Laboratory Tools to Predict CFTR Modulator Therapy Effectiveness and to Monitor Disease Severity in Cystic Fibrosis
Abstract
:1. Introduction
2. Laboratory Tools to Predict CFTR Modulator Effectiveness In Vivo
2.1. Primary Airway Cells Grown in Monolayers
2.2. Airway Organoids/Nasospheroids
2.3. Intestinal Organoids
3. Laboratory Biomarkers to Monitor Lung Disease Progression
3.1. Monitoring Ivacaftor Effects on CF Inflammation
3.2. Monitoring Lumacaftor/Ivacaftor and Tezacaftor/Ivacaftor Effects on CF Inflammation
3.3. Monitoring Elexacaftor/Tezacaftor/Ivacaftor Effects on CF Inflammation
4. Novel Laboratory Tools to Assess CF Status and Progression
4.1. Extracellular Vesicles
4.2. MicroRNAs
5. Concluding Remarks
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
Abbreviations
References
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Model System | CF Population/Genotypes | CFTR Modulator(s) | Key Findings/Correlations | Ref. |
---|---|---|---|---|
HNE cells | PwCF homozygous for p.Phe508del or carrying genotypes leading to minimal or residual CFTR function | LUMA TEZA IVA | The level of CFTR rescue significantly correlated with the ppFEV1 change at 6 months in 8 PwCF treated with CFTR modulators. | [25] |
Ten PwCF (<19 years) with a wide range of CFTR variants | LUMA IVA | CFTR modulation produced changes in CFTR function in nasal and bronchial cell cultures. There was a correlation between the residual CFTR function in both cell types from PwCF with SCC between 60 and 90 mmol·L−1. | [39] | |
Five healthy subjects (they were not genetically tested) and eight PwCF with variants associated with minimal or residual CFTR function | – | CFTR-mediated transepithelial chloride currents measured in vitro through Ussing chamber assay correlated with the SCC of subjects. | [40] | |
Twelve adults with CF with either the p.Gly551Asp or p.ArgR117His | IVA | A strong correlation between changes in SCC and in vitro CFTR activation was observed. Furthermore, a moderate correlation between in vitro CFTR activation and changes in ppFEV1 was reported. | [41] | |
Seven PwCF (≤16 years, clinically stable) with residual CFTR function variants | IVA | All subjects with decreased SCC in response to IVA treatment also had significant increases in chloride current in HNE cultures with IVA exposure. | [42] | |
Healthy volunteers, PwCF with p.PheF508del/p.Arg117His-7T, p.PheF508del/p.PheF508del, p.PheF508del/p.Met284fs, p.Arg334Trp/c.406-1G>A, and p.Ser18ArgfsX16/p.Ser18ArgfsX16 | LUMA TEZA IVA | In vitro CFTR chloride measurements correlated to changes in SCC. | [43] | |
Five PwCF: one homozygous for p.Ser737Phe and four compound heterozygous for p.Ser737Phe | TEZA ELX IVA | In vitro analysis demonstrated different levels of CFTR activity. Some degree of CFTR dysfunction was detected by evaluating chloride secretion in HNE cells derived from compound heterozygous subjects; CFTR activity was improved by IVA alone and even more by treatment with correctors. | [44] | |
Eleven PwCF carrying FDA-eligible variants for ELX/TEZA/IVA and twenty-eight PwCF carrying non-eligible variants | TEZA ELX IVA | There was a significant relationship between CFTR activity correction and changes in ppFEV1 or SCC. | [45] | |
