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PMC12842104
|
Breast cancer is a significant cause of death worldwide.
|
[] |
PMC12842104
|
Recent research has focused on identifying natural compounds for developing effective cancer treatments.
|
[] |
PMC12842104
|
Resiniferatoxin, a transient receptor potential vanilloid 1 (TRPV1) agonist, is a common diterpene in Euphorbia bicolor Engelm. &
|
[] |
PMC12842104
|
A. Gray (Euphorbiaceae), a plant native to the southern United States that has not been studied before.
|
[] |
PMC12842104
|
We investigated the antiproliferative activities and mechanisms of action of E. bicolor xylene extract in estrogen receptor-positive T47D and triple-negative MDA-MB-231 cell lines.
|
[
{
"end": 137,
"label": "CellLine",
"start": 133,
"text": "T47D"
},
{
"end": 168,
"label": "CellLine",
"start": 158,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
The extract significantly reduced the viability of T47D and MDA-MB-231 cells in a dose-dependent manner.
|
[
{
"end": 55,
"label": "CellLine",
"start": 51,
"text": "T47D"
},
{
"end": 70,
"label": "CellLine",
"start": 60,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
In MDA-MB-231 cells, the extract induced apoptosis via intracellular calcium overload, triggered by TRPV1 activation.
|
[
{
"end": 13,
"label": "CellLine",
"start": 3,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
This effect was diminished by the TRPV1 antagonist capsazepine and the calcium chelator BAPTA-AM.
|
[] |
PMC12842104
|
Intracellular calcium influx was confirmed through Fura-2 AM staining, revealing that E. bicolor phytochemicals activated TRPV1 in MDA-MB-231 cells.
|
[
{
"end": 141,
"label": "CellLine",
"start": 131,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
Treatment of T47D cells with E. bicolor xylene extract resulted in apoptosis associated with reactive oxygen species (ROS) generation (10-fold higher in T47D cells than in MDA-MB-231 cells) and mitochondrial calcium overload.
|
[
{
"end": 17,
"label": "CellLine",
"start": 13,
"text": "T47D"
},
{
"end": 157,
"label": "CellLine",
"start": 153,
"text": "T47D"
},
{
"end": 182,
"label": "CellLine",
"start": 172,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
These effects were significantly blocked when cells were pretreated with N-acetyl-l-cysteine (NAC), a ROS inhibitor.
|
[] |
PMC12842104
|
Both cell lines underwent apoptosis via multiple mitochondrial- and endoplasmic reticulum stress–mediated pathways.
|
[] |
PMC12842104
|
This was supported by the activation of caspases 3, 8, and 9; increased expression of FAS, XBP1s, and CHOP; upregulation of BAX; and downregulation of BCL-2.
|
[] |
PMC12842104
|
In addition, PI3K, AKT, and pAKT protein expressions were also reduced in both cell lines, indicating downregulation of PI3K/Akt signaling pathway.
|
[] |
PMC12842104
|
Phytochemicals in E. bicolor xylene extract could become promising ingredients for developing breast cancer therapeutics.
|
[] |
PMC12842104
|
Breast cancer has emerged as a significant concern for women globally, with 2.26 million reported cases in 2020, surpassing all other forms of cancer and becoming the leading cause of cancer-related deaths in women .
|
[] |
PMC12842104
|
The number of new cases in the United States had increased by 31% in 2023 .
|
[] |
PMC12842104
|
Despite significant advances in cancer diagnosis and treatment, the development of chemotherapeutic agents remains an area of intensive research .
|
[] |
PMC12842104
|
For centuries, plants have served as a foundation of traditional medicine, with many species containing bioactive compounds that exhibit strong anticancer properties .
|
[] |
PMC12842104
|
Plant secondary metabolites with anticancer properties, such as alkaloids, terpenoids, and phenolics, may provide a broad range of therapeutic benefits .
