NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE242311 Query DataSets for GSE242311
Status Public on Sep 08, 2023
Title Spatial heterogeneity of integrins and their ligands in primary breast tumors
Organism Homo sapiens
Experiment type Other
Summary The diversity of cell-cell interactions in different regions of a tumor reflects the functional heterogeneity of cancer, which poses challenges in early diagnosis, selection of treatment strategies, and prognosis of breast cancer. Cancer cells interact with each other to form different morphological structures in the tumor and stromal host cells via integrins. The objective of this study was to characterize the morphological and spatial heterogeneity of primary breast tumors in the context of expression profiles of integrins and their ligands. We studied spatial transcriptomics using the 10X Visium approach and the NICHES algorithm to map ligand-receptor signaling pathways and visualize the heterogeneity of signaling archetypes in tumor clusters. Cluster analysis of the expression profiles of tumor spots from the samples indicated pronounced inter-tumoral heterogeneity. Integrin-ligand functional clusters were associated with intratumoral heterogeneity, which was manifested by the presence of several morphological loci as observed in histological tumor samples. Inter-tumoral heterogeneity was manifested by a different number of functional clusters, ranging from 2 to 9 for each tumor sample. The main characteristic of these clusters was the significant predominance of non-complementary integrin subunits. Of the 42 functional integrin-ligand pairs in 21 clusters of five samples, 41 pairs occurred only once. The exception was the LAMA5-ITGB4 pair, which was detected in two clusters of different samples. The spatial heterogeneity of integrin-ligand expression clusters in breast cancer contributes significantly to the functional heterogeneity of the tumor, which sets the stage for many scenarios of parenchymatous-stromal relationships, some of which may be effective in the emergence of metastasizing tumor seed cells. The intra- and inter-tumoral spatio-functional heterogeneity of the tumor tissue that we discovered may largely explain why it is difficult to achieve success in most patients with breast cancer using any therapeutic strategy targeting one molecule of the vast array, regardless of the importance of its pathogenetic significance.
 
Overall design Six breast cancer samples were included in this study. Spatial transcriptomics using the 10X Visium approach and the NICHES algorithm to map ligand-receptor signaling pathways and visualize the heterogeneity of signaling archetypes in tumor clusters.
 
Contributor(s) Tashireva L, Grigorieva E, Alifanov V, Iamshchikov P, Zavyalova M, Perelmuter V
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Sep 05, 2023
Last update date Sep 08, 2023
Contact name Tashireva Liubov
E-mail(s) tashireva@oncology.tomsk.ru
Organization name Tomsk National Research Medical Center
Department Cancer Research Institute
Street address 5 Kooperativny Street, Tomsk
City Tomsk
ZIP/Postal code 634050
Country Russia
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (16)
GSM7757970 breast cancer, R1-S1
GSM7757971 breast cancer, R1-S2
GSM7757972 breast cancer, R1-S3
Relations
BioProject PRJNA1013084

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE242311_R1-S31_processed_files.zip 16.9 Mb (ftp)(http) ZIP
GSE242311_R1-S32_processed_files.zip 18.1 Mb (ftp)(http) ZIP
GSE242311_R1-S51_processed_files.zip 38.2 Mb (ftp)(http) ZIP
GSE242311_R1-S52_processed_files.zip 22.8 Mb (ftp)(http) ZIP
GSE242311_R2-S51_processed_files.zip 19.8 Mb (ftp)(http) ZIP
GSE242311_R2-S52_processed_files.zip 26.7 Mb (ftp)(http) ZIP
GSE242311_R3-S21_processed_files.zip 25.1 Mb (ftp)(http) ZIP
GSE242311_R3-S22_processed_files.zip 22.5 Mb (ftp)(http) ZIP
GSE242311_RAW.tar 666.2 Mb (http)(custom) TAR (of CSV, JPG, JSON, MTX, PNG, TSV)
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap