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  1. Article: Tracing vitamins on the long non-coding lane of the transcriptome: vitamin regulation of LncRNAs.

    Yazarlou, Fatemeh / Alizadeh, Fatemeh / Lipovich, Leonard / Giordo, Roberta / Ghafouri-Fard, Soudeh

    Genes & nutrition

    2024  Volume 19, Issue 1, Page(s) 5

    Abstract: A major revelation of genome-scale biological studies in the post-genomic era has been that two-thirds of human genes do not encode proteins. The majority of non-coding RNA transcripts in humans are long non-coding RNA (lncRNA) molecules, non-protein- ... ...

    Abstract A major revelation of genome-scale biological studies in the post-genomic era has been that two-thirds of human genes do not encode proteins. The majority of non-coding RNA transcripts in humans are long non-coding RNA (lncRNA) molecules, non-protein-coding regulatory transcripts with sizes greater than 500 nucleotides. LncRNAs are involved in nearly every aspect of cellular physiology, playing fundamental regulatory roles both in normal cells and in disease. As result, they are functionally linked to multiple human diseases, from cancer to autoimmune, inflammatory, and neurological disorders. Numerous human conditions and diseases stem from gene-environment interactions; in this regard, a wealth of reports demonstrate that the intake of specific and essential nutrients, including vitamins, shapes our transcriptome, with corresponding impacts on health. Vitamins command a vast array of biological activities, acting as coenzymes, antioxidants, hormones, and regulating cellular proliferation and coagulation. Emerging evidence suggests that vitamins and lncRNAs are interconnected through several regulatory axes. This type of interaction is expected, since lncRNA has been implicated in sensing the environment in eukaryotes, conceptually similar to riboswitches and other RNAs that act as molecular sensors in prokaryotes. In this review, we summarize the peer-reviewed literature to date that has reported specific functional linkages between vitamins and lncRNAs, with an emphasis on mammalian models and humans, while providing a brief overview of the source, metabolism, and function of the vitamins most frequently investigated within the context of lncRNA molecular mechanisms, and discussing the published research findings that document specific connections between vitamins and lncRNAs.
    Language English
    Publishing date 2024-03-12
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2416599-2
    ISSN 1865-3499 ; 1555-8932
    ISSN (online) 1865-3499
    ISSN 1555-8932
    DOI 10.1186/s12263-024-00739-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Dietary iron and the risk of lung cancer.

    Mohammadzadeh, Milad / Bahrami, Alireza / Ghafouri-Taleghani, Fatemeh / Khalesi, Saman / Abdi, Fatemeh / Hejazi, Ehsan

    International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition

    2023  

    Abstract: Animal models have suggested the carcinogenic effect of iron due to its oxidative potential. The lung is particularly vulnerable to oxidative stress. However, epidemiological studies investigating the association between dietary iron and the risk of lung ...

    Abstract Animal models have suggested the carcinogenic effect of iron due to its oxidative potential. The lung is particularly vulnerable to oxidative stress. However, epidemiological studies investigating the association between dietary iron and the risk of lung cancer have reported inconclusive results. In this systematic review and meta-analysis, we aimed to clarify this association.
    Language English
    Publishing date 2023-07-20
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 120692-8
    ISSN 0300-9831
    ISSN 0300-9831
    DOI 10.1024/0300-9831/a000789
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  3. Article ; Online: Biological treatment of triclosan using a novel strain of Enterobacter cloacae and introducing naphthalene dioxygenase as an effective enzyme.

    Ghafouri, Mahsa / Pourjafar, Fatemeh / Ghobadi Nejad, Zahra / Yaghmaei, Soheila

    Journal of hazardous materials

    2023  Volume 459, Page(s) 131833

    Abstract: In recent years, triclosan (TCS) has been widely used as an antibacterial agent in personal care products due to the spread of the Coronavirus. TSC is an emerging contaminant, and due to its stability and toxicity, it cannot be completely degraded ... ...

