Dataset Information

Multi-omics sequencing reveals the signature of the genome, cell composition and transcriptome of nodal RDD [ST]

ABSTRACT: RDD is a poorly understood disease with low incidence. Here, we performed whole genome sequencing, single cell RNA-seq and spatial transcriptome sequencing of a nodal RDD, describing its cell composition, spatial arrangement and molecular characteristics from a multi-omics perspective. By integrating single cell RNA-seq data, we found that compared with lymph node and LCH, RDD harbors completely different cell composition and molecular feature. Compared with lymph node, a subset of ion-responded macrophage appeared in RDD. Compared with LCH, macrophages in RDD are enriched for RHO GTPase pathway. And RHO GTPase high macrophages have unique cell-cell interactions and are the most actively proliferating cells in RDD. Our results provide a valuable insight for understanding the molecular basis of nodal RDD.

ORGANISM(S): Homo sapiens

PROVIDER: GSE263860 | GEO | 2025/04/16

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Head and neck squamous cell carcinoma (HNSCC) often present with locoregional or distant disease, despite multimodal therapeutic approaches, which include surgical resection, chemoradiotherapy, and more recently immunotherapy for metastatic, or recurrent HNSCC. Therapies often target the primary and nodal regional HNSCC sites, and efficacy at controlling occult distant sites remains poor. Whilst our understanding of the tumour microenvironment, conducive for effective therapies is increasing, the biology underpinning locoregional sites remains unclear. Here, we applied targeted spatial proteomic approaches to primary and lymph node metastasis from an oropharyngeal SCC (OPSCC) cohort, to understand the expression of proteins within tumour, and stromal compartments of the respective sites in both matched and unmatched patients’ samples. In unmatched analyses of n=43 primary and 11 nodal metastasis, our data indicated that tumour cells in nodal metastases had higher levels of Ki-67, PARP, BAD and cleaved caspase 9, suggesting a role for increased proliferation, DNA repair and apoptosis within these metastatic cells. Conversely, in matched analyses (n=7), pro-apoptotic markers BIM and BAD were enriched in the stroma of primary tumours. Univariate, overall survival (OS) analysis indicated CD25 in tumour regions of primary tumours to be associated with reduced survival (HR=3.3, p=0.003), while partial response (PR) was associated with an improved OS (HR=0.33, p=0.015). This study highlights the utility of spatial proteomics for delineating tumour and stroma compartment composition, and the utility towards understanding these properties in locoregional metastasis. These findings indicate the unique biological properties of lymph node metastases that may elucidate further understanding of the subsequent distant metastatic potential of OPSCC. In this dataset, we applied GeoMx DSP protein profiling to tumour and tumour microenvironment regions of primary and lymphnode metastasis FFPE samples. The files here represent the Ncounter readout from this assay.

Dataset Information

Multi-omics sequencing reveals the signature of the genome, cell composition and transcriptome of nodal RDD [ST]

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets