Background: Recent studies have validated the role of Pericentriolar Material 1 (PCM1) in several malignant tumour cell lines, but its specific biological function in lung adenocarcinoma (LUAD) remains unclear. Objective: To address this gap, this study analyzed 411 LUAD and control samples to evaluate the prognostic value of PCM1 using Cox regression analysis. objective: To address this gap, this study analyzed 411 LUAD and control samples to evaluate the prognostic value of PCM1 using Cox regression analysis. Methods: Multiple genes co-expressed with PCM1 were also analyzed to investigate the biological processes and roles involved in PCM1. An endogenous competitive network with PCM1 as the key gene was constructed to uncover its regulatory and competitive relationships in LUAD. The study further explored the immunological characteristics of PCM1 in different expression groups based on immune infiltration analysis. Results: These findings indicated that higher PCM1 expression levels were associated with better survival prognoses, possibly due to its antagonistic effects on RHOC. Immunological infiltration analysis revealed a significant correlation between PCM1 and various immune cell infiltration levels, including CD4+ T cells, naïve B cells, M2 macrophages, and mast cells. However, there was no significant relationship between PCM1 and MSI, TMB, or stemness, although it was positively correlated with m6A genes. Patients with lower PCM1 expression responded better to CTLA-4 therapy. The study also estimated that some chemotherapeutic and targeted agents might be effective in treating patients with high PCM1 levels. PCM1 was mainly expressed in the cytoplasmic and membranous structures. Conclusion: PCM1 shows potential as a prognostic biomarker for LUAD due to its strong correlation with immune cell infiltration and its ability to enhance anticancer treatment sensitivity. other: No.
{"title":"PCM1: A Potential Prognostic Biomarker Correlated with Immune Infiltration in Lung Adenocarcinoma","authors":"Zhihua Guo, Jinghao Liang, Xin Zhang, Qing Ai, Zixian Xie, Haonan Zhao, Fayuan Wu, Zhaofeng Tan, Weiqiang Yin, Linghua Ji","doi":"10.2174/0115701646270898231123065507","DOIUrl":"https://doi.org/10.2174/0115701646270898231123065507","url":null,"abstract":"Background: Recent studies have validated the role of Pericentriolar Material 1 (PCM1) in several malignant tumour cell lines, but its specific biological function in lung adenocarcinoma (LUAD) remains unclear. Objective: To address this gap, this study analyzed 411 LUAD and control samples to evaluate the prognostic value of PCM1 using Cox regression analysis. objective: To address this gap, this study analyzed 411 LUAD and control samples to evaluate the prognostic value of PCM1 using Cox regression analysis. Methods: Multiple genes co-expressed with PCM1 were also analyzed to investigate the biological processes and roles involved in PCM1. An endogenous competitive network with PCM1 as the key gene was constructed to uncover its regulatory and competitive relationships in LUAD. The study further explored the immunological characteristics of PCM1 in different expression groups based on immune infiltration analysis. Results: These findings indicated that higher PCM1 expression levels were associated with better survival prognoses, possibly due to its antagonistic effects on RHOC. Immunological infiltration analysis revealed a significant correlation between PCM1 and various immune cell infiltration levels, including CD4+ T cells, naïve B cells, M2 macrophages, and mast cells. However, there was no significant relationship between PCM1 and MSI, TMB, or stemness, although it was positively correlated with m6A genes. Patients with lower PCM1 expression responded better to CTLA-4 therapy. The study also estimated that some chemotherapeutic and targeted agents might be effective in treating patients with high PCM1 levels. PCM1 was mainly expressed in the cytoplasmic and membranous structures. Conclusion: PCM1 shows potential as a prognostic biomarker for LUAD due to its strong correlation with immune cell infiltration and its ability to enhance anticancer treatment sensitivity. other: No.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138572021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-07DOI: 10.2174/0115701646254996231130050528
Ajoy Basak, Euridice Carmona, Sanjukta Basak, Felicia Au, Rosa Anna Maria Barbarulo Borgheresi
Background: Snake venom has become a key source of many bioactive peptides, enzymes, and toxins associated with blood coagulation and neuronal toxicity. In the past, a number of bradykinin potentiating peptides have been isolated from snake venom that display hypotensive activity due to their inhibitory activity towards Angiotensin-Converting Enzyme (ACE). Significant interest has developed to isolate, characterize, and subsequently design peptide analogs as potent ACE-inhibitors which may find therapeutic applications for the treatment of hypertension and associated diseases. Aim: The aim of this study is to search for new bioactive peptide/s in the venom of the snake Bothrops Jararaca (Bj). Objective: The objective is to isolate and characterize new hypotensive peptides from BJ venom. Methodology: We examined the venom of Bj which is known to host a range of bioactive peptides. We have isolated