    Abstract In recent years, triclosan (TCS) has been widely used as an antibacterial agent in personal care products due to the spread of the Coronavirus. TSC is an emerging contaminant, and due to its stability and toxicity, it cannot be completely degraded through traditional wastewater treatment methods. In this study, a novel strain of Enterobacter cloacae was isolated and identified that can grow in high TCS concentrations. Also, we introduced naphthalene dioxygenase as an effective enzyme in TCS biodegradation, and its role during the removal process was investigated along with the laccase enzyme. The change of cell surface hydrophobicity during TCS removal revealed that a glycolipid biosurfactant called rhamnolipid was involved in TCS removal, leading to enhanced biodegradation of TCS. The independent variables, such as initial TCS concentration, pH, removal duration, and temperature, were optimized using the response surface method (RSM). As a result, the maximum TCS removal (97%) was detected at a pH value of 7 and a temperature of 32 °C after 9 days and 12 h of treatment. Gas chromatography-mass spectrometry (GC/MS) analysis showed five intermediate products and a newly proposed pathway for TCS degradation. Finally, the phytotoxicity experiment conducted on Cucumis sativus and Lens culinaris seeds demonstrated an increase in germination power and growth of stems and roots in comparison to untreated water. These results indicate that the final treated water was less toxic.
    MeSH term(s) Triclosan/analysis ; Enterobacter cloacae/metabolism ; Multienzyme Complexes ; Dioxygenases ; Water Pollutants, Chemical/chemistry
    Chemical Substances Triclosan (4NM5039Y5X) ; naphthalene dioxygenase (EC 1.14.12.-) ; Multienzyme Complexes ; Dioxygenases (EC 1.13.11.-) ; Water Pollutants, Chemical
    Language English
    Publishing date 2023-06-12
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1491302-1
    ISSN 1873-3336 ; 0304-3894
    ISSN (online) 1873-3336
    ISSN 0304-3894
    DOI 10.1016/j.jhazmat.2023.131833
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Dietary Diabetes Risk Reduction Score (DDRRS) and Breast Cancer Risk: A Case-Control Study in Iran.

    Mohammadzadeh, Milad / Bahrami, Alireza / Abdi, Fatemeh / Ghafouri-Taleghani, Fatemeh / Paydareh, Amin / Jalali, Saba / Heidari, Zeinab / Rashidkhani, Bahram

    Nutrition and cancer

    2023  Volume 76, Issue 1, Page(s) 106–113

    Abstract: Introduction: Given the role of type 2 diabetes and insulin resistance in tumor initiation, we hypothesized that following a diet that reduces the risk of type 2 diabetes could also reduce the risk of breast cancer. Herein, we conducted a case-control ... ...

    Abstract Introduction: Given the role of type 2 diabetes and insulin resistance in tumor initiation, we hypothesized that following a diet that reduces the risk of type 2 diabetes could also reduce the risk of breast cancer. Herein, we conducted a case-control study to investigate the association between dietary diabetes risk reduction score and breast cancer risk in Iranian women.
    Method: We recruited 136 newly diagnosed cases and 272 age-matched hospitalized controls from referral hospitals. A valid and reliable 168-item food frequency questionnaire (FFQ) was used to collect the data on dietary intake. We used Multivariate Logistic regression to assess the odds ratio (OR) with 95% confidence interval (CI) of breast cancer by the dietary diabetes risk reduction score tertiles.
    Results: After adjusting for confounding variables, no association was seen between dietary diabetes risk reduction score and breast cancer risk (OR = 0.65, 95% CI: 0.37-1.14). However, after stratification by menopausal status, a decreased risk was observed between adherence to dietary diabetes risk reduction score and breast cancer risk in postmenopausal individuals (OR = 0.43, 95% CI: 0.19-0.99).
    Conclusion: The present study states that there is no significant relationship between the dietary diabetes risk reduction score and the risk of breast cancer. However, adherence to dietary diabetes risk reduction score could have a preventive role for breast cancer among postmenopausal women.
    MeSH term(s) Female ; Humans ; Iran/epidemiology ; Breast Neoplasms/epidemiology ; Breast Neoplasms/etiology ; Breast Neoplasms/prevention & control ; Diabetes Mellitus, Type 2/prevention & control ; Case-Control Studies ; Diet ; Risk Factors ; Risk Reduction Behavior
    Language English
    Publishing date 2023-12-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 424433-3
    ISSN 1532-7914 ; 0163-5581
    ISSN (online) 1532-7914
    ISSN 0163-5581
    DOI 10.1080/01635581.2023.2281025
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Ciprofloxacin antibiotic removal from aqueous solutions by ZnO nanoparticles coated on ACA: modeling and optimization.

