1
|
Poddar NK, Agarwal D, Agrawal Y, Wijayasinghe YS, Mukherjee A, Khan S. Deciphering the enigmatic crosstalk between prostate cancer and Alzheimer's disease: A current update on molecular mechanisms and combination therapy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166524. [PMID: 35985445 DOI: 10.1016/j.bbadis.2022.166524] [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: 06/02/2022] [Revised: 08/05/2022] [Accepted: 08/11/2022] [Indexed: 11/26/2022]
Abstract
Alzheimer's disease (AD) and prostate cancer (PCa) are considered the leading causes of death in elderly people worldwide. Although both these diseases have striking differences in their pathologies, a few underlying mechanisms are similar when cell survival is considered. In the current study, we employed an in-silico approach to decipher the possible role of bacterial proteins in the initiation and progression of AD and PCa. We further analyzed the molecular connections between these two life-threatening diseases. The androgen deprivation therapy used against PCa has been shown to promote castrate resistant PCa as well as AD. In addition, cell signaling pathways, such as Akt, IGF, and Wnt contribute to the progression of both AD and PCa. Besides, various proteins and genes are also common in disease progression. One such similarity is mTOR signaling. mTOR is the common downstream target for many signaling pathways and plays a vital role in both PCa and AD. Targeting mTOR can be a favorable line of treatment for both AD and PCa. However, drug resistance is one of the challenges in effective drug therapy. A few drugs that target mTOR have now become ineffective due to the development of resistance. In that regard, phytochemicals can be a rich source of novel drug candidates as they can act via multiple mechanisms. This review also presents mTOR targeting phytochemicals with promising anti-PCa, anti-AD activities, and approaches to overcome the issues associated with phytochemical-based therapies in clinical trials.
Collapse
Affiliation(s)
- Nitesh Kumar Poddar
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India.
| | - Disha Agarwal
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Yamini Agrawal
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | | | - Arunima Mukherjee
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Shahanavaj Khan
- Department of Health Sciences, Novel Global Community Educational Foundation, NSW, Australia; Department of Pharmaceutics, College of Pharmacy, PO Box 2457, King Saud University, Riyadh 11451, Saudi Arabia; Department of Medical Lab Technology, Indian Institute of health and Technology (IIHT), Deoband, 247554 Saharanpur, UP, India.
| |
Collapse
|
2
|
Martini G, Ciardiello D, Dallio M, Famiglietti V, Esposito L, Della Corte CM, Napolitano S, Fasano M, Gravina AG, Romano M, Loguercio C, Federico A, Maiello E, Tuccillo C, Morgillo F, Troiani T, Di Maio M, Martinelli E, Ciardiello F. Gut microbiota correlates with antitumor activity in patients with
mCRC
and
NSCLC
treated with cetuximab plus avelumab. Int J Cancer 2022; 151:473-480. [PMID: 35429341 PMCID: PMC9321613 DOI: 10.1002/ijc.34033] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022]
Abstract
Gut microbiota is involved in immune modulation and immune checkpoint inhibitors (ICIs) efficacy. Single‐arm phase II CAVE‐mCRC and CAVE‐LUNG clinical trials investigated cetuximab + avelumab combination in RAS wild‐type (WT) metastatic colorectal cancer (mCRC) and chemo‐refractory nonsmall cell lung cancer (NSCLC) patients, respectively. A comprehensive gut microbiota genetic analysis was done in basal fecal samples of 14 patients from CAVE‐mCRC trial with circulating tumor DNA (ctDNA) RAS/BRAF WT and microsatellite stable (MSS) disease. Results were validated in a cohort of 10 patients from CAVE‐Lung trial. 16S rRNA sequencing revealed 23 027 bacteria species in basal fecal samples of 14 patients from CAVE‐mCRC trial. In five long‐term responding patients (progression‐free survival [PFS], 9‐24 months) significant increases in two butyrate‐producing bacteria, Agathobacter M104/1 (P = .018) and Blautia SR1/5 (P = .023) were found compared to nine patients with shorter PFS (2‐6 months). A significantly better PFS was also observed according to the presence or absence of these species in basal fecal samples. For Agathobacter M104/1, median PFS (mPFS) was 13.5 months (95% confidence interval [CI], 6.5‐20.5 months) vs 4.6 months (95% CI, 1.8‐7.4 months); P = .006. For Blautia SR1/5, mPFS was 5.9 months (95% CI, 2.2‐9.7 months) vs 3.6 months (95% CI, 3.3‐4.0 months); P = .021. Similarly, in CAVE‐Lung validation cohort, Agathobacter M104/1 and Blautia SR1/5 expression were associated with PFS according to their presence or absence in basal fecal samples. Agathobacter and Blautia species could be potential biomarkers of outcome in mCRC, and NSCLC patients treated with cetuximab + avelumab. These findings deserve further investigation.
