Pub Date : 2025-01-01DOI: 10.1016/j.abst.2025.01.001
Abdullahi Tunde Aborode , Ridwan Olamilekan Adesola , Godfred Yawson Scott , Emele Arthur-Hayford , Oche Joseph Otorkpa , Somuah Daniel Kwaku , Emmanuel Ebuka Elebesunu , Eghaghe Osadebamwen Nibokun , Ibude Jane Aruorivwooghene , Adetolase A. Bakre , Oluwaseun Adeolu Ogundijo , Olamilekan Gabriel Banwo , Oluwatobiloba Ige , Ibrahim O. Adelakun , Isreal Ayobami Onifade , Segun E. Ogungbemi , Boluwatife T. Dosunmu , Oluwaseunayo Deborah Ayando , Nike Idowu , Grace A. Adegoye , Olusegun Oluwaseun Jimoh
Tropical diseases present major health challenges in regions with limited resources, where access to advanced laboratory facilities is often scarce. This study explores the innovative techniques emerging in point-of-care (POC) diagnostics that are transforming the detection and treatment of tropical diseases. These advancements aim to provide faster diagnosis, better medical care, and ongoing monitoring in areas where traditional diagnostic methods are not practical, combining the precision of laboratory testing with the accessibility of field-based solutions. The review focuses on rapid diagnostic tests, molecular diagnostic tools, and smartphone-based applications, analyzing their advantages, limitations, and potential impact on healthcare delivery. It also addresses the challenges and opportunities involved in deploying these technologies in resource-constrained environments. Key to their success is the need for interdisciplinary collaboration, sustainable funding models, and strong regulatory frameworks to ensure their effective integration into healthcare systems. The review emphasizes how point-of-care diagnostics can play a crucial role in reducing the burden of tropical diseases and advancing health equity on a global scale.
{"title":"Bringing lab to the field: Exploring innovations in point-of-care diagnostics for the rapid detection and management of tropical diseases in resource-limited settings","authors":"Abdullahi Tunde Aborode , Ridwan Olamilekan Adesola , Godfred Yawson Scott , Emele Arthur-Hayford , Oche Joseph Otorkpa , Somuah Daniel Kwaku , Emmanuel Ebuka Elebesunu , Eghaghe Osadebamwen Nibokun , Ibude Jane Aruorivwooghene , Adetolase A. Bakre , Oluwaseun Adeolu Ogundijo , Olamilekan Gabriel Banwo , Oluwatobiloba Ige , Ibrahim O. Adelakun , Isreal Ayobami Onifade , Segun E. Ogungbemi , Boluwatife T. Dosunmu , Oluwaseunayo Deborah Ayando , Nike Idowu , Grace A. Adegoye , Olusegun Oluwaseun Jimoh","doi":"10.1016/j.abst.2025.01.001","DOIUrl":"10.1016/j.abst.2025.01.001","url":null,"abstract":"<div><div>Tropical diseases present major health challenges in regions with limited resources, where access to advanced laboratory facilities is often scarce. This study explores the innovative techniques emerging in point-of-care (POC) diagnostics that are transforming the detection and treatment of tropical diseases. These advancements aim to provide faster diagnosis, better medical care, and ongoing monitoring in areas where traditional diagnostic methods are not practical, combining the precision of laboratory testing with the accessibility of field-based solutions. The review focuses on rapid diagnostic tests, molecular diagnostic tools, and smartphone-based applications, analyzing their advantages, limitations, and potential impact on healthcare delivery. It also addresses the challenges and opportunities involved in deploying these technologies in resource-constrained environments. Key to their success is the need for interdisciplinary collaboration, sustainable funding models, and strong regulatory frameworks to ensure their effective integration into healthcare systems. The review emphasizes how point-of-care diagnostics can play a crucial role in reducing the burden of tropical diseases and advancing health equity on a global scale.</div></div>","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"7 ","pages":"Pages 28-43"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143098985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.abst.2024.12.001
Zhengjun Zhang
The origin of COVID-19 remains unclear despite extensive research. Theoretical models can simplify complex epigenetic landscapes by reducing vast methylation sites into manageable sets, revealing fundamental pathogen interactions that leap medical advances for the first time in tracing virus origin in the literature and practices. In our study, a max-logistic intelligence classifier analyzed 865,859 Infinium MethylationEPIC sites (CpGs), identifying eight CpGs that achieved 100 % accuracy in distinguishing COVID-19 patients from other respiratory disease patients and healthy controls. One CpG, cg07126281, linked to the SAMM50 gene, shares genetic ties with rare infectious diseases like Sennetsu fever and glanders, suggesting a potential connection between COVID-19 and these diseases, possibly transmitted through contaminated seafood or glanders-infected individuals. Identifying such links among 865,859 CpG sites is challenging, with a random correlation probability of less than one in ten million. However, the likelihood of finding meaningful associations with rare diseases lowers this probability to one in one hundred million, reinforcing the credibility of our findings. These results highlight the importance of investigating seafood markets and global supply chains in tracing COVID-19's origins and emphasize the need for ongoing biosafety and biosecurity measures to prevent future outbreaks.
