Identification of candidate genes and pathways in retinopathy of prematurity by whole exome sequencing of preterm infants enriched in phenotypic extremes

Abstract

Retinopathy of prematurity (ROP) is a vasoproliferative retinal disease affecting premature infants. In addition to prematurity itself and oxygen treatment, genetic factors have been suggested to predispose to ROP. We aimed to identify potentially pathogenic genes and biological pathways associated with ROP by analyzing variants from whole exome sequencing (WES) data of premature infants. As part of a multicenter ROP cohort study, 100 non-Hispanic Caucasian preterm infants enriched in phenotypic extremes were subjected to WES. Gene-based testing was done on coding nonsynonymous variants. Genes showing enrichment of qualifying variants in severe ROP compared to mild or no ROP from gene-based tests with adjustment for gestational age and birth weight were selected for gene set enrichment analysis (GSEA). Mean BW of included infants with pre-plus, type-1 or type 2 ROP including aggressive posterior ROP (n = 58) and mild or no ROP (n = 42) were 744 g and 995 g, respectively. No single genes reached genome-wide significance that could account for a severe phenotype. GSEA identified two significantly associated pathways (smooth endoplasmic reticulum and vitamin C metabolism) after correction for multiple tests. WES of premature infants revealed potential pathways that may be important in the pathogenesis of ROP and in further genetic studies.

Genome-wide association identifies novel ROP risk loci in a multiethnic cohort

“…To identify genetic susceptibility regions for ROP, we conducted a genome-wide association study (GWAS) using the Illumina Infinium Global Screening Array with information from these infants. As published by our group, ROP phenotype was rigorously determined by a team of ophthalmologists and image graders with clinical expertise in ROP and phenotype assigned by consensus of 3 or more graders 8 , 24 – 29 . This subset of iROP patients represents multiple ethnic and racial groups, including 44.5% Hispanic, 35.4% White, 12.1% African American, and 8% unidentified race individuals as noted in Table 1 .…”

“…However, this understanding of risk and pathogenesis is incomplete as only approximately 50–65% of infants with these risk factors will develop ROP disease 4 , 6 , 7 . For example, phenotypic extremes that do not conform to current risk profiles exist; preterm infants born at large birth weights and/or older gestational ages may develop treatment-warranted ROP whereas those within the risk profiles of GA and BW do not always develop treatment-warranted ROP 8 . The current stratification also does not address prevention; although post-natal oxygen exposure is the most modifiable risk, limiting oxygen increases infant mortality 9 – 11 .…”

“…ROP risk is multifactorial and although genetic risk is not fully elucidated, there is a growing body of evidence supporting a genetic basis for ROP, including twin studies 13 – 15 . To date, no GWAS has been published for ROP; case control and whole exome candidate gene approaches have reported significant risk associations between single nucleotide polymorphisms (SNP) in brain-derived neurotrophic factor ( BDNF ; rs7934165 and rs2049046), thrombospondin type-1 domain-containing protein 4 ( THSD4 ), TNF -308G/A polymorphism and angiotensin 1 converting enzyme insertion deletion (ACE ID) polymorphism 8 , 16 – 18 (Supplementary Table 1 ). By contrast, recent candidate work demonstrated significant protective associations between the BDNF SNP rs7929344 and ROP and severe ROP risk associations between SNPs within VEGF A, NOS3, and EPAS1 19 .…”

Studying the Pathogenesis of Retinopathy of Prematurity - From Theory to Practice

“…Work on the study of the pathogenesis of ROP has been carried out by several scientists from different countries for more than a decade [1][2][3][4][5][6][7], but a number of questions still remain open, so this research does not lose its relevance and promise. It is important to note that a holistic work on the study of the mechanisms of ROP development should include an assessment of both local and systemic factors, and since the study of local factors of pathogenesis in the clinic meets natural limitations, experimental studies are of great importance here, allowing to significantly expand the possibilities of analyzing molecular participants in the pathological process in situ.…”

Role of studying the pathogenesis of retinopathy of prematurity in optimizing disease screening

“…Ретинопатия недоношенных (РН) остаётся одной из ведущих причин слепоты и слабовидения у детей во всем мире, несмотря на разработку и активное применение современных стандартов диагностики и лечения данной патологии и достижения современной неонатальной службы [1]. В определённой степени ретинопатия проявляется даже как следствие этих достижений медицины, поскольку особенно тяжёлые «неклассические» формы заболевания, резистентные к существующим методам лечения, развиваются именно у выхаживаемых и выживающих сегодня глубоко недоношенных детей [2].…”