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The colony stimulating factor 2 receptor subunit beta (CSF2RB) is the common signaling subunit of the cytokine receptors for IL‐3, IL‐5, and GM‐CSF. Several studies have shown that spontaneous and random mutants of CSF2RB can lead to ligand independence in vitro. To date, no report(s) have been shown for the presence of potentially transforming and oncogenic CSF2RB mutation(s) clinically in cancer patients until the first reported case of a leukemia patient in 2016 harboring a germline‐activating mutation (R461C). We combined exome sequencing, pathway analyses, and functional assays to identify novel somatic mutations in KAIMRC1 cells and breast tumor specimen. The patient’s peripheral blood mononuclear cell (PBMC) exome served as a germline control in the identification of somatic mutations. Here, we report the discovery of a novel potentially transforming and oncogenic somatic mutation (S230I) in the CSF2RB gene of a breast cancer patient and the cell line, KAIMRC1 established from her breast tumor tissue. KAIMRC1 cells are immortalized and shown to survive and proliferate in ligand starvation condition. Immunoblot analysis showed that mutant CSF2RB signals through JAK2/STAT and PI3K/mTOR pathways in ligand starvation conditions. Screening a small molecule kinase inhibitor library revealed potent JAK2 inhibitors against KAIMRC1 cells. We, for the first time, identified a somatic, potentially transforming, and oncogenic CSF2RB mutation (S230I) in breast cancer patients that seem to be an actionable mutation leading to the development of new therapeutics for breast cancer., CSF2RB S230I mutation in breast tumor seems to confer ligand‐independence to breast tumor cells and the KAIMRC1 cell line established from this breast tumor. KAIMRC1 cells harboring this mutation showed constitutive activation of JAK2/STAT and PI3K/mTOR pathways in ligand starvation condition. We found KAIMRC1 cells highly sensitive to JAK2 inhibitors. Together these findings conclude that CSF2RB S230I mutation could be actionable and might help in developing novel therapeutics for breast cancer patients.

Quantitative phase imaging (QPI) measures the growth rate of individual cells by quantifying changes in mass versus time. Here, we use the breast cancer cell lines MCF-7, BT-474, and MDA-MB-231 to validate QPI as a multiparametric approach for determining response to single-agent therapies. Our method allows for rapid determination of drug sensitivity, cytotoxicity, heterogeneity, and time of response for up to 100,000 individual cells or small clusters in a single experiment. We find that QPI EC50 values are concordant with CellTiter-Glo (CTG), a gold standard metabolic endpoint assay. In addition, we apply multiparametric QPI to characterize cytostatic/cytotoxic and rapid/slow responses and track the emergence of resistant subpopulations. Thus, QPI reveals dynamic changes in response heterogeneity in addition to average population responses, a key advantage over endpoint viability or metabolic assays. Overall, multiparametric QPI reveals a rich picture of cell growth by capturing the dynamics of single-cell responses to candidate therapies.

In the search for potential anticancer agents from fruits, the present research work was carried out to examine the in vitro cytotoxic potential of kernel part of Prunus armeniaca (apricot) against eight distinct human cancer cell lines from six different tissues: lung (A-549), colon (HCT-116), breast (MCF-7, MDAMB-231), pancreatic (MIAPaCa-2, Panc-1), prostrate (PC- 3) and CNS (N2A). Methanolic extract and subsequent fractions (n-hexane, chloroform, ethyl acetate, acetone and methanol) were used as test material and anticancer activity was determined via SRB assay at 100g/mL. Results revealed that chloroform fraction of kernel suppressed the proliferation of human breast cancer cellline with growth inhibition of 89%. The fraction of kernel was then evaluated at lower concentrations of 50, 40, 30, 20 and 10g/mL. Further IC50 value was calculated and it was observed that the fraction showed IC5038.66. To conclude, kernel part of Prunus armeniaca possesses certain constituents with cytotoxic properties that can be used to develop anticancer agents especially for breast cancer therapy and to provide a great service to cancer patients.Further studies are required for the isolation of active ingredients from the kernel part.

Motivation Recent studies have shown the potential of using long-read whole-genome sequencing (WGS) approaches and optical mapping (OM) for the detection of clinically relevant structural variants (SVs) in cancer research. Three main long-read WGS platforms are currently in use: Pacific Biosciences (PacBio), Oxford Nanopore Technologies (ONT) and 10x Genomics. Recently, whole-genome OM technology (Bionano Genomics) has been introduced into human diagnostics. Questions remain about the accuracy of these long-read sequencing platforms, how comparable/interchangeable they are when searching for SVs and to what extent they can be replaced or supplemented by OM. Moreover, no tool can effectively compare SVs obtained by OM and WGS. Results This study compared optical maps of the breast cancer cell line SKBR3 with AnnotSV outputs from WGS platforms. For this purpose, a software tool with comparative and filtering features was developed. The majority of SVs up to a 50 kbp distance variance threshold found by OM were confirmed by all WGS platforms, and ∼99% of translocations and ∼80% of deletions found by OM were confirmed by both PacBio and ONT, with ∼70% being confirmed by 10x Genomics in combination with PacBio and/or ONT. Interestingly, long deletions (>100 kbp) were detected only by 10x Genomics. Regarding insertions, ∼74% was confirmed by PacBio and ONT, but none by 10x Genomics. Inversions and duplications detected by OM were not detected by WGS. Moreover, the tool enabled the confirmation of SVs that overlapped in the same gene(s) and was applied to the filtering of disease-associated SVs. Availability and implementation https://github.com/novosadt/om-annotsv-svc.

