Mammary Carcinoma, Human
It is characterized by the abnormal growth and proliferation of cells within the breast tissue.
This condition can range from non-invasive forms, such as ductal carcinoma in situ, to invasive forms that spread to surrounding tissues and lymph nodes.
Mammary Carcinoma is a complex disease with various subtypes and genetic profiles, requiring personalized treatment approaches.
Early detection and prompt management are crucial for improving patient outcomes.
PubCompare.ai's AI-driven platform can help optimize research on Mammary Carcinoma by facilitating access to the best protocols, products, and literature, enhancing reproducibility and accuracy in the research process.
Most cited protocols related to «Mammary Carcinoma, Human»
Differential gene expression was corrected for promiscuity across metabolic pathways by dividing the Wald t-value statistics obtained from DESeq analysis by the number of associated pathways (promiscuity). Corrected t-values were then used as input for GSEA. GSEA was performed by applying the manually curated metabolic gene signature to promiscuity-corrected t-values according to the algorithm developed by Subramanian et al.7 (link) by using the R package ‘piano' (version 1.6.2)31 (link).
Validation of the core metabolic signature in primary cancers (
We applied a mild variation filter using Cancer Outlier Profiler Analysis (COPA, 95th percentile) [34 (link)] to select the top 10,000 genes to be clustered in each of the human breast cancer datasets (GSE1456, GSE3494, GSE7390, GSE11121). In each dataset expression values were centered by setting the median value of each gene to zero (subtracting the gene-specific medians) and clustering analyses were performed for each dataset and species independently using hierarchical clustering with three different similarity metrics or distance metrics, respectively:
• Context-Specific Infinite Mixture Models (CSIMM) [22 (link)]. For any given pair or genes, this Bayesian method estimates the posterior pairwise probability (PPP) of the genes being co-clustered. The resulting PPP matrix is used as the similarity measure for the hierarchical clustering algorithm.
• Pearson Correlation of gene expression values as the similarity measure.
• Euclidian Distance based on per-gene normalized expression values as the distance measure.
All three hierarchical clustering algorithms used Average Linkage.
Each clustering analysis was then repeated after further variance based re-scaling each dataset by dividing expression levels by their standard deviation for each gene and each datasets separately. When computing the Pearson correlation, expression values are implicitly divided by the standard deviation. Thus, this additional normalization step did not significantly affect Pearson's correlations.
All statistical analyses were performed using the statistical programming environment R version 2.7.1 [36 ] and Bioconductor release 2.2 [37 (link)].
Most recents protocols related to «Mammary Carcinoma, Human»
Example 23
We have demonstrated that LXR agonists inhibit in vitro cancer progression phenotypes in breast cancer, pancreatic cancer, and renal cancer. To investigate if LXR agonist treatment inhibits breast cancer primary tumor growth in vivo, mice injected with MDA-468 human breast cancer cells were treated with either a control diet or a diet supplemented with LXR agonist GW3965 2 (
To determine the effect of orally delivered GW3965 2 on breast cancer tumor growth, 2×106 MDA-468 human breast cancer cells were resuspended in 50 μL PBS and 50 μL matrigel and the cell suspension was injected into both lower memory fat pads of 7-week-old Nod Scid gamma female mice. The mice were assigned to a control diet treatment or a GW3965-supplemented diet treatment (75 mg/kg/day) two days prior to injection of the cancer cells. The GW3965 2 drug compound was formulated in the mouse chow by Research Diets, Inc. Tumor dimensions were measured using digital calipers, and tumor volume was calculated as (small diameter)2×(large diameter)/2.
Treatment with GW3965 resulted in significant reduction in breast cancer tumor size in vivo (
Example 25
This experiment was to evaluate the effect of killing cancer cells by treating MDA-MB-231 cells (human breast cancer cells) with the test substance GI-101 alone or in combination with the TGF-beta signal inhibitor Vactosertib substance in an in vitro environment.
MDA-MB-231 cells were purchased from the Korea cell line bank and cultured in RPMI1640 medium (Gibco) containing 10% FBS (Gibco) and 1% antibiotic/antifungal agent (Gibco). For use in cancer cell killing test, the cells were harvested using trypsin (Gibco), and then suspended in RPMI1640 medium, and then dead cells and debris were removed using Ficoll (GE Healthcare Life Sciences) solution. The cells suspended in RPMI1640 medium were carefully layered on ficoll solution. The cell layer with a low specific gravity formed by centrifuging at room temperature at 350×g for 20 minutes was collected with a pipette, washed with PBS (Gibco), and then centrifuged at room temperature at 350×g for 5 minutes. The separated cell layer was made into a suspension of 2×105 cells/mL with FBS-free RPMI1640 medium. The cancer cell suspension was stained at 37° C. for 1 hour using CELLTRACKER™ Deep Red Dye (Thermo) in order to track proliferation or inhibition of the proliferation of cancer cells. After staining, it was centrifuged at 1300 rpm for 5 minutes, and then it was washed with FBS-free RPMI1640 medium, and then suspended in RPMI1640 medium containing 5% human AB serum (Sigma) to a concentration of 2×105 cells/mL. The cancer cell suspension was added to each well of a 96-well microplate (Corning) by 50 μl (1×104 cells), and then stabilized in an incubator (37° C., 5% CO2) for 1 hour.