{"title":"Etiological connections between initial COVID-19 and two rare infectious diseases","authors":"Zhengjun Zhang","doi":"10.1016/j.abst.2024.12.001","DOIUrl":"10.1016/j.abst.2024.12.001","url":null,"abstract":"<div><div>The origin of COVID-19 remains unclear despite extensive research. Theoretical models can simplify complex epigenetic landscapes by reducing vast methylation sites into manageable sets, revealing fundamental pathogen interactions that leap medical advances for the first time in tracing virus origin in the literature and practices. In our study, a max-logistic intelligence classifier analyzed 865,859 Infinium MethylationEPIC sites (CpGs), identifying eight CpGs that achieved 100 % accuracy in distinguishing COVID-19 patients from other respiratory disease patients and healthy controls. One CpG, cg07126281, linked to the SAMM50 gene, shares genetic ties with rare infectious diseases like Sennetsu fever and glanders, suggesting a potential connection between COVID-19 and these diseases, possibly transmitted through contaminated seafood or glanders-infected individuals. Identifying such links among 865,859 CpG sites is challenging, with a random correlation probability of less than one in ten million. However, the likelihood of finding meaningful associations with rare diseases lowers this probability to one in one hundred million, reinforcing the credibility of our findings. These results highlight the importance of investigating seafood markets and global supply chains in tracing COVID-19's origins and emphasize the need for ongoing biosafety and biosecurity measures to prevent future outbreaks.</div></div>","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"7 ","pages":"Pages 8-20"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143099112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.abst.2025.01.002
Yvette K. Kalimumbalo , Rosaline W. Macharia , Peter W. Wagacha
Background
The COVID-19 pandemic has highlighted the need for reliable biomarkers to predict disease severity and guide treatment strategies. However, the analysis of RNASeq data for biomarker discovery using machine learning is constrained by limited sample sizes, primarily due to cost and privacy considerations. In this study, we applied Generative Adversarial Networks (GANs) to RNASeq data in the process of identifying biomarkers associated with COVID-19 severity.
Methods
RNASeq data from COVID-19 patients, along with severity metadata, were collected from the GEO database. Differential expression analysis was conducted and GAN models were trained to augment the original dataset. This enhanced subsequent machine learning models’ robustness and accuracy for biomarker discovery. Feature selection using Recursive Feature Elimination with Cross-Validation (RFECV) identified key biomarkers on cGAN- and cWGAN-augmented datasets.
Results
Several key biomarkers significantly associated with disease severity were identified. Gene Ontology Enrichment analysis revealed upregulation of neutrophil degranulation and downregulation of T-cell activity, consistent with previous findings. The ROC analysis using a Random Forest machine learning model and the five most important biomarkers (CCDC65, ZNF239, OTUD7A, CEP126, and TCTN2) achieved high accuracy (AUC: 0.98, Acc: 0.94) in predicting disease severity. These genes are associated with processes such as cilium assembly, IFN activation, and NF-kB pathway suppression.
Conclusions
Our results demonstrate that GANs can effectively augment RNASeq data, leading to consistent findings that align with known mechanisms and providing new insights into severe COVID-19 transcriptional responses. Further experimental validation is needed to confirm the applicability of these biomarkers in diverse populations.
