Study of KMT2B (MLL2) gene expression changes in patients with breast cancer

Aim: This study aimed to demonstrate misregulation of KMT2B gene expression in breast cancer tissue. Materials & methods: Cancerous and marginal tissue samples were collected from 43 female patients. After RNA extraction and cDNA synthesis, quantitative-PCR was used to evaluate the expression level of the KMT2B gene. REST, Sigma plot and SPSS software were used to analyze data. Results: KMT2B gene expression was significantly decreased in tumor tissue compared with marginal tissue (p = 0.02). No significant correlation was found between expression levels of KMT2B and clinical parameters of patients (p > 0.05) Conclusion: Our study demonstrated that downregulation of KMT2B is associated with breast cancer and its misregulation may play an important role in tumorigenesis.

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Analysis of human aldehyde dehydrogenases (ALDH) gene expression pattern in breast cancer tissue samples: rutin-copper complex inhibit the breast cancer cell proliferation

Egyptian Journal of Medical Human Genetics ◽

10.1186/s43042-021-00143-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Shridhar V. Pattar ◽

Manisha R. Mirjankar ◽

Suyamindra Kulkarni ◽

Pramod B. Gai ◽

Namadev K. Pujar ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Single Nucleotide Polymorphism ◽

Copper Complex ◽

Breast Cancer Tissue ◽

Cancer Tissue ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Tissue Samples ◽

Aldehyde Dehydrogenases

Abstract Background Higher aldehyde dehydrogenases (ALDH) activity is one of the important signatures of breast cancer appearance and has been associated with poor prognosis. ALDH1A3 has been over-expressed in breast cancer patients. This study aims to analyze gene expression patterns of 18 ALDH isozymes in breast cancer tissue samples. It is carried out using a chip-based microarray, next-generation DNA sequencing of ALDH2 gene following in silico study to identify the natural products which act as inhibitors for over-expressed ALDH isoforms. The synthesis of rutin-copper complex and cell viability assay is carried out on MDA-MB-468 cell line. Results ALDH1A3 and ALDH18A1 have shown the highest positive mean fold of variation; whereas, ALDH2 and ALDH1A2 have shown the highest negative mean fold variation. In silico studies revealed that rutin has the highest binding affinity with both ALDH1A3 and ALDH18A1 and supported with IC50 value of rutin against MDA-MB-468 cells (144.50 μg/ml). Chemically synthesized rutin-copper complex significantly lowered the IC50 value to 119.40 μg/ml. The next-generation sequencing study provides the novel single nucleotide polymorphism (SNP) from T to G in the ALDH2 gene. Conclusion The present study signifies that, along with ALDH1A3, ALDH18A1 also acts as a marker for breast cancer. Apart from that, inhibitors of ALDH1A3 and ALDH18A1 were attained. Perhaps the single nucleotide polymorphism (SNP) obtained during the mutation analysis may be the probable cause of the highest downregulation of ALDH2 in breast cancer.

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The BIRC Family Genes Expression in Patients with Triple Negative Breast Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms22041820 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1820

Author(s):

Anna Makuch-Kocka ◽

Janusz Kocki ◽

Anna Brzozowska ◽

Jacek Bogucki ◽

Przemysław Kołodziej ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Clinical Data ◽

Triple Negative Breast Cancer ◽

Triple Negative ◽

Lymphatic Vessels ◽

The Cancer Genome Atlas ◽

Expression Level ◽

Cancer Tissue ◽

Expression Levels

The BIRC (baculoviral IAP repeat-containing; BIRC) family genes encode for Inhibitor of Apoptosis (IAP) proteins. The dysregulation of the expression levels of the genes in question in cancer tissue as compared to normal tissue suggests that the apoptosis process in cancer cells was disturbed, which may be associated with the development and chemoresistance of triple negative breast cancer (TNBC). In our study, we determined the expression level of eight genes from the BIRC family using the Real-Time PCR method in patients with TNBC and compared the obtained results with clinical data. Additionally, using bioinformatics tools (Ualcan and The Breast Cancer Gene-Expression Miner v4.5 (bc-GenExMiner v4.5)), we compared our data with the data in the Cancer Genome Atlas (TCGA) database. We observed diverse expression pattern among the studied genes in breast cancer tissue. Comparing the expression level of the studied genes with the clinical data, we found that in patients diagnosed with breast cancer under the age of 50, the expression levels of all studied genes were higher compared to patients diagnosed after the age of 50. We observed that in patients with invasion of neoplastic cells into lymphatic vessels and fat tissue, the expression levels of BIRC family genes were lower compared to patients in whom these features were not noted. Statistically significant differences in gene expression were also noted in patients classified into three groups depending on the basis of the Scarff-Bloom and Richardson (SBR) Grading System.

