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Proteomics and Metabolomics Approaches on Cancer Research
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Proteomics and Metabolomics Approaches on Cancer Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Oncology".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 13554

Special Issue Editors

Dr. Susan Costantini

E-Mail Website
Guest Editor
Experimental Pharmacology Unit, Laboratory of Mercogliano, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, Napoli, Italy
Interests: cancer; cytokines; metabolome; lipidome; NMR; LC-MS; systems biology; computational biology; molecular biology
Special Issues, Collections and Topics in MDPI journals
Dr. Biagio Pucci

E-Mail Website
Guest Editor
Mercogliano Laboratory, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, Napoli, Italy
Interests: cancer; proteome; metabolome; lipidome; LC-MS; cellular biology; experimental pharmacology; molecular biology

Special Issue Information

Dear Colleagues,

High-throughput technologies provide a great amount of data at multiple levels capable of revealing the complexity of cancer cells and their micro- and macro-environment, whereas the analyses of single data layers provide only causal relations. Therefore, multi-omics data integration strategies, including genome, epigenome, transcriptome, proteome, metabolome, microbiomes, lipidome and miRNome, also with bioinformatics and systems biology approaches, offer fantastic opportunities to understand the biology behind complex diseases, such as cancer.

In recent years, multi-omics approaches have been applied to many cancer studies for better identification of clinical subtypes or drug resistance, and the discovery of novel biomarkers able to predict the cancer progression, the patient’s outcome and the efficacy of new drugs and combination therapies.

In this context, so-called “liquid biopsies” allow a snapshot of a patient’s patho-physiological state at a given time and provide dynamic monitoring with insight into the spatial and temporal clonal evolution processes of the tumor, including secondary resistance to treatment, which is prohibited by the invasiveness of tissue biopsies.

The aim of this Special Issue is to present the latest research and new studies based on proteomics and metabolomics approaches applied to cancer research on different biological matrices such as cancer cells, tissues and biological fluids.

Dr. Susan Costantini
Dr. Biagio Pucci
Guest Editors

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • cancer
  • proteome
  • metabolome
  • microbiome
  • lipidome
  • LC-MS
  • NMR
  • GC-MS
  • cell biology/tissue
  • liquid biopsy
  • systems biology

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Published Papers (4 papers)

