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Phenomapping of Patients with Primary Breast Cancer Using Machine Learning-Based Unsupervised Cluster Analysis. J Pers Med 2021; 11:jpm11040272. [PMID: 33916398 PMCID: PMC8067194 DOI: 10.3390/jpm11040272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Primary breast cancer (PBC) is a heterogeneous disease at the clinical, histopathological, and molecular levels. The improved classification of PBC might be important to identify subgroups of the disease, relevant to patient management. Machine learning algorithms may allow a better understanding of the relationships within heterogeneous clinical syndromes. This work aims to show the potential of unsupervised learning techniques for improving classification in PBC. A dataset of 712 women with PBC is used as a motivating example. A set of variables containing biological prognostic parameters is considered to define groups of individuals. Four different clustering methods are used: K-means, self-organising maps, hierarchical agglomerative (HAC), and Gaussian mixture models clustering. HAC outperforms the other clustering methods. With an optimal partitioning parameter, the methods identify two clusters with different clinical profiles. Patients in the first cluster are younger and have lower values of the oestrogen receptor (ER) and progesterone receptor (PgR) than patients in the second cluster. Moreover, cathepsin D values are lower in the first cluster. The three most important variables identified by the HAC are: age, ER, and PgR. Unsupervised learning seems a suitable alternative for the analysis of PBC data, opening up new perspectives in the particularly active domain of dissecting clinical heterogeneity.
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Liu Y, Wang Y, Zhou L, Yin K, Yin W, Lu J. Prognostic effect of menstrual cycle on timing of surgery in premenopausal breast cancer patients. Am J Surg 2015; 210:506-11. [PMID: 26066864 DOI: 10.1016/j.amjsurg.2015.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/30/2014] [Accepted: 01/07/2015] [Indexed: 01/18/2023]
Abstract
BACKGROUND It is controversial whether surgery during different menstrual phases (a kind of host milieu may influence biological characteristics of micrometastatic foci) affects clinical outcomes. METHODS Survival outcomes were compared between patients who underwent surgery during the follicular (cycle days 1 to 14) and luteal (days 15 to 31) phases. A range of cutoff days from day 10 to 22 was used to observe the risk trend. RESULTS The follicular phase was associated with a more favorable prognosis than the luteal phase in disease-free survival (DFS) [hazard ratio (HR) .318, 95% confidence interval (CI) .10 to .99, P = .049] and overall survival (OS) (HR .260, 95% CI .07 to .92, P = .036). Similar results were detected when the cutoff day was set at days 14, 18, and 19 in DFS and days 11, 13, and 14 in OS. A low HR flat fluctuation was observed from cutoff days 10 to 22, and the risk went up thereafter for both DFS and OS. CONCLUSION Surgery performed during the follicular phase provides a more favorable prognosis compared with the luteal phase.
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Affiliation(s)
- Yu Liu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yaohui Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liheng Zhou
- Department of Breast Surgery, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Kai Yin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenjin Yin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Jinsong Lu
- Department of Breast Surgery, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200127, China.
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Markićević M, Džodić R, Buta M, Kanjer K, Mandušić V, Nešković-Konstantinović Z, Nikolić-Vukosavljević D. Trefoil factor 1 in early breast carcinoma: a potential indicator of clinical outcome during the first 3 years of follow-up. Int J Med Sci 2014; 11:663-73. [PMID: 24843314 PMCID: PMC4025164 DOI: 10.7150/ijms.8194] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/15/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND A role of an estrogen-regulated, autocrine motogenic factor was assumed to be a major biological role of trefoil factor 1 (TFF1) in breast cancer. TFF1 is regarded as a predictive factor for positive response to endocrine therapy in breast cancer patients. The aim of our study was to examine TFF1 level distribution in breast carcinomas in order to distinguish estrogen-independent from estrogen-dependent TFF1 expression and to evaluate clinical usefulness of TFF1 status in early breast cancer during the first 3 years of follow-up. METHODS The study included 226 patients with primary operable invasive early breast carcinomas for whom an equal, a 3-year follow-up was conducted. TFF1 levels as well as estrogen receptor (ER) and progesterone receptor (PR) levels were measured in cytosolic extracts of tumor samples by immunoradiometric assay or by use of classical biochemical method, respectively. Non-parametric statistical tests were applied for data analyses. RESULTS Statistical analysis revealed that TFF1 levels were significantly higher in premenopausal patients (p=0.02), or in tumors with: lower histological grade (p<0.001), positive ER or PR status (p<0.001, in both cases). On the basis of TFF1 level distribution between ER-negative and ER-positive postmenopausal patients with tumors of different histological grade, 14 ng/mg was set as the cut-off value to distinguish estrogen-independent from estrogen-dependent TFF1 expression in breast cancer. Depending on menopausal and PR status, positive TFF1 status identified patients at opposite risk for relapse among ER-positive patients with grade II tumors. Among ER- and PR-positive premenopausal patients with grade II tumors, TFF1 status alone identified patients at opposite risk for relapse. CONCLUSIONS Determination of TFF1 status might identify patients at different risk for relapse and help in making decision on administering adjuvant therapy for early breast cancer patients during the first 3 years of follow-up.
