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Theranostics by testing CFTR modulators in patient-derived materials: The current status and a proposal for subjects with rare CFTR mutations.

Amaral MD, de Boeck K; ECFS Strategic Planning Task Force on ‘Speeding up access to new drugs for CF’.

J Cyst Fibros. 2019 Jul 17. pii: S1569-1993(19)30814-8. doi: 10.1016/j.jcf.2019.06.010. [Epub ahead of print] Review.


Inhibition of calpain 1 restores plasma membrane stability to pharmacologically rescued Phe508del-CFTR variant.

Matos AM, Pinto FR, Barros P, Amaral MD, Pepperkok R, Matos P.

J Biol Chem. 2019 Jul 19. pii: jbc.RA119.008738. doi: 10.1074/jbc.RA119.008738. [Epub ahead of print]


Speeding up access to new drugs for CF: Considerations for clinical trial design and delivery.

Davies JC, Drevinek P, Elborn JS, Kerem E, Lee T; European CF Society (ECFS) Strategic Planning Task Force on ‘Speeding up access to new 4 drugs for CF’, Amaral MD, de Boeck K, Davies JC, Drevinek P, Elborn JS, Kerem E, Lee T.

J Cyst Fibros. 2019 Jul 11. pii: S1569-1993(19)30815-X. doi: 10.1016/j.jcf.2019.06.011. [Epub ahead of print]


Folding Status Is Determinant over Traffic-Competence in Defining CFTR Interactors in the Endoplasmic Reticulum.

Santos JD, Canato S, Carvalho AS, Botelho HM, Aloria K, Amaral MD, Matthiesen R, Falcao AO, Farinha CM.

Cells. 2019 Apr 14;8(4). pii: E353. doi: 10.3390/cells8040353.


Extent of rescue of F508del-CFTR function by VX-809 and VX-770 in human nasal epithelial cells correlates with SNP rs7512462 in SLC26A9 gene in F508del/F508del Cystic Fibrosis patients.

Kmit A, Marson FAL, Pereira SV, Vinagre AM, Leite GS, Servidoni MF, Ribeiro JD, Ribeiro AF, Bertuzzo CS, Amaral MD.

Biochim Biophys Acta Mol Basis Dis. 2019 Jun 1;1865(6):1323-1331. doi: 10.1016/j.bbadis.2019.01.029. Epub 2019 Feb 1.


Increases in cytosolic Ca2+ induce dynamin- and calcineurin-dependent internalisation of CFTR.

Patel W, Moore PJ, Sassano MF, Lopes-Pacheco M, Aleksandrov AA, Amaral MD, Tarran R, Gray MA.

Cell Mol Life Sci. 2019 Mar;76(5):977-994. doi: 10.1007/s00018-018-2989-3. Epub 2018 Dec 13.


The effect of premature termination codon mutations on CFTR mRNA abundance in human nasal epithelium and intestinal organoids: a basis for read-through therapies in cystic fibrosis.

Clarke LA, Awatade NT, Felício VM, Silva IA, Calucho M, Pereira L, Azevedo P, Cavaco J, Barreto C, Bertuzzo C, Gartner S, Beekman J, Amaral MD.

Hum Mutat. 2019 Mar;40(3):326-334. doi: 10.1002/humu.23692. Epub 2018 Dec 10.


Human epididymis protein 4 (HE4) levels inversely correlate with lung function improvement (delta FEV1) in cystic fibrosis patients receiving ivacaftor treatment.

Nagy B Jr, Bene Z, Fejes Z, Heltshe SL, Reid D, Ronan NJ, McCarthy Y, Smith D, Nagy A, Joseloff E, Balla G, Kappelmayer J, Macek M Jr, Bell SC, Plant BJ, Amaral MD, Balogh I.

J Cyst Fibros. 2019 Mar;18(2):271-277. doi: 10.1016/j.jcf.2018.08.013. Epub 2018 Sep 27.


Prolonged co-treatment with HGF sustains epithelial integrity and improves pharmacological rescue of Phe508del-CFTR.

Matos AM, Gomes-Duarte A, Faria M, Barros P, Jordan P, Amaral MD, Matos P.

Sci Rep. 2018 Aug 29;8(1):13026. doi: 10.1038/s41598-018-31514-2.


Proteomic interaction profiling reveals KIFC1 as a factor involved in early targeting of F508del-CFTR to degradation.

