Early Melanoma Invasivity Correlates With gut Fungal and Bacterial Profiles

F. Vitali; R. Colucci; M. Di Paola; M. Pindo; C. De Filippo; S. Moretti; D. Cavalieri

The British Journal of Dermatology. 2022;186(1):106-116.

Abstract and Introduction

Abstract

Background: The microbiome is emerging as a crucial player of the immune checkpoint in cancer. Melanoma is a highly immunogenic tumour, and the composition of the gut microbiome has been correlated to prognosis and evolution of advanced melanoma and proposed as a biomarker for immune checkpoint therapy.

Objectives: We investigated the gut fungal and bacterial compositions in early-stage melanoma and correlated microbial profiles with histopathological features.

Methods: Sequencing of bacterial 16S rRNA and the fungal internal transcribed spacer region was performed on faecal samples of patients with stage I and II melanoma, and healthy controls. A meta-analysis with gut microbiota data from patients with metastatic melanoma was also carried out.

Results: We found a combination of gut fungal and bacterial profiles significantly discriminating patients with melanoma from controls. In patients with melanoma, we observed an abundance of Prevotella copri and yeasts belonging to the order Saccharomycetales. We found that the bacterial and fungal community correlated to melanoma invasiveness, whereas the specific fungal profile correlated to melanoma regression. Bacteroides was identified as general marker of immunogenicity, being shared by regressive and invasive melanoma. In addition, the bacterial communities in patients with stage I and II melanoma were different in structure and richer than those from patients with metastatic melanoma.

Conclusions: The composition of the gut microbiota in early-stage melanoma changes along the gradient from in situ to invasive (and metastatic) melanoma. Changes in the microbiota and mycobiota are correlated to the histological features of early-stage melanoma, and to the clinical course and response to immune therapies of advanced-stage melanoma, through direct or indirect immunomodulation.

Introduction

Melanoma is a malignant tumour arising from melanocytes.^[1] It causes the greatest number of skin-cancer-related deaths worldwide, and despite the recent advances in therapeutic strategies, its prognosis in advanced stages remains poor.^[1] The environmental determinants of melanoma remain elusive, although a well-known risk factor is sun exposure.^[2,3]

In the past 10 years, it has become increasingly evident that in addition to our genome, health status depends on complex interactions with our symbiotic microbial community (the microbiota) and the genes and functions associated with it (the microbiome). The human microbiota is emerging as a crucial player in several types of cancer, and is an excellent predictor of the outcome of cancer immune checkpoint therapy.^[4–6] Patients with melanoma under nivolumab or pembrolizumab therapy showed a significantly higher alpha diversity and enrichment of selected microbial species positively associated with enhanced systemic or local antitumour immune reaction.^[6] A specific gut bacterial composition was found to be a predictive biomarker for the clinical outcome and the possible development of adverse gastrointestinal effects to ipilimumab treatment,^[6–10] suggesting that the gut microbiota is able to modulate both anticancer mechanisms and immune surveillance.^[11] Nevertheless, none of these studies investigated the gut fungal community. Fungi are well known for their immunogenicity traits, as recently observed in autoimmune diseases, such as Crohn disease.^[12] Moreover, neither gut bacterial nor fungal communities have yet been investigated in patients with early-stage (nonmetastatic) melanoma.

This study aimed to assess the gut bacterial and fungal community composition in a group of patients with stage I and II melanoma and to compare it with that of healthy controls. We correlated clinical and histopathological features of early-stage melanoma with the identified microbial profiles in order to discover putative microbial biomarkers. Finally, a comparison with patients with advanced-stage metastatic melanoma was achieved with a meta-analysis.

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Table 1. Results of PERMANOVA and ANOSIM tests for evaluation of the relationship between microbial community structure and histopathological parameters of melanoma
		Invasivity	Breslow	Inflammation (yes/no)	Regression (yes/no)	Mitosis
Bacteria
PERMANOVA	R ²	0.069	0.044	0.053	0.062	0.042
PERMANOVA	P-value	0.074	0.95	0.56	0.18	0.99
ANOSIM	R	0.33	–	0.071	0.073	–
ANOSIM	P-value	0.008	–	0.13	0.12	–
Fungi
PERMANOVA	R ²	0.083	0.054	0.064	0.094	0.058
PERMANOVA	P-value	0.042	0.5	0.25	0.013	0.38
ANOSIM	R	0.36	–	0.078	0.094	–
ANOSIM	P-value	0.006	–	0.1	0.074	–
Bacteria + fungi
PERMANOVA	R ²	0.071	0.045	0.055	0.066	0.043
PERMANOVA	P-value	0.039	0.94	0.48	0.095	0.98
ANOSIM	R	0.36	–	0.078	0.094	–
ANOSIM	P-value	0.006	–	0.1	0.074	–

Statistically significant P-values are shown in bold.

