1
|
Yuan M, Hu X, Xing W, Wu X, Pu C, Guo W, Zhu X, Yao M, Ao L, Li Z, Xu X. B2M is a Biomarker Associated With Immune Infiltration In High Altitude Pulmonary Edema. Comb Chem High Throughput Screen 2024; 27:168-185. [PMID: 37165489 PMCID: PMC10804239 DOI: 10.2174/1386207326666230510095840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/15/2023] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND High altitude pulmonary edema (HAPE) is a serious mountain sickness with certain mortality. Its early diagnosis is very important. However, the mechanism of its onset and progression is still controversial. AIM This study aimed to analyze the HAPE occurrence and development mechanism and search for prospective biomarkers in peripheral blood. METHODS The difference genes (DEGs) of the Control group and the HAPE group were enriched by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and then GSEA analysis was performed. After identifying the immune-related hub genes, QPCR was used to verify and analyze the hub gene function and diagnostic value with single-gene GSEA and ROC curves, and the drugs that acted on the hub gene was found in the CTD database. Immune infiltration and its association with the hub genes were analyzed using CIBERSORT. Finally, WGCNA was employed to investigate immune invasion cells' significantly related gene modules, following enrichment analysis of their GO and KEGG. RESULTS The dataset enrichment analysis, immune invasion analysis and WGCNA analysis showed that the occurrence and early progression of HAPE were unrelated to inflammation. The hub genes associated with immunity obtained with MCODE algorithm of Cytoscape were JAK2 and B2M.. RT-qPCR and ROC curves confirmed that the hub gene B2M was a specific biomarker of HAPE and had diagnostic value, and single-gene GSEA analysis confirmed that it participated in MHC I molecule-mediated antigen presentation ability decreased, resulting in reduced immunity. CONCLUSION Occurrence and early progression of high altitude pulmonary edema may not be related to inflammation. B2M may be a new clinical potential biomarker for HAPE for early diagnosis and therapeutic evaluation as well as therapeutic targets, and its decrease may be related to reduced immunity due to reduced ability of MCH I to participate in antigen submission.
Collapse
Affiliation(s)
- Mu Yuan
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Xueting Hu
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Wei Xing
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Xiaofeng Wu
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Chengxiu Pu
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Wei Guo
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Xiyan Zhu
- Department of Military Traffic Injury Prevention and Treatment, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Mengwei Yao
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Luoquan Ao
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Zhan Li
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| | - Xiang Xu
- Department of Stem Cell and Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
- Central Laboratory, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University, 400010, Chongqing, China
| |
Collapse
|
2
|
Gupta A, Pathak S, Varshney R, Ahmad Y, Khurana P. HighAltitudeOmicsDB, an integrated resource for high-altitude associated genes and proteins, networks and semantic-similarities. Sci Rep 2023; 13:9307. [PMID: 37291174 PMCID: PMC10250374 DOI: 10.1038/s41598-023-35792-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
Millions of people worldwide visit, live or work in the hypoxic environment encountered at high altitudes and it is important to understand the biomolecular responses to this stress. This would help design mitigation strategies for high altitude illnesses. In spite of a number of studies spanning over 100 years, still the complex mechanisms controlling acclimatization to hypoxia remain largely unknown. To identify potential diagnostic, therapeutic and predictive markers for HA stress, it is important to comprehensively compare and analyse these studies. Towards this goal, HighAltitudeOmicsDB is a unique resource that provides a comprehensive, curated, user-friendly and detailed compilation of various genes/proteins which have been experimentally validated to be associated with various HA conditions, their protein-protein interactions (PPIs) and gene ontology (GO) semantic similarities. For each database entry, HighAltitudeOmicsDB additionally stores the level of regulation (up/down-regulation), fold change, study control group, duration and altitude of exposure, tissue of expression, source organism, level of hypoxia, method of experimental validation, place/country of study, ethnicity, geographical location etc. The database also collates information on disease and drug association, tissue-specific expression level, GO and KEGG pathway associations. The web resource is a unique server platform that offers interactive PPI networks and GO semantic similarity matrices among the interactors.These unique features help to offer mechanistic insights into the disease pathology. Hence, HighAltitudeOmicsDBis a unique platform for researchers working in this area to explore, fetch, compare and analyse HA-associated genes/proteins, their PPI networks, and GO semantic similarities. The database is available at http://www.altitudeomicsdb.in .
Collapse
Affiliation(s)
- Apoorv Gupta
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, New Delhi, 110054, India
| | - Sandhya Pathak
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, New Delhi, 110054, India
| | - Rajeev Varshney
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, New Delhi, 110054, India
| | - Yasmin Ahmad
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, New Delhi, 110054, India
| | - Pankaj Khurana
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, New Delhi, 110054, India.
