HTAPP_Acquisition and allocation of fresh metastatic breast cancer sample. v1

Author(s):  
Karla Helvie ◽  
Laura DelloStritto ◽  
Lori Marini ◽  
Nelly Oliver ◽  
Miraj Patel ◽  
...  

This standard operating procedure was established by the Center for Cancer Genomics at Dana-Farber Cancer Institute, the Brigham and Women's Hospital and the Klarman Cell Observatory at the Broad Institute, to standardize the collection of fresh metastatic breast cancer biopsies and their allocation to various bulk and single cell assays, including whole exome and bulk RNA-sequencing, single-cell RNA sequencing, and spatial profiling of RNA and protein. The use of a well defined workflow has allowed us to generate high quality data from these different assays, by implementing efficient modes of communication, minimizing the time elapsed from sample collection to preservation or processing, and ensuring optimal transportation conditions. Visual Abstract

2021 ◽  
Author(s):  
Karla Helvie ◽  
Laura DelloStritto ◽  
Lori Marini ◽  
Nelly Oliver ◽  
Miraj Patel ◽  
...  

This standard operating procedure was established by the Center for Cancer Genomics at Dana-Farber Cancer Institute, the Brigham and Women's Hospital and the Klarman Cell Observatory at the Broad Institute, to standardize the collection of fresh metastatic breast cancer biopsies and their allocation to various bulk and single cell assays, including whole exome and bulk RNA-sequencing, single-cell RNA sequencing, and spatial profiling of RNA and protein. The use of a well defined workflow has allowed us to generate high quality data from these different assays, by implementing efficient modes of communication, minimizing the time elapsed from sample collection to preservation or processing, and ensuring optimal transportation conditions. Visual Abstract


2013 ◽  
Vol 8 ◽  
pp. 9 ◽  
Author(s):  
Kristine Raaby Jakobsen ◽  
Emilie Sørensen ◽  
Karin Kathrine Brøndum ◽  
Tina Fuglsang Daugaard ◽  
Rune Thomsen ◽  
...  

2018 ◽  
Vol 5 (12) ◽  
pp. 1801158 ◽  
Author(s):  
Jialang Zhuang ◽  
Yongjian Wu ◽  
Liang Chen ◽  
Siping Liang ◽  
Minhao Wu ◽  
...  

2014 ◽  
Vol 9 (4) ◽  
pp. 749-757 ◽  
Author(s):  
Marta Pestrin ◽  
Francesca Salvianti ◽  
Francesca Galardi ◽  
Francesca De Luca ◽  
Natalie Turner ◽  
...  

Nature ◽  
2015 ◽  
Vol 526 (7571) ◽  
pp. 131-135 ◽  
Author(s):  
Devon A. Lawson ◽  
Nirav R. Bhakta ◽  
Kai Kessenbrock ◽  
Karin D. Prummel ◽  
Ying Yu ◽  
...  

2019 ◽  
Vol 21 (1) ◽  
pp. 170 ◽  
Author(s):  
József Á. Balog ◽  
László Hackler Jr. ◽  
Anita K. Kovács ◽  
Patrícia Neuperger ◽  
Róbert Alföldi ◽  
...  

The treatment of metastatic breast cancer remained a challenge despite the recent breakthrough in the immunotherapy regimens. Here, we addressed the multidimensional immunophenotyping of 4T1 metastatic breast cancer by the state-of-the-art single cell mass cytometry (CyTOF). We determined the dose and time dependent cytotoxicity of cisplatin on 4T1 cells by the xCelligence real-time electronic sensing assay. Cisplatin treatment reduced tumor growth, number of lung metastasis, and the splenomegaly of 4T1 tumor bearing mice. We showed that cisplatin inhibited the tumor stroma formation, the polarization of carcinoma-associated fibroblasts by the diminished proteolytic activity of fibroblast activating protein. The CyTOF analysis revealed the emergence of CD11b+/Gr-1+/CD44+ or CD11b+/Gr-1+/IL-17A+ myeloid-derived suppressor cells (MDSCs) and the absence of B220+ or CD62L+ B-cells, the CD62L+/CD4+ and CD62L+/CD8+ T-cells in the spleen of advanced cancer. We could show the immunomodulatory effect of cisplatin via the suppression of splenic MDSCs and via the promotion of peripheral IFN-γ+ myeloid cells. Our data could support the use of low dose chemotherapy with cisplatin as an immunomodulatory agent for metastatic triple negative breast cancer.


2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 10527-10527
Author(s):  
Nicole Margo Grogan ◽  
Yi-Mi Wu ◽  
Dan R. Robinson ◽  
James M. Rae ◽  
Norah Lynn Henry ◽  
...  

10527 Background: Among patients with early-stage breast cancer, approximately 6-10% have a pathogenic germline variant (PGV) conferring inherited cancer predisposition. In contrast, few studies have explored the frequency and types of PGVs identified in patients with metastatic breast cancer (MBC); therefore, additional data is needed. Methods: From 2011-2020, 278 patients with MBC underwent fresh tumor biopsy and blood sample collection for paired tumor/normal DNA (targeted exome capture with analysis of 1700 genes) and RNA (tumor transcriptome) sequencing through the Michigan Oncology Sequencing (Mi-ONCOSEQ) program. Somatic and germline alterations were annotated and classified according to degree of clinical actionability with results returned to treating oncologists. Retrospective chart review was performed to determine if: 1) a PGV was identified prior to Mi-ONCOSEQ testing, 2) patients met National Comprehensive Cancer Network (NCCN) guideline criteria for genetic testing on the basis of personal or family cancer history and 3) patients received subsequent therapy informed by a PGV. Results: Forty-eight of the 278 patients (17.3%) had at least one PGV identified, with a total of 50 PGVs identified in this cohort. Only twelve of these PGVs (24%) had been identified prior to Mi-ONCOSEQ testing. The most frequent PGVs identified were in CHEK 2 (n = 9, 18%), MUTYH (n = 6, 12%), BRCA 1 (n = 5, 10%), BRCA2 (n = 5, 10%), ATM (n = 4, 8%) and PALB2 (n = 4, 8%). Somatic loss of heterozygosity events (LOH) occurred in 30 of the 50 cases with PGVs identified (60%). LOH events were observed in 83.3% of BRCA1, BRCA2, ATM and PALB2 PGVs, but were less frequently observed with CHEK2 (33.3%) and MUTYH (66.7%). Two hundred sixteen out of 278 patients (77.7%) in this cohort met NCCN criteria for genetic testing, although six patients with a PGV identified (CHEK2: n = 5; MUTYH: n = 1) did not meet NCCN criteria. Twenty-nine PGVs identified (58%) had potential therapeutic relevance and 11 patients (22.9%) received targeted therapy based on the PGV. Conclusions: The frequency of PGVs identified in this cohort is nearly double the frequency reported for patients with early-stage disease, suggesting that certain PGVs may confer worse prognosis. CHEK2, the most frequently identified PGV, was less likely to have an identifiable LOH event. The direct role of CHEK2 PGVs in tumor pathogenesis is uncertain, but other mechanisms of silencing the wild type allele must be considered. Despite the majority of patients meeting NCCN criteria for genetic testing, those with PGVs in CHEK2 were less reliably identified by this mechanism. The majority of PGVs identified were of potential therapeutic relevance, supporting the recommendation for genetic testing in all patients with MBC.


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