|
[] |
PMC12842104
|
Recent research suggests that phytochemicals could have various therapeutic effects, such as preventing tumor growth by activating several cellular signaling pathways and targeting specific receptors .
|
[] |
PMC12842104
|
One of the well-known receptors that can be activated by phytochemicals is the transient receptor potential vanilloid 1 (TRPV1) receptor.
|
[] |
PMC12842104
|
TRPV1 receptors are ion channels belonging to the TRP channel superfamily, modulated by several phytochemicals and activating several cell death signaling pathways, thus exhibiting antiproliferative effects .
|
[] |
PMC12842104
|
The TRPV1 channel is a non-selective cation channel classically associated with nociception and thermosensation .
|
[] |
PMC12842104
|
However, accumulating evidence indicates that TRPV1 also participates in diverse physiological and pathological processes, including cancer , and is expressed in different carcinoma tissues, including all types of breast cancers .
|
[] |
PMC12842104
|
Various plant phytochemicals, including capsaicin, gingerol, piperine, and resiniferatoxin (RTX), are the commonly known activators of the TRPV1 channel .
|
[] |
PMC12842104
|
In cancer cells, TRPV1 activation leads to an influx of calcium, initiating subsequent signaling cascades and triggering antiproliferative effects .
|
[] |
PMC12842104
|
Further study is required to fully understand the potential of phytochemicals targeting TRPV1 in cancer therapy.
|
[] |
PMC12842104
|
One genus known to have antiproliferative effects is Euphorbia (Euphorbiaceae).
|
[] |
PMC12842104
|
Many species of Euphorbia are used in traditional folk medicine to treat different diseases and have been extensively studied because of their wide range of biological activities, including antiproliferative, anti-inflammatory, and analgesic properties .
|
[] |
PMC12842104
|
Extracts of Euphorbia species, such as E. helioscopia L., and E. macroclada Boiss.,
|
[] |
PMC12842104
|
applied to different breast cancer cell lines, inhibit cell proliferation through cell cycle arrest and apoptosis and were able to reverse multidrug resistance .
|
[] |
PMC12842104
|
Euphorbia bicolor Engelm. &
|
[] |
PMC12842104
|
A. Gray, also known as Snow-on-the-prairie, is native to south-central USA.
|
[] |
PMC12842104
|
No scientific research has been done on this species.
|
[] |
PMC12842104
|
Our previous research found that the latex extract of E. bicolor and its phytochemicals showed antiproliferative properties in ER-positive MCF-7 and T47D, as well as triple-negative MDA-MB-231 and MDA-MB-469 breast carcinomas, but the mechanisms of action were not determined .
|
[
{
"end": 144,
"label": "CellLine",
"start": 139,
"text": "MCF-7"
},
{
"end": 153,
"label": "CellLine",
"start": 149,
"text": "T47D"
},
{
"end": 192,
"label": "CellLine",
"start": 182,
"text": "MDA-MB-231"
},
{
"end": 207,
"label": "CellLine",
"start": 197,
"text": "MDA-MB-469"
}
] |
PMC12842104
|
The present study aims to determine the antiproliferative mechanisms of action of E. bicolor xylene extract on ER-positive T47D and triple-negative MDA-MB-231 cell lines.
|
[
{
"end": 127,
"label": "CellLine",
"start": 123,
"text": "T47D"
},
{
"end": 158,
"label": "CellLine",
"start": 148,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
Resiniferatoxin, a common diterpene present in E. bicolor , was reported to activate the TRPV1 channel in neurons and cancer cells .
|
[] |
PMC12842104
|
We hypothesized that E. bicolor xylene extract, containing diterpenes, would activate TRPV1 and induce TRPV1-dependent antiproliferative mechanisms of action in the breast cancer cell lines.
|
[] |
PMC12842104
|
We report that E. bicolor xylene extract possesses antiproliferative properties in both breast cancer cell lines under study and induces apoptosis through multiple cell death pathways.
