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Proteomes
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Cancer Proteomics
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Cancer Proteomics

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (31 March 2017) | Viewed by 29606

Special Issue Editor

Prof. Dr. Karl-Friedrich Becker

E-Mail Website
Guest Editor
Institute of Pathology, Technische Universität München, München, Germany
Interests: quantitative (phospho)protein analysis of clinical tissue samples; development and validation of molecular biomarkers; improvement of tissue quality for diagnosis and research; intratumoral heterogeneity of human cancers; tissue proteomics; reverse phase protein array; protein biomarkers in cancer tissues; diagnosis; therapy; pathology; tumor heterogeneity; preanalytics; standardization; personalized medicine

Special Issue Information

Dear Colleagues,

While human cancers evolve from benign to malignant lesions by acquiring a series of gene mutations over time, the results of gene mutations translate to dysregulation or dysfunction of proteins, which are attractive molecular biomarkers and drug targets. Proteomics technologies have much improved during the last five years. Powerful extract-based and section-based methods and their targeted and discovery-based variations are available to establish comprehensive protein profiling maps in human cancers.

One goal for clinical proteomics will be to characterize the information flow within single cells, tissues or entire organisms under normal or disease conditions. Although tissue samples will continue to be the material of choice for definitive cancer diagnosis, evaluation of treatment response and disease monitoring may be performed using less invasive samples, for example, blood samples or other body fluids, such as urine or saliva. In addition, assays that can measure protein interactions will complement current protein profiling technologies. In order to improve assay results and patient outcomes, the pre-analytical workflow for clinical proteomics needs to be standardized.

This Special Issue on cancer proteomics will highlight the opportunities and possibilities of proteomic studies in cancer research. The newest proteomics technologies in different fields of cancer biology will be reviewed and challenges for their implementation in future clinical workflows addressed.

Prof. Dr. Karl-Friedrich Becker
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • proteomics
  • tissues
  • blood
  • diagnosis
  • therapy
  • biomarkers
  • post translational modifications
  • preanalytics
  • standardization
  • tumor heterogeneity
  • personalized medicine
  • mass spectrometry
  • MALDI Imaging
  • Reverse Phase Protein Arrays

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Published Papers (4 papers)

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5048 KiB  
Article
Retrospective Proteomic Screening of 100 Breast Cancer Tissues
by Ida Pucci-Minafra, Gianluca Di Cara, Rosa Musso, Patrizia Cancemi, Nadia Ninfa Albanese, Elena Roz and Salvatore Minafra
Proteomes 2017, 5(3), 15; https://doi.org/10.3390/proteomes5030015 - 7 Jul 2017
Cited by 10 | Viewed by 7193
Abstract
The present investigation has been conducted on one hundred tissue fragments of breast cancer, collected and immediately cryopreserved following the surgical resection. The specimens were selected from patients with invasive ductal carcinoma of the breast, the most frequent and potentially aggressive type of [...] Read more.
The present investigation has been conducted on one hundred tissue fragments of breast cancer, collected and immediately cryopreserved following the surgical resection. The specimens were selected from patients with invasive ductal carcinoma of the breast, the most frequent and potentially aggressive type of mammary cancer, with the objective to increase the knowledge of breast cancer molecular markers potentially useful for clinical applications. The proteomic screening; by 2D-IPG and mass spectrometry; allowed us to identify two main classes of protein clusters: proteins expressed ubiquitously at high levels in all patients; and proteins expressed sporadically among the same patients. Within the group of ubiquitous proteins, glycolytic enzymes and proteins with anti-apoptotic activity were predominant. Among the sporadic ones, proteins involved in cell motility, molecular chaperones and proteins involved in the detoxification appeared prevalent. The data of the present study indicates that the primary tumor growth is reasonably supported by concurrent events: the inhibition of apoptosis and stimulation of cellular proliferation, and the increased expression of glycolytic enzymes with multiple functions. The second phase of the evolution of the tumor can be prematurely scheduled by the occasional presence of proteins involved in cell motility and in the defenses of the oxidative stress. We suggest that this approach on large-scale 2D-IPG proteomics of breast cancer is currently a valid tool that offers the opportunity to evaluate on the same assay the presence and recurrence of individual proteins, their isoforms and short forms, to be proposed as prognostic indicators and susceptibility to metastasis in patients operated on for invasive ductal carcinoma of the breast. Full article
(This article belongs to the Special Issue Cancer Proteomics)
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1808 KiB  
Article
Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes
by Roger Higdon, Jessie Kala, Devan Wilkins, Julia Fangfei Yan, Manveen K. Sethi, Liang Lin, Siqi Liu, Elizabeth Montague, Imre Janko, John Choiniere, Natali Kolker, William S. Hancock, Eugene Kolker and Susan Fanayan
Proteomes 2017, 5(1), 5; https://doi.org/10.3390/proteomes5010005 - 3 Feb 2017
Cited by 20 | Viewed by 6346
Abstract
Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Patient survival has remained largely the same for the past 20 years, with therapies causing significant health, cognitive, behavioral and developmental complications for those who survive the tumor. In this study, we profiled [...] Read more.
Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Patient survival has remained largely the same for the past 20 years, with therapies causing significant health, cognitive, behavioral and developmental complications for those who survive the tumor. In this study, we profiled the total transcriptome and proteome of two established MB cell lines, Daoy and UW228, using high-throughput RNA sequencing (RNA-Seq) and label-free nano-LC-MS/MS-based quantitative proteomics, coupled with advanced pathway analysis. While Daoy has been suggested to belong to the sonic hedgehog (SHH) subtype, the exact UW228 subtype is not yet clearly established. Thus, a goal of this study was to identify protein markers and pathways that would help elucidate their subtype classification. A number of differentially expressed genes and proteins, including a number of adhesion, cytoskeletal and signaling molecules, were observed between the two cell lines. While several cancer-associated genes/proteins exhibited similar expression across the two cell lines, upregulation of a number of signature proteins and enrichment of key components of SHH and WNT signaling pathways were uniquely observed in Daoy and UW228, respectively. The novel information on differentially expressed genes/proteins and enriched pathways provide insights into the biology of MB, which could help elucidate their subtype classification. Full article
(This article belongs to the Special Issue Cancer Proteomics)
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Review