Background: Cancer is the second cause of death in developed countries. Colon and breast cancers are among the most prevalent ones. Research focusing on finding new natural products with fewer side effects to fight cancer is increasing. Objectives: The present study aimed to evaluate the cytotoxicity of Centaurea albonitens Turrill methanol extract and its fractions against colon and breast cancer cell lines and a normal cell line of bovine kidney cells. Methods: The methanol extract and petroleum ether, chloroform and aqueous fractions were provided from the aerial parts of C. albonitens by maceration method in three days. Each day the solvent was refreshed. Colon (HT-29) and breast (MCF-7) cell lines were treated with the extract/fractions for 48 h for evaluating the cytotoxic activity by MTT assay. The apoptotic induction potential was also evaluated with the Hoechst 33258 staining method. Results: The most considerable effect was reported from the chloroform fraction with IC50 values of 25.6 and 25.1 μg/mL in MCF-7 and HT-29 cells, respectively. In Hoechst staining, condensed chromatin of the apoptotic cells was observed in both cell lines. Conclusion: Centaurea albonites can be suggested for further cancer research studies.

Background: By considering [6]-gingerol as an important polyphenol, ginger has been related to cancer. Objective: The main objective of this study is to evaluate the ginger extract on the expressions of four genes from different categories involved in breast cancer in Balb/C mice after 14 days. Methods: In terms of this research, ethanol extraction methods for extracting ginger rhizomes with the goal of increasing [6]-gingerol were used. In this regard, a MTT test was accomplished for the whole ginger extract to confirm its effect on the 4T1 breast cancer cell line (murine mammary carcinoma cell). Afterward, the transplanted breast cancer Balb/C mouse was used to be treated with the whole ginger extract (0.02 g/kg of mouse weight). The expressions of STAT3, β-catenin, P53, APC, genes were evaluated, after 14-day of treatment. Results: The results showed that 70% ethanol and microwave extraction method can be considered as the best method for extracting ginger extract. The expression of β-catenin has decreased in the blood and liver of the treated group. Moreover, the expression of STAT3 oncogenes has significantly decreased in the liver tissue. In addition, the expressions of APC suppressor genes have increased in the blood and liver. Conclusion: In conclusion, treatment by 0.02 g/kg of mouse weight of ginger extract after 14 days increased the expressions of APC as suppressor genes and a β-catenin oncogene in blood and liver of the breast cancer group.

In this study, we present initial data for the potential anti-cancer effects of standardized Bulgarian Petasites hybridus root extract against breast cancer cells. The results showed that Butterbur extract (BE) caused a dose-dependent selective reduction in viability with concomitant increase of apoptosis in human breast cancer cells after 72 h treatment. We found the highest cytotoxicity of BE to MDA-MB-231 cells (IC50 – 520 μg/mL), followed by the MCF-7 cancer cell line (IC50 – 865 μg/mL). At the same time, the extract exhibited very low cytotoxicity to the non-tumorigenic L929 cell line (two-fold higher inhibitory concentration – 1252 μg/mL). As a result of our experiments we made the conclusion that Butterbur root extract shows selective high cytotoxicity and nucleus alterations in cancer cells comparing to non-cancerous cells.

The biomolecule-coated nanotitania catalysts were synthesised using rhizome extract of Gloriosa superba and the characteristics of the synthesised nanocatalysts were investigated by using various physiochemical methodologies. The antibacterial activity of the biomolecule coated nanotitania catalysts was tested against harmful microbial human pathogens. Nanotitania catalysts were found to be the most potential agent against gram negative bacterium i.e. Staphylococcus epidermidis. An efficient anti-biofilm activity was also observed against biofilm developing bacteria namely S. epidermidis and Pseudomonas aeruginosa. The 50% inhibitory concentration (IC50) of nanotitania catalysts noticed was 46.64 and 61.81 µg/mL for MCF-7 (cancer) L929 (normal) cell lines, respectively. Bioengineered nanotitania catalysts exhibited potential anticancer activity against breast cancer cell line. AO/EtBr staining results show distinct morphological variations such as orange and red coloured apoptotic bodies were identified in cancer cells that were treated with nanotitania catalysts. Further, the nuclear changes, mitochondrial depolarization and increased reactive oxygen species (ROS) level were also detected in nanotitania catalysts treated MCF-7 cells by Hoechst, rhodamine and DCFH-DA probe staining techniques. COMET assay confirmed the DNA destruction in the nanotitania treated cancer cells. In addition, the nanotitania catalysts exhibited potential photocatalytic activity against inorganic toxic dyes and the maximum rate of dye degradation was observed for crystal violet. The present results strongly suggest that the biomolecule coated nanotitania catalysts could be used as potential and novel compound towards biomedical as well as photocatalytic applications.

Aim and Objectives: The present study aimed to examine the antiproliferative activity of ethanol extract derived from the Boswellia dalzielii stem bark in breast carcinoma. Methodology: Ethanolic extract of stem bark of Boswellia dalzielii were prepared. Antiproliferative activity was assessed in estrogen receptor (ER)-negative breast carcinoma (MDA-MB-231) cells by 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide assay. Results: Obtained results in 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide assay indicated that ethanol extract of Boswellia dalzielii stem bark showed significant antiproliferative activity in MDA-MB-231 cells in a dose-dependent manner. IC50 of Boswellia dalzielii stem bark ethanol extract in MDA-MB231 was 98. 12 μg/mL. Conclusion: The results obtained suggest that Boswellia dalzielii stem bark extract possesses significant antiproliferative potential which could be mediated by the chemical constituents present in the plant. However, further research needs to be carried out to determine the effect of the extract on the cell cycle and also to determine the type of cell death produced by the extract.

Metastases are the main cause of cancer-related mortality in breast cancer. Although significant progress has been made in the field of tumor metastasis, the exact molecular mechanisms involved in tumor metastasis are still unclear. Here, we report that ATOH8-V1, a novel isoform of ATOH8, is highly expressed in breast cancer and is a negative prognostic indicator of survival for patients. Forced expression of ATOH8-V1 dramatically enhances, while silencing of ATOH8-V1 decreases the metastasis of breast cancer cell lines. Moreover, ATOH8-V1 directly binds to the RhoC promoter and stimulates the expression of RhoC, which in turn enhances the metastasis of breast cancer. Altogether, our data demonstrate that ATOH8-V1 is a novel pro-metastatic factor that enhances cancer metastasis, suggesting that ATOH8-V1 is a potential therapeutic target for treatment of metastatic cancers.