|
[] |
PMC12842104
|
To the best of our knowledge, this is the first study on the antiproliferative mechanisms of action of E. bicolor xylene extract on ER-positive T47D and triple-negative MDA-MB-231 breast cancer cell lines.
|
[
{
"end": 148,
"label": "CellLine",
"start": 144,
"text": "T47D"
},
{
"end": 179,
"label": "CellLine",
"start": 169,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
ER-positive T47D and triple-negative MDA-MB-231 cell lines were treated with increasing concentrations of E. bicolor ethanol, xylene extracts, or capsaicin.
|
[
{
"end": 16,
"label": "CellLine",
"start": 12,
"text": "T47D"
},
{
"end": 47,
"label": "CellLine",
"start": 37,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
E. bicolor ethanol extract significantly inhibited the cell viability of ER-positive T47D cell lines at 500 µg/mL (Figure 1A).
|
[
{
"end": 89,
"label": "CellLine",
"start": 85,
"text": "T47D"
}
] |
PMC12842104
|
However, E. bicolor ethanol extract did not show a reduction in cell viability of triple-negative MDA-MB-231 cells (Figure 1B).
|
[
{
"end": 108,
"label": "CellLine",
"start": 98,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
E. bicolor xylene extract dose-dependently inhibited the proliferation of ER-positive T47D and triple-negative MDA-MB-231 cell lines (Figure 1C,D).
|
[
{
"end": 90,
"label": "CellLine",
"start": 86,
"text": "T47D"
},
{
"end": 121,
"label": "CellLine",
"start": 111,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
The xylene extract significantly inhibited cell viability, starting at 2 µg/mL in T47D and 8 µg/mL in MDA-MB-231 cell lines.
|
[
{
"end": 86,
"label": "CellLine",
"start": 82,
"text": "T47D"
},
{
"end": 112,
"label": "CellLine",
"start": 102,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
At 500 µg/mL, E. bicolor xylene extract significantly inhibited T47D and MDA-MB-231 cell viability by more than 95% (Figure 1C,D).
|
[
{
"end": 68,
"label": "CellLine",
"start": 64,
"text": "T47D"
},
{
"end": 83,
"label": "CellLine",
"start": 73,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
Since the xylene extract is significantly more potent than the ethanol extract in inducing antiproliferative effects, all follow-up experiments were performed with E. bicolor xylene extract.
|
[] |
PMC12842104
|
The proliferation of T47D cells was significantly inhibited by capsaicin treatment at 250 µg/mL and 500 µg/mL concentrations (Figure 1E), while MDA-MB-231 cell viability was significantly reduced at 500 µg/mL capsaicin (Figure 1F).
|
[
{
"end": 25,
"label": "CellLine",
"start": 21,
"text": "T47D"
},
{
"end": 154,
"label": "CellLine",
"start": 144,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
In contrast to E. bicolor ethanol extract, the xylene extract at higher concentrations (125 µg/mL–500 µg/mL) inhibited the growth of human mammary epithelial cells (HMECs) (Figure 1G,H).
|
[
{
"end": 163,
"label": "CellLine",
"start": 133,
"text": "human mammary epithelial cells"
}
] |
PMC12842104
|
Therefore, the rest of the experiments were set up to use 62.5 µg/mL xylene extract to determine the antiproliferative mechanisms.
|
[] |
PMC12842104
|
The half-maximal inhibitory concentration (IC50) of E. bicolor xylene extract for T47D cells was 0.7834 µg/mL (Figure 2A), and for MDA-MB-231 cells was 9.341 µg/mL (Figure 2B).
|
[
{
"end": 86,
"label": "CellLine",
"start": 82,
"text": "T47D"
},
{
"end": 141,
"label": "CellLine",
"start": 131,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
The IC50 of E. bicolor xylene extract for HMECs was 288.6 µg/mL (Figure 2C).