A 56-year-old male with CF and the p.Phe508del/p.Gln1291His genotype | TEZA ELX IVA | In HNE cells, p.Phe508del/p.Gln1291His resulted in reduced baseline CFTR activity, and showed minimal response to ELX/TEZA/IVA (individually or in combination), aligning with the individual’s clinical evaluation as a non-responder to these drugs. | [46] | |
Airway organoids | Nine healthy volunteers and three PwCF | LUMA IVA | Organoids treated with modulators displayed similar effects to clinical response; LUMA/IVA treatment promoted greater responses in organoids from p.PheF508del-homozygous subjects. | [26] |
Six healthy volunteers, nine PwCF homozygous for p.Phe508del, and ten with at least one non-p.Phe508del variant | LUMA IVA | p.Phe508del/p.Phe508del organoids treated with LUMA/IVA exhibited a positive change in swelling responses; a relationship between organoid response to drug and in vivo clinical response was observed for three subjects treated. | [47] | |
Eighteen PwCF and five healthy volunteers | TEZA ELX IVA | In vitro responses to CFTR modulators correlated well with clinical measurements. | [48] | |
Five PwCF: p.Phe508del/p.Phe508del, p.Phe508del/p.Gly542X, and F508del/G542X and p.Arg334Trp/p.Arg334Trp | LUMA IVA | Responses of organoids correlated well with clinical findings. | [49] | |
Intestinal organoids | Twelve healthy volunteers, four CF carriers (WT/p.Phe508del), thirty-five PwCF carrying class II and III variants, and eighteen PwCF carrying class IV and V variants | LUMA IVA | Responses of organoids to CFTR modulators correlated with outcome data from clinical trials. | [24] |
Twenty-four PwCF: fifteen carrying at least one p.Ser1251Asn and nine carrying at least one (ultra)rare CFTR variant | LUMA IVA | Responses to CFTR modulators in organoids correlated with in vivo measurements (SCC and ppFEV1). | [50] | |
Thirty-four children with CF carrying a wide range of CFTR variants | – | Organoid swelling significantly correlated with SCC and ICM. | [51] | |
Thirty-four PwCF with p.Phe508del/p.Phe508del | – | Variability in CFTR residual function appeared to contribute to the clinical heterogeneity and organoid swelling values; responses in organoids correlated with ppFEV1 and BMI. | [52] | |
Ninety-seven PwCF with well-characterized and rare CFTR variants | LUMA IVA | Measurements of residual CFTR function and rescue by CFTR modulators in organoids correlated with clinical data, namely changes in ppFEV1 and SCC. | [53] | |
A 56-year-old female with CF carrying p.Phe508del/c.3717+5G>T | LUMA TEZA IVA | No baseline swelling was observed in organoids, suggesting minimal CFTR function; however, limited swelling was detected after LUMA/IVA or TEZA/IVA treatment. | [54] | |
Twenty-one PwCF homozygous for p.Phe508del | LUMA IVA | No correlations were found between organoid swelling and changes in the in vivo biomarkers, namely SCC and NPD. | [55] | |
A total of 173 PwCF carrying a wide range of CFTR variants | – | Organoid swelling values were associated with long-term ppFEV1 decline and the probability of developing different CF-related comorbidities, namely pancreatic insufficiency, CF-related liver disease, and CF-related diabetes. | [56] | |
