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Budhbaware T, Rathored J, Shende S. Molecular methods in cancer diagnostics: a short review. Ann Med 2024; 56:2353893. [PMID: 38753424 PMCID: PMC11100444 DOI: 10.1080/07853890.2024.2353893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required. OBJECTIVE In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer. METHODS We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria. RESULTS The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes. LIMITATION The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field. CONCLUSION After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.
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Affiliation(s)
- Tanushree Budhbaware
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Jaishriram Rathored
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Sandesh Shende
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
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Pérez-Fuentes N, Alvariño R, Alfonso A, González-Jartín J, Vieytes MR, Botana LM. In vitro assessment of emerging mycotoxins co-occurring in cheese: a potential health hazard. Arch Toxicol 2024:10.1007/s00204-024-03872-6. [PMID: 39322822 DOI: 10.1007/s00204-024-03872-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 09/19/2024] [Indexed: 09/27/2024]
Abstract
Some Penicillium strains used in cheese ripening produce emerging mycotoxins, notably roquefortine C (ROQC) and cyclopiazonic acid (CPA), as well as enniatins (ENNs) and beauvericin (BEA). Co-occurrence of these mycotoxins in natural samples has been reported worldwide, however, most studies focus on the toxicity of a single mycotoxin. In the present study, the effects of ROQC and CPA alone and in combination with BEA and ENNs A, A1, B, and B1 were analysed in human neuroblastoma cells. ROQC and CPA reduced cell viability, with IC50 values of 49.5 and 7.3 µM, respectively, and induced caspase-8-mediated apoptosis. When ROQC and CPA were binary combined with ENNs, an enhancement of their individual effects was observed. Furthermore, a clear synergism was produced when ROQC and CPA were mixed with the four ENNs. An additive effect was also described for the combination of CPA + ENNs (A, A1, B, B1) + BEA. Finally, the effects of commercial cheese extracts containing the mentioned mycotoxins were evaluated, finding a strong reduction in cell viability. These results suggest that the co-occurrence of emerging mycotoxins in natural matrices could pose a potential health risk.
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Affiliation(s)
- Nadia Pérez-Fuentes
- Departamento de Farmacología, Facultad de Veterinaria, IDIS, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - Rebeca Alvariño
- Departamento de Fisiología, Facultad de Veterinaria, IDIS, Universidad de Santiago de Compostela, 27002, Lugo, Spain.
| | - Amparo Alfonso
- Departamento de Farmacología, Facultad de Veterinaria, IDIS, Universidad de Santiago de Compostela, 27002, Lugo, Spain.
| | - Jesús González-Jartín
- Departamento de Farmacología, Facultad de Veterinaria, IDIS, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - Mercedes R Vieytes
- Departamento de Fisiología, Facultad de Veterinaria, IDIS, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - Luis M Botana
- Departamento de Farmacología, Facultad de Veterinaria, IDIS, Universidad de Santiago de Compostela, 27002, Lugo, Spain
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Nayagam SM, Ramachandran K, Selvaraj G, Sunmathi R, Easwaran M, Palraj ND, Anand K S SV, Muthurajan R, Tangavel C, Rajasekaran S. Identification of extracellular matrix proteins in plasma as a potential biomarker for intervertebral disc degeneration. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2024:10.1007/s00586-024-08481-6. [PMID: 39299936 DOI: 10.1007/s00586-024-08481-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
PURPOSE Recently, there has been significant focus on extracellular matrix proteolysis due to its importance in the pathological progression of intervertebral disc degeneration (IVDD). The present study investigates the circulating levels of extracellular matrix proteins in the plasma of IVDD and determines their potential relevance as biomarkers in disc degeneration. METHODS Global proteomic analysis was performed in the plasma samples of 10 healthy volunteers (HV) and 10 diseased subjects (DS) after depletion of highly abundant proteins such as albumin and IgG. RESULTS We identified 144 and 135 matrix-associated proteins in plasma samples from healthy volunteers (HV) and patients with disc degeneration (DS), respectively. Among these, 49 of the matrix-associated proteins were identical to the proteins found in intervertebral disc (IVD) tissues retrieved from the in-house library. Applying stringent parameters, we selected 28 proteins, with 26 present in DS and 21 in HV. 19 proteins were found common between the groups, two of which-aggrecan (ACAN) and fibulin 1 (FBLN1) - showed statistically significant differences. Specifically, ACAN was up-regulated and FBLN1 was down-regulated in the DS-plasma. In particular, DS-plasma exhibited specific expression of collagen type 2a1 (COL2A1), native to the nucleus pulposus. CONCLUSION The distinct presence of collagen type 2a1 and the elevated expression of aggrecan in IVDD plasma may serve as the basis for the development of a potential biomarker for monitoring the progression of disc degeneration.
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Affiliation(s)
| | - Karthik Ramachandran
- Department of Spine Surgery, Ganga Hospital, 313, Mettupalayam Road, Coimbatore, India
| | - Ganesh Selvaraj
- Ganga Research Centre, 442, Vattamalaipalayam Road, NGGO colony, Coimbatore, India
| | - R Sunmathi
- Ganga Research Centre, 442, Vattamalaipalayam Road, NGGO colony, Coimbatore, India
| | - Murugesh Easwaran
- Ganga Research Centre, 442, Vattamalaipalayam Road, NGGO colony, Coimbatore, India
| | - Narmatha Devi Palraj
- Ganga Research Centre, 442, Vattamalaipalayam Road, NGGO colony, Coimbatore, India
| | - Sri Vijay Anand K S
- Department of Spine Surgery, Ganga Hospital, 313, Mettupalayam Road, Coimbatore, India
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Lawley Road, Coimbatore, India
| | - Chitraa Tangavel
- Ganga Research Centre, 442, Vattamalaipalayam Road, NGGO colony, Coimbatore, India
| | - S Rajasekaran
- Department of Spine Surgery, Ganga Hospital, 313, Mettupalayam Road, Coimbatore, India.
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Bulangalire N, Claeyssen C, Douffi S, Agbulut O, Cieniewski-Bernard C. A novel 2D-electrophoresis method for the simultaneous visualization of phosphorylated and O-GlcNAcylated proteoforms of a protein. Electrophoresis 2024; 45:1618-1629. [PMID: 38700120 DOI: 10.1002/elps.202400043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
Post-translational modifications (PTMs), such as phosphorylation and O-N-acetyl-β-d-glucosaminylation (O-GlcNAcylation), are involved in the fine spatiotemporal regulation of protein functions, and their dynamic interplay is at the heart of protein language. The coexistence of phosphorylation and O-GlcNAcylation on a protein leads to the diversification of proteoforms. It is therefore essential to decipher the phosphorylation/O-GlcNAcylation interplay on protein species that orchestrates cellular processes in a specific physiological or pathophysiological context. However, simultaneous visualization of phosphorylation and O-GlcNAcylation patterns on a protein of interest remains a challenge. To map the proteoforms of a protein, we have developed an easy-to-use two-dimensional electrophoresis method with a single sample processing permitting simultaneous visualization of the phosphorylated and the O-GlcNAcylated forms of the protein of interest. This method, we termed 2D-WGA-Phos-tag-PAGE relies on proteoforms retardation by affinity gel electrophoresis. With this novel approach, we established the cartography of phospho- and glycoforms of αB-crystallin and desmin in the whole extract and the cytoskeleton protein subfraction in skeletal muscle cells. Interestingly, we have shown that the pattern of phosphorylation and O-GlcNAcylation depends of the subcellular subfraction. Moreover, we have also shown that proteotoxic stress condition increased the complexity of the pattern of PTMs on αB-crystallin.
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Affiliation(s)
- Nathan Bulangalire
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
- CHU Lille, Université de Lille, F-59000, Lille, France
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Charlotte Claeyssen
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
| | - Sana Douffi
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
| | - Onnik Agbulut
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Caroline Cieniewski-Bernard
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
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Van Bockstal L, Prims S, Van Cruchten S, Ayuso M, Che L, Van Ginneken C. Cell migration and proliferation capacity of IPEC-J2 cells after short-chain fatty acid exposure. PLoS One 2024; 19:e0309742. [PMID: 39213333 PMCID: PMC11364292 DOI: 10.1371/journal.pone.0309742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Novel antimicrobial strategies are necessary to tackle using antibiotics during the suckling and weaning period of piglets, often characterized by E. coli-induced diarrhea. In the last decades, acetate, propionate, and butyrate, all short-chain fatty acids (SCFAs), have been proposed as an alternative to antibiotics. SCFAs are instrumental in promoting the proliferation of enterocytes, preserving intestinal integrity, and modulating the microbial community by suppressing the growth of pathogenic bacteria in pigs. The effect of individual SCFAs (proprionate, acetate and butyrate) on the regenerative capacity of intestinal cells was investigated via an optimized wound-healing assay in IPEC-J2 cells, a porcine jejunal epithelial cell line. IPEC-J2 cells proved a good model as they express the free fatty acid receptor 2 (FFAR2), an important SCFA receptor with a high affinity for proprionate. Our study demonstrated that propionate (p = 0.005) and acetate (p = 0.037) were more effective in closing the wound than butyrate (p = 0.190). This holds promise in using SCFA's per os as an alternative to antibiotics.
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Affiliation(s)
- Lieselotte Van Bockstal
- Comparative Perinatal Development, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Sara Prims
- Comparative Perinatal Development, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Steven Van Cruchten
- Comparative Perinatal Development, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Miriam Ayuso
- Biogenesis Bagó, Development of Biotech Products, Madrid, Spain
| | - Lianqiang Che
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu City, Sichuan Province, China
| | - Chris Van Ginneken
- Comparative Perinatal Development, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
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Zhou H, Wu Z, Zhang Y, Yu Z, Nie Z, Fan J, Zhu Z, Chen F, Wang T. In vitro anticancer study of novel curcumin derivatives via targeting PI3K/Akt/p53 signaling pathway. Mol Divers 2024:10.1007/s11030-024-10833-9. [PMID: 38951417 DOI: 10.1007/s11030-024-10833-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/28/2024] [Indexed: 07/03/2024]
Abstract
Four new series of curcumin derivatives bearing NO-donating moiety were synthesized via etherification, nucleophilic substitution, and Knoevenagel condensation etc. The cytotoxicity activity of curcumin derivatives against five human tumor cell lines (A549, Hela, HepG2, MCF-7 and HT-29) and two normal cell lines (LO-2 and HK-2) has been studied. The results showed that compound 6a could inhibit the proliferation of MCF-7 cells remarkably and exhibit low toxicity to normal cells. Also, the underlying mechanism in vitro of compound 6a on MCF-7 was investigated. It has been found that compound 6a induced G2/M arrest and apoptosis of MCF-7 in a dose-dependent manner. Compound 6a-induced the fluorescence changes of ROS in MCF-7 cells confirmed the occurrence of apoptosis. Western Blot suggested that compound 6a decreased the expression of PI3K, as well as increased the expression of p53, cleaved caspase-9 and cleaved caspase-3. Furthermore, molecular docking revealed that compound 6a could bind well at active site of PI3K (3zim) with total score 9.59. Together, compound 6a, a potential PI3K inhibitor, may inhibit the survival of MCF-7 cells via interfering with PI3K/Akt/p53 pathway.
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Affiliation(s)
- Huixian Zhou
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Zhiwen Wu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Yannan Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Zikai Yu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Zhengyang Nie
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Jinbiao Fan
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Zuchang Zhu
- Technological R&D department, Lizhu Pharmaceutical Co., Ltd, Zhuhai, Guangdong, 519000, People's Republic of China
| | - Fenglian Chen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, People's Republic of China.
| | - Tao Wang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, People's Republic of China.
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Baltazar-García EA, Vargas-Guerrero B, Lima A, Boavida Ferreira R, Mendoza-Magaña ML, Ramírez-Herrera MA, Baltazar-Díaz TA, Domínguez-Rosales JA, Salazar-Montes AM, Gurrola-Díaz CM. Deflamin Attenuated Lung Tissue Damage in an Ozone-Induced COPD Murine Model by Regulating MMP-9 Catalytic Activity. Int J Mol Sci 2024; 25:5063. [PMID: 38791100 PMCID: PMC11121448 DOI: 10.3390/ijms25105063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/26/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is comprised of histopathological alterations such as pulmonary emphysema and peribronchial fibrosis. Matrix metalloproteinase 9 (MMP-9) is one of the key enzymes involved in both types of tissue remodeling during the development of lung damage. In recent studies, it was demonstrated that deflamin, a protein component extracted from Lupinus albus, markedly inhibits the catalytic activity of MMP-9 in experimental models of colon adenocarcinoma and ulcerative colitis. Therefore, in the present study, we investigated for the first time the biological effect of deflamin in a murine COPD model induced by chronic exposure to ozone. Ozone exposure was carried out in C57BL/6 mice twice a week for six weeks for 3 h each time, and the treated group was orally administered deflamin (20 mg/kg body weight) after each ozone exposure. The histological results showed that deflamin attenuated pulmonary emphysema and peribronchial fibrosis, as evidenced by H&E and Masson's trichrome staining. Furthermore, deflamin administration significantly decreased MMP-9 activity, as assessed by fluorogenic substrate assay and gelatin zymography. Interestingly, bioinformatic analysis reveals a plausible interaction between deflamin and MMP-9. Collectively, our findings demonstrate the therapeutic potential of deflamin in a COPD murine model, and suggest that the attenuation of the development of lung tissue damage occurs by deflamin-regulated MMP-9 catalytic activity.
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Affiliation(s)
- Elia Ana Baltazar-García
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - Belinda Vargas-Guerrero
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - Ana Lima
- CECAV—Centro de Ciência Animal e Veterinária, Faculty of Veterinary Medicine, Lusófona University, Campo Grande, 376, 1749-024 Lisbon, Portugal;
| | - Ricardo Boavida Ferreira
- LEAF—Landscape Environment Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal;
| | - María Luisa Mendoza-Magaña
- Laboratorio de Neurofisiología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (M.L.M.-M.); (M.A.R.-H.)
| | - Mario Alberto Ramírez-Herrera
- Laboratorio de Neurofisiología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (M.L.M.-M.); (M.A.R.-H.)
| | - Tonatiuh Abimael Baltazar-Díaz
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - José Alfredo Domínguez-Rosales
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - Adriana María Salazar-Montes
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - Carmen Magdalena Gurrola-Díaz
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
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Barros O, D'Agostino VG, Lara Santos L, Vitorino R, Ferreira R. Shaping the future of oral cancer diagnosis: advances in salivary proteomics. Expert Rev Proteomics 2024; 21:149-168. [PMID: 38626289 DOI: 10.1080/14789450.2024.2343585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/19/2024] [Indexed: 04/18/2024]
Abstract
INTRODUCTION Saliva has gained increasing attention in the quest for disease biomarkers. Because it is a biological fluid that can be collected is an easy, painless, and safe way, it has been increasingly studied for the identification of oral cancer biomarkers. This is particularly important because oral cancer is often diagnosed at late stages with a poor prognosis. AREAS COVERED The review addresses the evolution of the experimental approaches used in salivary proteomics studies of oral cancer over the years and outlines advantages and pitfalls related to each one. In addition, examines the current landscape of oral cancer biomarker discovery and translation focusing on salivary proteomic studies. This discussion is based on an extensive literature search (PubMed, Scopus and Google Scholar). EXPERT OPINION The introduction of mass spectrometry has revolutionized the study of salivary proteomics. In the future, the focus will be on refining existing methods and introducing powerful experimental techniques such as mass spectrometry with selected reaction monitoring, which, despite their effectiveness, are still underutilized due to their high cost. In addition, conducting studies with larger cohorts and establishing standardized protocols for salivary proteomics are key challenges that need to be addressed in the coming years.
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Affiliation(s)
- Oriana Barros
- Department of Medical Sciences, Institute of Biomedicine iBiMED, University of Aveiro, Aveiro, Portugal
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network) and Surgical Department of Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Vito G D'Agostino
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Lucio Lara Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network) and Surgical Department of Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Rui Vitorino
- Department of Medical Sciences, Institute of Biomedicine iBiMED, University of Aveiro, Aveiro, Portugal
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network) and Surgical Department of Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
- UnIC, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rita Ferreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
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Lee HN, Lee SE, Inn KS, Seong J. Optical sensing and control of T cell signaling pathways. Front Physiol 2024; 14:1321996. [PMID: 38269062 PMCID: PMC10806162 DOI: 10.3389/fphys.2023.1321996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
T cells regulate adaptive immune responses through complex signaling pathways mediated by T cell receptor (TCR). The functional domains of the TCR are combined with specific antibodies for the development of chimeric antigen receptor (CAR) T cell therapy. In this review, we first overview current understanding on the T cell signaling pathways as well as traditional methods that have been widely used for the T cell study. These methods, however, are still limited to investigating dynamic molecular events with spatiotemporal resolutions. Therefore, genetically encoded biosensors and optogenetic tools have been developed to study dynamic T cell signaling pathways in live cells. We review these cutting-edge technologies that revealed dynamic and complex molecular mechanisms at each stage of T cell signaling pathways. They have been primarily applied to the study of dynamic molecular events in TCR signaling, and they will further aid in understanding the mechanisms of CAR activation and function. Therefore, genetically encoded biosensors and optogenetic tools offer powerful tools for enhancing our understanding of signaling mechanisms in T cells and CAR-T cells.
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Affiliation(s)
- Hae Nim Lee
- Brain Science Institute, Korea Institute of Science and Technoloy, Seoul, Republic of Korea
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Seung Eun Lee
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Soo Inn
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Jihye Seong
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, Republic of Korea
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10
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Ajithkumar P, Vasantharajan SS, Pattison S, McCall JL, Rodger EJ, Chatterjee A. Exploring Potential Epigenetic Biomarkers for Colorectal Cancer Metastasis. Int J Mol Sci 2024; 25:874. [PMID: 38255946 PMCID: PMC10815915 DOI: 10.3390/ijms25020874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Metastatic progression is a complex, multistep process and the leading cause of cancer mortality. There is growing evidence that emphasises the significance of epigenetic modification, specifically DNA methylation and histone modifications, in influencing colorectal (CRC) metastasis. Epigenetic modifications influence the expression of genes involved in various cellular processes, including the pathways associated with metastasis. These modifications could contribute to metastatic progression by enhancing oncogenes and silencing tumour suppressor genes. Moreover, specific epigenetic alterations enable cancer cells to acquire invasive and metastatic characteristics by altering cell adhesion, migration, and invasion-related pathways. Exploring the involvement of DNA methylation and histone modification is crucial for identifying biomarkers that impact cancer prediction for metastasis in CRC. This review provides a summary of the potential epigenetic biomarkers associated with metastasis in CRC, particularly DNA methylation and histone modifications, and examines the pathways associated with these biomarkers.
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Affiliation(s)
- Priyadarshana Ajithkumar
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Sai Shyam Vasantharajan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Sharon Pattison
- Department of Medicine, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - John L. McCall
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
- School of Health Sciences and Technology, UPES University, Dehradun 248007, India
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11
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Samandari-Bahraseman MR, Ismaili A, Esmaeili-Mahani S, Ebrahimie E, Loit E. Bunium persicum Seeds Extract in Combination with Vincristine Mediates Apoptosis in MCF-7 Cells through Regulation of Involved Genes and Proteins Expression. Anticancer Agents Med Chem 2024; 24:213-223. [PMID: 38038013 DOI: 10.2174/0118715206277444231124051035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Bunium persicum seeds, a member of the Apiaceae family, have historically been consumed as part of the Iranian diet. OBJECTIVE While many of this herb's biological properties have been fully investigated, there is currently no reliable information about its anticancer/cytotoxic properties. METHODS Herein, we first determined the major bioactive compounds of B. persicum seed extract (BPSE) via GC-Mass analysis. We evaluated the cytotoxicity of the extract alone as well as in combination with vincristine (VCR), a commonly used chemotherapy drug, using MTT assays on two breast cancer cell lines, MCF-7 and MDA-MB-231, as well as a normal breast cancer cell line, MCF-10A. Moreover, these compounds were evaluated in vitro for their anticancer activity using ROS assays, Real-Time PCR, Western blots, flow cytometry, and cell cycle assays. RESULTS As a result of our investigation, it was determined that the extract significantly reduced the viability of cancerous cells while remaining harmless to normal cells. The combination of BPSE and VCR also resulted in synergistic effects. BPSE and/or BPSE-VCR treatment increased the intracellular ROS of MCF-7 cells by over twofold. Moreover, the IC30 of BPSE (100 μg/ml) significantly increased the BAX/BCL-2 and P53 gene expression while reducing the expression of the MYC gene. Moreover, treated cells were arrested in the G2 phase of the cell cycle. The BPSE-VCR combination synergistically reduced the NF-κB and increased the Caspase-7 proteins' expression. The percent of apoptosis in the cells treated with the extract, VCR, and their combination was 27, 11, and 50, respectively. CONCLUSIONS The present study demonstrated the anticancer activity of the BPSE and its potential for application in combination therapy with VCR.
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Affiliation(s)
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran Iran
| | - Saeed Esmaeili-Mahani
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Esmaeil Ebrahimie
- La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne, VIC 3086, Australia
| | - Evelin Loit
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
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12
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Kutyrieva-Nowak N, Leszczuk A, Zdunek A. A practical guide to in situ and ex situ characterisation of arabinogalactan proteins (AGPs) in fruits. PLANT METHODS 2023; 19:117. [PMID: 37915041 PMCID: PMC10621164 DOI: 10.1186/s13007-023-01100-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Arabinogalactan proteins (AGPs) are plant cell components found in the extracellular matrix that play crucial roles in fruit growth and development. AGPs demonstrate structural diversity due to the presence of a protein domain and an expanded carbohydrate moiety. Considering their molecular structure, the modification of glycosylation is a primary factor contributing to the functional variety of AGPs. MAIN BODY Immunocytochemical methods are used for qualitative and quantitative analyses of AGPs in fruit tissues. These include in situ techniques such as immunofluorescence and immunogold labelling for visualising AGP distribution at different cellular levels and ex situ methods such as Western blotting and enzyme-linked immunoenzymatic assays (ELISA) for molecular characterisation and quantitative detection of isolated AGPs. The presented techniques were modified by considering the structure of AGPs and the changes that occur in fruit tissues during the development and ripening processes. These methods are based on antibodies that recognise carbohydrate chains, which are the only commercially available highly AGP-specific tools. These probes recognise AGP epitopes and identify structural modifications and changes in spatio-temporal distribution, shedding light on their functions in fruit. CONCLUSION This paper provides a concise overview of AGP research methods, emphasising their use in fruit tissue analysis and demonstrating the accessibility gaps in other tools used in such research (e.g. antibodies against protein moieties). It underscores fruit tissue as a valuable source of AGPs and emphasises the potential for future research to understand of AGP synthesis, degradation, and their roles in various physiological processes. Moreover, the application of advanced probes for AGP visualisation is a milestone in obtaining more detailed insights into the localisation and function of these proteins within fruit.