a new peptide (BJ-1) which displayed in vitro potent hypotensive activity. The peptide was purified via Sephadex G25 column chromatography and RP-HPLC. It was characterized by mass spectrometry, amino acid analysis, N-terminal sequencing, and chemical synthesis. Result: The peptide was identified as an octa-decapeptide with an amino acid sequence as DCPSDWSSYEGHCYKPFS where the two Cys residues are likely present in a free state, although they can form an internal S-S bond upon oxidation. It was fully confirmed by comparing it with synthetic peptides prepared by solid phase chemistry. Both have the same molecular mass (2,108 Da) and identical bioactivity. Furthermore, we rationalize that BJ-1 may be derived from precursor protein “Coagulation factor IX/factor X binding protein (CF-IX/X-BP)” by proteolytic cleavage at the Nterminus of its A-chain within the sequence KPFS18ↆE 19PKN. This cleavage site contains the recognition motif of enzyme PCSK8 (Proprotein Convertase Subtilisin Kexin8) also known as Subtilisin Kexin Isozyme 1 (SKI-1) or Site 1 Protease (S1P). Despite this observation, using a synthetic peptide encompassing the proposed cleavage site and recombinant PCSK8 enzyme, we found that the enzyme responsible for the generation of BJ-1 is not PCSK8. Further studies will be needed to identify the associated enzyme and fully characterize the pharmacological and biological properties of the peptide. Conclusion: Our study revealed the presence of a novel hypotensive octa-decapeptide in the venom of the snake Bothrops jararaca. It is likely derived from the A-chain of protein CF-IX/X-BP via proteolytic cleavage at the N-terminus by a protease yet to be characterized
{"title":"Characterization of a New Hypotensive Peptide from the Venom of Snake bothrops jararaca (Bj)","authors":"Ajoy Basak, Euridice Carmona, Sanjukta Basak, Felicia Au, Rosa Anna Maria Barbarulo Borgheresi","doi":"10.2174/0115701646254996231130050528","DOIUrl":"https://doi.org/10.2174/0115701646254996231130050528","url":null,"abstract":"Background: Snake venom has become a key source of many bioactive peptides, enzymes, and toxins associated with blood coagulation and neuronal toxicity. In the past, a number of bradykinin potentiating peptides have been isolated from snake venom that display hypotensive activity due to their inhibitory activity towards Angiotensin-Converting Enzyme (ACE). Significant interest has developed to isolate, characterize, and subsequently design peptide analogs as potent ACE-inhibitors which may find therapeutic applications for the treatment of hypertension and associated diseases. Aim: The aim of this study is to search for new bioactive peptide/s in the venom of the snake Bothrops Jararaca (Bj). Objective: The objective is to isolate and characterize new hypotensive peptides from BJ venom. Methodology: We examined the venom of Bj which is known to host a range of bioactive peptides. We have isolated a new peptide (BJ-1) which displayed in vitro potent hypotensive activity. The peptide was purified via Sephadex G25 column chromatography and RP-HPLC. It was characterized by mass spectrometry, amino acid analysis, N-terminal sequencing, and chemical synthesis. Result: The peptide was identified as an octa-decapeptide with an amino acid sequence as DCPSDWSSYEGHCYKPFS where the two Cys residues are likely present in a free state, although they can form an internal S-S bond upon oxidation. It was fully confirmed by comparing it with synthetic peptides prepared by solid phase chemistry. Both have the same molecular mass (2,108 Da) and identical bioactivity. Furthermore, we rationalize that BJ-1 may be derived from precursor protein “Coagulation factor IX/factor X binding protein (CF-IX/X-BP)” by proteolytic cleavage at the Nterminus of its A-chain within the sequence KPFS18ↆE 19PKN. This cleavage site contains the recognition motif of enzyme PCSK8 (Proprotein Convertase Subtilisin Kexin8) also known as Subtilisin Kexin Isozyme 1 (SKI-1) or Site 1 Protease (S1P). Despite this observation, using a synthetic peptide encompassing the proposed cleavage site and recombinant PCSK8 enzyme, we found that the enzyme responsible for the generation of BJ-1 is not PCSK8. Further studies will be needed to identify the associated enzyme and fully characterize the pharmacological and biological properties of the peptide. Conclusion: Our study revealed the presence of a novel hypotensive octa-decapeptide in the venom of the snake Bothrops jararaca. It is likely derived from the A-chain of protein CF-IX/X-BP via proteolytic cleavage at the N-terminus by a protease yet to be characterized","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Leech therapy has been used for centuries as a recommended approach to cure several diseases, such as; psoriasis, arthrosclerosis, urinary tract diseases, and wound healing. The present study aimed to analyze the number, quantity, and distribution differences of medicinal leech (Hirudo orientalis) proteins throughout various seasons and in laboratory conditions as well. Protein profiling of salivary gland secretion from leech was studied by SDS-PAGE and 2D Electrophoresis on the proteins with the molecular weight range of 5 - 250 KDa in the lyophilized salivary gland secretion (SGS) during the seasons of summer and winter, and also in the laboratory conditions. Our results indicated differences in the number and quality of leech saliva proteins in different seasons. We observed a higher number of proteins in summer than in winter. These results demonstrated the presence of Calin and Manillase in summer and Hyaluronidase and Collagenase in winter. This study could help us in choosing the best and most favorable conditions for using H. orientalis proteins for the treatment of different diseases