|
[] |
PMC12842104
|
The IC50 of capsaicin for T47D cells was 173.4 µg/mL (Figure 2D), and MDA-MB-231 cells were 439.3 µg/mL (Figure 2E).
|
[
{
"end": 30,
"label": "CellLine",
"start": 26,
"text": "T47D"
},
{
"end": 80,
"label": "CellLine",
"start": 70,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
Three days after E. bicolor xylene extract treatment (62.5 μg/mL), fewer cells as well as cell morphological changes were observed in both cell lines.
|
[] |
PMC12842104
|
Cells were smaller and more spherical, partially or completely detached from the bottom of the wells after treatment, indicative of the cytotoxic effects of E. bicolor xylene extract (Figure 2F).
|
[] |
PMC12842104
|
T47D and MDA-MB-231 cells were treated with E. bicolor xylene extract (62.5 µg/mL) for 24 h, and TUNEL assays were performed to detect apoptosis.
|
[
{
"end": 4,
"label": "CellLine",
"start": 0,
"text": "T47D"
},
{
"end": 19,
"label": "CellLine",
"start": 9,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
Typical DNA fragmentation in T47D and MDA-MB-231 cell lines was observed (Figure 3A).
|
[
{
"end": 33,
"label": "CellLine",
"start": 29,
"text": "T47D"
},
{
"end": 48,
"label": "CellLine",
"start": 38,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
The number of apoptotic T47D and MDA-MB-231 cells significantly increased with E. bicolor xylene extract treatments, as indicated by the relative red fluorescence intensity of Alexa 594 (Figure 3B).
|
[
{
"end": 28,
"label": "CellLine",
"start": 24,
"text": "T47D"
},
{
"end": 43,
"label": "CellLine",
"start": 33,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
T47D and MDA-MB-231 cells were treated with E. bicolor xylene extract, and reactive oxygen species (ROS) production was monitored using 2′,7′-dichlorofluorescin diacetate (DCFDA) to investigate whether E. bicolor treatment could generate ROS accumulation in cells.
|
[
{
"end": 4,
"label": "CellLine",
"start": 0,
"text": "T47D"
},
{
"end": 19,
"label": "CellLine",
"start": 9,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
The DCFDA fluorescence intensity increased in a dose-dependent manner with increasing time of E. bicolor xylene extract treatment in both T47D and MDA-MB-231 cells (Figure 4A,B).
|
[
{
"end": 142,
"label": "CellLine",
"start": 138,
"text": "T47D"
},
{
"end": 157,
"label": "CellLine",
"start": 147,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
E. bicolor xylene extract treatment significantly and dose-dependently triggered intracellular ROS accumulation in T47D and MDA-MB-231 cells compared to the negative control and 20× and 30× higher than the positive control (Figure 4C,D).
|
[
{
"end": 119,
"label": "CellLine",
"start": 115,
"text": "T47D"
},
{
"end": 134,
"label": "CellLine",
"start": 124,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
At higher doses of E. bicolor xylene extract treatments, intracellular ROS accumulation was found to be ten times greater in T47D cells than in MDA-MB-231 cells (Figure 4C).
|
[
{
"end": 129,
"label": "CellLine",
"start": 125,
"text": "T47D"
},
{
"end": 154,
"label": "CellLine",
"start": 144,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
To determine whether ROS generation was associated with E. bicolor-induced apoptosis, T47D and MDA-MB-231 cells were pretreated with the ROS inhibitor N-Acetyl-L-cysteine (NAC) for 1 h and then treated with E. bicolor xylene extract.
|
[
{
"end": 90,
"label": "CellLine",
"start": 86,
"text": "T47D"
},
{
"end": 105,
"label": "CellLine",
"start": 95,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
Pretreatment with NAC significantly ameliorated the effect of E. bicolor in T47D cells (Figure 4E), suggesting that ROS generation is involved in E. bicolor diterpene extract-induced apoptosis in T47D cells.
