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Cells
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New Advances in Proteomics in Cancer
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New Advances in Proteomics in Cancer

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Methods".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 5930

Special Issue Editors

Dr. Arun Wiita

E-Mail Website
Guest Editor
1. Department of Laboratory Medicine, University of California, San Francisco, CA, USA
2. Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
Interests: surface proteomics; drug target discovery; cellular therapy development; mechanisms of therapy resistance in cancer
Prof. Dr. Sanjeeva Srivastava

E-Mail Website
Guest Editor
Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay Powai, Mumbai 400076, India
Interests: clinical proteomics; biomarker discovery in infectious diseases and cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Proteomic technologies have rapidly expanded over the past two decades to address the crucial observation: Biology Happens at the Protein Level. In cancer biology, we have seen proteomic approaches play a foundational role in uncovering potential mechanisms of cancer initiation, metastasis, and treatment, as well as biomarker discovery and precision medicine strategies. These achievements have come through the systematic and extensive high-throughput analysis of protein expression profiles, protein sequences, structures, variants, PTMs, and functional effects. The emergence of fields featuring multi-omics integration, such as proteogenomics, as well as the incorporation of artificial intelligence into data analysis, have unlocked new capabilities of acquired datasets to provide biological insight into cancer. The goal of this Special Issue is to showcase key advances on applying proteomic approaches to the study of cancer, both related to advances in underlying technologies and key biological discoveries. The topics to be included, but not limited to, are proteomic research with a cancer focus involving the development of high-throughput proteomic methods, proteomics-based biological and clinical findings, small molecule and immunotherapeutic target discovery, therapeutic mechanism of action, cancer immunology, advancements in sample preparation techniques, PTM analysis, single cell analysis, comprehensive metadata analysis, AI/statistics technology, etc. While tandem mass spectrometry-based strategies will be emphasized, other important technologies such as protein microarrays, mass cytometry, and direct protein sequencing will also be included. Interdisciplinary research is highly valued and encouraged. We welcome the submission of both original research articles and reviews.

Dr. Arun Wiita
Prof. Dr. Sanjeeva Srivastava
Guest Editors

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. Cells is an international peer-reviewed open access semimonthly 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 2700 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
  • cancer
  • biomarkers
  • surface proteomics
  • immunotherapeutic
  • cancer immunology
  • proteogenomics
  • protein microarrays
  • mass cytometry
  • single cell proteomics
  • immunopeptidomics
  • label-free detection platforms
  • sample prep for HT cancer proteomics

Published Papers (3 papers)