Collapse
Affiliation(s)
- Giulia Martini
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Davide Ciardiello
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
- Medical Oncology Fondazione IRCCS Casa Sollievo della Sofferenza San Giovanni Rotondo Italy
| | - Marcello Dallio
- Gastroenterology, Department of Precision Medicine Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Vincenzo Famiglietti
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Lucia Esposito
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | | | - Stefania Napolitano
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Morena Fasano
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Antonietta Gerarda Gravina
- Gastroenterology, Department of Precision Medicine Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Marco Romano
- Gastroenterology, Department of Precision Medicine Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Carmelina Loguercio
- Gastroenterology, Department of Precision Medicine Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Alessandro Federico
- Gastroenterology, Department of Precision Medicine Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Evaristo Maiello
- Medical Oncology Fondazione IRCCS Casa Sollievo della Sofferenza San Giovanni Rotondo Italy
| | - Concetta Tuccillo
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Floriana Morgillo
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Teresa Troiani
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Massimo Di Maio
- Department of Oncology University of Turin, at Ordine Mauriziano Hospital Turin Italy
| | - Erika Martinelli
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| | - Fortunato Ciardiello
- Medical Oncology Università degli Studi della Campania “Luigi Vanvitelli” Naples Italy
| |
Collapse
|
3
|
Kato I, Zhang J, Sun J. Bacterial-Viral Interactions in Human Orodigestive and Female Genital Tract Cancers: A Summary of Epidemiologic and Laboratory Evidence. Cancers (Basel) 2022; 14:425. [PMID: 35053587 PMCID: PMC8773491 DOI: 10.3390/cancers14020425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Infectious agents, including viruses, bacteria, fungi, and parasites, have been linked to pathogenesis of human cancers, whereas viruses and bacteria account for more than 99% of infection associated cancers. The human microbiome consists of not only bacteria, but also viruses and fungi. The microbiome co-residing in specific anatomic niches may modulate oncologic potentials of infectious agents in carcinogenesis. In this review, we focused on interactions between viruses and bacteria for cancers arising from the orodigestive tract and the female genital tract. We examined the interactions of these two different biological entities in the context of human carcinogenesis in the following three fashions: (1) direct interactions, (2) indirect interactions, and (3) no interaction between the two groups, but both acting on the same host carcinogenic pathways, yielding synergistic or additive effects in human cancers, e.g., head and neck cancer, liver cancer, colon cancer, gastric cancer, and cervical cancer. We discuss the progress in the current literature and summarize the mechanisms of host-viral-bacterial interactions in various human cancers. Our goal was to evaluate existing evidence and identify gaps in the knowledge for future directions in infection and cancer.
Collapse
Affiliation(s)
- Ikuko Kato
- Department of Oncology and Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jilei Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Sun
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| |
Collapse
|
4
|
Ruan Z, Yu Y, Feng Y. The global dissemination of bacterial infections necessitates the study of reverse genomic epidemiology. Brief Bioinform 2021; 21:741-750. [PMID: 30715167 DOI: 10.1093/bib/bbz010] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/17/2018] [Accepted: 01/06/2019] [Indexed: 01/29/2023] Open
Abstract
Whole genome sequencing (WGS) has revolutionized the genotyping of bacterial pathogens and is expected to become the new gold standard for tracing the transmissions of bacterial infectious diseases for public health purposes. Traditional genomic epidemiology often uses WGS as a verification tool, namely, when a common source or epidemiological link is suspected, the collected isolates are sequenced for the determination of clonal relationships. However, increasingly frequent international travel and food transportation, and the associated potential for the cross-border transmission of bacterial pathogens, often lead to an absence of information on bacterial transmission routes. Here we introduce the concept of 'reverse genomic epidemiology', i.e. when isolates are inspected by genome comparisons to be sufficiently similar to one another, they are assumed to be a consequence of infection from a common source. Through BacWGSTdb (http://bacdb.org/BacWGSTdb/), a database we have developed for bacterial genome typing and source tracking, we have found that almost the entire analyzed 20 bacterial species exhibit the phenomenon of cross-border clonal dissemination. Five networks were further identified in which isolates sharing nearly identical genomes were collected from at least five different countries. Three of these have been documented as real infectious disease outbreaks, therefore demonstrating the feasibility and authority of reverse genomic epidemiology. Our survey and proposed strategy would be of potential value in establishing a global surveillance system for tracing bacterial transmissions and outbreaks; the related database and techniques require urgent standardization.
