Background Tumour Infiltrating Lymphocytes (TILs) is a modality of ACT under development in solid tumours. Unfortunately, prior lymphodepletion is a key step that frequently requires the administration of antibiotics and antifungics for long periods of time. Although there is evidence that gut microbiome may influence tumour response in patients treated with checkpoint-inhibitors, it has not been extensively studied in ACT.¹

Methods Analysis of gut microbiome at three different times (T1: before lymphodepletion, T2: before TIL infusion and T3: day +15) has been performed in patients treated with ACT between 2018 and 2020. The composition and structure of the sampled microbial communities was assessed through the amplification and sequencing the V3-V4 variable regions of the 16S rRNA gene. The Illumina Miseq sequencing 300×2 approach was used. Taxonomic assignment of phylotypes was performed using a Bayesian Classifier trained with Silva database version 132 (99% OTUs full-length sequences). The following metrics were measured: observed OTUs (community richness), evenness (Pielou’s index) and Shannon’s diversity index. Differential abundance of taxa was tested using ANCOM test and Kruskal Wallis test.

Results A total of 21 patients have been treated with TILs between 2018 and 2020 at our institution. 67% were female. Median age was 43 (range 26–70 years). All patients had stage IV pre-treated solid tumours: 55% cervical cancer, 33% melanoma, 10% lung adenocarcinoma and 5% head and neck cancer. Median previous treatment lines was 3 (range 2–4). Analysis of gut microbiome has been performed in 3 of these patients: one achieved PR, one progressed and the third one suffered an unexpected death. 971 phylotypes were detected. Analysis revealed differences in terms of observed OTUs, evenness and Shannon’s index when comparing T1 and T2 with T3. At T3 a tendency towards less diversity and evenness was observed when compared with T1 and T2 (H 3.0, p-value 0.083, not statistically significant). Comparing the distribution of considered taxa in ACT responders vs. non-responders, we observed significant differences for both class (Bacteroidia, Clostridia and Gammaproteobacteria) and order (Bacteroidales, Lactobacillales, Clostridiales and Enterobacteriales) levels.

Conclusions A deep change in gut microbiome composition along TILs therapy was observed. Though preliminary, differences between responders and non-responders were observed but should be confirmed in larger populations.

Reference

1. Gopalakrishnan V, Spencer CN, Nezi L, et al. Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Science 2018;359:97–103.