Canato S, Santos JD, Carvalho AS, Aloria K, Amaral MD, Matthiesen R, Falcao AO, Farinha CM.

Cell Mol Life Sci. 2018 Dec;75(24):4495-4509. doi: 10.1007/s00018-018-2896-7. Epub 2018 Jul 31.


R560S: A class II CFTR mutation that is not rescued by current modulators.

Awatade NT, Ramalho S, Silva IAL, Felício V, Botelho HM, de Poel E, Vonk A, Beekman JM, Farinha CM, Amaral MD.

J Cyst Fibros. 2019 Mar;18(2):182-189. doi: 10.1016/j.jcf.2018.07.001. Epub 2018 Jul 18.


CFTR modulator theratyping: Current status, gaps and future directions.

Clancy JP, Cotton CU, Donaldson SH, Solomon GM, VanDevanter DR, Boyle MP, Gentzsch M, Nick JA, Illek B, Wallenburg JC, Sorscher EJ, Amaral MD, Beekman JM, Naren AP, Bridges RJ, Thomas PJ, Cutting G, Rowe S, Durmowicz AG, Mense M, Boeck KD, Skach W, Penland C, Joseloff E, Bihler H, Mahoney J, Borowitz D, Tuggle KL.

J Cyst Fibros. 2019 Jan;18(1):22-34. doi: 10.1016/j.jcf.2018.05.004. Epub 2018 Jun 20. Review.


Cystic fibrosis: Beyond the airways. Report on the meeting of the basic science working group in Loutraki, Greece.

Amaral MD, Boj SF, Shaw J, Leipziger J, Beekman JM.

J Cyst Fibros. 2018 Jul;17(4):441-443. doi: 10.1016/j.jcf.2018.05.008. Epub 2018 Jun 2. Review.


Genomic sequencing identifies secondary findings in a cohort of parent study participants.

Thompson ML, Finnila CR, Bowling KM, Brothers KB, Neu MB, Amaral MD, Hiatt SM, East KM, Gray DE, Lawlor JMJ, Kelley WV, Lose EJ, Rich CA, Simmons S, Levy SE, Myers RM, Barsh GS, Bebin EM, Cooper GM.

Genet Med. 2018 Dec;20(12):1635-1643. doi: 10.1038/gim.2018.53. Epub 2018 Apr 12.


Functional variants in TBX2 are associated with a syndromic cardiovascular and skeletal developmental disorder.

Liu N, Schoch K, Luo X, Pena LDM, Bhavana VH, Kukolich MK, Stringer S, Powis Z, Radtke K, Mroske C, Deak KL, McDonald MT, McConkie-Rosell A, Markert ML, Kranz PG, Stong N, Need AC, Bick D, Amaral MD, Worthey EA, Levy S; Undiagnosed Diseases Network (UDN), Wangler MF, Bellen HJ, Shashi V, Yamamoto S.

Hum Mol Genet. 2018 Jul 15;27(14):2454-2465. doi: 10.1093/hmg/ddy146.


Systematic reanalysis of genomic data improves quality of variant interpretation.

Hiatt SM, Amaral MD, Bowling KM, Finnila CR, Thompson ML, Gray DE, Lawlor JMJ, Cochran JN, Bebin EM, Brothers KB, East KM, Kelley WV, Lamb NE, Levy SE, Lose EJ, Neu MB, Rich CA, Simmons S, Myers RM, Barsh GS, Cooper GM.

Clin Genet. 2018 Jul;94(1):174-178. doi: 10.1111/cge.13259. Epub 2018 May 10.


A Mathematical Model of the Phosphoinositide Pathway.

Olivença DV, Uliyakina I, Fonseca LL, Amaral MD, Voit EO, Pinto FR.

Sci Rep. 2018 Mar 2;8(1):3904. doi: 10.1038/s41598-018-22226-8.


Partial rescue of F508del-cystic fibrosis transmembrane conductance regulator channel gating with modest improvement of protein processing, but not stability, by a dual-acting small molecule.

Liu J, Bihler H, Farinha CM, Awatade NT, Romão AM, Mercadante D, Cheng Y, Musisi I, Jantarajit W, Wang Y, Cai Z, Amaral MD, Mense M, Sheppard DN.