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Research

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25 pages, 6108 KiB  
Article
Functional Proteomics Characterization of the Role of SPRYD7 in Colorectal Cancer Progression and Metastasis
by Ana Montero-Calle, Sofía Jiménez de Ocaña, Ruth Benavente-Naranjo, Raquel Rejas-González, Rubén A. Bartolomé, Javier Martínez-Useros, Rodrigo Sanz, Jana Dziaková, María Jesús Fernández-Aceñero, Marta Mendiola, José Ignacio Casal, Alberto Peláez-García and Rodrigo Barderas
Cells 2023, 12(21), 2548; https://doi.org/10.3390/cells12212548 - 31 Oct 2023
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Abstract
SPRY domain-containing protein 7 (SPRYD7) is a barely known protein identified via spatial proteomics as being upregulated in highly metastatic-to-liver KM12SM colorectal cancer (CRC) cells in comparison to its isogenic poorly metastatic KM12C CRC cells. Here, we aimed to analyze SPRYD7’s role in [...] Read more.
SPRY domain-containing protein 7 (SPRYD7) is a barely known protein identified via spatial proteomics as being upregulated in highly metastatic-to-liver KM12SM colorectal cancer (CRC) cells in comparison to its isogenic poorly metastatic KM12C CRC cells. Here, we aimed to analyze SPRYD7’s role in CRC via functional proteomics. Through immunohistochemistry, the overexpression of SPRYD7 was observed to be associated with the poor survival of CRC patients and with an aggressive and metastatic phenotype. Stable SPRYD7 overexpression was performed in KM12C and SW480 poorly metastatic CRC cells and in their isogenic highly metastatic-to-liver-KM12SM-and-to-lymph-nodes SW620 CRC cells, respectively. Upon upregulation of SPRYD7, in vitro and in vivo functional assays confirmed a key role of SPRYD7 in the invasion and migration of CRC cells and in liver homing and tumor growth. Additionally, transient siRNA SPRYD7 silencing allowed us to confirm in vitro functional results. Furthermore, SPRYD7 was observed as an inductor of angiogenesis. In addition, the dysregulated SPRYD7-associated proteome and SPRYD7 interactors were elucidated via 10-plex TMT quantitative proteins, immunoproteomics, and bioinformatics. After WB validation, the biological pathways associated with the stable overexpression of SPRYD7 were visualized. In conclusion, it was demonstrated here that SPRYD7 is a novel protein associated with CRC progression and metastasis. Thus, SPRYD7 and its interactors might be of relevance in identifying novel therapeutic targets for advanced CRC. Full article
(This article belongs to the Special Issue New Advances in Proteomics in Cancer)
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20 pages, 3862 KiB  
Article
Integrated Meta-Omics Analysis Unveils the Pathways Modulating Tumorigenesis and Proliferation in High-Grade Meningioma
by Deeptarup Biswas, Ankit Halder, Abhilash Barpanda, Susmita Ghosh, Aparna Chauhan, Lipika Bhat, Sridhar Epari, Prakash Shetty, Aliasgar Moiyadi, Graham Roy Ball and Sanjeeva Srivastava
Cells 2023, 12(20), 2483; https://doi.org/10.3390/cells12202483 - 18 Oct 2023
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Abstract
Meningioma, a primary brain tumor, is commonly encountered and accounts for 39% of overall CNS tumors. Despite significant progress in clinical research, conventional surgical and clinical interventions remain the primary treatment options for meningioma. Several proteomics and transcriptomics studies have identified potential markers [...] Read more.
Meningioma, a primary brain tumor, is commonly encountered and accounts for 39% of overall CNS tumors. Despite significant progress in clinical research, conventional surgical and clinical interventions remain the primary treatment options for meningioma. Several proteomics and transcriptomics studies have identified potential markers and altered biological pathways; however, comprehensive exploration and data integration can help to achieve an in-depth understanding of the altered pathobiology. This study applied integrated meta-analysis strategies to proteomic and transcriptomic datasets comprising 48 tissue samples, identifying around 1832 common genes/proteins to explore the underlying mechanism in high-grade meningioma tumorigenesis. The in silico pathway analysis indicated the roles of extracellular matrix organization (EMO) and integrin binding cascades in regulating the apoptosis, angiogenesis, and proliferation responsible for the pathobiology. Subsequently, the expression of pathway components was validated in an independent cohort of 32 fresh frozen tissue samples using multiple reaction monitoring (MRM), confirming their expression in high-grade meningioma. Furthermore, proteome-level changes in EMO and integrin cell surface interactions were investigated in a high-grade meningioma (IOMM-Lee) cell line by inhibiting integrin-linked kinase (ILK). Inhibition of ILK by administrating Cpd22 demonstrated an anti-proliferative effect, inducing apoptosis and downregulating proteins associated with proliferation and metastasis, which provides mechanistic insight into the disease pathophysiology. Full article
(This article belongs to the Special Issue New Advances in Proteomics in Cancer)
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Review

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38 pages, 3172 KiB  
Review
Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome
by Tim M. G. MacKenzie, Rocío Cisneros, Rajan D. Maynard and Michael P. Snyder
Cells 2023, 12(14), 1860; https://doi.org/10.3390/cells12141860 - 14 Jul 2023
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Abstract
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of [...] Read more.
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a ‘reverse-ChIP’ approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a ‘reverse-ChIP’ technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens. Full article
(This article belongs to the Special Issue New Advances in Proteomics in Cancer)
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