{"title":"Protein Profiling of Hirudo orientalis During Different Seasons for Obtaining Accurate Results in Leech Therapy","authors":"Leili Amani, Mehran Mirabzadeh Ardakani, Nasrin Motamed, Masuomeh Malek, Marzieh Dehghan Shasaltaneh","doi":"10.2174/0115701646257568231130053824","DOIUrl":"https://doi.org/10.2174/0115701646257568231130053824","url":null,"abstract":"Leech therapy has been used for centuries as a recommended approach to cure several diseases, such as; psoriasis, arthrosclerosis, urinary tract diseases, and wound healing. The present study aimed to analyze the number, quantity, and distribution differences of medicinal leech (Hirudo orientalis) proteins throughout various seasons and in laboratory conditions as well. Protein profiling of salivary gland secretion from leech was studied by SDS-PAGE and 2D Electrophoresis on the proteins with the molecular weight range of 5 - 250 KDa in the lyophilized salivary gland secretion (SGS) during the seasons of summer and winter, and also in the laboratory conditions. Our results indicated differences in the number and quality of leech saliva proteins in different seasons. We observed a higher number of proteins in summer than in winter. These results demonstrated the presence of Calin and Manillase in summer and Hyaluronidase and Collagenase in winter. This study could help us in choosing the best and most favorable conditions for using H. orientalis proteins for the treatment of different diseases","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-30DOI: 10.2174/0115701646243074231113071548
Diba Aslani Firozabadi, Mohammad Reza Bozorgmehr, S. Ali Beiramabadi, Sharareh Mohseni
Background: The formation of plaque from protein fibrils is the major source of diseases, such as Alzheimer's and Prion diseases. Amyloid beta (Aβ) is a peptide with different lengths, which is one of the main components of the plaque in the brain of people with Alzheimer's. Of the amyloid beta of various lengths in the brain cells plaque, beta-amyloid with 40 amino acids (Aβ1- 40) is more abundant than the rest. Aβ monomers are in a dynamic equilibrium of various conformations with beta sheets that aggregate as oligomers or larger structures. The misfolding of betaamyloid peptide is involved in its accumulation. On the other hand, various species that exist in the cell environment can affect the structure of beta-amyloid peptides. background: The accumulation of beta-amyloid peptide is one of the effective mechanisms in creating amyloid plaques in nerve cells. These plaques are responsible for causing Alzheimer's disease Aims: This study aimed to study the interaction of truncated forms of beta-amyloid peptide with human albumin serum protein. objective: Interaction of beta-amyloid peptide with other proteins is effective in causing Alzheimer's disease. These include interactions between beta-amyloid and cell surface proteins such as prions and extracellular proteins such as clusterins and human serum albumin (HSA). Because HSA concentrations are higher than other proteins, more than half of the interaction of beta-amyloid with proteins is related to interaction with this protein. Interaction of HSA with beta-amyloid somewhat reduces the aggregation of beta amyloid. However, due to the diversity of beta-amyloid peptides with different lengths, the mechanism of their interaction with HSA has not been well understood. In this work, the interaction of C-terminal truncated beta-amyloid peptides with HSA has been investigated. Objective: Interaction of beta-amyloid peptide with other proteins is effective in causing Alzheimer's disease. These include interactions between beta-amyloid and cell surface proteins, such as prions and extracellular proteins, such as clusterins and human serum albumin (HSA). As HSA concentrations are higher than other proteins, more than half of the interaction of beta-amyloid with proteins is related to interaction with this protein. Interaction of HSA with beta-amyloid reduces the aggregation of beta-amyloid. However, due to the diversity of beta-amyloid peptides with different lengths, the mechanism of their interaction with HSA has not been well understood. In this work, the interaction of C-terminal truncated beta-amyloid peptides with HSA has been investigated. Method: The C-terminal truncated forms of beta-amyloid peptides, Aβ1 − 26, Aβ1 − 30, and Aβ1 − 36 and Aβ1 − 40, were designed in silico. Docking between these truncated peptides was performed with serum albumin. A molecular dynamics simulation of the interaction of designed peptides with serum albumin was also performed. Results and Discussion