| |
Collapse
|
3
|
Li C, Wu Y, Chen B, Cai Y, Guo J, Leonard AS, Kalds P, Zhou S, Zhang J, Zhou P, Gan S, Jia T, Pu T, Suo L, Li Y, Zhang K, Li L, Purevdorj M, Wang X, Li M, Wang Y, Liu Y, Huang S, Sonstegard T, Wang MS, Kemp S, Pausch H, Chen Y, Han JL, Jiang Y, Wang X. Markhor-derived Introgression of a Genomic Region Encompassing PAPSS2 Confers High-altitude Adaptability in Tibetan Goats. Mol Biol Evol 2022; 39:6830663. [PMID: 36382357 PMCID: PMC9728798 DOI: 10.1093/molbev/msac253] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the genetic mechanism of how animals adapt to extreme conditions is fundamental to determine the relationship between molecular evolution and changing environments. Goat is one of the first domesticated species and has evolved rapidly to adapt to diverse environments, including harsh high-altitude conditions with low temperature and poor oxygen supply but strong ultraviolet radiation. Here, we analyzed 331 genomes of domestic goats and wild caprid species living at varying altitudes (high > 3000 m above sea level and low < 1200 m), along with a reference-guided chromosome-scale assembly (contig-N50: 90.4 Mb) of a female Tibetan goat genome based on PacBio HiFi long reads, to dissect the genetic determinants underlying their adaptation to harsh conditions on the Qinghai-Tibetan Plateau (QTP). Population genomic analyses combined with genome-wide association studies (GWAS) revealed a genomic region harboring the 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (PAPSS2) gene showing strong association with high-altitude adaptability (PGWAS = 3.62 × 10-25) in Tibetan goats. Transcriptomic data from 13 tissues revealed that PAPSS2 was implicated in hypoxia-related pathways in Tibetan goats. We further verified potential functional role of PAPSS2 in response to hypoxia in PAPSS2-deficient cells. Introgression analyses suggested that the PAPSS2 haplotype conferring the high-altitude adaptability in Tibetan goats originated from a recent hybridization between goats and a wild caprid species, the markhor (Capra falconeri). In conclusion, our results uncover a hitherto unknown contribution of PAPSS2 to high-altitude adaptability in Tibetan goats on QTP, following interspecific introgression and natural selection.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Peter Kalds
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shiwei Zhou
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China,College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Jingchen Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Shangqu Gan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, China
| | - Tianchun Pu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, China
| | - Langda Suo
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Yan Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ke Zhang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Lan Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Myagmarsuren Purevdorj
- Lab of Animal Genetics and Animal Reproductive Technology, Research Institute of Animal Husbandry, Mongolian University of Life Sciences, Ulaanbaatar 17024, Mongolia
| | - Xihong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ming Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yu Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yao Liu
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shuhong Huang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 94720
| | - Stephen Kemp
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 30709-00100, Kenya
| | - Hubert Pausch
- Animal Genomics, ETH Zürich, 8092 Zürich, Switzerland
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Yu Jiang
- Corresponding authors: E-mails: ; ;
| | | |
Collapse
|
4
|
Singh T, Banerjee P, Uditi, Kumari S, Chopra A, Singh N, Qamar I. Expression of Regucalcin, a calcium-binding protein is regulated by hypoxia-inducible factor-1α. Life Sci 2022; 292:120278. [PMID: 35041836 DOI: 10.1016/j.lfs.2021.120278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/18/2021] [Accepted: 12/26/2021] [Indexed: 01/16/2023]
Abstract
Regucalcin (RGN) regulates intracellular Ca2+ homeostasis and the activity of several proteins involved in intracellular signaling pathways, which highlights its importance in cell biology. Regucalcin has cytoprotective effects reducing intracellular levels of oxidative stress, also playing a crucial role in the control of cell survival and apoptosis. In an effort to assess its gene regulation, we initially identified the expression of Regucalcin in rat lungs treated with hypoxia at various time points. Previously, HIF-1α expression was also reported to be upregulated in hypoxia. Interestingly hypoxic induced Regucalcin expression in a fashion similar to that of HIF-1α expression in rat lungs. Sequence analysis of the Regucalcin promoter region revealed the presence of putative HRE binding motifs. Further analysis of the 1 kb Regucalcin promoter region with 5' deletion and point mutants of HRE binding motif showed that the HRE binding site was critical for high promoter activity. In addition, HIF-1α protein binds directly to the HRE binding motifs within the Regucalcin promoter in-vivo, and regulates Regucalcin gene expression. All together, these findings suggest that Regucalcin is the novel target gene of HIF-1α and that Regucalcin gene expression in hypoxia may be regulated by the control of HIF-1α expression.
Collapse
Affiliation(s)
- Tripti Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Pallabi Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Uditi
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Sarita Kumari
- Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Anita Chopra
- Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India.
| |
Collapse
|
5
|
Patel JC, Singh A, Tulswani R, Sharma YK, Khurana P, Ragumani S. Identification of VEGFA-centric temporal hypoxia-responsive dynamic cardiopulmonary network biomarkers. Life Sci 2021; 281:119718. [PMID: 34147483 DOI: 10.1016/j.lfs.2021.119718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
AIMS Hypoxia, a pathophysiological condition, is profound in several cardiopulmonary diseases (CPD). Every individual's lethality to a hypoxia state differs in terms of hypoxia exposure time, dosage units and dependent on the individual's genetic makeup. Most of the proposed markers for CPD were generally aim to distinguish disease samples from normal samples. Although, as per the 2018 GOLD guidelines, clinically useful biomarkers for several cardio pulmonary disease patients in stable condition have yet to be identified. We attempt to address these key issues through the identification of Dynamic Network Biomarkers (DNB) to detect hypoxia induced early warning signals of CPD before the catastrophic deterioration. MATERIALS AND METHODS The human microvascular endothelial tissues microarray datasets (GSE11341) of lung and cardiac expose to hypoxia (1% O2) for 3, 24 and 48 h were retrieved from the public repository. The time dependent differentially expressed genes were subjected to tissue specificity and promoter analysis to filtrate the noise levels in the networks and to dissect the tissue specific hypoxia induced genes. These filtered out genes were used to construct the dynamic segmentation networks. The hypoxia induced dynamic differentially expressed genes were validated in the lung and heart tissues of male rats. These rats were exposed to hypobaric hypoxia (simulated altitude of 25,000 or PO2 - 282 mm of Hg) progressively for 3, 24 and 48 h. KEY FINDINGS To identify the temporal key genes regulated in hypoxia, we ranked the dominant genes based on their consolidated topological features from tissue specific networks, time dependent networks and dynamic networks. Overall topological ranking described VEGFA as a single node dynamic hub and strongly communicated with tissue specific genes to carry forward their tissue specific information. We named this type of VEGFAcentric dynamic networks as "V-DNBs". As a proof of principle, our methodology helped us to identify the V-DNBs specific for lung and cardiac tissues namely V-DNBL and V-DNBC respectively. SIGNIFICANCE Our experimental studies identified VEGFA, SLC2A3, ADM and ENO2 as the minimum and sufficient candidates of V-DNBL. The dynamic expression patterns could be readily exploited to capture the pre disease state of hypoxia induced pulmonary vascular remodelling. Whereas in V-DNBC the minimum and sufficient candidates are VEGFA, SCL2A3, ADM, NDRG1, ENO2 and BHLHE40. The time dependent single node expansion indicates V-DNBC could also be the pre disease state pathological hallmark for hypoxia-associated cardiovascular remodelling. The network cross-talk and expression pattern between V-DNBL and V-DNBC are completely distinct. On the other hand, the great clinical advantage of V-DNBs for pre disease predictions, a set of samples during the healthy condition should suffice. Future clinical studies might further shed light on the predictive power of V-DNBs as prognostic and diagnostic biomarkers for CPD.
