1
|
Altendorf T, Mohrlüder J, Willbold D. TSAT: Efficient evaluation software for NGS data of phage/mirror-image phage display selections. BIOPHYSICAL REPORTS 2024; 4:100166. [PMID: 38909902 PMCID: PMC11269273 DOI: 10.1016/j.bpr.2024.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/31/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Phage display and mirror-image phage display are commonly used techniques for the identification of binders that are specific to predefined targets. Recent studies demonstrated the effectiveness of next-generation sequencing (NGS) by increasing the amount of information extracted from selections. This allows for a better analysis and increases the possibility to select effective binders. A potential downside to NGS analysis of phage display selections is the increased workload that is needed to analyze the obtained information. Here, we report on the development of TSAT (target-specific analysis tool), software for user-friendly and efficient analysis of peptide sequence data from NGS of phage display selections.
Collapse
Affiliation(s)
- Tim Altendorf
- Institut für Biologische Informationsprozesse, IBI-7, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jeannine Mohrlüder
- Institut für Biologische Informationsprozesse, IBI-7, Forschungszentrum Jülich, Jülich, Germany.
| | - Dieter Willbold
- Institut für Biologische Informationsprozesse, IBI-7, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
| |
Collapse
|
2
|
Inchanalkar M, Srivatsa S, Ambatipudi S, Bhosale PG, Patil A, Schäffer AA, Beerenwinkel N, Mahimkar MB. Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers. Clin Epigenetics 2023; 15:93. [PMID: 37245006 DOI: 10.1186/s13148-023-01510-z] [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: 09/13/2022] [Accepted: 05/21/2023] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND Gingivobuccal complex oral squamous cell carcinoma (GBC-OSCC) is an aggressive malignancy with high mortality often preceded by premalignant lesions, including leukoplakia. Previous studies have reported genomic drivers in OSCC, but much remains to be elucidated about DNA methylation patterns across different stages of oral carcinogenesis. RESULTS There is a serious lack of biomarkers and clinical application of biomarkers for early detection and prognosis of gingivobuccal complex cancers. Hence, in search of novel biomarkers, we measured genome-wide DNA methylation in 22 normal oral tissues, 22 leukoplakia, and 74 GBC-OSCC tissue samples. Both leukoplakia and GBC-OSCC had distinct methylation profiles as compared to normal oral tissue samples. Aberrant DNA methylation increases during the different stages of oral carcinogenesis, from premalignant lesions to carcinoma. We identified 846 and 5111 differentially methylated promoters in leukoplakia and GBC-OSCC, respectively, with a sizable fraction shared between the two sets. Further, we identified potential biomarkers from integrative analysis in gingivobuccal complex cancers and validated them in an independent cohort. Integration of genome, epigenome, and transcriptome data revealed candidate genes with gene expression synergistically regulated by copy number and DNA methylation changes. Regularised Cox regression identified 32 genes associated with patient survival. In an independent set of samples, we validated eight genes (FAT1, GLDC, HOXB13, CST7, CYB5A, MLLT11, GHR, LY75) from the integrative analysis and 30 genes from previously published reports. Bisulfite pyrosequencing validated GLDC (P = 0.036), HOXB13 (P < 0.0001) promoter hypermethylation, and FAT1 (P < 0.0001) hypomethylation in GBC-OSCC compared to normal controls. CONCLUSIONS Our findings identified methylation signatures associated with leukoplakia and gingivobuccal complex cancers. The integrative analysis in GBC-OSCC identified putative biomarkers that enhance existing knowledge of oral carcinogenesis and may potentially help in risk stratification and prognosis of GBC-OSCC.