Objectives Breast cancer (BC) is the most commonly diagnosed cancer in women worldwide with a high mortality rate, despite early detection and treatment. Spindle and kinetochore-associated complex subunit 3 (SKA3) is closely correlated with patient outcomes in several cancers. The present study aimed to elucidate the role of SKA3 in BC. Methods The biological functions of SKA3 was investigated by proliferation and migration assays in MDA-MB-231 cells with stable SKA3 knockdown and Hs578T cells ectopically expressing SKA3. Gene Expression Omnibus datasets were utilised to determine the correlation between SKA3 expression and clinical features of BC patients. Results We confirmed that SKA3 mRNA expression is higher in breast tumour tissue than in normal tissue, and that higher SKA3 expression is associated with poor survival rate of BC patients. Knockdown of SKA3 reduced MDA-MB-231 cell proliferation and migration, whereas SKA3 overexpression enhanced the proliferative and migratory ability of Hs578T cells. We also found that SKA3 is involved in regulating cell cycle progression in mitotic exit. Conclusions These results suggest that SKA3 is correlated with BC cell proliferation and migration by promoting cell cycle progression, and could be a novel potential therapeutic target for BC treatment.

Long non-coding RNAs (lncRNAs) have recently been found to be important in gene regulation. lncRNA H19 has been reported to play an oncogenic role in many human cancers. Its specific regulatory role is still elusive. In this study, we developed a novel analytic approach by integrating the synergistic regulation among lncRNAs (e.g., H19), transcription factors (TFs), target genes, and microRNAs (miRNAs) and then applied it to the pan-cancer expression datasets from The Cancer Genome Atlas (TCGA). Using linear regression models, we identified 88 H19-TF-gene co-regulatory triplets, in which 93% of the TF-gene pairs were related to cancer, indicating that our approach was effective to identify disease-related lncRNA-TF-gene co-regulation mechanisms. lncRNAs can function as miRNA sponges. Our further experiments found that H19 might regulate SP1-TGFBR2 through let-7b and miR-200b, ETS1-TGFBR2 through miR-29a and miR-200b, and STAT3-KLF11 through miR-17 in breast cancer cell lines. Our work suggests that miRNA-mediated lncRNA-TF-gene co-regulation is complicated yet important in cancer., Graphical Abstract, Li et al. developed a novel analytic approach by integrating the synergistic regulation among lncRNAs, miRNAs, TFs, and genes, and then applied it to pan-cancer expression data from TCGA. Using linear regression models, they identified 88 H19-TF-gene co-regulatory triplets. Their study shows that lncRNAs can interfere with miRNA-mediated TF-gene interactions.

Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression. We performed whole-genome sequencing of the SKBR3 breast cancer cell line and patient-derived tumor and normal organoids from two breast cancer patients using Illumina/10x Genomics, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT) sequencing. We then inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ensemble of methods. Our findings show that long-read sequencing allows for substantially more accurate and sensitive SV detection, with between 90% and 95% of variants supported by each long-read technology also supported by the other. We also report high accuracy for long reads even at relatively low coverage (25×–30×). Furthermore, we integrated SV and CNV data into a unifying karyotype-graph structure to present a more accurate representation of the mutated cancer genomes. We find hundreds of variants within known cancer-related genes detectable only through long-read sequencing. These findings highlight the need for long-read sequencing of cancer genomes for the precise analysis of their genetic instability.

Our work includes the study of synergistic efficiency of turmeric crude extracts and electrical pulses on breast cancer cell line, MCF-7 (an Estrogen Receptor alpha positive, weakly invasive, lumin...

Background: Apoptosis is a normal physiological phenomenon that plays a pivotal role during embryonic development, retention of tissue homeostasis and pathology. The experimental investigation of apoptotic processes is still challenging and routinely based on the assessment of molecular events like chromatin fragmentation and caspase enzyme activity. The present study was conducted to evaluate the apoptosis inducing effect of the Methanol, aqueous and chloroform extracts of Prunus persica leaves. Methods: Different extracts were obtained by cold extraction process using Methanol, water and Chloroform as solvents. Crude extracts were screened for different phytochemical constituents like flavonoids, tannins, sugars, saponins, and glycosides etc. The apoptotic effect of Prunus persica leaves was examined by DAPI staining assay against MDA-MB-231 (Human breast cancer cell line) and HeLa (Human cervical cancer cell line). Results: The results of the studies revealed that the Chloroform extract have tremendous apoptotic activity on MDA-MB-231 cells and methanolic extract have good apoptotic activity on HeLa cells. Nuclear morphological changes assessed by DAPI shows changes in morphology, apoptotic body formation, cell shrinkage, nuclei that were broken into discrete fragments and cell budding that resulted in cells of various sizes. Conclusion: The phytochemical screening reveals the presence of alkaloids, tannins, Saponins, steroids and flavonoids. The Chloroform extract has shown more effectiveness and less toxicity against MDA-MB-231 and Methanol extract was more apoptotic against HeLa in comparison to others. The present findings clearly indicated that Prunus persica leaves showed dose dependant cytotoxicity.

Chemical investigation into the stems of the medicinal plant Schisandra sphaerandra led to the isolation and identification of a new dibenzocyclooctadiene lignan sphaerandrin A (1) and 11 known ones gomisin B (2), schirubrisin B (3), kadsuphilin B (4), schizandrin (5), benzoylgomisin Q (6), angeloylgomisin Q (7), gomisin G (8), schisanwilsonin O (9), isogomisin O (10), schisantherin D (11), and wuweizisu C (12). The structure of the new compound was elucidated by comprehensive spectroscopic methods including 1 D/2D NMR, HRESIMS, and CD spectrometry. To the best of our knowledge, compounds 2 – 11 were obtained from this species for the first time. All the compounds were evaluated for the cytotoxic activity against the triple-negative breast cancer cell lines MDA-MB-231 and HCC-1937.