Collapse
Affiliation(s)
- Jai Chand Patel
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Ajeet Singh
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Rajkumar Tulswani
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Yogendra Kumar Sharma
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Pankaj Khurana
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Sugadev Ragumani
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India.
| |
Collapse
|
6
|
Modulation of lung cytoskeletal remodeling, RXR based metabolic cascades and inflammation to achieve redox homeostasis during extended exposures to lowered pO 2. Apoptosis 2021; 26:431-446. [PMID: 34002323 DOI: 10.1007/s10495-021-01679-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
Extended exposure to low pO2 has multiple effects on signaling cascades. Despite multiple exploratory studies, omics studies elucidating the signaling cascades essential for surviving extended low pO2 exposures are lacking. In this study, we simulated low pO2 (PB = 40 kPa; 7620 m) exposure in male Sprague-Dawley rats for 3, 7 and 14 days. Redox stress assays and proteomics based network biology were performed using lungs and plasma. We observed that redox homeostasis was achieved after day 3 of exposure. We investigated the causative events for this. Proteo-bioinformatics analysis revealed STAT3 to be upstream of lung cytoskeletal processes and systemic lipid metabolism (RXR) derived inflammatory processes, which were the key events. Thus, during prolonged low pO2 exposure, particularly those involving slowly decreasing pressures, redox homeostasis is achieved but energy metabolism is perturbed and this leads to an immune/inflammatory signaling impetus after third day of exposure. We found that an interplay of lung cytoskeletal elements, systemic energy metabolism and inflammatory proteins aid in achieving redox homeostasis and surviving extended low pO2 exposures. Qualitative perturbations to cytoskeletal stability and innate immunity/inflammation were also observed during extended low pO2 exposure in humans exposed to 14,000 ft for 7, 14 and 21 days.
Collapse
|
7
|
Paul S, Gangwar A, Bhargava K, Ahmad Y. D4F prophylaxis enables redox and energy homeostasis while preventing inflammation during hypoxia exposure. Biomed Pharmacother 2021; 133:111083. [PMID: 33378979 DOI: 10.1016/j.biopha.2020.111083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/18/2020] [Accepted: 11/28/2020] [Indexed: 02/02/2023] Open
Abstract
Apo-A1 is correlated with conditions like hyperlipidemia, cardiovascular diseases, high altitude pulmonary edema and etc. where hypoxia constitutes an important facet.Hypoxia causes oxidative stress, vaso-destructive and inflammatory outcomes.Apo-A1 is reported to have vasoprotective, anti-oxidative, anti-apoptotic, and anti-inflammatory effects. However, effects of Apo-A1 augmentation during hypoxia exposure are unknown.In this study, we investigated the effects of exogenously supplementing Apo-A1-mimetic peptide on SD rats during hypoxia exposure. For easing the processes of delivery, absorption and bio-availability, Apo-A1 mimetic peptide D4F was used. The rats were given 10 mg/kg BW dose (i.p.) of D4F for 7 days and then exposed to hypoxia. D4F was observed to attenuate both oxidative stress and inflammation during hypoxic exposure. D4F improved energy homeostasis during hypoxic exposure. D4F did not affect HIF-1a levels during hypoxia but increased MnSOD levels while decreasing CRP and Apo-B levels. D4F showed promise as a prophylactic against hypoxia exposure.
Collapse
Affiliation(s)
- Subhojit Paul
- Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi, 110054, India
| | - Anamika Gangwar
- Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi, 110054, India
| | - Kalpana Bhargava
- Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi, 110054, India
| | - Yasmin Ahmad
- Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi, 110054, India.
| |
Collapse
|
8
|
Sharma Kandel R, Mishra R, Gautam J, Alaref A, Hassan A, Jahan N. Patchy Vasoconstriction Versus Inflammation: A Debate in the Pathogenesis of High Altitude Pulmonary Edema. Cureus 2020; 12:e10371. [PMID: 33062494 PMCID: PMC7556690 DOI: 10.7759/cureus.10371] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
High altitude pulmonary edema (HAPE) occurs in individuals rapidly ascending at altitudes greater than 2,500 m within one week of arrival. HAPE is characterized by orthopnea, breathlessness at rest, cough, and pink frothy sputum. Several mechanisms to describe the pathophysiology of HAPE have been proposed in different kinds of literature where most of the mechanisms are reported to be activated before a drop in oxygen saturation levels. The majority of the current studies favor diffuse hypoxic pulmonary vasoconstriction (HPV) as a pathophysiological basis for HAPE. However, some of the studies described inflammation in the lungs and genetic basis as the pathophysiology of HAPE. So, there is a major disagreement regarding the exact pathophysiology of HAPE in the current literature, which raises a question as to what is the exact pathophysiology of HAPE. So, we reviewed 23 different articles which include clinical trials, review articles, randomized controlled trials (RCTs), and original research published from 2010 to 2020 to find out widely accepted pathophysiology of HAPE. In our study, we found out sympathetic stimulation, reduced nitric oxide (NO) bioavailability, increased endothelin, increased pulmonary artery systolic pressure (PASP) resulting in diffuse HPV, and reduced reabsorption of interstitial fluid to be the most important determinants for the development of HAPE. Similarly, with the evaluation of the role of inflammatory mediators like C-reactive protein (CRP) and interleukin (IL-6), we found out that inflammation in the lungs seems to modulate but not cause the process of development of HAPE. Genetic basis as evidenced by increased transcription of certain gene products seems to be another promising hypoxic change leading to HAPE. However, comprehensive studies are still needed to decipher the pathophysiology of HAPE in greater detail.
