolism ; Amino Acid Sequence ; Animals ; COVID-19/pathology ; Cell Line ; Chiroptera/virology ; Coronavirus 3C Proteases/genetics ; Coronavirus 3C Proteases/metabolism ; Coronavirus Papain-Like Proteases/genetics ; Coronavirus Papain-Like Proteases/metabolism ; HEK293 Cells ; Humans ; Interferon Regulatory Factor-3/metabolism ; Intracellular Signaling Peptides and Proteins/metabolism ; Mice ; SARS-CoV-2/enzymology ; SARS-CoV-2/genetics
Chemical Substances	Adaptor Proteins, Signal Transducing ; IRF3 protein, human ; Interferon Regulatory Factor-3 ; Intracellular Signaling Peptides and Proteins ; NLRP12 protein, human ; TAB1 protein, human ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus Papain-Like Proteases (EC 3.4.22.2) ; papain-like protease, SARS coronavirus (EC 3.4.22.2) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2020-12-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2681359-2
ISSN	2222-1751 ; 2222-1751
ISSN (online)	2222-1751
ISSN	2222-1751
DOI	10.1080/22221751.2020.1870414
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Article ; Online: Evolutionary Landscape of

Underwood, Adam / Rasicci, Daniel T / Hinds, David / Mitchell, Jackson T / Zieba, Jacob K / Mills, Joshua / Arnold, Nicholas E / Cook, Taylor W / Moustaqil, Mehdi / Gambin, Yann / Sierecki, Emma / Fontaine, Frank / Vanderweele, Sophie / Das, Akansha S / Cvammen, William / Sirpilla, Olivia / Soehnlen, Xavier / Bricker, Kristen / Alokaili, Maram /

Green, Morgan / Heeringa, Sadie / Wilstermann, Amy M / Freeland, Thomas M / Qutob, Dinah / Milsted, Amy / Jauch, Ralf / Triche, Timothy J / Krawczyk, Connie M / Bupp, Caleb P / Rajasekaran, Surender / Francois, Mathias / Prokop, Jeremy W

Genes

2023 Volume 14, Issue 1

Abstract: The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in ... ...

Abstract	The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood-brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.
MeSH term(s)	Humans ; High Mobility Group Proteins/chemistry ; High Mobility Group Proteins/genetics ; High Mobility Group Proteins/metabolism ; SOX Transcription Factors/genetics ; Amino Acid Sequence ; Dimerization ; Genotype ; SOXF Transcription Factors/genetics ; SOXF Transcription Factors/metabolism ; SOXB2 Transcription Factors/genetics ; SOXB2 Transcription Factors/metabolism ; SOXE Transcription Factors/genetics
Chemical Substances	High Mobility Group Proteins ; SOX Transcription Factors ; SOX7 protein, human ; SOXF Transcription Factors ; SOX18 protein, human ; SOX14 protein, human ; SOXB2 Transcription Factors ; SOX8 protein, human ; SOXE Transcription Factors
Language	English
Publishing date	2023-01-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14010222
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Article ; Online: A Split-Luciferase Reporter Recognizing GFP and mCherry Tags to Facilitate Studies of Protein-Protein Interactions.

Moustaqil, Mehdi / Bhumkar, Akshay / Gonzalez, Laura / Raoul, Lisa / Hunter, Dominic J B / Carrive, Pascal / Sierecki, Emma / Gambin, Yann

International journal of molecular sciences

2017 Volume 18, Issue 12

Abstract: The use of fluorescently-tagged proteins in microscopy has become routine, and anti-GFP (Green fluorescent protein) affinity matrices are increasingly used in proteomics protocols. However, some protein-protein interactions assays, such as protein ... ...

Abstract	The use of fluorescently-tagged proteins in microscopy has become routine, and anti-GFP (Green fluorescent protein) affinity matrices are increasingly used in proteomics protocols. However, some protein-protein interactions assays, such as protein complementation assays (PCA), require recloning of each protein as a fusion with the different parts of the complementation system. Here we describe a generic system where the complementation is separated from the proteins and can be directly used with fluorescently-tagged proteins. By using nanobodies and performing tests in cell-free expression systems, we accelerated the development of multiple reporters, detecting heterodimers and homodimers or oligomers tagged with GFP or mCherry. We demonstrate that the system can detect interactions at a broad range of concentrations, from low nanomolar up to micromolar.
MeSH term(s)	Cell-Free System/metabolism ; Genes, Reporter ; Genetic Engineering ; Green Fluorescent Proteins/metabolism ; Luciferases/genetics ; Luciferases/metabolism ; Luminescent Proteins/metabolism ; Microscopy, Fluorescence ; Protein Interaction Maps ; Proteomics ; Red Fluorescent Protein
Chemical Substances	Luminescent Proteins ; Green Fluorescent Proteins (147336-22-9) ; Luciferases (EC 1.13.12.-)
Language	English
Publishing date	2017-12-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms18122681
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Article ; Online: Correction

Jeroen Overman / Frank Fontaine / Mehdi Moustaqil / Deepak Mittal / Emma Sierecki / Natalia Sacilotto / Johannes Zuegg / Avril AB Robertson / Kelly Holmes / Angela A Salim / Sreeman Mamidyala / Mark S Butler / Ashley S Robinson / Emmanuelle Lesieur / Wayne Johnston / Kirill Alexandrov / Brian L Black / Benjamin M Hogan / Sarah De Val /

Robert J Capon / Jason S Carroll / Timothy L Bailey / Peter Koopman / Ralf Jauch / Matthew A Cooper / Yann Gambin / Mathias Francois

eLife, Vol

Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice

2023 Volume 12

Keywords	Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-08-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evolutionary Landscape of SOX Genes to Inform Genotype-to-Phenotype Relationships

Green, Morgan / Heeringa, Sadie / Wilstermann, Amy M / Freeland, Thomas M. / Qutob, Dinah / Milsted, Amy / Jauch, Ralf / Triche, Timothy J / Krawczyk, Connie M / Bupp, Caleb P / Rajasekaran, Surender / Francois, Mathias / Prokop, Jeremy W.

Genes (Basel). 2023 Jan. 14, v. 14, no. 1

2023

Abstract: The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype–phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in ... ...

Abstract	The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype–phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood–brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.
Keywords	amino acid sequences ; amino acids ; blood-brain barrier ; dimerization ; evolution ; eyes ; genes ; genotype-phenotype correlation ; heterozygosity ; humans ; open reading frames ; transcription factors
Language	English
Dates of publication	2023-0114
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14010222
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