Human peripheral blood mononuclear cells (PBMCs) were used in order to identify the effect of killing cancer cells by GI-101. The human PBMCs were purchased from Zen-Bio, and the PBMCs stored frozen were placed in a 37° C. water bath, and thawed as quickly as possible, and then transferred to RPMI1640 medium (Gibco) containing 10% FBS (Gibco) and 1% antibiotic/antifungal agent (Gibco), and centrifuged at 1300 rpm for 5 minutes. The separated cell layer was suspended in RPMI1640 medium, and then dead cells and debris were removed using Ficoll (GE Healthcare Life Sciences) solution in the same manner as the cancer cell line. The cells suspended in RPMI1640 medium were carefully layered on ficoll solution. The cell layer with a low specific gravity formed by centrifuging at room temperature at 350×g for 20 minutes was collected with a pipette, washed with PBS (Gibco), and then centrifuged at room temperature at 350×g for 5 minutes. The separated cell layer was suspended in RPMI1640 medium containing 5% human AB serum (Sigma) to a concentration of 5×105 cells/mL. The PBMC suspension was dispensed 50 μl into each well of a 96-well microplate (Corning) in which cancer cell line has been dispensed, depending on the conditions.
In order to identify the effect of killing the cells, a CytoTox Green reagent (INCUCYTE™ CytoTox Green, Satorius) that binds to the DNA of cells to be killed was prepared in 1 μl per 1 mL of RPMI1640 medium containing 5% human AB serum (Sigma). The prepared medium was used for dilution of the test substance, and the effect of killing the cells could be quantitatively identified by staining the cells to be killed when the test substance was co-cultured with cancer cell lines and PBMCs.
Vactosertib power was dissolved in DMSO (Sigma) to a concentration of 48.4 mM, and diluted using RPMI1640 medium containing a CytoTox Green reagent, and then used in the experiment at a final concentration of 12.1 nM (50 μL) per well of a 96-well microplate.
GI-101 was diluted by ⅓ using RPMI1640 medium containing a CytoTox Green reagent, and then used in the experiment at final concentrations of 0.4 nM, 1.2 nM, 3.7 nM, 11.1 nM, 33.3 nM, and 100 nM by 50 μl per well of a 96-well microplate.
The prepared test substance was placed in each well of a 96-well microplate in which cancer cell lines and PBMCs were dispensed depending on the conditions, and cultured in an incubator (37° C., 5% CO2) for 24 hours, and the proliferation or death of cancer cells was observed through the real-time cell imaging analysis equipment IncuCyte S3 (Satorious). The death of cancer cells was quantified by the integrated intensity of the cells stained in green with a CytoTox Green reagent.
As a result, it was identified that the group having received a combination of GI-101 and Vactosertib exhibited the excellent effect of killing cancer cells as compared with the group having received each drug alone.
Example 11
MPV.10.34.d IRC Effectiveness in Human Assays
While the in vitro functional test results of the above experiments were promising, the next desired step in the analysis was to perform similar experiments in human-based assays. To this end, the response of mock human cellular immune system components to tumor cells exposed to MPV.10.34.d IRC was examined in vitro. Human CMV (HCMV) was selected for this study since human CMV is highly prevalent (infecting 50-90% of the human population) and mostly asymptomatic in healthy individuals. (See, Longmate et al., Immunogenetics, 52(3-4):165-73, 2001; Pardieck et al., F1000Res, 7, 2018; and van den Berg et al., Med. Microbiol. Immunol., 208(3-4):365-373, 2019). Importantly, HCMV establishes a life-long persistent infection that requires long-lived cellular immunity to prevent disease. Hence, it is rational to hypothesize that a complex adaptive cell-mediated anti-viral immunity developed over many years to strongly control a viral infection in an aging person can be repurposed and harnessed to treat cancer.
In these experiments, CD8+ T cell responses to CMV peptides were tested in three different human tumor cell lines, including HCT116, OVCAR3, and MCF7. All three of these human tumor cell lines are HLA-A*0201 positive.
In vitro cytotoxicity assays. HTC112, human colon cancer cells, MCF7, human breast cancer cells, and OVCAR3, human ovarian cancer cells (all from ATCC, Manassas, VA, US) were seeded overnight at 0.01 to 0.2×106 per well per 100 μL per 96 well plate. The next day (about 20 to 22 hrs later), each cell line was incubated for one hour at 37° C. under the following conditions: (1) CMV peptide at a final concentration of 1 μg/mL (positive control), (2) MPV.10.34.d at a final concentration of 2.5 μg/mL (negative control), (3) CMV-conjugated MPV.10.34.d IRC at a final concentration of 2.5 μg/mL, (4) CMV-conjugated HPV16 IRC at a final concentration of 2.5 μg/mL, and (5) no antigen (negative control). After 1 hour, the cells were washed vigorously with 200 μL of media for three times to remove non-specific binding. Human patient donor CMV T cells (ASTARTE Biologics, Seattle, WA, US) were added at the E:T (effector cell:target cell) ratio of 10:1 and incubated in a tissue culture incubator for 24 hrs at 37 C, 5% CO2. The total final volume of each sample after co-culture was 200 μL. Cell viability was measured after co-culturing. Cell viability was measured with CELLTITER-GLO® (Promega, Madison, WI, US). This assay provides a luciferase-expressing chemical probe that detects and binds to ATP, a marker of cell viability. The amount of ATP generated from tumor cells was quantified according to manufacturer protocols. In these assays, reduced luciferase activity indicates cell death and suggests greater immune redirection and greater cytotoxicity.
