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Kumarasamy G, Mohd Salim NH, Mohd Afandi NS, Hazlami Habib MA, Mat Amin ND, Ismail MN, Musa M. Glycoproteomics-based liquid biopsy: translational outlook for colorectal cancer clinical management in Southeast Asia. Future Oncol 2023; 19:2313-2332. [PMID: 37937446 DOI: 10.2217/fon-2023-0704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
Colorectal cancer (CRC) signifies a significant healthcare challenge in Southeast Asia. Despite advancements in screening approaches and treatment modalities, significant medical gaps remain, ranging from prevention and early diagnosis to determining targeted therapy and establishing personalized approaches to managing CRC. There is a need to expand more validated biomarkers in clinical practice. An advanced technique incorporating high-throughput mass spectrometry as a liquid biopsy to unravel a repertoire of glycoproteins and glycans would potentially drive the development of clinical tools for CRC screening, diagnosis and monitoring, and it can be further adapted to the existing standard-of-care procedure. Therefore this review offers a perspective on glycoproteomics-driven liquid biopsy and its potential integration into the clinical care of CRC in the southeast Asia region.
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Affiliation(s)
- Gaayathri Kumarasamy
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Pulau Pinang, 11800, Malaysia
| | - Nurul Hakimah Mohd Salim
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, 16150, Malaysia
| | - Nur Syafiqah Mohd Afandi
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Nor Datiakma Mat Amin
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
- Nature Products Division, Forest Research Institute Malaysia, Kepong, Selangor, 52109, Malaysia
| | - Mohd Nazri Ismail
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Pulau Pinang, 11800, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Marahaini Musa
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, 16150, Malaysia
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Habib MAH, Ismail MN. Correction to: Hevea brasiliensis latex proteomics: a review of analytical methods and the way forward. J Plant Res 2023; 136:431. [PMID: 36943551 DOI: 10.1007/s10265-023-01451-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia (USM), 11800, Pulau Pinang, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia (USM), 11800, Pulau Pinang, Malaysia.
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia (USM), 11800, Pulau Pinang, Malaysia.
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Adebayo IA, Habib MAH, Sarmiento ME, Acosta A, Yaacob NS, Ismail MN. Proteomic analysis of Malaysian Horseshoe crab (Tachypleus gigas) hemocytes gives insights into its innate immunity host defence system and other biological processes. PLoS One 2022; 17:e0272799. [PMID: 35947629 PMCID: PMC9365167 DOI: 10.1371/journal.pone.0272799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
Horseshoe crabs are one of the most studied invertebrates due to their remarkable innate immunity mechanism and biological processes. In this work, the proteins of the lipopolysaccharides (LPS)-stimulated and non-stimulated hemocytes of Malaysian Tachypleus gigas were profiled using LC-MS/MS. A total of 154 proteins were identified in both types of samples. Additionally, seventy-seven proteins were commonly found in both conditions, while 52 and 25 proteins were uniquely found in the LPS-stimulated and non-stimulated hemocytes, respectively. ATP-dependent energy-generating proteins such as actins and BLTX actin-related proteins were detected in both stimulated and non-stimulated T. gigas hemocytes, but more of such proteins were found in the former type. Proteins such as tachylectin-2, coagulogen, c-reactive proteins, histones, hemocyanin, and DNA polymerase, which play key roles in the organism’s innate immunity, were differentially expressed in the hemocytes following LPS challenge. In conclusion, the proteins identified in the hemolymph of T. gigas are vital for the organism’s molecular functions, biological processes, and activation of innate immunity.
