
Our Interstitial Lung Disease (ILD) Biobank is dedicated to advancing translational research in fibrotic lung diseases, with a particular focus on idiopathic pulmonary fibrosis (IPF). By systematically collecting and curating high-quality biospecimens from patients with ILD, the biobank serves as a critical resource for understanding disease mechanisms, identifying biomarkers, and developing novel therapeutic strategies.
The biobank includes a comprehensive set of specimens, including bronchoalveolar lavage fluid (BALF), lung biopsy tissues, and peripheral blood samples. These samples are collected under standardized protocols and are linked with detailed clinical data, enabling integrative analyses across molecular, cellular, and clinical dimensions.
Given the progressive and heterogeneous nature of IPF, access to well-annotated patient samples is essential for uncovering disease-driving pathways, including aberrant immune responses, fibroblast activation, and extracellular matrix remodeling. Our biobank aims to support studies that explore these mechanisms and facilitate the discovery of diagnostic and prognostic biomarkers, as well as therapeutic targets.
We actively promote collaboration and welcome investigators interested in utilizing this resource to accelerate research in ILD and IPF. Through these efforts, we hope to contribute to improved patient outcomes and the development of precision medicine approaches for fibrotic lung diseases.
Research Applications
The ILD Biobank supports a wide range of advanced translational research applications aimed at understanding the molecular and cellular mechanisms underlying fibrotic lung diseases, particularly idiopathic pulmonary fibrosis (IPF). Biospecimens from the biobank are suitable for high-resolution analyses, including single-cell RNA sequencing and bulk RNA sequencing to characterize cellular heterogeneity and gene expression profiles. Spatial transcriptomics further enables the investigation of tissue architecture and cell–cell interactions within the diseased lung microenvironment. In addition, proteomics and metabolomics approaches can be applied to uncover dysregulated signaling pathways and metabolic alterations. Comprehensive immune profiling, including flow cytometry, CyTOF, and imaging mass cytometry (IMC), allows detailed characterization of immune cell populations and their functional states. These integrated approaches facilitate in-depth studies of fibrosis-related pathways, such as TGF-β signaling and PI3K/AKT signaling, ultimately contributing to the identification of novel biomarkers and therapeutic targets.

John Vang
Specialist
Publications
- Maddali MV, Pugashetti JV, Pienkos SM, Moore AR, Konkol SB, Kim JS, Ma SF, Newton CA, Garcia CK, Adegunsoye A, Strek ME, Chen CH, Linderholm AL, Zemans RL, Moore BB, Wolters PJ, Raj R, Chen JH, Martinez FJ, Noth I, Rogers AJ, Oldham JM. Molecular endotypes predict differential response to immunosuppressant therapy in non-IPF interstitial lung disease. Am J Respir Crit Care Med. 2026 Jan 30:aamag006. doi: 10.1093/ajrccm/aamag006. Epub ahead of print. PMID: 41738192.
- Oldham J, Molyneaux P, Maddali M, Newton C, Kim J, Konkol S, Pugashetti J, Liu G, Goobie G, Adegunsoye A, Ma SF, Bornstein D, Murray S, Wain L, Saini G, Stewart I, Johnson S, Jenkins G, Strek M, Linderholm A, Chen CH, Fahy W, Zemans R, Moore B, Khanna D, Ryerson C, Flaherty K, Suresh M, Hoffmann-Vold AM, Maher T, Garcia C, Wolters P, Martinez F, Noth I, Smith JA. Prioritizing Therapeutic Targets for Interstitial Lung Disease: A Causal Mediation Analysis. Res Sq [Preprint]. 2026 Feb 5:rs.3.rs-8714555. doi: 10.21203/rs.3.rs-8714555/v1. PMID: 41674845; PMCID: PMC12889817.
- Tan DBA, Stentenbach M, Bolitho E, Tedja C, Aresgado E, Chen CH, Linderholm A, Oldham J, Moodley Y; AIPFR. Let-7f-5p Has Antifibrotic Properties and Is Reduced in Circulatory Small Extracellular Vesicles in Progressive Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2025 Dec;211(12):2410-2413. doi: 10.1164/rccm.202504-0882RL. PMID: 40961262; PMCID: PMC12700245.