Collapse
Affiliation(s)
- Zhi Ruan
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
5
|
Henriquez FL, Mooney R, Bandel T, Giammarini E, Zeroual M, Fiori PL, Margarita V, Rappelli P, Dessì D. Paradigms of Protist/Bacteria Symbioses Affecting Human Health: Acanthamoeba species and Trichomonas vaginalis. Front Microbiol 2021; 11:616213. [PMID: 33488560 PMCID: PMC7817646 DOI: 10.3389/fmicb.2020.616213] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
Ever since the publication of the seminal paper by Lynn Margulis in 1967 proposing the theory of the endosymbiotic origin of organelles, the study of the symbiotic relationships between unicellular eukaryotes and prokaryotes has received ever-growing attention by microbiologists and evolutionists alike. While the evolutionary significance of the endosymbiotic associations within protists has emerged and is intensively studied, the impact of these relationships on human health has been seldom taken into account. Microbial endosymbioses involving human eukaryotic pathogens are not common, and the sexually transmitted obligate parasite Trichomonas vaginalis and the free-living opportunistic pathogen Acanthamoeba represent two unique cases in this regard, to date. The reasons of this peculiarity for T. vaginalis and Acanthamoeba may be due to their lifestyles, characterized by bacteria-rich environments. However, this characteristic does not fully explain the reason why no bacterial endosymbiont has yet been detected in unicellular eukaryotic human pathogens other than in T. vaginalis and Acanthamoeba, albeit sparse and poorly investigated examples of morphological identification of bacteria-like microorganisms associated with Giardia and Entamoeba were reported in the past. In this review article we will present the body of experimental evidences revealing the profound effects of these examples of protist/bacteria symbiosis on the pathogenesis of the microbial species involved, and ultimately their impact on human health.
Collapse
Affiliation(s)
- Fiona L Henriquez
- School of Health and Life Sciences, University of West Scotland, Paisley, United Kingdom
| | - Ronnie Mooney
- School of Health and Life Sciences, University of West Scotland, Paisley, United Kingdom
| | - Timothy Bandel
- School of Health and Life Sciences, University of West Scotland, Paisley, United Kingdom
| | - Elisa Giammarini
- School of Health and Life Sciences, University of West Scotland, Paisley, United Kingdom
| | - Mohammed Zeroual
- School of Health and Life Sciences, University of West Scotland, Paisley, United Kingdom.,Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Pier Luigi Fiori
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy.,Mediterrenean Center for Disease Control, Sassari, Italy
| | - Valentina Margarita
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Paola Rappelli
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy.,Mediterrenean Center for Disease Control, Sassari, Italy
| | - Daniele Dessì
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy.,Mediterrenean Center for Disease Control, Sassari, Italy
| |
Collapse
|
6
|
Salahuddin N, Gaber M, Mousa M, Abdelwahab MA. Poly(3-hydroxybutyrate)/poly(amine)-coated nickel oxide nanoparticles for norfloxacin delivery: antibacterial and cytotoxicity efficiency. RSC Adv 2020; 10:34046-34058. [PMID: 35519075 PMCID: PMC9056780 DOI: 10.1039/d0ra04784h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
Sustained release dosage forms enable prolonged and continuous release of a drug in the gastrointestinal tract for medication characterized by a short half lifetime. In this study, the effect of blending polyamine on poly(3-hydroxybutyrate) (PHB) as a carrier for norfloxacin (NF) was studied. The prepared blend was mixed with different amounts of NiO nanoparticles and characterized using FTIR analysis, X-ray diffraction analysis, thermogravimetric analysis, dynamic light scattering, transmission electron microscopy and scanning electron microscopy. It was found that the drug released from the nanocomposite has a slow rate in comparison with NiO, PHB, and PHB/polyamine blend. The highest ratio of NiO content to the matrix (highest NF loading), leads to a slower rate of drug release. The release from the nanocomposites showed a faster rate at pH = 2 than that at pH = 7.4. The mechanisms of NF adsorption and release were studied on PHB/polyamine-3% NiO nanocomposite. In addition, the antimicrobial efficacy of nanocomposites loaded with the drug was determined and compared with the free drug. Inclusion of NiO into PHB/polyamine showed a higher efficacy against Streptococcus pyogenes and Pseudomonas aeruginosa than the free NF. Moreover, the cytotoxicity of PHB/polyamine-3% NiO against HePG-2 cells was investigated and compared with PHB and PHB/polyamine loaded with the drug. The most efficient IC50 was found for NF@PHB/polyamine-3% NiO (29.67 μg mL-1). No effect on cell proliferation against the normal human cell line (WISH) was observed and IC50 was detected to be 44.95 and 70 μg mL-1 for NiO nanoparticles and the PHB/polyamine-3% NiO nanocomposite, respectively indicating a selectivity of action towards tumor cells coupled with a lack of cytotoxicity towards normal cells.
