scholarly journals MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sevan Omer Majed ◽  
Suhad Asad Mustafa
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Small Rnas ◽  
Target Genes ◽  
Target Prediction ◽  
Ffpe Tissue ◽  
Differentially Expressed ◽  
Expression Level ◽  
Formalin Fixed Paraffin Embedded ◽  
Cancer Tumor

Abstract Introduction Disruption of cellular processes in the breast by abnormally expressed miRNA is characterized to develop cancer. We aimed to identify the differential expression of small RNAs (sRNAs) and mRNAs in formalin-fixed paraffin-embedded (FFPE) tissue of the breast cancer (BC) and normal adjacent tissue (NAT). Another aim is to determine the differential expression of miR-1275 as a novel biomarker for BC and also identify its target genes. Methods TrueQuant method for analysis of sRNA expression and MACE-sequencing method for analysis of gene expression were used analyzing. The RT-qPCR technique was used to confirm miR-1275 down expression. Target genes of miR-1275 were computationally identified using target prediction sites and also the expression level of them was experimentally determined among the expressed genes. Results TrueQuant findings showed that 1400 sRNAs were differentially expressed in the FFPE tissue of two Kurdish cases with BC, as compared to NAT. Among the sRNAs, 29 small RNAs were shown to be significantly downregulated in BC cells. The RT-qPCR results confirmed that miR-1275 was significantly down-expressed in 20 Kurdish cases with BC compared to NAT. However, Overall survival (OS) analysis revealed that the correlation between the expression level of miR-1275 and clinical significance was highly corrected in cases with BC (OS rate: P = 0.0401). The MACE-seq results revealed that 26,843 genes were differentially expressed in the BC tissue compared to NAT, but 7041 genes were displayed in a scatter plot. Furthermore, putative target genes (DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA) were computationally identified as direct targets of miR-1275 in several target predicted sites. The MACE-seq results revealed that the expression level of these targets was increased in BC tissue compared to NAT. The level of these targets was negatively associated with miR-1275 expression. Finally, the role of down-regulated miR-1275 on its targets in biological mechanisms of BC cells was identified; including cell growth, proliferation, movement, invasion, metastasis, and apoptosis. Conclusion Down-expressed miR-1275, a tumor suppressor, is a novel biomarker for early detection of BC. DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA are newly identified to be targeted by miR-1275.

scholarly journals MACE-Seq-based coding RNA and TrueQuant-based small RNA profiles in breast cancer: tumor-suppressive miR-1275 identified as a novel marker 

2020 ◽  
Author(s):  
Sevan Majed ◽  
Suhad Mustafa
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Small Rnas ◽  
Target Genes ◽  
Target Prediction ◽  
Ffpe Tissue ◽  
Differentially Expressed ◽  
Expression Level ◽  
Formalin Fixed Paraffin Embedded ◽  
Cancer Tumor

Abstract Introduction: Disruption of cellular processes in the breast by abnormally expressed miRNA is characterized to develop cancer. We aimed to identify the differential expression of small RNAs (sRNAs) and mRNAs in formalin-fixed paraffin-embedded (FFPE) tissue of the breast cancer (BC) and normal adjacent tissue (NAT). Another aim is to determine the differential expression of miR-1275 as a novel biomarker for BC and also identify its target genes. Methods: TrueQuant method for analysis of sRNA expression and MACE-sequencing method for analysis of gene expression were used analyzing. The RT-qPCR technique was used to confirm miR-1275 down expression. Target genes of miR-1275 were computationally identified using target prediction sites and also the expression level of them was experimentally determined among the expressed genes.Results: TrueQuant findings showed that 1400 sRNAs were differentially expressed in the FFPE tissue of two Kurdish cases with BC, as compared to NAT. Among the sRNAs, 29 small RNAs were shown to be significantly downregulated in BC cells. The RT-qPCR results confirmed that miR-1275 was significantly down-expressed in 20 Kurdish cases with BC compared to NAT. However, Overall survival (OS) analysis revealed that the correlation between the expression level of miR-1275 and clinical significance was highly corrected in cases with BC (OS rate: P = 0.0401). The MACE-seq results revealed that 26843 genes were differentially expressed in the BC tissue compared to NAT, but 7041 genes were displayed in a scatter plot. Furthermore, putative target genes (DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA) were computationally identified as direct targets of miR-1275 in several target predicted sites. The MACE-seq results revealed that the expression level of these targets was increased in BC tissue compared to NAT. The level of these targets was negatively associated with miR-1275 expression. Finally, the role of down-regulated miR-1275 on its targets in biological mechanisms of BC cells was identified; including cell growth, proliferation, movement, invasion, metastasis, and apoptosis.Conclusion: down-expressed miR-1275, a tumor suppressor, is a novel biomarker for early detection of breast cancer. DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA are newly identified to be targeted by miR-1275.

