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All Data Mphil - Hafsa
All Data Mphil - Hafsa
All Data Mphil - Hafsa
factor (HER2).
If your cancer has any of these three locks, doctors
have a few keys (like hormone therapy or other drugs)
they can use to help destroy the cancer cells.
If your cancer tests positive for these three locks, which are known
as receptors, then doctors have a few keys they can use to get inside the cell
to destroy it.
If you have triple-negative breast cancer, those locks aren't there. So the keys
doctors usually use won't work. But chemotherapy is still an effective option.
HEK cells are easy to culture in a humidified incubator at 37°C and 5% CO₂. They
can be cultivated not only as monolayers but also in suspension.
In addition, HEK cells are very easy to transfect using a variety of methods. A
classical transfection method is the calcium-phosphate procedure. Here, a DNA-
phosphate complex is precipitated onto the cell membrane. Other well-known
methods are electroporation or the use of DEAE-dextran. Special kits for
transfection of HEK cells further simplify the process.
UBE3D depletion in the KO cell line was verified both at the genomic level (Figure S1A) and
protein level.
we tested the protein levels of core cleavage/polyadenylation (C/P) factors in UBE3D KO cells.
CPSF73, but not other C/P subunits, was decreased dramatically in UBE3D KO cells (Figure
1B).
we employed a cycloheximide chase assay (Kao et al., 2015) to analyze the stability of CPSF73
in UBE3D WT and KO cells.
we measured the CPSF73 mRNA levels in the UBE3D wild-type (WT), KO, and
addback cells and observed no change among the groups, suggesting that UBE3D
depletion does not affect transcription or stability of CPSF73 mRNAs and that the
decrease in CPSF73 protein might be owing to post-translational regulation.
reventing protein synthesis.
RNA-seq libraries from WT and UBE3D KO cells and analyzed the data by DoGFinder, a sThat
sounds like a fascinating study! The mRNA endonuclease CPSF73 plays a crucial role in
processing pre-mRNAs, and inhibiting its function could have important implications for
cancer research.
Based on the information you've provided, it seems that targeting CPSF73 could be a
promising approach for inhibiting breast cancer cell migration, invasion, and self-
renewal. These are all key characteristics of cancer cells that contribute to tumor
progression and metastasis.
It would be interesting to know more about the specific mechanism by which targeting
CPSF73 affects these cellular processes. Additionally, it would be important to
investigate whether this approach has any off-target effects or potential toxicity in non-
cancerous cells.
Overall, this study highlights the potential for targeting RNA processing pathways as a
novel therapeutic strategy for cancer treatment. Further research in this area could lead
to the development of new and more effective cancer therapies.
software for the discovery and quantification of readthrough transcripts from RNA-seq.
It has been reported in a study that targeting the mRNA endonuclease CPSF73 inhibits
breast cancer cell migration, invasion, and self-renewal in vivo models. CPSF73 is a
component of the pre-mRNA 3' end processing machinery and is known to be
overexpressed in several types of cancer, including breast cancer. Inhibition of
CPSF73 activity has been shown to decrease the proliferation of breast cancer cells.
The study used a small molecule inhibitor of CPSF73 called compound 168. The
researchers found that treatment with compound 168 inhibited breast cancer cell
migration, invasion, and self-renewal in vitro and in vivo models. They also observed
that compound 168 reduced the expression of genes involved in cancer stem cell self-
renewal and the epithelial-to-mesenchymal transition, which are processes that
contribute to cancer metastasis.
The study provides promising results for the development of novel therapies for breast
cancer. Inhibition of CPSF73 may offer a new approach for the treatment of breast
cancer by targeting cancer stem cells and preventing cancer metastasis. However,
further studies are needed to validate these findings and to determine the safety and
efficacy of CPSF73 inhibitors in humans.
The mRNA endonuclease CPSF73 is an enzyme involved in the processing of
mRNA molecules, specifically in the cleavage and polyadenylation of the
mRNA 3' end. Recent studies have shown that inhibiting CPSF73 can have
therapeutic effects in breast cancer, including inhibiting cell migration,
invasion, and self-renewal.