Fifteen PwCF homozygous for p.Phe508del, fifteen PwCF carrying p.Phe508del/class I variant, and twenty-two PwCF with rare variant non-eligible for CFTR modulator therapy | TEZA ELX IVA | Responses to modulators in organoids from p.Phe508del/p.Phe508del or p.Phe508del/class I variant correlated with changes in ppFEV1. In CF organoids with 11 rare genotypes, CFTR function restoration was reported upon ELX/TEZA/IVA treatment. | [57] | |
A 19-year-old female with CF carrying p.Tyr515X/p.Arg334Trp | LUMA TEZA ELX IVA | Organoids treated with IVA alone or in combination with correctors demonstrated similar rescue of CFTR-dependent fluid secretion. In vivo measurements demonstrated significant clinical improvements in SCC, ppFEV1, and respiratory symptoms after 7 days of IVA initiation that were sustained for the 9-month follow-up. | [58] | |
A 6-year-old male with CF carrying p.Phe508del/p.Glu217Gly-Gly509Asp | LUMA TEZA ELX IVA | The p.Glu217Gly-Gly509Asp complex allele was characterized by a high residual function of the CFTR channel; organoid swelling values demonstrated rescue of CFTR function by all tested modulators. | [59] |
CFTR Modulator(s) | Sample | CF Population/Genotypes | Key Findings | Ref. |
---|---|---|---|---|
IVA | Sputum | A total of 151 PwCF (≥6 years) carrying p.Gly551Asp | ↓ bacterial load. | [94] |
Sputum | Three children with CF carrying p.Gly551Asp | No differences in airway microbiota density. | [95] | |
Blood | Seven PwCF (≥6 years) carrying at least one residual function variant: p.Gln715X/p.Gly1349Asp; p.Glu1418ArgfsX14/p.Gly1349Asp; p.Gly1349Asp/p.Gly1349Asp; p.Ile1295PhefsX33/p.Gly1349Asp; p.Arg352AlafsX11/p.Gly1349Asp; p.Glu1418ArgfsX14/p.Ser549Arg; p.Phe508del/p.Gly1244Glu | ↑ circulating mononuclear cell count after 2 months of IVA treatment. | [96] | |
Sputum | Twelve PwCF (≥6 years) carrying p.Gly551Asp | ↓ IL-8, IL-1β and NE levels; ↓ bacterial relative abundance; ↓ arginase-1, myeloperoxidase, calprotectin and S100A9. | [97] | |
Blood/Sputum | Thirty-three PwCF (≥6 years) carrying p.Gly551Asp | Blood: ↓ CRP, IL-1β, IL-6, IL-8 and IL-10 levels. Sputum: ↓ bacterial relative abundance. | [98] | |
Sputum | Thirty-one PwCF (≥6 years) carrying p.Gly551Asp | Despite improvements in SCC and ppFEV1, there were no significant changes in airway microbiota density, or in IL-6, IL-8, NE, IL-1β, SLPI, or A1AT levels. | [99] | |
Epithelial lining fluid | Ten PwCF (≥6 years) carrying p.Gly551Asp | ↓ IL-1β, IL-6, and IL-8 levels. | [100] | |
Blood | Twenty PwCF carrying p.Gly551Asp | ↓ white blood cell count and IL-6 and IL-8 levels. | [101] | |
Blood | Ten PwCF (≥6 years) carrying p.Gly551Asp | ↓ CXCL7, IL-8 and sTNFR1 levels. | [102] | |
BALF | Thirty-nine children with CF carrying at least a gating variant | No differences in neutrophil count and free NE and IL-8 levels. | [103] | |
LUMA/IVA | Blood | Fourteen PwCF homozygous for p.Phe508del | No differences in white blood cell count or CRP levels. | [104] |
Blood/Sputum | Fourteen PwCF (≥16 years) homozygous for p.Phe508del | Blood: ↓ IL-8, IL-1β and TNF-α levels. Sputum: ↓ IL-6, IL-8, IL-1β and TNF-α levels. | [105] | |
Sputum | Thirty PwCF (≥12 years) homozygous for p.Phe508del | ↓ bacterial relative abundance and IL-1β levels. | [106] | |
Sputum | Forty-one PwCF (≥12 years) homozygous for p.Phe508del | No differences in calprotectin levels or bacterial and fungal relative abundance. | [107] | |