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Affiliation(s)
| | - Agata Leszczuk
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland.
| | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland
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13
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Yaghoubi Naei V, Bordhan P, Mirakhorli F, Khorrami M, Shrestha J, Nazari H, Kulasinghe A, Ebrahimi Warkiani M. Advances in novel strategies for isolation, characterization, and analysis of CTCs and ctDNA. Ther Adv Med Oncol 2023; 15:17588359231192401. [PMID: 37692363 PMCID: PMC10486235 DOI: 10.1177/17588359231192401] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Over the past decade, the detection and analysis of liquid biopsy biomarkers such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have advanced significantly. They have received recognition for their clinical usefulness in detecting cancer at an early stage, monitoring disease, and evaluating treatment response. The emergence of liquid biopsy has been a helpful development, as it offers a minimally invasive, rapid, real-time monitoring, and possible alternative to traditional tissue biopsies. In resource-limited settings, the ideal platform for liquid biopsy should not only extract more CTCs or ctDNA from a minimal sample volume but also accurately represent the molecular heterogeneity of the patient's disease. This review covers novel strategies and advancements in CTC and ctDNA-based liquid biopsy platforms, including microfluidic applications and comprehensive analysis of molecular complexity. We discuss these systems' operational principles and performance efficiencies, as well as future opportunities and challenges for their implementation in clinical settings. In addition, we emphasize the importance of integrated platforms that incorporate machine learning and artificial intelligence in accurate liquid biopsy detection systems, which can greatly improve cancer management and enable precision diagnostics.
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Affiliation(s)
- Vahid Yaghoubi Naei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pritam Bordhan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Science, Institute for Biomedical Materials & Devices, University of Technology Sydney, Australia
| | - Fatemeh Mirakhorli
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Motahare Khorrami
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Arutha Kulasinghe
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, 1, Broadway, Ultimo New South Wales 2007, Australia
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14
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Ramalhete L, Vigia E, Araújo R, Marques HP. Proteomics-Driven Biomarkers in Pancreatic Cancer. Proteomes 2023; 11:24. [PMID: 37606420 PMCID: PMC10443269 DOI: 10.3390/proteomes11030024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Pancreatic cancer is a devastating disease that has a grim prognosis, highlighting the need for improved screening, diagnosis, and treatment strategies. Currently, the sole biomarker for pancreatic ductal adenocarcinoma (PDAC) authorized by the U.S. Food and Drug Administration is CA 19-9, which proves to be the most beneficial in tracking treatment response rather than in early detection. In recent years, proteomics has emerged as a powerful tool for advancing our understanding of pancreatic cancer biology and identifying potential biomarkers and therapeutic targets. This review aims to offer a comprehensive survey of proteomics' current status in pancreatic cancer research, specifically accentuating its applications and its potential to drastically enhance screening, diagnosis, and treatment response. With respect to screening and diagnostic precision, proteomics carries the capacity to augment the sensitivity and specificity of extant screening and diagnostic methodologies. Nonetheless, more research is imperative for validating potential biomarkers and establishing standard procedures for sample preparation and data analysis. Furthermore, proteomics presents opportunities for unveiling new biomarkers and therapeutic targets, as well as fostering the development of personalized treatment strategies based on protein expression patterns associated with treatment response. In conclusion, proteomics holds great promise for advancing our understanding of pancreatic cancer biology and improving patient outcomes. It is essential to maintain momentum in investment and innovation in this arena to unearth more groundbreaking discoveries and transmute them into practical diagnostic and therapeutic strategies in the clinical context.
