Case report: Tracing in parallel the salivary and gut microbiota profiles to assist Larotrectinib anticancer treatment for NTRK fusion-positive glioblastoma

Abstract

Oncotherapy can shape intestinal microbiota, which, in turn, may influence therapy effectiveness. Furthermore, microbiome signatures during treatments can be leveraged for the development of personalised therapeutic protocols in cancer treatment based on the identification of microbiota profiles as prognostic tools. Here, for the first time, the trajectory of gut and salivary microbiota in a patient treated with Larotrectinib, a targeted therapy approved for diagnosed glioblastoma multiforme neurotrophic tyrosine receptor kinase (NTRK) gene fusion-positive, has been accurately investigated. We based our analyses on histological diagnosis, genomic and epigenomic profiling of tumour DNA, and faecal and salivary full-length 16S rRNA gene sequencing. The study clearly evidenced a remodelling of the bacterial communities following 1 month of the NTRK-inhibitor treatment, at both gut and oral levels. We reported a boosting of specific bacteria also described in response to other chemotherapeutic approaches, such as Enterococcus faecium, E. hirae, Akkermansia muciniphila, Barnesiella intestinihominis, and Bacteroides fragilis. Moreover, several bacterial species were similarly modulated upon Larotrectinib in faecal and saliva samples. Our results suggest a parallel dynamism of microbiota profiles in both body matrices possibly useful to identify microbial biomarkers as contributors to precision medicine in cancer therapies.

Keywords: NTRK-gene fusion; full-length 16S rRNA gene sequencing; glioblastoma multiforme; oncotherapy; saliva and feces microbiota profiles.

Figure 1

Timeline experiment. A 66-year-old man diagnosed with a high-grade glioma underwent a right temporal craniotomy with a gross total resection: the histological diagnosis was a glioblastoma. The next-generation sequencing fusion panel identified an NTRK2 gene fusion (left-side figure). After the neurosurgical intervention, the patient received the Stupp protocol, a standard treatment as the first line with radio- and chemotherapy based on temozolomide. Due to neurological symptoms, the patient started a second-line therapy with Larotrectinib. Faecal and salivary samples were collected at the beginning of the treatment and the follow-up was done after 1 month.

Figure 2

Gut microbial communities’ arrangement at the genus level. (A) The taxon bar chart shows the relative abundance (%) of the 30 predominant bacteria at the genus level before and after treatment. (B) List of genera selected from the 30 most abundant ones with a log₂ fold change of at least ±2. For each genus, the percentage of its relative abundance before and after treatment, the log₂ fold change, and the species annotation are reported. The log₂ fold change has been calculated as the difference between the log₂ of the after-treatment relative abundance (%) and the log₂ of the before-treatment relative abundance (%). The corresponding species were selected considering from all the species identified only those contributing at least 10% to the variation of the corresponding genus. Green and red bars represent a positive and negative fold change to the baseline, respectively.

Figure 3

Impact of Larotrectinib intake on bacterial species within the gut and salivary microbiota. (A) Subset of species sorted out from the 484 overall identified in the gut microbiota by applying a cutoff criterion of a log₂ fold change of at least ±3. (B) Subset of species sorted out from the 265 overall identified in the salivary microbiota by applying a cutoff criterion of a log₂ fold change of at least ±2. For each species featured, the percentage of its relative abundance before and after treatment and the log₂ fold change are presented. The log₂ fold change has been calculated as the difference between the log₂ of the after-treatment relative abundance (%) and the log₂ of the before-treatment relative abundance (%). Green and red bars represent a positive and negative fold change to the baseline, respectively.

Figure 4

Intersectional analysis of the gut and salivary microbiota. Venn diagrams showing the species shared before and after treatment at the gut level and within the salivary microbiota, independently. On the right side, the Venn diagram present the shared species between the gut and the salivary microbiota at the two different experimental time points.