Br J Pharmacol. 2018 Apr;175(7):1017-1038. doi: 10.1111/bph.14141. Epub 2018 Feb 22.


A novel microscopy-based assay identifies extended synaptotagmin-1 (ESYT1) as a positive regulator of anoctamin 1 traffic.

Lérias JR, Pinto MC, Botelho HM, Awatade NT, Quaresma MC, Silva IAL, Wanitchakool P, Schreiber R, Pepperkok R, Kunzelmann K, Amaral MD.

Biochim Biophys Acta Mol Cell Res. 2018 Feb;1865(2):421-431. doi: 10.1016/j.bbamcr.2017.11.009. Epub 2017 Nov 15.


Evaluation of the acaricidal activity of thymol incorporated in two formulations for topical use against immature stages of Rhipicephalus sanguineus sensu lato (Latreille, 1806) (Acari: Ixodidae).

Delmonte C, Cruz PB, Zeringóta V, de Mello V, Ferreira F, Amaral MDPH, Daemon E.

Parasitol Res. 2017 Nov;116(11):2957-2964. doi: 10.1007/s00436-017-5604-x. Epub 2017 Sep 5.


Genomic diagnosis for children with intellectual disability and/or developmental delay.

Bowling KM, Thompson ML, Amaral MD, Finnila CR, Hiatt SM, Engel KL, Cochran JN, Brothers KB, East KM, Gray DE, Kelley WV, Lamb NE, Lose EJ, Rich CA, Simmons S, Whittle JS, Weaver BT, Nesmith AS, Myers RM, Barsh GS, Bebin EM, Cooper GM.

Genome Med. 2017 May 30;9(1):43. doi: 10.1186/s13073-017-0433-1.


Investigating Alternative Transport of Integral Plasma Membrane Proteins from the ER to the Golgi: Lessons from the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).

Amaral MD, Farinha CM, Matos P, Botelho HM.

Methods Mol Biol. 2016;1459:105-26. doi: 10.1007/978-1-4939-3804-9_7.


Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium.

Amendola LM, Jarvik GP, Leo MC, McLaughlin HM, Akkari Y, Amaral MD, Berg JS, Biswas S, Bowling KM, Conlin LK, Cooper GM, Dorschner MO, Dulik MC, Ghazani AA, Ghosh R, Green RC, Hart R, Horton C, Johnston JJ, Lebo MS, Milosavljevic A, Ou J, Pak CM, Patel RY, Punj S, Richards CS, Salama J, Strande NT, Yang Y, Plon SE, Biesecker LG, Rehm HL.

Am J Hum Genet. 2016 Jul 7;99(1):247. doi: 10.1016/j.ajhg.2016.06.001. No abstract available.


Classification of CFTR mutation classes - Authors' reply.

De Boeck K, Amaral MD.

Lancet Respir Med. 2016 Aug;4(8):e39. doi: 10.1016/S2213-2600(16)30189-8. Epub 2016 Jul 1. No abstract available.


EPAC1 activation by cAMP stabilizes CFTR at the membrane by promoting its interaction with NHERF1.

Lobo MJ, Amaral MD, Zaccolo M, Farinha CM.

J Cell Sci. 2016 Jul 1;129(13):2599-612. doi: 10.1242/jcs.185629. Epub 2016 May 20.


Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium.

Amendola LM, Jarvik GP, Leo MC, McLaughlin HM, Akkari Y, Amaral MD, Berg JS, Biswas S, Bowling KM, Conlin LK, Cooper GM, Dorschner MO, Dulik MC, Ghazani AA, Ghosh R, Green RC, Hart R, Horton C, Johnston JJ, Lebo MS, Milosavljevic A, Ou J, Pak CM, Patel RY, Punj S, Richards CS, Salama J, Strande NT, Yang Y, Plon SE, Biesecker LG, Rehm HL.

Am J Hum Genet. 2016 Jun 2;98(6):1067-1076. doi: 10.1016/j.ajhg.2016.03.024. Epub 2016 May 12. Erratum in: Am J Hum Genet. 2016 Jul 7;99(1):247.


mRNA-based detection of rare CFTR mutations improves genetic diagnosis of cystic fibrosis in populations with high genetic heterogeneity.

Felício V, Ramalho AS, Igreja S, Amaral MD.

Clin Genet. 2017 Mar;91(3):476-481. doi: 10.1111/cge.12802. Epub 2016 Jun 1.


