Molecular Biomarkers in Solid Tumors

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 January 2021) | Viewed by 47469

Special Issue Editors


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Guest Editor
1. Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
2. Division of Pathology, IRCCS European Institute of Oncology (IEO), Milan, Italy
Interests: translational research; breast cancer; biomarkers; immunology; molecular pathology; TILs; precision medicine
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
1. Department of Medical Sciences, University of Turin, Turin, Italy
2. Division of Pathology, FPO-IRCCS Candiolo Cancer Institute, Candiolo, Italy
Interests: breast cancer; molecular pathology; HER2 status; tumor heterogeneity; tumor microenvironment

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Guest Editor
1. Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
2. Department of Oncology, Pisa University Hospital, 56126 Pisa, Italy
Interests: pathology; tumour microenvironment; molecular genetics; breast cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Our understanding of the pathogenesis of solid tumors at the molecular level is expanding day by day. Due to unprecedented technological developments, coupled with novel holistic approaches in translational research, a multitude of biomarkers at genomic, transcriptomic, proteomic, and immunologic levels have been discovered. These biomarkers are strongly impacting treatment decision making in patients with solid tumors.

This Special Issue in Genes on “Molecular Biomarkers in Solid Tumors” will provide a monographic portrait of the current state of knowledge of biomarkers for the clinical management of cancer patients. We especially welcome review articles (either systematic or discursive), original translational research studies, and short communications of preliminary, but significant, experimental results.

Prof. Nicola Fusco
Prof. Caterina Marchiò
Dr. Cristian Scatena
Dr. Michele Ghidini
Guest Editors

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Keywords

  • Cancer
  • Biomarkers
  • Translational research
  • Precision medicine

Published Papers (12 papers)

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Editorial

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3 pages, 187 KiB  
Editorial
Special Issue: Molecular Biomarkers in Solid Tumors
by Nicola Fusco, Caterina Marchiò, Michele Ghidini and Cristian Scatena
Genes 2021, 12(7), 984; https://doi.org/10.3390/genes12070984 - 28 Jun 2021
Cited by 1 | Viewed by 1902
Abstract
Diagnostic strategies using a next-generation systematic approach have the potential to radically improve the outcome and subsequent quality of life of patients with cancer [...] Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)