Collapse
Affiliation(s)
- Rajan Sharma Kandel
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Rohi Mishra
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Jeevan Gautam
- Neurology, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Amer Alaref
- Diagnostic Radiology, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA.,Diagnostic Radiology, Thunder Bay Regional Health Sciences Centre, Thunder Bay, CAN.,Diagnostic Imaging, Northern Ontario School of Medicine, Sudbury, CAN.,Breast Imaging, Thunder Bay Regional Health Sciences Centre/Linda Buchan Centre, Thunder Bay, CAN
| | - Abdallah Hassan
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Nusrat Jahan
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| |
Collapse
|
9
|
Ramos P, McCoy J, Wambier C, Shapiro J, Vañó‐Galvan S, Sinclair R, Goren A. Novel topical booster enhances follicular sulfotransferase activity in patients with androgenetic alopecia: a new strategy to improve minoxidil response. J Eur Acad Dermatol Venereol 2020; 34:e799-e800. [DOI: 10.1111/jdv.16645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/02/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Affiliation(s)
- P.M. Ramos
- Department of Dermatology and Radiotherapy São Paulo State University (UNESP) Botucatu SP Brazil
| | | | - C. Wambier
- Department of Dermatology The Warren Alpert Medical School Brown University Providence RI USA
| | - J. Shapiro
- The Ronald O. Perelman Department of Dermatology New York University School of Medicine New York NY USA
| | - S. Vañó‐Galvan
- Servício de Dermatología Hospital Universitario Ramón y Cajal Madrid Spain
| | - R. Sinclair
- Sinclair Dermatology Melbourne VIC Australia
| | | |
Collapse
|
10
|
Wan XL, Zhou ZL, Wang P, Zhou XM, Xie MY, Mei J, Weng J, Xi HT, Chen C, Wang ZY, Wang ZB. Small molecule proteomics quantifies differences between normal and fibrotic pulmonary extracellular matrices. Chin Med J (Engl) 2020; 133:1192-1202. [PMID: 32433051 PMCID: PMC7249707 DOI: 10.1097/cm9.0000000000000754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pulmonary fibrosis is a respiratory disease caused by the proliferation of fibroblasts and accumulation of the extracellular matrix (ECM). It is known that the lung ECM is mainly composed of a three-dimensional fiber mesh filled with various high-molecular-weight proteins. However, the small-molecular-weight proteins in the lung ECM and their differences between normal and fibrotic lung ECM are largely unknown. METHODS Healthy adult male Sprague-Dawley rats (Rattus norvegicus) weighing about 150 to 200 g were randomly divided into three groups using random number table: A, B, and C and each group contained five rats. The rats in Group A were administered a single intragastric (i.g.) dose of 500 μL of saline as control, and those in Groups B and C were administered a single i.g. dose of paraquat (PQ) dissolved in 500 μL of saline (20 mg/kg). After 2 weeks, the lungs of rats in Group B were harvested for histological observation, preparation of de-cellularized lung scaffolds, and proteomic analysis for small-molecular-weight proteins, and similar procedures were performed on Group C and A after 4 weeks. The differentially expressed small-molecular-weight proteins (DESMPs) between different groups and the subcellular locations were analyzed. RESULTS Of the 1626 small-molecular-weight proteins identified, 1047 were quantifiable. There were 97 up-regulated and 45 down-regulated proteins in B vs. A, 274 up-regulated and 31 down-regulated proteins in C vs. A, and 237 up-regulated and 28 down-regulated proteins identified in C vs. B. Both the up-regulated and down-regulated proteins in the three comparisons were mainly distributed in single-organism processes and cellular processes within biological process, cell and organelle within cellular component, and binding within molecular function. Further, more up-regulated than down-regulated proteins were identified in most sub-cellular locations. The interactions of DESMPs identified in extracellular location in all comparisons showed that serum albumin (Alb) harbored the highest degree of node (25), followed by prolyl 4-hydroxylase beta polypeptide (12), integrin β1 (10), apolipoprotein A1 (9), and fibrinogen gamma chain (9). CONCLUSIONS Numerous PQ-induced DESMPs were identified in de-cellularized lungs of rats by high throughput proteomics analysis. The DESMPs between the control and treatment groups showed diversity in molecular functions, biological processes, and pathways. In addition, the interactions of extracellular DESMPs suggested that the extracellular proteins Alb, Itgb1, Apoa1, P4hb, and Fgg in ECM could be potentially used as biomarker candidates for pulmonary fibrosis. These results provided useful information and new insights regarding pulmonary fibrosis.
Collapse
Affiliation(s)
- Xin-Long Wan
- Platform for Radiation Protection and Emergency Preparedness of Southern Zhejiang, School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Center for Health Assessment, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zhi-Liang Zhou
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Peng Wang
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xiao-Ming Zhou
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Meng-Ying Xie
- Department of Geriatric Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Jin Mei
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jie Weng
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Hai-Tao Xi
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Chan Chen
- Department of Geriatric Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Zhi-Yi Wang
- Center for Health Assessment, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zhi-Bin Wang
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| |
Collapse
|
11
|
Paul S, Gangwar A, Bhargava K, Khan N, Khurana P, Ahmad Y. Plasma protein(s)-based conceptual diagnostic tool for assessing high-altitude acclimation in humans. Funct Integr Genomics 2019; 20:191-200. [PMID: 31444657 DOI: 10.1007/s10142-019-00712-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/30/2019] [Accepted: 08/20/2019] [Indexed: 11/24/2022]
Abstract
Exposure to high altitude above 3000 m leads to two outcomes-acclimation or high-altitude maladies. To reach a particular outcome, the plasma proteome is modified differentially, either in context of an acclimation response or mal-acclimation response leading to disease. This ensures that hypoxia-responsive plasma protein trends reflect acclimation in acclimated individuals when compared with their levels prior to acclimation. Such protein trends could be used to assess acclimation in an individual and any significant deviation from this trend may indicate non-acclimation, thereby preventing high-altitude illnesses before they manifest. In this study, we investigate and statistically evaluate the trendlines of various hypoxia-responsive plasma protein levels, reported significantly perturbed in our previous studies, in individuals (male; n = 20) exposed to 3520 m at high-altitude day 1 (HAD1), HAD4, and HAD7L and to 4420 m at HAD7H, HAD30, and HAD120. We observe that thioredoxin (Trx), glutathione peroxidase 3 (GPx-3), and apolipoprotein AI (Apo-AI) are statistically robust markers to assess acclimation across the exposure duration while sulfotransferase 1A1 (ST1A1) is a capable negative control whose levels increase only in cases of HAPE. We also observe exposure day-specific and resident altitude-specific proteins capable of accurately assessing acclimation when compared with baseline levels or the lower altitude zone.