The third dimension: new developments in cell culture models for colorectal research.

Pereira JF, Awatade NT, Loureiro CA, Matos P, Amaral MD, Jordan P.

Cell Mol Life Sci. 2016 Nov;73(21):3971-89. doi: 10.1007/s00018-016-2258-2. Epub 2016 May 4. Review.


Human Epididymis Protein 4: A Novel Serum Inflammatory Biomarker in Cystic Fibrosis.

Nagy B Jr, Nagy B, Fila L, Clarke LA, Gönczy F, Bede O, Nagy D, Újhelyi R, Szabó Á, Anghelyi A, Major M, Bene Z, Fejes Z, Antal-Szalmás P, Bhattoa HP, Balla G, Kappelmayer J, Amaral MD, Macek M Jr, Balogh I.

Chest. 2016 Sep;150(3):661-72. doi: 10.1016/j.chest.2016.04.006. Epub 2016 Apr 19.


Progress in therapies for cystic fibrosis.

De Boeck K, Amaral MD.

Lancet Respir Med. 2016 Aug;4(8):662-674. doi: 10.1016/S2213-2600(16)00023-0. Epub 2016 Apr 1. Review.


Correction of a Cystic Fibrosis Splicing Mutation by Antisense Oligonucleotides.

Igreja S, Clarke LA, Botelho HM, Marques L, Amaral MD.

Hum Mutat. 2016 Feb;37(2):209-15. doi: 10.1002/humu.22931. Epub 2015 Dec 2.


Hallmarks of therapeutic management of the cystic fibrosis functional landscape.

Amaral MD, Balch WE.

J Cyst Fibros. 2015 Nov;14(6):687-99. doi: 10.1016/j.jcf.2015.09.006. Epub 2015 Oct 29. Review.


Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators.

Clarke LA, Botelho HM, Sousa L, Falcao AO, Amaral MD.

Genomics. 2015 Nov;106(5):268-77. doi: 10.1016/j.ygeno.2015.07.005. Epub 2015 Jul 29.


Increased efficacy of VX-809 in different cellular systems results from an early stabilization effect of F508del-CFTR.

Farinha CM, Sousa M, Canato S, Schmidt A, Uliyakina I, Amaral MD.

Pharmacol Res Perspect. 2015 Aug;3(4):e00152. doi: 10.1002/prp2.152. Epub 2015 Jun 11.


Measurements of Functional Responses in Human Primary Lung Cells as a Basis for Personalized Therapy for Cystic Fibrosis.

Awatade NT, Uliyakina I, Farinha CM, Clarke LA, Mendes K, Solé A, Pastor J, Ramos MM, Amaral MD.

EBioMedicine. 2014 Dec 17;2(2):147-53. doi: 10.1016/j.ebiom.2014.12.005. eCollection 2015.


A molecular switch in the scaffold NHERF1 enables misfolded CFTR to evade the peripheral quality control checkpoint.

Loureiro CA, Matos AM, Dias-Alves Â, Pereira JF, Uliyakina I, Barros P, Amaral MD, Matos P.

Sci Signal. 2015 May 19;8(377):ra48. doi: 10.1126/scisignal.aaa1580.


Protein traffic disorders: an effective high-throughput fluorescence microscopy pipeline for drug discovery.

Botelho HM, Uliyakina I, Awatade NT, Proença MC, Tischer C, Sirianant L, Kunzelmann K, Pepperkok R, Amaral MD.

Sci Rep. 2015 Mar 12;5:9038. doi: 10.1038/srep09038.


Comparative ex vivo, in vitro and in silico analyses of a CFTR splicing mutation: Importance of functional studies to establish disease liability of mutations.

Ramalho AS, Clarke LA, Sousa M, Felicio V, Barreto C, Lopes C, Amaral MD.

J Cyst Fibros. 2016 Jan;15(1):21-33. doi: 10.1016/j.jcf.2015.02.002. Epub 2015 Feb 27.


Novel personalized therapies for cystic fibrosis: treating the basic defect in all patients.

Amaral MD.

J Intern Med. 2015 Feb;277(2):155-166. doi: 10.1111/joim.12314. Review.


Experimental assessment of splicing variants using expression minigenes and comparison with in silico predictions.

