scholarly journals Analysis of the BRCA1 gene coding regions in patients with luminal B breast cancer

Author(s):  
А.М. Певзнер ◽  
М.К. Ибрагимова ◽  
М.М. Цыганов

Наши предыдущие исследования показали, что дефицит гена BRCA1, вызванный изменениями в опухоли, такими как низкая экспрессия, делеция, потеря гетерозиготности, может быть связан с эффективностью химиотерапии и прогнозом заболевания. Однако даже при отсутствии этих факторов эффективность терапии таксотером была переменной. Это может быть связано с наличием других соматических изменениий гена BRCA1 в опухолевой ткани, и их определение поможет определить индивидуальную стратегию лечения для каждого пациента с раком молочной железы. Здесь мы исследовали весь спектр герминальных и соматических мутаций кодирующей области генов BRCA1/2 в опухолевой ткани. В целом, наши результаты показывают, что имеет смысл принимать во внимание не только выявленные герминальные мутации, но и соматические изменения в генах BRCA1/2 при назначении терапии. Our previous studies have shown that BRCA1 gene deficiency caused by changes in the tumor such as low expression, deletion, loss of heterozygosity, etc., can be associated with the effectiveness of chemotherapy and the disease prognosis. However, even in the absence of these factors, the effectiveness of taxotere therapy was variable. This may be due to the availability of another BRCA1 gene somatic changes in the tumor tissue and their determination will help to define the personalize treatment strategy for each breast cancer patient. Here we investigated the entire spectrum germline and somatic mutation of coding region of the BRCA1/2 gene in tumor tissue. Overall, our results suggest that it makes sense to take into account not only identified germline mutations, but also somatic changes in the BRCA1/2 gene when appointment taxotere

Gene Reports ◽  
2020 ◽  
Vol 21 ◽  
pp. 100859
Author(s):  
Alina Pevzner ◽  
Matvey Tsyganov ◽  
Marina Ibragimova ◽  
Alexey Zarubin ◽  
Nikolay Litviakov

Author(s):  
М.М. Цыганов ◽  
М.К. Ибрагимова ◽  
А.М. Певзнер ◽  
Е.Ю. Гарбуков ◽  
К.А. Гаптулбарова ◽  
...  

Целью работы явилась оценка связи хромосомных аберраций генов BRCA1, NF-κB1, PARP1 в опухолевой ткани молочной железы с эффектом химиотерапии и прогнозом заболевания. В исследование включены 85 больных люминальным В раком молочной железы IIA-IIIB стадии, с морфологически верифицированным диагнозом, в возрасте 25-68 лет (47,8±1,1). Было установлено, что наибольшая частота делеций наблюдается в гене BRCA1 (36%, 30 случаев из 85). Частота амплификаций PARP1 в исследуемой группе больных РМЖ достигает 62% (53 случая из 85). Наименьшее число хромосомных аберраций наблюдается в гене NF-κB1, всего у 22 больных наблюдаются делеции и амплификации данного гена (26%). Показано, что делеция гена BRCA1 сопряжена с хорошим ответом на неоадъювантную химиотерапию вне зависимости от наличия хромосомных аберраций других генов. При этом амплификация PARP1 связана с плохим прогнозом заболевания. The aim of the work was to assess the relationship of chromosomal aberrations of the BRCA1, NF-κB1, PARP1 genes in breast tumor tissue with the effect of chemotherapy and prognosis of the disease. The study included 85 patients with luminal stage IIA-IIIB breast cancer, with a morphologically verified diagnosis, aged 25-68 years (47.8±1.1). As a result of the study, the CNA frequency of the studied genes was estimated. It was found that the highest deletion rate is observed in the BRCA1 gene (36%, 30 cases out of 85). The frequency of amplification of PARP1 in the studied group of breast cancer patients reaches 62% (53 cases out of 85). The smallest number of chromosomal aberrations is observed in the NF-κB1 gene; in only 22 patients, deletions and amplifications of this gene are observed (26%). it was found that the deletion of the BRCA1 gene is associated with a good response to neoadjuvant chemotherapy, regardless of the presence of chromosomal aberrations of other genes. Moreover, amplification of PARP1 is associated with a poor prognosis of the disease.