|
[
{
"end": 80,
"label": "CellLine",
"start": 76,
"text": "T47D"
},
{
"end": 200,
"label": "CellLine",
"start": 196,
"text": "T47D"
}
] |
PMC12842104
|
However, NAC could not inhibit the effect of E. bicolor xylene extracts in MDA-MB-231 cells (Figure 4F), suggesting that E. bicolor extracts induced apoptosis in a TRPV1-dependent manner and only partially through ROS generation.
|
[
{
"end": 85,
"label": "CellLine",
"start": 75,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
Resiniferatoxin, commonly known as a TRPV1 agonist, is present in E. bicolor .
|
[] |
PMC12842104
|
Therefore, we hypothesized that TRPV1 would be activated by E. bicolor xylene extract, causing an influx of calcium that would lead to cell death.
|
[] |
PMC12842104
|
The T47D cells were treated with E. bicolor xylene extract after pretreating them with 10 μM of capsazepine (CAPZ), a TRPV1 antagonist.
|
[
{
"end": 8,
"label": "CellLine",
"start": 4,
"text": "T47D"
}
] |
PMC12842104
|
TRPV1 inhibition increased the cell proliferation only at E. bicolor extract concentrations of 2–16 µg/mL. Capsazepine could not completely block the effect of higher concentrations of E. bicolor xylene extract (Figure 5A).
|
[] |
PMC12842104
|
To determine the calcium involvement in apoptosis, 1 μM of the calcium chelator BAPTA-AM was used to pretreat T47D cells, after which they were treated with E. bicolor xylene extract.
|
[
{
"end": 114,
"label": "CellLine",
"start": 110,
"text": "T47D"
}
] |
PMC12842104
|
Chelating calcium increased the cell proliferation only at concentrations of 2–8 µg/mL of E. bicolor extract.
|
[] |
PMC12842104
|
Chelating calcium could not completely block the effect of higher concentrations of E. bicolor extract (Figure 5B).
|
[] |
PMC12842104
|
Fura2-AM staining was employed to check intracellular calcium concentrations and activation of TRPV1.
|
[] |
PMC12842104
|
Fluorescence followed a downward trend immediately after the E. bicolor treatment (Figure 5C), revealing that TRPV1 may not be involved in the antiproliferative mechanism of action.
|
[] |
PMC12842104
|
In search of calcium-regulated apoptotic mechanism of action, an endoplasmic reticulum-targeted low-affinity GCaMP6-210 plasmid variant, a fluorescent reporter for ER calcium signaling, was used to visualize ER Ca dynamics.
|
[] |
PMC12842104
|
T47D cells were transfected with the GCaMP6-210 variant, and immediately after E. bicolor xylene extract treatment, calcium concentration (green fluorescence) was observed.
|
[
{
"end": 4,
"label": "CellLine",
"start": 0,
"text": "T47D"
}
] |
PMC12842104
|
GCaMP6-210 fluorescence followed a downward trend (Figure 5D), suggesting that E. bicolor treatment in T47D cells triggers the release of calcium from ER.
|
[
{
"end": 107,
"label": "CellLine",
"start": 103,
"text": "T47D"
}
] |
PMC12842104
|
This suggests that TRPV1 might not be involved in the cell death of E. bicolor-treated T47D cells.
|
[
{
"end": 91,
"label": "CellLine",
"start": 87,
"text": "T47D"
}
] |
PMC12842104
|
Rhod2-AM was used to monitor mitochondrial calcium.
|
[] |
PMC12842104
|
Twenty-seven seconds after E. bicolor xylene extract treatment, Rhod2-AM was localized within the mitochondria of T47D cells (Figure 5E).
|
[
{
"end": 118,
"label": "CellLine",
"start": 114,
"text": "T47D"
}
] |
PMC12842104
|
MDA-MB-231 cells were pretreated with 10 μM of CAPZ and treated with E. bicolor xylene extract.