{"title":"Interaction of C-terminal Truncated Beta-amyloid Peptides with Human Serum Albumin","authors":"Diba Aslani Firozabadi, Mohammad Reza Bozorgmehr, S. Ali Beiramabadi, Sharareh Mohseni","doi":"10.2174/0115701646243074231113071548","DOIUrl":"https://doi.org/10.2174/0115701646243074231113071548","url":null,"abstract":"Background: The formation of plaque from protein fibrils is the major source of diseases, such as Alzheimer's and Prion diseases. Amyloid beta (Aβ) is a peptide with different lengths, which is one of the main components of the plaque in the brain of people with Alzheimer's. Of the amyloid beta of various lengths in the brain cells plaque, beta-amyloid with 40 amino acids (Aβ1- 40) is more abundant than the rest. Aβ monomers are in a dynamic equilibrium of various conformations with beta sheets that aggregate as oligomers or larger structures. The misfolding of betaamyloid peptide is involved in its accumulation. On the other hand, various species that exist in the cell environment can affect the structure of beta-amyloid peptides. background: The accumulation of beta-amyloid peptide is one of the effective mechanisms in creating amyloid plaques in nerve cells. These plaques are responsible for causing Alzheimer's disease Aims: This study aimed to study the interaction of truncated forms of beta-amyloid peptide with human albumin serum protein. objective: Interaction of beta-amyloid peptide with other proteins is effective in causing Alzheimer's disease. These include interactions between beta-amyloid and cell surface proteins such as prions and extracellular proteins such as clusterins and human serum albumin (HSA). Because HSA concentrations are higher than other proteins, more than half of the interaction of beta-amyloid with proteins is related to interaction with this protein. Interaction of HSA with beta-amyloid somewhat reduces the aggregation of beta amyloid. However, due to the diversity of beta-amyloid peptides with different lengths, the mechanism of their interaction with HSA has not been well understood. In this work, the interaction of C-terminal truncated beta-amyloid peptides with HSA has been investigated. Objective: Interaction of beta-amyloid peptide with other proteins is effective in causing Alzheimer's disease. These include interactions between beta-amyloid and cell surface proteins, such as prions and extracellular proteins, such as clusterins and human serum albumin (HSA). As HSA concentrations are higher than other proteins, more than half of the interaction of beta-amyloid with proteins is related to interaction with this protein. Interaction of HSA with beta-amyloid reduces the aggregation of beta-amyloid. However, due to the diversity of beta-amyloid peptides with different lengths, the mechanism of their interaction with HSA has not been well understood. In this work, the interaction of C-terminal truncated beta-amyloid peptides with HSA has been investigated. Method: The C-terminal truncated forms of beta-amyloid peptides, Aβ1 − 26, Aβ1 − 30, and Aβ1 − 36 and Aβ1 − 40, were designed in silico. Docking between these truncated peptides was performed with serum albumin. A molecular dynamics simulation of the interaction of designed peptides with serum albumin was also performed. Results and Discussion","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138514629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-27DOI: 10.2174/0115701646244648231014153217
Farideh Ghalamfarsa, Amir Savardashtaki, Cambyz Irajie, Amir Emami, Navid Nezafat, Younes Ghasemi
Background: Chlamydiasis is a widespread bacterial infection in the world. Serological tests are expensive, and in addition, intrinsic antigens can cause cross-reactions and make the diagnosis process difficult. Multi-epitope protein antigens are novel and potential diagnostic markers that have the capability of more accurate and cheaper diagnosis. Therefore, in this study, the main goal is to design a new protein vaccine, including multiple epitopes of B cells with dominant immunity from three proteins named MOMP, ompA and Pgp3D from C. trachomatis Methods: The amino acid sequences were obtained from the UniProt database. The areas with the highest antigenicity were identified using the EMBOSS server. Linear B cell epitopes were determined using BCPRED, ABCpred, and Bepipred servers. Epitopes with the highest antigenicity were connected using the EAAAK linker. Results: Two epitopes from MOMP, two from ompA, and one from Pgp3D were selected. These epitopes were connected to each other with the EAAAK linker. Three residues (0.592), 16 residues (0.76), 36 residues (0.578), and 37 residues (0.734) were obtained from the prediction of the spatial structure of the B cell multiple epitopes designed with ElliPro. Model 1 of RaptorX was selected as the best structure. In this model, the ERRAT quality, ProSA-web z-score, and Verify3D were 83.1169, - 5.17 and 84.62% with PASS score, respectively. Moreover, the Ramachandran plot showed that 86.093% of the amino acid residues were located in the favored region. To achieve the highest level of protein expression, the designed multi-epitope reverse-translated with the Genscript server and was cloned in E. coli. The highest level of expression was achieved, and a CAI score of 0.91 was reported. The gene GC content was 51.98%, and the contribution of low-frequency codons was 0%. Conclusion: The results confirmed that the designed construct could identify C. trachomatis with high sensitivity and specificity in serum samples of patients with chlamydiasis. However, further experimental studies are needed for final confirmation.