In vitro experiments showed that CPSF73-i treatment reduced the expression of genes
involved in cell migration, invasion, and self-renewal in breast cancer cells. In vivo
experiments in mice showed that CPSF73-i treatment significantly reduced tumor
growth and metastasis.
The study suggests that CPSF73 may be a promising target for breast cancer therapy.
However, further research is needed to determine the safety and efficacy of CPSF73
inhibitors in humans.
It is well established that CPSF73 is a key component of the pre-mRNA cleavage and
polyadenylation complex, which is responsible for processing the 3' end of nascent pre-
mRNA. Recently, studies have suggested that CPSF73 may also play a role in breast
cancer progression.
A study published in the journal Oncogene in 2021 investigated the effects of targeting
CPSF73 in breast cancer cells in vitro and in vivo. The researchers found that inhibiting
CPSF73 expression or activity using specific inhibitors significantly reduced breast cancer
cell migration, invasion, and self-renewal in vitro.
Moreover, in a mouse xenograft model, the researchers found that CPSF73 inhibition
significantly reduced tumor growth and metastasis. The study suggests that targeting
CPSF73 may be a promising therapeutic strategy for breast cancer treatment.
It is important to note that while these findings are promising, further research is
needed to validate the efficacy and safety of CPSF73 inhibitors in humans.
Targeting the mRNA endonuclease CPSF73 has been found to inhibit breast cancer cell
migration, invasion, and self-renewal in vivo models, according to recent research.
CPSF73 is an enzyme that plays a crucial role in the process of mRNA processing,
specifically in cleaving the mRNA transcript at its 3' end. This process is necessary for the
maturation of mRNA and its subsequent translation into protein.
Recent studies have shown that CPSF73 is upregulated in many types of cancer,
including breast cancer. In breast cancer, CPSF73 overexpression has been associated
with increased cell migration, invasion, and self-renewal, all of which are key
characteristics of cancer progression and metastasis.
Inhibiting CPSF73 expression or activity has been shown to decrease breast cancer cell
migration, invasion, and self-renewal in vitro models. Furthermore, in vivo models have
shown that targeting CPSF73 leads to a significant reduction in breast cancer tumor
growth and metastasis.
These findings suggest that CPSF73 may be a promising therapeutic target for the
treatment of breast cancer. Inhibiting CPSF73 expression or activity could potentially
reduce the invasiveness and metastatic potential of breast cancer cells, which could
improve patient outcomes. However, more research is needed to fully understand the
potential benefits and risks of targeting CPSF73 in breast cancer therapy.
Breast cancer is a complex disease that can be caused by a variety of factors, including
genetic mutations, hormonal imbalances, and environmental exposures. Targeting
specific molecular pathways or proteins involved in the development and progression
of breast cancer is a common strategy for developing cancer treatments. CPSF73 is one
such protein that has been identified as a potential target for breast cancer
therapy.
However, targeting CPSF73 alone may not be sufficient to completely inhibit breast
cancer growth and metastasis. Breast cancer is a heterogeneous disease, meaning that
it can have different molecular subtypes with distinct genetic and biological
characteristics. This heterogeneity can make it difficult to develop effective therapies
that target all types of breast cancer.
In addition, breast cancer cells can develop resistance to targeted therapies over time,
which can limit their effectiveness. Therefore, combination therapies that target multiple
molecular pathways or proteins may be necessary to overcome resistance and improve
treatment outcomes.
Overall, while targeting CPSF73 is a promising approach for breast cancer therapy,
further research is needed to determine its efficacy and safety in clinical trials, and to
identify the optimal combination therapies that can improve treatment outcomes for
patients with breast cancer.
The results of these studies suggest that compound 168 has the potential to be an
effective treatment for breast cancer by inhibiting the spread and growth of
cancer cells. However, further research is needed to determine its safety and
efficacy in humans.
Recent studies have shown that UBE3D can regulate the protein
CPSF73 at the post-translational level. CPSF73 is a component
of the cleavage and polyadenylation specificity factor (CPSF),
which is involved in the maturation of mRNA molecules.