Collapse
Affiliation(s)
- Subhojit Paul
- Defence R&D Organization (DRDO), Defence Institute of Physiology & Allied Sciences (DIPAS), Lucknow Road, Timarpur, New Delhi, 110054, India
| | - Anamika Gangwar
- Defence R&D Organization (DRDO), Defence Institute of Physiology & Allied Sciences (DIPAS), Lucknow Road, Timarpur, New Delhi, 110054, India
| | - Kalpana Bhargava
- Defence R&D Organization (DRDO), Defence Institute of Physiology & Allied Sciences (DIPAS), Lucknow Road, Timarpur, New Delhi, 110054, India
| | - Nilofar Khan
- Defence R&D Organization (DRDO), Defence Institute of Physiology & Allied Sciences (DIPAS), Lucknow Road, Timarpur, New Delhi, 110054, India
| | - Pankaj Khurana
- Defence R&D Organization (DRDO), Defence Institute of Physiology & Allied Sciences (DIPAS), Lucknow Road, Timarpur, New Delhi, 110054, India
| | - Yasmin Ahmad
- Defence R&D Organization (DRDO), Defence Institute of Physiology & Allied Sciences (DIPAS), Lucknow Road, Timarpur, New Delhi, 110054, India.
| |
Collapse
|
12
|
Paul S, Gangwar A, Patir H, Bhargava K, Ahmad Y. Reverse translating SULT1A1, a potential biomarker in roentgenographically tested rat model of rapid HAPE induction. Life Sci 2019; 229:132-138. [DOI: 10.1016/j.lfs.2019.05.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/13/2019] [Accepted: 05/13/2019] [Indexed: 01/22/2023]
|
13
|
Ghoneim MT, Nguyen A, Dereje N, Huang J, Moore GC, Murzynowski PJ, Dagdeviren C. Recent Progress in Electrochemical pH-Sensing Materials and Configurations for Biomedical Applications. Chem Rev 2019; 119:5248-5297. [PMID: 30901212 DOI: 10.1021/acs.chemrev.8b00655] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
pH-sensing materials and configurations are rapidly evolving toward exciting new applications, especially those in biomedical applications. In this review, we highlight rapid progress in electrochemical pH sensors over the past decade (2008-2018) with an emphasis on key considerations, such as materials selection, system configurations, and testing protocols. In addition to recent progress in optical pH sensors, our main focus in this review is on electromechanical pH sensors due to their significant advances, especially in biomedical applications. We summarize developments of electrochemical pH sensors that by virtue of their optimized material chemistries (from metal oxides to polymers) and geometrical features (from thin films to quantum dots) enable their adoption in biomedical applications. We further present an overview of necessary sensing standards and protocols. Standards ensure the establishment of consistent protocols, facilitating collective understanding of results and building on the current state. Furthermore, they enable objective benchmarking of various pH-sensing reports, materials, and systems, which is critical for the overall progression and development of the field. Additionally, we list critical issues in recent literary reporting and suggest various methods for objective benchmarking. pH regulation in the human body and state-of-the-art pH sensors (from ex vivo to in vivo) are compared for suitability in biomedical applications. We conclude our review by (i) identifying challenges that need to be overcome in electrochemical pH sensing and (ii) providing an outlook on future research along with insights, in which the integration of various pH sensors with advanced electronics can provide a new platform for the development of novel technologies for disease diagnostics and prevention.
Collapse
|
14
|
Wade BE, Zhao J, Ma J, Hart CM, Sutliff RL. Hypoxia-induced alterations in the lung ubiquitin proteasome system during pulmonary hypertension pathogenesis. Pulm Circ 2018; 8:2045894018788267. [PMID: 29927354 PMCID: PMC6146334 DOI: 10.1177/2045894018788267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pulmonary hypertension (PH) is a clinical disorder characterized by sustained
increases in pulmonary vascular resistance and pressure that can lead to right
ventricular (RV) hypertrophy and ultimately RV failure and death. The molecular
pathogenesis of PH remains incompletely defined, and existing treatments are
associated with suboptimal outcomes and persistent morbidity and mortality.
Reports have suggested a role for the ubiquitin proteasome system (UPS) in PH,
but the extent of UPS-mediated non-proteolytic protein alterations during PH
pathogenesis has not been previously defined. To further examine UPS
alterations, the current study employed C57BL/6J mice exposed to normoxia or
hypoxia for 3 weeks. Lung protein ubiquitination was evaluated by mass
spectrometry to identify differentially ubiquitinated proteins relative to
normoxic controls. Hypoxia stimulated differential ubiquitination of 198
peptides within 131 proteins (p < 0.05). These proteins were
screened to identify candidates within pathways involved in PH pathogenesis.
Some 51.9% of the differentially ubiquitinated proteins were implicated in at
least one known pathway contributing to PH pathogenesis, and 13% were involved
in three or more PH pathways. Anxa2, App, Jak1, Lmna, Pdcd6ip, Prkch1, and Ywhah
were identified as mediators in PH pathways that undergo differential
ubiquitination during PH pathogenesis. To our knowledge, this is the first study
to report global changes in protein ubiquitination in the lung during PH
pathogenesis. These findings suggest signaling nodes that are dynamically
regulated by the UPS during PH pathogenesis. Further exploration of these
differentially ubiquitinated proteins and related pathways can provide new
insights into the role of the UPS in PH pathogenesis.
Collapse
Affiliation(s)
- Brandy E Wade
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - Jingru Zhao
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - Jing Ma
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - C Michael Hart
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| | - Roy L Sutliff
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Atlanta Veterans' Affairs and Emory University Medical Centers, Decatur, Georgia, USA
| |
Collapse
|
15
|
Paul S, Gangwar A, Bhargava K, Khurana P, Ahmad Y. Diagnosis and prophylaxis for high-altitude acclimatization: Adherence to molecular rationale to evade high-altitude illnesses. Life Sci 2018; 203:171-176. [PMID: 29698652 DOI: 10.1016/j.lfs.2018.04.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 04/13/2018] [Accepted: 04/21/2018] [Indexed: 11/25/2022]
Abstract
Lack of zero side-effect, prescription-less prophylactics and diagnostic markers of acclimatization status lead to many suffering from high altitude illnesses. Although not fully translated to the clinical setting, many strategies and interventions are being developed that are aimed at providing an objective and tangible answer regarding the acclimatization status of an individual as well as zero side-effect prophylaxis that is cost-effective and does not require medical supervision. This short review brings together the twin problems associated with high-altitude acclimatization, i.e. acclimatization status and zero side-effect, easy-to-use prophylaxis, for the reader to comprehend as cogs of the same phenomenon. We describe current research aimed at preventing all the high-altitude illnesses by considering them an assault on redox and energy homeostasis at the molecular level. This review also entails some proteins capable of diagnosing either acclimatization or high-altitude illnesses. The future strategies based on bioinformatics and systems biology is also discussed.