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Affiliation(s)
- Luís Ramalhete
- Blood and Transplantation Center of Lisbon—Instituto Português do Sangue e da Transplantação, Alameda das Linhas de Torres, n° 117, 1769-001 Lisbon, Portugal
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- iNOVA4Health—Advancing Precision Medicine, RG11: Reno-Vascular Diseases Group, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
| | - Emanuel Vigia
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
| | - Rúben Araújo
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- CHRC—Comprehensive Health Research Centre, NOVA Medical School, 1150-199 Lisbon, Portugal
| | - Hugo Pinto Marques
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
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15
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Su HC, Sun YT, Yang MY, Wu CY, Hsu CM. Dihydroisotanshinone I and BMAL-SIRT1 Pathway in an In Vitro 6-OHDA-Induced Model of Parkinson's Disease. Int J Mol Sci 2023; 24:11088. [PMID: 37446264 DOI: 10.3390/ijms241311088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Danshen has been widely used for the treatment of central nervous system diseases. We investigated the effect of dihydroisotanshinone I (DT), a compound extracted from Danshen, as well as the corresponding mechanisms in an in vitro-based 6-OHDA-induced Parkinson's disease (PD) model. SH-SY5Y human neuroblastoma cell lines were pretreated with 6-hydroxydopamine (6-OHDA) and challenged with DT. Subsequently, the cell viability and levels of reactive oxygen species (ROS) and caspase-3 were analyzed. The effect of DT on the 6-OHDA-treated SH-SY5Y cells and the expression of the core circadian clock genes were measured using a real-time quantitative polymerase chain reaction. Our results indicated that DT attenuated the 6-OHDA-induced cell death in the SH-SY5Y cells and suppressed ROS and caspase-3. Moreover, DT reversed both the RNA and protein levels of BMAL1 and SIRT1 in the 6-OHDA-treated SH-SY5Y cells. Additionally, the SIRT1 inhibitor attenuated the effect of DT on BMAL1 and reduced the cell viability. The DT and SIRT1 activators activated SIRT1 and BMAL1, and then reduced the death of the SH-SY5Y cells damaged by 6-OHDA. SIRT1 silencing was enhanced by DT and resulted in a BMAL1 downregulation and a reduction in cell viability. In conclusion, our investigation suggested that DT reduces cell apoptosis, including an antioxidative effect due to a reduction in ROS, and regulates the circadian genes by enhancing SIRT1 and suppressing BMAL1. DT may possess novel therapeutic potential for PD in the future, but further in vivo studies are still needed.
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Affiliation(s)
- Hui-Chen Su
- Department of Neurology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yuan-Ting Sun
- Department of Neurology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ming-Yu Yang
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Ching-Yuan Wu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi 61363, Taiwan
| | - Cheng-Ming Hsu
- Department of Otolaryngology-Head and Neck Surgery, Chiayi Chang Gung Memorial Hospital, Chiayi 61363, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Cancer Center, Chiayi Chang Gung Memorial Hospital, Chiayi 61363, Taiwan
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16
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Long MA, Benman W, Petrikas N, Bugaj LJ, Hughes AJ. Enhancing single-cell western blotting sensitivity using diffusive analyte blotting and antibody conjugate amplification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544857. [PMID: 37398364 PMCID: PMC10312704 DOI: 10.1101/2023.06.13.544857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
While there are many techniques to achieve highly sensitive, multiplex detection of RNA and DNA from single cells, detecting protein contents often suffers from low limits of detection and throughput. Miniaturized, high-sensitivity western blots on single cells (scWesterns) are attractive since they do not require advanced instrumentation. By physically separating analytes, scWesterns also uniquely mitigate limitations to target protein multiplexing posed by affinity reagent performance. However, a fundamental limitation of scWesterns is their limited sensitivity for detecting low-abundance proteins, which arises from transport barriers posed by the separation gel against detection species. Here we address sensitivity by decoupling the electrophoretic separation medium from the detection medium. We transfer scWestern separations to a nitrocellulose blotting medium with distinct mass transfer advantages over traditional in-gel probing, yielding a 5.9-fold improvement in limit of detection. We next amplify probing of blotted proteins with enzyme-antibody conjugates which are incompatible with traditional in-gel probing to achieve further improvement in the limit of detection to 103 molecules, a 520-fold improvement. This enables us to detect 85% and 100% of cells in an EGFP-expressing population using fluorescently tagged and enzyme-conjugated antibodies respectively, compared to 47% of cells using in-gel detection. These results suggest compatibility of nitrocellulose-immobilized scWesterns with a variety of affinity reagents - not previously accessible for in-gel use - for further signal amplification and detection of low abundance targets.