Background: DNA methylation plays an important role in the regulation of gene expression in mammalian cells and often occurs at CpG islands in the genome. It is more reversible than genetic variations and has therefore attracted much attention for the treatment of many diseases, especially cancer. In the present study, we investigated the effect of Solanum nigrum Extract (SNE) on the methylation status of the VIM and CXCR4 genes in breast cancer cell lines. Methods: The Trypan blue assay was used to study the effect of SNE at various concentrations of 0, 0.1, 1.5, 2.5, 3.5 and 5 mg/ml for 48 h on the survival of three human breast cancer cell lines MCF7, MDA-MB-468, MDA-MB-231. Methylation status of VIM and CXCR4 genes in breast cancer cell lines was assessed by Methylation-Specific PCR (MSP) method. Also, methylation changes of VIM and CXCR4 genes in breast cancer cell lines after treatment with 0.1 mg/ml of SNE for 6 days were analyzed by MSP method. To confirm the effect of SNE on methylation of VIM and CXCR4 genes, Real-Time PCR was performed. Results: The Trypan blue assay results indicated that treatment with SNE reduced cell viability in a dose-dependent manner in breast cancer cells. Our results showed that treatment of breast cancer cells with 0.1 mg/ml of SNE hypermethylated the VIM, CXCR4 genes and significantly reduced the expression levels of their mRNA (P Conclusion: Our findings reveal for the first time the impact of SNE on the methylation of breast cancer cells.

Breast cancer research has traditionally centred on genomic alterations, hormone receptor status and changes in cancer-related proteins to provide new avenues for targeted therapies. Due to advances in next generation sequencing technologies, there has been the emergence of long, non-coding RNAs (lncRNAs) as regulators of normal cellular events, with links to various disease states, including breast cancer. Here we describe our bioinformatic analyses of a previously published RNA sequencing (RNA-seq) dataset to identify lncRNAs with altered expression levels in a subset of breast cancer cell lines. Using a previously published RNA-seq dataset of 675 cancer cell lines, a subset of 18 cell lines was selected for our analyses that included 16 breast cancer lines, one ductal carcinoma in situ line and one normal-like breast epithelial cell line. Principal component analysis demonstrated correlation with well-established categorisation methods of breast cancer (i.e. luminal A/B, HER2 enriched and basal-like A/B). Through detailed comparison of differentially expressed lncRNAs in each breast cancer sub-type with normal-like breast epithelial cells, we identified 15 lncRNAs with consistently altered expression, including three uncharacterised lncRNAs. Utilising data from The Cancer Genome Atlas (TCGA) and The Genotype Tissue Expression (GETx) project via Gene Expression Profiling Interactive Analysis (GEPIA2), we assessed clinical relevance of several identified lncRNAs with invasive breast cancer. Lastly, we determined the relative expression level of six lncRNAs across a spectrum of breast cancer cell lines to experimentally confirm the findings of our bioinformatic analyses. Overall, we show that the use of existing RNA-seq datasets, if re-analysed with modern bioinformatic tools, can provide a valuable resource to identify lncRNAs that could have important biological roles in oncogenesis and tumour progression.

CD40 is an important tumor necrosis factor receptor TNFR family protein for the development of antitumor response against cancer cells, apart from its role in the regulation of the immune system as a costimulatory molecule. It is broadly expressed on the surface of immune cells and in diverse cancer types, including breast cancer. Here, we analyzed both CD40/CD40 ligand expression in breast cancer cells and tissues using public data sets and overall survival analysis in ungrouped breast cancer patients, as well as in the triple-negative breast cancer subtype. We detected CD40 gene expression along with its 3 different splice variants variants 1-3 , predominantly in the triple-negative subgroup of breast cancer cell lines. The results of the overall survival analysis showed that high CD40 gene expression, particularly in the triple-negative subgroup of breast cancer patients, is associated with better survival. In addition to the transcriptional levels of CD40 splice variants, investigation of protein levels of these variants will allow the categorization of breast cancer cells and reveal their potential as an immunotherapeutic target.

The ocean is abundant in organisms beneficial to living beings, including cyanobacteria that are widely studied for their bioactive compounds. This research was conducted to observe the compounds and concomitant cytotoxic activities of cyanobacteria in Udar Island waters, Sabah, Malaysia, against cancer cells. The samples were identified by the 16S DNA method, and a phylogenetic tree was built to check similarities in the genus. The samples were extracted using ethyl acetate and butanol. Afterward, the compounds were determined by Liquid Chromatography-Mass Spectrometry (LCMS), while the cytotoxicity activities were examined by the MTT assay. Several known compounds in ethyl acetate crude extract, such as several types of Apratoxins, and possible new compounds were observed. The compounds examined were mainly peptide. The crude ethyl acetate extracts of Moorea sp. in Udar Island waters were found to contain cytotoxic compounds, with the IC 50 value of 0.072 µg/mL against the MCF-7 breast cancer cell lines, that were more potent compared to the butanol crude extract, whose IC 50 was 2.031 µg/mL. Further isolation and cytotoxic tests are necessary to confirm which compounds are responsible as cytotoxic agents. This finding provides an opportunity for the discovery of anticancer compounds from marine cyanobacteria.

In this work, the synthesizing procedure of superparamagnetic iron oxide nanoparticles (SPIONs), which were observed with small ranged sizes, has been successfully performed by an ecological and green methodology. The report includes the synthesis and characterization of superparamagnetic iron oxide nanoparticles from iron salts in the aqueous extracts of (Aloe Vera leaves) and (Flaxseed) that had been achieved through a green co-precipitation technique. Although in accordance with the obtained X-ray diffraction (XRD), the composed samples have been pure Fe3O4 that contained a spinel structure, yet there have not been any phase changes in regards to the coating of herbal extracts. As it has been indicated by the field emission scanning electron microscopy (FESEM), the ordinary spheres of Fe3O4 particles, coated by herbal extracts, have been regular spheres that measured to be in sizes of about ~ 54 emu/g) and the flaxseed/SPIONs ( ~ 51 emu/g), the in vitro cytotoxicity assessments on MCF-7 Breast cancer cell line have reported the observation of a dose-dependent toxicity with low toxic effect in regards to concentrations below 4.7 μg/mL.

