1
|
Idrees S, Paudel KR, Sadaf T, Hansbro PM. Uncovering domain motif interactions using high-throughput protein-protein interaction detection methods. FEBS Lett 2024; 598:725-742. [PMID: 38439692 DOI: 10.1002/1873-3468.14841] [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: 10/17/2023] [Revised: 01/09/2024] [Accepted: 02/18/2024] [Indexed: 03/06/2024]
Abstract
Protein-protein interactions (PPIs) are often mediated by short linear motifs (SLiMs) in one protein and domain in another, known as domain-motif interactions (DMIs). During the past decade, SLiMs have been studied to find their role in cellular functions such as post-translational modifications, regulatory processes, protein scaffolding, cell cycle progression, cell adhesion, cell signalling and substrate selection for proteasomal degradation. This review provides a comprehensive overview of the current PPI detection techniques and resources, focusing on their relevance to capturing interactions mediated by SLiMs. We also address the challenges associated with capturing DMIs. Moreover, a case study analysing the BioGrid database as a source of DMI prediction revealed significant known DMI enrichment in different PPI detection methods. Overall, it can be said that current high-throughput PPI detection methods can be a reliable source for predicting DMIs.
Collapse
Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Tayyaba Sadaf
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| |
Collapse
|
2
|
Chen Y, Dong J, Gong L, Hong Y, Hu C, Bao Y, Chen H, Liu L, Huang L, Zhao Y, Zhang J, He S, Yan X, Wu X, Cui W. Fucoxanthin, a marine derived carotenoid, attenuates surgery-induced cognitive impairments via activating Akt and ERK pathways in aged mice. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 120:155043. [PMID: 37639810 DOI: 10.1016/j.phymed.2023.155043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/31/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Fucoxanthin is the most abundant marine carotenoid derived from brown seaweeds, possesses antioxidant, anti-inflammatory, and neuroprotective properties, and might be benefit for the treatment of neurological disorders. Post-operative cognitive dysfunction (POCD) is a neurological symptom with learning and memory impairments, mainly affecting the elderly after surgery. However, there is no effective treatments for this symptom. PURPOSES In this study, we evaluated the neuroprotective effects of fucoxanthin against POCD in aged mice after surgery. STUDY DESIGN AND METHODS The animal model of POCD was established in 12 - 14 month aged mice with a laparotomy. Curcumin was used as a positive control. The beneficial effects of fucoxanthin on POCD was analyzed by behavioral tests. Pro-inflammatory cytokines were measured by Enzyme-linked Immunosorbent Assay (ELISA). And the expressions of key proteins in the Akt and ERK signaling pathways were analyzed by Western blotting analysis. The morphology of microglial cells and astrocytes was explored by immunohistochemical staining. The activity of antioxidant superoxide dismutase (SOD) and catalase (CAT) were measured by anti-oxidative enzyme activity assays. RESULTS Fucoxanthin at 100 - 200 mg/kg significantly attenuated cognitive dysfunction, with a similar potency as curcumin, in aged mice after surgery. In addition, fucoxanthin and curcumin significantly increased the expression of pAkt, prevented the activation of microglial cells and astrocytes, and inhibited the secretion of pro-inflammatory interleukin-1β (IL - 1β) and tumor necrosis factor-α (TNF-α). Furthermore, fucoxanthin and curcumin elevated the ERK pathway and potently increased the activity of antioxidant enzymes. Most importantly, U0126, an inhibitor of the ERK pathway, and wortmannin, an inhibitor of the Akt pathway, significantly abolished the cognitive-enhancing effects, as well as the inhibition of neuroinflammation and the reduction of oxidative stress, induced by fucoxanthin in aged mice after surgery. CONCLUSION Fucoxanthin might be developed as a functional food or drug for the treatment of POCD by inhibiting neuroinflammation and enhancing antioxidant capacity via the activation of the Akt and ERK signaling pathways.
Collapse
Affiliation(s)
- Yuan Chen
- The First Hospital of Ningbo University, Ningbo 315010, China; Translational Medicine Center of Pain, Emotion and Cognition, Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Jiahui Dong
- The First Hospital of Ningbo University, Ningbo 315010, China; Translational Medicine Center of Pain, Emotion and Cognition, Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Luyun Gong
- Translational Medicine Center of Pain, Emotion and Cognition, Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Yirui Hong
- Translational Medicine Center of Pain, Emotion and Cognition, Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Chenwei Hu
- Translational Medicine Center of Pain, Emotion and Cognition, Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Yongjie Bao
- Translational Medicine Center of Pain, Emotion and Cognition, Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Huiyue Chen
- Translational Medicine Center of Pain, Emotion and Cognition, Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Lin Liu
- Ningbo Women & Children Hospital, Ningbo 315012, China
| | - Ling Huang
- Ningbo Kangning Hospital, Ningbo 315201, China
| | | | - Jinrong Zhang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Xiaojun Yan
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Xiang Wu
- The First Hospital of Ningbo University, Ningbo 315010, China.
| | - Wei Cui
- The First Hospital of Ningbo University, Ningbo 315010, China; Translational Medicine Center of Pain, Emotion and Cognition, Ningbo Key Laboratory of Behavioral Neuroscience, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo 315211, China; Ningbo Kangning Hospital, Ningbo 315201, China.
| |
Collapse
|
3
|
Zhang R, Datta S. asmbPLS: Adaptive Sparse Multi-block Partial Least Square for Survival Prediction using Multi-Omics Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535442. [PMID: 37066143 PMCID: PMC10103991 DOI: 10.1101/2023.04.03.535442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Background As high-throughput studies advance, more and more high-dimensional multi-omics data are available and collected from the same patient cohort. Using multi-omics data as predictors to predict survival outcomes is challenging due to the complex structure of such data. Results In this article, we introduce an adaptive sparse multi-block partial least square (asmbPLS) regression method by assigning different penalty factors to different blocks in different PLS components for feature selection and prediction. We compared the proposed method with several competitive algorithms in many aspects including prediction performance, feature selection and computation efficiency. The performance and the efficiency of our method were demonstrated using both the simulated and the real data. Conclusions In summary, asmbPLS achieved a competitive performance in prediction, feature selection, and computation efficiency. We anticipate asmbPLS to be a valuable tool for multi-omics research. An R package called asmbPLS implementing this method is made publicly available on GitHub.
Collapse
|
4
|
Valdés A, Álvarez-Rivera G, Socas-Rodríguez B, Herrero M, Ibáñez E, Cifuentes A. Foodomics: Analytical Opportunities and Challenges. Anal Chem 2022; 94:366-381. [PMID: 34813295 PMCID: PMC8756396 DOI: 10.1021/acs.analchem.1c04678] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alberto Valdés
- Laboratory of Foodomics, Institute
of Food Science Research, CIAL, CSIC, Nicolas Cabrera 9, Madrid, 28049, Spain
| | - Gerardo Álvarez-Rivera
- Laboratory of Foodomics, Institute
of Food Science Research, CIAL, CSIC, Nicolas Cabrera 9, Madrid, 28049, Spain
| | - Bárbara Socas-Rodríguez
- Laboratory of Foodomics, Institute
of Food Science Research, CIAL, CSIC, Nicolas Cabrera 9, Madrid, 28049, Spain
| | - Miguel Herrero
- Laboratory of Foodomics, Institute
of Food Science Research, CIAL, CSIC, Nicolas Cabrera 9, Madrid, 28049, Spain
| | - Elena Ibáñez
- Laboratory of Foodomics, Institute
of Food Science Research, CIAL, CSIC, Nicolas Cabrera 9, Madrid, 28049, Spain
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute
of Food Science Research, CIAL, CSIC, Nicolas Cabrera 9, Madrid, 28049, Spain
| |
Collapse
|
5
|
Metaproteomics insights into fermented fish and vegetable products and associated microbes. FOOD CHEMISTRY. MOLECULAR SCIENCES 2021; 3:100045. [PMID: 35415649 PMCID: PMC8991600 DOI: 10.1016/j.fochms.2021.100045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
Increasing global population means higher demand for healthy food. Fish and vegetables are healthy foods, but overproduction leads to spoilage. Fermentation of fish/vegetables elongate their shelf lives, improved flavour and functions. Microbes associated with Fish/vegetable fermentation produce health conferring peptides. There is little review on peptides elicited during fish/vegetable fermentations.