Research

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18 pages, 4876 KiB  
Article
Identification of Diagnostic Biomarkers and Subtypes of Liver Hepatocellular Carcinoma by Multi-Omics Data Analysis
by Xiao Ouyang, Qingju Fan, Guang Ling, Yu Shi and Fuyan Hu
Genes 2020, 11(9), 1051; https://doi.org/10.3390/genes11091051 - 6 Sep 2020
Cited by 12 | Viewed by 5077
Abstract
As liver hepatocellular carcinoma (LIHC) has high morbidity and mortality rates, improving the clinical diagnosis and treatment of LIHC is an important issue. The advent of the era of precision medicine provides us with new opportunities to cure cancers, including the accumulation of [...] Read more.
As liver hepatocellular carcinoma (LIHC) has high morbidity and mortality rates, improving the clinical diagnosis and treatment of LIHC is an important issue. The advent of the era of precision medicine provides us with new opportunities to cure cancers, including the accumulation of multi-omics data of cancers. Here, we proposed an integration method that involved the Fisher ratio, Spearman correlation coefficient, classified information index, and an ensemble of decision trees (DTs) for biomarker identification based on an unbalanced dataset of LIHC. Then, we obtained 34 differentially expressed genes (DEGs). The ability of the 34 DEGs to discriminate tumor samples from normal samples was evaluated by classification, and a high area under the curve (AUC) was achieved in our studied dataset and in two external validation datasets (AUC = 0.997, 0.973, and 0.949, respectively). Additionally, we also found three subtypes of LIHC, and revealed different biological mechanisms behind the three subtypes. Mutation enrichment analysis showed that subtype 3 had many enriched mutations, including tumor protein p53 (TP53) mutations. Overall, our study suggested that the 34 DEGs could serve as diagnostic biomarkers, and the three subtypes could help with precise treatment for LIHC. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
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15 pages, 2812 KiB  
Article
Comprehensive Genomic Analysis Reveals the Prognostic Role of LRRK2 Copy-Number Variations in Human Malignancies
by Gianluca Lopez, Giulia Lazzeri, Alessandra Rappa, Giuseppe Isimbaldi, Fulvia Milena Cribiù, Elena Guerini-Rocco, Stefano Ferrero, Valentina Vaira and Alessio Di Fonzo
Genes 2020, 11(8), 846; https://doi.org/10.3390/genes11080846 - 24 Jul 2020
Cited by 3 | Viewed by 2138
Abstract
Genetic alterations of leucine-rich repeat kinase 2 (LRRK2), one of the most important contributors to familial Parkinson’s disease (PD), have been hypothesized to play a role in cancer development due to demographical and preclinical data. Here, we sought to define the [...] Read more.
Genetic alterations of leucine-rich repeat kinase 2 (LRRK2), one of the most important contributors to familial Parkinson’s disease (PD), have been hypothesized to play a role in cancer development due to demographical and preclinical data. Here, we sought to define the prevalence and prognostic significance of LRRK2 somatic mutations across all types of human malignancies by querying the publicly available online genomic database cBioPortal. Ninety-six different studies with 14,041 cases were included in the analysis, and 761/14,041 (5.4%) showed genetic alterations in LRRK2. Among these, 585 (76.9%) were point mutations, indels or fusions, 168 (22.1%) were copy number variations (CNVs), and 8 (1.0%) showed both types of alterations. One case showed the somatic mutation R1441C. A significant difference in terms of overall survival (OS) was noted between cases harboring somatic LRRK2 whole deletions, amplifications, and CNV-unaltered cases (median OS: 20.09, 57.40, and 106.57 months, respectively; p = 0.0008). These results suggest that both LRRK2 amplifications and whole gene deletions could play a role in cancer development, paving the way for future research in terms of potential treatment with LRRK2 small molecule inhibitors for LRRK2-amplified cases. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
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15 pages, 1694 KiB  
Article
Prognostic Significance of RAS Mutations and P53 Expression in Cutaneous Squamous Cell Carcinomas
by Manuel António Campos, Sofia Macedo, Margarida Sá Fernandes, Ana Pestana, Joana Pardal, Rui Batista, João Vinagre, Agostinho Sanches, Armando Baptista, José Manuel Lopes and Paula Soares
Genes 2020, 11(7), 751; https://doi.org/10.3390/genes11070751 - 6 Jul 2020
Cited by 13 | Viewed by 2834
Abstract
TP53 is considered the most commonly-altered gene in cutaneous squamous cell carcinoma (cSCC). Conversely, RAS mutations have been reported in a low percentage of cSCC. The objective of our study was to evaluate the frequency of p53 expression and RAS mutations in cSCC [...] Read more.
TP53 is considered the most commonly-altered gene in cutaneous squamous cell carcinoma (cSCC). Conversely, RAS mutations have been reported in a low percentage of cSCC. The objective of our study was to evaluate the frequency of p53 expression and RAS mutations in cSCC and correlate them with clinicopathological features and patient outcome. We performed immunohistochemistry for p53 and genetic profiling for RAS mutations in a retrospective series of cSCC. The predictive value of p53 expression, RAS mutations, and clinicopathological parameters was assessed using logistic regression models. The overall frequency of RAS mutations was 9.3% (15/162), and 82.1% of the cases (133/162) had p53 overexpression. RAS mutations rate was 3.2% (1/31) of in situ cSCCs and 10.7% (14/131) of invasive cSCCs. RAS mutations were more frequently associated with an infiltrative than an expansive pattern of invasion (p = 0.046). p53 overexpression was a predictor of recurrence in the univariate analysis. Our results indicate that RAS mutations associate with features of local aggressiveness. Larger studies with more recurrent and metastatic cSCCs are necessary to further address the prognostic significance of p53 overexpression in patients’ risk stratification. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
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Review

