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| Status |
Public on Jul 28, 2021 |
| Title |
Recurrence biomarkers of triple negative breast cancer treated with neoadjuvant chemotherapy combined with anti-EGFR antibodies [Agilent] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
To find metastatic recurrence biomarkers of triple negative breast cancer (TNBC) treated by neoadjuvant chemotherapy and anti-EGFR antibodies (NAT), we evaluated tumor genomic, transcriptomic and immune features, using MSK-IMPACT assay, gene arrays, Nanostring technology and TIL assessment on H&E. Six patients experienced a rapid fatal recurrence (RR) and other 6 had later non-fatal recurrences (LR). Before NAT, RR had low expression of 6 MHC class I and 13 MHC class II genes but were enriched in upregulated genes involved in the cell cycle-related pathways. Their TIL number before NAT in RR was very low (<5%) and did not increase after treatment. In post-NAT residual tumors, RR cases showed high expression of SOX2 and CXCR4. Our results indicate that high expression of cell cycle genes, combined with cold immunological phenotype, may predict strong TNBC resistance to NAT and rapid progression after it. This biomarker combination is worth validation in larger studies.
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| Overall design |
Nucleic acids were extracted from frozen tumor tissue (pre-NAT samples) using AllPrep DNA/RNA mini kit (Qiagen France SAS, Courtaboeuf, France) according to the manufacturer’s protocol. RNA quality was verified using the 2100 BioAnalyzer (Agilent Technologies). The extracted material was sent to Helixio (Saint-Beauzire, France), where it was hybridized with gene arrays (Human SurePrint, Agilent Technologies France, Les Ullis, France).
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| Contributor(s) |
Scaltriti M, Reis-Filho JS, Radosevic-Robin N, Zhu Y |
| Citation(s) |
34535679 |
| Submission date |
Jul 25, 2021 |
| Last update date |
Oct 13, 2021 |
| Contact name |
Yingjie Zhu |
| Organization name |
Memorial Sloan Kettering Cancer Center
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| Street address |
1275 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL13607 |
Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version) |
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| Samples (41)
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| Relations |
| BioProject |
PRJNA749501 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE180775_RAW.tar |
510.6 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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