Collapse
Affiliation(s)
- Mayuri Inchanalkar
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Sumana Srivatsa
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Srikant Ambatipudi
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, Kerala, India
| | - Priyanka G Bhosale
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Centre for Gene Therapy and Regenerative Medicine, Guy's Hospital, King's College London, Tower Wing, London, UK
| | - Asawari Patil
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, and National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Manoj B Mahimkar
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
| |
Collapse
|
3
|
CD47-targeted optical molecular imaging and near-infrared photoimmunotherapy in the detection and treatment of bladder cancer. Mol Ther Oncolytics 2022; 24:319-330. [PMID: 35118190 PMCID: PMC8784304 DOI: 10.1016/j.omto.2021.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 12/03/2022] Open
Abstract
Transurethral resection of bladder tumor (TURBT) followed by intravesical therapy remains the most effective strategy for the management of non-muscle-invasive bladder cancer worldwide. TURBT has two purposes: to remove all visible tumors and to obtain tumor specimens for histopathological analysis. However, the detection of flat and small malignant lesions under white-light cystoscopy is extremely challenging, and residual lesions are still the main reason for the high recurrence rate of bladder cancer. We hypothesized that visual enhancement of malignant lesions using targeted optical molecular imaging could potentially highlight residual tumors in the bladder during surgery, and near-infrared photoimmunotherapy (NIR-PIT) could kill exfoliated cancer cells and residual tumors. A mouse model of complete or partial bladder tumor resection was established under the guidance of optical molecular imaging mediated by indocyanine green and anti-CD47-Alexa Fluor 790, respectively. Once the tumor recurred, mouse model received repeated CD47-targeted NIR-PIT. After complete resection, there was no tumor recurrence. Furthermore, the growth rate of recurrent tumor decreased significantly after repeated NIR-PIT. Therefore, CD47-targeted optical molecular imaging can potentially assist urologists to detect and remove all tumors, and repeated NIR-PIT shows the potential to reduce tumor recurrence rates and inhibit the growth of recurrent tumor.
Collapse
|
4
|
Zheng B, Zhang P, Wang H, Wang J, Liu ZH, Zhang D. Advances in Research on Bladder Cancer Targeting Peptides: a Review. Cell Biochem Biophys 2021; 79:711-718. [PMID: 34468956 PMCID: PMC8558283 DOI: 10.1007/s12013-021-01019-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2021] [Indexed: 12/04/2022]
Abstract
Bladder cancer (Bca) is the second most common malignant tumor of the genitourinary system in Chinese male population with high potential of recurrence and progression. The overall prognosis has not been improved significantly for the past 30 years due to the lack of early theranostic technique. Currently the early theranostic technique for bladder cancer is mainly through the intravesical approach, but the clinical outcomes are poor due to the limited tumor-targeting efficiency. Therefore, the targeting peptides for bladder cancer provide possibility to advance intravesical theranostic technique. However, no systematic review has covered the wide use of the targeting peptides for intravesical theranostic techniques in bladder cancer. Herein, a summary of original researches introduces all aspects of the targeting peptides for bladder cancer, including the peptide screening, the targeting mechanism and its preclinical application.
Collapse
Affiliation(s)
- Bin Zheng
- Zhejiang Chinese Medical University, 310053, HangZhou, China
- Zhejiang Provincial People's Hospital, Hangzhou Medical College, 310014, Hangzhou, China
| | - Pu Zhang
- Zhejiang Provincial People's Hospital, Hangzhou Medical College, 310014, Hangzhou, China
| | - Heng Wang
- Zhejiang Provincial People's Hospital, Hangzhou Medical College, 310014, Hangzhou, China
| | - Jinxue Wang
- Handan Central hospital, 056001, Handan, China
| | - Zheng Hong Liu
- Zhejiang Chinese Medical University, 310053, HangZhou, China
| | - DaHong Zhang
- Zhejiang Chinese Medical University, 310053, HangZhou, China.
