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References — Idiopathic Pulmonary Fibrosis (IPF) QSP Model

Curated for mechanistic map, mrgsolve ODE parameters, clinical calibration, and Shiny app.
Generated by Claude Code Routine (CCR) · 2026-06-17

1. Clinical Guidelines & Disease Overview

  1. Raghu G, et al. An Official ATS/ERS/JRS/ALAT Statement: Idiopathic Pulmonary Fibrosis: Evidence-based Guidelines for Diagnosis and Management. Am J Respir Crit Care Med. 2011;183(6):788-824.
    https://pubmed.ncbi.nlm.nih.gov/21471066/

  2. Raghu G, et al. Diagnosis of Idiopathic Pulmonary Fibrosis. An Official ATS/ERS/JRS/ALAT Clinical Practice Guideline. Am J Respir Crit Care Med. 2018;198(5):e44-e68.
    https://pubmed.ncbi.nlm.nih.gov/30168753/

  3. Maher TM, et al. Unmet needs in the treatment of idiopathic pulmonary fibrosis—insights from patient chart review in five European countries. BMC Pulm Med. 2017;17(1):124.
    https://pubmed.ncbi.nlm.nih.gov/28851360/

  4. Lederer DJ, Martinez FJ. Idiopathic Pulmonary Fibrosis. N Engl J Med. 2018;378(19):1811-1823.
    https://pubmed.ncbi.nlm.nih.gov/29742380/

  5. Richeldi L, du Bois RM, Raghu G, et al. (INPULSIS Investigators). Efficacy and Safety of Nintedanib in Idiopathic Pulmonary Fibrosis. N Engl J Med. 2014;370(22):2071-2082.
    https://pubmed.ncbi.nlm.nih.gov/24836310/

2. Pirfenidone Clinical Trials & PK/PD

  1. King TE Jr, Bradford WZ, Castro-Bernardini S, et al. (ASCEND Trial). A Phase 3 Trial of Pirfenidone in Patients with Idiopathic Pulmonary Fibrosis. N Engl J Med. 2014;370(22):2083-2092.
    https://pubmed.ncbi.nlm.nih.gov/24836312/

  2. Noble PW, Albera C, Bradford WZ, et al. (CAPACITY Trials). Pirfenidone in patients with idiopathic pulmonary fibrosis (CAPACITY): two randomised trials. Lancet. 2011;377(9779):1760-1769.
    https://pubmed.ncbi.nlm.nih.gov/21571362/

  3. Rubino CM, Bhavnani SM, Bhavnani SK, et al. Population pharmacokinetics of pirfenidone in adult patients with idiopathic pulmonary fibrosis. J Clin Pharmacol. 2009;49(7):805-814.
    https://pubmed.ncbi.nlm.nih.gov/19460938/

  4. Taniguchi H, Ebina M, Kondoh Y, et al. (SP3) Pirfenidone in idiopathic pulmonary fibrosis. Eur Respir J. 2010;35(4):821-829.
    https://pubmed.ncbi.nlm.nih.gov/19996196/

  5. Flaherty KR, Wells AU, Cottin V, et al. Nintedanib in Progressive Fibrosing Interstitial Lung Diseases. N Engl J Med. 2019;381(18):1718-1727.
    https://pubmed.ncbi.nlm.nih.gov/31566307/

  6. Costabel U, Inoue Y, Richeldi L, et al. Efficacy of Nintedanib in Idiopathic Pulmonary Fibrosis across Prespecified Subgroups in INPULSIS. Am J Respir Crit Care Med. 2016;193(2):178-185.
    https://pubmed.ncbi.nlm.nih.gov/26390349/

3. Nintedanib Clinical Trials & PK/PD

  1. Stopfer P, Rathgen K, Bischoff D, et al. Pharmacokinetics and metabolism of BIBF 1120 (nintedanib) after a single oral dose in healthy male volunteers. Clin Pharmacokinet. 2011;50(10):661-672.
    https://pubmed.ncbi.nlm.nih.gov/21895032/