The interest in proteomic studies of fermented food is increasing; the role of proteins derived from fermentation extends beyond preservation, they also improve the organoleptic, anti-pathogenic, anti-cancer, anti-obesogenic properties, and other health conferring properties of fermented food. Traditional fermentation processes are still in use in certain cultures, but recently, the controlled process is gaining wider acceptance due to consistency and predictability. Scientists use modern biotechnological approaches to evaluate reactions and component yields from fermentation processes. Pieces of literature on fermented fish and vegetable end-products are scanty (compared to milk and meat), even though fish and vegetables are considered health conferring diets with high nutritional contents. Evaluations of peptides from fermented fish and vegetables show they have anti-obesity, anti-oxidative, anti-inflammatory, anti-pathogenic, anti-anti-nutrient, improves digestibility, taste, nutrient content, texture, aroma properties, etc. Despite challenges impeding the wider applications of the metaproteomic analysis of fermented fish and vegetables, their potential benefits cannot be underestimated.
Collapse
|
6
|
|
7
|
Foerster H, Battey JND, Sierro N, Ivanov NV, Mueller LA. Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. Brief Bioinform 2021; 22:bbaa136. [PMID: 32662816 PMCID: PMC8138835 DOI: 10.1093/bib/bbaa136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/19/2020] [Accepted: 06/04/2020] [Indexed: 01/09/2023] Open
Abstract
Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e. NicotianaCyc as well as six species-specific databases for Nicotiana tabacum TN90, N. tabacum K326, Nicotiana benthamiana, N. sylvestris, N. tomentosiformis and N. attenuata. New pathways were created through the extraction, examination and verification of related data from the literature and the aid of external database guided by an expert-led curation process. Here we describe the curation progress that has been achieved in these databases since the first release version 1.0 in 2016, the curation flow and the curation process using the example metabolic pathway for cholesterol in plants. The current content of our databases comprises 266 pathways and 36 superpathways in SolanaCyc and 143 pathways plus 21 superpathways in NicotianaCyc, manually curated and validated specifically for the Solanaceae family and Nicotiana genus, respectively. The curated data have been propagated to the respective Nicotiana-specific databases, which resulted in the enrichment and more accurate presentation of their metabolic networks. The quality and coverage in those databases have been compared with related external databases and discussed in terms of literature support and metabolic content.
Collapse
|
8
|
Grozdanic SD, Lazic T, Kecova H, Mohan K, Adamus G, Kuehn MH. Presumed cancer-associated retinopathy (CAR) mimicking Sudden Acquired Retinal Degeneration Syndrome (SARDS) in canines. Vet Ophthalmol 2020; 24:125-155. [PMID: 33369040 PMCID: PMC8048582 DOI: 10.1111/vop.12853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To describe functional and structural features of presumed cancer-associated retinopathy (CAR) mimicking sudden acquired retinal degeneration syndrome (SARDS) in dogs and describe treatment outcomes. ANIMALS Subjects were 17 dogs from 8 eight US states and Canada diagnosed with SARDS or immune-mediated retinitis (IMR) by 12 ophthalmologists. Nine eyes from seven deceased patients were used for microarray (MA), histology, or immunohistochemical (IHC) analysis. PROCEDURES Dogs underwent complete ophthalmic examination, including retinal photography, optical coherence tomography (OCT), chromatic pupil light reflex testing (cPLR), and electroretinography (ERG), in addition to complete systemic examination. Histology, microarray, and IHC analysis were performed in CAR retinas to evaluate histological and molecular changes in retinal tissue. RESULTS None of the patients evaluated satisfied previously established criteria for diagnosis of SARDS (flat ERG+ no red - good blue PLR), and all were diagnosed with IMR. All patients were diagnosed with a cancer: meningioma (24%), sarcoma (18%), pituitary tumor (12%), and squamous cell carcinoma (12%), other (34%). Median survival time was 6 months from diagnosis (range 1-36 months). Most frequent systemic abnormalities were as follows: proteinuria (78%); elevated liver enzymes (47%); and metabolic changes (PU/PD, polyphagia - 24%). Immunosuppressive therapy resulted in the reversal of blindness in 44% of treated patients, with 61% of all treated patients recovering and/or maintaining vision. Median time for preservation of vision was 5 months (range 1-35 months). CONCLUSIONS Observed changes are highly suggestive of immune-mediated damage in IMR-CAR eyes. A relatively high percentage of patients with CAR responded positively to immunosuppressive therapy.