Collapse
Affiliation(s)
- Nehal Salahuddin
- Chemistry Department, Faculty of Science, Tanta University Tanta 31527 Egypt
| | - Mohamed Gaber
- Chemistry Department, Faculty of Science, Tanta University Tanta 31527 Egypt
| | - Maie Mousa
- Chemistry Department, Faculty of Science, Tanta University Tanta 31527 Egypt
| | | |
Collapse
|
7
|
Zhang C, Ju Y, Tang N, Li Y, Zhang G, Song Y, Fang H, Yang L, Feng J. Systematic analysis of supervised machine learning as an effective approach to predicate β-lactam resistance phenotype in Streptococcus pneumoniae. Brief Bioinform 2020; 21:1347-1355. [PMID: 31192359 DOI: 10.1093/bib/bbz056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is the most common human respiratory pathogen, and β-lactam antibiotics have been employed to treat infections caused by S. pneumoniae for decades. β-lactam resistance is steadily increasing in pneumococci and is mainly associated with the alteration in penicillin-binding proteins (PBPs) that reduce binding affinity of antibiotics to PBPs. However, the high variability of PBPs in clinical isolates and their mosaic gene structure hamper the predication of resistance level according to the PBP gene sequences. In this study, we developed a systematic strategy for applying supervised machine learning to predict S. pneumoniae antimicrobial susceptibility to β-lactam antibiotics. We combined published PBP sequences with minimum inhibitory concentration (MIC) values as labelled data and the sequences from NCBI database without MIC values as unlabelled data to develop an approach, using only a fragment from pbp2x (750 bp) and a fragment from pbp2b (750 bp) to predicate the cefuroxime and amoxicillin resistance. We further validated the performance of the supervised learning model by constructing mutants containing the randomly selected pbps and testing more clinical strains isolated from Chinese hospital. In addition, we established the association between resistance phenotypes and serotypes and sequence type of S. pneumoniae using our approach, which facilitate the understanding of the worldwide epidemiology of S. pneumonia.
Collapse
Affiliation(s)
- Chaodong Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University 60 Nanyang Drive, Singapore, Singapore
| | - Yingjiao Ju
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Na Tang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Gang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuqin Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hailing Fang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Khan S, Zaidi S, Alouffi AS, Hassan I, Imran A, Khan RA. Computational Proteome-Wide Study for the Prediction of Escherichia coli Protein Targeting in Host Cell Organelles and Their Implication in Development of Colon Cancer. ACS OMEGA 2020; 5:7254-7261. [PMID: 32280866 PMCID: PMC7143404 DOI: 10.1021/acsomega.9b04042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/16/2020] [Indexed: 05/08/2023]
Abstract
Enterohemorrhagic Escherichia coli infection is associated with gastrointestinal disorders, including diarrhea and colorectal cancer. Although evidences have established the involvement of E. coli in the growth of colon cancer, the molecular mechanisms of carcinogenesis of cancer growth and development are not well understood. We analyzed E. coli protein targeting in host cell organelles and the implication in colon cancer using in silico approaches. Our results indicated that many E. coli proteins targeted the endoplasmic reticulum (ER), ER membranes, Golgi apparatus, Golgi apparatus membranes, peroxisomes, nucleus, nuclear membrane, mitochondria, and mitochondrial membrane of host cells. These targeted proteins in ER, Golgi apparatus, peroxisomes, nucleus, and mitochondria may alter the normal functioning of various pathways including DNA repair, apoptosis, replication, transcription, and protein folding in E. coli-infected host cells. The results of the current in silico study provide insights into E. coli pathogenesis and may aid in designing new preventive and therapeutic strategies.