    Mohammadi, Fatemeh / Farahmandkia, Zohre / Mehrasbi, Mohammad Reza / Mahmoudian, Mohammad Hassan / Tabatabaei, Fatemeh Sadat / Mostafaloo, Roqiyeh / Ghafouri, Nasim / Asadi-Ghalhari, Mahdi

    Environmental monitoring and assessment

    2023  Volume 195, Issue 12, Page(s) 1443

    Abstract: Antibiotics are one of the most widely used drug groups. The presence of antibiotics in urban water sources and sewage creates many environmental and medical risks for humans and other living organisms. In this study, the potential of zinc oxide (ZnO) ... ...

    Abstract Antibiotics are one of the most widely used drug groups. The presence of antibiotics in urban water sources and sewage creates many environmental and medical risks for humans and other living organisms. In this study, the potential of zinc oxide (ZnO) coated on almond shell activated carbon (ACA-ZnO) in removing ciprofloxacin (CIP) from aqueous solutions was investigated. Almond shell was used to make activated carbon. Zinc oxide nanoparticles were prepared by the sol-gel method, and finally, ZnO nanoparticles were bonded to activated carbon. The effect of independent parameters pH, contact time, adsorbent dose, and initial CIP concentration on CIP removal efficiency using ACA-ZnO was investigated by response surface methodology. Optimal removal was obtained at pH = 5.4, CIP initial concentration = 7.4 mg/L, adsorbent dose = 0.82 g/L, and reaction time = 67.3 min. This study followed a quadratic model (R
    MeSH term(s) Humans ; Anti-Bacterial Agents/chemistry ; Ciprofloxacin/chemistry ; Zinc Oxide/chemistry ; Charcoal ; Environmental Monitoring ; Water/chemistry ; Nanoparticles ; Adsorption ; Water Pollutants, Chemical/chemistry ; Kinetics ; Hydrogen-Ion Concentration
    Chemical Substances Anti-Bacterial Agents ; Ciprofloxacin (5E8K9I0O4U) ; Zinc Oxide (SOI2LOH54Z) ; Charcoal (16291-96-6) ; Water (059QF0KO0R) ; Water Pollutants, Chemical
    Language English
    Publishing date 2023-11-10
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 782621-7
    ISSN 1573-2959 ; 0167-6369
    ISSN (online) 1573-2959
    ISSN 0167-6369
    DOI 10.1007/s10661-023-12041-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Gene cloning and characterization of a novel recombinant 40-kDa heat shock protein from Mesobacillus persicus B48.

    Fathinejad, Fatemeh / Ghafouri, Hossein / Barzegari, Ebrahim / Sarikhan, Sajjad / Alizadeh, Arghavan / Howard, Newton

    World journal of microbiology & biotechnology

    2023  Volume 39, Issue 9, Page(s) 248

    Abstract: The present study reports the recognition and characterization of the gene encoding the co-chaperone DnaJ in the halophilic strain Mesobacillus persicus B48. The new extracted gene was sequenced and cloned in E. coli, followed by protein purification ... ...