scholarly journals Identification of Tumor-Suppressive miRNA-1275 as a Novel Marker for Breast Cancer (BC) by MACE-Sequencing and RT-qPCR Techniques

2020 ◽  
Author(s):  
Sevan Omer Majed ◽  
Suhad Asad Mustafa
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Small Rnas ◽  
Target Genes ◽  
The Cancer Genome Atlas ◽  
Expression Level ◽  
Formalin Fixed Paraffin ◽  
Number Of Patients ◽  
Sequencing Technique ◽  
Formalin Fixed Paraffin Embedded

Abstract IntroductionDisruption of cellular processes in the breast by abnormally expressed miRNA is characterized to develop cancer. We aimed to determine the differential expression of coding and non-coding RNAs in formalin fixed paraffin embedded (FFPE) blocks of breast cancer (BC) tissue and normal adjacent tissue (NAT). Another aim is to determine differential expression of has-miR-1275 as novel biomarker for BC and identify its target genes using prediction sites and experimentally expression level of them via the MACE-sequencing technique. MethodsMACE-sequencing technique was utilized to analyze differential expression of coding RNAs and small RNAs (sRNAs). Among small RNAs, miRNA-1275 expression was focused and confirmed using RT-qPCR technique in 20 Kurdish cases with BC . Moreover, clinical significance of miR- 1275 and its target genes was studied in a large number of patients with BC using the data obtained from The Cancer Genome Atlas database.ResultsThe MACE-seq findings showed that 1400 sRNAs and 26843 coding RNAs were differentially expressed in FFPE of BC tissue compared to NAT. Among these sRNAs, miRNA-1275 expression was found to be decreased in BC tissue compared to NAT. The decreased expression level of which was then confirmed via RT-qPCR technique to farther prove in 20 Kurdish cases with BC . Furthermore, the correlation between the expression level of miRNA-1275 and clinical data were evaluated to be highly corrected in cases with BC (overall survival rate: P = 0.0401). However, putative target genes ( DVL3, PPP 2R2D, THSD4, CREB1, SYT7, and PRKACA) were computationally identified as direct targets of miRNA-1275 in several target predicted sites. Among coding RNAs, the expression level of these targets was increased in BC tissue compared to NAT. The levels of these targets were negatively associated with miRNA-1275 expression. Finally, the role of down-expressed miRNA-1275 and its targets in BC cells were identified to attenuated biological mechanisms; including cell growth, proliferation, movement, invasion, metastasis, and apoptosis.Conclusiondown-expressed miR-1275 , a tumor suppressor, is as a novel biomarker for early detection of breast cancer. DVL3, PPP 2R2D, THSD4, CREB1, SYT7, and PRKACA are novely identified to be targeted by miR-1275 in BC cells.

