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Thongbut J, Laengsri V, Raud L, Promwong C, I-Na-Ayudhya C, Férec C, Nuchnoi P, Fichou Y. Nation-wide investigation of RHD variants in Thai blood donors: Impact for molecular diagnostics. Transfusion 2020; 61:931-938. [PMID: 33377204 DOI: 10.1111/trf.16242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/23/2020] [Accepted: 12/06/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Knowledge of the molecular determinants driving antigen expression is critical to design, optimize, and implement a genotyping approach on a population-specific basis. Although RHD gene variability has been extensively reported in Caucasians, Africans, and East-Asians, it remains to be explored in Southeast Asia. Thus the molecular basis of non-D+ blood donors was investigated in Thailand. STUDY DESIGN AND METHODS First, 1176 blood samples exhibiting an inconclusive or negative result by automated serological testing were collected in the 12 Regional Blood Centres of the Thai Red Cross located throughout Thailand. Second, the RHD gene was analyzed in all samples by 1) quantitative multiplex PCR of short fluorescent fragments, and 2) direct sequencing, when necessary, for identifying structural variants and single nucleotide variants, respectively. RESULTS Additional serological typing yielded 51 and 1125 samples with weak/partial D and D-negative (D-) phenotype, respectively. In the first subset, partial RHD*06.03 was the most common variant allele (allele frequency: 18.6%). In the second subset, the whole deletion of the gene is largely the most frequent (allele frequency: 84.9%), followed by the Asian DEL allele found in 15.6% of the samples. Eight novel alleles with various mutational mechanisms were identified. CONCLUSION We report, for the first time at the national level, the molecular basis of weak/partial D and serologically D- phenotypes in Thai blood donors. The design and implementation of a dedicated diagnostic strategy in blood donors and patients are the very next steps for optimizing the management and supply of RBC units in Thailand.
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Affiliation(s)
- Jairak Thongbut
- Center of Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,National Blood Centre, Thai Red Cross Society, Bangkok, Thailand
| | - Vishuda Laengsri
- Center of Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | | | - Charuporn Promwong
- National Blood Centre, Thai Red Cross Society, Bangkok, Thailand.,Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Chartchalerm I-Na-Ayudhya
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Claude Férec
- Univ Brest, Inserm, EFS, Brest, France.,Service de Génétique Médicale, CHRU Brest, Brest, France
| | - Pornlada Nuchnoi
- Center of Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Yann Fichou
- Univ Brest, Inserm, EFS, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
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Laengsri V, Shoombuatong W, Adirojananon W, Nantasenamat C, Prachayasittikul V, Nuchnoi P. Correction to: ThalPred: a web-based prediction tool for discriminating thalassemia trait and iron deficiency anemia. BMC Med Inform Decis Mak 2019; 19:228. [PMID: 31744481 PMCID: PMC6862745 DOI: 10.1186/s12911-019-0977-7] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- V Laengsri
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - W Shoombuatong
- Center of Data Mining and Medical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - W Adirojananon
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - C Nantasenamat
- Center of Data Mining and Medical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - V Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - P Nuchnoi
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand. .,Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.
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Laengsri V, Shoombuatong W, Adirojananon W, Nantasenamat C, Prachayasittikul V, Nuchnoi P. ThalPred: a web-based prediction tool for discriminating thalassemia trait and iron deficiency anemia. BMC Med Inform Decis Mak 2019; 19:212. [PMID: 31699079 PMCID: PMC6836478 DOI: 10.1186/s12911-019-0929-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 10/14/2019] [Indexed: 01/07/2023] Open
Abstract
Background The hypochromic microcytic anemia (HMA) commonly found in Thailand are iron deficiency anemia (IDA) and thalassemia trait (TT). Accurate discrimination between IDA and TT is an important issue and better methods are urgently needed. Although considerable RBC formulas and indices with various optimal cut-off values have been developed, distinguishing between IDA and TT is still a challenging problem due to the diversity of various anemic populations. To address this problem, it is desirable to develop an improved and automated prediction model for discriminating IDA from TT. Methods We retrospectively collected laboratory data of HMA found in Thai adults. Five machine learnings, including k-nearest neighbor (k-NN), decision tree, random forest (RF), artificial neural network (ANN) and support vector machine (SVM), were applied to construct a discriminant model. Performance was assessed and compared with thirteen existing discriminant formulas and indices. Results The data of 186 patients (146 patients with TT and 40 with IDA) were enrolled. The interpretable rules derived from the RF model were proposed to demonstrate the combination of RBC indices for discriminating IDA from TT. A web-based tool ‘ThalPred’ was implemented using an SVM model based on seven RBC parameters. ThalPred achieved prediction results with an external accuracy, MCC and AUC of 95.59, 0.87 and 0.98, respectively. Conclusion ThalPred and an interpretable rule were provided for distinguishing IDA from TT. For the convenience of health care team experimental scientists, a web-based tool has been established at http://codes.bio/thalpred/ by which users can easily get their desired screening test result without the need to go through the underlying mathematical and computational details.
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Affiliation(s)
- V Laengsri
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - W Shoombuatong
- Center of Data Mining and Medical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - W Adirojananon
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - C Nantasenamat
- Center of Data Mining and Medical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - V Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - P Nuchnoi
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand. .,Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.
