The CF Canada-Sick Kids Program in individual CF therapy: A resource for the advancement of personalized medicine in CF

Abstract

Background: Therapies targeting certain CFTR mutants have been approved, yet variations in clinical response highlight the need for in-vitro and genetic tools that predict patient-specific clinical outcomes. Toward this goal, the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT) is generating a "first of its kind", comprehensive resource containing patient-specific cell cultures and data from 100 CF individuals that will enable modeling of therapeutic responses. Methods: The CFIT program is generating: 1) nasal cells from drug naïve patients suitable for culture and the study of drug responses in vitro, 2) matched gene expression data obtained by sequencing the RNA from the primary nasal tissue, 3) whole genome sequencing of blood derived DNA from each of the 100 participants, 4) induced pluripotent stem cells (iPSCs) generated from each participant's blood sample, 5) CRISPRedited isogenic control iPSC lines and 6) prospective clinical data from patients treated with CF modulators. Results: To date, we have recruited 57 of 100 individuals to CFIT, most of whom are homozygous for F508del (to assess in-vitro: in-vivo correlations with respect to ORKAMBI response) or heterozygous for F508del and a minimal function mutation. In addition, several donors are homozygous for rare nonsense and missense mutations. Nasal epithelial cell cultures and matched iPSC lines are available for many of these donors.

The CFTR Mutation c.3453G > C (D1152H) Confers an Anion Selectivity Defect in Primary Airway Tissue that Can be Rescued by Ivacaftor

“…Once confluent, the media was changed to air liquid interface (ALI) with basal differentiation media (PneumaCult TM ALI, StemCell Tech.). By 2 to 3 weeks, cells were well differentiated with a ciliated phenotype [ 20 , 21 , 23 ].…”

Gene modifiers of cystic fibrosis lung disease: A systematic review

“…Whilst such testing may seem invasive, they are already being conducted regularly in cohorts such as AREST CF 107 and the Toronto Sick Kids CF Cohort. 108 Using insensitive measures of lung disease may result in an inaccurate assessment of the contribution of gene-modifiers to lung disease severity. Moving forward, a challenge in phenotyping lung disease severity will be accounting for the effect of CFTR modulating therapies, given differences in lung disease severity may be related to eligibility and access to these therapies rather than true differences in lung disease severity.…”

LocusFocus: A web-based colocalization tool for the annotation and functional follow-up of GWAS

“…Our GWAS on lung disease severity in CF, however, revealed no association at this locus [20]. To further investigate ATP12A in the lungs in the event that the CF lung GWAS was confounded, we tested colocalization at the CF MI GWAS locus with eQTLs in lung tissue from GTEx [11] and eQTLs from RNAseq of human nasal epithelia (HNE) from individuals with CF [21]. eQTLs for ATP12A from the lung and HNE [22] do not colocalize with the MI GWAS locus ( Figure 2).…”