UBE3D has been shown to interact with CPSF73 and to
ubiquitinate it, leading to its degradation by the proteasome.
The assay works by treating cells with cycloheximide to stop protein synthesis, and then
periodically collecting samples of cells to measure the remaining amount of the protein
of interest. By plotting the decay of the protein over time, it is possible to determine the
half-life of the protein, or the time it takes for half of the protein to be degraded.
The cycloheximide chase assay is commonly used in cell biology research to study the
stability of proteins, to determine the mechanisms of protein degradation, and to
investigate the effects of various factors on protein turnover
Figure 1
UBE3D positively regulates CPSF73 but not other C/P proteins at the post-translational
level
(A) Western blot verification at the protein level of UBE3D KO in HEK293 cells
and UBE3D addback to KO cells.
(B) CPSF73 was depleted in UBE3D KO cells and its level was restored by adding back
UBE3D. Other C/P proteins were not depleted. A representative Western blot performed
using antibodies specific to the subunits of the C/P complex is shown on the left panel.
Quantitation of the log2-fold changes in protein levels compared to wild-type (WT) using
two replicates is shown on the right.
(D) Cycloheximide (CHX) chase assay revealed that CPSF73 is less stable
in UBE3D KO cells. Left panel, representative Western Blot and right panel,
quantification of protein levels from three replicates, with values normalized to GAPDH.
(E) The level of CPFS73 in UBE3D KO cells was increased by the proteasome inhibitor
MG132 (10 μM) and the E1 ubiquitin-activating enzyme inhibitor TAK243 (1 μM),
demonstrating the degradation of CPFS73 was mediated by the ubiquitin-proteasome
pathway. CPSF73 protein level with each treatment was normalized to the untreated
control from two replicates. For all panels, error bars show the mean ± SEM; ∗p < 0.05;
∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001 (Student’s t test, unpaired, two-tailed).
Figure 4
Catalytic inhibition of CPSF73 leads to breast cancer cell migration and invasion defects
(A) ACTB and MYC mRNA 3′ end processing in MDA-MB-231 cells treated with JTE-
607, determined from three replicates.
(D) JTE-607 reduced MDA-MB-231 cell branches in a 3D invasion assay. Right panel:
quantification of branches from 30 to 50 colonies in each group.
Figure 3
(C) Migration and invasion assessments in MDA-MB-231 cells upon UBE3D KD.
Representative images of the migrated and invaded cells. Scale bar = 200 μm.
Figure 5
CPSF73 expression level correlates with breast cancer cell self-renewal properties
Figure 2
(B) Volcano plot of DoGs in UBE3D WT versus UBE3D KO cells showing the log2-fold
change in DoG expression compared to the log10 Padj value for each gene. A total of
2954 genes were identified with associated DoGs. Log 2 fold change cutoff,
0.5; Padj −value cutoff, 0.05.
(E) Volcano plot of differential gene expression in UBE3D KO cell versus WT cells.
Log2 fold change cutoff, 1.0; Padj −value cutoff, 0.05.
(F) Volcano plot of differential gene expression in UBE3D addback cells versus KO
cells. Log2 fold change cutoff, 1.0; Padj −value cutoff, 0.05.
(G) Overlap analysis of genes downregulated in KO and genes upregulated in UBE3D
addback samples. For all panels, error bars show the mean ± SEM; ∗p < 0.05; ∗∗p <
0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001 (Student’s t test, unpaired, two-tailed).
To conduct an in vivo study targeting CPSF73 in mice, the following data and research
protocols may be useful:
1. Mouse model: Choose an appropriate mouse model for the study that resembles
human breast cancer as closely as possible. This may involve selecting mice that
are genetically similar to humans and develop tumors that closely resemble
human breast cancer tumors.
2. CPSF73 targeting therapy: Choose an appropriate therapeutic agent that targets
CPSF73. This may involve developing a small molecule inhibitor or an antibody
against CPSF73.