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The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues

BMC Cancer ◽

10.1186/s12885-019-6363-0 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 4

Author(s):

Michal Marczyk ◽

Chunxiao Fu ◽

Rosanna Lau ◽

Lili Du ◽

Alexander J. Trevarton ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Rna Sequencing ◽

Rna Extraction ◽

Formalin Fixed Paraffin ◽

Ffpe Samples ◽

Formalin Fixed Paraffin Embedded ◽

The Impact ◽

Formalin Fixed

Abstract Background Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretation of the impact of pre-analytical variables on the data obtained, particularly the methods used to preserve samples and to purify RNA. Methods Matched tissue samples from 12 breast cancers were fresh frozen (FF) and preserved in RNAlater or fixed in formalin and processed as FFPE tissue. Total RNA was extracted and purified from FF samples using the Qiagen RNeasy kit, and in duplicate from FFPE tissue sections using three different kits (Norgen, Qiagen and Roche). All RNA samples underwent whole transcriptome RNA sequencing (wtRNAseq) and targeted RNA sequencing for 31 transcripts included in a signature of sensitivity to endocrine therapy. We assessed the effect of RNA extraction kit on the reliability of gene expression levels using linear mixed-effects model analysis, concordance correlation coefficient (CCC) and differential analysis. All protein-coding genes in the wtRNAseq and three gene expression signatures for breast cancer were assessed for concordance. Results Despite variable quality of the RNA extracted from FFPE samples by different kits, all had similar concordance of overall gene expression from wtRNAseq between matched FF and FFPE samples (median CCC 0.63–0.66) and between technical replicates (median expression difference 0.13–0.22). More than half of genes were differentially expressed between FF and FFPE, but with low fold change (median |LFC| 0.31–0.34). Two out of three breast cancer signatures studied were highly robust in all samples using any kit, whereas the third signature was similarly discordant irrespective of the kit used. The targeted RNAseq assay was concordant between FFPE and FF samples using any of the kits (CCC 0.91–0.96). Conclusions The selection of kit to purify RNA from FFPE did not influence the overall quality of results from wtRNAseq, thus variable reproducibility of gene signatures probably relates to the reliability of individual gene selected and possibly to the algorithm. Targeted RNAseq showed promising performance for clinical deployment of quantitative assays in breast cancer from FFPE samples, although numerical scores were not identical to those from wtRNAseq and would require calibration.

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NPY and sbGnRH gene expression in juvenile and adult male Brazilian flounder Paralichthys orbignyanus

Ciência Rural ◽

10.1590/s0103-84782011001100013 ◽

2011 ◽

Vol 41 (11) ◽

pp. 1927-1930 ◽

Cited By ~ 4

Author(s):

Vinicius Farias Campos ◽

Tiago Veiras Collares ◽

Fabiana Kömmling Seixas ◽

João Carlos Deschamps ◽

Luis Fernando Fernandes Marins ◽

...

Keyword(s):

Gene Expression ◽

Rna Extraction ◽

Sea Bream ◽

Mrna Levels ◽

Adult Males ◽

Adult Fish ◽

Cdna Synthesis ◽

Hypothalamic Regulation ◽

Measure Gene Expression ◽

Paralichthys Orbignyanus

The objective of this study was to evaluate neuropeptide Y (NPY) and sea bream gonadotropin-release hormone (sbGnRH) gene expression in juvenile and adult males of Brazilian flounder. Hypothalamuses from fish were sampled for total RNA extraction. After cDNA synthesis, real-time PCR was used to measure gene expression. NPY showed approximately 2-fold increases in their mRNA levels while sbGnRH showed 3-fold increases in adult fish. These results suggest that these peptides could be involved on hypothalamic regulation of Brazilian flounder sexual maturation.

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Strategy for SRM-based Verification of Biomarker Candidates Discovered by iTRAQ Method in Limited Breast Cancer Tissue Samples

Journal of Proteome Research ◽

10.1021/pr300322q ◽

2012 ◽

Vol 11 (8) ◽

pp. 4201-4210 ◽

Cited By ~ 52

Author(s):

Satoshi Muraoka ◽

Hideaki Kume ◽

Shio Watanabe ◽

Jun Adachi ◽

Masayoshi Kuwano ◽

...