Gene expression profiling involved in response to neoadjuvant therapy in breast cancer.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e12618-e12618
Author(s):  
Salvador Bofill ◽  
Carmen Garrigos ◽  
Marta Benavent ◽  
Rosario Gonzalez ◽  
Alvaro Montaño ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Neoadjuvant Therapy ◽  
Differential Expression ◽  
Tumor Stage ◽  
Lymph Node Involvement ◽  
Differentially Expressed ◽  
Breast Cancers ◽  
Neoadjuvant Systemic Therapy ◽  
Limma Package ◽  
Formalin Fixed Paraffin Embedded

e12618 Background: Neoadjuvant systemic therapy for breast cancer is used increasingly but, there is a group of patients which do not benefit from this therapy. With these premises, we stablished that our main objective was to identify differential expression genes patterns in patients (pts) with the ER/PR- Her2+, ER/PR+ Her2+ and triple negative (TN) subtypes breast cancers according to response to neoadjuvant therapy. Methods: RNA from formalin fixed paraffin embedded tumor samples from 54 pts with breast cancer that had received neoadjuvant therapy was extracted with mirVana miRNA isolation kit (Ambion). Patients with TN subtype received neoadjuvant chemotherapy based on anthracyclines and taxanes and patients with the Her2+ subtype received treatment with taxanos-trastuzumab and anthracyclines. The RNA expression levels were identified by ClariomD Asssay (ThermoFisher). Results were analyzed with Transcriptome Analysis Console and with in-house scripts in R (version 3.5.1). Data were corrected and normalized using Robust Multichip Average method from the oligo package. Expression was summarized at gene level using the corresponding annotation for ClariomD array BrainArray. Expression analyses were performed with limma package. A fold change ≥ 2 and p < 0.05 was considered statistically significant. We defined to groups: R (response, RCB 0) and NR (not response, RCB III) pts. Results: The median age of the pts was 52 years and 58% were menopausal and 42% pre-menopausal. Tumor stage were T1 9%, T2 50%, T3 30%, T4 11% and lymph node involvement were N0 31%, N1 41%, N2 24%, N3 4%. We obtained twelve genes differentially expressed in R vs NR groups. Respect to TN, two genes (AC053503.12, C9orf153) were differentially expressed between R (n = 11) and NR (n = 11). In ER/PR+ Her2+ subgroup, NBPF4 showed a differential expression in R (n = 8) vs NR (n = 7). In pts with ER/PR- Her2+, nine genes (DHRS2, SLCO1B3, UGT2B15, RGS2, SULT1E1, MED23, FKBP5, MIEN1, HER2) were differentially expressed in R (n = 10) vs NR (n = 7). We have started a validation in an independent cohort of pts in ER/PR+ Her2+ subgroup, confirming the results previously obtained. Conclusions: We found twelve genes differentially expressed in the different molecular subtypes of breast cancer involved in the response to neoadjuvant therapy. Several of these genes, especially UGT2B15, SULT1E1, FKBP5, MIEN1 and HER2 have been reported as key genes in tumoral processes, such as cell proliferation, invasion and drug resistant pathways, suggesting that its could be good biomarkers of response to neoadjuvant therapy in breast cancer.

Screening candidate microR-15a- IRAK2 regulatory pairs for predicting the response to Staphylococcus aureus-induced mastitis in dairy cows

2019 ◽  
Vol 86 (4) ◽  
pp. 425-431 ◽  
Author(s):  
Zhi Chen ◽  
Jingpeng Zhou ◽  
Xiaolong Wang ◽  
Yang Zhang ◽  
Xubin Lu ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Differential Expression ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Interleukin 1 ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Expression Of Genes ◽  
Chinese Holstein Cows ◽  
Reporter Assays