Collapse
Affiliation(s)
- Sinisa D Grozdanic
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.,Animal Eye Consultants of Iowa, Hiawatha, IA, USA.,TL VetPath International Consultants, Hiawatha, IA, USA
| | - Tatjana Lazic
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.,Animal Eye Consultants of Iowa, Hiawatha, IA, USA.,TL VetPath International Consultants, Hiawatha, IA, USA
| | - Helga Kecova
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.,Animal Eye Consultants of Iowa, Hiawatha, IA, USA
| | - Kabhilan Mohan
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Grazyna Adamus
- Department of Ophthalmology, Oregon Health & Science University, Portland, OR, USA
| | - Markus H Kuehn
- Department of Ophthalmology and Visual Sciences, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, USA
| |
Collapse
|
9
|
Mihara Y, Maekawa R, Sato S, Shimizu N, Doi-Tanaka Y, Takagi H, Shirafuta Y, Shinagawa M, Tamura I, Taketani T, Tamura H, Abe T, Asai Y, Sugino N. An Integrated Genomic Approach Identifies HOXC8 as an Upstream Regulator in Ovarian Endometrioma. J Clin Endocrinol Metab 2020; 105:5900720. [PMID: 32877504 DOI: 10.1210/clinem/dgaa618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
PURPOSE To identify the upstream regulators (URs) involved in the onset and pathogenesis of ovarian endometrioma. METHODS Recently, a method called Significance-based Modules Integrating the Transcriptome and Epigenome (SMITE) that uses transcriptome data in combination with publicly available data for identifying URs of cellular processes has been developed. Here, we used SMITE with transcriptome data from ovarian endometrioma stromal cells (ovESCs) and eutopic endometrium stromal cells (euESCs) in combination with publicly available gene regulatory network data. To confirm the URs identified by SMITE, we developed a Boolean network simulation to see if correcting aberrant expressions of the identified genes could restore the entire gene expression profile of ovESCs to a profile similar to that of euESCs. We then established euESCs overexpressing the identified gene and characterized them by cell function assays and transcriptome analysis. RESULTS SMITE identified 12 potential URs in ovarian endometrioma that were confirmed by the Boolean simulation. One of the URs, HOXC8, was confirmed to be overexpressed in ovESCs. HOXC8 overexpression significantly enhanced cell proliferation, migration, adhesion, and fibrotic activities, and altered expression statuses of the genes involved in transforming growth factor (TGF)-β signaling. HOXC8 overexpression also increased the expression levels of phosphorylated SMAD2/SMAD3. The increased adhesion and fibrosis activities by HOXC8 were significantly inhibited by E-616452, a selective inhibitor of TGF-β receptor type I kinases. MAIN CONCLUSIONS Integrated genomic approaches identified HOXC8 as an UR in ovarian endometrioma. The pathological features of ovarian endometrioma including cell proliferation, adhesion, and fibrosis were induced by HOXC8 and its subsequent activation of TGF-β signaling.
Collapse
Affiliation(s)
- Yumiko Mihara
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Natsuko Shimizu
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yumiko Doi-Tanaka
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Haruka Takagi
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yuichiro Shirafuta
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Masahiro Shinagawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Toshiaki Taketani
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroshi Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Takeshi Abe
- Department of Systems Bioinformatics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yoshiyuki Asai
- Department of Systems Bioinformatics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| |
Collapse
|
10
|
Duggan BM, Cullum R, Fenical W, Amador LA, Rodríguez AD, La Clair JJ. Searching for Small Molecules with an Atomic Sort. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography University of California, San Diego La Jolla CA 92093-0204 USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography University of California, San Diego La Jolla CA 92093-0204 USA
| | - Luis A. Amador
- Molecular Sciences Research Center University of Puerto Rico 1390 Ponce de León Avenue San Juan 00926 Puerto Rico
| | - Abimael D. Rodríguez
- Molecular Sciences Research Center University of Puerto Rico 1390 Ponce de León Avenue San Juan 00926 Puerto Rico
| | - James J. La Clair
- Department of Chemistry and Biochemistry University of California San Diego 9500 Gilman Drive, La Jolla CA 92093 USA
| |
Collapse
|
11
|
Duggan BM, Cullum R, Fenical W, Amador LA, Rodríguez AD, La Clair JJ. Searching for Small Molecules with an Atomic Sort. Angew Chem Int Ed Engl 2020; 59:1144-1148. [PMID: 31696595 PMCID: PMC6942196 DOI: 10.1002/anie.201911862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/24/2019] [Indexed: 12/14/2022]
Abstract
The discovery of biologically active small molecules requires sifting through large amounts of data to identify unique or unusual arrangements of atoms. Here, we develop, test and evaluate an atom-based sort to identify novel features of secondary metabolites and demonstrate its use to evaluate novelty in marine microbial and sponge extracts. This study outlines an important ongoing advance towards the translation of autonomous systems to identify, and ultimately elucidate, atomic novelty within a complex mixture of small molecules.
