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Related Experiment Video

Updated: Dec 29, 2025

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Microscaled proteogenomic methods for precision oncology.

Shankha Satpathy¹, Eric J Jaehnig², Karsten Krug³

¹Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. shankha@broadinstitute.org.

Nature Communications

|January 29, 2020

Summary

This summary is machine-generated.

This study introduces a new proteogenomics method for small cancer biopsies, enabling detailed analysis of ERBB2 positive breast cancer treatment response and resistance mechanisms.

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Area of Science:

Proteomics
Genomics
Cancer Biology

Background:

Proteogenomics integrates multi-omics data for cancer insights.
Current methods require large sample inputs, limiting clinical application.

Purpose of the Study:

To develop and demonstrate a tissue-sparing proteogenomics approach for core biopsies.
To analyze ERBB2 positive breast cancer response to neoadjuvant chemotherapy.

Main Methods:

Developed a microscaled proteomics workflow for core needle biopsies.
Analyzed ERBB2 positive breast cancer biopsies before and after trastuzumab therapy.

Main Results:

Observed greater ERBB2 and mTOR pathway suppression in complete responders.
Identified resistance mechanisms including lack of ERBB2 amplification, androgen receptor signaling, mucin overexpression, and an inactive immune microenvironment.

Conclusions:

Biopsy-scale proteogenomics is clinically valuable and facilitates discovery.
This approach can reveal mechanisms of treatment resistance in breast cancer.