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Affiliation(s)
- Mariia Alibekova Long
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
| | - Nathan Petrikas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Currently at Tempus Labs Inc., Chicago, IL, USA
| | - Lukasz J. Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alex J. Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, PA, 19104, USA
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17
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Connolly EA, Grimison PS, Horvath LG, Robinson PJ, Reddel RR. Quantitative proteomic studies addressing unmet clinical needs in sarcoma. Front Oncol 2023; 13:1126736. [PMID: 37197427 PMCID: PMC10183589 DOI: 10.3389/fonc.2023.1126736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/31/2023] [Indexed: 05/19/2023] Open
Abstract
Sarcoma is a rare and complex disease comprising over 80 malignant subtypes that is frequently characterized by poor prognosis. Challenges in clinical management include uncertainties in diagnosis and disease classification, limited prognostic and predictive biomarkers, incompletely understood disease heterogeneity among and within subtypes, lack of effective treatment options, and limited progress in identifying new drug targets and novel therapeutics. Proteomics refers to the study of the entire complement of proteins expressed in specific cells or tissues. Advances in proteomics have included the development of quantitative mass spectrometry (MS)-based technologies which enable analysis of large numbers of proteins with relatively high throughput, enabling proteomics to be studied on a scale that has not previously been possible. Cellular function is determined by the levels of various proteins and their interactions, so proteomics offers the possibility of new insights into cancer biology. Sarcoma proteomics therefore has the potential to address some of the key current challenges described above, but it is still in its infancy. This review covers key quantitative proteomic sarcoma studies with findings that pertain to clinical utility. Proteomic methodologies that have been applied to human sarcoma research are briefly described, including recent advances in MS-based proteomic technology. We highlight studies that illustrate how proteomics may aid diagnosis and improve disease classification by distinguishing sarcoma histologies and identify distinct profiles within histological subtypes which may aid understanding of disease heterogeneity. We also review studies where proteomics has been applied to identify prognostic, predictive and therapeutic biomarkers. These studies traverse a range of histological subtypes including chordoma, Ewing sarcoma, gastrointestinal stromal tumors, leiomyosarcoma, liposarcoma, malignant peripheral nerve sheath tumors, myxofibrosarcoma, rhabdomyosarcoma, synovial sarcoma, osteosarcoma, and undifferentiated pleomorphic sarcoma. Critical questions and unmet needs in sarcoma which can potentially be addressed with proteomics are outlined.
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Affiliation(s)
- Elizabeth A. Connolly
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Department of Medical Oncology, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- *Correspondence: Elizabeth A. Connolly,
| | - Peter S. Grimison
- Department of Medical Oncology, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Lisa G. Horvath
- Department of Medical Oncology, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Phillip J. Robinson
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Roger R. Reddel
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
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18
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Souza IMFNBD, Siqueira VDS, Ribeiro IDC, Moraes LSP, Prado DPGD, Rezende SR, Costa WLGD, Rezende HHA. Molecular and serological diagnosis of toxoplasmosis: a systematic review and meta-analysis. Rev Inst Med Trop Sao Paulo 2023; 65:e19. [PMID: 36921207 PMCID: PMC10013468 DOI: 10.1590/s1678-9946202365019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/06/2023] [Indexed: 03/17/2023] Open
Abstract
Toxoplasmosis is an infection of vast worldwide distribution whose etiologic agent is Toxoplasma gondii. This disease can cause problems ranging from mild symptoms to serious conditions, such as encephalitis, miscarriage and blindness. Therefore, it is of utmost importance to perform a diagnosis with reproducible techniques in order to obtain a good prognosis. The aim of this review was to analyze the efficiency of toxoplasmosis diagnostic techniques based on sensitivity and specificity results. Five research platforms in English language were used (Eric, Elsevier, Google Scholar, PubMed and SciELO), which contained data on the diagnosis of toxoplasmosis. The search and selection were performed for studies published prior to June 2021. The search resulted in the inclusion of 13 articles published from 2005 to 2020. The data revealed the use of different samples in the standardization of techniques such as serum, total blood, colostrum and amniotic fluid. The flow cytometry, lateral flow immunoassay and qPCR techniques showed 100% sensitivity, whereas the ELISA, western blotting, qPCR and RE-LAMP techniques achieved 100% specificity. Significantly, the qPCR and LAMP techniques were more accurate when the likelihood ratio was assessed. The meta-analysis identified that ISAGA and western blotting have low sensitivity values and LIASON, ELFA and ELISA, using a silica bioconjugate, also have low specificity values. It was noted that a wide range of methods have high values of sensitivity and specificity. Therefore, the choice of the method will be based on the conditions and its financial viability.
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Affiliation(s)
| | - Victor da Silva Siqueira
- Universidade Federal de Jatai, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Jataí, Goiás, Brazil
| | | | | | | | | | - Webster Leonardo Guimarães da Costa
- Universidade Federal de Jatai, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Jataí, Goiás, Brazil.,Universidade Estadual de Campinas, Instituto de Biologia, Programa de Pós-Graduação em Genética e Biologia Molecular (Imunologia), Campinas, São Paulo, Brazil
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