| |
Collapse
|
5
|
Yang Y, Liu C, Yan X, Li J, Yang X. En Bloc Tumor Resection, Optical Molecular Imaging, and the Potential Synergy of the Combination of the Two Techniques in Bladder Cancer. Front Oncol 2021; 11:638083. [PMID: 33796465 PMCID: PMC8008058 DOI: 10.3389/fonc.2021.638083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/04/2021] [Indexed: 12/14/2022] Open
Abstract
Although transurethral resection of bladder tumor is the golden standard for the treatment of non-muscle invasive bladder cancer, this surgical procedure still has some serious drawbacks. For example, piecemeal resection of tumor tissue results in exfoliated tumor cells dissemination and implantation, and fragmented tumor specimens make it difficult for pathologists to accurately assess the pathological stage and histologic grade. En bloc tumor resection follows the basic principle of oncological surgery and provides an intact tumor specimen containing detrusor muscle for pathologists to make accurate histopathological assessment. However, there is no robust clinical evidence that en bloc tumor resection is superior to conventional resection in terms of oncological outcomes. Considering the high recurrence rate, small or occult tumor lesions may be overlooked and incomplete tumor resection may occur during white light cystoscopy-assisted transurethral resection. Molecular fluorescent tracers have the ability to bind tumor cells with high sensitivity and specificity. Optical molecular imaging mediated by it can detect small or occult malignant lesions while minimizing the occurrence of false-positive results. Meanwhile, optical molecular imaging can provide dynamic and real-time image guidance in the surgical procedure, which helps urologists to accurately determine the boundary and depth of tumor invasion, so as to perform complete and high-quality transurethral tumor resection. Integrating the advantages of these two technologies, optical molecular imaging-assisted en bloc tumor resection shows the potential to improve the positive detection rate of small or occult tumor lesions and the quality of transurethral resection, resulting in high recurrence-free and progression-free survival rates.
Collapse
Affiliation(s)
- Yongjun Yang
- First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Chao Liu
- First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Xiaoting Yan
- First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Jiawei Li
- First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Xiaofeng Yang
- First Clinical Medical College, Shanxi Medical University, Taiyuan, China
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, China
| |
Collapse
|
6
|
Zhou C, Li H, Han X, Pang H, Wu M, Tang Y, Luo X. Prognostic Value and Molecular Mechanisms of Proteasome 26S Subunit, Non-ATPase Family Genes for Pancreatic Ductal Adenocarcinoma Patients after Pancreaticoduodenectomy. J INVEST SURG 2021; 35:330-346. [PMID: 33525943 DOI: 10.1080/08941939.2020.1863527] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Objective: Pancreatic cancer (PC) is an extremely malignant tumor with similar morbidity and mortality and lack of an effective treatment. This study explored the prognostic value and molecular mechanisms of proteasome 26S subunit, non-ATPase (PSMD) family genes in pancreatic ductal adenocarcinoma (PDAC).Methods: Survival analyses were performed to elucidate the relationship between prognosis and the level of PSMD expression. ROC curves and nomograms were constructed to predict the prognosis. A bioinformatics analysis was used to explore the co-expression and complex interaction networks of PSMDs. The potential mechanisms were further explored via gene set enrichment analysis (GSEA).Results: We find high levels of PSMD6, PSMD9, PSMD11, and PSMD14 expression were significantly associated with a poorer OS. High PSMD6 and PSMD11 expression was associated with a poorer relapse-free survival (RFS). A risk score model was constructed based on prognosis-related genes. The area under ROC curves (AUC) was 53.3%, 59.3%, and 62.9% for 1-, 2-, 3 years, respectively.Conclusion: GSEA revealed that PSMD6 and PSMD11 play a role in PDAC through various biological processes and signaling pathways, including TP53, CDKN2A, MYC pathway, DNA repair, KRAS, cell cycle checkpoint, NIK, NF-κB signaling pathway, and proteasomes. This study demonstrated that PSMD6 and PSMD11 could serve as a potential prognostic and diagnostic biomarkers for patients with early-stage PDAC after pancreaticoduodenectomy.
Collapse
Affiliation(s)
- Caifu Zhou
- Research Department, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Haixia Li
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiao Han
- Research Department, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hongbing Pang
- Research Department, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Manya Wu
- Research Department, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yanping Tang
- Research Department, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiaoling Luo
- Research Department, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China.,School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| |
Collapse
|
7
|
Tyagi A, Daliri EBM, Kwami Ofosu F, Yeon SJ, Oh DH. Food-Derived Opioid Peptides in Human Health: A Review. Int J Mol Sci 2020; 21:E8825. [PMID: 33233481 PMCID: PMC7700510 DOI: 10.3390/ijms21228825] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
World Health Organization data suggest that stress, depression, and anxiety have a noticeable prevalence and are becoming some of the most common causes of disability in the Western world. Stress-related disorders are considered to be a challenge for the healthcare system with their great economic and social impact. The knowledge on these conditions is not very clear among many people, as a high proportion of patients do not respond to the currently available medications for targeting the monoaminergic system. In addition, the use of clinical drugs is also associated with various side effects such as vomiting, dizziness, sedation, nausea, constipation, and many more, which prevents their effective use. Therefore, opioid peptides derived from food sources are becoming one of the safe and natural alternatives because of their production from natural sources such as animals and plant proteins. The requirement for screening and considering dietary proteins as a source of bioactive peptides is highlighted to understand their potential roles in stress-related disorders as a part of a diet or as a drug complementing therapeutic prescription. In this review, we discussed current knowledge on opioid endogenous and exogenous peptides concentrating on their production, purification, and related studies. To fully understand their potential in stress-related conditions, either as a drug or as a therapeutic part of a diet prescription, the need to screen more dietary proteins as a source of novel opioid peptides is emphasized.