Collapse
Affiliation(s)
- Brendan M Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0204, USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0204, USA
| | - Luis A Amador
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, 00926, Puerto Rico
| | - Abimael D Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, 00926, Puerto Rico
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| |
Collapse
|
12
|
He QL, Qin SY, Tao L, Ning HJ, Jiang HX. Prognostic value and prospective molecular mechanism of miR-100-5p in hepatocellular carcinoma: A comprehensive study based on 1,258 samples. Oncol Lett 2019; 18:6126-6142. [PMID: 31788087 PMCID: PMC6865135 DOI: 10.3892/ol.2019.10962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023] Open
Abstract
The prognostic value and molecular mechanism of microRNA-100-5p (miR-100-5p) in hepatocellular carcinoma (HCC) are still unclear. To explore the prognostic value and the mechanism of miR-100-5p in HCC, the present study analyzed the results of 18 previous studies and bioinformatic datasets. The clinical significance of miR-100-5p and its targets in HCC were investigated using The Cancer Genome Atlas and the Gene Expression Omnibus, as well as relevant literature. In total, 12 online tools were used to predict the target genes of miR-100-5p. Bioinformatics analysis and Spearman correlation analysis were performed, and genomic alterations of the hub genes were evaluated. A meta-analysis with 1,258 samples revealed that miR-100-5p was significantly downregulated in HCC [standard mean difference (SMD), -0.94; 95% confidence interval (CI), -1.14 to -0.74; I2, 35.2%]. Lower miR-100-5p expression was associated with poorer clinical characteristics and a poorer prognosis for patients with HCC. Additionally, bioinformatics analysis revealed that the 'regulation of transcription', 'chromatin remodeling complex', 'transcription regulator activity', 'pathways in cancer' and 'heparan sulfate biosynthesis' were the most enriched terms. Furthermore, expression of histone deacetylase (HDAC)2, HDAC3, SHC-transforming protein 1 (SHC1), Ras-related protein Rac1 (RAC1) and E3 ubiquitin-protein ligase CBL (CBL) was negatively correlated with miR-100-5p expression. Among these, upregulated HDAC2 [hazard ratio (HR), 1.910; 95% CI, 1.309-2.787; P=0.0007], HDAC3 (HR, 1.474; 95% CI, 1.012-2.146; P=0.0435), SHC1 (HR, 1.52; 95% CI, 1.043-2.215; P=0.0281) and RAC1 (HR, 1.817; 95% CI, 1.248-2.645; P=0.0022) were associated with shorter survival. Alterations in HDAC2, SHC1, RAC1 and IGF1R were linked with a poorer outcome for HCC, and alternative splicing of SHC and RAC1 were significantly decreased and increased in HCC, respectively. In summary, the downregulation of miR-100-5p may be involved in the progression and prognosis of HCC. The upregulation of HDAC2, HDAC3, SHC1 and RAC1 may indicate a poorer survival rate for patients with HCC. Thus, miR-100-5p and these 4 potential target genes may provide novel therapeutic targets and prognostic predictors for patients with HCC.