Collapse
Affiliation(s)
- Subhojit Paul
- Peptide & Proteomics Division, Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India
| | - Anamika Gangwar
- Peptide & Proteomics Division, Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India
| | - Kalpana Bhargava
- Peptide & Proteomics Division, Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India
| | - Pankaj Khurana
- Peptide & Proteomics Division, Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India
| | - Yasmin Ahmad
- Peptide & Proteomics Division, Defence Institute of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, New Delhi 110054, India.
| |
Collapse
|
16
|
Global Proteomics Deciphered Novel-Function of Osthole Against Pulmonary Arterial Hypertension. Sci Rep 2018; 8:5556. [PMID: 29615702 PMCID: PMC5882969 DOI: 10.1038/s41598-018-23775-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/19/2018] [Indexed: 12/13/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a progressive cardiovascular-disease with high mortality lacking high-efficiency drug. Our efforts attempted to delineate therapeutic action of osthole produced by Angelica Pubescens Maxim, which has the capacity to treat PAH by exploiting an iTRAQ-based proteomic method. Excitingly, osthole was observed to significantly restore 98 of 315 differential proteins significantly modified by PAH progression. They were primarily annotated into 24 signaling pathways. Four mostly affected proteins (RPL15, Cathepsin S, Histone H3.3 and HMGB1) were experimentially validated which belonged to ribosome pathway, oxidative phosphorylation pathway, systemic lupus erythematosus pathway, complement and coagulation cascades pathway, whose modifications and modulations mostly accounted for therapeutic capacity of this compound against PAH. Altogether, our findings demonstrated that global proteomics is a promising systems-biology approach for deciphering therapeutic actions and associated mechanisms of natural products derived from traditional Chinese medicine. Importantly, osthole is supposed to be a candidate compound for new drug development to treat PAH.
Collapse
|
17
|
Analysis of Housekeeping Genes for Accurate Normalization of qPCR Data During Early Postnatal Brain Development. J Mol Neurosci 2018; 64:431-439. [DOI: 10.1007/s12031-018-1037-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/02/2018] [Indexed: 10/17/2022]
|
18
|
Quantitative proteomics reveals molecular mechanism of gamabufotalin and its potential inhibition on Hsp90 in lung cancer. Oncotarget 2018; 7:76551-76564. [PMID: 27384878 PMCID: PMC5363529 DOI: 10.18632/oncotarget.10388] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/05/2016] [Indexed: 12/24/2022] Open
Abstract
Gamabufotalin (CS-6) is a major bufadienolide of Chansu, which shows desirable metabolic stability and less adverse effect in cancer therapy. CS-6 treatment inhibited the proliferation of NSCLC in a nanomolar range. And CS-6 could induce G2/M cell cycle arrest and apoptosis in A549 cells. However, its molecular mechanism in antitumor activity remains poorly understood. We employed a quantitative proteomics approach to identify the potential cellular targets of CS-6, and found 38 possible target-related proteins. Among them, 31 proteins were closely related in the protein-protein interaction network. One of the regulatory nodes in key pathways was occupied by Hsp90. Molecular docking revealed that CS-6 interacted with the ATP-binding sites of Hsp90. In addition, CS-6 inhibited the chaperone function of Hsp90 and reduced expression of Hsp90-dependent client proteins. Moreover, CS-6 markedly down-regulated the protein level of Hsp90 in tumor tissues of the xenograft mice. Taken together, our results suggest that CS-6 might be a novel inhibitor of Hsp90, and the possible network associated with CS-6 target-related proteins was constructed, which provided experimental evidence for the preclinical value of using CS-6 as an effective antitumor agent in treatment of NSCLC.
Collapse
|
19
|
Jain BP, Pandey S, Saleem N, Tanti GK, Mishra S, Goswami SK. SG2NA is a regulator of endoplasmic reticulum (ER) homeostasis as its depletion leads to ER stress. Cell Stress Chaperones 2017; 22:853-866. [PMID: 28634818 PMCID: PMC5655373 DOI: 10.1007/s12192-017-0816-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/19/2017] [Accepted: 05/26/2017] [Indexed: 01/24/2023] Open
Abstract
SG2NA belongs to a three-member striatin subfamily of WD40 repeat superfamily of proteins. It has multiple protein-protein interaction domains involved in assembling supramolecular signaling complexes. Earlier, we had demonstrated that there are at least five variants of SG2NA generated by alternative splicing, intron retention, and RNA editing. Such versatile and dynamic mode of regulation implicates it in tissue development. In order to shed light on its role in cell physiology, total proteome analysis was performed in NIH3T3 cells depleted of 78 kDa SG2NA, the only isoform expressing therein. A number of ER stress markers were among those modulated after knockdown of SG2NA. In cells treated with the ER stressors thapsigargin and tunicamycin, expression of SG2NA was increased at both mRNA and protein levels. The increased level of SG2NA was primarily in the mitochondria and the microsomes. A mouse injected with thapsigargin also had an increase in SG2NA in the liver but not in the brain. Cell cycle analysis suggested that while loss of SG2NA reduces the level of cyclin D1 and retains a population of cells in the G1 phase, concurrent ER stress facilitates their exit from G1 and traverse through subsequent phases with concomitant cell death. Thus, SG2NA is a component of intrinsic regulatory pathways that maintains ER homeostasis.