{"title":"Developing Multi-epitope Antigen Construct from Immunodominant Proteins for Serological Diagnosis of Chlamydia trachomatis: An In Silico Approach","authors":"Farideh Ghalamfarsa, Amir Savardashtaki, Cambyz Irajie, Amir Emami, Navid Nezafat, Younes Ghasemi","doi":"10.2174/0115701646244648231014153217","DOIUrl":"https://doi.org/10.2174/0115701646244648231014153217","url":null,"abstract":"Background: Chlamydiasis is a widespread bacterial infection in the world. Serological tests are expensive, and in addition, intrinsic antigens can cause cross-reactions and make the diagnosis process difficult. Multi-epitope protein antigens are novel and potential diagnostic markers that have the capability of more accurate and cheaper diagnosis. Therefore, in this study, the main goal is to design a new protein vaccine, including multiple epitopes of B cells with dominant immunity from three proteins named MOMP, ompA and Pgp3D from C. trachomatis Methods: The amino acid sequences were obtained from the UniProt database. The areas with the highest antigenicity were identified using the EMBOSS server. Linear B cell epitopes were determined using BCPRED, ABCpred, and Bepipred servers. Epitopes with the highest antigenicity were connected using the EAAAK linker. Results: Two epitopes from MOMP, two from ompA, and one from Pgp3D were selected. These epitopes were connected to each other with the EAAAK linker. Three residues (0.592), 16 residues (0.76), 36 residues (0.578), and 37 residues (0.734) were obtained from the prediction of the spatial structure of the B cell multiple epitopes designed with ElliPro. Model 1 of RaptorX was selected as the best structure. In this model, the ERRAT quality, ProSA-web z-score, and Verify3D were 83.1169, - 5.17 and 84.62% with PASS score, respectively. Moreover, the Ramachandran plot showed that 86.093% of the amino acid residues were located in the favored region. To achieve the highest level of protein expression, the designed multi-epitope reverse-translated with the Genscript server and was cloned in E. coli. The highest level of expression was achieved, and a CAI score of 0.91 was reported. The gene GC content was 51.98%, and the contribution of low-frequency codons was 0%. Conclusion: The results confirmed that the designed construct could identify C. trachomatis with high sensitivity and specificity in serum samples of patients with chlamydiasis. However, further experimental studies are needed for final confirmation.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136316945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Cold exposure can induce inflammation-related injury in lung tissue, but the exact mechanism is still unclear. Objective: The study aimed to clarify the proteomic characteristics of lung tissue under cold exposure. Methods: Forty mice were randomly equally divided into a control group and a model group. The model group was exposed to - 20 °C for two weeks (4 hours per day), while the control group was maintained at 22 ± 2 °C. H&E staining and ELISA were used to verify the injury of lung tissue. Furthermore, a quantitative analysis of the overall proteome in the lung of mice exposed to cold stress was conducted by using LC-MS/MS. 15 differentially expressed proteins were selected for PRM validation. Results: According to our results, cold exposure induced lung injury, and the expressions of 151 proteins were upregulated and those of 95 proteins were downregulated. Bioinformatics analysis showed that differentially expressed proteins were associated with tricarboxylic acid cycle, fat metabolism, glycolysis, and oxidative phosphorylation. The expression of gabra2, Klkb1, and complement-related proteins was significantly upregulated. The results of PRM validation were consistent with those of proteomics. Conclusion: We found changes in glycolysis, gabra2, Klkb1, and the complement system in the lung tissue of cold-stressed mice, which may play an important role in cold stress-induced lung injury
{"title":"Effects of Chronic Cold Exposure on Proteomics of Lung Tissue in Mice","authors":"Moyou Li, Ying Liu, Xiaoye Tian, Zhuojun Wang, Feng Cheng, Xiao Han, Zheyuan Chen, Ruihang Ma, Hongxu Jin","doi":"10.2174/0115701646245422231013072302","DOIUrl":"https://doi.org/10.2174/0115701646245422231013072302","url":null,"abstract":"Background: Cold exposure can induce inflammation-related injury in lung tissue, but the exact mechanism is still unclear. Objective: The study aimed to clarify the proteomic characteristics of lung tissue under cold exposure. Methods: Forty mice were randomly equally divided into a control group and a model group. The model group was exposed to - 20 °C for two weeks (4 hours per day), while the control