This study brought significant innovations establishing; lung tissue bank; ILD Research Laboratory/expertise in RNA extraction, RT-PCR, immunohistochemistry and RNA sequencing analysis and interpretation; prospective, longitudinal cohort study registered at clinicaltrials.gov (NCT03836417). Study is transformative in respect to diagnostic approach to fibrosing ILD. While discussion of pathology results is standard of care, no biomarkers are currently used. Once validated, integration of spatially-resolved molecular markers into diagnostic algorithm is expected to: avoid unclassifiable cases; qualify the transcriptional relevance of smaller, less invasive (transbronchial) biopsies; match patients with appropriate treatment right from the time of diagnosis. With the need for more accurate diagnostic tools for fibrosing ILD, and the decreased cost of RNA sequencing, validated and spatially-resolved molecular markers will be applicable in numerous clinical contexts at other institutions.

The aim of study is matching patients with fibrosing interstitial lung disease (ILD) with most effective treatment right from start, improving their survival and quality of life. Fibrosing ILDs are heterogeneous group of scarring disorders of lungs (mainly including idiopathic interstitial pneumonias) causing progressive loss of lung function, shortness of breath on minimal exertion, respiratory failure and in the absence of lung transplantation, premature death. This study represented first step in introduction of molecular diagnosis techniques in diagnostic algorithm of fibrosing ILDs. Diagnostic uncertainty even after obtaining lung biopsy and lack of personalized medicine approaches are central problems in the management of these conditions. We applied for the first time digital spatial profiling (DSP) techniques to lung biopsies from patients with fibrosing ILD. DSP is an innovative computational procedure providing spatially-resolved RNA sequencing in selected areas of histology slides. We were able to correlate histologic features to transcriptional signatures, matching peculiar lung microenvironments to expression of certain genes. With this new approach genes that are not only quantitatively prominent, but also located in lung microenvironments of key biological importance were found. Identification of molecular markers biologically relevant in the most common types of fibrosing ILD will have a major impact on health care delivery, helping clarify the diagnosis of unclassifiable cases, qualify transcriptional relevance of smaller, less invasive biopsies for clinical use, and assign specific therapies to patients. Introduction of molecular markers in clinical practice will represent our measure of success. As research continues, two more grants from AMOSO and from the PSI foundation were recently awarded. Next goal is to identify and validate genetic spatially-resolved biomarkers used for diagnostic and prognostic purposes in fibrosing ILD.

https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-022-02067-w
Keow J, Cecchini M, Jayawardena N, Zompatori M, Joseph M, Mura M. Digital quantification of p16-positive foci in fibrotic interstitial lung disease identifies a senescent phenotype of idiopathic pulmonary fibrosis with reduced survival. Respiratory Research 2022:23:147
DOI: 10.1186/s12931-022-02067-w

The second manuscript “Digital spatial profiling of fibrosing ILDs” is currently being drafted.