Author(s):  
Francesca Rossiello, et al. (#)

Germ line mutations in the coding sequence of some genes, mainly BRCA1 and BRCA2, confer a high risk of developing breast cancer. However, about 70% of tumors cases are not associated with any known mutation. By screening by sequencing peripheral blood of patients and healthy controls, we identified some previously unknown germline mutations in the 3 'UTR non-coding region of the BRCA1 gene. These mutations can modify gene expression, and can therefore be useful to predict, with greater accuracy, familiar breast cancer predisposition. Subsequently, to understand the mechanisms of aging in non-proliferating cells we studied the persistent DNA damage response (DDR) signal in senescent cells, both in cell cultures and in animal tissues, and we found that these signals mainly localize to telomeres, independently from their length. The accumulation of damage at the telomeric DNA, due to the inhibition of the repair mechanisms, causes cellular and individual aging, but it is also an important anti-tumor mechanism, as it prevents the uncontrolled cell growth during the early stages of neoplastic transformation.


2020 ◽  
Vol 12 (8) ◽  
pp. 979-986
Author(s):  
Yang Sun ◽  
Qianlong Chen ◽  
Yujing Zhang ◽  
Wenke Li ◽  
Kun Zhao ◽  
...  

Considering the lack of information regarding the role and mechanism of low expression of PRKAR1α in cardiac myxoma, we investigated the relationship between the low expression of PRKAR1α and the cAMP responsive element binding protein (CREB) and the expression of its phosphorylated form (p-CREB) in cardiac myxoma tissue. For this purpose, we conducted a retrospective analysis of 130 cases of CM tissue obtained by surgical resection, from which paraffin-fixed tissue DNA was extracted, followed by detection of PRKAR1A DNA mutation by Sanger sequencing and detection of CREB, p-CREB, and PKAR1α protein expression by immunohistochemical SP method. Mutations in the PRKAR1A gene coding region were detected in 35 (46.05%) of 76 sporadic CM tissues, of which 48.57% (17/35 cases) had more than two mutations, and 28.57% (10/35 cases) had exon4: C.349-4-C.349-5insertTmutation. Compared with the surrounding normal tissues, 55.26% (42/76 cases) of PKAR1α protein was not expressed or weakly expressed, CREB was not expressed in myxoma and myocardial tissues, p-CREB was expressed in 51 (67.11%) CM-positive tissues, and PKAR1α and p-CREB expression demonstrated no correlation (P > 0.05). These results indicate the presence of a high level of CREB phosphorylation in cardiac myxoma tissue; however, its phosphorylation is not associated with mutations in the PRKAR1A gene coding region and PKAR1α expression.


2020 ◽  
Vol 27 (5) ◽  
Author(s):  
M.A. Elbaiomy ◽  
T. Akl ◽  
R. Elhelaly ◽  
W. El-Beshbishi ◽  
M.S. El-Ghonemy ◽  
...  