group was maintained at 22 ± 2 °C. H&E staining and ELISA were used to verify the injury of lung tissue. Furthermore, a quantitative analysis of the overall proteome in the lung of mice exposed to cold stress was conducted by using LC-MS/MS. 15 differentially expressed proteins were selected for PRM validation. Results: According to our results, cold exposure induced lung injury, and the expressions of 151 proteins were upregulated and those of 95 proteins were downregulated. Bioinformatics analysis showed that differentially expressed proteins were associated with tricarboxylic acid cycle, fat metabolism, glycolysis, and oxidative phosphorylation. The expression of gabra2, Klkb1, and complement-related proteins was significantly upregulated. The results of PRM validation were consistent with those of proteomics. Conclusion: We found changes in glycolysis, gabra2, Klkb1, and the complement system in the lung tissue of cold-stressed mice, which may play an important role in cold stress-induced lung injury","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134910347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-25DOI: 10.2174/0115701646253656231013141100
Xiaowu Fan
Background: Non-small cell lung cancer (NSCLC) consists of a class of heterogeneous diseases. Objective: LncRNAs are exceedingly implicated in the pathogenesis of NSCLC. Herein, the current study set out to illustrate the molecular mechanism of SH3BP5-AS1 in NSCLC cells. Methods: SH3BP5-AS1 expression in clinical NSCLC tissues and its impact on prognosis were analyzed by bioinformatics database. SH3BP5-AS1 expression patterns in NSCLC cell lines (A549/H1299/H1975/H460) and human normal lung epithelial cell lines (BEAS-2B) were examined by RT-qPCR. SH3BP5-AS1 was overexpressed in A549 or silenced in H1975 cells through transfection to assess its effect on proliferation, cell cycle distribution, and apoptosis, apoptosisrelated protein (Cleaved Caspase-3, Bax, Bcl-2) levels, invasive, migratory, and healing capacity through CCK-8, colony formation assay, flow cytometry, Western blot, Transwell, and cell scratch test. Results: SH3BP5-AS1 was under-expressed in NSCLC clinical tissues, and NSCLC patients with low SH3BP5-AS1 expression showed poor prognosis. A549/H1299/H1975/H460 cells had reduced levels of SH3BP5-AS1, with the relative level lowest/highest expression in A549/H1975 cells, respectively. SH3BP5-AS1 overexpression repressed A549 cell proliferation, slowed down cell cycle progression, enhanced apoptosis, elevated Cleared Caspase-3, Bax, suppressed Bcl-2 protein levels, and inhibited migratory, invasive, and scratch healing capacities, while SH3BP5-AS1 silencing brought about the opposite results in H1975 cells. Conclusion: SH3BP5-AS1 could suppress NSCLC cell proliferation, slow down cell cycle progression, stimulate apoptosis, and limit invasion and migration.
{"title":"LncRNA SH3BP5-AS1 Regulates the Proliferation and Cell Cycle of Non- Small Cell Lung Cancer Cells","authors":"Xiaowu Fan","doi":"10.2174/0115701646253656231013141100","DOIUrl":"https://doi.org/10.2174/0115701646253656231013141100","url":null,"abstract":" Background: Non-small cell lung cancer (NSCLC) consists of a class of heterogeneous diseases. Objective: LncRNAs are exceedingly implicated in the pathogenesis of NSCLC. Herein, the current study set out to illustrate the molecular mechanism of SH3BP5-AS1 in NSCLC cells. Methods: SH3BP5-AS1 expression in clinical NSCLC tissues and its impact on prognosis were analyzed by bioinformatics database. SH3BP5-AS1 expression patterns in NSCLC cell lines (A549/H1299/H1975/H460) and human normal lung epithelial cell lines (BEAS-2B) were examined by RT-qPCR. SH3BP5-AS1 was overexpressed in A549 or silenced in H1975 cells through transfection to assess its effect on proliferation, cell cycle distribution, and apoptosis, apoptosisrelated protein (Cleaved Caspase-3, Bax, Bcl-2) levels, invasive, migratory, and healing capacity through CCK-8, colony formation assay, flow cytometry, Western blot, Transwell, and cell scratch test. Results: SH3BP5-AS1 was under-expressed in NSCLC clinical tissues, and NSCLC patients with low SH3BP5-AS1 expression showed poor prognosis. A549/H1299/H1975/H460 cells had reduced levels of SH3BP5-AS1, with the relative level lowest/highest expression in A549/H1975 cells, respectively. SH3BP5-AS1 overexpression repressed A549 cell proliferation, slowed down cell cycle progression, enhanced apoptosis, elevated Cleared Caspase-3, Bax, suppressed Bcl-2 protein levels, and inhibited migratory, invasive, and scratch healing capacities, while SH3BP5-AS1 silencing brought about the opposite results in H1975 cells. Conclusion: SH3BP5-AS1 could suppress NSCLC cell proliferation, slow down cell cycle progression, stimulate apoptosis, and limit invasion and migration.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138816628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-20DOI: 10.2174/0115701646256131231013111220