|
[
{
"end": 10,
"label": "CellLine",
"start": 0,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
TRPV1 inactivation by CAPZ significantly increased the cell viability of extract-treated cells (Figure 6A), indicating that E. bicolor extract reduces the viability of MDA-MB-231 cells in a TRPV1-dependent manner.
|
[
{
"end": 178,
"label": "CellLine",
"start": 168,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
To see the effect of calcium chelation, which could oppose the above scenario and increase cell viability, MDA-MB-231 cells were exposed to E. bicolor xylene extract after pretreatment with 1 μM of the calcium chelator BAPTA-AM.
|
[
{
"end": 117,
"label": "CellLine",
"start": 107,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
At low extract concentrations (2–16 μg/mL), chelating calcium with BAPTA-AM increases the cell viability by blocking the effect of E. bicolor extract (Figure 6B).
|
[] |
PMC12842104
|
However, at higher extract concentrations (62.5–500 μg/mL), MDA-MB-231 cells exhibited a significant decrease in viability, likely attributable to the cytotoxic effects of E. bicolor xylene extract at elevated doses.
|
[
{
"end": 70,
"label": "CellLine",
"start": 60,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
To check the calcium dynamics induced by the activation of TRPV1, Fura2-AM staining was used and an increase in intracellular calcium was observed.
|
[] |
PMC12842104
|
Fluorescence intensity followed an upward trend immediately after the E. bicolor xylene extract treatment, which lasted for 6–10 s (Figure 6C).
|
[] |
PMC12842104
|
To determine if this activation could lead to the accumulation of calcium in mitochondria, Rhod2-AM was used to monitor mitochondrial calcium.
|
[] |
PMC12842104
|
An immediate accumulation of calcium in the mitochondria was observed.
|
[] |
PMC12842104
|
Within 8 s after E. bicolor xylene extract treatment, Rhod2-AM was predominantly localized in the mitochondria of MDA-MB-231 cells (Figure 6D).
|
[
{
"end": 124,
"label": "CellLine",
"start": 114,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
Mitochondria are critical mediators of apoptotic signaling pathways.
|
[] |
PMC12842104
|
Activated/cleaved caspase 3 (green fluorescence) was detected in both T47D and MDA-MB-231 cells treated with E. bicolor xylene extract (62.5 μg/mL).
|
[
{
"end": 74,
"label": "CellLine",
"start": 70,
"text": "T47D"
},
{
"end": 89,
"label": "CellLine",
"start": 79,
"text": "MDA-MB-231"
}
] |
PMC12842104
|
Activation of caspase 3 was significantly higher in MDA-MB-231 cells compared with T47D cells (Figure 7A,B).
|
[
{
"end": 62,
"label": "CellLine",
"start": 52,
"text": "MDA-MB-231"
},
{
"end": 87,
"label": "CellLine",
"start": 83,
"text": "T47D"
}
] |
PMC12842104
|
Capsaicin (positive control) and E. bicolor extract treatments were also associated with the expression of caspase 8 and FAS, indicating induction of mitochondrial extrinsic apoptosis (Figure 7C).
|
[] |
PMC12842104
|
Capsaicin and E. bicolor xylene extract treatments led to the expression of caspase 9 and reduction in anti-apoptotic BCL-2 protein compared to the DMSO control (Figure 7D).
|
[] |
PMC12842104
|
However, the expression of BCL-2 was significantly lower in E. bicolor extract-treated cells than in control and capsaicin (Figure 7E).
|
[] |
PMC12842104
|
The proapoptotic BAX protein showed a higher molecular weight band (47 KDa) in capsaicin and E. bicolor extract-treated cells, compared to its known average molecular weight (21 KDa) (Figure 7F).
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PMC12842104
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The fold activation of BAX is significantly higher than that of DMSO control (Figure 7G), indicating that E. bicolor xylene extract treatment also led to mitochondrial intrinsic apoptotic pathway.
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PMC12842104
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The protein kinase B (AKT) plays essential roles in cell survival, growth, and proliferation by regulating cellular signaling .