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Affiliation(s)
- Milan Markićević
- 1. Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Radan Džodić
- 2. Surgical Oncology Clinic, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia; ; 3. University of Belgrade School of Medicine, Dr Subotića 8, 11000 Belgrade, Serbia
| | - Marko Buta
- 2. Surgical Oncology Clinic, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Ksenija Kanjer
- 1. Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Vesna Mandušić
- 4. Vinča Institute of Nuclear Science, Mike Petrovića Alasa 12-14, 11000 Belgrade, Serbia
| | - Zora Nešković-Konstantinović
- 5. Clinic of Medical Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Dragica Nikolić-Vukosavljević
- 1. Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
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Corte MD, Tamargo F, Alvarez A, Rodríguez JC, Vázquez J, Sánchez R, Lamelas ML, González LO, Allende MT, García-Muñiz JL, Fueyo A, Vizoso F. Cytosolic levels of TFF1/pS2 in breast cancer: Their relationship with clinical-pathological parameters and their prognostic significance. Breast Cancer Res Treat 2005; 96:63-72. [PMID: 16267614 DOI: 10.1007/s10549-005-9041-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2005] [Accepted: 07/27/2005] [Indexed: 12/14/2022]
Abstract
BACKGROUND The Trefoil Factor 1 (TFF1/pS2), a peptide consisting of 60 amino acids, is the most abundant estrogen-induced messenger RNA present in MCF-7 breast cancer cells. The objective of this work was to evaluate the cytosolic TFF1 content in breast carcinomas, its possible relationship with different clinical-pathological parameters, and its potential prognostic significance and predictive value. METHODS Cytosolic TFF1 levels were examined by immunoradiometric assay in 1031 patients with invasive breast cancer. The median follow-up period was of 50 months. RESULTS There was a wide variability of cytosolic TFF1 levels in tumors (0.9-743.2 ng/mg protein). Statistical analysis showed that TFF1 levels were significantly higher in premenopausal patients (p = 0.001), as well as in tumors showing any of the following characteristics: good differentiation (p = 0.0001), ER and PgR positivity (p = 0.0001 and p = 0.001, respectively), diploidy (p = 0.045) and a high S-phase fraction (p = 0.001). In addition, the presence of high intratumoral TFF1 levels (cut-off: 2 ng/mg protein) was independently associated with a shorter overall survival in the group of patients as a whole (p = 0.001) as well as in the subgroup with node-negative breast cancer (p = 0.0004). Likewise, high intratumoral TFF1 levels were associated with a more prolonged overall survival in patients who received adjuvant tamoxifen (p = 0.004). CONCLUSIONS In breast cancer patients, intratumoral TFF1 levels are associated with a better clinical outcome, especially in those with node-negative tumors. In addition, TFF1 levels have a low but significant predictive value in regards to response to adjuvant therapy with tamoxifen.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Breast Neoplasms/therapy
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/therapy
- Carcinoma, Lobular/metabolism
- Carcinoma, Lobular/pathology
- Carcinoma, Lobular/therapy
- Combined Modality Therapy
- Cytosol/metabolism
- Female
- Flow Cytometry
- Follow-Up Studies
- Humans
- Immunoradiometric Assay
- Middle Aged
- Neoplasm Invasiveness/pathology
- Premenopause
- Prognosis
- Receptors, Estrogen/metabolism
- Receptors, Progesterone/metabolism
- Survival Rate
- Trefoil Factor-1
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Maria D Corte
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
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Rochefort H, Rouayrenc J, Roger P. Cathepsin D in Breast Cancer—20 Years Later. Breast Cancer 2002. [DOI: 10.1201/b14039-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Suzumori N, Ozaki Y, Ogasawara M, Suzumori K. Increased concentrations of cathepsin D in peritoneal fluid from women with endometriosis. Mol Hum Reprod 2001; 7:459-62. [PMID: 11331669 DOI: 10.1093/molehr/7.5.459] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To assess the release of the proteolytic enzyme cathepsin D in endometriosis, concentrations in peritoneal fluid and serum were measured by ELISA in 54 women with (n = 33) and without (n = 21) endometriosis. Surgery was scheduled in either the proliferative or secretory phase of the menstrual cycle. The concentrations of cathepsin D in the peritoneal fluid were markedly elevated in the endometriosis patients (median 58 ng/ml, interquartile range 0-166 ng/ml) as compared to the controls (5 ng/ml, 0-86 ng/ml), especially in women with late stage disease (n = 19, stages III/IV) and in those not undergoing gonadotrophin-releasing hormone (GnRH) agonist therapy (n = 15). No significant difference was determined in cathepsin D concentrations of the serum from women with and without endometriosis. We conclude that cathepsin D is an important factor that may contribute to the pathogenesis of endometriosis, possibly by promoting digestion of extracellular matrix proteins. These results have implications for the therapeutic efficacy of GnRH agonists.
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Affiliation(s)
- N Suzumori
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya, Japan.