{"title":"Application of Generative Adversarial Networks on RNASeq data to uncover COVID-19 severity biomarkers","authors":"Yvette K. Kalimumbalo , Rosaline W. Macharia , Peter W. Wagacha","doi":"10.1016/j.abst.2025.01.002","DOIUrl":"10.1016/j.abst.2025.01.002","url":null,"abstract":"<div><h3>Background</h3><div>The COVID-19 pandemic has highlighted the need for reliable biomarkers to predict disease severity and guide treatment strategies. However, the analysis of RNASeq data for biomarker discovery using machine learning is constrained by limited sample sizes, primarily due to cost and privacy considerations. In this study, we applied Generative Adversarial Networks (GANs) to RNASeq data in the process of identifying biomarkers associated with COVID-19 severity.</div></div><div><h3>Methods</h3><div>RNASeq data from COVID-19 patients, along with severity metadata, were collected from the GEO database. Differential expression analysis was conducted and GAN models were trained to augment the original dataset. This enhanced subsequent machine learning models’ robustness and accuracy for biomarker discovery. Feature selection using Recursive Feature Elimination with Cross-Validation (RFECV) identified key biomarkers on cGAN- and cWGAN-augmented datasets.</div></div><div><h3>Results</h3><div>Several key biomarkers significantly associated with disease severity were identified. Gene Ontology Enrichment analysis revealed upregulation of neutrophil degranulation and downregulation of T-cell activity, consistent with previous findings. The ROC analysis using a Random Forest machine learning model and the five most important biomarkers (CCDC65, ZNF239, OTUD7A, CEP126, and TCTN2) achieved high accuracy (AUC: 0.98, Acc: 0.94) in predicting disease severity. These genes are associated with processes such as cilium assembly, IFN activation, and NF-kB pathway suppression.</div></div><div><h3>Conclusions</h3><div>Our results demonstrate that GANs can effectively augment RNASeq data, leading to consistent findings that align with known mechanisms and providing new insights into severe COVID-19 transcriptional responses. Further experimental validation is needed to confirm the applicability of these biomarkers in diverse populations.</div></div>","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"7 ","pages":"Pages 44-58"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143098984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.abst.2024.11.003
Noha Maher Galal , Salem Said Al Touby , Yahya Bin Abdullah Alrashdi , Mohammad Amzad Hossain
Zygophyllum simplex (Z. simplex) is a plant that has been used for a long time for the treatment of human diseases. Therefore, this present research study aims to prepare various plant extracts and screen their antioxidant and cytotoxic activities. To attain the present objectives, different crude extracts were prepared from the leaves and stems of Z. simplex by using a maceration method. The activities of antioxidant and cytotoxic were prepared from aerial crude extracts of Z. simplex which were determined by 2,2-diphenyl-1-1-picrylhydrazyl (DPPH) and brine shrimp lethality (BSL) methods, respectively. All the prepared leaves and stems extracts of the selected plant at six different concentrations showed significant antioxidant activity against the DPPH method. The ethyl acetate crude extract showed the highest antioxidant activity and the lowest activity was in butanol extract. However, all the leaves and stems crude extracts of Z. simplex were prepared at different concentrations also showed promising cytotoxic activity against the BSL method. However, based on the antioxidant activity results, the ethyl acetate extract was selected for the isolation of bioactive compounds by using the column chromatographic method. The ethyl acetate was purified by using column chromatography in which different ratios of mobile phase (dichlorometane: methanol) were used. A series of test tubes were collected with a volume of 3 mL and depending on the similar retention mobility (Rf) behavior a total of twelve fractions were prepared. Similarly, the antioxidant activity of the obtained twelve fractions from column chromatography was determined by the same DPPH method. All the fractions showed significant antioxidant activity. Among the fractions from the column, fraction 6 give the highest antioxidant activity and the lowest was fraction 1. In conclusion, all the leaves and stems showed encouraging activities against DPPH and the fraction with the highest antioxidant activity could be used as a natural antioxidant to prevent cell damage.