Collapse
Affiliation(s)
- Shahanavaj Khan
- Bioinformatics
and Biotechnology Unit, Department of Biosciences, SRGC, Muzaffarnagar 251001, UP, India
- Department
of Pharmaceutics, College of Pharmacy, King
Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
- . Phone: +91
9219993262
| | - Sabika Zaidi
- Bioinformatics
and Biotechnology Unit, Department of Biosciences, SRGC, Muzaffarnagar 251001, UP, India
| | | | - Iftekhar Hassan
- Department
of Zoology, College of Science, King Saud
University, Riyadh 11451, Saudi Arabia
| | - Ahmad Imran
- King
Abdullah Institute for Nanotechnology, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Rais Ahmad Khan
- Department
of Chemistry, College of Science, King Saud
University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
9
|
Zhou J, Hui X, Mao Y, Fan L. Identification of novel genes associated with a poor prognosis in pancreatic ductal adenocarcinoma via a bioinformatics analysis. Biosci Rep 2019; 39:BSR20190625. [PMID: 31311829 PMCID: PMC6680377 DOI: 10.1042/bsr20190625] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/01/2019] [Accepted: 07/12/2019] [Indexed: 01/18/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a class of the commonest malignant carcinomas. The present study aimed to elucidate the potential biomarker and prognostic targets in PDAC. The array data of GSE41368, GSE43795, GSE55643, and GSE41369 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) and differentially expressed microRNAs (DEmiRNAs) in PDAC were obtained by using GEO2R, and overlapped DEGs were acquired with Venn Diagrams. Functional enrichment analysis of overlapped DEGs and DEmiRNAs was conducted with Metascape and FunRich, respectively. The protein-protein interaction (PPI) network of overlapped DEGs was constructed by STRING and visualized with Cytoscape. Overall survival (OS) of DEmiRNAs and hub genes were investigated by Kaplan-Meier (KM) plotter (KM plotter). Transcriptional data and correlation analyses among hub genes were verified through GEPIA and Human Protein Atlas (HPA). Additionally, miRNA targets were searched using miRTarBase, then miRNA-DEG regulatory network was visualized with Cytoscape. A total of 32 DEmiRNAs and 150 overlapped DEGs were identified, and Metascape showed that DEGs were significantly enriched in cellular chemical homeostasis and pathways in cancer, while DEmiRNAs were mainly enriched in signal transduction and Glypican pathway. Moreover, seven hub genes with a high degree, namely, V-myc avian myelocytomatosis viral oncogene homolog (MYC), solute carrier family 2 member 1 (SLC2A1), PKM, plasminogen activator, urokinase (PLAU), peroxisome proliferator activated receptor γ (PPARG), MET proto-oncogene, receptor tyrosine kinase (MET), and integrin subunit α 3 (ITGA3), were identified and found to be up-regulated between PDAC and normal tissues. miR-135b, miR-221, miR-21, miR-27a, miR-199b-5p, miR-143, miR-196a, miR-655, miR-455-3p, miR-744 and hub genes predicted poor OS of PDAC. An integrative bioinformatics analysis identified several hub genes that may serve as potential biomarkers or targets for early diagnosis and precision target treatment of PDAC.
Collapse
Affiliation(s)
- Jun Zhou
- Department of General Ward 1, Zhejiang Hospital of Lingyin District, Zhejiang, China
| | - Xiaoliang Hui
- Department of General Ward 1, Zhejiang Hospital of Lingyin District, Zhejiang, China
| | - Ying Mao
- Department of General Ward 1, Zhejiang Hospital of Lingyin District, Zhejiang, China
| | - Liya Fan
- Department of Gastroenterology, Zhejiang Hospital of Sandun District, Zhejiang, China
| |
Collapse
|
10
|
Liang X, Zhu W, Lv Z, Zou Q. Molecular Computing and Bioinformatics. Molecules 2019; 24:E2358. [PMID: 31247973 PMCID: PMC6651761 DOI: 10.3390/molecules24132358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 02/06/2023] Open
Abstract
Molecular computing and bioinformatics are two important interdisciplinary sciences that study molecules and computers. Molecular computing is a branch of computing that uses DNA, biochemistry, and molecular biology hardware, instead of traditional silicon-based computer technologies. Research and development in this area concerns theory, experiments, and applications of molecular computing. The core advantage of molecular computing is its potential to pack vastly more circuitry onto a microchip than silicon will ever be capable of-and to do it cheaply. Molecules are only a few nanometers in size, making it possible to manufacture chips that contain billions-even trillions-of switches and components. To develop molecular computers, computer scientists must draw on expertise in subjects not usually associated with their field, including organic chemistry, molecular biology, bioengineering, and smart materials. Bioinformatics works on the contrary; bioinformatics researchers develop novel algorithms or software tools for computing or predicting the molecular structure or function. Molecular computing and bioinformatics pay attention to the same object, and have close relationships, but work toward different orientations.