Collapse
Affiliation(s)
| | | | | | | | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 200-701, Korea; (A.T.); (E.B.-M.D.); (F.K.O.); (S.-J.Y.)
| |
Collapse
|
8
|
Li C, Li J, Xu Y, Zhan Y, Li Y, Song T, Zheng J, Yang H. Application of Phage-Displayed Peptides in Tumor Imaging Diagnosis and Targeting Therapy. Int J Pept Res Ther 2020; 27:587-595. [PMID: 32901205 PMCID: PMC7471523 DOI: 10.1007/s10989-020-10108-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022]
Abstract
Phage display is an effective and powerful technique that provides a route to discovery unique peptides targeting to tumor cells. Specifically binding peptides are considered as the valuable target directing molecule fragments with potential efficiency to improve the current tumor clinic, and offer new approaches for tumor prevention, diagnosis and treatment. We focus on the recent advances in the isolation of tumor-targeting peptides by biopanning methods, with particular emphasis on molecular imaging, and pharmaceutical targeting therapy.
Collapse
Affiliation(s)
- Chunyan Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, 127 West ChangLe Road, Xi'an, 710032 Shaanxi China
| | - Jia Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, 127 West ChangLe Road, Xi'an, 710032 Shaanxi China
| | - Ying Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, 127 West ChangLe Road, Xi'an, 710032 Shaanxi China
| | - Ying Zhan
- 518 Hospital of PLA, Xi'an, 710043 Shaanxi China
| | - Yu Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, 127 West ChangLe Road, Xi'an, 710032 Shaanxi China
| | - Tingting Song
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, 127 West ChangLe Road, Xi'an, 710032 Shaanxi China
| | - Jiao Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, 127 West ChangLe Road, Xi'an, 710032 Shaanxi China
| | - Hong Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Air Force Medical University, 127 West ChangLe Road, Xi'an, 710032 Shaanxi China
| |
Collapse
|
9
|
Yang Y, Liu C, Yang X. Endoscopic Molecular Imaging plus Photoimmunotherapy: A New Strategy for Monitoring and Treatment of Bladder Cancer. MOLECULAR THERAPY-ONCOLYTICS 2020; 18:409-418. [PMID: 32913890 PMCID: PMC7452043 DOI: 10.1016/j.omto.2020.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Due to the high recurrence and progression rate of non-muscle invasive bladder cancer after transurethral resection of bladder tumor, some new optical imaging technologies have arisen as auxiliary imaging modes for white light cystoscopy to improve the detection rate of small or occult tumor lesions, such as photodynamic diagnosis, narrow-band imaging, and molecular imaging. White light cystoscopy is inadequate and imperfect for bladder cancer detection, and thus residual tumors or coexisting flat malignant lesions, especially carcinoma in situ, would be ignored during conventional resection. The bladder, a hollow organ with high compliance, provides an ideal closed operation darkroom for endoscopic molecular imaging free from interference of external light sources. Also, intravesical instillation of a molecular fluorescent tracer is simple and convenient before surgery through the urethra. Molecular fluorescent tracer has high sensitivity and specificity to tumor cells, and its mediated molecular imaging allows small or occult tumor lesion detection while minimizing false-positive results. Meanwhile, endoscopic molecular imaging provides a real-time and dynamic image during surgery, which helps urologists to perform high-quality and complete tumor resection through accurate judgment of tumor boundaries and depth of invasion. Photoimmunotherapy is a novel molecular targeted therapeutic pattern of photodynamic therapy that kills malignant cells selectively and minimizes the cytotoxicity to normal tissues. The combination of endoscopic molecular imaging and photoimmunotherapy used in initial treatment may avoid the need of repeat transurethral resection in strictly selected patients and improve oncological outcomes such as recurrence-free survival and overall survival after operation.