{"title":"Evaluation of toxicity and antioxidant activities of various crude extracts of leaves and stems of Zygophyllum simplex","authors":"Noha Maher Galal , Salem Said Al Touby , Yahya Bin Abdullah Alrashdi , Mohammad Amzad Hossain","doi":"10.1016/j.abst.2024.11.003","DOIUrl":"10.1016/j.abst.2024.11.003","url":null,"abstract":"<div><div><em>Zygophyllum simplex</em> (<em>Z</em>. <em>simplex</em>) is a plant that has been used for a long time for the treatment of human diseases. Therefore, this present research study aims to prepare various plant extracts and screen their antioxidant and cytotoxic activities. To attain the present objectives, different crude extracts were prepared from the leaves and stems of <em>Z. simplex</em> by using a maceration method. The activities of antioxidant and cytotoxic were prepared from aerial crude extracts of <em>Z. simplex</em> which were determined by 2,2-diphenyl-1-1-picrylhydrazyl (DPPH) and brine shrimp lethality (BSL) methods, respectively. All the prepared leaves and stems extracts of the selected plant at six different concentrations showed significant antioxidant activity against the DPPH method. The ethyl acetate crude extract showed the highest antioxidant activity and the lowest activity was in butanol extract. However, all the leaves and stems crude extracts of <em>Z. simplex</em> were prepared at different concentrations also showed promising cytotoxic activity against the BSL method. However, based on the antioxidant activity results, the ethyl acetate extract was selected for the isolation of bioactive compounds by using the column chromatographic method. The ethyl acetate was purified by using column chromatography in which different ratios of mobile phase (dichlorometane: methanol) were used. A series of test tubes were collected with a volume of 3 mL and depending on the similar retention mobility (Rf) behavior a total of twelve fractions were prepared. Similarly, the antioxidant activity of the obtained twelve fractions from column chromatography was determined by the same DPPH method. All the fractions showed significant antioxidant activity. Among the fractions from the column, fraction 6 give the highest antioxidant activity and the lowest was fraction 1. In conclusion, all the leaves and stems showed encouraging activities against DPPH and the fraction with the highest antioxidant activity could be used as a natural antioxidant to prevent cell damage.</div></div>","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"7 ","pages":"Pages 1-7"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143099099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ankylosing spondylitis (AS) is a chronic inflammatory arthritis primarily affecting the spine and sacroiliac joints. Gut microbiota significantly affects ankylosing spondylitis (AS) pathophysiology. Environmental factors, like smoking, and genetic predispositions can worsen AS. Patients often have altered fecal microbiota, decreased Bacteroides and Lachnospiraceae, and increased Proteobacteria and Enterobacteriaceae. Bacteroides coprophilus and Prevotella copri are particularly enriched in AS. This condition is associated with the HLA-B27 genetic marker and involves various immunological cells and inflammatory cytokines. To develop more effective treatments, research is ongoing to identify specific signaling pathways and genetic markers associated with AS.Gender prevalence of AS is now more evenly distributed, with women experiencing longer diagnostic delays and increased disease activity. Treatment regimens and responses to medication may vary between genders. Some case studies suggest that an Ayurvedic approach, including Panchakarma treatments and specific Ayurvedic medications, may be beneficial in managing AS. HLA-B27 and non-HLA genes such as IL23R, ERAP1, and RUNX3 are linked to AS susceptibility. The Th17 lymphocyte system, associated with IL23R, plays a role in AS pathogenesis, highlighting potential treatment targets. Over 100 genes related to AS were identified in genome-wide association studies, many connected to IL-23-driven inflammation and antigen processing. AS is regulated by various immunological cells, and changes in bone structure are caused by the interaction of immune cells with bone cells. Ankylosing spondylitis (AS) involves inflammatory cytokines like IL-1β IL-17 and IL-23. The immune system plays a crucial role in the disease, with certain proteins linked to AS risk. However, further research is needed to determine the effectiveness of this approach.
