1
|
Limbu S, Dakshanamurthy S. Predicting Dose-Dependent Carcinogenicity of Chemical Mixtures Using a Novel Hybrid Neural Network Framework and Mathematical Approach. TOXICS 2023; 11:605. [PMID: 37505571 PMCID: PMC10383376 DOI: 10.3390/toxics11070605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
This study addresses the challenge of assessing the carcinogenic potential of hazardous chemical mixtures, such as per- and polyfluorinated substances (PFASs), which are known to contribute significantly to cancer development. Here, we propose a novel framework called HNNMixCancer that utilizes a hybrid neural network (HNN) integrated into a machine-learning framework. This framework incorporates a mathematical model to simulate chemical mixtures, enabling the creation of classification models for binary (carcinogenic or noncarcinogenic) and multiclass classification (categorical carcinogenicity) and regression (carcinogenic potency). Through extensive experimentation, we demonstrate that our HNN model outperforms other methodologies, including random forest, bootstrap aggregating, adaptive boosting, support vector regressor, gradient boosting, kernel ridge, decision tree with AdaBoost, and KNeighbors, achieving a superior accuracy of 92.7% in binary classification. To address the limited availability of experimental data and enrich the training data, we generate an assumption-based virtual library of chemical mixtures using a known carcinogenic and noncarcinogenic single chemical for all the classification models. Remarkably, in this case, all methods achieve accuracies exceeding 98% for binary classification. In external validation tests, our HNN method achieves the highest accuracy of 80.5%. Furthermore, in multiclass classification, the HNN demonstrates an overall accuracy of 96.3%, outperforming RF, Bagging, and AdaBoost, which achieved 91.4%, 91.7%, and 80.2%, respectively. In regression models, HNN, RF, SVR, GB, KR, DT with AdaBoost, and KN achieved average R2 values of 0.96, 0.90, 0.77, 0.94, 0.96, 0.96, and 0.97, respectively, showcasing their effectiveness in predicting the concentration at which a chemical mixture becomes carcinogenic. Our method exhibits exceptional predictive power in prioritizing carcinogenic chemical mixtures, even when relying on assumption-based mixtures. This capability is particularly valuable for toxicology studies that lack experimental data on the carcinogenicity and toxicity of chemical mixtures. To our knowledge, this study introduces the first method for predicting the carcinogenic potential of chemical mixtures. The HNNMixCancer framework offers a novel alternative for dose-dependent carcinogen prediction. Ongoing efforts involve implementing the HNN method to predict mixture toxicity and expanding the application of HNNMixCancer to include multiple mixtures such as PFAS mixtures and co-occurring chemicals.
Collapse
Affiliation(s)
- Sarita Limbu
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Sivanesan Dakshanamurthy
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| |
Collapse
|
2
|
Smith KJ, Skelton H. Arachidonic Acid-Derived Bioactive Lipids: Their Role and the Role for Their Inhibitors in Dermatology. J Cutan Med Surg 2016. [DOI: 10.1177/120347540200600309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: In addition to corticosteroids, there are increasing numbers of anti-inflammatory agents that specifically target bioactive lipids generated from arachidonic acid. Knowledge of the diverse mechanisms of action of these different bioactive lipids holds promise in the therapy of a wide spectrum of cutaneous and systemic disorders. Objective: Therapeutic manipulations of these lipid molecules through inhibition, stimulation, or direct replacement have broad physiologic effects. These therapeutic strategies not only modulate inflammation, pain, and hemostatic parameters, they also play a role in cardiac, respiratory, renal, and gastrointestinal function and disease, as well as in angiogenesis and in factors that control cell growth and apoptosis important in carcinogenesis. Conclusion: Newer drug discovery methods, including combinatorial chemistry with molecular modeling, have made it possible to develop inhibitors and analogs with increasing specificity and bioactivity and decreasing toxicity. Although the application of these analogs and inhibitors for cutaneous disease is limited today, either as primary agents or adjuvant therapy, these drugs will have a place in our therapeutic regimes of the future. We present a review of the therapeutic agents now available from manipulation of these bioactive lipids, and their role and future in dermatology.