A new study in Nature determines metastatic tropism in xenograft mouse models. This results in a metastasis map for 21 tumor types, the utility of which is demonstrated by identifying lipid metabolism to be uniquely altered in breast cancer cell lines that metastasize to the brain.

Normalization of gene expression using internal controls or reference genes (RGs) has been the method of choice for standardizing the technical variations in reverse transcription quantitative polymerase chain reactions (RT-qPCR). Conventionally, ACTB and GAPDH have been used as reference genes despite evidence from literature discouraging their use. Hence, in the present study we identified and investigated novel reference genes in SK-BR-3, an HER2-enriched breast cancer cell line. Transcriptomic data of 82 HER2-E breast cancer samples from TCGA database were analyzed to identify twelve novel genes with stable expression. Additionally, thirteen RGs from the literature were analyzed. The expression variations of the candidate genes were studied over five successive passages (p) in two parallel cultures S1 and S2 and in acute and chronic hypoxia using various algorithms. Finally, the most stable RGs were selected and validated for normalization of the expression of three genes of interest (GOIs) in normoxia and hypoxia. Our results indicate that HSP90AB1, DAD1, PFN1 and PUM1 can be used in any combination of three (triplets) for optimizing intra- and inter-assay gene expression differences in the SK-BR-3 cell line. Additionally, we discourage the use of conventional RGs (ACTB, GAPDH, RPL13A, RNA18S and RNA28S) as internal controls for RT-qPCR in SK-BR-3 cell line.

Recent technological developments allow us to measure the status of dozens of proteins in individual cells. This opens the way to understand the heterogeneity of complex multi‐signaling networks across cells and cell types, with important implications to understand and treat diseases such as cancer. These technologies are, however, limited to proteins for which antibodies are available and are fairly costly, making predictions of new markers and of existing markers under new conditions a valuable alternative. To assess our capacity to make such predictions and boost further methodological development, we organized the Single Cell Signaling in Breast Cancer DREAM challenge. We used a mass cytometry dataset, covering 36 markers in over 4,000 conditions totaling 80 million single cells across 67 breast cancer cell lines. Through four increasingly difficult subchallenges, the participants predicted missing markers, new conditions, and the time‐course response of single cells to stimuli in the presence and absence of kinase inhibitors. The challenge results show that despite the stochastic nature of signal transduction in single cells, the signaling events are tightly controlled and machine learning methods can accurately predict new experimental data., This study presents the results and conclusions of the ‘Single Cell Signaling in Breast Cancer DREAM challenge’, where teams were challenged to use state‐of‐the‐art methods for predicting single‐cell signaling from single‐cell and bulk proteomics, transcriptomics and genomics data.

Background Breast cancer cell lines (BCCLs) and patient-derived xenografts (PDXs) are the most frequently used models in breast cancer research. Despite their widespread usage, genome sequencing of these models is incomplete, with previous studies only focusing on targeted gene panels, whole exome or shallow whole genome sequencing. Deep whole genome sequencing is the most sensitive and accurate method to detect single nucleotide variants and indels, gene copy number and structural events such as gene fusions. Results Here we describe deep whole genome sequencing (WGS) of commonly used BCCL and PDX models using the Illumina X10 platform with an average ~ 60 × coverage. We identify novel genomic alterations, including point mutations and genomic rearrangements at base-pair resolution, compared to previously available sequencing data. Through integrative analysis with publicly available functional screening data, we annotate new genomic features likely to be of biological significance. CSMD1, previously identified as a tumor suppressor gene in various cancer types, including head and neck, lung and breast cancers, has been identified with deletion in 50% of our PDX models, suggesting an important role in aggressive breast cancers. Conclusions Our WGS data provides a comprehensive genome sequencing resource of these models.

Microtubules are critical for a variety of cellular processes such as chromosome segregation, intracellular transport and cell shape. Drugs against microtubules have been widely used in cancer chemotherapies, though the acquisition of drug resistance has been a significant issue for their use. To identify novel small molecules that inhibit microtubule organization, we conducted sequential phenotypic screening of fission yeast and human cells. From a library of diverse 10 371 chemicals, we identified 11 compounds that inhibit proper mitotic progression both in fission yeast and in HeLa cells. An in vitro assay revealed that five of these compounds are strong inhibitors of tubulin polymerization. These compounds directly bind tubulin and destabilize the structures of tubulin dimers. We showed that one of the compounds, L1, binds to the colchicine-binding site of microtubules and exhibits a preferential potency against a panel of human breast cancer cell lines compared with a control non-cancer cell line. In addition, L1 overcomes cellular drug resistance mediated by βIII tubulin overexpression and has a strong synergistic effect when combined with the Plk1 inhibitor BI2536. Thus, we have established an economically effective drug screening strategy to target mitosis and microtubules, and have identified a candidate compound for cancer chemotherapy.