Collapse
Affiliation(s)
- Buddhi Prakash Jain
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
- Department of Zoology, School of Life Sciences, Mahatma Gandhi Central University Bihar, Motihari, 845401, India
| | - Shweta Pandey
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
| | - Nikhat Saleem
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
| | - Goutam K Tanti
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
- Neuro-Kopf-Zentrum, Department of Neurology, Klinikumrechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str.22, 81675, Muenchen, Germany
| | - Shalini Mishra
- Peptide and Proteomics Division, Defence Institute of Physiology and Allied Sciences (DIPAS), DRDO, New Delhi, -110054, India
| | - Shyamal K Goswami
- School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
| |
Collapse
|
20
|
STAT3-RXR-Nrf2 activates systemic redox and energy homeostasis upon steep decline in pO 2 gradient. Redox Biol 2017; 14:423-438. [PMID: 29078168 PMCID: PMC5680518 DOI: 10.1016/j.redox.2017.10.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 08/30/2017] [Accepted: 10/15/2017] [Indexed: 01/04/2023] Open
Abstract
Hypobaric hypoxia elicits several patho-physiological manifestations, some of which are known to be lethal. Among various molecular mechanisms proposed so far, perturbation in redox state due to imbalance between radical generation and antioxidant defence is promising. These molecular events are also related to hypoxic status of cancer cells and therefore its understanding has extended clinical advantage beyond high altitude hypoxia. In present study, however, the focus was to understand and propose a model for rapid acclimatization of high altitude visitors to enhance their performance based on molecular changes. We considered using simulated hypobaric hypoxia at some established thresholds of high altitude stratification based on known physiological effects. Previous studies have focused on the temporal aspect while overlooking the effects of varying pO2 levels during exposure to hypobaric hypoxia. The pO2 levels, indicative of altitude, are crucial to redox homeostasis and can be the limiting factor during acclimatization to hypobaric hypoxia. In this study we present the effects of acute (24h) exposure to high (3049m; pO2: 71kPa), very high (4573m; pO2: 59kPa) and extreme altitude (7620m; pO2: 40kPa) zones on lung and plasma using semi-quantitative redox specific transcripts and quantitative proteo-bioinformatics workflow in conjunction with redox stress assays. It was observed that direct exposure to extreme altitude caused 100% mortality, which turned into high survival rate after pre-exposure to 59kPa, for which molecular explanation were also found. The pO2 of 59kPa (very high altitude zone) elicits systemic energy and redox homeostatic processes by modulating the STAT3-RXR-Nrf2 trio. Finally we posit the various processes downstream of STAT3-RXR-Nrf2 and the plasma proteins that can be used to ascertain the redox status of an individual.
Collapse
|
21
|
Marto N, Morello J, Monteiro EC, Pereira SA. Implications of sulfotransferase activity in interindividual variability in drug response: clinical perspective on current knowledge. Drug Metab Rev 2017; 49:357-371. [PMID: 28554218 DOI: 10.1080/03602532.2017.1335749] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The interindividual variability in drug response is a major issue in clinical practice and in drug development. Sulfoconjugation is an important Phase II reaction catalyzed by cytosolic sulfotransferases (SULTs), playing a major role in homeostatic functions, xenobiotic detoxification, and carcinogen bioactivation. SULT display wide interindividual variability, explained only partially by genetic variation, suggesting that other non-genetic, epigenetic, and environmental influences could be major determinants of variability in SULT activity. This review focuses on the factors known to influence SULT variability in expression and activity and the available evidence regarding the impact of SULT variability on drug response.
Collapse
Affiliation(s)
- Natalia Marto
- a CEDOC, Chronic Diseases Research Centre, NOVA Medical School Faculdade de Ciências Médicas, Universidade NOVA de Lisboa , Lisboa , Portugal.,b Department of Internal Medicine , Hospital da Luz , Lisboa , Portugal
| | - Judit Morello
- a CEDOC, Chronic Diseases Research Centre, NOVA Medical School Faculdade de Ciências Médicas, Universidade NOVA de Lisboa , Lisboa , Portugal
| | - Emilia C Monteiro
- a CEDOC, Chronic Diseases Research Centre, NOVA Medical School Faculdade de Ciências Médicas, Universidade NOVA de Lisboa , Lisboa , Portugal
| | - Sofia A Pereira
- a CEDOC, Chronic Diseases Research Centre, NOVA Medical School Faculdade de Ciências Médicas, Universidade NOVA de Lisboa , Lisboa , Portugal
| |
Collapse
|
22
|
Gao Z, Luo G, Ni B. Progress in Mass Spectrometry-Based Proteomics in Hypoxia-Related Diseases and High-Altitude Medicine. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:305-313. [PMID: 28486083 DOI: 10.1089/omi.2016.0187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human migration, influenced by social conflict and natural disasters as well as global climate change, has become recognized as a major "planetary force." It has also brought to the forefront, new specialties of integrative biology-such as high-altitude medicine-and the impact of hitherto understudied environmental factors on human pathophysiology in these new geographical settings. For people migrating to or living in high-altitude regions, environmental hypoxia is a primary challenge. Decreased partial pressure of oxygen in environmental air, caused by lower barometric pressure, puts living organisms in a hypoxic state. When there is a serious inability to adapt, death may ensue. Research efforts over the past few years have applied mass spectrometry-based proteomics analyses to uncover the mechanisms of hypoxia-related high-altitude pathophysiology. The differential proteomic profiles in plasma and tissues under high-altitude hypoxia conditions, as compared with sea level controls, and the multitudinous hypoxia-specific proteins identified elucidate mechanisms underlying high-altitude hypoxia acclimatization and diseases, and provide a foundation for development of new therapeutic, prophylactic, and diagnostic approaches. In this expert review and innovation analysis, we highlight the current proteomics findings on high-altitude hypoxia, and suggest paths forward toward effective interventions to address this key challenge in high-altitude medicine.
Collapse
Affiliation(s)
- Zhiqi Gao
- Department of Pathophysiology and High-Altitude Pathology/Key Laboratory of High-Altitude Environment Medicine (Third Military Medical University), Ministry of Education/Key Laboratory of High-Altitude Medicine, College of High-Altitude Military Medicine, Third Military Medical University , Chongqing, PR China
| | - Gang Luo
- Department of Pathophysiology and High-Altitude Pathology/Key Laboratory of High-Altitude Environment Medicine (Third Military Medical University), Ministry of Education/Key Laboratory of High-Altitude Medicine, College of High-Altitude Military Medicine, Third Military Medical University , Chongqing, PR China
| | - Bing Ni
- Department of Pathophysiology and High-Altitude Pathology/Key Laboratory of High-Altitude Environment Medicine (Third Military Medical University), Ministry of Education/Key Laboratory of High-Altitude Medicine, College of High-Altitude Military Medicine, Third Military Medical University , Chongqing, PR China
| |
Collapse
|
23
|
Paul S, Bhargava K, Ahmad Y. The meta-analytical paradigm in an in silico hybrid: Pathways and networks perturbed during exposure to varying degrees of hypobaric hypoxia. Proteomics Clin Appl 2017; 11. [PMID: 28155252 DOI: 10.1002/prca.201600160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/23/2017] [Accepted: 01/31/2017] [Indexed: 01/11/2023]
Abstract
PURPOSE Computational biology has opened a gateway to omics data analysis and shifted the focus from molecules to systemic molecular networks in the domain of hypobaric hypoxia (HH). Yet there are no meta-analytical investigations circumventing constraints such as organism (rat/human), HH exposure conditions (acute/chronic), and the tissues that can be investigated simultaneously in the realm of wet lab experiments. EXPERIMENTAL DESIGN We analyzed 154 differentially expressed proteins upon HH exposure using Ingenuity Pathway Analysis (IPA) tool, without the constraint of using a single organism or tissue type, to determine the most significant pathways and networks that are perturbed across a range of HH conditions. RESULTS We found acute phase response signaling, farsenoid X receptor/retinoid X receptor activation, liver X receptor/retinoid X receptor activation, clathrin-mediated endocytosis signaling, mitochondrial dysfunction, production of nitric oxide and ROS in macrophages, and integrin signaling to be the most significant universally perturbed pathways. Unique protein-function relationships have also been highlighted. CONCLUSION AND CLINICAL RELEVANCE This meta-analysis provides a list of specific pathways and networks across two model organisms that are perturbed due to HH exposure irrespective of its duration/intensity. Thus, it will be a map of important pathways and proteins to look at when exploring effects of HH exposure irrespective of tissue/organism chosen, particularly in the context of prophylactic/therapeutic targets.