Collapse
Affiliation(s)
- Kathleen J. Smith
- The opinions and assertions contained herein are the private views of the authors and are not to be construed as official or as reflecting the views of the Department of the Army, the Department of the Navy, or the Department of Defense
| | - Henry Skelton
- The opinions and assertions contained herein are the private views of the authors and are not to be construed as official or as reflecting the views of the Department of the Army, the Department of the Navy, or the Department of Defense
| |
Collapse
|
3
|
Karunagaran D, Joseph J, Kumar TRS. CELL GROWTH REGULATION. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 595:245-68. [PMID: 17569215 DOI: 10.1007/978-0-387-46401-5_11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Curcumin, the active ingredient of turmeric (Curcuma longa) used in culinary and medical practices in Asia, has immense potential for being used in cancer chemotherapy because of its control over the cell growth regulatory mechanisms. The present chapter throws light on the role of curcumin in modulating the various phases of the cell cycle and its apoptosis-inducing effects. This is followed by a discussion on the implications of these effects of curcumin for its use as a chemotherapeutic agent in cancer. Curcumin affects various cell cycle proteins and checkpoints involving downregulation of some of the cyclins and cyclin-dependent kinases, upregulation of cdk inhibitors, and inhibition of DNA synthesis. In addition, curcumin also exerts indirect control over cell division such as inhibition of telomerase activity. Remarkably, some studies point toward a selective growth-inhibitory effect of curcumin on transformed cell lines compared to nontransformed cell lines. Curcumin has also been demonstrated to have proapoptotic effects in several in vitro studies, mostly through the mitochondria-mediated pathway of apoptosis. Curcumin-mediated regulation of apoptosis involves caspases, Bcl2 family members, inhibitors of apoptosis proteins, and heat shock proteins. The accumulating data on the in vitro and in vivo actions of curcumin together with the ongoing human clinical trials will provide a better understanding of curcumin-mediated cell growth regulation, ultimately catering to the needs of human welfare.
Collapse
Affiliation(s)
- Devarajan Karunagaran
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, India.
| | | | | |
Collapse
|
4
|
Aggarwal BB, Sundaram C, Malani N, Ichikawa H. CURCUMIN: THE INDIAN SOLID GOLD. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 595:1-75. [PMID: 17569205 DOI: 10.1007/978-0-387-46401-5_1] [Citation(s) in RCA: 842] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Turmeric, derived from the plant Curcuma longa, is a gold-colored spice commonly used in the Indian subcontinent, not only for health care but also for the preservation of food and as a yellow dye for textiles. Curcumin, which gives the yellow color to turmeric, was first isolated almost two centuries ago, and its structure as diferuloylmethane was determined in 1910. Since the time of Ayurveda (1900 Bc) numerous therapeutic activities have been assigned to turmeric for a wide variety of diseases and conditions, including those of the skin, pulmonary, and gastrointestinal systems, aches, pains, wounds, sprains, and liver disorders. Extensive research within the last half century has proven that most of these activities, once associated with turmeric, are due to curcumin. Curcumin has been shown to exhibit antioxidant, anti-inflammatory, antiviral, antibacterial, antifungal, and anticancer activities and thus has a potential against various malignant diseases, diabetes, allergies, arthritis, Alzheimer's disease, and other chronic illnesses. These effects are mediated through the regulation of various transcription factors, growth factors, inflammatory cytokines, protein kinases, and other enzymes. Curcumin exhibits activities similar to recently discovered tumor necrosis factor blockers (e.g., HUMIRA, REMICADE, and ENBREL), a vascular endothelial cell growth factor blocker (e.g., AVASTIN), human epidermal growth factor receptor blockers (e.g., ERBITUX, ERLOTINIB, and GEFTINIB), and a HER2 blocker (e.g., HERCEPTIN). Considering the recent scientific bandwagon that multitargeted therapy is better than monotargeted therapy for most diseases, curcumin can be considered an ideal "Spice for Life".