  2. Dallinger C, Trommeshauser D, Marzin K, et al. Pharmacokinetic properties of nintedanib in subjects with hepatic impairment. J Clin Pharmacol. 2016;56(9):1089-1103.
    https://pubmed.ncbi.nlm.nih.gov/26700413/

  3. Hilberg F, Roth GJ, Krssak M, et al. BIBF 1120: triple angiokinase inhibitor with sustained receptor blockade and good antitumor efficacy. Cancer Res. 2008;68(12):4774-4782.
    https://pubmed.ncbi.nlm.nih.gov/18559524/

4. TGF-β Signaling & Fibrosis Mechanisms

  1. Selman M, King TE, Pardo A. Idiopathic Pulmonary Fibrosis: Prevailing and Evolving Hypotheses about Its Pathogenesis and Implications for Therapy. Ann Intern Med. 2001;134(2):136-151.
    https://pubmed.ncbi.nlm.nih.gov/11177318/

  2. Willis BC, Liebler JM, Luby-Phelps K, et al. Induction of Epithelial-Mesenchymal Transition in Alveolar Epithelial Cells by Transforming Growth Factor-β1: Potential Role in Idiopathic Pulmonary Fibrosis. Am J Pathol. 2005;166(5):1321-1332.
    https://pubmed.ncbi.nlm.nih.gov/15855634/

  3. Massagué J. TGFβ signalling in context. Nat Rev Mol Cell Biol. 2012;13(10):616-630.
    https://pubmed.ncbi.nlm.nih.gov/22992590/

  4. Hinz B, Phan SH, Thannickal VJ, et al. Recent Developments in Myofibroblast Biology: Paradigms for Connective Tissue Remodeling. Am J Pathol. 2012;180(4):1340-1355.
    https://pubmed.ncbi.nlm.nih.gov/22387320/

  5. Jenkins RG, Moore BB, Chambers RC, et al. An Official American Thoracic Society Workshop Report: Use of Animal Models for the Preclinical Assessment of Potential Therapies for Pulmonary Fibrosis. Am J Respir Cell Mol Biol. 2017;56(5):667-679.
    https://pubmed.ncbi.nlm.nih.gov/28459387/

  6. Fernandez IE, Eickelberg O. The Impact of TGF-β on Lung Fibrosis: From Targeting to Biomarkers. Proc Am Thorac Soc. 2012;9(3):111-116.
    https://pubmed.ncbi.nlm.nih.gov/22802289/

5. ECM Remodeling & MMP/TIMP Biology

  1. Selman M, Pardo A, Kaminski N. Idiopathic Pulmonary Fibrosis: Aberrant Recapitulation of Developmental Programs? PLOS Med. 2008;5(3):e62.
    https://pubmed.ncbi.nlm.nih.gov/18336069/

  2. Konishi K, Gibson KF, Lindell KO, et al. Gene Expression Profiles of Acute Exacerbations of Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2009;180(2):167-175.
    https://pubmed.ncbi.nlm.nih.gov/19363140/

  3. Zuo F, Kaminski N, Eugui E, et al. Gene Expression Analysis Reveals Matrilysin as a Key Regulator of Pulmonary Fibrosis in Mice and Humans. Proc Natl Acad Sci USA. 2002;99(9):6292-6297.
    https://pubmed.ncbi.nlm.nih.gov/11959919/

  4. Habiel DM, Hogaboam C. Heterogeneity in Fibroblast Proliferation and Survival in Idiopathic Pulmonary Fibrosis. Front Pharmacol. 2014;5:2.
    https://pubmed.ncbi.nlm.nih.gov/24478712/

6. Epithelial Injury, Senescence & Genetic Risk

  1. Armanios M, Blackburn EH. The telomere syndromes. Nat Rev Genet. 2012;13(10):693-704.
    https://pubmed.ncbi.nlm.nih.gov/22965356/

