scholarly journals Iterative Variable Selection for High-Dimensional Data: Prediction of Pathological Response in Triple-Negative Breast Cancer

Mathematics ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 222
Author(s):  
Juan C. Laria ◽  
M. Carmen Aguilera-Morillo ◽  
Enrique Álvarez ◽  
Rosa E. Lillo ◽  
Sara López-Taruella ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Variable Selection ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
A Priori ◽  
Simulated Data ◽  
Point Of View ◽  
High Dimensional ◽  
Whole Genome ◽  
Genome Context

Over the last decade, regularized regression methods have offered alternatives for performing multi-marker analysis and feature selection in a whole genome context. The process of defining a list of genes that will characterize an expression profile remains unclear. It currently relies upon advanced statistics and can use an agnostic point of view or include some a priori knowledge, but overfitting remains a problem. This paper introduces a methodology to deal with the variable selection and model estimation problems in the high-dimensional set-up, which can be particularly useful in the whole genome context. Results are validated using simulated data and a real dataset from a triple-negative breast cancer study.

Triple negative breast cancer: a study from the point of view of basal CK5/6 and HER-1

2009 ◽  
Vol 62 (7) ◽  
pp. 624-628 ◽  
Author(s):  
S Pintens ◽  
P Neven ◽  
M Drijkoningen ◽  
V Van Belle ◽  
P Moerman ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Point Of View

scholarly journals A High-Dimensional Window into the Micro-Environment of Triple Negative Breast Cancer

Cancers ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 316
Author(s):  
Iris Nederlof ◽  
Hugo M. Horlings ◽  
Christina Curtis ◽  
Marleen Kok
Keyword(s):  
Breast Cancer ◽  
Tumor Microenvironment ◽  
Tumor Cell ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
High Dimensional ◽  
Mass Cytometry ◽  
Cell Repertoire ◽  
Cellular Phenotypes ◽  
The Impact

Providing effective personalized immunotherapy for triple negative breast cancer (TNBC) patients requires a detailed understanding of the composition of the tumor microenvironment. Both the tumor cell and non-tumor components of TNBC can exhibit tremendous heterogeneity in individual patients and change over time. Delineating cellular phenotypes and spatial topographies associated with distinct immunological states and the impact of chemotherapy will be necessary to optimally time immunotherapy. The clinical successes in immunotherapy have intensified research on the tumor microenvironment, aided by a plethora of high-dimensional technologies to define cellular phenotypes. These high-dimensional technologies include, but are not limited to, single cell RNA sequencing, spatial transcriptomics, T cell repertoire analyses, advanced flow cytometry, imaging mass cytometry, and their integration. In this review, we discuss the cellular phenotypes and spatial patterns of the lymphoid-, myeloid-, and stromal cells in the TNBC microenvironment and the potential value of mapping these features onto tumor cell genotypes.

scholarly journals Whole Genome Transcriptome Analysis of the Association between Obesity and Triple Negative Breast Cancer in Caucasian Women

2018 ◽  
Author(s):  
Tarun Mamidi ◽  
Jiande Wu ◽  
Paul B. Tchounwou ◽  
Lucio Miele ◽  
Chindo Hicks
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Postmenopausal Women ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Normal Weight ◽  
Biological Pathways ◽  
Molecular Networks ◽  
Whole Genome ◽  
Caucasian Women

Background: Triple negative breast cancer (TNBC) is the most aggressive form of breast cancer with poor outcomes. The molecular basis of TNBC remains poorly understood. The objective of this study was to explore the relationship between obesity and TNBC in premenopausal and postmenopausal Caucasian women using whole genome transcription profiling. Methods: We compared gene expression levels of tumor samples drawn from normal weight, overweight and obese in pre and postmenopausal women diagnosed with TNBC. We performed hierarchical clustering to assess similarity in patterns of gene expression profiles, and conducted network and pathway analysis to identify molecular networks and biological pathways. Results: We discovered gene signatures distinguishing normal weight from obese, normal weight from overweight and overweight from obese individuals in both premenopausal and postmenopausal women. The analysis revealed molecular networks and biological pathways dysregulated in response to obesity. Among the discovered pathways included the unfolded protein response, endoplasmatic reticulum stress, B cell receptor and the autophagy signaling pathways in obese premenopausal women and the integrin, axonal guidance, ERK/MAPK and Glutathione biosynthesis signaling pathways obese postmenopausal women. Conclusions: The results suggest that both overweight and obesity are associated with TNBC, highlighting the need for conformation of these results in independent studies.

scholarly journals Differential expression of methyltransferase METTL1 associates with death in a cohort of patients with triple negative breast cancer.