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Pujol P, Daures JP, Brouillet JP, Chang S, Rouanet P, Bringer J, Grenier J, Maudelonde T. A prospective prognostic study of the hormonal milieu at the time of surgery in premenopausal breast carcinoma. Cancer 2001. [DOI: 10.1002/1097-0142(20010515)91:10<1854::aid-cncr1206>3.0.co;2-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Roger P, Daures JP, Maudelonde T, Pignodel C, Gleizes M, Chapelle J, Marty-Double C, Baldet P, Mares P, Laffargue F, Rochefort H. Dissociated overexpression of cathepsin D and estrogen receptor alpha in preinvasive mammary tumors. Hum Pathol 2000; 31:593-600. [PMID: 10836299 DOI: 10.1053/hp.2000.6687] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The role of estrogen as a promoter agent of sporadic breast cancer has been considered by assaying, in benign breast disease (BBD) and in situ carcinomas (CIS), 2 markers, the estrogen receptor alpha (ERalpha) and cathepsin D (cath-D) involved in estrogen action on mammary tissue. ERalpha and cath-D were assayed by quantitative immunohistochemistry using an image analyzer in 170 lesions of varying histological risk (94 BBD and 76 CIS), and in "normal" glands close to these lesions. The ERalpha level increased significantly in proliferative BBD with atypia (P < .001), in non-high-grade CIS (P < .001), and in adjacent "normal" glands. ERalpha level was decreased in high-grade ductal CIS (DCIS) and also in adjacent "normal" glands. Cath-D level increased in ductal proliferative BBD (P < or = .01) and in high-grade DCIS (P < or = .003), but not in the other lesions. After menopause, ERalpha level was increased (P = .012) but not cath-D level. According to Mac Neman test, the high-grade DCIS were predominantly ERalpha negative and cath-D positive (P = .0017), and the other CIS were predominantly ERalpha positive and cath-D negative (P = .0002). The 2 markers are overexpressed early in premalignant lesions, but independently. This dissociation suggests a branched model of mammary carcinogenesis involving 1 estrogen-independent pathway with high cath-D and low ERalpha levels (including high-grade DCIS) and 1 estrogen-dependent pathway, with high ERalpha level (including proliferative BBD with atypia and low-grade DCIS). We propose that ERalpha-negative breast cancers may develop directly from high-grade DCIS and that ERalpha assay in preinvasive lesions should be considered in prevention trials with antiestrogens.
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Affiliation(s)
- P Roger
- Unité Hormones et Cancer (U 148) Inserm, Montpellier, France
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9
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Rochefort H, Garcia M, Glondu M, Laurent V, Liaudet E, Rey JM, Roger P. Cathepsin D in breast cancer: mechanisms and clinical applications, a 1999 overview. Clin Chim Acta 2000; 291:157-70. [PMID: 10675721 DOI: 10.1016/s0009-8981(99)00226-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A short review of the literature first confirms the clinical value of cathepsin D as a prognostic marker in breast cancer, when using well standardized assays. We then summarize results of studies, mostly performed in our laboratory, aimed at understanding the effect of cathepsin D overexpression on metastasis and the molecular mechanisms involved. Cathepsin D-cDNA transfection increases tumor cell proliferation in vitro and the metastatic potential of 3Y1-Ad12 embryonic rat tumorigenic cells when injected in vivo into nude mice. The mechanism by which cathepsin D increases the incidence of clinical metastasis involves increased cell growth and decreased contact inhibition rather than escape of cancer cells through the basement membrane. Different mechanisms are considered to explain this mitogenic activity. Cathepsin D could act as a protease following its activation at an acidic pH, or as a ligand of different membrane receptors at a more neutral pH. In this case cathepsin D can displace IGFII from the mannose-6-phosphate/IGFII receptor to the IGFI receptor or activate another membrane receptor to be identified. The nature of the mechanisms involved in vivo may depend on the micro environment of the tumor cells. These studies should guide in the development of new therapies aimed at inhibiting the deleterious effect of overexpressed cathepsin D.
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Affiliation(s)
- H Rochefort
- Faculté de Médecine, Université de Montpellier 1, Unité Hormones and Cancer (U 148), 60, rue de Navacelles, 34090, Montpellier, France.
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10
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Dooley W. Surgery in breast cancer. Curr Opin Oncol 1999; 11:447-62. [PMID: 10550008 DOI: 10.1097/00001622-199911000-00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This year (1999) has been filled with new information on the prevention of breast cancer and new literature trying to address some of the long-term adverse consequences of our surgical therapies. As the complexities of our therapies continue to increase at exponential rates, we now also have the ability to more accurately predict the consequences of both our therapeutic actions and our failure to act. Nowhere is this more evident than in the literature devoted to long-term consequences of treatment for breast cancer. As we are more successful in achieving our goals of increased survival from this dreaded disease, the future needs of these long-term survivors must play an ever-increasing role in our current management. Advances reported this year are laying down a new basis for efforts to improve the quality of life for breast cancer survivors.
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Affiliation(s)
- W Dooley
- Johns Hopkins Oncology Center, Baltimore, Maryland 21287, USA.
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