Identifying Unique Pathogenic Macrophages in Systemic Sclerosis-ILD

Using cutting-edge single cell RNA-Seq technology, we will identify in the BAL fluid of
subjects of SSc-ILD emerging pathogenic cell populations in the lung that were previously
unrecognized using standard RNA-Seq and microarray technologies, which lack the resolution to
analyze transcriptomes of individual cells. Alveolar macrophages isolated from
bronchoalveolar lavage (BAL) fluid from SSc patients with clinically significant lung
fibrosis will be studied at baseline and at 6 months after enrollment to assess
longitudinally the presence and persistence of an emergent, pro-fibrotic alveolar macrophage
population.

Subjects with SSc-ILD will be recruited from the Scleroderma Program. We will recruit adults
who fulfill 2013 American College of Rheumatology SSc criteria and clinically relevant
SSc-interstitial lung disease. Patients will undergo bronchoscopy with bronchoalveolar lavage
at month 0 and then at month 6. Healthy control subjects will complete demographic and basic
medical forms to ensure health. Pertinent clinical data will be downloaded from the
Enterprise Data Warehouse, an electronic database in use at Northwestern that was designed to
aggregate and store patient data from various medical systems, or through manual chart
review, and entered into a RedCap database created specifically for this project.

During an elective bronchoscopy procedure in SSc and healthy control subjects the
bronchoscope will be wedged into an affected lung segment guided by CT scanning. After
wedging the bronchoscope, 120ml of sterile 0.09% normal saline will be instilled. All
subsequent aliquots will be pooled. Up to 40-60 mL of BAL fluid will be obtained for analysis
during each sampling. Alveolar macrophages will be sorted on a FACS Aria III instrument.
High-throughput single cell transcriptomic (Drop-seq) data will be processed on Northwestern
high-performance computational cluster using Cell Ranger pipeline and post-processed using
modified AltAnalyze pipeline.

Inclusion Criteria:

- forearm modified Rodnan skin scores/mRSS ≥1

- have radiographic evidence for ILD and a forced vital capacity <70% on PFT

Exclusion Criteria:

-patients currently taking immunosuppression (methotrexate, IVIg, cyclophosphamide, etc.)
in the preceding 2 months will be excluded.