Ht 12 v3

SLC7A8 gene copy number and gene expression were evaluated using the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort of invasive BC (n = 1980) [17 (link)]. In this study, DNA/RNA was isolated from fresh frozen samples and transcriptional profiling was acquired using the Illumina HT-12v3 platforms. Data were pre-processed and normalised as described previously [17 (link)]. Patients involved in the study who were Oestrogen Receptor-negative (ER-) and Lymph Node (LN)-positive received adjuvant chemotherapy, while ER+ and/or LN− patients did not receive adjuvant chemotherapy. Dichotomisation of SLC7A8 mRNA was achieved using X-tile (version 3.6.1, Yale University, USA), based on prediction of Breast Cancer Specific Survival (BCSS). SLC7A8 mRNA expression was associated with clinicopathological parameters, molecular subtypes and patient outcome.
The online dataset, Breast Cancer Gene-Expression Miner v4.0 (https://bcgenex.centregauducheau.fr), was used for external validation of SLC7A8 mRNA expression.

Breast cancer patients were all treated at Nottingham University Hospitals between 1998 and 2006. Patients underwent a wide local excision or mastectomy, decided by disease characteristics or patient choice, followed by radiotherapy if indicated. Nottingham Prognostic Index (NPI), ER and menopausal status determined if patients received systemic adjuvant treatment. Patients with an NPI score less than 3.4 did not receive adjuvant treatment, and patients with an NPI score of 3.4 and above were candidates for CMF combination chemotherapy (cyclophosphamide, methotrexate and 5‐fluorouracil) if they were ER‐negative or pre‐menopausal; and hormonal therapy if they were ER‐positive.
PKA mRNA expression and PP‐1 mRNA expression were determined in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) data set (n = 1980).²² DNA and RNA were isolated from samples and hybridized to the Affymetrix SNP 6.0 and Illumina HT‐12 v3 platforms for genomic and transcriptional profiling as described by Curtis et al.²² Tumours were collected by five centres in the UK and Canada between 1977 and 2005, and almost all ER‐negative and lymph node–positive patients received adjuvant chemotherapy, whereas ER‐positive and/or lymph node–positive patient did not. No patients with HER2 overexpression received trastuzumab.

The microarray (Illumina HT12 v3, United States) of GCA patients of Severance Hospital (Republic of Korea, Seoul, from 2000 to 2010, IRB 4–2016-0013) was analyzed for the effects and the associations of molecular markers [15 (link)]. A pathologist and surgeon both confirmed the Lauren classification and tumor size. TNM staging was designated according to the AJCC 8th edition. Histology was divided into Moderately-differentiated (MD), Poorly-differentiated (PD), Signet-ring carcinoma (SRC), Well-differentiated (WD).

METABRIC-normalized Illumina HT12v3 data were downloaded from the European Bioinformatics Institute, quantile-normalized, and corrected for age [27 (link)]. Samples were stratified as TNBC or receptor-positive as follows: samples with negative expression of ER, PR, and Her2, as reported by Curtis et al. [27 (link)] in the columns “ER.Expr,” “PR.Expr”, and “Her2.Expr,” respectively, and not classified as luminal A, luminal B, or Her2 by PAM50 subtyping, also reported by Curtis et al. [27 (link)], were labeled TNBC (n = 276); all other samples were labeled receptor-positive (n = 1698). PRKCQ expression was extracted and log expression was compared in the TNBC and receptor-positive samples using the one-sided Student t test.

Details of the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) data set (n = 1980) data set have been published elsewhere^{27 (link)}. Tumours were collected by five centres in the UK and Canada between 1977–2005 and almost all ER negative and lymph node positive patients received adjuvant chemotherapy, whereas ER negative and/or lymph node positive patient did not. No patients with HER2 overexpression received trastuzumab. Median follow-up was 141 months determined using the reverse Kaplan-Meier method. DNA and RNA were isolated from samples and hybridised to the Affymetrix SNP 6.0 and Illumina HT-12 v3 platforms for genomic and transcriptional profiling as described by Curtis et al. (2012)^{27 (link)}. This cohort was used to assess the prognostic significance of DARPP-32 at the mRNA level and determine associations with other genes using artificial neural network analysis.