Collapse
Affiliation(s)
- Qing-Lin He
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shan-Yu Qin
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Lin Tao
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong-Jian Ning
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hai-Xing Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| |
Collapse
|
13
|
Bioinformatics to Tackle the Biological Meaning of Human Cerebrospinal Fluid Proteome. Methods Mol Biol 2019. [PMID: 31432428 DOI: 10.1007/978-1-4939-9706-0_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cerebrospinal fluid (CSF) is a source of valuable information concerning brain disorders. The technical advances of high-throughput omics platforms to analyze body fluids can generate a huge amount of data, whose translation to biological meaning is a challenge. Several bioinformatic tools have emerged to help handling this data into systems biology comprehensively. Herein, we describe a step-by-step tutorial for CSF proteome data analysis in the set of neurodegenerative diseases using (1) ClueGO+CluePedia tool to perform cluster-based analysis envisioning the characterization of the biological processes dysregulated in neurodegenerative diseases including Alzheimer's and Parkinson's diseases; (2) Cytoscape to map disease-specific proteins; (3) SecretomeP to inquire the secretion pathway of CSF proteins; and (4) STRING to identify biological processes modulated by secreted CSF proteins based on protein-protein interaction analysis. This step-by-step guide might help researchers to better characterize disease pathogenesis and to identify putative disease biomarkers.
Collapse
|
14
|
Manfredi M, Brandi J, Di Carlo C, Vita Vanella V, Barberis E, Marengo E, Patrone M, Cecconi D. Mining cancer biology through bioinformatic analysis of proteomic data. Expert Rev Proteomics 2019; 16:733-747. [PMID: 31398064 DOI: 10.1080/14789450.2019.1654862] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Discovery proteomics for cancer research generates complex datasets of diagnostic, prognostic, and therapeutic significance in human cancer. With the advent of high-resolution mass spectrometers, able to identify thousands of proteins in complex biological samples, only the application of bioinformatics can lead to the interpretation of data which can be relevant for cancer research. Areas covered: Here, we give an overview of the current bioinformatic tools used in cancer proteomics. Moreover, we describe their applications in cancer proteomics studies of cell lines, serum, and tissues, highlighting recent results and critically evaluating their outcomes. Expert opinion: The use of bioinformatic tools is a fundamental step in order to manage the large amount of proteins (from hundreds to thousands) that can be identified and quantified in a cancer biological samples by proteomics. To handle this challenge and obtain useful data for translational medicine, it is important the combined use of different bioinformatic tools. Moreover, a particular attention to the global experimental design, and the integration of multidisciplinary skills are essential for best setting of tool parameters and best interpretation of bioinformatics output.
Collapse
Affiliation(s)
- Marcello Manfredi
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale , Novara , Italy.,Department of Translation Medicine, University of Piemonte Orientale , Novara , Italy
| | - Jessica Brandi
- Department of Biotechnology, University of Verona , Verona , Italy
| | - Claudia Di Carlo
- Department of Biotechnology, University of Verona , Verona , Italy
| | - Virginia Vita Vanella
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale , Novara , Italy.,Department of Sciences and Technological Innovation, University of Piemonte Orientale , Alessandria , Italy
| | - Elettra Barberis
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale , Novara , Italy.,Department of Sciences and Technological Innovation, University of Piemonte Orientale , Alessandria , Italy.,ISALIT , Novara , Italy
| | - Emilio Marengo
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale , Novara , Italy.,Department of Sciences and Technological Innovation, University of Piemonte Orientale , Alessandria , Italy.,ISALIT , Novara , Italy
| | - Mauro Patrone
- Department of Sciences and Technological Innovation, University of Piemonte Orientale , Alessandria , Italy
| | - Daniela Cecconi
- Department of Biotechnology, University of Verona , Verona , Italy
| |
Collapse
|
15
|
Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics Approaches. PROGRESS IN BOTANY 2019. [DOI: 10.1007/124_2019_32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
16
|
A decade of Nucleic Acid Programmable Protein Arrays (NAPPA) availability: News, actors, progress, prospects and access. J Proteomics 2018; 198:27-35. [PMID: 30553075 DOI: 10.1016/j.jprot.2018.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/04/2018] [Accepted: 12/10/2018] [Indexed: 12/29/2022]
Abstract
Understanding the dynamic of the proteome is a critical challenge because it requires high sensitive methodologies in high-throughput formats in order to decipher its modifications and complexity. While molecular biology provides relevant information about cell physiology that may be reflected in post-translational changes, High-Throughput (HT) experimental proteomic techniques are essential to provide valuable functional information of the proteins, peptides and the interconnections between them. Hence, many methodological developments and innovations have been reported during the last decade. To study more dynamic protein networks and fine interactions, Nucleic Acid Programmable Protein Arrays (NAPPA) was introduced a decade ago. The tool is rapidly maturing and serving as a gateway to characterize biological systems and diseases thanks primarily to its accuracy, reproducibility, throughput and flexibility. Currently, NAPPA technology has proved successful in several research areas adding valuable information towards innovative diagnostic and therapeutic applications. Here, the basic and latest advances within this modern technology in basic, translational research are reviewed, in addition to presenting its exciting new directions. Our final goal is to encourage more scientists/researchers to incorporate this method, which can help to remove bottlenecks in their particular research or biomedical projects. SIGNIFICANCE: Nucleic Acid Programmable Protein Arrays (NAPPA) is becoming an essential tool for functional proteomics and protein-protein interaction studies. The technology impacts decisively on projects aiming massive screenings and the latest innovations like the multiplexing capability or printing consistency make this a promising method to be integrated in novel and combinatorial proteomic approaches.