Zhenling Ma, Lei Wang, Kun Cheng, Guozhen Xing, Jiajia Zhang, Wei Liu
abstract: Introduction: Ovarian cancer is a common gynecological malignancy. It is one of the leading causes of death among women worldwide. The incidence of ovarian cancer ranks third, and mortality is the first among gynecological malignant tumors. CCL2 (Chemokine C-C motif Ligand 2) is associated with the progression of a variety of tumors, including ovarian cancer. However, the mechanism of CCL2 in A2780 cell growth has not been clarified. Method: In this study, we found that exogenous CCL2 promoted A2780 cell activity. RNA sequencing was used to identify the transcriptomic changes in CCL2-treated A2780 cells. Based on a p-value less than 0.05 and |log2 Fold Change| greater than 1, 190 differentially expressed genes were selected. Of these genes, 82 were observed to be upregulated and 108 downregulated. Result: The GO (gene ontology) analysis of differentially expressed genes was used to identify the underlying functions and biological processes. In addition, the expression of the topmost upregulated genes was verified by qPCR. Conclusion: This work may provide new markers and reveal the underlying mechanism of exogenous CCL2 in A2780 cell proliferation. other: /
{"title":"RNA Sequencing of A2780 Cells Treated with CCL2 Identified Genes Associated with A2780 Cell Growth","authors":"Zhenling Ma, Lei Wang, Kun Cheng, Guozhen Xing, Jiajia Zhang, Wei Liu","doi":"10.2174/0115701646256131231013111220","DOIUrl":"https://doi.org/10.2174/0115701646256131231013111220","url":null,"abstract":"abstract: Introduction: Ovarian cancer is a common gynecological malignancy. It is one of the leading causes of death among women worldwide. The incidence of ovarian cancer ranks third, and mortality is the first among gynecological malignant tumors. CCL2 (Chemokine C-C motif Ligand 2) is associated with the progression of a variety of tumors, including ovarian cancer. However, the mechanism of CCL2 in A2780 cell growth has not been clarified. Method: In this study, we found that exogenous CCL2 promoted A2780 cell activity. RNA sequencing was used to identify the transcriptomic changes in CCL2-treated A2780 cells. Based on a p-value less than 0.05 and |log2 Fold Change| greater than 1, 190 differentially expressed genes were selected. Of these genes, 82 were observed to be upregulated and 108 downregulated. Result: The GO (gene ontology) analysis of differentially expressed genes was used to identify the underlying functions and biological processes. In addition, the expression of the topmost upregulated genes was verified by qPCR. Conclusion: This work may provide new markers and reveal the underlying mechanism of exogenous CCL2 in A2780 cell proliferation. other: /","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135666282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-27DOI: 10.2174/1570164620666230727104921
R. Vitorino, Luís Perpétuo, H. Rocha, R. Ferreira, B. Manadas, Francisco Amado, Sofia Guedes, Atef Mahmoud Mannaa, J. Vialaret, C. Hirtz
Dry blood spots (DBS) have been used in combination with liquid chromatography-mass spectrometry for targeted proteomics to identify sensitive and specific novel biomarkers. DBS presents several advantages over other traditional blood sampling methods. This re-view discusses the past, present and future of the technology, focusing on studies with clin-ical and population relevance. Arguments for and against DBS are presented by discussing technological advances, particularly those related to mass spectrometry (MS) and multiple reaction monitoring (MRM), sample preparation issues, disease biomarkers, pharmacoki-netics, and pharmacodynamics. There will be a focus on proteomic studies that rely on DBS as a sampling method. In this context, numerous studies on the diagnosis and treatment of several diseases. To date, proteomic reports of studies using DBS have shown that DBS can facilitate diagnosis and prognosis. DBS offers several advantages that make it a viable op-tion for many fields. Moreover, some of its disadvantages can be easily overcome through automation to increase reproducibility and reduce protocol variability and standardization of parameters such as the volume of sample used. Within this context, here we propose to review the advantages and disadvantages of using DBS for blood proteomics and provide an understanding of how current DBS-based protocols are being conducted for future stand-ardization and protocol optimization.