Background Cancer initiation typically occurs when a proto-oncogene’s coding region undergoes mutation, result­ing in uncontrollable cell growth and division, or when a tumour suppressor gene’s coding region is affected by a mutation that inhibits activity of the resulting gene product. The pathophysiologic result is, respectively, exaggerated cell-cycle growth or deficient programmed cell death. Osteopontin (opn) is an integrin-binding phosphoprotein that is expressed on the surface of normal cells. Osteopontin has a major role in diverse tumour components, especially those implicated in invasion and metastasis. In the present study, we aimed to illustrate the value of opn as a possible contributor in breast cancer (bca). Methods This prospective study included 115 patients newly diagnosed with bca and distant metastasis who were recruited from the Oncology Center, Mansoura University, and the Department of Clinical Oncology and Nuclear Medicine, Mansoura University Hospital, Egypt. The patients recruited had been diagnosed with disseminated visceral metastasis (visceral crisis), with or without bone metastasis; patients with cranial metastasis were excluded from the study. All patients received first-line chemotherapy with docetaxel 75 mg/m2 plus cisplatin 75 mg/m2 or carboplatin 6 auc (area under the curve) on day 1 every 21 days for a maximum of 6 cycles or till development of toxicity. Trastu­zumab (in cases of her2-positive disease) was given whenever possible (if government assistance or personal finances permitted). Serum levels of opn were assessed by enzyme-linked immunosorbent assay (elisa) before treatment was started. A group of 30 matched healthy women whose median serum opn level was 15 ng/dL were included, and that level was therefore defined as the cut-off value. In addition, opn gene mutation was determined by polymerase chain reaction (pcr). Correlations of pretreatment serum opn and opn gene mutation with various patient clinicopathologic criteria, response to the treatment, progression-free survival (pfs), and overall survival (os) were assessed. Results Mean serum opn was highest in her2-amplified bca (64.4 ± 42.3 ng/dL), and then in triple-negative bca (55.9 ± 34.7 ng/dL), followed by the luminal B and A subtypes (38.4 ± 33.1 ng/dL and 36.3 ± 32.2 ng/dL respectively, p = 0.017). Testing by pcr revealed that opn gene mutation was highest in triple-negative bca (85% opn mutant vs. 15% non-mutant), and then in her2-overexpressed bca (80% opn mutant vs. 20% non-mutant), followed by luminal B bca (61.9% opn mutant vs. 38.1% non-mutant); the least expression was detected in luminal A bca (57.9% opn mutant vs. 42.1% non-mutant). Interestingly, patients with high serum opn and opn gene mutation experienced both poor pfs (median: 12 months vs. 14 months; p = 0.001) and poor os (median: 14 months vs. 18 months; p = 0.001). Moreover, participants with opn gene mutation experienced a poor response: of those with progressive disease, 74% had opn mutation and 26% had unmutated opn (p = 0.04). Additionally, high pretreatment serum opn was correlated with poor treatment response: 49.1 ± 33.8 ng/dL in patients with progressive disease and 35.5 ± 34.3 ng/dL in those who achieved a complete response, a partial response, or stable disease (p = 0.05). Strong concordance was found between high serum opn and opn gene mutation in 69 tumours (79.3%), and strong concordance was detected between normal or low serum opn and non-mutant opn in 28 tumours (60.8%). Conclusions The current prospective work helps to highlight opn as a valid prognostic biomarker for patients with metastatic bca and reveals that high pretreatment serum opn and opn gene mutation are both strongly linked with poor response and survival. Concordance between elisa and pcr results indicates that either method can be used for the evaluation of opn. Increased opn gene mutation in triple-negative bca could assist in tailoring the treatment response in this very aggressive tumour subtype and could be considered a targetable molecule in future studies.


Author(s):  
Л.В. Якушевич ◽  
L.V. Yakushevich

Coding regions (CDS) being an integral part of any gene sequence, play an important role in the process of transcription. One of the tasks associated with the CDS regions, consists in the modeling of the passage of transcription bubbles named also open states or DNA kinks through the coding regions. In this paper, we present a simple and convenient approach to the modeling of the passage. It includes the calculation of the energy profile of the sequence and reducing the initial task to the modeling of the movement of a quasi particle in the field with this energy profile. To illustrate the method, we present the results of the calculations of the trajectories of the DNA kinks moving in the sequence of gene coding interferon alpha 17 (IFNA17) that consists of the three regions: the coding region and the two regions with unknown functional properties. To analyze the kink dynamics, we apply approximation where the DNA parameters are being averaged separately over each of the three regions. In the absences of dissipation, the total kink energy is constant. At the same time the kink velocity is constant only inside each of the regions. In the presence of dissipation, the total kink energy decreases. It is shown that the greater the total initial energy of the kink, the faster the energy decrease. It is suggested that the proposed approach could be useful in finding the ways to govern the movement of transcription bubbles at the first stage of the process of transcription.


2009 ◽  
Vol 2009 ◽  
pp. 1-7 ◽  
Author(s):  
Elias Daura-Oller ◽  
Maria Cabré ◽  
Miguel A. Montero ◽  
José L. Paternáin ◽  
Antoni Romeu

In the present study, a positive training set of 30 known human imprinted gene coding regions are compared with a set of 72 randomly sampled human nonimprinted gene coding regions (negative training set) to identify genomic features common to human imprinted genes. The most important feature of the present work is its ability to use multivariate analysis to look at variation, at coding region DNA level, among imprinted and non-imprinted genes. There is a force affecting genomic parameters that appears through the use of the appropriate multivariate methods (principle components analysis (PCA) and quadratic discriminant analysis (QDA) to analyse quantitative genomic data. We show that variables, such as CG content, [bp]% CpG islands, [bp]% Large Tandem Repeats, and [bp]% Simple Repeats, are able to distinguish coding regions of human imprinted genes.