- Alqalyoobi S, Smith JA, Maddali MV, Pugashetti JV, Newton CA, Kim JS, Linderholm AL, Chen CH, Ma SF, Bose S, Murray S, Adegunsoye A, Strek ME, Garcia CK, Wolters PJ, Martinez FJ, Noth I, Oldham JM. Proteomic Biomarkers of Survival in Non-Idiopathic Pulmonary Fibrosis Interstitial Lung Disease. Am J Respir Crit Care Med. 2025 Aug;211(8):1452-1462. doi: 10.1164/rccm.202407-1506OC. PMID: 40208180; PMCID: PMC12369864.
- Maddali MV, Moore AR, Sinha P, Newton CA, Kim JS, Adegunsoye A, Ma SF, Strek ME, Chen CH, Linderholm AL, Zemans RL, Moore BB, Wolters PJ, Martinez FJ, Rogers AJ, Raj R, Noth I, Oldham JM. Molecular Endotypes of Idiopathic Pulmonary Fibrosis: A Latent Class Analysis of Two Multicenter Observational Cohorts. Am J Respir Crit Care Med. 2024 Jun 24. doi: 10.1164/rccm.202402-0339OC. Epub ahead of print. PMID: 38913573.
- Pugashetti JV, Kim JS, Bose S, Adegunsoye A, Linderholm AL, Chen CH, Strek ME, Flaherty KR, Murray S, Newton CA, Alqalyoobi S, Ma SF, Mychaleckyj JC, Bowler RP, Han MK, Curtis JL, Martinez FJ, Smith JA, Noth I, Oldham JM. Biological Age, Chronological Age and Survival in Pulmonary Fibrosis: A Causal Mediation Analysis. Am J Respir Crit Care Med. 2024 Jun 6. doi: 10.1164/rccm.202310-1887OC. Epub ahead of print. PMID: 38843133.
- Pugashetti JV, Kim JS, Combs MP, Ma SF, Adegunsoye A, Linderholm AL, Strek ME, Chen CH, Dilling DF, Whelan TPM, Flaherty KR, Martinez FJ, Noth I, Oldham JM. A multidimensional classifier to support lung transplant referral in patients with pulmonary fibrosis. J Heart Lung Transplant. 2024 Jul;43(7):1174-1182. doi: 10.1016/j.healun.2024.03.018. Epub 2024 Mar 29. PMID: 38556070.
- Oldham JM, Huang Y, Bose S, Ma SF, Kim JS, Schwab A, Ting C, Mou K, Lee CT, Adegunsoye A, Ghodrati S, Vu Pugashetti J, Nazemi N, Strek ME, Linderholm AL, Chen CH, Murray S, Zemans RL, Flaherty KR, Martinez FJ, Noth I. Proteomic Biomarkers of Survival in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2023 Oct 17. doi: 10.1164/rccm.202301-0117OC. Epub ahead of print. PMID: 37847691.
- Yang DC#, Hsu SW#, Li JM, Oldham J, Chen CH. Spatial Decoding of Immune Cell Contribution to Fibroblastic Foci in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2023 Jul 24. doi: 10.1164/rccm.202303-0372LE. Epub ahead of print. PMID: 37487177. Featured on the cover of the journal’s Sept. 2023 issue. #Equally contributed to this work.
- Li JM, Chang WH, Li L, Yang DC, Hsu SW, Kenyon NJ, Chen CH. Inositol possesses antifibrotic activity and mitigates pulmonary fibrosis. Respir Res. 2023 May 16;24(1):132. doi: 10.1186/s12931-023-02421-6. PMID: 37194070; PMCID: PMC10189934.
- Yang DC, Gu S, Li JM, Hsu SW, Chen SJ, Chang WH, Chen CH. Targeting the AXL Receptor in Combating Smoking-related Pulmonary Fibrosis. Am J Respir Cell Mol Biol. 2021 Jun;64(6):734-746. doi: 10.1165/rcmb.2020-0303OC. PMID: 33730527.
- Li JM, Yang DC, Oldham J, Linderholm A, Zhang J, Liu J, Kenyon NJ, Chen CH. Therapeutic targeting of argininosuccinate synthase 1 (ASS1)-deficient pulmonary fibrosis. Mol Ther. 2021 Apr 7;29(4):1487-1500. doi: 10.1016/j.ymthe.2021.01.028. Epub 2021 Jan 26.PMID: 33508432.
- Yang DC, Li JM, Xu J, Oldham J, Phan SH, Last JA, Wu R, Chen CH. Tackling MARCKS-PIP3 circuit attenuates fibroblast activation and fibrosis progression. FASEB J. 2019 Dec;33(12):14354-14369. doi: 10.1096/fj.201901705R. Epub 2019 Oct 26. PubMed PMID: 31661644; PubMed Central PMCID: PMC6894092.