Collapse
Affiliation(s)
- Yongjun Yang
- First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Chao Liu
- First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaofeng Yang
- First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| |
Collapse
|
10
|
Xu H, Cao B, Li Y, Mao C. Phage nanofibers in nanomedicine: Biopanning for early diagnosis, targeted therapy, and proteomics analysis. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1623. [PMID: 32147974 DOI: 10.1002/wnan.1623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/02/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Abstract
Display of a peptide or protein of interest on the filamentous phage (also known as bacteriophage), a biological nanofiber, has opened a new route for disease diagnosis and therapy as well as proteomics. Earlier phage display was widely used in protein-protein or antigen-antibody studies. In recent years, its application in nanomedicine is becoming increasingly popular and encouraging. We aim to review the current status in this research direction. For better understanding, we start with a brief introduction of basic biology and structure of the filamentous phage. We present the principle of phage display and library construction method on the basis of the filamentous phage. We summarize the use of the phage displayed peptide library for selecting peptides with high affinity against cells or tissues. We then review the recent applications of the selected cell or tissue targeting peptides in developing new targeting probes and therapeutics to advance the early diagnosis and targeted therapy of different diseases in nanomedicine. We also discuss the integration of antibody phage display and modern proteomics in discovering new biomarkers or target proteins for disease diagnosis and therapy. Finally, we propose an outlook for further advancing the potential impact of phage display on future nanomedicine. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
Collapse
Affiliation(s)
- Hong Xu
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Binrui Cao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Yan Li
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| |
Collapse
|
11
|
Novel real-time optical imaging modalities for the detection of neoplastic lesions in urology: a systematic review. Surg Endosc 2018; 33:1349-1367. [PMID: 30421080 PMCID: PMC6484817 DOI: 10.1007/s00464-018-6578-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 11/02/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Current optical diagnostic techniques for malignancies are limited in their diagnostic accuracy and lack the ability to further characterise disease, leading to the rapidly increasing development of novel imaging methods within urology. This systematic review critically appraises the literature for novel imagining modalities, in the detection and staging of urological cancer and assesses their effectiveness via their utility and accuracy. METHODS A systematic literature search utilising MEDLINE, EMBASE and Cochrane Library Database was conducted from 1970 to September 2018 by two independent reviewers. Studies were included if they assessed real-time imaging modalities not already approved in guidelines, in vivo and in humans. Outcome measures included diagnostic accuracy and utility parameters, including feasibility and cost. RESULTS Of 5475 articles identified from screening, a final 46 were included. Imaging modalities for bladder cancer included optical coherence tomography (OCT), confocal laser endomicroscopy, autofluorescence and spectroscopic techniques. OCT was the most widely investigated, with 12 studies demonstrating improvements in overall diagnostic accuracy (sensitivity 74.5-100% and specificity 60-98.5%). Upper urinary tract malignancy diagnosis was assessed using photodynamic diagnosis (PDD), narrow band imaging, optical coherence tomography and confocal laser endomicroscopy. Only PDD demonstrated consistent improvements in overall diagnostic accuracy in five trials (sensitivity 94-96% and specificity 96.6-100%). Limited evidence for optical coherence tomography in percutaneous renal biopsy was identified, with anecdotal evidence for any modality in penile cancer. CONCLUSIONS Evidence supporting the efficacy for identified novel imaging modalities remains limited at present. However, OCT for bladder cancer and PDD in upper tract malignancy demonstrate the best potential for improvement in overall diagnostic accuracy. OCT may additionally aid intraoperative decision making via real-time staging of disease. Both modalities require ongoing investigation through larger, well-conducted clinical trials to assess their diagnostic accuracy, use as an intraoperative staging aid and how to best utilise them within clinical practice.