2019 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Differentially Expressed Gene ◽  
Whole Genome ◽  
Disease Course ◽  
The Third ◽  
Genome Profiling ◽  
Whole Genome Profiling

Whole genome profiling data of 226 patients with triple negative breast cancer using a published dataset (1) was stratified based on survival. When comparing the transcriptomes of 87 patients that expired versus 123 patients that survived, the methyltransferase like 1 METTL1 was the third most differentially expressed gene in the entire transcriptome. METTL1 mediates 7-methylguanosine modification of microRNAs and tRNAs (2,3,4,5,6). Increased expression of METTL1 is an indication that the disease course will likely result in fatality in patients with triple negative breast cancer and should be treated accordingly.

scholarly journals Olfactory receptors OR5B21 and OR6C76 are differentially expressed in humans with triple negative breast cancer.

2019 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Olfactory Receptor ◽  
Triple Negative ◽  
Olfactory Receptors ◽  
Differentially Expressed ◽  
Survival Outcomes ◽  
Whole Genome ◽  
Genome Profiling ◽  
Whole Genome Profiling

Whole genome profiling data of 226 patients with triple negative breast cancer (1) was stratified based on survival. When comparing the transcriptomes of 87 patients that expired versus 123 patients that survived, two olfactory receptors were among the genes whose expression was most different. We previously reported that genes of the olfactory receptor superfamily were differentially expressed in metastases in the HER2+ Balb-NeuT mouse model of breast cancer (2). The data here indicate that differential expression of OR5B21 and OR6C76 associates with survival outcomes in humans with triple negative breast cancer.

scholarly journals TRIPLE NEGATIVE BREAST CANCER, EXPERIENCE OF MILITARY HOSPITAL RABAT: ABOUT 52 CASES

2021 ◽  
Vol 9 (11) ◽  
pp. 1177-1186
Author(s):  
Moad Belouad ◽  
◽  
Abdelhamid Benlghazi ◽  
Saad Benali ◽  
Yassine Bouhtouri ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Ductal Carcinoma ◽  
Point Of View ◽  
Response To Treatment ◽  
Military Hospital ◽  
Predictive Parameters ◽  
Evolutionary Level ◽  
Cancer Experience

Objective: to review the epidemiological, clinical, anatomopathological, biological, therapeutic and prognostic characteristics of this histo-prognostic subgroup, namely triple-negative breast cancer Material and Method: Our work consists of a retrospective study carried out at the military hospital of instruction Med v rabat between January 2010 and December 2017 on 52 cases of invasive breast carcinoma with a triple negative phenotype. Result: From an epidemiological point of view: a peak in frequency was noted between 45 and 50 years old, and 48.1% of patients still in genital activity. On the anatomo-pathological level: invasive ductal carcinoma is the most predominant type representing 68.3% of cases with an average tumor size of 30mm. Histopronostic grades II and III each represent 43.2% and 56.8% of cases. Therapeutically: more than 42.3% received conservative treatment and 57.7% underwent radical surgery of the Pateytype.Adjuvant systemic chemotherapy was given in 86.5% of cases and 5.8% received neoadjuvant chemotherapy On the evolutionary level, 17.3% or 9 cases developed systemic metastases with predilection for the lungs. Conclusion: Despite advances in treatments and the emergence of targeted therapies, breast cancer remains the leading cause of death in women. Current clinical and histological classifications do not fully establish the prognostic and predictive parameters of response to treatment.

Abstract LB-267: Whole-genome and transcriptome interrogation of metastatic chemo-resistant triple negative breast cancer from African American patients

2011 ◽  
Author(s):  
David W. Craig ◽  
Joyce A. O'Shaughnessy ◽  
Jeffrey Kiefer ◽  
Tracy M. Moses ◽  
Shripad Sinari ◽  
...  
Keyword(s):  
Breast Cancer ◽  
African American ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Whole Genome

Identification of new therapeutic leads for triple negative breast cancer subtypes

Planta Medica ◽  
2015 ◽  
Vol 81 (11) ◽  
Author(s):  
AJ Robles ◽  
L Du ◽  
S Cai ◽  
RH Cichewicz ◽  
SL Mooberry
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Breast Cancer Subtypes ◽  
Cancer Subtypes ◽  
Therapeutic Leads
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