{"title":"Unraveling ankylosing spondylitis: Exploring the genetic and immunological factors and latest treatment innovations","authors":"Nilasree Hazra , Sudeshna Sengupta , Dipannita Burman , Jyoti Sekhar Banerjee , Malavika Bhattacharya","doi":"10.1016/j.abst.2024.12.002","DOIUrl":"10.1016/j.abst.2024.12.002","url":null,"abstract":"<div><div>Ankylosing spondylitis (AS) is a chronic inflammatory arthritis primarily affecting the spine and sacroiliac joints. Gut microbiota significantly affects ankylosing spondylitis (AS) pathophysiology. Environmental factors, like smoking, and genetic predispositions can worsen AS. Patients often have altered fecal microbiota, decreased Bacteroides and Lachnospiraceae, and increased Proteobacteria and Enterobacteriaceae. <em>Bacteroides coprophilus</em> and <em>Prevotella copri</em> are particularly enriched in AS. This condition is associated with the HLA-B27 genetic marker and involves various immunological cells and inflammatory cytokines. To develop more effective treatments, research is ongoing to identify specific signaling pathways and genetic markers associated with AS.Gender prevalence of AS is now more evenly distributed, with women experiencing longer diagnostic delays and increased disease activity. Treatment regimens and responses to medication may vary between genders. Some case studies suggest that an Ayurvedic approach, including Panchakarma treatments and specific Ayurvedic medications, may be beneficial in managing AS. HLA-B27 and non-HLA genes such as IL23R, ERAP1, and RUNX3 are linked to AS susceptibility. The Th17 lymphocyte system, associated with IL23R, plays a role in AS pathogenesis, highlighting potential treatment targets. Over 100 genes related to AS were identified in genome-wide association studies, many connected to IL-23-driven inflammation and antigen processing. AS is regulated by various immunological cells, and changes in bone structure are caused by the interaction of immune cells with bone cells. Ankylosing spondylitis (AS) involves inflammatory cytokines like IL-1β IL-17 and IL-23. The immune system plays a crucial role in the disease, with certain proteins linked to AS risk. However, further research is needed to determine the effectiveness of this approach.</div></div>","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"7 ","pages":"Pages 21-27"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143099100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-01DOI: 10.1016/j.abst.2024.02.001
Onifade Isreal Ayobami, Oluwatomiwa Jubilee Sunbare-Funto, Chinedu Endurance Mbah, O. Ajibade, O. Oyawoye, A. Aborode, S. C. Ogunleye, A. Jamiu, Basit Bolarinwa, Mosope F. Abanikannda, Zainab Tiamiyu, A. R. Idowu, O. Ige, Opara Julia Kelechi, Jeremiah I. Abok, Eniola A. Lawal, Ibude Jane Aruorivwooghene, Adekunle Fatai Adeoye, Olowo Roqeebah, Emmanuel Akinloye Ojewole, R. Adesola
{"title":"Faecal microbial transplant","authors":"Onifade Isreal Ayobami, Oluwatomiwa Jubilee Sunbare-Funto, Chinedu Endurance Mbah, O. Ajibade, O. Oyawoye, A. Aborode, S. C. Ogunleye, A. Jamiu, Basit Bolarinwa, Mosope F. Abanikannda, Zainab Tiamiyu, A. R. Idowu, O. Ige, Opara Julia Kelechi, Jeremiah I. Abok, Eniola A. Lawal, Ibude Jane Aruorivwooghene, Adekunle Fatai Adeoye, Olowo Roqeebah, Emmanuel Akinloye Ojewole, R. Adesola","doi":"10.1016/j.abst.2024.02.001","DOIUrl":"https://doi.org/10.1016/j.abst.2024.02.001","url":null,"abstract":"","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"38 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139817822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oral cancer presents a significant global health challenge, driving ongoing research to enhance diagnostics and treatments. MicroRNAs, particularly miRNA99a, have emerged as key players in oral cancer's initiation, progression, and advanced development. However, their precise molecular mechanisms remain unclear. We analyze miRNA99a in modulating the PI3K/Akt1/mTOR signaling pathway within oral squamous cell carcinoma through in silico data analysis. Additionally, we examined miRNA99a levels in both oral submucous fibrosis (OSMF) and oral squamous cell carcinoma (OSCC).
Materials and methods
A comprehensive approach utilizing various insilico tools identified potential target genes regulated by miRNA99a and examined their interactions within the PI3K/Akt1/mTOR signaling pathway. The study involved meticulous screening, functional enrichment analyses, and network analyses to understand the regulatory networks influenced by miRNA99a. Additionally, RT-PCR was used to measure the CT levels of miR-99a in OSMF, OSCC and NM samples.
Results
The analysis revealed a cohort of putative target genes regulated by miRNA99a, demonstrating their involvement in crucial cellular processes linked to OSCC progression. Functional enrichment analyses highlighted the significant association of these target genes with the PI3K/Akt1/mTOR pathway, indicating their potential impact on pivotal oncogenic signaling pathways. Network analyses revealed complex regulatory networks orchestrated by miRNA99a, its action within the PI3K/Akt1/mTOR signalling pathway and influencing OSCC development. RT-PCR analysis revealed a significant downregulation of miR-99a in OSCC and OSMF samples compared to NM, with mean CT values of 39.0940 and 38.3986 respectively, versus 33.7540 in NM (p = 0.000).