Table 2. Zero-radius operational taxonomic units (zOTUs) found at significantly different abundance in multiple comparisons
zOTU	Intersection	Identification	Associated with
DENOVO40\|ITS	All	Cryptococcus_fuscescens\|SH215218.06FU	In situ, no regression, melanoma
DENOVO314\|16S	Invasivity ∩ regression	Phylum Firmicutes	In situ, no regression
DENOVO55\|16S	Invasivity ∩ regression	Genus Bacteroides	Invasive, regression
DENOVO256\|16S	Invasivity ∩ regression	Genus Prevotella	In situ, no regression
DENOVO590\|16S	Invasivity ∩ regression	Genus Victivallis	In situ, no regression
DENOVO124\|ITS	Invasivity ∩ regression	Mortierella_sp\|SH218045.06FU	In situ, no regression
DENOVO31\|ITS	Invasivity ∩ regression	Mortierella_sp\|SH217983.06FU	In situ, no regression
DENOVO16\|ITS	Invasivity ∩ regression	Malasseziales_sp\|SH206221.06FU	Invasive, no regression
DENOVO27\|ITS	Invasivity ∩ melanoma control	Davidiella_tassiana\|SH196750.06FU	In situ, control
DENOVO62\|16S	Regression ∩ melanoma control	Family Clostridiales	Regression, melanoma
DENOVO42\|ITS	Regression ∩ melanoma control	Sordariomycetes_sp\|SH219629.06FU	No regression, melanoma
DENOVO14\|ITS	Regression ∩ melanoma control	Tremellomycetes_sp\|SH219359.06FU	No regression, melanoma

Table 3. BLAST identification of the bacterial zero-radius operational taxonomic units (zOTUs) found at significantly different abundance in multiple comparisons
zOTU	Hit	Identity	Query cover	E-value	Max score	Total score	Associated with
DENOVO314\|16S	Christensenella massiliensis	88.6	100	2 × 10⁻¹³⁹	494	494	In situ, no regression
DENOVO55\|16S	Bacteroides ovatus	100	100	0.0	780	780	Invasive, regression
DENOVO256\|16S	Prevotella copri	97.9	100	0.0	732	732	In situ, no regression
DENOVO590\|16S	Victivallis vadensis	93.6	100	4 × 10⁻¹⁷¹	599	599	In situ, no regression
DENOVO62\|16S	Anaerobacterium chartisolvens	88.6	99	3 × 10⁻¹³⁷	486	486	Regression, melanoma

Table 4. BLAST identification of the 10 most important zero-radius operational taxonomic units (zOTUs) in explaining the random forest classification model of patients with *in situ* and invasive melanoma
	Hit	Identity	Query cover	E-value	Max score	Total score	Enriched in
zOTU 1559	Hungateiclostridium cellulolyticum	90.1	100	3 × 10⁻¹⁴⁷	520	520	In situ
zOTU 231	Agathobaculum butyriciproducens	99.8	100	0.0	743	743	Invasive
zOTU 530	Kineothrix alysoides	97.0	100	0.0	678	678	In situ
zOTU 392	Kineothrix alysoides	98.3	100	0.0	704	704	In situ
zOTU 2266	Desulfosporosinus fructosivorans	89.0	99	6 × 10⁻¹⁵⁰	529	529	In situ
zOTU 232	Christensenella massiliensis	90.4	100	4 × 10⁻¹⁵¹	532	532	In situ
zOTU 1804	[Eubacterium] rectale	99.7	96	0.0	710	710	Invasive
zOTU 240	Intestinimonas butyriciproducens	93.1	100	2 × 10⁻¹⁶⁹	593	593	In situ
zOTU 517	Sporobacter termitidis	93.3	100	3 × 10⁻¹⁷²	603	603	In situ
zOTU 197	Saccharofermentans acetigenes	88.9	100	4 × 10⁻¹⁴¹	499	499	In situ