Collapse
MESH Headings
- Animals
- Anti-Bacterial Agents/chemistry
- Anti-Bacterial Agents/pharmacology
- Anti-Bacterial Agents/therapeutic use
- Anti-Inflammatory Agents, Non-Steroidal/chemistry
- Anti-Inflammatory Agents, Non-Steroidal/pharmacology
- Anti-Inflammatory Agents, Non-Steroidal/therapeutic use
- Antifungal Agents/chemistry
- Antifungal Agents/pharmacology
- Antifungal Agents/therapeutic use
- Antineoplastic Agents, Phytogenic/chemistry
- Antineoplastic Agents, Phytogenic/pharmacology
- Antineoplastic Agents, Phytogenic/therapeutic use
- Antioxidants/chemistry
- Antioxidants/pharmacology
- Antioxidants/therapeutic use
- Antiviral Agents/chemistry
- Antiviral Agents/pharmacology
- Antiviral Agents/therapeutic use
- Arthritis, Rheumatoid/drug therapy
- Curcuma/chemistry
- Curcumin/analogs & derivatives
- Curcumin/chemistry
- Curcumin/metabolism
- Curcumin/pharmacology
- Curcumin/therapeutic use
- Humans
- India
- Medicine, Ayurvedic
- Models, Biological
- Molecular Structure
- Neoplasms/drug therapy
- Phytotherapy
- Plants, Medicinal
- Spices
- Structure-Activity Relationship
Collapse
Affiliation(s)
- Bharat B Aggarwal
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| | | | | | | |
Collapse
|
5
|
Smith KJ, Williams J, Skelton H. Metastatic adenocarcinoma of the esophagus to the skin: new patterns of tumor recurrence and alternate treatments for palliation. J Cutan Pathol 2001; 28:425-31. [PMID: 11493381 DOI: 10.1034/j.1600-0560.2001.028008425.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Esophageal cancer, particularly adenocarcinoma of the esophagus (ACE), has been steadily increasing in incidence in the United States. In the past, patients usually died rapidly with locoregional disease that leads to inanition and aspiration. However, today when patients with ACE are treated successfully with induction chemotherapy and radiation therapy, followed by surgical excision, ACE usually does not recur locally, but presents with metatastic disease. We present a 62-year-old white male with ACE, which was treated with induction chemotherapy and radiation therapy followed by surgical excision. After approximately 1 year with no evidence of locoregional recurrence, the patient presented with diffuse cutaneous metastatic disease. METHODS In addition to routine staining immunohistochemical stains for CK(AE1/AE3), CK7, CK 20, EMA, alpha-smooth muscle (SM) actin, S-100 protein, CD34, P53, Bcl-2, c-erbB-2 were performed. RESULTS The immunohistochemical profile was consistent with an esophageal origin showing positive staining with CK20 and CK7 as well as AE1/AE3 and EMA. In addition, there was marked nuclear expression of p53, as well as membrane expression of c-erb-B2; consistent with progression of the disease and poor response to further cytotoxic therapeutic regimes. CONCLUSIONS With new therapeutic protocols, we can expect to see more metastatic disease with recurrences of ACE. The histopathologic features and the immunohistochemical profile of the recurrent tumors may be helpful in determining alternate forms of therapy that either alone or in combination could be useful in palliation and delaying progression.
Collapse
Affiliation(s)
- K J Smith
- Department of Dermatology, National Naval Medical Center, Bethesda, Maryland, USA.