Collapse
Affiliation(s)
- Xin Liang
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China
| | - Wen Zhu
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China
| | - Zhibin Lv
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China.
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| |
Collapse
|
11
|
Culture-independent studies on bacterial dysbiosis in oral and oropharyngeal squamous cell carcinoma: A systematic review. Crit Rev Oncol Hematol 2019; 139:31-40. [PMID: 31112880 DOI: 10.1016/j.critrevonc.2019.04.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 01/01/2019] [Accepted: 04/16/2019] [Indexed: 12/28/2022] Open
Abstract
Imbalance within the resident bacterial community (dysbiosis), rather than the presence and activity of a single organism, has been proposed to be associated with, and to influence, the development and progression of various diseases; however, the existence and significance of dysbiosis in oral/oropharyngeal cancer is yet to be clearly established. A systematic search (conducted on 25/01/2018 and updated on 25/05/2018) was performed on three databases (Pubmed, Web of Science & Scopus) to identify studies employing culture-independent methods which investigated the bacterial community in oral/oropharyngeal cancer patients compared to control subjects. Of the 1546 texts screened, only fifteen publications met the pre-determined selection criteria. Data extracted from 731 cases and 809 controls overall, could not identify consistent enrichment of any particular taxon in oral/oropharyngeal cancers, although common taxa could be identified between studies. Six studies reported the enrichment of Fusobacteria in cancer at different taxonomic levels whereas four studies reported an increase in Parvimonas. Changes in microbial diversity remained inconclusive, with four studies showing a higher diversity in controls, three studies showing a higher diversity in tumors and three additional studies showing no difference between tumors and controls. Even though most studies identified a component of dysbiosis in oral/oropharyngeal cancer, methodological and analytical variations prevented a standardized summary, which highlights the necessity for studies of superior quality and magnitude employing standardized methodology and reporting. Indeed an holistic metagenomic approach is likely to be more meaningful, as is understanding of the overall metabolome, rather than a mere enumeration of the organisms present.
Collapse
|
12
|
Abstract
Trichomonas vaginalis is an anaerobic protist, responsible for the most prevalent non-viral sexually transmitted infection in humans. One of the most intriguing aspects of T. vaginalis pathobiology is the complex relationship with intracellular microbial symbionts: a group of dsRNA viruses belonging to family of Totiviridae (T. vaginalis virus), and eubacteria belonging to the Mycoplasma genus, in particular Mycoplasma hominis. Both microorganisms seem to strongly influence the lifestyle of T. vaginalis, suggesting a role of the symbiosis in the high variability of clinical presentation and sequelae during trichomoniasis. In the last few years many aspects of this unique symbiotic relationship have been investigated: M. hominis resides and replicates in the protozoan cell, and T. vaginalis is able to pass the bacterial infection to both mycoplasma-free protozoan isolates and human epithelial cells; M. hominis synergistically upregulates the proinflammatory response of human monocytes to T. vaginalis. Furthermore, the influence of M. hominis over T. vaginalis metabolism and physiology has been characterized. The identification of a novel species belonging to the class of Mollicutes (Candidatus Mycoplasma girerdii) exclusively associated to T. vaginalis opens new perspectives in the research of the complex series of events taking place in the multifaceted world of the vaginal microbiota, both under normal and pathological conditions.
Collapse
|
13
|
Intracellular Delivery: An Overview. TARGETED INTRACELLULAR DRUG DELIVERY BY RECEPTOR MEDIATED ENDOCYTOSIS 2019. [DOI: 10.1007/978-3-030-29168-6_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|