Data and metadata supporting the published article: Skeletal muscle reprogramming by breast cancer regardless of treatment history or tumor molecular subtype.

Increased susceptibility to fatigue is a negative predictor of survival commonly experienced by women with breast cancer (BC). In this study, the authors sought to identify molecular changes induced in human skeletal muscle by BC regardless of treatment history or tumor molecular subtype using RNA-sequencing (RNA-seq) and proteomic analyses.

Data access: The processed RNA-Seq and proteomics datasets generated during this study are publicly available in the figshare repository as part of this figshare data record: https://doi.org/10.6084/m9.figshare.12248951. The dataset ClinicalCharacteristics.xlsx is not publicly available in order to protect patient privacy, but will be made available on reasonable request from the corresponding author. The patients who took part in this study, did not give consent to have their genetic data made publicly available, and therefore the raw transcriptomic and proteomics data are not publicly available. Raw RNA-Seq and proteomics data will be made available on reasonable request from the corresponding author, to researchers who have completed a Data Usage Agreement. Corresponding author details: Dr. Emidio E. Pistilli, West Virginia University School of Medicine, email address: epistilli2@hsc.wvu.edu.

Study approval and patient consent: The procedures in this study were reviewed and approved by the West Virginia University Institutional Review Board (IRB). Informed written consent was obtained from each subject or each subject’s guardian.

Study aims and methodology:

Muscle dysfunction in individuals with cancer is commonly thought to be a consequence of muscle atrophy, which is a major component of the paraneoplastic syndrome known as cancer cachexia. In this study, the authors tested the hypothesis that breast cancer induces a common molecular response in skeletal muscle that is independent of the molecular subtype of the tumor and the patient’s treatment history.

A total of 71 female surgical patients provided informed consent for inclusion in this study (control n=20; BC n=51).

Women with BC provided muscle biopsies from the pectoralis major muscle intraoperatively at the time of mastectomy, and control patients provided pectoralis major muscle samples intraoperatively during other breast surgeries. Women with BC were classified into four molecular subtypes based on immunohistochemical staining of their primary tumors:

positive for estrogen receptor (ER) and progesterone receptor (PR)- ERPR (n=20), overexpression of HER2/neu in the absence of ER and PR expression- HER2 (n=9), triple negative —absence of ER, PR, and HER2/neu expression- TN (n=11), or triple positive—presence of ER and PR expression, and overexpression of HER2/neuTP-TP (n=11).

Information on BMI at multiple time points was collected in 12 control and 50 BC patients.

The following techniques are described in more detail in the published article: RNA sequencing, proteomics (including sample preparation, mass spectrometry, and mass spectrometry analysis), Western blotting, and patient muscle ATP quantification.

Animal experiments were approved by the WVU Institutional Animal Care and Use Committee, and conducted in accordance with the Guidelines for Ethical Conduct in the Care and Use of Nonhuman Animals in Research. BC-PDOX mice were created by implanting human BC tumor fragments into the

mammary fat pad of female NOD.CG-Prkdscid Il2rgtm1 Wjl/SzJ/ 0557 (NSG) mice (n=6).

For the in vitro experiments, the following cell lines were used: EpH4-EV (immortalized normal murine mammary epithelium), EO771 (murine luminal BC), NF639 (murine HER2/neu-overexpressing BC), HEK293 (human embryonic kidney), and C2C12 (murine myoblasts).

3000pts.csv in .csv file format

AlbuminAndWeightLoss.csv in .csv file format

ATPContentHuman.xlsx in .xlsx file format

ATPContentPDOX.xlsx in .xlsx file format

ATPProduction.xlsx in .xlsx file format

GFP.xlsx in .xlsx file format

RNASeqProteomicsCorrelation.xlsx in .xlsx file format, contains log-transformed gene and protein expression data for 8 patients with matched RNA-seq and proteomics data

Supplementary Data 3.xlsx in .xlsx file format

Supplementary Data1.xlsx in .xlsx file format

Supplementary Data2.xlsx in .xlsx file format

WBdata.xlsx

Dataset ClinicalCharacteristics.xlsx contains clinical information on study patients (i.e. body composition, race, treatment history, etc.) and will be made available on request.

Figure/Supplementary table supported by the datasets listed above:

Figure 1> SupplementaryData1.xlsx

Figure 2> AlbuminAndWeightLoss.csv, 3000pts.csv

Figure 3> SupplementaryData1.xlsx

Figure 4> SupplementaryData1.xlsx

Figure 5> SupplementaryData2.xlsx, WBdata.xlsx, SupplementaryData3.xlsx

Figure 6> SupplementaryData1.xlsx, ATPContentHuman.xlsx, ATPContentPDOX, ATPProduction.xlsx,GFP.xlsx

Supplementary table 1> SupplementaryData1.xlsx

Supplementary table 2> SupplementaryData2.xlsx

Supplementary table 3> SupplementaryData3.xlsx