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Research

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12 pages, 1248 KiB  
Article
Loco-Regional Control and Sustained Difference in Serum Immune Protein Expression in Patients Treated for p16-Positive and p16-Negative Head and Neck Squamous Cell Carcinoma
by Karl Sandström, Ylva Tiblom Ehrsson, Felix Sellberg, Hemming Johansson and Göran Laurell
Int. J. Mol. Sci. 2023, 24(4), 3838; https://doi.org/10.3390/ijms24043838 - 14 Feb 2023
Cited by 1 | Viewed by 1877
Abstract
The main prognostic factors for patients with head and neck cancer are the tumour site and stage, yet immunological and metabolic factors are certainly important, although knowledge is still limited. Expression of the biomarker p16INK4a (p16) in oropharyngeal cancer tumour tissue is one [...] Read more.
The main prognostic factors for patients with head and neck cancer are the tumour site and stage, yet immunological and metabolic factors are certainly important, although knowledge is still limited. Expression of the biomarker p16INK4a (p16) in oropharyngeal cancer tumour tissue is one of the few biomarkers for the diagnosis and prognosis of head and neck cancer. The association between p16 expression in the tumour and the systemic immune response in the blood compartment has not been established. This study aimed to assess whether there is a difference in serum immune protein expression profiles between patients with p16+ and p16- head and squamous cell carcinoma (HNCC). The serum immune protein expression profiles, using the Olink® immunoassay, of 132 patients with p16+ and p16- tumours were compared before treatment and one year after treatment. A significant difference in the serum immune protein expression profile was observed both before and one year after treatment. In the p16- group, a low expression of four proteins: IL12RB1, CD28, CCL3, and GZMA before treatment conferred a higher rate of failure. Based on the sustained difference between serum immune proteins, we hypothesise that the immunological system is still adapted to the tumour p16 status one year after tumour eradication or that a fundamental difference exists in the immunological system between patients with p16+ and p16- tumours. Full article
(This article belongs to the Special Issue Proteomics and Metabolomics Approaches on Cancer Research)
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24 pages, 10901 KiB  
Article
Metabolomics and Lipidomics Screening Reveal Reprogrammed Signaling Pathways toward Cancer Development in Non-Alcoholic Steatohepatitis
by Eman A. Ahmed, Marwa O. El-Derany, Ali Mostafa Anwar, Essa M. Saied and Sameh Magdeldin
Int. J. Mol. Sci. 2023, 24(1), 210; https://doi.org/10.3390/ijms24010210 - 22 Dec 2022
Cited by 18 | Viewed by 5287
Abstract
With the rising incidence of hepatocellular carcinoma (HCC) from non-alcoholic steatohepatitis (NASH), identifying new metabolic readouts that function in metabolic pathway perpetuation is still a demand. The study aimed to compare the metabolic signature between NASH and NASH-HCC patients to explore novel reprogrammed [...] Read more.
With the rising incidence of hepatocellular carcinoma (HCC) from non-alcoholic steatohepatitis (NASH), identifying new metabolic readouts that function in metabolic pathway perpetuation is still a demand. The study aimed to compare the metabolic signature between NASH and NASH-HCC patients to explore novel reprogrammed metabolic pathways that might modulate cancer progression in NASH patients. NASH and NASH-HCC patients were recruited and screened for metabolomics, and isotope-labeled lipidomics were targeted and profiled using the EXION-LCTM system equipped with a Triple-TOFTM 5600+ system. Results demonstrated significantly (p ≤ 0.05) higher levels of triacylglycerol, AFP, AST, and cancer antigen 19-9 in NASH-HCC than in NASH patients, while prothrombin time, platelet count, and total leukocyte count were decreased significantly (p ≤ 0.05). Serum metabolic profiling showed a panel of twenty metabolites with 10% FDR and p ≤ 0.05 in both targeted and non-targeted analysis that could segregate NASH-HCC from NASH patients. Pathway analysis revealed that the metabolites are implicated in the down-regulation of necroptosis, amino acid metabolism, and regulation of lipid metabolism by PPAR-α, biogenic amine synthesis, fatty acid metabolism, and the mTOR signaling pathway. Cholesterol metabolism, DNA repair, methylation pathway, bile acid, and salts metabolism were significantly upregulated in NASH-HCC compared to the NASH group. Metabolite–protein interactions network analysis clarified a set of well-known protein encoding genes that play crucial roles in cancer, including PEMT, IL4I1, BAAT, TAT, CDKAL1, NNMT, PNP, NOS1, and AHCYL. Taken together, reliable metabolite fingerprints are presented and illustrated in a detailed map for the most predominant reprogrammed metabolic pathways that target HCC development from NASH. Full article
(This article belongs to the Special Issue Proteomics and Metabolomics Approaches on Cancer Research)
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15 pages, 1370 KiB  
Article
Serum Proteomics in Patients with Head and Neck Cancer: Peripheral Blood Immune Response to Treatment
by Thorsteinn Astradsson, Felix Sellberg, Ylva Tiblom Ehrsson, Karl Sandström and Göran Laurell
Int. J. Mol. Sci. 2022, 23(11), 6304; https://doi.org/10.3390/ijms23116304 - 4 Jun 2022
Cited by 9 | Viewed by 2831
Abstract
In this real-world study, the aims were to prospectively evaluate the expression of inflammatory proteins in serum collected from head and neck cancer patients before and after treatment, and to assess whether there were differences in expression associated with treatment modalities. The mixed [...] Read more.
In this real-world study, the aims were to prospectively evaluate the expression of inflammatory proteins in serum collected from head and neck cancer patients before and after treatment, and to assess whether there were differences in expression associated with treatment modalities. The mixed study cohort consisted of 180 patients with head and neck cancer. The most common tumor sites were the oropharynx (n = 81), the oral cavity (n = 53), and the larynx (n = 22). Blood tests for proteomics analysis were carried out before treatment, 7 weeks after the start of treatment, and 3 and 12 months after the termination of treatment. Sera were analyzed for 83 proteins using an immuno-oncology biomarker panel (Olink, Uppsala, Sweden). Patients were divided into four treatment groups: surgery alone (Surg group, n = 24), radiotherapy with or without surgery (RT group, n = 94), radiotherapy with concomitant cisplatin (CRT group, n = 47), and radiotherapy with concomitant targeted therapy (RT Cetux group, n = 15). For the overall cohort, the expression levels of 15 of the 83 proteins changed significantly between the pretreatment sample and the sample taken 7 weeks after the start of treatment. At 7 weeks after the start of treatment, 13 proteins showed lower expression in the CRT group compared to the RT group. The majority of the inflammatory proteins had returned to their pretreatment levels after 12 months. It was clearly demonstrated that cisplatin-based chemoradiation has immunological effects in patients with head and neck cancer. This analysis draws attention to several inflammatory proteins that are of interest for further studies. Full article
(This article belongs to the Special Issue Proteomics and Metabolomics Approaches on Cancer Research)
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Review

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20 pages, 1734 KiB  
Review
Bioactive Compounds from Marine Sponges and Algae: Effects on Cancer Cell Metabolome and Chemical Structures
by Roberta Esposito, Serena Federico, Francesca Glaviano, Emanuele Somma, Valerio Zupo and Maria Costantini
Int. J. Mol. Sci. 2022, 23(18), 10680; https://doi.org/10.3390/ijms231810680 - 14 Sep 2022
Cited by 9 | Viewed by 2753
Abstract
Metabolomics represent the set of small organic molecules generally called metabolites, which are located within cells, tissues or organisms. This new “omic” technology, together with other similar technologies (genomics, transcriptomics and proteomics) is becoming a widely used tool in cancer research, aiming at [...] Read more.
Metabolomics represent the set of small organic molecules generally called metabolites, which are located within cells, tissues or organisms. This new “omic” technology, together with other similar technologies (genomics, transcriptomics and proteomics) is becoming a widely used tool in cancer research, aiming at the understanding of global biology systems in their physiologic or altered conditions. Cancer is among the most alarming human diseases and it causes a considerable number of deaths each year. Cancer research is one of the most important fields in life sciences. In fact, several scientific advances have been made in recent years, aiming to illuminate the metabolism of cancer cells, which is different from that of healthy cells, as suggested by Otto Warburg in the 1950s. Studies on sponges and algae revealed that these organisms are the main sources of the marine bioactive compounds involved in drug discovery for cancer treatment and prevention. In this review, we analyzed these two promising groups of marine organisms to focus on new metabolomics approaches for the study of metabolic changes in cancer cell lines treated with chemical extracts from sponges and algae, and for the classification of the chemical structures of bioactive compounds that may potentially prove useful for specific biotechnological applications. Full article
(This article belongs to the Special Issue Proteomics and Metabolomics Approaches on Cancer Research)
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