Collapse
|
17
|
Costanzo M, Zacchia M, Bruno G, Crisci D, Caterino M, Ruoppolo M. Integration of Proteomics and Metabolomics in Exploring Genetic and Rare Metabolic Diseases. KIDNEY DISEASES 2017; 3:66-77. [PMID: 28868294 DOI: 10.1159/000477493] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/15/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inherited metabolic disorders or inborn errors of metabolism are caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders include aminoacidopathies, urea cycle defects, organic acidemias, defects of oxidation of fatty acids, and lysosomal storage diseases. Inborn errors of metabolism constitute a significant proportion of genetic diseases, particularly in children; however, they are individually rare. Clinical phenotypes are very variable, some of them remain asymptomatic, others manifest metabolic decompensation in neonatal age, and others encompass mental retardation at later age. The clinical manifestation of these disorders can involve different organs and/or systems. Some disorders are easily managed if promptly diagnosed and treated, whereas in other cases neither diet, vitamin therapy, nor transplantation appears to prevent multi-organ impairment. SUMMARY Here, we discuss the principal challenges of metabolomics and proteomics in inherited metabolic disorders. We review the recent developments in mass spectrometry-based proteomic and metabolomic strategies. Mass spectrometry has become the most widely used platform in proteomics and metabolomics because of its ability to analyze a wide range of molecules, its optimal dynamic range, and great sensitivity. The fast measurement of a broad spectrum of metabolites in various body fluids, also collected in small samples like dried blood spots, have been facilitated by the use of mass spectrometry-based techniques. These approaches have enabled the timely diagnosis of inherited metabolic disorders, thereby facilitating early therapeutic intervention. Due to its analytical features, proteomics is suited for the basic investigation of inborn errors of metabolism. Modern approaches enable detailed functional characterization of the pathogenic biochemical processes, as achieved by quantification of proteins and identification of their regulatory chemical modifications. KEY MESSAGE Mass spectrometry-based "omics" approaches most frequently used to study the molecular mechanisms underlying inherited metabolic disorders pathophysiology are described.
Collapse
Affiliation(s)
- Michele Costanzo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II," Naples, Italy
| | - Miriam Zacchia
- Prima Divisione di Nefrologia, Dipartimento di Scienze Cardio-Toraciche e Respiratorie, Università degli studi della Campania "Luigi Vanvitelli," Scuola di Medicina, Naples, Italy
| | | | - Daniela Crisci
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II," Naples, Italy.,CEINGE - Biotecnologie Avanzate scarl, Naples, Italy
| | - Marianna Caterino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II," Naples, Italy.,CEINGE - Biotecnologie Avanzate scarl, Naples, Italy.,Associazione culturale DiSciMuS RCF, Naples, Italy
| | - Margherita Ruoppolo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II," Naples, Italy.,CEINGE - Biotecnologie Avanzate scarl, Naples, Italy.,Associazione culturale DiSciMuS RCF, Naples, Italy
| |
Collapse
|