Collapse
|
12
|
Peng L, Shang W, Guo P, He K, Wang H, Han Z, Jiang H, Tian J, Wang K, Xu W. Phage Display-Derived Peptide-Based Dual-Modality Imaging Probe for Bladder Cancer Diagnosis and Resection Postinstillation: A Preclinical Study. Mol Cancer Ther 2018; 17:2100-2111. [PMID: 30082470 DOI: 10.1158/1535-7163.mct-18-0212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/09/2018] [Accepted: 08/02/2018] [Indexed: 11/16/2022]
Abstract
Bladder cancer is a common human malignancy. Conventional ultrasound and white-light cystoscopy are often used for bladder cancer diagnosis and resection, but insufficient specificity results in a high bladder cancer recurrence rate. New strategies for the diagnosis and resection of bladder cancer are needed. In this study, we developed a highly specific peptide-based probe for bladder cancer photoacoustic imaging (PAI) diagnosis and near-infrared (NIR)-imaging-guided resection after instillation. A bladder cancer-specific peptide (PLSWT7) was selected by in vivo phage-display technology and labeled with IRDye800CW to synthesize a bladder cancer-specific dual-modality imaging (DMI) probe (PLSWT7-DMI). The feasibility of PLSWT7-DMI-based dual-modality PAI-NIR imaging was assessed in vitro, in mouse models, and ex vivo human bladders. An air-pouch bladder cancer (APBC) model suitable for probe instillation was established to evaluate the probe-based bladder cancer PAI diagnosis and NIR-imaging-guided resection. Human bladders were used to assess whether the PLSWT7-DMI-based DMI strategy is a translatable approach for bladder cancer detection and resection. The probe exhibited excellent selectivity and specificity both in vitro and in vivo Postinstillation of the probe, tumors <3 mm were detectable by PAI, and NIR-imaging-guided tumor resection decreased the bladder cancer recurrence rate by 90% and increased the survival in the mouse model. Additionally, ex vivo NIR imaging of human bladders indicated that PLSWT7-DMI-based imaging would potentially allow precise resection of bladder cancer in clinical settings. This PLSWT7-DMI-based DMI strategy was a translatable approach for bladder cancer diagnosis and resection and could potentially lower the bladder cancer recurrence rate. Mol Cancer Ther; 17(10); 2100-11. ©2018 AACR.
Collapse
Affiliation(s)
- Li Peng
- Urology Surgery Department, The Fourth Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China.,CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P.R. China.,Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, Heilongjiang, P.R. China
| | - Wenting Shang
- CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P.R. China.,The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Pengyu Guo
- Urology Surgery Department, The Fourth Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China.,CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P.R. China.,Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, Heilongjiang, P.R. China
| | - Kunshan He
- CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P.R. China.,The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Hongzhi Wang
- Urology Surgery Department, The Fourth Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China.,Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, Heilongjiang, P.R. China
| | - Ziyu Han
- CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P.R. China.,The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jiang
- CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P.R. China.,The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Jie Tian
- CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P.R. China. .,The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,Beihang University, Beijing, P.R. China
| | - Kun Wang
- CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P.R. China. .,The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Wanhai Xu
- Urology Surgery Department, The Fourth Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China. .,Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, Heilongjiang, P.R. China
| |
Collapse
|
13
|
Selection and identification of novel peptides specifically targeting human cervical cancer. Amino Acids 2018; 50:577-592. [DOI: 10.1007/s00726-018-2539-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/18/2018] [Indexed: 12/30/2022]
|
14
|
Abstract
Novel affinity agents with high specificity are needed to make progress in disease diagnosis and therapy. Over the last several years, peptides have been considered to have fundamental benefits over other affinity agents, such as antibodies, due to their fast blood clearance, low immunogenicity, rapid tissue penetration, and reproducible chemical synthesis. These features make peptides ideal affinity agents for applications in disease diagnostics and therapeutics for a wide variety of afflictions. Virus-derived peptide techniques provide a rapid, robust, and high-throughput way to identify organism-targeting peptides with high affinity and selectivity. Here, we will review viral peptide display techniques, how these techniques have been utilized to select new organism-targeting peptides, and their numerous biomedical applications with an emphasis on targeted imaging, diagnosis, and therapeutic techniques. In the future, these virus-derived peptides may be used as common diagnosis and therapeutics tools in local clinics.
Collapse
Affiliation(s)
- Mingying Yang
- Institute of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Kegan Sunderland
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| |
Collapse
|