{"title":"Current understanding of dried spots platform for blood proteomics","authors":"R. Vitorino, Luís Perpétuo, H. Rocha, R. Ferreira, B. Manadas, Francisco Amado, Sofia Guedes, Atef Mahmoud Mannaa, J. Vialaret, C. Hirtz","doi":"10.2174/1570164620666230727104921","DOIUrl":"https://doi.org/10.2174/1570164620666230727104921","url":null,"abstract":"\u0000\u0000Dry blood spots (DBS) have been used in combination with liquid chromatography-mass spectrometry for targeted proteomics to identify sensitive and specific novel biomarkers. DBS presents several advantages over other traditional blood sampling methods. This re-view discusses the past, present and future of the technology, focusing on studies with clin-ical and population relevance. Arguments for and against DBS are presented by discussing technological advances, particularly those related to mass spectrometry (MS) and multiple reaction monitoring (MRM), sample preparation issues, disease biomarkers, pharmacoki-netics, and pharmacodynamics. There will be a focus on proteomic studies that rely on DBS as a sampling method. In this context, numerous studies on the diagnosis and treatment of several diseases. To date, proteomic reports of studies using DBS have shown that DBS can facilitate diagnosis and prognosis. DBS offers several advantages that make it a viable op-tion for many fields. Moreover, some of its disadvantages can be easily overcome through automation to increase reproducibility and reduce protocol variability and standardization of parameters such as the volume of sample used. Within this context, here we propose to review the advantages and disadvantages of using DBS for blood proteomics and provide an understanding of how current DBS-based protocols are being conducted for future stand-ardization and protocol optimization.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73676095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-17DOI: 10.2174/1570164620666230717114018
L. Hernández-Ochoa, M. Martínez-Ceniceros, L. O. Nevarez-Prado, David Neder‐Suárez, F. Sandoval-Salas, L. Rodríguez-Valdez, L. Landeros-Martínez, Karla Bernal-Alvarado
Ricin is the most toxic protein known. It is part of the ribosome-inactivating proteins, RIPs, type 2, which has generated importance in his research; it is possible to detoxify this protein with phenolic compounds; however, it is essential to understand how this detoxification occurs. To analyze using electrophoresis, UV-visible spectroscopy, and high-performance liquid chromatography (HPLC) the protein ricin with the flavonol quercetin, understanding the detoxification process. The UV-visible analysis was performed on both the supernatant and the precipitate of the samples; these results were analyzed using one-factor analysis of variance (ANOVA) and a Tukey test with a significance level of 0.05. 34.9 μg / mL of total protein and 4.2 μg / mL of ricin were obtained in the extraction method. Eight interactions were carried out, and all presented precipitation, observing through the electrophoresis technique a decrease in the bands corresponding to the protein; these results were analyzed with HPLC observing a decrease in the size of the area of the peaks in the chromatograms. The results obtained in this study suggest an agglomeration of the protein, generating a precipitate that could benefit the protein's inactivation as a detoxification process.
蓖麻毒素是已知毒性最强的蛋白质。它是核糖体失活蛋白(RIPs, type 2)的一部分，在他的研究中产生了重要意义;用酚类化合物来解毒这种蛋白质是可能的;然而，有必要了解这种解毒是如何发生的。采用电泳、紫外可见光谱和高效液相色谱分析蓖麻毒素蛋白与槲皮素黄酮醇的解毒过程。对样品的上清液和沉淀物进行紫外可见分析;采用单因素方差分析(ANOVA)和Tukey检验对提取结果进行分析，总蛋白含量显著水平为0.05.34.9 μg / mL，蓖麻毒素含量显著水平为4.2 μg / mL。共进行了8次相互作用，均出现沉淀，通过电泳技术观察到蛋白质对应的条带减少;用高效液相色谱法分析这些结果，观察到色谱峰面积的大小减小。在这项研究中获得的结果表明，蛋白质的团聚，产生沉淀，可能有利于蛋白质的失活作为一个解毒过程。
{"title":"Evaluation of the interaction between ricin protein and quercetin using different analytical methods","authors":"L. Hernández-Ochoa, M. Martínez-Ceniceros, L. O. Nevarez-Prado, David Neder‐Suárez, F. Sandoval-Salas, L. Rodríguez-Valdez, L. Landeros-Martínez, Karla Bernal-Alvarado","doi":"10.2174/1570164620666230717114018","DOIUrl":"https://doi.org/10.2174/1570164620666230717114018","url":null,"abstract":"\u0000\u0000Ricin is the most toxic protein known. It is part of the ribosome-inactivating proteins, RIPs, type 2, which has generated importance in his research; it is possible to detoxify this protein with phenolic compounds; however, it is essential to understand how this detoxification occurs.\u0000To analyze using electrophoresis, UV-visible spectroscopy, and high-performance liquid chromatography (HPLC) the protein ricin with the flavonol quercetin, understanding the detoxification process.\u0000\u0000\u0000\u0000The UV-visible analysis was performed on both the supernatant and the precipitate of the samples; these results were analyzed using one-factor analysis of variance (ANOVA) and a Tukey test with a significance level of 0.05.\u0000\u0000\u0000\u000034.9 μg / mL of total protein and 4.2 μg / mL of ricin were obtained in the extraction method. Eight interactions were carried out, and all presented precipitation, observing through the electrophoresis technique a decrease in the bands corresponding to the protein; these results were analyzed with HPLC observing a decrease in the size of the area of the peaks in the chromatograms.\u0000\u0000\u0000\u0000The results obtained in this study suggest an agglomeration of the protein, generating a precipitate that could benefit the protein's inactivation as a detoxification process.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83189338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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