Conclusion
miRNA99a′s potential as a crucial regulator of the PI3K/Akt1/mTOR pathway in OSCC. The identified target genes and their interactions offer a foundation for further experimental validations, presenting opportunities for discovering novel therapeutic avenues or prognostic markers in managing OSCC. Integrating multi-omics data reinforces the significance of miRNA99a-mediated regulatory mechanisms in the intricate landscape of oral cancer biology.
{"title":"miRNA99a as a Potential target in P13K/Akt1/mTOR signaling pathway in progression of OSCC","authors":"Shazia Fathima J H , Selvaraj Jayaram , Vishnu Priya Veeraraghavan , Mohmed Isaqali Karobar","doi":"10.1016/j.abst.2024.10.003","DOIUrl":"10.1016/j.abst.2024.10.003","url":null,"abstract":"<div><h3>Background</h3><div>Oral cancer presents a significant global health challenge, driving ongoing research to enhance diagnostics and treatments. MicroRNAs, particularly miRNA99a, have emerged as key players in oral cancer's initiation, progression, and advanced development. However, their precise molecular mechanisms remain unclear. We analyze miRNA99a in modulating the PI3K/Akt1/mTOR signaling pathway within oral squamous cell carcinoma through in silico data analysis. Additionally, we examined miRNA99a levels in both oral submucous fibrosis (OSMF) and oral squamous cell carcinoma (OSCC).</div></div><div><h3>Materials and methods</h3><div>A comprehensive approach utilizing various insilico tools identified potential target genes regulated by miRNA99a and examined their interactions within the PI3K/Akt1/mTOR signaling pathway. The study involved meticulous screening, functional enrichment analyses, and network analyses to understand the regulatory networks influenced by miRNA99a. Additionally, RT-PCR was used to measure the CT levels of miR-99a in OSMF, OSCC and NM samples.</div></div><div><h3>Results</h3><div>The analysis revealed a cohort of putative target genes regulated by miRNA99a, demonstrating their involvement in crucial cellular processes linked to OSCC progression. Functional enrichment analyses highlighted the significant association of these target genes with the PI3K/Akt1/mTOR pathway, indicating their potential impact on pivotal oncogenic signaling pathways. Network analyses revealed complex regulatory networks orchestrated by miRNA99a, its action within the PI3K/Akt1/mTOR signalling pathway and influencing OSCC development. RT-PCR analysis revealed a significant downregulation of miR-99a in OSCC and OSMF samples compared to NM, with mean CT values of 39.0940 and 38.3986 respectively, versus 33.7540 in NM (p = 0.000).</div></div><div><h3>Conclusion</h3><div>miRNA99a′s potential as a crucial regulator of the PI3K/Akt1/mTOR pathway in OSCC. The identified target genes and their interactions offer a foundation for further experimental validations, presenting opportunities for discovering novel therapeutic avenues or prognostic markers in managing OSCC. Integrating multi-omics data reinforces the significance of miRNA99a-mediated regulatory mechanisms in the intricate landscape of oral cancer biology.</div></div>","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"6 ","pages":"Pages 242-259"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142586766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-01DOI: 10.1016/j.abst.2024.06.002
Xiaotong Wang , Yunqiu Shen , Yan Chen , Shuang Yang
Persistent inflammation can trigger the development of colorectal cancer, especially in patients with inflammatory bowel disease (IBD). The precise molecular mechanisms underlying this process are not fully understood. This study investigated the molecular modifications that occur in the cellular microenvironment during inflammation-induced and colitis-associated cancers. Studies showed that genetic mutations and post-translational modifications of oncogene proteins can alter the biological functions of macrophage inflammatory proteins, complicating the intricate interactions between inflammation and cancer. The researchers also observed abnormal glycosylation patterns in cases of inflammation and colitis-associated cancers. This observation suggests that glycoproteins present in bodily fluids could potentially serve as valuable disease markers. Additionally, the researchers investigated general signaling alterations that manifest in cases of colitis-associated cancer. They proposed a provisional molecular model that suggests the involvement of endoplasmic reticulum (ER) stress during the transition from inflammation to cancer. This potential pathway is mediated through the FKBP/c-Myc/p53 signaling axis. In the context of protein glycosylation, we summarize the potential molecular mechanisms of IBD-induced carcinogenesis. This knowledge could potentially lead to the development of novel targets for the clinical treatment of colorectal cancer.