Keyword(s):

Breast Cancer ◽

Breast Cancer Tissue ◽

Cancer Tissue ◽

Tissue Samples

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Comparison of the Results of PCR Analysis of Gene Expression in Breast Cancer Tissue Specimens Stabilized in Formalin and RNAlater

Bulletin of Experimental Biology and Medicine ◽

10.1007/s10517-014-2381-8 ◽

2014 ◽

Vol 156 (4) ◽

pp. 486-490 ◽

Cited By ~ 3

Author(s):

N. A. Khaustova ◽

D. S. Makeeva ◽

O. V. Kondrashina ◽

N. N. Fedotov ◽

I. N. Nechaev ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Breast Cancer Tissue ◽

Pcr Analysis ◽

Cancer Tissue ◽

Tissue Specimens ◽

Comparison Of The Results

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RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens

Biomedicines ◽

10.3390/biomedicines8050114 ◽

2020 ◽

Vol 8 (5) ◽

pp. 114

Author(s):

Maxim Sorokin ◽

Kirill Ignatev ◽

Elena Poddubskaya ◽

Uliana Vladimirova ◽

Nurshat Gaifullin ◽

...

Keyword(s):

Breast Cancer ◽

Lung Cancer ◽

Rna Sequencing ◽

Expression Profiles ◽

Correlation Study ◽

Cancer Tissue ◽

Transcriptional Level ◽

Tissue Samples ◽

Protein Levels ◽

Formalin Fixed Paraffin Embedded

RNA sequencing is considered the gold standard for high-throughput profiling of gene expression at the transcriptional level. Its increasing importance in cancer research and molecular diagnostics is reflected in the growing number of its mentions in scientific literature and clinical trial reports. However, the use of different reagents and protocols for RNA sequencing often produces incompatible results. Recently, we published the Oncobox Atlas of RNA sequencing profiles for normal human tissues obtained from healthy donors killed in road accidents. This is a database of molecular profiles obtained using uniform protocol and reagents settings that can be broadly used in biomedicine for data normalization in pathology, including cancer. Here, we publish new original 39 breast cancer (BC) and 19 lung cancer (LC) RNA sequencing profiles obtained for formalin-fixed paraffin-embedded (FFPE) tissue samples, fully compatible with the Oncobox Atlas. We performed the first correlation study of RNA sequencing and immunohistochemistry-measured expression profiles for the clinically actionable biomarker genes in FFPE cancer tissue samples. We demonstrated high (Spearman’s rho 0.65–0.798) and statistically significant (p < 0.00004) correlations between the RNA sequencing (Oncobox protocol) and immunohistochemical measurements for HER2/ERBB2, ER/ESR1 and PGR genes in BC, and for PDL1 gene in LC; AUC: 0.963 for HER2, 0.921 for ESR1, 0.912 for PGR, and 0.922 for PDL1. To our knowledge, this is the first validation that total RNA sequencing of archived FFPE materials provides a reliable estimation of marker protein levels. These results show that in the future, RNA sequencing can complement immunohistochemistry for reliable measurements of the expression biomarkers in FFPE cancer samples.

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Diagonistic Value of ARFI in Breast Lesions

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2021/v33i50b33421 ◽

2021 ◽

pp. 24-30

Author(s):

J. Jayapriya ◽

S. Arul Murugan

Keyword(s):

Breast Cancer ◽

Acoustic Radiation ◽

Radiation Force ◽

Acoustic Radiation Force Impulse ◽

Stiffness Index ◽

Cancer Tissue ◽

Cancer Type ◽

Tissue Samples ◽

Biopsy Confirmation ◽

Index Value

Breast cancer became the most prominent cancer type in women worldwide. Its prevalence increased in recent years due to changes in life style and relapse among the patients seemed to be higher. Acoustic radiation force impulse (ARFI) imaging in based on the principle of the ultrasonic elasticity and the elestography accurately predict and measure the changes in breast cancer tissue compared to the normal tissue. It is a technical alternative to the palpation and able to measure lesser than 10 mm size. In contrast to biopsy, where the reduced deformability would occur and lead to biopsy failing. In fibroadenoma, due to its complications, many false positives could be detected and the ARFI elastography serve as an effective alternative method for breast cancer confirmation. The tissue stiffness index value is used to differentiate the benign and malignant tissue samples. ARFI further, use B- mode elasticity and help in recommending the biopsy confirmation.

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