scholarly journals Lift the Veil of Breast Cancers Using Four or Fewer Critical Genes

2021 ◽  
Author(s):  
Zhengjun Zhang
Keyword(s):  
Breast Cancer ◽  
Differentially Expressed Gene ◽  
Gene Interaction ◽  
Differentially Expressed ◽  
Biological Knowledge ◽  
Interaction Patterns ◽  
Breast Cancers ◽  
Luminal A ◽  
Cancer Study ◽  
Breast Cancer Study

Tackling breast cancer problems is like mastering a puzzle, and the mystery is not yet solved. Reported key genes in the literature could not be confirmed whether they are vital to breast cancer formations due to lack of convincing accuracy, although they may be biologically directly related to breast cancer based on present biological knowledge. It is hoped vital genes can be identified with the highest possible accuracy, e.g., 100% accuracy and convincing causal patterns beyond what has been known in breast cancer. One hope is that finding gene-gene interaction signatures and functional effects may solve the puzzle. This research uses a recently developed competing linear factor analysis method in differentially expressed gene detection to advance the study of breast cancer formation to its deepest root level as deep as possible. Surprisingly, three genes are detected to be differentially expressed in TNBC, and non-TNBC (Her2, Luminal A, Luminal B) samples with 100% sensitivity and 100% specificity in one study of triple-negative breast cancers (TNBC, with 54675 genes and 265 samples). These three genes show a clear signature pattern of how TNBC patients can be grouped. For another TNBC study (with 54673 genes and 66 samples), four genes bring the same accuracy of 100% sensitivity and 100% specificity. Four genes are found to have the same accuracy of 100% sensitivity and 100% specificity in one breast cancer study (with 54675 genes and 121 samples), and the same four genes bring an accuracy of 100% sensitivity and 96.5% specificity in the fourth breast cancer study (with 60483 genes and 1217 samples.) These results show the four-gene-based classifiers are robust and accurate. The detected genes naturally classify patients into subtypes, e.g., seven subtypes. These findings demonstrate the clearest gene-gene interaction patterns and functional effects with the smallest numbers of genes and the highest accuracy compared with findings reported in the literature. The four genes are considered to be essential for breast cancer studies and practice. They can provide focused, targeted researches and precision medicine for each subtype of breast cancer. New breast cancer disease types may be detected using the classified subtypes, and hence new effective therapies can be developed.

scholarly journals Race-associated biological differences among luminal A and basal-like breast cancers in the Carolina Breast Cancer Study

2017 ◽  
Vol 19 (1) ◽  
Author(s):  
Humberto Parada ◽  
Xuezheng Sun ◽  
Jodie M. Fleming ◽  
ClarLynda R. Williams-DeVane ◽  
Erin L. Kirk ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Breast Cancers ◽  
Luminal A ◽  
Cancer Study ◽  
Breast Cancer Study ◽  
Biological Differences ◽  
Carolina Breast Cancer Study

scholarly journals Differential expression of mab-21 like 1 in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Molecular Subtype ◽  
Differentially Expressed Gene ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Luminal A ◽  
Significant Differential Expression ◽  
Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding mab-21 like 1, MAB21L1, when comparing primary tumors of the breast to the tissue of origin, the normal breast. MAB21L1 was also differentially expressed in the tumor cells of patients with triple negative breast cancer. MAB21L1 mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of MAB21L1 in primary tumors of the breast was correlated with overall survival in patients with luminal A subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by molecular subtype. MAB21L1 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

scholarly journals Differential expression of defective in cullin neddylation 1 domain-containing 3 in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Molecular Subtype ◽  
Differentially Expressed Gene ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Luminal A ◽  
Significant Differential Expression ◽  
Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding defective in cullin neddylation 1 domain-containing 3, DCUN1D3, when comparing primary tumors of the breast to the tissue of origin, the normal breast. DCUN1D3 mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of DCUN1D3 in primary tumors of the breast was correlated with recurrence-free survival in patients with basal, luminal A and luminal B subtype cancers, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by PAM50 molecular subtype. DCUN1D3 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

scholarly journals Differential expression of dystrophin in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Molecular Subtype ◽  
Differentially Expressed Gene ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Luminal A ◽  
Significant Differential Expression ◽  
Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding dystrophin, DMD, when comparing primary tumors of the breast to the tissue of origin, the normal breast. DMD was also differentially expressed in the tumor cells of patients with triple negative breast cancer. DMD mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of DMD in primary tumors of the breast was correlated with overall survival in patients with basal and luminal A subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by molecular subtype. DMD may be of relevance to initiation, maintenance or progression of cancers of the female breast.

scholarly journals Differential expression of RHOJ in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Molecular Subtype ◽  
Differentially Expressed Gene ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Luminal A ◽  
Significant Differential Expression ◽  
Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding ras homolog family member J, RHOJ, when comparing primary tumors of the breast to the tissue of origin, the normal breast. RHOJ was also differentially expressed in the tumor cells of patients with triple negative breast cancer. RHOJ mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of RHOJ in primary tumors of the breast was correlated with recurrence-free survival in patients with luminal A subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by molecular subtype. RHOJ may be of relevance to initiation, maintenance or progression of cancers of the female breast.

scholarly journals Differential expression of dermatopontin in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Molecular Subtype ◽  
Differentially Expressed Gene ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Luminal A ◽  
Significant Differential Expression ◽  
Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding dermatopontin, DPT, when comparing primary tumors of the breast to the tissue of origin, the normal breast. DPT mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of DPT in primary tumors of the breast was correlated with overall survival in patients with luminal A subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by molecular subtype. DPT may be of relevance to initiation, maintenance or progression of cancers of the female breast.

scholarly journals Differential expression of prospero homeobox 1 in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Molecular Subtype ◽  
Differentially Expressed Gene ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Luminal A ◽  
Significant Differential Expression ◽  
Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding prospero homeobox 1, PROX1, when comparing primary tumors of the breast to the tissue of origin, the normal breast. PROX1 was also differentially expressed in the tumor cells of patients with triple negative breast cancer. PROX1 mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of PROX1 in primary tumors of the breast was correlated with recurrence-free survival in patients with luminal A and luminal B subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by molecular subtype. PROX1 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

scholarly journals Differential expression of SDPR in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Molecular Subtype ◽  
Differentially Expressed Gene ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Luminal A ◽  
Significant Differential Expression ◽  
Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding serum deprivation response, SDPR, when comparing primary tumors of the breast to the tissue of origin, the normal breast. SDPR was also differentially expressed in the tumor cells of patients with triple negative breast cancer. SDPR mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of SDPR in primary tumors of the breast was correlated with overall survival in patients with luminal A, basal subtype, and HER2+ cancer, but not in luminal B subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by molecular subtype. SDPR may be of relevance to initiation, maintenance or progression of cancers of the female breast.

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