Background Breast cancer is one of the most important causes of mortality in the world, and Tamoxifen therapy is known as a medication strategy for estrogen receptor-positive breast cancer. In current study, two hypotheses of Tamoxifen consumption in breast cancer cell line (MCF7) were investigated. First, the effect of Tamoxifen on genes expression profile at transcriptome level was evaluated between the control and treated samples. Second, due to the fact that Tamoxifen is known as a mutagenic factor, there may be an association between the alterations of genetic variants and Tamoxifen treatment, which can impact on the drug response. Methods In current study, the whole-transcriptome (RNA-seq) dataset of four investigations (19 samples) were derived from European Bioinformatics Institute (EBI). At transcriptome level, the effect of Tamoxifen was investigated on gene expression profile between control and treatment samples. Moreover, Tamoxifen is known as a mutagenic factor, therefore, its contribution to alterations of genetic variants and drug response were examined. Results Results achieved from RNA-seq analysis indicated the contribution of several candidate genes to tumor suppression process and consequently, the achievement of an effective treatment. For instance, XIAP-associated factor 1 (XAF1) was reported as an up-regulated gene under Tamoxifen therapy. XAF1 is a tumor suppressor that contributes to the apoptosis induction and tumor growth inhibition along with TP53. Results of gene ontology enrichment analysis of differential gene expressions indicated that most of them could considerably lead to the cell death, apoptosis, and negative regulation of proteolysis process. Findings achieved from evaluating Tamoxifen mutagenicity effect on drug response was not confirmed perfectly. The most reported candidate genes, which were related to differential genetic variants between control and treated samples, played the oncogene and tumor suppressor dual roles and also their exact roles in breast cancer were not investigated precisely. Conclusion At transcriptome level, Tamoxifen consumption in MCF7 cell line could be associated with candidate genes and biological pathways that contribute to the apoptosis, proteolysis, and tumor suppression. The mutagenicity effect of Tamoxifen and its contribution to drug response was not confirmed perfectly.

Bone is one of the most common metastatic sites of breast cancer, and bone metastasis profoundly affects the quality of life of breast cancer patients. Bone metastasis is commonly observed among all the subtypes of breast cancer; however, its molecular mechanism has been analyzed only in triple-negative subtype of breast cancer (TNBC). To characterize the molecular mechanisms of bone metastasis of luminal breast cancer, we established a bone-metastatic model of the MCF7, luminal breast cancer cell line, with enhanced osteolytic activity by intracaudal arterial injection (CAI). Pathological analysis of the established cell lines revealed that they exhibited fierce osteolytic ability by promoting osteoclast differentiation and activity. The signature genes extracted from highly osteolytic MCF7 cell lines were differed from those of bone-metastatic TNBC cell lines. Our results suggest that unique mechanisms of osteolysis in bone-metastatic lesions of luminal breast cancer. In addition, several up-regulated genes in MCF7-BM (Bone Metastasis) 02 cell lines correlated with poor prognosis with luminal breast cancer patients. Our findings support further study on the bone-metastatic mechanisms of luminal breast cancer.

Drug sensitivity biomarkers are molecular features informative for drug response. Previous studies have identified many candidate drug-sensitivity signatures at the transcript level based on significant p values. However, the potential of sensitivity biomarkers has not been sufficiently understood because these investigations have focused on individual biomarkers and have not been carried out at the systems level. In this study, we applied a meta-analytical framework to compute co-expression between isoform pairs in two large datasets of RNA-seq profiles of breast cancer cell lines. We then built hallmark-related direct (HRD) networks by integrating a breast cancer specific isoform co-expression (BCIC) network and hallmark-related isoforms. Next, we explored the associations between isoform biomarkers and the functional clusters of the HRD network. The crucial isoform-based biomarkers for drugs were identified by functional clusters analysis and elucidated by combining isoform expression profiles with clinical information for breast cancer in The Cancer Genome Atlas.

Isoliquiritigenin (2’,4’,4-trihydroxychalcone, ISL) is one of the most important chalcone compounds which is mainly derived from licorice root and many other plants. It exhibits a remarkable range of potent biological and pharmacological activities such as antioxidative, antitumor, antiaging, anti-inflammatory, anti-diabetic activities, etc. Numerous research teams have demonstrated that ISL posseses the ability to carry out antigrowth and proliferation in various cancer cells in vitro and in vivo. Meanwhile, the underlying mechanisms of ISL that inhibit cancer cell proliferation have not been well explored. However, the poor bioavailability and low water-soluble limit its clinical application. This review aims at providing a comprehensive overview of the pharmacology antitumor activity of ISL and its mechanisms in different malignancy especially in breast cancer cell line and summarize developments of formulation utilized to overcome the barrier between its delivery characteristics and application in clinics over the past 20 years.

Background and Objectives: Given the rising prevalence of breast cancer in Iran over the past two decades and also high mortality rate of the patients, and on the other hand, according to oral administration, low cost, and easy public access to hyssop (Hyssopus officinalis), in this study, the effectiveness of this herbal product, was investigated on MCF-7 breast cancer cell line. Methods: In this experimental study, MCF-7 cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum (FBS) and 5% CO2 at 37°C with concentrations of 10-1000µg/mL of the hyssop extract. To evaluate the cytotoxic effect of the extract on the cells, colorimetric method MTT, was used and the viability rate of the cells was determined. The results were analyzed by t-test. Results: In this study, using colorimetric method MTT, after 72 hours, the methanol extract of hyssop flower in the concentration of more than 500µg/mL, could reduce the chances of viability of MCF-7 cells from 100% to 60%, while the ethanol extract of hyssop leaves has little effect on death of MCF-7 cancer cells. Conclusion: According to the results of this study, it seems that methanol extract of hyssop flower has a significant cytotoxic effect on MCF-7 cell. Therefore, with further research on active substancesof this plant, it can be used in the treatment of cancer in the future.

Mass spectrometry (MS) has become the technique of choice for large-scale analysis of histone post-translational modifications (hPTMs) and their combinatorial patterns, especially in untargeted settings where novel discovery-driven hypotheses are being generated. However, MS-based histone analysis requires a distinct sample preparation, acquisition, and data analysis workflow when compared to traditional MS-based approaches. To this end, sequential window acquisition of all theoretical fragment ion spectra (SWATH) has great potential, as it allows for untargeted accurate identification and quantification of hPTMs. Here, we present a complete SWATH workflow specifically adapted for the untargeted study of histones (hSWATH). We assess its validity on a technical dataset of time-lapse deacetylation of a commercial histone extract using HDAC1, which contains a ground truth, i.e., acetylated substrate peptides reduce in intensity. We successfully apply this workflow in a biological setting and subsequently investigate the differential response to HDAC inhibition in different breast cancer cell lines.