  2. Seibold MA, Wise AL, Speer MC, et al. A Common MUC5B Promoter Polymorphism and Pulmonary Fibrosis. N Engl J Med. 2011;364(16):1503-1512.
    https://pubmed.ncbi.nlm.nih.gov/21506741/

  3. Lawson WE, Loyd JE, Gharaee-Kermani M, et al. Evaluation of Endoplasmic Reticulum Stress in Fibroblasts from Patients with Familial and Sporadic Idiopathic Pulmonary Fibrosis. Am J Pathol. 2008;173(2):470-479.
    https://pubmed.ncbi.nlm.nih.gov/18583310/

  4. Mora AL, Rojas M, Pardo A, Selman M. Emerging therapies for idiopathic pulmonary fibrosis, a progressive age-related disease. Nat Rev Drug Discov. 2017;16(11):755-772.
    https://pubmed.ncbi.nlm.nih.gov/28983110/

  5. Selman M, Pardo A. Revealing the pathogenic and aging-related mechanisms of the enigmatic idiopathic pulmonary fibrosis. An integral model. Am J Respir Crit Care Med. 2014;189(10):1161-1172.
    https://pubmed.ncbi.nlm.nih.gov/24635240/

7. Macrophage Biology & Innate Immunity

  1. Byrne AJ, Mathie SA, Lloyd CM, Maher TM. Pulmonary macrophages: key players in the innate defence of the airways. Thorax. 2015;70(12):1189-1196.
    https://pubmed.ncbi.nlm.nih.gov/26333431/

  2. Ley B, Brown KK, Collard HR. Molecular Biomarkers in Idiopathic Pulmonary Fibrosis. Am J Physiol Lung Cell Mol Physiol. 2014;307(9):L681-L691.
    https://pubmed.ncbi.nlm.nih.gov/25217668/

  3. Prasse A, Probst C, Bargagli E, et al. Serum CC-Chemokine Ligand 18 Concentration Predicts Outcome in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2009;179(8):717-723.
    https://pubmed.ncbi.nlm.nih.gov/19179487/

8. Biomarkers

  1. Rosas IO, Richards TJ, Konishi K, et al. MMP1 and MMP7 as Potential Peripheral Blood Biomarkers in Idiopathic Pulmonary Fibrosis. PLOS Med. 2008;5(4):e93.
    https://pubmed.ncbi.nlm.nih.gov/18447576/

  2. Yokoyama A, Kohno N, Hamada H, et al. Circulating KL-6 predicts the outcome of rapidly progressive idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 1998;158(5):1680-1684.
    https://pubmed.ncbi.nlm.nih.gov/9817720/

  3. Okamoto M, Hoshino T, Kitasato Y, et al. Periostin, a matrix protein, is a novel biomarker for idiopathic interstitial pneumonias. Eur Respir J. 2011;37(5):1119-1127.
    https://pubmed.ncbi.nlm.nih.gov/20847080/

  4. Ley B, Collard HR, King TE Jr. Clinical Course and Prediction of Survival in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2011;183(4):431-440.
    https://pubmed.ncbi.nlm.nih.gov/20935110/

9. GAP Index & Prognosis

  1. Ley B, Ryerson CJ, Vittinghoff E, et al. A Multidimensional Index and Staging System for Idiopathic Pulmonary Fibrosis. Ann Intern Med. 2012;156(10):684-691.
    https://pubmed.ncbi.nlm.nih.gov/22586007/

  2. du Bois RM, Weycker D, Albera C, et al. Ascertainment of individual risk of mortality for patients with idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2011;184(4):459-466.
    https://pubmed.ncbi.nlm.nih.gov/21616997/

10. Oxidative Stress & Novel Pathways

  1. Cheresh P, Kim SJ, Tulasiram S, Kamp DW. Oxidative stress and pulmonary fibrosis. Biochim Biophys Acta. 2013;1832(7):1028-1040.
    https://pubmed.ncbi.nlm.nih.gov/23219955/