| | | | | |
Collapse
|
6
|
Lord RV, Tsai PI, Danenberg KD, Peters JH, Demeester TR, Tsao-Wei DD, Groshen S, Salonga D, Park JM, Crookes PF, Kiyabu M, Chandrasoma P, Danenberg PV. Retinoic acid receptor-alpha messenger RNA expression is increased and retinoic acid receptor-gamma expression is decreased in Barrett's intestinal metaplasia, dysplasia, adenocarcinoma sequence. Surgery 2001; 129:267-76. [PMID: 11231454 DOI: 10.1067/msy.2001.110856] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Expression levels of the retinoic acid receptors (RAR-alpha, RAR-beta, and RAR-gamma) are significantly different in neoplastic tissues compared with non-neoplastic tissues for some tumors. This study investigated whether retinoic acid receptor messenger RNA (mRNA) expression levels are altered in Barrett's esophagus and Barrett's adenocarcinoma tissues. METHODS Relative mRNA expression levels of the RARs were quantified by using the ABI 7700 Sequence Detector (Taqman) system in Barrett's intestinal metaplasia (n = 15), dysplasia (n = 6), adenocarcinoma (n = 17), and matching normal esophagus tissues (n = 36). RESULTS RAR-alpha expression was significantly increased, and RAR-gamma expression was significantly decreased, at higher stages in the Barrett's sequence. There was almost complete loss of RAR-gamma expression (relative expression level < or = 1) in a majority (70%) of the dysplasia and adenocarcinoma tissues. There were significant differences in RAR-alpha and RAR-gamma expression in histopathologically normal tissues in patients with cancer versus patients without cancer. RAR-beta expression levels were significantly elevated in adenocarcinoma versus normal esophagus tissues. The RAR expression profile was similar for cancers arising within the esophagus and for cancers arising at the gastroesophageal junction. CONCLUSIONS RAR mRNA expression levels are significantly different in Barrett's tissues compared with normal esophagus tissues, and these levels are significantly different in Barrett's dysplasia and adenocarcinoma tissues compared with nondysplastic tissues. These results suggest that RAR mRNA levels may be useful biomarkers for this disease and that gastroesophageal junction adenocarcinomas are genetically similar to esophageal adenocarcinomas. These results also suggest that a cancer field is present in the esophagus in patients with cancer and that genetic alterations can precede histopathologic alterations in this disease.
Collapse
Affiliation(s)
- R V Lord
- Department of Surgery, University of Southern California Keck School of Medicine and USC/Norris Cancer Center, Los Angeles, Calif., USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Abstract
Increasing emphasis has been placed on chemoprevention as understanding of the genetic and molecular events of carcinogenesis has evolved. More than 1000 compounds that inhibit cancer development in vitro or in animal models have been identified, and active research is under way to determine which of these agents will be both effective and nontoxic in human beings. Currently, 13-cis-retinoic acid is the most studied chemopreventive agent against head and neck cancers. Unfortunately, this vitamin A derivative has significant clinical toxicity, which limits its utility in a practice setting. The efficacy of the retinoids, however, has stimulated efforts to find other chemopreventive compounds that are both effective and nontoxic. This review discusses head and neck premalignancy, chemoprevention strategies, retinoids, and several other classes of chemopreventive agents with potential efficacy against head and neck premalignancy.
Collapse
Affiliation(s)
- W B Armstrong
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Chao Family Comprehensive Cancer Center, Orange, USA
| | | |
Collapse
|
8
|
Armstrong WB, Meyskens FL. Chemoprevention of head and neck cancer. Otolaryngol Head Neck Surg 2000. [DOI: 10.1067/mhn.2000.104627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Increasing emphasis has been placed on chemo-prevention as understanding of the genetic and molecular events of carcinogenesis has evolved. More than 1000 compounds that inhibit cancer development in vitro or in animal models have been identified, and active research is under way to determine which of these agents will be both effective and nontoxic in human beings. Currently, 13-cis-retinoic acid is the most studied chemopreventive agent against head and neck cancers. Unfortunately, this vitamin A derivative has significant clinical toxicity, which limits its utility in a practice setting. The efficacy of the retinoids, however, has stimulated efforts to find other chemopreventive compounds that are both effective and non-toxic. This review discusses head and neck premalignancy, chemoprevention strategies, retinoids, and several other classes of chemopreventive agents with potential efficacy against head and neck premalignancy.
Collapse
Affiliation(s)
| | - Frank L. Meyskens
- Medicine (Dr Meyskens), University of California, Irvine, Chao Family Comprehensive Cancer Center
| |
Collapse
|