Two highly oxygenated nortriterpenes, picraviane A and B, were isolated from the ethanolic extract of Picramnia glazioviana Engl. The structures were determined by analysis of HRMS and 2D NMR spectroscopic data. Single-crystal X-ray diffraction data was also obtained for picraviane B. The absolute configuration of both compounds were assigned by comparison of experimental and calculated vibrational and electronic circular dichroism spectroscopy, respectively. Picraviane A showed a moderate cytotoxic activity against the triple negative MDA-MB-231 breast cancer cell line. These compounds represent an undescribed class of natural products with limonoid-like skeletons containing a heptanolide as the E-ring.

Background: Given the scarcity of cell lines from underrepresented populations, it is imperative that genetic ancestry for these cell lines is characterized. Consequences of cell line mischaracterization include squandered resources and publication retractions. Methods: We calculated genetic ancestry proportions for 15 cell lines to assess the accuracy of previous race/ethnicity classification and determine previously unknown estimates. DNA was extracted from cell lines and genotyped for ancestry informative markers representing West African (WA), Native American (NA), and European (EUR) ancestry. Results: Of the cell lines tested, all previously classified as White/Caucasian were accurately described with mean EUR ancestry proportions of 97%. Cell lines previously classified as Black/African American were not always accurately described. For instance, the 22Rv1 prostate cancer cell line was recently found to carry mixed genetic ancestry using a much smaller panel of markers. However, our more comprehensive analysis determined the 22Rv1 cell line carries 99% EUR ancestry. Most notably, the E006AA-hT prostate cancer cell line, classified as African American, was found to carry 92% EUR ancestry. We also determined the MDA-MB-468 breast cancer cell line carries 23% NA ancestry, suggesting possible Afro-Hispanic/Latina ancestry. Conclusions: Our results suggest predominantly EUR ancestry for the White/Caucasian-designated cell lines, yet high variance in ancestry for the Black/African American–designated cell lines. In addition, we revealed an extreme misclassification of the E006AA-hT cell line. Impact: Genetic ancestry estimates offer more sophisticated characterization leading to better contextualization of findings. Ancestry estimates should be provided for all cell lines to avoid erroneous conclusions in disparities literature.

Cell lines are widely-used models to study metastatic cancer although the extent to which they recapitulate the disease in patients remains unknown. The recent accumulation of genomic data provides an unprecedented opportunity to evaluate the utility of them for metastatic cancer research. Here, we reveal substantial genomic differences between breast cancer cell lines and metastatic breast cancer patient samples. We also identify cell lines that more closely resemble the different subtypes of metastatic breast cancer seen in the clinic and show that surprisingly, MDA-MB-231 cells bear little genomic similarities to basal-like metastatic breast cancer patient samples. Further comparison suggests that organoids more closely resemble the transcriptome of metastatic breast cancer samples compared to cell lines. Our work provides a guide for cell line selection in the context of breast cancer metastasis and highlights the potential of organoids in these studies., While cell lines and organoids are extensively used to study cancer, how closely they resemble the disease in patients remains unclear. Here, Liu et al. shed light on this issue by comparing the genomic and transcriptomic profiles of different breast cancer cell lines and organoids to data from patient-derived breast cancer metastases.

Background and Objectives: Breast cancer is one of the most common cancers in women around the world. Problems, such as treatment failure, drug resistance, heavy costs, other problems associated with the treatment of this type of cancer, have attracted the interest of many researchers to cyanobacteria, since these microorganisms have fewer side-effects compared to chemical drugs. In the present research, the effect of Oscillatoria extract was investigated on the viability of MCF7 cell line as well as caspase-9 gene expression. Methods: In this experimental study, MCF7 cell lines, were treated with different concentrations of extract of Oscillatoria cyanobacteria (0.078, 0.15, 0.3, 0.6, 1.2, 2.5, 5, and 10mg/ml) for 24 hours. The effect of the extract on cell viability was assessed using MTT assay. Then, RNA extraction was carried out, and after synthesis of cDNA, real time PCR was performed to assess the expression rate of caspase-9 gene. Results: With increasing the concentration of the extract, cell viability significantly decreased compared to the control sample. Real time PCR results also showed that the expression of caspase-9 gene increased by 5.59 ± 0.83 (p

Objective: The objective of this study was to determine the new bioactive compounds through gas chromatography–mass spectrometry analysis and the cytotoxic activity of two rodent tuber mutant plants against breast cancer cells (MCF-7). Methods: The bioactive compounds in rodent tuber mutant plants were successfully increased by somaclonal variation using gamma rays irradiation technique. Further, the cytotoxicity activity of rodent tuber mutant plants was tested on breast cancer cell line (MCF-7) performed by 3-(4,5-dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide assay method. Results: This results study confirmed that the presence of phytochemical composition in the tuber of rodent tuber mutant plants KB 6–1–3–4 and KB 6–9–5 was found six bioactive compounds from fatty acid groups which have the potential as an anticancer compound, such as octadecanoic acid, hexadecanoic acid, hexadecanoic acid methyl ester, 9-octadecanoic acid, linolelaidic acid methyl ester, and butanoic acid. The results showed that extracts from rodent tuber mutant plants had a cytotoxicity effect on MCF-7 cancer cells with half maximal inhibitory concentration (IC50) values that were lower than the control (mother plant). In vitro tests of KB 6–1–3–4 and KB 6–9–5 against MCF-7 cancer cell lines have IC50 values of 12.482 μg/mL and 7.043 μg/mL, respectively, while it had a lower cytotoxicity effect with the IC50 value of control plant was 19.113 μg/mL. The mutant plants of KB 6-9-5 have 3 times more effective than control. Conclusion: The results of this study clearly indicated that rodent tuber mutant plants have shown promising as an anticancer drug on breast cancer.