LUMA/IVA or TEZA/IVA | Blood | LUMA/IVA: 13 PwCF homozygous for p.Phe508del TEZA/IVA: 8 PwCF homozygous for p.Phe508del | LUMA/IVA: ↓ IL-18, TNF-α, and caspase-1 levels. TEZA/IVA: ↓ IL-18, IL-1β, TNF-α, and caspase-1 levels. | [108] |
ELX/TEZA/IVA | Blood | Forty-eight PwCF carrying at least one p.Phe508del | Of the cultures, 30% were negative to P. aeruginosa, and Meticilin-resistant S. aureus. ↓ IL-6, IL-8, IL-17A levels and neutrophil count. | [109] |
Sputum | Seventy-nine PwCF (≥12 years) carrying at least one p.Phe508del | ↓ P. aeruginosa relative abundance, IL-1β, IL-8, NE, A1AT, and cathepsin-G levels. ↑ SLPI levels. | [110] | |
BALF | Eight PwCF (≥12 years) carrying at least one p.Phe508del | ↓ polymorphonuclear cell count. Bacterial cultures were negative for all subjects. | [111] | |
Blood/Sputum | Thirty PwCF (≥12 years) carrying at least one p.Phe508del | Sputum: ↓ NE, PR3, cathepsin-G, IL-8, IL-1β levels and P. aeruginosa density. ↑ SLPI levels. Blood: ↓ IL-6, CRP, and A1AT levels. | [112] |
MicroRNA | Target | Key Mechanism(s) | Ref. |
---|---|---|---|
miR-17 | IL-8 | ↓ IL-8 levels P. aeruginosa infection reduced miR-17 levels | [143] |
miR-31 | IRF-1 | ↓ cathepsin-S production | [144] |
miR-93 | IL-8 | P. aeruginosa infection reduced miR-93 levels and increased IL-8 production | [145] |
miR-126 | TOM1 | ↑ IL-8 levels and NF-κB signaling | [146] |
miR-145 | CFTR SMAD3 | Repression of CFTR 3′-UTR reporter ↓ TGF-β signaling | [147,148,149] [147,150] |
miR-155 | SHIP1 | ↓ SHIP1 levels ↑ IL-8 levels and PI3K/Akt signaling | [151] |
miR-199a-5p | CAV1 | ↓ CAV1 levels ↑ TLR4 signaling | [152] |
miR-223 | CFTR | Repression of CFTR 3′-UTR reporter | [148] |
miR-384 | CFTR and SLC12A2 | ↓ CFTR and SLC12A2 expression levels | [149] |
miR-494 | CFTR and SLC12A2 | ↓ CFTR and SLC12A2 expression levels Repression of CFTR 3′-UTR reporter ↑ NF-κB signaling, TNF-α, and IL-1β levels increased miR-494 activity | [149] [147,148,149] [153] |
miR-509-3p | CFTR | ↑ NF-κB signaling, TNF-α, and IL-1β levels increased miR-494 activity | [153] |
miR-1246 | CFTR and SLC12A2 | ↓ CFTR and SLC12A2 expression levels | [149] |
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Bacalhau, M.; Camargo, M.; Lopes-Pacheco, M. Laboratory Tools to Predict CFTR Modulator Therapy Effectiveness and to Monitor Disease Severity in Cystic Fibrosis. J. Pers. Med. 2024, 14, 93. https://doi.org/10.3390/jpm14010093
Bacalhau M, Camargo M, Lopes-Pacheco M. Laboratory Tools to Predict CFTR Modulator Therapy Effectiveness and to Monitor Disease Severity in Cystic Fibrosis. Journal of Personalized Medicine. 2024; 14(1):93. https://doi.org/10.3390/jpm14010093
Chicago/Turabian StyleBacalhau, Mafalda, Mariana Camargo, and Miquéias Lopes-Pacheco. 2024. "Laboratory Tools to Predict CFTR Modulator Therapy Effectiveness and to Monitor Disease Severity in Cystic Fibrosis" Journal of Personalized Medicine 14, no. 1: 93. https://doi.org/10.3390/jpm14010093
APA StyleBacalhau, M., Camargo, M., & Lopes-Pacheco, M. (2024). Laboratory Tools to Predict CFTR Modulator Therapy Effectiveness and to Monitor Disease Severity in Cystic Fibrosis. Journal of Personalized Medicine, 14(1), 93. https://doi.org/10.3390/jpm14010093