scholarly journals Integrated transcriptomic meta-analysis provides novel insights into breast cancer molecular subtypes

2021 ◽  
Author(s):  
Akhilesh Kumar Bajpai ◽  
Sravanthi Davuluri ◽  
Kavitha Thirumurugan ◽  
Kshitish K Acharya
Keyword(s):  
Breast Cancer ◽  
Signaling Pathways ◽  
Candidate Genes ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Meta Analysis ◽  
Interaction Network ◽  
Luminal A ◽  
Cancer Subtypes ◽  
Luminal B

Breast cancer is the most common cancer in women worldwide. There are four major breast cancer subtypes (luminal A, luminal B, HER2-enriched and triple-negative/TNBC). TNBC is the most aggressive form with the worst prognosis. However, the differences among the subtypes have not been completely established at the molecular level, thereby limiting therapeutic and diagnostic options for TNBC. We performed a meta-analysis of microarray and RNA-sequencing data to identify candidate genes with an expression-based association in each molecular subtype of breast cancer. The protein interaction network of the candidate genes was analyzed to discover functionally significant gene clusters and hub genes. Potential therapeutic candidates for TNBC were explored through gene-miRNA interactions. We identified 316, 347, 382, and 442 candidate genes in luminal A, luminal B, HER2 and TNBC subtypes, respectively. A total of 135 (26 up- and 109 down-regulated) candidate genes were shared by all four subtypes. Functional analysis of the candidate genes indicated up-regulation of 'cell cycle' and 'p53 signaling' pathways and down-regulation of multiple signaling pathways. COL10A1 was found to be highly up-regulated in all subtypes. It may be a good target for research towards multiple types of applications, including therapeutics. KIF4A, a commonly up-regulated X-chromosome gene was significantly associated with the survival of breast cancer patients. Protein interaction network and centrality analysis revealed that low-moderately differentially regulated genes play an important role in functional cascades across proteins in breast cancer subtypes and may be potential candidates for therapeutics. Targeting FN1 (fibronectin 1), the key up-regulated hub gene by miR-1271 5p may be an important molecular event to be targeted for potential therapeutic application in TNBC.

scholarly journals The association of women’s birth size with risk of molecular breast cancer subtypes: a cohort study

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Marie S. Sandvei ◽  
Signe Opdahl ◽  
Marit Valla ◽  
Pagona Lagiou ◽  
Ellen Veronika Vesterfjell ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Birth Weight ◽  
Breast Cancer Risk ◽  
Cancer Risk ◽  
Head Circumference ◽  
Birth Length ◽  
Birth Size ◽  
Luminal A ◽  
Cancer Subtypes ◽  
Luminal B

Abstract Background Because birth size appears to be positively associated with breast cancer risk, we have studied whether this risk may differ according to molecular breast cancer subtypes. Methods A cohort of 22,931 women born 1920–1966 were followed up for breast cancer occurrence from 1961 to 2012, and 870 were diagnosed during follow-up. Archival diagnostic material from 537 patients was available to determine molecular breast cancer subtype, specified as Luminal A, Luminal B (human epidermal growth factor receptor 2 (HER2)-), Luminal B (HER2+), HER2 type, and Triple negative (TN) breast cancer. Information on the women’s birth weight, birth length and head circumference at birth was used to estimate hazard ratios (HR) with 95% confidence intervals (CI) for each molecular subtype, applying Cox regression, and stratified by maternal height. Results Birth length (per 2 cm increments) was positively associated with Luminal A (HR = 1.2, 95% CI, 1.0–1.3), Luminal B (HER2+) (HR = 1.3, 95% CI, 1.0–1.7), and TN breast cancer (HR = 1.4, 95% CI, 1.0–1.9). No clear association was found for birth weight and head circumference. The positive associations of birth length were restricted to women whose mothers were relatively tall (above population median). Conclusion We found a positive association of birth length with risk of Luminal A, Luminal B (HER2+) and TN breast cancer that appears to be restricted to women whose mothers were relatively tall. This may support the hypothesis that breast cancer risk is influenced by determinants of longitudinal growth and that this finding deserves further scrutiny.

scholarly journals Survival of Spinal Metastasis Disease based on Immunohistochemistry Subtype of Breast Cancer: A Systematic Review and Meta-analysis

2021 ◽  
Vol 9 (F) ◽  
pp. 101-105
Author(s):  
Ivan Hugo Hadisaputra ◽  
Tjokorda Gde Bagus Mahadewa ◽  
Putu Eka Mardhika
Keyword(s):  
Breast Cancer ◽  
Systematic Review ◽  
Survival Time ◽  
Spinal Metastasis ◽  
Meta Analysis ◽  
Spinal Metastases ◽  
Luminal A ◽  
Luminal B ◽  
Moderate Growth ◽  
Her 2