2020 ◽  
Vol 3 ◽  
pp. 6-12
Author(s):  
Yuriy Vinnik ◽  
Yulia Belevtsova ◽  
Marina Sadchikova

Improving the efficiency of treatment of locally distributed forms of breast cancer (BC) patients is relevant. The aim of the study: to determine the possibility of increasing the efficiency of treatment of patients with locally distributed BC by supplementing it with the determination of the expression of TOP2 alpha and beta-tubulin III genes in the primary tumor during various chemotherapy regimens. Method. 139 patients with locally distributed BC were examined. Patients received 2-4 courses of neoadjuvant chemotherapy (NAChT) according to the TC (docetaxel + cyclophosphamide) and TAC (docetaxel + doxorubicin + cyclophosphamide) regimens, subsequent surgical intervention and 2–4 courses of AchT according to the FAC regimen. Immunohistochemical (IHCh) study of the levels of estrogen receptors (ER), progesterone (PR), epidermal growth factor (HER2) in tumors was conducted. The expression of TOP2 alpha and beta-tubulin class III genes was determined using PCR. Statistical data processing was performed using the program Stastistica for Windows 6. 0, Excel. Results. In the third cycle of chemotherapy, patients were transferred from the TC scheme to the TAC scheme. The frequency of the FPR increased 4 times in the group of patients with a triple negative tumor subtype compared with patients with luminal B. A combination of low expression of the class III beta-tubulin gene with high expression of TOP2 alpha in tumor tissue was found in 64.5 % of patients treated according to the TAC + cross over regimen and in 56.3 % of cases according to the TC regimen. A change in the receptor status of MLN after NAChT was detected in some cases. Conclusions. The combination of high expression of TOP2 alpha with low expression of class III beta-tubulins can be considered as a predictive sign of full pathomorphological response when using taxane-containing locally distributed BC. These markers can be recommended for determination in MLN (along with definition of ER, PR, HER2) in order to increase the effectiveness of AchT.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Glauco Akelinghton Freire Vitiello ◽  
Marla Karine Amarante ◽  
Jefferson Crespigio ◽  
Bruna Karina Banin Hirata ◽  
Nathalia de Sousa Pereira ◽  
...  

Abstract Background TGFβ signaling exerts context-specific effects in breast cancer (BC) pathogenesis and single nucleotide polymorphisms (SNPs) in TGFβ-signaling components play a role in the genetic control of their expression and in BC susceptibility and clinical presentation. However, studies investigating the association between the TGFβ-signaling molecules and BC prognosis rarely considered disease subtypes and SNPs. Therefore, the present study aimed to evaluate the expression of TGFβ-signaling components in BC tissue from patients with available data regarding TGFB1 and TGFBR2 SNPs and plasmatic TGFβ1 levels. Methods Immunostaining for TGFβ1, TGFβRII and phosphorylated (p)-SMAD2/3 was investigated in primary tumor tissue from 34 patients with luminal-B-HER2+ (LB-HER2), HER2-enriched (HER2) and triple negative (TN) BC subtypes genotyped for TGFB1 (rs1800468, rs1800469, rs1800470 and rs1800471) and TGFBR2 (rs3087465) SNPs. Results Strong positive correlations were observed between TGFβ1, TGFβRII and p-SMAD2/3 in tumor tissue, and an inverse correlation was observed between intratumor and plasmatic TGFβ1 levels in TN BCs. In LB-HER2+ tumors, p-SMAD2/3 was associated with older age at diagnosis and inversely correlated with p53 staining and lymph-node metastasis, while tumor-size negatively correlated with TGFβ1 and TGFβRII in this BC subgroup. Also, in p53-negative BCs, tumor size and Ki67 negatively correlated with both TGFβ1, TGFβRII and p-SMAD2/3. No correlation was found between SNPs and TGFβ1-signaling components expression. Conclusion TGFβ1 canonical signaling is activated in approximately half of BCs, and correlation between TGFβ components indicate a paracrine activation, which may exert tumor suppressor effects in p53-negative or Luminal-B-HER2+ subgroups.


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