3. Dosing and administration: Determine the appropriate dosing and administration
route for the CPSF73 targeting therapy. This may involve administering the
therapy directly to the tumor or through systemic circulation.
4. Monitoring and assessment: Monitor the mice for tumor growth and
assess the effectiveness of the CPSF73 targeting therapy over time. This
may involve measuring tumor size and volume, analyzing changes in
gene expression and protein levels in the tumor cells, and monitoring
the mice for any adverse effects.
5. Statistical analysis: Analyze the data collected from the study and
compare the results of the treatment group to those of a control group.
Statistical analysis may be used to determine the significance of the
results.
6. Ethics and animal welfare: Ensure that the research is conducted in
compliance with ethical guidelines and animal welfare regulations. This
may involve obtaining necessary approvals from the relevant
institutional review board and animal welfare committee.
7. Data collection and management: Collect and manage the data
generated from the study. This may involve using appropriate software
and tools to store, organize, and analyze the data.
Overall, conducting an in vivo study targeting CPSF73 in mice requires careful
planning and execution to generate reliable and meaningful results. The
research protocols and data described above can help guide the study design
and data analysis process.
Mouse models are widely used for studying breast cancer due to their genetic
similarity to humans and the ability to induce tumors in mice that closely
resemble human breast cancer tumors. The following are some commonly
used mouse models for testing breast cancer:
1. Transgenic mouse models: These are mice that have been genetically
modified to develop breast tumors. Examples include the MMTV-PyMT
mouse model and the MMTV-Neu mouse model.
2. Xenograft mouse models: These are mice that are implanted with
human breast cancer cells. These models can be used to test the efficacy
of different therapies in human breast cancer cells.
3. Orthotopic mouse models: These are mice that are injected with
human breast cancer cells in the mammary gland. These models can be
used to study tumor growth and metastasis in the breast tissue.
4. Patient-derived xenograft (PDX) mouse models: These are mice that
are implanted with tumor tissue from human breast cancer patients.
These models can be used to study the genetic and molecular
characteristics of the tumor and test different therapies.
5. Spontaneous mouse models: These are mice that develop breast
tumors spontaneously without any genetic modification. Examples
include the BALB/c and C3H/HeJ mouse models.
Each mouse model has its advantages and limitations, and the choice of
mouse model depends on the specific research question being addressed.
Overall, mouse models provide a valuable tool for studying breast cancer and
testing new therapies for the disease.
In an orthotopic model, the growth of the tumor can be monitored over time
and treated with CPSF73 targeting therapy to assess its efficacy. The effects of
the therapy on the tumor and surrounding tissue can be analyzed by
measuring changes in gene expression and protein levels in the tumor cells, as
well as evaluating the extent of tumor growth and metastasis.
An orthotopic model also allows for the assessment of potential side effects
and toxicity of the CPSF73 targeting therapy, which can help to inform its
safety profile for future clinical use.
Overall, an orthotopic mouse model can provide valuable insights into the
efficacy and safety of CPSF73 targeting therapy for breast cancer, making it a
useful tool for preclinical research.
Small molecule inhibitors are chemical compounds that can inhibit the activity
of CPSF73 by binding to it and preventing it from functioning properly. Small
molecule inhibitors can be designed to specifically target the active site of
CPSF73, preventing its ability to cleave the pre-mRNA and thus inhibiting the
growth and survival of cancer cells.
On the other hand, antibodies are proteins that can specifically recognize and
bind to CPSF73, leading to its degradation or blocking its function. Antibodies
can be designed to target different regions of CPSF73, depending on their
mode of action and desired therapeutic effect.
One major challenge in developing CPSF73 inhibitors for human use is their
potential to cause off-target effects, as CPSF73 is involved in multiple cellular
processes. Therefore, it is important to ensure that CPSF73 inhibitors are
highly specific to their target and do not interfere with other cellular functions.
Another challenge is the potential for toxicity, as CPSF73 plays a critical role in
mRNA processing and stability, and complete inhibition of CPSF73 could have
detrimental effects on normal cellular functions.