BACKGROUND: Breast cancer is categorized as a slow-growth tumor in the spinal metastases disease (SMD) scoring system. Based on immunohistochemistry, breast cancer has four subtypes: Luminal A (LumA), luminal B (LumB), human epidermal growth factor 2 (Her-2) type, and triple-negative breast cancer (TNBC). TNBC has the poorest prognosis. AIM: This study aimed to describe the survival time of breast cancer with SMD based on immunohistochemistry subtypes through systematic review and meta-analysis. METHODS: This is a systematic review and meta-analysis study. This study used electronic articles published in PubMed and CENTRAL online database. We used keywords ([breast] AND [cancer] AND [spine] AND [metastasis]) to find eligible studies. Articles included were full-text studies in English. Survival time as the outcome was pooled according to the immunohistochemistry subtype of breast cancer. Statistical analysis was performed using software Stata. RESULTS: Five articles met our inclusion and exclusion criteria. LumA, LumB, Her-2 type, and TNBC have a survival time of 32.84 months, 35.20 months, 60.8 months, and 14.27 months, respectively. CONCLUSION: TNBC has the lowest survival time in the pooled analysis. We proposed TNBC be categorized as a moderate growth primary tumor.

scholarly journals Data Perturbation Independent Diagnosis and Validation of Breast Cancer Subtypes Using Clustering and Patterns

2006 ◽  
Vol 2 ◽  
pp. 117693510600200 ◽  
Author(s):  
G. Alexe ◽  
G.S. Dalgin ◽  
R. Ramaswamy ◽  
C. Delisi ◽  
G. Bhanot
Keyword(s):  
Breast Cancer ◽  
Data Perturbation ◽  
Luminal A ◽  
Cancer Subtypes ◽  
Luminal B ◽  
Molecular Stratification ◽  
Core Cluster ◽  
Therapeutic Decisions ◽  
Disease Subtypes

Molecular stratification of disease based on expression levels of sets of genes can help guide therapeutic decisions if such classifications can be shown to be stable against variations in sample source and data perturbation. Classifications inferred from one set of samples in one lab should be able to consistently stratify a different set of samples in another lab. We present a method for assessing such stability and apply it to the breast cancer (BCA) datasets of Sorlie et al. 2003 and Ma et al. 2003. We find that within the now commonly accepted BCA categories identified by Sorlie et al. Luminal A and Basal are robust, but Luminal B and ERBB2+ are not. In particular, 36% of the samples identified as Luminal B and 55% identified as ERBB2+ cannot be assigned an accurate category because the classification is sensitive to data perturbation. We identify a “core cluster” of samples for each category, and from these we determine “patterns” of gene expression that distinguish the core clusters from each other. We find that the best markers for Luminal A and Basal are (ESR1, LIV1, GATA-3) and (CCNE1, LAD1, KRT5), respectively. Pathways enriched in the patterns regulate apoptosis, tissue remodeling and the immune response. We use a different dataset (Ma et al. 2003) to test the accuracy with which samples can be allocated to the four disease subtypes. We find, as expected, that the classification of samples identified as Luminal A and Basal is robust but classification into the other two subtypes is not.

scholarly journals Ki-67 (30-9) scoring and differentiation of Luminal A- and Luminal B-like breast cancer subtypes

2019 ◽  
Vol 178 (2) ◽  
pp. 451-458 ◽  
Author(s):  
Giuseppe Viale ◽  
Amy E. Hanlon Newell ◽  
Espen Walker ◽  
Greg Harlow ◽  
Isaac Bai ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Breast Cancer Subtypes ◽  
Luminal A ◽  
Ki 67 ◽  
Cancer Subtypes ◽  
Luminal B

Response to neoadjuvant chemotherapy and outcome based on breast cancer subtype

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e11516-e11516
Author(s):  
A. Guerrero-Zotano ◽  
J. Gavila ◽  
M. A. Climent ◽  
M. J. Juan ◽  
V. Guillem ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Neoadjuvant Chemotherapy ◽  
Breast Cancer Subtypes ◽  
Nuclear Staining ◽  
Luminal A ◽  
Long Term Outcome ◽  
Cancer Subtypes ◽  
Luminal B ◽  
Her 2