Collapse
Affiliation(s)
- Subhojit Paul
- Peptide & Proteomics Division, Defence Institute Of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Ministry of Defence, Timarpur, New Delhi, India
| | - Kalpana Bhargava
- Peptide & Proteomics Division, Defence Institute Of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Ministry of Defence, Timarpur, New Delhi, India
| | - Yasmin Ahmad
- Peptide & Proteomics Division, Defence Institute Of Physiology & Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Ministry of Defence, Timarpur, New Delhi, India
| |
Collapse
|
24
|
Ma D, Zheng J, Tang P, Xu W, Qing Z, Yang S, Li J, Yang R. Quantitative Monitoring of Hypoxia-Induced Intracellular Acidification in Lung Tumor Cells and Tissues Using Activatable Surface-Enhanced Raman Scattering Nanoprobes. Anal Chem 2016; 88:11852-11859. [DOI: 10.1021/acs.analchem.6b03590] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Dandan Ma
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jing Zheng
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Pinting Tang
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weijian Xu
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Zhihe Qing
- School
of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, Hunan 410004, China
| | - Sheng Yang
- School
of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, Hunan 410004, China
| | - Jishan Li
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Ronghua Yang
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, China
- School
of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, Hunan 410004, China
| |
Collapse
|
25
|
Yang J, Li W, Liu S, Yuan D, Guo Y, Jia C, Song T, Huang C. Identification of novel serum peptide biomarkers for high-altitude adaptation: a comparative approach. Sci Rep 2016; 6:25489. [PMID: 27150491 PMCID: PMC4858689 DOI: 10.1038/srep25489] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/18/2016] [Indexed: 01/06/2023] Open
Abstract
We aimed to identify serum biomarkers for screening individuals who could adapt to high-altitude hypoxia at sea level. HHA (high-altitude hypoxia acclimated; n = 48) and HHI (high-altitude hypoxia illness; n = 48) groups were distinguished at high altitude, routine blood tests were performed for both groups at high altitude and at sea level. Serum biomarkers were identified by comparing serum peptidome profiling between HHI and HHA groups collected at sea level. Routine blood tests revealed the concentration of hemoglobin and red blood cells were significantly higher in HHI than in HHA at high altitude. Serum peptidome profiling showed that ten significantly differentially expressed peaks between HHA and HHI at sea level. Three potential serum peptide peaks (m/z values: 1061.91, 1088.33, 4057.63) were further sequence identified as regions of the inter-α trypsin inhibitor heavy chain H4 fragment (ITIH4 347–356), regions of the inter-α trypsin inhibitor heavy chain H1 fragment (ITIH1 205–214), and isoform 1 of fibrinogen α chain precursor (FGA 588–624). Expression of their full proteins was also tested by ELISA in HHA and HHI samples collected at sea level. Our study provided a novel approach for identifying potential biomarkers for screening people at sea level who can adapt to high altitudes.
Collapse
Affiliation(s)
- Juan Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Wenhua Li
- Xizang Minzu University Medical School, Xianyang 712082, P. R. China
| | - Siyuan Liu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Dongya Yuan
- Xizang Minzu University Medical School, Xianyang 712082, P. R. China
| | - Yijiao Guo
- Xizang Minzu University Medical School, Xianyang 712082, P. R. China
| | - Cheng Jia
- Xizang Minzu University Medical School, Xianyang 712082, P. R. China
| | - Tusheng Song
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
| |
Collapse
|
26
|
Revisiting cobalt chloride preconditioning to prevent hypobaric hypoxia-induced damage: identification of global proteomic alteration and key networks. Funct Integr Genomics 2016; 16:281-95. [PMID: 26882918 DOI: 10.1007/s10142-016-0483-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/24/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
Several studies have supported the hypoxia mimetic roles and cytoprotective properties of cobalt chloride in vitro and in vivo. However, a clear understanding of biological process-based mechanism that integrates the available information remains unknown. This study was aimed to explore the potential mechanism of cobalt chloride deciphering its benefits and well-known physiological challenge caused by hypobaric hypoxia that reportedly affects nearly 24 % of the global population. In order to explore the mechanism of CoCl2, we used global proteomic and systems biology approach in rat model to provide a deeper insight into molecular mechanisms of preconditioning. Furthermore, key conclusions were drawn based on biological network analysis and their enrichment with ontological overlaps. The study was further strengthened by consistent identification of validation of proteins using immunoblotting. CoCl2-pretreated animals exposed to hypoxia showed two significant networks, one lipid metabolism and other cell cycle associated, with a total score of 23 and eight focus molecules. In this study, we delineated two primary routes: one, by direct modulation of reactive oxygen species metabolism and, second, by regulation of lipid metabolism which was not known until now. The previously known benefits of cobalt chloride during physiological challenge by hypobaric hypoxia are convincing and could be explained by some basic set of metabolic and molecular reorganization within the hypoxia model. Interestingly, we also observed some of the completely unknown roles of cobalt chloride such as regulation of lipid that could undulate the translational roles of cobalt chloride supplementation beyond hypoxia preconditioning.
Collapse
|