AbstractWe established a mastitis model using exogenous infection of the mammary gland of Chinese Holstein cows with Staphylococcus aureus and extracted total RNA from S. aureus-infected and healthy mammary quarters. Differential expression of genes due to mastitis was evaluated using Affymetrix technology and results revealed a total of 1230 differentially expressed mRNAs. A subset of affected genes was verified via Q-PCR and pathway analysis. In addition, Solexa high-throughput sequencing technology was used to analyze profiles of miRNA in infected and healthy quarters. These analyses revealed a total of 52 differentially expressed miRNAs. A subset of those results was verified via Q-PCR. Bioinformatics techniques were used to predict and analyze the correlations among differentially expressed miRNA and mRNA. Results revealed a total of 329 pairs of negatively associated miRNA/mRNA, with 31 upregulated pairs of mRNA and 298 downregulated pairs of mRNA. Differential expression of miR-15a and interleukin-1 receptor-associated kinase-like 2 (IRAK2), were evaluated by western blot and luciferase reporter assays. We conclude that miR-15a and miR-15a target genes (IRAK2) constitute potential miRNA–mRNA regulatory pairs for use as biomarkers to predict a mastitis response.

scholarly journals Differential expression of cyclin A2 in triple negative breast cancer.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Overall Survival ◽  
Differential Expression ◽  
Tumor Cells ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Differentially Expressed ◽  
Primary Tumors ◽  
Ductal Cells ◽  
Cyclin A2

Women diagnosed with triple negative breast cancer can benefit neither from endocrine therapy nor from HER2-targeted therapies (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 cyclin A2, CCNA2, when comparing the tumor cells of patients with triple negative breast cancer to normal mammary ductal cells (2). CCNA2 was also differentially expressed in bulk tumor in human breast cancer (3). CCNA2 mRNA was present at significantly increased quantities in TNBC tumor cells relative to normal mammary ductal cells. Analysis of human survival data revealed that expression of CCNA2 in primary tumors of the breast was correlated with overall survival in patients with basal-like type cancer, while within triple negative breast cancer, primary tumor expression of CCNA2 was correlated with overall survival in patients with basal-like 1, basal-like 2, and mesenchymal subtype disease. CCNA2 may be of relevance to initiation, maintenance or progression of triple negative breast cancers.

scholarly journals Differential expression of LIM domain binding 2 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 ◽  
Lim Domain ◽  
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 LIM domain binding 2, LDB2, when comparing primary tumors of the breast to the tissue of origin, the normal breast. LDB2 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 LDB2 in primary tumors of the breast was correlated with recurrence-free survival in patients with luminal A subtype cancers, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by molecular subtype. LDB2 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

scholarly journals Differential expression of Rho GTPase-activating protein 20 in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Rho Gtpase ◽  
Differentially Expressed Gene ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Gtpase Activating Protein ◽  
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 Rho GTPase-activating protein 20, ARHGAP20, when comparing primary tumors of the breast to the tissue of origin, the normal breast. ARHGAP20 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 ARHGAP20 in primary tumors of the breast was correlated with overall survival in patients with HER2+ subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by PAM50 molecular subtype. ARHGAP20 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

scholarly journals Differential expression of CKS2 in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Regulatory Subunit ◽  
Luminal A ◽  
Gene Encoding ◽  
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 the CDC28 protein kinase regulatory subunit 2, CKS2, when comparing primary tumors of the breast to the tissue of origin, the normal breast. CKS2 was also differentially expressed in the tumor cells of patients with triple negative breast cancer. CKS2 mRNA was present at significantly higher quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of CKS2 in primary tumors of the breast was correlated with overall survival in patients with basal and luminal A subtype cancer, but in a contrary manner. CKS2 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

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 dCTP pyrophosphatase 1 in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Normal Breast ◽  
Differentially Expressed ◽  
Tissue Analysis ◽  
Gene Encoding ◽  
Significant Differential Expression ◽  
Primary Tumors ◽  
Microarray Datasets

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 dCTP pyrophosphatase 1, DCTPP1, when comparing primary tumors of the breast to the tissue of origin, the normal breast. DCTPP1 was also differentially expressed in the tumor cells of patients with triple negative breast cancer. DCTPP1 mRNA was present at significantly higher quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of DCTPP1 in primary tumors of the breast was correlated with overall survival in patients with basal subtype cancer. DCTPP1 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

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