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Affiliation(s)
- Ismail Abiola Adebayo
- Faculty of Biomedical Sciences, Department of Microbiology and Immunology, Kampala International University, Ishaka, Bushenyi, Uganda
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
- Department of Clinical Biology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
| | - Maria E. Sarmiento
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Nik Soriani Yaacob
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kelantan, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
- * E-mail:
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Mohd Afandi NS, Habib MAH, Ismail MN. Recent insights on gene expression studies on Hevea Brasiliensis fatal leaf fall diseases. Physiol Mol Biol Plants 2022; 28:471-484. [PMID: 35400887 PMCID: PMC8943083 DOI: 10.1007/s12298-022-01145-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Hevea brasiliensis is one of the most important agricultural commodities globally, heavily cultivated in Southeast Asia. Fatal leaf fall diseases cause aggressive leaf defoliation, linked to lower latex yield and death of crops before maturity. Due to the significant consequences of the disease to H. brasiliensis, the recent gene expression studies from four fall leaf diseases of H. brasiliensis were gathered; South American leaf blight, powdery mildew, Corynespora cassiicola and Phytophthora leaf fall disease. The differential analysis observed the pattern of commonly expressed genes upon fungi triggers using RT-PCR, DDRT-PCR, Real-time qRT-PCR and RNA-Seq. We have observed that RNA-Seq is the best tool to seek novel genes. Among the identified genes with defence-against fungi were pathogenesis-related genes such as β-1,3-glucanase and chitinase, the reactive oxygen species, and the phytoalexin biosynthesis. This manuscript also provided functional elaboration on the responsive genes and predicted possible biosynthetic pathways to identify and characterise novel genes in the future. At the end of the manuscript, the PCR methods and proteomic approaches were presented for future molecular and biochemical studies in the related diseases to H. brasiliensis.
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Affiliation(s)
- Nur Syafiqah Mohd Afandi
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 USM Penang, Malaysia
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Habib MAH, Ismail MN. Extraction and identification of biologically important proteins from the medicinal plant God's crown (Phaleria macrocarpa). J Food Biochem 2021; 45:e13817. [PMID: 34137461 DOI: 10.1111/jfbc.13817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 11/30/2022]
Abstract
The fruit and leaf of God's crown (Phaleria macrocarpa) have been traditionally used to treat a wide variety of diseases. However, the proteins of this tropical plant are still heavily understudied. Three protein extraction methods; phenol (Phe), trichloroacetic acid (TCA)-acetone-phenol (TCA-A-Phe), and ultrasonic (Ult) were compared on the fruit and leaf of P. macrocarpa. The Phe extraction method showed the highest percentage of recovered protein after the resolubilization process for both leaf (12.24%) and fruit (30.41%) based on protein yields of the leaf (6.15 mg/g) and fruit (36.98 mg/g). Phe and TCA-A-Phe extraction methods gave well-resolved bands over a wide range of molecular weights through sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Following liquid chromatography-tandem mass spectrometry analysis, proteins identified through the Phe extraction method were 30%-35% enzymatic proteins, including oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases that possess various biological functions. PRACTICAL APPLICATIONS: Every part of God's crown plant is traditionally consumed to treat various illnesses. While plant's benefits are well known and have led to a plethora of health products, the proteome remains mostly unknown. This study compares three protein extraction methods for the leaf and fruit of P. macrocarpa and identifies their proteins thru LC-MS/MS coupled with PEAKS. These method comparisons can be a guide for works on other plants as well. In addition, the proteomics data from this study may shed light on the functional properties of these plant parts and their products.
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Affiliation(s)
- Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia (USM), Bayan Lepas, Penang, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia (USM), Bayan Lepas, Penang, Malaysia.,Institute For Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), Bayan Lepas, Penang, Malaysia
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Habib MAH, Ismail MN. Hevea brasiliensis latex proteomics: a review of analytical methods and the way forward. J Plant Res 2021; 134:43-53. [PMID: 33108557 DOI: 10.1007/s10265-020-01231-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
Natural rubber or latex from the Hevea brasiliensis is an important commodity in various economic sectors in today's modern society. Proteins have been detected in latex since the early twentieth century, and they are known to regulate various biological pathways within the H. brasiliensis trees such as the natural rubber biosynthesis, defence against pathogens, wound healing, and stress tolerance. However, the exact mechanisms of the pathways are still not clear. Proteomic analyses on latex have found various proteins and revealed how they fit into the mechanisms of the biological pathways. In the past three decades, there has been rapid latex protein identification due to the improvement of latex protein extraction methods, as well as the emergence of two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). In this manuscript, we reviewed the methods of latex protein extraction that keeps on improving over the past three decades as well as the results of numerous latex protein identification and quantitation.