    Abstract The present study reports the recognition and characterization of the gene encoding the co-chaperone DnaJ in the halophilic strain Mesobacillus persicus B48. The new extracted gene was sequenced and cloned in E. coli, followed by protein purification using a C-terminal His-tag. The stability and function of the recombinant DnaJ protein under salt and pH stress conditions were evaluated. SDS-PAGE revealed a band on nearly 40-kDa region. The homology model structure of new DnaJ demonstrated 56% similarity to the same protein from Streptococcus pneumonia. Fluorescence spectra indicated several hydrophobic residues located on the protein surface, which is consistent with the misfolded polypeptide recognition function of DnaJ. Spectroscopic results showed 56% higher carbonic anhydrase activity in the presence of the recombinant DnaJ homolog compared to its absence. In addition, salt resistance experiments showed that the survival of recombinant E. coli+DnaJ was 2.1 times more than control cells in 0.5 M NaCl. Furthermore, the number of recombinant E. coli BL21+DnaJ colonies was 7.7 times that of the control colonies in pH 8.5. Based on the results, DnaJ from the M. persicus can potentially be employed for improving the functional features of enzymes and other proteins in various applications.
    MeSH term(s) Heat-Shock Proteins/chemistry ; Heat-Shock Proteins/genetics ; Heat-Shock Proteins/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; HSP70 Heat-Shock Proteins/genetics ; Escherichia coli Proteins/genetics ; HSP40 Heat-Shock Proteins/genetics ; Cloning, Molecular ; Recombinant Proteins/metabolism ; Bacterial Proteins/metabolism
    Chemical Substances Heat-Shock Proteins ; HSP70 Heat-Shock Proteins ; Escherichia coli Proteins ; HSP40 Heat-Shock Proteins ; Recombinant Proteins ; Bacterial Proteins
    Language English
    Publishing date 2023-07-12
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1499109-3
    ISSN 1573-0972 ; 0959-3993
    ISSN (online) 1573-0972
    ISSN 0959-3993
    DOI 10.1007/s11274-023-03693-2
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  7. Article ; Online: Modeling and optimization of the coagulation/flocculation process in turbidity removal from water using poly aluminum chloride and rice starch as a natural coagulant aid.

    Asadi-Ghalhari, Mahdi / Usefi, Saideh / Ghafouri, Nassim / Kishipour, Amin / Mostafaloo, Roqiyeh / Tabatabaei, Fatemeh Sadat

    Environmental monitoring and assessment

    2023  Volume 195, Issue 4, Page(s) 527

    Abstract: The application of the coagulation/flocculation process is very important due to its simplicity in removing turbidity. Due to the disadvantages of using chemical coagulants in water and the lack of sufficient effect of natural materials alone in removing ...

    Abstract The application of the coagulation/flocculation process is very important due to its simplicity in removing turbidity. Due to the disadvantages of using chemical coagulants in water and the lack of sufficient effect of natural materials alone in removing turbidity for proper performance, the simultaneous use of chemical and natural coagulants is the best way to reduce the harmful effects of chemical coagulants in water. In this study, the application of poly aluminum chloride (PAC) as a chemical coagulant and rice starch as a natural coagulant aid to remove turbidity from aqueous solutions was investigated. Effects of the above coagulants on the four main factors, coagulant dose (0-10 mg/L), coagulant adjuvant dose (0-0.1 mg/L), pH (5-9), turbidity (NTU 0-50), and each five levels were assessed using a central composite design (CCD). Under the optimized conditions, the maximum turbidity elimination efficiency was found to be 96.6%. The validity and adequacy of the proposed model (quadratic model) were confirmed by the corresponding statistics (i.e., F-value of 23.3, p-values of 0.0001, and lack of fit of 0.877 for the model, respectively, R
    MeSH term(s) Aluminum Chloride/chemistry ; Flocculation ; Oryza ; Starch/chemistry ; Water ; Water Purification/methods ; Models, Chemical
    Chemical Substances Aluminum Chloride (3CYT62D3GA) ; Starch (9005-25-8) ; Water (059QF0KO0R)
    Language English
    Publishing date 2023-03-31
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 782621-7
    ISSN 1573-2959 ; 0167-6369
    ISSN (online) 1573-2959
    ISSN 0167-6369
    DOI 10.1007/s10661-023-11150-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Emerging role of let-7 family in the pathogenesis of hematological malignancies.