e11516 Background: Gene expression profiling identifies several breast cancer subtypes with different chemosensitivity and outcome. We used immunohistochemistry surrogate markers to classify tumors according to known breast cancer subtypes and examined the relationship between neoadjuvant chemotherapy (NAC) response and long-term end points, including distant disease-free survival (DDFS) and overall survival (OS). Methods: Review of clinical and pathological data from 271 breast cancer patients treated in our institution with NAC between 1991–2008. Breast cancer subtypes were defined as follows: Luminal A: Estrogen receptor positive (ER+) and/or progesterone peceptor positive (PR+), human epidermal growth factor receptor 2-positive (Her-2+); Luminal B: ER+ and/or PR+,Her-2+; Basal: ER-,PR-,Her-2-;HER2: ER-,PR-,Her-2 +. ER and PR positive scored as positive if tumor cell nuclear staining was at least 2+. Her-2 scored as positive if test DAKO scored 3+ or FISH ratio Her-2/CEP-17>2.2. Results: 121 (45.8%) patients were classifed as Luminal A; 22 (8.1%) as Luminal B; 75 (27.7%) as Basal, and 50 (18.5%) as HER2. Most patients (63%) received NAC based on anthracyclines and taxanes. 36% Her-2+ patients were treated with NAC based on trastuzumab, and 43% received trastuzumab as adjuvant treatment. Response and outcome results are shown below (Table). Independently from subtype, only four patients out of 58 with pCR relapsed. Among patients who didn´t achieved pathologic complete response (pCR), basal and HER2 subtypes have the worst outcome (4 years SG 80% and 72% respectevely) compared with Luminal A (4 years SG: 94.7%), (log-rank p=0.009). Conclusions: Basal and HER2 tumor despite high chemosensitivity have worst long term outcome, particularly if pCR is not achieved after NAC. [Table: see text] No significant financial relationships to disclose.

Epigenetic aspects of triple-negative in patients with breast cancer.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 1041-1041
Author(s):  
Joaquina Martínez-Galan ◽  
Sandra Rios ◽  
Juan Ramon Delgado ◽  
Blanca Torres-Torres ◽  
Jesus Lopez-Peñalver ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Dna Methylation ◽  
Triple Negative ◽  
Breast Cancer Subtype ◽  
Regulation Of Gene Expression ◽  
Breast Cancer Subtypes ◽  
Luminal A ◽  
Cancer Subtypes ◽  
Luminal B

1041 Background: Identification of gene expression-based breast cancer subtypes is considered a critical means of prognostication. Genetic mutations along with epigenetic alterations contribute to gene-expression changes occurring in breast cancer. However, the reproducibility of differential DNA methylation discoveries for cancer and the relationship between DNA methylation and aberrant gene expression have not been systematically analysed. The present study was undertaken to dissect the breast cancer methylome and to deliver specific epigenotypes associated with particular breast cancer subtypes. Methods: By using Real Time QMSPCR SYBR green we analyzed DNA methylation in regulatory regions of 107 pts with breast cancer and analyzed association with prognostics factor in triple negative breast cancer and methylation promoter ESR1, APC, E-Cadherin, Rar B and 14-3-3 sigma. Results: We identified novel subtype-specific epigenotypes that clearly demonstrate the differences in the methylation profiles of basal-like and human epidermal growth factor 2 (HER2)-overexpressing tumors. Of the cases, 37pts (40%) were Luminal A (LA), 32pts (33%) Luminal B (LB), 14pts (15%) Triple-negative (TN), and 9pts (10%) HER2+. DNA hypermethylation was highly inversely correlated with the down-regulation of gene expression. Methylation of this panel of promoter was found more frequently in triple negative and HER2 phenotype. ESR1 was preferably associated with TN(80%) and HER2+(60%) subtype. With a median follow up of 6 years, we found worse overall survival (OS) with more frequent ESR1 methylation gene(p>0.05), Luminal A;ESR1 Methylation OS at 5 years 81% vs 93% when was ESR1 Unmethylation. Luminal B;ESR1 Methylation 86% SG at 5 years vs 92% in Unmethylation ESR1. Triple negative;ESR1 Methylation SG at 5 years 75% vs 80% in unmethylation ESR1. HER2;ESR1 Methylation SG at 5 years was 66.7% vs 75% in unmethylation ESR1. Conclusions: Our results provide evidence that well-defined DNA methylation profiles enable breast cancer subtype prediction and support the utilization of this biomarker for prognostication and therapeutic stratification of patients with breast cancer.

First results of the prospective Neoadjuvant Breast Registry Symphony Trial (NBRST).

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e22117-e22117
Author(s):  
Pat W. Whitworth ◽  
Mark Gittleman ◽  
Stephanie Akbari ◽  
Lisette Stork ◽  
Femke De Snoo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Endocrine Therapy ◽  
Complete Response ◽  
Adjuvant Endocrine Therapy ◽  
Excision Biopsy ◽  
Luminal A ◽  
Cancer Subtypes ◽  
Luminal B ◽  
Prior Therapy ◽  
Basal Type

