Table S1.
Selected instances from literature search
| 1st author | Year | Journal | Pubmed ID | Cancer biology underpinning | Related clinical indicator | Major contribution/conclusion |
|---|---|---|---|---|---|---|
| van ’t Veer1 | 2002 | Nature | 11823860 | Gene expression patterns | Lymph node status | Provides a powerful tool to tailor adjuvant systemic treatment that could greatly reduce the cost of BC treatment. |
| Rennstam2 | 2003 | Cancer Research | 14695203 | Chromosomal copy number aberrations | Patterns of copy number gains and losses define BCs with distinct clinicopathological features and patient prognosis. | |
| Paik3 | 2004 | New England Journal of Medicine | 15591335 | Gene expression patterns | Node-negative, ER-positive, tamoxifen treatment | A novel recurrence score based on 21 genes to quantify the likelihood of distant recurrence in patients as well as overall survival time. |
| Kronenwett4 | 2006 | Cancer Epidemiology, Biomarkers and Prevention | 16985023 | Genomic stability | Objective classification of BCs into stable and unstable subtypes that are a prognostic indicator independent of established clinical factors. | |
| Bacac5 | 2006 | PLoS One | 17183660 | Stromal cells | Human genes expressed in mouse stromal response to tumor invasion predicts BC patient survival. | |
| Suh6 | 2007 | Clinical Cancer Research | 17200346 | CLIC4 (chloride intracellular channel 4) | Reactivation and restoration of CLIC4 in tumor cells or the converse in tumor stromal cells could provide a novel approach to inhibit tumor growth. | |
| Conlin7 | 2007 | Molecular Diagnosis and Therapy | 18078353 | Oncotype DX recurrence score assay | Lymph node negative, ER-expressing BC | The Oncotype DX assay and others aim to help improve risk classification and recurrence prediction and optimize selection of patients for adjuvant chemotherapy. |
| Rodriguez8 | 2008 | Carcinogenesis | 18499701 | HOXB13 (homeobox B13) and IL17BR (interleukin 17 receptor B) | Estrogen signaling | Hypermethylation of HOXB13 is a later event of tumor progression and a prognostic indicator of advanced BC. |
| Wei9 | 2008 | Molecular Carcinogenesis | 18176935 | H3K27me3 | Loss of H3K27me3 is a predictor of poor outcome in BCs. | |
| Kim10 | 2008 | Annals of Oncology | 17956886 | CDKs | Patients recruited for study underwent mastectomy or breast-conserving surgery | Tumors with high CDK1SA and high CDK2SA showed significantly poorer 5-year relapse-free survival than those with low CDK1SA and low CDK2SA, respectively. |
| Han11 | 2008 | Nature | 18337816 | SATB1 (SATB homeobox 1) | SATB1 is a genome organizer that tethers multiple genomic loci and recruits chromatin-remodeling enzymes to regulate chromatin structure and gene expression. | |
| Ben-Porath12 | 2008 | Nature Genetics | 18443585 | Stem cell genetic expression signatures | Detailed characterization of the stem-cell regulatory networks active in cancer is likely to yield powerful diagnostic and prognostic markers. | |
| Parker13 | 2009 | Journal of Clinical Oncology | 19204204 | A 50-gene set (PAM50) | “Intrinsic” subtypes, pathologic staging, histologic grade | The intrinsic subtype and risk predictors based on the PAM50 gene set adds significant prognostic and predictive value. |
| Sung14 | 2010 | Cancer Science | 20412117 | SIRT1 (sirtuin 1) and CCAR2 (also known as DBC1, deleted in breast cancer 1, KIAA1967) | Luminal subtype, ER and PR expressions | Correlation between SIRT1 and DBC1 is a more useful prognostic factor than their individual expressions. Correlation between the two is decreased in tumor cells. |
| Gevensleben15 | 2010 | International Journal of Molecular Medicine | 21042777 | 70-gene expression profile MammaPrint® | Size, age, histological grade, hormone receptor status, peritumoral vascular invasion and HER2 status | Gene signature MammaPrint® is shown to provide additional independent prognostic information. |
| Lanigan16 | 2010 | Breast Cancer Research | 20682066 | Msx2 (msh homeobox 2) | Msx2 expression results in improved outcome for BCs, possibly by increasing the likelihood of tumor cell death by apoptosis. | |
| Creighton17 | 2010 | Breast Cancer Research | 20569503 | PI3K pathway | Luminal ER+ breast tumors | Luminal B tumors have hyperactive GFR/PI3K signaling associated with lower ER levels, which has been correlated with resistance to endocrine therapy. Targeting PI3K in these tumors may reverse loss of ER expression and signaling and restore hormonal sensitivity. |
| Xu18 | 2011 | Breast Cancer Research | 21255398 | RAD21 (RAD21 homolog [S. pombe]) | N/A | RAD21 expression confers poor prognosis and resistance to chemotherapy in high-grade luminal, basal, and HER2 BCs. |
| Littlepage19 | 2012 | Cancer Discovery | 22728437 | ZNF217 (zinc finger protein 217) | Amplification of the human chromosomal region 20q13 | ZNF217 (amplified in numerous cancers) is a poor prognostic indicator and therapeutic target in patients with BC and may be a strong biomarker of triciribine treatment efficacy in patients. |
| Pitroda20 | 2012 | PLoS One | 23056240 | Endothelial inflammatory pathways | The first prognostic cancer gene signature derived from an experimental model of tumor-associated endothelial inflammation. | |
| Kim21 | 2012 | Journal of Breast Cancer | 22807942 | Gene expression patterns | Histological grade, size, number of metastatic lymph nodes, ER, lymphovascular invasion, local invasion of tumor, and number of tumors | As the selected prognostic factors can be easily obtained in clinical practice, the proposed model might prove useful in the prediction of BR recurrence. |
| Faryna22 | 2012 | FASEB Journal | 22930747 | Aberrant DNA methylation | Low-grade ER- and/or PR-positive BC | Early methylation changes are frequent in the low-grade pathway of BC and may be useful in the development of prognostic markers. |
| Fasching23 | 2012 | Human Molecular Genetics | 22532573 | TOX3 (TOX high mobility group box family member 3) | With the exception of rs3803662 (TOX3), there was no evidence that any of the SNPs associated with BC susceptibility were associated with BC survival. | |
| Huang24 | 2013 | Cell and Bioscience | 23497677 | MACC1 (metastasis associated in colon cancer 1) | Clinicopathologic features | The over expression of MACC1 in BR is significantly correlated with adverse clinicopathological features, including metastasis and patient survival. |
| Yang25 | 2013 | PLoS One | 23441166 | Mediation of transcription factor GRHL2 (grainyhead-like 2 [Drosophila]) on its targets is prognostic in BC | Histological grade | Proposed the RXA-GSP (relative expression analysis with gene-set pairs) method, shows promise as both a valid prediction model as well as high potential for clinical utility. |
| Nagata26 | 2014 | Breast Cancer | 22528804 | Induced pluripotent stem cell inducing factors | Strong expression of NANOG is an indicator of poor prognosis for BC patients, whereas KLF4 is a favorable prognostic indicator. |
Note: Each key word (genomic, transcriptional, epigenetic, sequence, novel) respectively together with “breast cancer” and “prognostic indicator” was searched in PubMed, from Jan 2005–July 2013.
Abbreviations: BC, breast cancer; ER, estrogen receptor; PAM, prediction analysis of microarray; RXA-GSP, relative expression analysis of gene set pair; SNPs, single-nucleotide polymorphisms.