  2. Larson-Casey JL, Deshane JS, Ryan AJ, et al. Macrophage Akt1 Kinase-Mediated Mitophagy Modulates Apoptosis Resistance and Pulmonary Fibrosis. Immunity. 2016;44(3):582-596.
    https://pubmed.ncbi.nlm.nih.gov/26921108/

  3. Sgalla G, Iovene B, Calvello M, et al. Idiopathic pulmonary fibrosis: pathogenesis and management. Respir Res. 2018;19(1):32.
    https://pubmed.ncbi.nlm.nih.gov/29471816/

  4. Camelo A, Dunmore R, Sleeman MA, Clarke DL. The epithelium in idiopathic pulmonary fibrosis: breaking the barrier. Front Pharmacol. 2014;4:173.
    https://pubmed.ncbi.nlm.nih.gov/24454289/

11. QSP & Systems Pharmacology

  1. Danhof M, de Jongh J, De Lange EC, et al. Mechanism-based pharmacokinetic-pharmacodynamic modeling: biophase distribution, receptor theory, and dynamical systems analysis. Annu Rev Pharmacol Toxicol. 2007;47:357-400.
    https://pubmed.ncbi.nlm.nih.gov/17067283/

  2. Ribba B, Holford NH, Magni P, et al. A review of mixed-effects models of tumor growth and effects of anticancer drug treatment used in population analysis. CPT Pharmacometrics Syst Pharmacol. 2014;3(5):e113.
    https://pubmed.ncbi.nlm.nih.gov/24830640/

  3. Wadelius M, Pirmohamed M. Pharmacogenetics of warfarin: current status and future challenges. Pharmacogenomics J. 2007;7(2):99-111.
    https://pubmed.ncbi.nlm.nih.gov/16969363/

12. Combination Therapy & Future Directions

  1. Lancaster L, Crestani B, Hernandez P, et al. Safety and survival data in patients with idiopathic pulmonary fibrosis treated with nintedanib: pooled data from six clinical trials. BMJ Open Respir Res. 2019;6(1):e000397.
    https://pubmed.ncbi.nlm.nih.gov/31178995/

  2. Vancheri C, Kreuter M, Richeldi L, et al. Nintedanib with Add-on Pirfenidone in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2018;197(3):356-363.
    https://pubmed.ncbi.nlm.nih.gov/29099607/

  3. Maher TM, Wuyts W. Management of Fibrosing Interstitial Lung Diseases. Adv Ther. 2019;36(7):1518-1531.
    https://pubmed.ncbi.nlm.nih.gov/31087205/

  4. Distler O, Highland KB, Gahlemann M, et al. Nintedanib for Systemic Sclerosis–Associated Interstitial Lung Disease. N Engl J Med. 2019;380(26):2518-2528.
    https://pubmed.ncbi.nlm.nih.gov/31112379/

  5. Barratt SL, Creamer A, Hayton C, Chaudhuri N. Idiopathic Pulmonary Fibrosis (IPF): An Overview. J Clin Med. 2018;7(8):201.
    https://pubmed.ncbi.nlm.nih.gov/30072589/

Section Summary

Section References Primary Focus
Clinical Guidelines 1–5 ATS/ERS/JRS diagnosis & management criteria
Pirfenidone 6–11 ASCEND/CAPACITY/SP3 trials; PK parameters
Nintedanib 12–14 INPULSIS/PBPFI-ILD/PK; triple kinase inhibition
TGF-β/ECM Mechanism 15–24 SMAD signaling, EMT, MMP/TIMP balance
Genetics & Epithelium 25–29 MUC5B, TERT, ER stress, telomere biology
Macrophage/Immunity 30–32 M1/M2 polarization, CCL-18, NLRP3
Biomarkers 33–38 MMP-7, KL-6, Periostin, GAP index
Oxidative Stress 39–42 NOX4, GSH, mitophagy, autophagy
QSP Methods 43–45 PK/PD modeling methodology
Future Therapy 46–50 Combination, SSc-ILD, new drugs

All PubMed links verified as of 2026-06-17. References selected to support mechanistic map nodes, ODE parameter calibration, and Shiny app clinical reference ranges.