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Related Concept Videos

lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Updated: Jun 19, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Spatial Transcriptomic Profiling Reveals Gene Expression Characteristics in Lymph Node-positive Breast Carcinoma.

Yumin Chung1, Jinah Chu1, Sung-Im DO2

  • 1Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.

Anticancer Research
|July 26, 2024
PubMed
Summary

Breast cancer gene expression differs with lymph node metastasis. Spatially resolved transcriptomics revealed distinct transcriptional activities, highlighting the need for personalized treatments for breast carcinoma patients with lymph node involvement.

Keywords:
Breastinvasive carcinomalymph node metastasisspatial transcriptomicstumor microenvironment

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Area of Science:

  • Oncology
  • Genomics
  • Molecular Biology

Background:

  • Limited understanding of gene expression differences in breast carcinoma based on lymph node metastasis.
  • Need for spatially resolved transcriptomic data to differentiate node-positive and node-negative tumors.

Purpose of the Study:

  • To compare spatially resolved transcriptomic profiles between node-positive and node-negative breast carcinomas.
  • To identify key genes and pathways associated with lymph node metastasis in breast cancer.

Main Methods:

  • Digital spatial profiling and bioinformatic analysis of tumor samples from eight breast carcinoma patients.
  • Investigation of spatial transcriptomes to identify differentially expressed genes.

Main Results:

  • Upregulation of nuclear receptor subfamily 4 group A member 1 (NR4A1) and Jun proto-oncogene, activating protein-1 transcription factor subunit (JUN) in the epithelial compartment.
  • Gene ontology analysis revealed significant upregulation of myeloid differentiation, mononuclear cell differentiation, and hematopoietic regulation genes in node-positive tumors.
  • Gene set enrichment analysis showed enrichment of inflammatory cytokine regulation pathways in both epithelial and stromal compartments of node-positive breast carcinomas.

Conclusions:

  • Significant differences in gene expression and transcriptional activity exist between node-positive and node-negative breast carcinomas.
  • Findings emphasize the importance of personalized treatment strategies for breast carcinoma patients with lymph node metastasis.