A Single-cell Approach to Identify Biomarkers of Pulmonary Toxicity for Immune Checkpoint Blockade

The main goal of this prospective non-interventional exploratory monocentric study is to characterize the immune cell composition of bronchoalveolar lavage (BAL) fluid from cancer patients experiencing cancer therapy-induced pneumonitis on a single-cell scale. These mechanistic insights can directly lead to putative diagnostic biomarkers and therapeutic targets.

A second highly clinically relevant hypothesis is that single-cell profiling of blood samples will reveal circulating biomarkers of ICB toxicity, making non-invasive diagnosis feasible.

Study Overview

• Status: Recruiting
• Conditions: Immunotherapy; Pneumonitis, Interstitial; Immune-related Adverse Events
• Intervention / Treatment: Drug: Immune checkpoint blockade; Radiation: Radiotherapy; Drug: Targeted therapy

Detailed Description

The investigators will apply single cell RNA- and TCR-sequencing on up to 5,000 single cells per sample. Additionally, cell surface protein expression can be integrated with the transcriptional information. Various bioinformatics pipelines, including Seurat, will be used to identify different cell clusters, which through marker gene expression will be assigned to known cell types, cellular subtypes or phenotypes. For instance, this will make it possible to monitor the abundance of PD-1/PD-L1 expressing T-cells, cytotoxic T-cells, immune-suppressive myeloid cells etc. The following parameters at single-cell level will be relevant, amongst others:

• The composition and relative abundancies of established immune cell types (e.g. T cells (CD4+, CD8+ and regulatory subsets), NK cells, B cells, MDSCs, macrophages, neutrophils, dendritic cells). Transcriptomic data for each of these immune cell subtypes will be analyzed, allowing characterization of specific gene expression programs that define specific phenotypic states.
• Composition of all stromal cellular subtypes identified by single-cell transcriptomics.
• A gene regulatory network for each cell type and cellular subtype (or cell state) will be established and master transcriptional regulators will be identified. Individual T-cells and T-cell subclusters will be classified based on interferon activation, high rates of proliferation and transcription and increased granzyme expression, which are all indicative of T-cell activation.

Blood samples will be subjected to similar single-cell experimental procedures. First, peripheral blood mononuclear cells (PBMC) are isolated using Ficoll density gradient centrifugation. Single-cell transcriptome analysis in combination with CITE-seq will be performed on 5000 PBMC. Cellular composition will be determined using the same bioinformatic pipelines as used for processing the BAL fluid cells.

• Study Type: Observational
• Enrollment (Anticipated): 60

Contacts and Locations

• Study Contact: Name: Els Wauters, MD, PhD; Phone Number: +3216340942; Email: els.wauters@uzleuven.be

Study Locations

• Belgium
  • Flemish Brabant
    • Leuven, Flemish Brabant, Belgium, 3000
      • Recruiting
      • Universitaire Ziekenhuizen Leuven
      • Contact: Els Wauters, MD, PhD; Phone Number: 016340942; Email: els.wauters@uzleuven.be

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years to 120 years (Adult, Older Adult)
• Accepts Healthy Volunteers: No
• Genders Eligible for Study: All

• Sampling Method: Non-Probability Sample

Study Population

Patients experiencing cancer-treatment induced pneumonitis, undergoing bronchoscopy with BAL

Description

Inclusion criteria:

• Adult M/F/X (>= 18 years)
• Patients receiving or having received treatment per guidelines
• Patients undergoing bronchoscopy with BAL, for possible cancer treatment-induced pneumonitis
• Not included in other clinical trials
• Signed informed consent form

Exclusion criteria:

• Collected material not suitable for further processing in this study (e.g. bad quality). This decision will be made in consultation with a lab technician and/or bio-informatician, specialized in single-cell analysis.

Study Plan

How is the study designed?

Design Details

• Observational Models: Cohort
• Time Perspectives: Prospective

Number of groups / cohorts

3

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
ICI-pneumonitis; Cancer patients experiencing ICI-pneumonitis	Drug: Immune checkpoint blockade; ICI, administered as standard-of-care treatment; Other Names: Pembrolizumab; Durvalumab
Radiotherapy induced pneumonitis; Cancer patients experiencing RT-pneumonitis	Radiation: Radiotherapy; RT, administered as standard-of-care treatment
TKI-induced pneumonitis; Cancer patients experiencing TKI-induced pneumonitis	Drug: Targeted therapy; TKI, administered as standard-of-care treatment; Other Names: TKI

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Immune cell proportions, as determined by scRNA-seq, present in ICI-/RT-/TKI-induced pneumonitis BAL fluid	By identifying and statistically comparing the percentages of immune cell subtypes present in ICI-/RT-/TKI-induced pneumonitis BAL fluid, we aim to i) understand which immune processes drive these adverse events ii) identify putative molecular biomarkers iii) identify putative therapeutic targets	From date of inclusion until study completion, on average 2 years
Differentially expressed genes in BAL fluid, as determined by scRNA-seq, discriminating ICI-/RT-/TKI-induced pneumonitis	By identifying differentially expressed genes in ICI- vs. RT- vs. TKI-induced pneumonitis BAL fluid, we aim to i) understand which immune processes drive these adverse events ii) identify putative molecular biomarkers iii) identify putative therapeutic targets	From date of inclusion until study completion, on average 2 years

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Immune cell proportions, as determined by scRNA-seq, present in ICI-/RT-/TKI-induced pneumonitis peripheral blood mononuclear cells	By identifying and statistically comparing the percentages of immune cell subtypes present in ICI-/RT-/TKI-induced pneumonitis peripheral blood mononuclear cells, we aim to i) understand which immune processes drive these adverse events ii) identify putative molecular biomarkers iii) identify putative therapeutic targets	From date of inclusion until study completion, on average 2 years
Differentially expressed genes in PBMC, as determined by scRNA-seq, discriminating ICI-/RT-/TKI-induced pneumonitis	By identifying differentially expressed genes in ICI- vs. RT- vs. TKI-induced pneumonitis PBMC, we aim to i) understand which immune processes drive these adverse events ii) identify putative molecular biomarkers iii) identify putative therapeutic targets	From date of inclusion until study completion, on average 2 years

Collaborators and Investigators

• Sponsor: Universitaire Ziekenhuizen KU Leuven
• Collaborators: KU Leuven
• Investigators: Principal Investigator: Els Wauters, MD, PhD, University Hospitals - KU Leuven

Study record dates

Study Major Dates

• Study Start (Actual): February 1, 2020
• Primary Completion (Anticipated): January 31, 2024
• Study Completion (Anticipated): January 31, 2024

Study Registration Dates

• First Submitted: March 10, 2021
• First Submitted That Met QC Criteria: March 18, 2021
• First Posted (Actual): March 19, 2021

Study Record Updates

• Last Update Posted (Actual): March 28, 2023
• Last Update Submitted That Met QC Criteria: March 27, 2023
• Last Verified: March 1, 2023

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Infections; Respiratory Tract Infections; Respiratory Tract Diseases; Lung Diseases; Pneumonia; Lung Diseases, Interstitial; Molecular Mechanisms of Pharmacological Action; Antineoplastic Agents; Antineoplastic Agents, Immunological; Durvalumab; Pembrolizumab; Immune Checkpoint Inhibitors
• Other Study ID Numbers: S63357

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No