{"title":"Inflammation-induced cellular changes: Genetic mutations, oncogene impact, and novel glycoprotein biomarkers","authors":"Xiaotong Wang , Yunqiu Shen , Yan Chen , Shuang Yang","doi":"10.1016/j.abst.2024.06.002","DOIUrl":"https://doi.org/10.1016/j.abst.2024.06.002","url":null,"abstract":"<div><p>Persistent inflammation can trigger the development of colorectal cancer, especially in patients with inflammatory bowel disease (IBD). The precise molecular mechanisms underlying this process are not fully understood. This study investigated the molecular modifications that occur in the cellular microenvironment during inflammation-induced and colitis-associated cancers. Studies showed that genetic mutations and post-translational modifications of oncogene proteins can alter the biological functions of macrophage inflammatory proteins, complicating the intricate interactions between inflammation and cancer. The researchers also observed abnormal glycosylation patterns in cases of inflammation and colitis-associated cancers. This observation suggests that glycoproteins present in bodily fluids could potentially serve as valuable disease markers. Additionally, the researchers investigated general signaling alterations that manifest in cases of colitis-associated cancer. They proposed a provisional molecular model that suggests the involvement of endoplasmic reticulum (ER) stress during the transition from inflammation to cancer. This potential pathway is mediated through the FKBP/c-Myc/p53 signaling axis. In the context of protein glycosylation, we summarize the potential molecular mechanisms of IBD-induced carcinogenesis. This knowledge could potentially lead to the development of novel targets for the clinical treatment of colorectal cancer.</p></div>","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"6 ","pages":"Pages 91-104"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2543106424000097/pdfft?md5=718031484392d22ce87e2421b57cf8f9&pid=1-s2.0-S2543106424000097-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141438577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biliary atresia (BA) is a disease of the intrahepatic or extrahepatic bile ducts with an unknown etiology. It presents in neonates with jaundice, clay-colored stool, and often hepatomegaly. Early diagnosis of the disease is pivotal for long-term prognosis. If the BA is left untreated, progressive liver cirrhosis and death can occur. Persisting jaundice in infants born at term should lead to further examination of liver diseases. A range of laboratory analyses is used, but none is specific for BA. In this review, we investigate whether the level of matrix metalloproteinase 7 (MMP-7) in serum can be used as an early diagnostic biomarker for BA.
Method
A systematic literature search of the PubMed database revealed the two terms “matrix metalloproteinase 7” and “biliary atresia”. A total of 24 articles were identified; these articles were screened, and eight articles were found to be relevant for this literature review, each describing an independent study.
Results
In all eight articles, the diagnostic cut-off values for serum MMP-7 in BA patients vs. non-BA patients were determined by receiver operating characteristic (ROC) curve analysis and by determining the area under the curve (AUC). The AUC ranged from 0.96 to 0.99. All studies had a sensitivity of 95 % or above and a specificity of 83 % or above. The cut-off values were discordant and ranged from 1.43 ng/ml to 52.85 ng/ml. The calculated positive likelihood ratio (PLR) varied from 5.66 to 21.86, and the negative likelihood ratio (NLR) varied from 0.01 to 0.05 among the eight studies. Finally, the diagnostic odds ratio (DOR) varied from 168.64 to 1406.00 in seven out of the eight studies.
Conclusion
The serum MMP-7 concentration can be used as a diagnostic biomarker according to the eight studies investigated in this review. However, further assessments of MMP-7 in larger, multicenter, and multiethnic studies are needed to validate its potential for biomarker development and, ultimately, its standard use in clinical practice.