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Affiliation(s)
- Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia (USM), 11800, Pulau Pinang, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia (USM), 11800, Pulau Pinang, Malaysia.
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia (USM), 11800, Pulau Pinang, Malaysia.
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Habib MAH, Ismail MN. Characterization of erythropoietin biosimilars using mass spectrometric CID and HCD techniques. J LIQ CHROMATOGR R T 2019. [DOI: 10.1080/10826076.2019.1615502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, University Sains Malaysia, Minden, Malaysia
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Habib MAH, Gan CY, Abdul Latiff A, Ismail MN. Unrestrictive identification of post-translational modifications in Hevea brasiliensis latex. Biochem Cell Biol 2018; 96:818-824. [PMID: 30058361 DOI: 10.1139/bcb-2018-0020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The natural rubber latex extracted from the bark of Hevea brasiliensis plays various important roles in modern society. Post-translational modifications (PTMs) of the latex proteins are important for the stability and functionality of the proteins. In this study, latex proteins were acquired from the C-serum, lutoids, and rubber particle layers of latex without using prior enrichment steps; they were fragmented using collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron-transfer dissociation (ETD) activation methods. PEAKS 7 were used to search for unspecified PTMs, followed by analysis through PTM prediction tools to crosscheck both results. There were 73 peptides in 47 proteins from H. brasiliensis protein sequences derived from UniProtKB were identified and predicted to be post-translationally modified. The peptides with PTMs identified include phosphorylation, lysine acetylation, N-terminal acetylation, hydroxylation, and ubiquitination. Most of the PTMs discovered have yet to be reported in UniProt, which would provide great assistance in the research of the functional properties of H. brasiliensis latex proteins, as well as being useful biomarkers. The data are available via the MassIVE repository with identifier MSV000082419.
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Affiliation(s)
- Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 USM, Pulau, Pinang, Malaysia
| | - Chee-Yuen Gan
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 USM, Pulau, Pinang, Malaysia
| | | | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 USM, Pulau, Pinang, Malaysia
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Habib MAH, Yuen GC, Othman F, Zainudin NN, Latiff AA, Ismail MN. Proteomics analysis of latex from Hevea brasiliensis (clone RRIM 600). Biochem Cell Biol 2017; 95:232-242. [DOI: 10.1139/bcb-2016-0144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The natural rubber latex extracted from the bark of Hevea brasiliensis plays various important roles in today’s modern society. Following ultracentrifugation, the latex can be separated into 3 layers: C-serum, lutoids, and rubber particles. Previous studies have shown that a large number of proteins are present in these 3 layers. However, a complete proteome for this important plant is still unavailable. Protein sequences have been recently translated from the completed draft genome database of H. brasiliensis, leading to the creation of annotated protein databases of the following H. brasiliensis biosynthetic pathways: photosynthesis, latex allergens, rubberwood formation, latex biosynthesis, and disease resistance. This research was conducted to identify the proteins contained within the latex by way of de novo sequencing from mass spectral data obtained from the 3 layers of the latex. Peptides from these proteins were fragmented using collision-induced dissociation, higher-energy collisional dissociation, and electron-transfer dissociation activation methods. A large percentage of proteins from the biosynthetic pathways (63% to 100%) were successfully identified. In addition, a total of 1839 unique proteins were identified from the whole translated draft genome database (AnnHBM).
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Affiliation(s)
- Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Gan Chee Yuen
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | | | - Nurul Nabilah Zainudin
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | | | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
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