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Spatial Transcriptomics Reveals Local Subtype-Specific Identity and Signaling within Multifocal Small Intestinal Neuroendocrine Tumors

ABSTRACT: Small intestinal neuroendocrine tumors (SI-NETs) frequently present as multifocal lesions, but the spatial and molecular mechanisms underlying their development and heterogeneity remain unclear. This study aimed to characterize the phenotypic subtypes of tumor cells across anatomical sites in multifocal SI-NETs and identify local microenvironmental factors influencing tumor development.

ORGANISM(S): Homo sapiens

PROVIDER: GSE301265 | GEO | 2026/02/09

REPOSITORIES: GEO

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Project description:A significant proportion of breast cancer patients develop multiple synchronous unilateral breast tumors, also referred to as multifocal tumors, which represent a diagnostic and therapeutic challenge. Multifocality has been associated with a possible adverse patient outcome, propensity for axillary nodal involvement, and increased risk of local recurrence following breast conserving surgery when compared to unifocal tumors. Previous studies indicate that most lesions from multifocal tumors are concordant with regard to the currently used pathological parameters (histological subtype and grade, hormonal receptors and HER2 status). However, to our knowledge, no study has yet provided a detailed molecular analysis of multifocal breast cancer. Here, we aimed to better define the incidence of multifocal breast cancer using a systematic analysis of pathology reports of primary breast cancers and to compare different foci from 5 multifocal breast cancers in a global analysis using genomic, transcriptomic and epigenomic data. We demonstrate that multifocality is a frequent finding since it concerns 22% (945/4340) of breast cancer patients with primary ductal breast cancer. We find that different lesions from multifocal breast cancer can differ at the (epi)genomic and transcriptomic level even when the foci present similar histology, grading, hormonal and HER2 status despite having a common genetic background. Since the number of (epi)genetic alterations with potential clinical utility is rapidly growing due to increasing numbers of targeted therapies, these findings suggest that it might be necessary to interrogate the different lesions of multifocal breast cancers for adequate treatment management of these tumors. The biological characterization of multifocal breast cancer here is focused on 5 cancers for which the foci did not differ in terms of histological grade, hormonal receptors and HER2 status. The characterization of multifocal tumors involved the identification of somatic rearrangements in 2 foci from each patient via low-coverage whole genome sequencing. Putative rearrangements were amplified by polymerase chain reaction (PCR) and capillary sequenced in tumor and matching blood-derived germline DNA to validate the somatic rearrangements. For all patients, the presence of a number of validated rearrangements was assessed in different paraffin blocks of tumor-adjacent histologically normal tissue by nested PCR. We also performed transcriptomic and epigenomic profiling in 4 and 5 patients respectively using the HG-U133 Plus 2.0 Chips and Infinium Methylation 450K arrays (RNA was not available for patient E).

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Spatial Transcriptomics Reveals Local Subtype-Specific Identity and Signaling within Multifocal Small Intestinal Neuroendocrine Tumors

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