{"title":"Matrix metalloproteinase 7 as a diagnostic biomarker of biliary atresia: A systematic review","authors":"Pauline Louise Møllmann Lausten , Vibeke Brix Christensen , Hannelouise Kissow","doi":"10.1016/j.abst.2024.04.001","DOIUrl":"10.1016/j.abst.2024.04.001","url":null,"abstract":"<div><h3>Background</h3><p>Biliary atresia (BA) is a disease of the intrahepatic or extrahepatic bile ducts with an unknown etiology. It presents in neonates with jaundice, clay-colored stool, and often hepatomegaly. Early diagnosis of the disease is pivotal for long-term prognosis. If the BA is left untreated, progressive liver cirrhosis and death can occur. Persisting jaundice in infants born at term should lead to further examination of liver diseases. A range of laboratory analyses is used, but none is specific for BA. In this review, we investigate whether the level of matrix metalloproteinase 7 (MMP-7) in serum can be used as an early diagnostic biomarker for BA.</p></div><div><h3>Method</h3><p>A systematic literature search of the PubMed database revealed the two terms “matrix metalloproteinase 7” and “biliary atresia”. A total of 24 articles were identified; these articles were screened, and eight articles were found to be relevant for this literature review, each describing an independent study.</p></div><div><h3>Results</h3><p>In all eight articles, the diagnostic cut-off values for serum MMP-7 in BA patients vs. non-BA patients were determined by receiver operating characteristic (ROC) curve analysis and by determining the area under the curve (AUC). The AUC ranged from 0.96 to 0.99. All studies had a sensitivity of 95 % or above and a specificity of 83 % or above. The cut-off values were discordant and ranged from 1.43 ng/ml to 52.85 ng/ml. The calculated positive likelihood ratio (PLR) varied from 5.66 to 21.86, and the negative likelihood ratio (NLR) varied from 0.01 to 0.05 among the eight studies. Finally, the diagnostic odds ratio (DOR) varied from 168.64 to 1406.00 in seven out of the eight studies.</p></div><div><h3>Conclusion</h3><p>The serum MMP-7 concentration can be used as a diagnostic biomarker according to the eight studies investigated in this review. However, further assessments of MMP-7 in larger, multicenter, and multiethnic studies are needed to validate its potential for biomarker development and, ultimately, its standard use in clinical practice.</p></div>","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"6 ","pages":"Pages 72-82"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2543106424000061/pdfft?md5=af95e4928e71a8f2814b306292f1fb85&pid=1-s2.0-S2543106424000061-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140771555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The presence of toxic materials in water solutions, mainly harmful metals and metalloids, is a significant ecological and community issue. In village areas, hardness is major groundwater toxicity. Hardness, those are alkaline in nature, can reason problems to the eyes, respiratory tract failure, and epidermis in both its liquid and gaseous types. The natural parts of hardness in humans subsequent to severe exposures are concentrations-dependent and changes depending on the duration, times of effects, and quantity absorbed by the body. Biosorption is a physiochemical processes that happens mainly in the certain biomass, following it to inactively collect and attach impurities onto its cellular configuration. It is a metabolically inactive procedure that does not need energy. The composition and kinetic equilibrium of the sorbent's cellular surface determine the number of contaminants that the sorbent can eliminate. The biosorption procedures were facilitate by the single physical, biological and chemical characteristics of each biosorbents those applied the elimination of hardness from the water. In the hardness of the water has been removed, the biosorption procedures can be made highly cost-effective by recycling and reprocessing of the biosorbents. The removals of hardness from huge amounts of water can be done by the applications of a variety of bioreactors in the biosorption.
{"title":"Development and applications of different types of green biosorbents for eliminations of hardness from water: A review on treatment, kinetics mechanism and future scope","authors":"Subhashish Dey, G.T.N. Veerendra, A.V. Phani Manoj, Siva Shanmukha Anjaneya Babu Padavala, A.H.L. Swaroop","doi":"10.1016/j.abst.2024.11.001","DOIUrl":"10.1016/j.abst.2024.11.001","url":null,"abstract":"<div><div>The presence of toxic materials in water solutions, mainly harmful metals and metalloids, is a significant ecological and community issue. In village areas, hardness is major groundwater toxicity. Hardness, those are alkaline in nature, can reason problems to the eyes, respiratory tract failure, and epidermis in both its liquid and gaseous types. The natural parts of hardness in humans subsequent to severe exposures are concentrations-dependent and changes depending on the duration, times of effects, and quantity absorbed by the body. Biosorption is a physiochemical processes that happens mainly in the certain biomass, following it to inactively collect and attach impurities onto its cellular configuration. It is a metabolically inactive procedure that does not need energy. The composition and kinetic equilibrium of the sorbent's cellular surface determine the number of contaminants that the sorbent can eliminate. The biosorption procedures were facilitate by the single physical, biological and chemical characteristics of each biosorbents those applied the elimination of hardness from the water. In the hardness of the water has been removed, the biosorption procedures can be made highly cost-effective by recycling and reprocessing of the biosorbents. The removals of hardness from huge amounts of water can be done by the applications of a variety of bioreactors in the biosorption.</div></div>","PeriodicalId":72080,"journal":{"name":"Advances in biomarker sciences and technology","volume":"6 ","pages":"Pages 265-299"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142652860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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