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Chuanboon K, Na Nakorn P, Pannengpetch S, Laengsri V, Nuchnoi P, Isarankura-Na-Ayudhya C, Isarankura-Na-Ayudhya P. Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae. PeerJ 2019; 7:e6904. [PMID: 31534833 PMCID: PMC6727835 DOI: 10.7717/peerj.6904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023] Open
Abstract
Background Enterobacter cloacae (EC) is a Gram-negative bacterium that has been utilized extensively in biotechnological and environmental science applications, possibly because of its high capability for adapting itself and surviving in hazardous conditions. A search for the EC from agricultural and industrial areas that possesses high capability to tolerate and/or accumulate cadmium ions has been conducted in this study. Plausible mechanisms of cellular adaptations in the presence of toxic cadmium have also been proposed. Methods Nine strains of EC were isolated and subsequently identified by biochemical characterization and MALDI-Biotyper. Minimum inhibitory concentrations (MICs) against cadmium, zinc and copper ions were determined by agar dilution method. Growth tolerance against cadmium ions was spectrophotometrically monitored at 600 nm. Cadmium accumulation at both cellular and protein levels was investigated using atomic absorption spectrophotometer. Proteomics analysis by 2D-DIGE in conjunction with protein identification by QTOF-LC-MS/MS was used to study differentially expressed proteins between the tolerant and intolerant strains as consequences of cadmium exposure. Expression of such proteins was confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Bioinformatics tools were applied to propose the functional roles of cadmium-binding protein and its association in cadmium tolerance mechanisms. Results The cadmium-tolerant strain (EC01) and intolerant strain (EC07) with the MICs of 1.6 and 0.4 mM, respectively, were isolated. The whole cell lysate of EC01 exhibited approximately two-fold higher in cadmium binding capability than those of the EC07 and ATCC 13047, possibly by the expression of Cd-binding proteins. Our proteomics analysis revealed the higher expression of DUF326-like domain (a high cysteine-rich protein) of up to 220 fold in the EC01 than that of the EC07. Confirmation of the transcription level of this gene by qRT-PCR revealed a 14-fold induction in the EC01. Regulation of the DUF326-like domain in EC01 was more pronounced to mediate rapid cadmium accumulation (in 6 h) and tolerance than the other resistance mechanisms found in the ATCC 13047 and the EC07 strains. The only one major responsive protein against toxic cadmium found in these three strains belonged to an antioxidative enzyme, namely catalase. The unique proteins found in the ATCC 13047 and EC07 were identified as two groups: (i) ATP synthase subunit alpha, putative hydrolase and superoxide dismutase and (ii) OmpX, protein YciF, OmpC porin, DNA protection during starvation protein, and TrpR binding protein WrbA, respectively. Conclusion All these findings gain insights not only into the molecular mechanisms of cadmium tolerance in EC but also open up a high feasibility to apply the newly discovered DUF326-like domain as cadmium biosorbents for environmental remediation in the future.
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Affiliation(s)
- Kitipong Chuanboon
- Department of Medical Technology and Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand.,Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Piyada Na Nakorn
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Supitcha Pannengpetch
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Vishuda Laengsri
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Pornlada Nuchnoi
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | | | - Patcharee Isarankura-Na-Ayudhya
- Department of Medical Technology and Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
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Laengsri V, Nantasenamat C, Schaduangrat N, Nuchnoi P, Prachayasittikul V, Shoombuatong W. TargetAntiAngio: A Sequence-Based Tool for the Prediction and Analysis of Anti-Angiogenic Peptides. Int J Mol Sci 2019; 20:E2950. [PMID: 31212918 PMCID: PMC6628072 DOI: 10.3390/ijms20122950] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 11/21/2022] Open
Abstract
Cancer remains one of the major causes of death worldwide. Angiogenesis is crucial for the pathogenesis of various human diseases, especially solid tumors. The discovery of anti-angiogenic peptides is a promising therapeutic route for cancer treatment. Thus, reliably identifying anti-angiogenic peptides is extremely important for understanding their biophysical and biochemical properties that serve as the basis for the discovery of new anti-cancer drugs. This study aims to develop an efficient and interpretable computational model called TargetAntiAngio for predicting and characterizing anti-angiogenic peptides. TargetAntiAngio was developed using the random forest classifier in conjunction with various classes of peptide features. It was observed via an independent validation test that TargetAntiAngio can identify anti-angiogenic peptides with an average accuracy of 77.50% on an objective benchmark dataset. Comparisons demonstrated that TargetAntiAngio is superior to other existing methods. In addition, results revealed the following important characteristics of anti-angiogenic peptides: (i) disulfide bond forming Cys residues play an important role for inhibiting blood vessel proliferation; (ii) Cys located at the C-terminal domain can decrease endothelial formatting activity and suppress tumor growth; and (iii) Cyclic disulfide-rich peptides contribute to the inhibition of angiogenesis and cell migration, selectivity and stability. Finally, for the convenience of experimental scientists, the TargetAntiAngio web server was established and made freely available online.
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Affiliation(s)
- Vishuda Laengsri
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
| | - Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
| | - Pornlada Nuchnoi
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
| | - Virapong Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
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Affiliation(s)
- Vishuda Laengsri
- Center for Research & Innovation, Mahidol University, Bangkok, Thailand
- Department of Clinical Microscopy, Mahidol University, Bangkok, Thailand
| | - Usanee Kerdpin
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Chotiros Plabplueng
- Center for Research & Innovation, Mahidol University, Bangkok, Thailand
- Department of Clinical Microscopy, Mahidol University, Bangkok, Thailand
| | - Lertyot Treeratanapiboon
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Pornlada Nuchnoi
- Center for Research & Innovation, Mahidol University, Bangkok, Thailand
- Department of Clinical Microscopy, Mahidol University, Bangkok, Thailand
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