Traditional medicines, derived from plants, could present alternative treatment strategy for cancer therapy. One such plant is Momordica charantia (MC) which possesses anti-carcinogenic properties. This study investigated the anticancer effect of an ethanol extract of MC fruit, Kuguacin-J (K-J), an isolated compound from the leaves of MC and cisplatin, either alone or combination on healthy MCF-10A mammary cells and compared with breast cancer MCF-7 and MDAMB-231 cell lines. Cell viability was tested using 8 μg/mL and 80 μg/mL doses of MC extract, K-J and cisplatin individually or combined for 24 and 48 hours. Caspase-3- activity was measured in MCF-7 and MDA-MB-231 cells using established methods. The results revealed that MC extract and K-J had no effect on healthy MCF-10A cell viability as compared to cisplatin which induced dose and time-dependent cell death. Similarly, treatment of MCF-7 cells with cisplatin induced cell death at high concentration at both the time points, while MC extract and K-J only induce MCF-7 cell death at high dose after 48 hours only. During combination therapy, both doses of cisplatin enhanced MCF-7 cell death when combined with MC extract or K-J after 24 and 48 hours. In MDAMB-231 cells, the three drugs, either alone or combined, evoked significant cell death at both the doses and time points. All three drugs, at high dose, elicited significant increase in caspase-3- activity in MCF-7 and MDA-MB-231 cells as compared to untreated cells. The results revealed that either MC extract or K-J alone or combined with cisplatin, can elicit significant increase in cell death and caspase–3-activity in MCF-7 and MDA-MB-231cells as compared to untreated cells.

Isolation and identification of compounds and pharmacological activity of the Micromelum minutum grown in some countries has been done, but the Indonesian M. minutum has not been studied, either phytochemically or pharmacologically. This study aimed to determine the cytotoxic activity of Indonesian M. minutum leave extracts toward MCF-7 and 4T1 breast cancer cell lines. The leaves were obtained from M. minutum grow in Bantimurung National Park, Bulusaraung, South Sulawesi, and then were macerated gradually in hexane, ethyl acetate, and methanol. The cytotoxic activity of obtained extracts was determined by MTT assay. The extraction yielded hexane (HEM), ethyl acetate (EEM), and methanol (MEM) extracts of 2.65, 6.12, and 6.49%, respectively. HEM was the most potent extract with IC50 values of 148 and 87 µg/mL on MCF-7 and 4T1 cells, respectively, followed by EEM (185 and 170 µg/mL). MEM possessed a weak potency with an IC50 value of 384 µg/mL on MCF-7 cells and was not toxic toward 4T1 cells. Therefore, HEM is important to be further investigated for its active constituents.

The dysregulation of cyclin-CDK6 interactions has been implicated in human breast cancer, providing a rationale for more therapeutic options. Recently, ATP-competitive inhibitors have been employed for managing breast cancer. These molecules, like most natural CDKs inhibitors, potently bind in the ATP-binding site of CDK6 to regulate trans-activation. Nonetheless, only a few numbers of these molecules are approved to mitigate breast cancer, thus, ensuring that the search for more selective inhibitors continues. In this study, we attempted to establish the selective predictive models for identifying potent CDK6 inhibitors against a human breast cancer cell-line using a dataset of fifty-two 1,3,4-thiadiazole derivatives. The significant eight descriptor hybrid QSAR models generated exhibited encouraging statistical attributes including

Radioresistance-a living cell's response to, and development of resistance to ionising radiation-can lead to radiotherapy failure and/or tumour recurrence. We used Raman spectroscopy and machine learning to characterise biochemical changes that occur in acquired radioresistance for breast cancer cells. We were able to distinguish between wild-type and acquired radioresistant cells by changes in chemical composition using Raman spectroscopy and machine learning with 100% accuracy. In studying both hormone receptor positive and negative cells, we found similar changes in chemical composition that occur with the development of acquired radioresistance; these radioresistant cells contained less lipids and proteins compared to their parental counterparts. As well as characterising acquired radioresistance in vitro, this approach has the potential to be translated into a clinical setting, to look for Raman signals of radioresistance in tumours or biopsies; that would lead to tailored clinical treatments.

Under normal physiological conditions, IGF-1 (insulin-like growth factor-1) has important biological effects. However, many studies have found that IGF-1 is closely related to the occurrence and development of breast cancer. But up to now, the cellular properties of IGF-1 have not been systematically explored in breast cancer cell. It is well-known that the cellular properties and behaviors of IGF-1/IGF-1R are closely related to its biological functions. In the current study, we used the breast cancer cell line as a model to explore the biological characteristics of IGF-1/IGF-1R, and found that IGF-1/IGF-1R can be internalized into the cytoplasm. In addition, we also found that IGF-1R can also enter cell nuclei under the mediation of IGF-1. Further research found that the nuclear-localized IGF-1R has important potential biological effects, which is closely associated to the proliferation of breast cancer cell, this may be achieved by regulating IGF-1R-mediated intracellular signaling. The current research has laid the foundation for investigating the relationship between IGF-1/IGF-1R system and the occurrence and development of breast cancer.

We evaluated in vitro a series of telluride containing compounds bearing the benzenesulfonamide group, as effective inhibitors of the physiologically relevant human (h) expressed Carbonic Anhydrase (CA; EC 4.2.1.1) enzymes I, II, IV VII and IX. The potent effects of such compounds against the tumor-associated hCA IX being low nanomolar inhibitors (KI 2.2 to 2.9 nM) and with good selectivity over the ubiquitous hCA II, gave the possibility to evaluate their lethal effect in vitro against a breast cancer cell line (MDA-MB-231). Among the series, both compounds 3a and 3g induced significant toxic effects against tumor cells after 48 h incubation. Under normoxic condition 3a showed high efficacy killing over 94% of tumor cells at 1 µM, and derivative 3g reached the tumor cell viability under the 5% at 10 µM. In hypoxic condition, these two compounds showed less effective although retained excellent cancer cell killer. These unusual features make them interesting lead compounds acting as antitumor agents also in tumor types not dependent from hCA IX overexpression.