The results are provided in
Example 3
MDA-MB-231 and Hs578T cells were prepared and inoculated to a 6-pore plate with a density of 2.5×105 cells/pore. When the cells density reached 70%, add sh-LINC01614-1, sh-LINC01614-2 or sh-Control lentivirus (MOI=10) supernatant to the cell and transduce for 24 hour. Remove and discard the lentivirus-containing transduction medium and replace with fresh growth medium. Continue to incubate the cells for 72 hours. After 72 h, the GFP expression was analysis by a fluorescence microscope. When the expression reached more than 90% indicated a successful transfection.
line MDA-MB-231 was purchased from American Type Culture Collection
(ATCC), and HEK293 stably expressing the 6xHis-SUMO3-Q87R/Q88N mutant
(HEK293-SUMO3m)23 (link) was cultured in Dulbecco’s
modified Eagle’s medium (HyClone) supplemented with 10% fetal
bovine serum (Wisent), 1%
and 1% penicillin/streptomycin (Invitrogen) in 5% CO2 at
37 °C.
For gene knockout, the CRISPR/Cas9-based gene knockout
vectors pCRISPR were purchased from Genecopoeia, Inc. (Rockville,
MD). We ordered three different sgRNAs for each PIAS gene. The sgRNA
sequence for each gene is listed below. PIAS1-sgRNA1: 5′-TTCTGAACTCCAAGTACTGT-3′,
PIAS1-sgRNA2: 5′- GCCCTGCATTTGCTAAAGGC-3′, PIAS1-sgRNA3:
5′- ACTTGAATGTACGTTGGGGA-3′, PIAS2-sgRNA1: 5′-CAAGTATTACTAGGCTTTGC-3′,
PIAS2-sgRNA2: 5′-ATAAATGCAGCGCCCTCATC-3′, PIAS2-sgRNA3:
5′-CTCATCAAGCCCACGAGTTT-3′, PIAS3-sgRNA1: 5′-GCCCTTCTATGAAGTCTATG-3′,
PIAS3-sgRNA2: 5′- ATGGTGACATCAGGGTGCAC-3′, PIAS3-sgRNA3:
5′-GCCCTTCTATGAAGTCTATG-3′, PIAS4-sgRNA1: 5′-GGCTTCGCGCCGTAGTCTTAG-3′,
PIAS4-sgRNA2: 5′- GAAGCACGAGCTCGTCACCA-3′, PIAS4-sgRNA3:
5′-GAGCTTCACC AGGCGGACTTC-3′, and scrambled sgRNA: 5′-GGCTTCGCGCCGTAGTCTTA-3′.
MDA-MB-231 cells or HEK293-SUMO3m cells were transfected with 1 μg
of pCRISPR vector or a scrambled sgRNA vector as negative control
per million cells using JetPrime Reagent (Polyplus-transfection) according
to the manufacturer’s protocol. Single-cell sorting for clonal
cell line development was achieved by fluorescence-activated cell
sorting (FACS) based on Red Fluorescent Proteins-mCherry signals 48
h after transfection. mCherry-positive cells were cultured and expanded
for 2 weeks. PIAS knockout efficiency was confirmed by western blotting.
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More about "Mammary Carcinoma, Human"
This condition is characterized by the abnormal proliferation and growth of cells within the breast tissue, ranging from non-invasive forms like Ductal Carcinoma in Situ (DCIS) to invasive types that can spread to surrounding tissues and lymph nodes.
Mammary Carcinoma has various subtypes, each with unique genetic profiles, requiring personalized treatment approaches.
Understanding the underlying mechanisms and molecular characteristics of Mammary Carcinoma is crucial for developing effective therapeutic strategies.
Cell lines like MCF-7 and MDA-MB-231, commonly used in Mammary Carcinoma research, provide valuable insights into the disease.
These cell lines are typically cultured in media such as DMEM, RPMI 1640, and supplemented with antibiotics like Penicillin and Streptomycin to maintain optimal growth conditions.
Early detection and prompt management of Mammary Carcinoma are essential for improving patient outcomes.
PubCompare.ai's AI-driven platform can help optimize Mammary Carcinoma research by facilitating access to the best protocols, products, and literature, enhancing reproducibility and accuracy in the research process.
This can lead to a deeper understanding of the disease and ultimately, more effective treatments for patients.