Integrative analysis of the tumour immune microenvironment of breast implant-associated anaplastic large cell lymphoma using multi-omics Free

Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is a recently identified T cell lymphoma that develops in women with textured breast implants and can have localised presentation (seroma-associated) or invasive disease (Stage II and above). Nevertheless, the mechanisms behind ALCL formation and the potential influence of the tumour microenvironment (TME) on ALCL's survival and growth in breast tissue remain unclear. To explore these questions, we examined the immunobiology of both ALCL and the endogenous immune cells present in both localised and invasive disease using a multimodal approach.

We conducted a multi-centre national cohort study and collected breast implant seroma samples, including benign cases and BIA-ALCL cases at surgery. We used single-cell RNA sequencing (scRNAseq) and bulk RNA sequencing to characterise immune cells and ALCL cells from both localised and invasive disease. Bulk RNA sequencing was also conducted on samples from patients with cutaneous ALCL (pcALCL). We performed TCR-seq to explore their clonal relationships. Additionally, we analysed the microenvironment by measuring seroma cytokine and chemokine levels and conducted an interactome analysis to identify potential cell-cell interactions. We also performed targeted sequencing to detect mutations and utilised spatial multiplex immunohistochemistry to examine the spatial relationships between tumour and immune cells, as well as differences between invasive and non-invasive disease.

scRNAseq data revealed that ALCL cells formed separate clusters, with distinct gene expression patterns observed between patients. ALCL cells expressed common gene signature genes such as BATF3, SERPIN family genes, TNFSFR8, and IL2RA; along with genes unique to each patient. Endogenous T cells from the BIA-ALCL seroma exhibited an activated or exhausted phenotype, along with immune checkpoints and endogenous T cell clonal expansion. In contrast, benign seroma endogenous T cells had a Th1/Th17 profile and limited T cell clonal expansion. Myeloid clusters were abundant in the BIA-ALCL seroma, but not in benign seroma. TME studies showed a significant increase in BIA-ALCL seroma for cytokines IL-13, TNF, IL-10, and secretory PDL-1. The single-cell interactome analysis using CellphoneDB revealed unique cell-cell interactions in the BIA-ALCL TME between tumour-tumour, tumour-myeloid DC, and tumour-CD8+ T effector memory cells. Mutational analysis revealed novel JAK1 mutations and STAT3 mutations along with chromosome 20 loss consistent with previous studies. Bulk RNAseq analysis revealed differences between BIA-ALCL and pcALCL with BIA-ALCL displaying a more inflamed immune TME.

BIA-ALCL cells vary between patients and from the body's own immune cells. Additionally, BIA-ALCL seroma contains endogenous T cells with an exhausted profile and clonal expansion, along with higher levels of IFN-γ and TNF, suggesting these T cells are responding to antigens in the tumour microenvironment (TME). The TME also shows increased IL-13 and IL-10 levels, produced through interactions between tumour cells and myeloid cells. Bulk RNA sequencing and spatial analysis indicated that the invasive BIA-ALCL TME is less inflamed and more immune-excluded compared to non-invasive early-stage disease. This is the first study to perform an in-depth characterisation of BIA-ALCL using a multi-omics approach, and the results enhance our understanding of this rare lymphoma, offering potential for improved treatments.