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874 KiB  
Review
Comprehensive Analysis of Cancer-Proteogenome to Identify Biomarkers for the Early Diagnosis and Prognosis of Cancer
by Hem D. Shukla
Proteomes 2017, 5(4), 28; https://doi.org/10.3390/proteomes5040028 - 25 Oct 2017
Cited by 30 | Viewed by 5872
Abstract
During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it [...] Read more.
During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment. The heterogeneous nature of cancer has hindered progress in understanding the underlying mechanisms that lead to abnormal cellular growth. Since, the start of The Cancer Genome Atlas (TCGA), and the International Genome consortium projects, there has been tremendous progress in genome sequencing and immense numbers of cancer genomes have been completed, and this approach has transformed our understanding of the diagnosis and treatment of different types of cancers. By employing Genomics and proteomics technologies, an immense amount of genomic data is being generated on clinical tumors, which has transformed the cancer landscape and has the potential to transform cancer diagnosis and prognosis. A complete molecular view of the cancer landscape is necessary for understanding the underlying mechanisms of cancer initiation to improve diagnosis and prognosis, which ultimately will lead to personalized treatment. Interestingly, cancer proteome analysis has also allowed us to identify biomarkers to monitor drug and radiation resistance in patients undergoing cancer treatment. Further, TCGA-funded studies have allowed for the genomic and transcriptomic characterization of targeted cancers, this analysis aiding the development of targeted therapies for highly lethal malignancy. High-throughput technologies, such as complete proteome, epigenome, protein–protein interaction, and pharmacogenomics data, are indispensable to glean into the cancer genome and proteome and these approaches have generated multidimensional universal studies of genes and proteins (OMICS) data which has the potential to facilitate precision medicine. However, due to slow progress in computational technologies, the translation of big omics data into their clinical aspects have been slow. In this review, attempts have been made to describe the role of high-throughput genomic and proteomic technologies in identifying a panel of biomarkers which could be used for the early diagnosis and prognosis of cancer. Full article
(This article belongs to the Special Issue Cancer Proteomics)
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1736 KiB  
Review
Advances of Salivary Proteomics in Oral Squamous Cell Carcinoma (OSCC) Detection: An Update
by Rabia Sannam Khan, Zohaib Khurshid, Shazia Akhbar and Syed Faraz Moin
Proteomes 2016, 4(4), 41; https://doi.org/10.3390/proteomes4040041 - 15 Dec 2016
Cited by 38 | Viewed by 9622
Abstract
Oral cancer refers to malignancies that have higher morbidity and mortality rates due to the late stage diagnosis and no early detection of a reliable diagnostic marker, while oral squamous cell carcinoma (OSCC) is amongst the world’s top ten most common cancers. Diagnosis [...] Read more.
Oral cancer refers to malignancies that have higher morbidity and mortality rates due to the late stage diagnosis and no early detection of a reliable diagnostic marker, while oral squamous cell carcinoma (OSCC) is amongst the world’s top ten most common cancers. Diagnosis of cancer requires highly sensitive and specific diagnostic tools which can support untraceable hidden sites of OSCC, yet to be unleashed, for which plenty of biomarkers are identified; the most recommended biomarker detection medium for OSCC includes biological fluids, such as blood and saliva. Saliva holds a promising future in the search for new clinical biomarkers that are easily accessible, less complex, accurate, and cost effective as well as being a non-invasive technique to follow, by analysing the malignant cells’ molecular pathology obtained from saliva through proteomic, genomic and transcriptomic approaches. However, protein biomarkers provide an immense potential for developing novel marker-based assays for oral cancer, hence this current review offers an overall focus on the discovery of a panel of candidates as salivary protein biomarkers, as well as the proteomic tools used for their identification and their significance in early oral cancer detection. Full article
(This article belongs to the Special Issue Cancer Proteomics)
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