    Yazarlou, Fatemeh / Kadkhoda, Sepideh / Ghafouri-Fard, Soudeh

    Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

    2021  Volume 144, Page(s) 112334

    Abstract: Let-7 includes a family of miRNA which are implicated in the developmental processes as well as carcinogenesis. This miRNA family has been shown to influence pathogenesis of a variety of hematological malignancies through changing expression of a number ... ...

    Abstract Let-7 includes a family of miRNA which are implicated in the developmental processes as well as carcinogenesis. This miRNA family has been shown to influence pathogenesis of a variety of hematological malignancies through changing expression of a number of oncogenic pathways, particularly those related with MYC. Expression of these miRNAs has been found to be different between distinct hematological malignancies or even between cytogenetically-defined subgroups of a certain malignancy. In the current review, we summarize the data regarding biogenesis, genomic locations, targets and regulatory network of this miRNA family in the context of hematological malignancies.
    MeSH term(s) Animals ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Hematologic Neoplasms/genetics ; Hematologic Neoplasms/metabolism ; Hematologic Neoplasms/pathology ; Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Signal Transduction
    Chemical Substances MicroRNAs ; mirnlet7 microRNA, human
    Language English
    Publishing date 2021-10-13
    Publishing country France
    Document type Journal Article ; Review
    ZDB-ID 392415-4
    ISSN 1950-6007 ; 0753-3322 ; 0300-0893
    ISSN (online) 1950-6007
    ISSN 0753-3322 ; 0300-0893
    DOI 10.1016/j.biopha.2021.112334
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Colorectal cancer-secreted exosomal circ_001422 plays a role in regulating KDR expression and activating mTOR signaling in endothelial cells by targeting miR-195-5p.

    Ghafouri, Iren / Pakravan, Katayoon / Razmara, Ehsan / Montazeri, Maryam / Rouhollah, Fatemeh / Babashah, Sadegh

    Journal of cancer research and clinical oncology

    2023  Volume 149, Issue 13, Page(s) 12227–12240

    Abstract: Background: As non-coding RNAs, exosomal circular RNAs (circRNAs) regulate colorectal cancer (CRC) progression, although the functional mechanisms by which such molecules affect the tumor microenvironment are still elusive. Herein, we aimed to explore ... ...

