Identification of non-coding genetic variants in samples from hypoxemic respiratory disease patients that affect the transcriptional response to hypoxia.
A wide range of diseases course with an unbalance between the consumption of oxygen by tissues and its supply. This situation triggers a transcriptional response, mediated by the hypoxia inducible factors (HIFs), that aims to restore oxygen homeostasis. Little is known about the inter-individual variation in this response and its role in the progression of disease. Herein, we sought to identify common genetic variants mapping to hypoxia response elements (HREs) and characterize their effect on transcription. To this end, we constructed a list of genome-wide HIF-binding regions from publicly available experimental datasets and studied the genetic variability in these regions by targeted re-sequencing of genomic samples from 96 chronic obstructive pulmonary disease and 144 obstructive sleep apnea patients. This study identified 14 frequent variants disrupting potential HREs. The analysis of the genomic regions containing these variants by means of reporter assays revealed that variants rs1009329, rs6593210 and rs150921338 impaired the transcriptional response to hypoxia. Finally, using genome editing we confirmed the functional role of rs6593210 in the transcriptional regulation of EGFR. In summary, we found that inter-individual variability in non-coding regions affect the response to hypoxia and could potentially impact on the progression of pulmonary diseases.
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain.|IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain.|Unidad de Medicina Molecular, laboratorio de Oncología, CRIB. Universidad de Castilla-La Mancha, 02006, Albacete, Spain.
Olga
O
Roche
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain.|IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain.
María Laura
ML
Deguiz
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain.|IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain.|Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain.
María
M
Tiana
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain.
Clara
C
Galiana-Ribote
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain.
Daniel
D
Martinez-Alcazar
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain.
Carlos
C
Rey-Serra
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain.
Beatriz
B
Ranz-Ribeiro
IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain.|Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain.|Hospital Universitario La Paz, IdiPAZ, Servicio de Neumología, 28029 Madrid, Spain.
Raquel
R
Casitas
IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain.|Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain.|Hospital Universitario La Paz, IdiPAZ, Servicio de Neumología, 28029 Madrid, Spain.
Raúl
R
Galera
Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain.|Hospital Universitario La Paz, IdiPAZ, Servicio de Neumología, 28029 Madrid, Spain.
Isabel
I
Fernández-Navarro
Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain.|Servicio de Neumología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del hospital de La Princesa, 28006 Madrid, Spain.
Silvia
S
Sánchez-Cuéllar
Departamento de Medicina, Universidad Autónoma de Madrid (UAM) 28029 Madrid, Spain.
Virginie
V
Bernard
Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain.|Servicio de Neumología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del hospital de La Princesa, 28006 Madrid, Spain.|Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada.
Julio
J
Ancochea
Departamento de Medicina, Universidad Autónoma de Madrid (UAM) 28029 Madrid, Spain.
Wyeth W
WW
Wasserman
IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain.|Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain.|Hospital Universitario La Paz, IdiPAZ, Servicio de Neumología, 28029 Madrid, Spain.|Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada.
Francisco
F
García-Rio
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain.|IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain.|Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain.
Benilde
B
Jimenez
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), 28029 Madrid, Spain luis.peso@uam.es.|IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain.|Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain.
Luis
L
Del Peso
D002460:Cell Line; D016000:Cluster Analysis; D005260:Female; D000072669:Gene Editing; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D018773:Genes, erbB-1; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D000860:Hypoxia / Q000235:genetics* / Q000378:metabolism; D008297:Male; D059372:Nucleotide Motifs; D010641:Phenotype; D010735:Phosphoglycerate Kinase / Q000235:genetics; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic; D012140:Respiratory Tract Diseases / Q000235:genetics* / Q000378:metabolism / Q000503:physiopathology; D014158:Transcription, Genetic; D059467:Transcriptome; D020506:Untranslated Regions
D020506:Untranslated Regions; C577282:PGK1 protein, human; D010735:Phosphoglycerate Kinase