e22117 Background: Classification into molecular subtypes may be important for the selection of therapy for patients with early breast cancer. Previous analyses had shown that breast cancer subtypes have distinct clinical outcome (Sorlie, PNAS 2001; Esserman, BCRT 2011). The aim of the prospective NBRST study is to measure chemosensitivity as defined by pathological Complete Response (pCR), or endocrine sensitivity as defined by partial response (PR) and metastasis-free survival in molecular subgroups. Methods: The study includes women aged 18–90 with histologically proven breast cancer, who are scheduled to start neo-adjuvant chemotherapy (CT) or neo-adjuvant endocrine therapy (ET), and who provide written informed consent. Additional inclusion criteria include no excision biopsy or axillary dissection, no confirmed distant metastatic disease, and no prior therapy for breast cancer. Treatment is at the discretion of the physician adhering to NCCN approved regimens. 500 Patients will be enrolled. Results: 128 Patients (median age 52, range 22-79), T1-4 N0-3, had definitive surgery and the overall pCR rate was 22%.14 (11%) patients are classified as Luminal A-type (BluePrint Luminal/MammaPrint Low Risk) of whom 11 received neo-adjuvant CT; none of these patients had a pCR. While 3 patients received neo-adjuvant ET and all 3 had a PR. 47 (37%) Patients are classified as Luminal B-type (BluePrint Luminal/MammaPrint High Risk). All but 1 patient received neo-adjuvant CT and 4 (9%) had a pCR. 20 (16%) Patients are classified as BluePrint HER2-type and received neo-adjuvant CT plus Trastuzumab; 8 (40%) had a pCR. 47 (37%) Patients are classified as BluePrint Basal-type and received neo-adjuvant CT; 15 (32%) had a pCR. Of the patients with IHC/FISH HER2+ cancer 13/39 (33%) had a pCR and 6/21 (29%) of the patients with IHC/FISH triple negative breast cancer. Conclusions: We observed differences in pCR to neo-adjuvant treatment in groups stratified by BluePrint and MammaPrint. Patients with Luminal A-type breast cancer have a high response to neo-adjuvant endocrine therapy (100% PR) and no pCR to neo-adjuvant CT. While patients with BluePrint HER2-type and Basal-type breast cancer have a high pCR rate to neo-adjuvant CT. Clinical trial information: NCT01479101.

Chemosensitivity and endocrine sensitivity prediction by MammaPrint and BluePrint in the Neoadjuvant Breast Registry Symphony Trial (NBRST).

2014 ◽  
Vol 32 (26_suppl) ◽  
pp. 29-29
Author(s):  
Pat W. Whitworth ◽  
Mark Gittleman ◽  
Stephanie Akbari ◽  
Lisette Stork ◽  
Femke De Snoo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative ◽  
Pathologic Complete Response ◽  
Complete Response ◽  
Excision Biopsy ◽  
Luminal A ◽  
Neoadjuvant Endocrine Therapy ◽  
Cancer Subtypes ◽  
Luminal B ◽  
Prior Therapy

29 Background: Classification into molecular subtypes is important for the selection of therapy for patients with breast cancer. Previous analyses demonstrated that breast cancer subtypes have distinct clinical outcome (Gluck, BCRT 2013). The aim of the prospective NBRST study is to measure chemosensitivity as defined by pathologic complete response (pCR), or endocrine sensitivity as defined by partial response (PR) and metastasis-free survival in molecular subgroups. Methods: The study includes women aged 18 to 90 with histologically proven breast cancer, who are scheduled to start neoadjuvant chemotherapy (NCT) or neoadjuvant endocrine therapy (NET), and who provide written informed consent. Additional inclusion criteria include no excision biopsy or axillary dissection, no confirmed distant metastatic disease, and no prior therapy for breast cancer. Treatment is at the discretion of the physician adhering to NCCN approved regimens. Results: Of 336 patients, T1-4 N0-3, had definitive surgery and the overall pCR rate was 24%. 32/167 (19%) IHC/FISH ERPR+/Her2- patients were reclassified by BluePrint (31 Basal). 43/95 (45%) IHC/FISH Her2+ patients were reclassified by BluePrint (25 Luminal and 18 Basal). 3/74 (3%) IHC/FISH triple-negative patients were not Basal by BluePrint. Of 45 (13%) patients classified as Luminal A 32 received NCT; one patient (3%) had a pCR; 13 patients received NET and 9 (70%) had a PR. Of 116 (35%) patients classified as Luminal B, 111 received NCT and seven (6%) had a pCR. The pCR rate (17/149 (11%)) in IHC/FISH ERPR+/HER2- patients was higher. Fifty-five (16%) are BluePrint HER2 and received NCT (51 plus trastuzumab); 27 (49%) had a pCR compared to 35/95 (37%) in IHC/FISH HER2+ patients. One-hundred twenty (36%) are BluePrint Basal and received NCT; 46 (38%) had a pCR, similar to the pCR percentage seen in the 74 patients designated triple-negative by IHC/FISH. Conclusions: Molecular subtyping using MammaPrint and BluePrint leads to a reclassification of 23% (78/336) of tumors. BluePrint reclassification resulted in better grouping of patients into expected response groups compared to local surrogate subtyping with immunostains.

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