    Abstract Background: As non-coding RNAs, exosomal circular RNAs (circRNAs) regulate colorectal cancer (CRC) progression, although the functional mechanisms by which such molecules affect the tumor microenvironment are still elusive. Herein, we aimed to explore the potential clinical significance of a signature of five serum-derived circRNAs in CRC and investigated the mechanisms underlying endothelial cell angiogenesis mediated by CRC-secreted exosomal circ_001422.
    Methods: The expression of a signature of five serum-derived circRNAs (circ_0004771, circ_0101802, circ_0082333, circ_0072309, and circ_001422) were measured by RT-qPCR, and their associations with tumor staging and lymph node metastasis were further evaluated in CRC patients. In silico analysis was used to show the relationship between circ_001422, miR-195-5p, and KDR, validated by dual-luciferase reporter and Western blotting assays. CRC cell-derived exosomes were isolated and characterized by scanning electron microscopy and Western blotting. Endothelial cell uptake of PKH26-labeled exosomes was demonstrated using a spectral confocal microscope. In vitro genetic strategies were used to exogenously alter the expression level of circ_001422 and miR-195-5p expression. Cell proliferation assay, transwell migration assay, and capillary tube formation assay were conducted to explore the role of CRC-secreted exosomal circ_001422 in endothelial cell function in vitro.
    Results: The expression levels of serum-derived circ_0004771, circ_0101802, circ_0082333, and circ_001422 were significantly higher in CRC and were positively correlated with the lymph node metastasis status. However, circ_0072309 showed a significant down-regulation in CRC than in healthy individuals. Furthermore, a higher expression level of circ_001422 in both cellular and exosomal fractions was found in HCT-116 CRC cells. We found that HCT-116 exosomes considerably enhanced proliferation and migration of endothelial cells through shuttling of circ_001422. We also observed that exosomes derived from HCT-116 cell, but not non-aggressive Caco-2 CRC cells, increased in vitro tubulogenesis of endothelial cells. Importantly, knockdown of circ_001422 impaired the capability of endothelial cells to form the capillary-like tube structures. CRC-secreted circ_001422 acted as an endogenous miR-195-5p sponge to inhibit miR-195-5p activity, which led to increased KDR expression and mTOR signaling activation in endothelial cells. Importantly, ectopic expression of miR-195-5p mimicked the effect of circ_001422 silencing on KDR/mTOR signaling in endothelial cells.
    Conclusion: This study attributed a biomarker role for circ_001422 in CRC diagnosis and proposed a novel mechanism whereby circ_001422 up-regulates KDR through sponging miR-195-5p. These interactions may give rise to the activation of mTOR signaling and may be a possible clarification for the pro-angiogenesis effects of CRC-secreted exosomal circ_001422 on endothelial cells.
    MeSH term(s) Humans ; Endothelial Cells ; Caco-2 Cells ; Lymphatic Metastasis ; RNA, Circular/genetics ; TOR Serine-Threonine Kinases/genetics ; Colorectal Neoplasms/genetics ; MicroRNAs/genetics ; Cell Proliferation ; Tumor Microenvironment ; Vascular Endothelial Growth Factor Receptor-2
    Chemical Substances RNA, Circular ; TOR Serine-Threonine Kinases (EC 2.7.11.1) ; MicroRNAs ; KDR protein, human (EC 2.7.10.1) ; Vascular Endothelial Growth Factor Receptor-2 (EC 2.7.10.1) ; MIRN195 microRNA, human
    Language English
    Publishing date 2023-07-11
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 134792-5
    ISSN 1432-1335 ; 0171-5216 ; 0084-5353 ; 0943-9382
    ISSN (online) 1432-1335
    ISSN 0171-5216 ; 0084-5353 ; 0943-9382
    DOI 10.1007/s00432-023-05095-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Roles of non-coding RNAs in cell death pathways involved in the treatment of resistance and recurrence of cancer.

    Motlagh, Fatemeh Movahedi / Kadkhoda, Sepideh / Motamedrad, Maryam / Javidzade, Parisa / Khalilian, Sheyda / Modarressi, Mohammad Hossein / Ghafouri-Fard, Soudeh

    Pathology, research and practice

    2023  Volume 247, Page(s) 154542

    Abstract: Considering the burden of cancer, a number of methods have been applied to control or stop it. However, because of drug resistance or cancer recurrence, these treatments usually face failure. Combination of modulation of expression of non-coding RNAs ( ... ...

    Abstract Considering the burden of cancer, a number of methods have been applied to control or stop it. However, because of drug resistance or cancer recurrence, these treatments usually face failure. Combination of modulation of expression of non-coding RNAs (ncRNAs) with other treatments can increase treatment-sensitivity of tumors but these approaches still face some challenges. Gathering information in this field is a prerequisite to find more efficient cures for cancer. Cancer cells use ncRNAs to enhance uncontrolled proliferation originated from inactivation of cell death routs. In this review article, the main routes of cell death and involved ncRNAs in these routes are discussed. Moreover, extant information in the role of different ncRNAs on cell death pathways involved in the treatment resistance and cancer recurrence is summarized.
    MeSH term(s) Humans ; RNA, Untranslated/genetics ; Neoplasms/genetics ; Cell Death/genetics ; RNA, Long Noncoding
    Chemical Substances RNA, Untranslated ; RNA, Long Noncoding
    Language English
    Publishing date 2023-05-18
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 391889-0
    ISSN 1618-0631 ; 0344-0338
    ISSN (online) 1618-0631
    ISSN 0344-0338
    DOI 10.1016/j.prp.2023.154542
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