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ChEMBL CellLine NER Data
Dataset Description
This dataset has been extracted from Europe PMC (EPMC), a free database offering comprehensive access to life sciences research literature. EPMC aggregates content from various sources, including PubMed, arXiv, and other repositories, and provides open access to millions of scientific articles. This dataset has been generated as part of a project collaboration between Europe PMC, Open Targets, and ChEMBL] at EMBL-EBI. Standard: Silver
Dataset Details
The dataset was extracted using assay descriptions from CheMBL andThe dataset has been annotated on mentions of cell lines. This makes it a valuable resource as it can be used for(but not limited to) the following downstream natural language processing (NLP) tasks in the biomedical domain.
NLP Tasks
Named Entity Recognition (NER): Identify and classify mentions of cell lines or related entities appearing in biomedical contexts.
Relationship Extraction: Extract relationships between cell lines and other biomedical entities, such as genes, diseases, or drugs.
Text Classification: Classify sentences or articles based on their relevance to specific cell lines, particularly in cancer research or drug development.
Sentiment Analysis: Analyze the sentiment or tone of texts discussing cell lines, such as the evaluation of experimental results (positive or negative).
Information Retrieval: Develop systems to retrieve articles or specific mentions of cell lines based on user queries.
Entity Linking: Link cell line mentions in text to standardized identifiers in cell line ontologies or databases.
Question Answering (QA): Build systems that can answer specific questions about cell lines, such as their role in particular diseases or experiments.
Topic Modeling: Analyze the dataset to uncover major themes or trends in research involving cell lines.
Text Summarization: Automatically generate summaries of articles or sections discussing cell lines.
Who funded the creation of the dataset?
Any other comments?
The dataset aims to provide a foundational resource for advancing NLP in biomedicine.
Dataset Composition
- What experiments were initially run on this dataset? No experiments have been conducted yet. Updates will follow as they occur.
Data Collection Process
How was the data collected? The dataset was collected using the Europe PMC API. Articles marked as "open access" were retrieved, and those labeled as "retraction of publication" were excluded. Duplicate entries were filtered by ensuring unique PMCIDs.
Who was involved in the data collection process? The data collection process was carried out by researchers at EMBL-EBI, leveraging automated tools for querying and processing the Europe PMC repository.
Are there any known errors, sources of noise, or redundancies in the data? None have been identified yet.
Data Preprocessing
What preprocessing/cleaning was done?
- Only open-access articles were retrieved.
- Articles labeled as "retraction of publication" were excluded.
- Duplicate entries based on the PMCID column were removed.
- Paragraph text from each section of an article was Extracted with the relevant section referenced in the 'Section Column'
- Extra whitespace, inlne math/latex formatting and irrelevant sections such "Disclosure", "Publisher's note", etc, were filtered
- Name identifiers and personal data was also removed from the dataset
Dataset Distribution
How is the dataset distributed? The dataset is freely available for use and reproduction. Proper citation of the authors is required(Information to be updated).
When will the dataset be released/first distributed? To be updated.
Dataset Maintenance
Who is supporting/hosting/maintaining the dataset?
Europe PMC, and ChEMBL team responsible for the dataset's maintenance.
How does one contact the owner/curator/manager of the dataset?
Contact can be made via the community discussion forums on GitHub or Hugging Face.
Will the dataset be updated?
Yes, updates will occur as the project progresses.
How often and by whom?
Updates will be carried out periodically by the team.
How will updates/revisions be documented and communicated?
Updates will be documented via GitHub, using version tags.
Is there a repository to link to any/all papers/systems that use this dataset?
Yes, a GitHub repository will track publications and systems using this dataset.
If others want to extend/augment/build on this dataset, is there a mechanism for them to do so?
Yes, contributions are encouraged via GitHub. Quality will be assessed through pull requests, and accepted contributions will be communicated to users via version tags and release notes.
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