Sharma N, Sosnay PR, Ramalho AS, Douville C, Franca A, Gottschalk LB, Park J, Lee M, Vecchio-Pagan B, Raraigh KS, Amaral MD, Karchin R, Cutting GR.

Hum Mutat. 2014 Oct;35(10):1249-59. doi: 10.1002/humu.22624. Epub 2014 Sep 10.


New pharmacological approaches for cystic fibrosis: promises, progress, pitfalls.

Bell SC, De Boeck K, Amaral MD.

Pharmacol Ther. 2015 Jan;145:19-34. doi: 10.1016/j.pharmthera.2014.06.005. Epub 2014 Jun 14.


CFTR functional measurements in human models for diagnosis, prognosis and personalized therapy: Report on the pre-conference meeting to the 11th ECFS Basic Science Conference, Malta, 26-29 March 2014.

Beekman JM, Sermet-Gaudelus I, de Boeck K, Gonska T, Derichs N, Mall MA, Mehta A, Martin U, Drumm M, Amaral MD.

J Cyst Fibros. 2014 Jul;13(4):363-72. doi: 10.1016/j.jcf.2014.05.007. Epub 2014 Jun 2. Review. No abstract available.


LMTK2-mediated phosphorylation regulates CFTR endocytosis in human airway epithelial cells.

Luz S, Cihil KM, Brautigan DL, Amaral MD, Farinha CM, Swiatecka-Urban A.

J Biol Chem. 2014 May 23;289(21):15080-93. doi: 10.1074/jbc.M114.563742. Epub 2014 Apr 11.


Revertant mutants modify, but do not rescue, the gating defect of the cystic fibrosis mutant G551D-CFTR.

Xu Z, Pissarra LS, Farinha CM, Liu J, Cai Z, Thibodeau PH, Amaral MD, Sheppard DN.

J Physiol. 2014 May 1;592(9):1931-47. doi: 10.1113/jphysiol.2014.271817. Epub 2014 Mar 3.


Assessing the residual CFTR gene expression in human nasal epithelium cells bearing CFTR splicing mutations causing cystic fibrosis.

Masvidal L, Igreja S, Ramos MD, Alvarez A, de Gracia J, Ramalho A, Amaral MD, Larriba S, Casals T.

Eur J Hum Genet. 2014 Jun;22(6):784-91. doi: 10.1038/ejhg.2013.238. Epub 2013 Oct 16.


High-content siRNA screen reveals global ENaC regulators and potential cystic fibrosis therapy targets.

Almaça J, Faria D, Sousa M, Uliyakina I, Conrad C, Sirianant L, Clarke LA, Martins JP, Santos M, Heriché JK, Huber W, Schreiber R, Pepperkok R, Kunzelmann K, Amaral MD.

Cell. 2013 Sep 12;154(6):1390-400. doi: 10.1016/j.cell.2013.08.045.


Neuronal reprograming of protein homeostasis by calcium-dependent regulation of the heat shock response.

Silva MC, Amaral MD, Morimoto RI.

PLoS Genet. 2013 Aug;9(8):e1003711. doi: 10.1371/journal.pgen.1003711. Epub 2013 Aug 29.


Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene.

Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, Ramalho AS, Amaral MD, Dorfman R, Zielenski J, Masica DL, Karchin R, Millen L, Thomas PJ, Patrinos GP, Corey M, Lewis MH, Rommens JM, Castellani C, Penland CM, Cutting GR.

Nat Genet. 2013 Oct;45(10):1160-7. doi: 10.1038/ng.2745. Epub 2013 Aug 25.


Revertants, low temperature, and correctors reveal the mechanism of F508del-CFTR rescue by VX-809 and suggest multiple agents for full correction.

Farinha CM, King-Underwood J, Sousa M, Correia AR, Henriques BJ, Roxo-Rosa M, Da Paula AC, Williams J, Hirst S, Gomes CM, Amaral MD.

Chem Biol. 2013 Jul 25;20(7):943-55. doi: 10.1016/j.chembiol.2013.06.004.


Control of cystic fibrosis transmembrane conductance regulator membrane trafficking: not just from the endoplasmic reticulum to the Golgi.

Farinha CM, Matos P, Amaral MD.

FEBS J. 2013 Sep;280(18):4396-406. doi: 10.1111/febs.12392. Epub 2013 Jul 5. Review.

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