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31 pages, 415 KiB  
Review
Circulating RNA in Kidney Cancer: What We Know and What We Still Suppose
by Alessandra Cinque, Riccardo Vago and Francesco Trevisani
Genes 2021, 12(6), 835; https://doi.org/10.3390/genes12060835 - 28 May 2021
Cited by 18 | Viewed by 3182
Abstract
Renal cancer represents the 7th most common tumor worldwide, affecting 400,000 people annually. This malignancy, which is the third most frequent cancer among urological diseases, displays a completely different prognosis if the tumor is detected in the early stages or advance phases. Unfortunately, [...] Read more.
Renal cancer represents the 7th most common tumor worldwide, affecting 400,000 people annually. This malignancy, which is the third most frequent cancer among urological diseases, displays a completely different prognosis if the tumor is detected in the early stages or advance phases. Unfortunately, more than 50% of renal cancers are discovered incidentally, with a consistent percentage of cases where the tumor remains clinically silent till the metastatic process is established. In day-to-day clinical practice, no available predictive biomarkers exist, and the existent imaging diagnostic techniques harbor several gaps in terms of diagnosis and prognosis. In the last decade, many efforts have been reported to detect new predictive molecular biomarkers using liquid biopsies, which are less invasive in comparison to renal biopsy. However, until now, there has been no clear evidence that a liquid biopsy biomarker could be relevant to the creation of a precise and tailored medical management in these oncological patients, even though circulating RNA biomarkers remain among the most promising. Given the idea that liquid biopsies will play a future key role in the management of these patients, in the present review, we summarize the current state of circulating RNA (miRNA, lncRNAs, and circRNAs) as possible biomarkers of renal cancer presence and aggressiveness in patients. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
24 pages, 1008 KiB  
Review
Decipher the Glioblastoma Microenvironment: The First Milestone for New Groundbreaking Therapeutic Strategies
by Giuseppe Nicolò Fanelli, Dario Grassini, Valerio Ortenzi, Francesco Pasqualetti, Nicola Montemurro, Paolo Perrini, Antonio Giuseppe Naccarato and Cristian Scatena
Genes 2021, 12(3), 445; https://doi.org/10.3390/genes12030445 - 20 Mar 2021
Cited by 67 | Viewed by 6055
Abstract
Glioblastoma (GBM) is the most common primary malignant brain tumour in adults. Despite the combination of novel therapeutical approaches, it remains a deadly malignancy with an abysmal prognosis. GBM is a polymorphic tumour from both molecular and histological points of view. It consists [...] Read more.
Glioblastoma (GBM) is the most common primary malignant brain tumour in adults. Despite the combination of novel therapeutical approaches, it remains a deadly malignancy with an abysmal prognosis. GBM is a polymorphic tumour from both molecular and histological points of view. It consists of different malignant cells and various stromal cells, contributing to tumour initiation, progression, and treatment response. GBM’s microenvironment is multifaceted and is made up of soluble factors, extracellular matrix components, tissue-resident cell types (e.g., neurons, astrocytes, endothelial cells, pericytes, and fibroblasts) together with resident (e.g., microglia) or recruited (e.g., bone marrow-derived macrophages) immune cells. These latter constitute the so-called immune microenvironment, accounting for a substantial GBM’s tumour volume. Despite the abundance of immune cells, an intense state of tumour immunosuppression is promoted and developed; this represents the significant challenge for cancer cells’ immune-mediated destruction. Though literature data suggest that distinct GBM’s subtypes harbour differences in their microenvironment, its role in treatment response remains obscure. However, an in-depth investigation of GBM’s microenvironment may lead to novel therapeutic opportunities to improve patients’ outcomes. This review will elucidate the GBM’s microenvironment composition, highlighting the current state of the art in immunotherapy approaches. We will focus on novel strategies of active and passive immunotherapies, including vaccination, gene therapy, checkpoint blockade, and adoptive T-cell therapies. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
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19 pages, 981 KiB  
Review
Current Knowledge on Genomic Profiling of Upper Tract Urothelial Carcinoma
by Elisa De Lorenzis, Giancarlo Albo, Fabrizio Longo, Carolina Bebi, Luca Boeri and Emanuele Montanari
Genes 2021, 12(3), 333; https://doi.org/10.3390/genes12030333 - 25 Feb 2021
Cited by 12 | Viewed by 2438
Abstract
Recent research in next-generation sequencing characterized the genomic landscape of urothelial cancer. However, the majority of the studies focused on bladder cancer (BC). Upper urinary tract urothelial carcinomas (UTUC) and BC share some histological characteristics, but, considering the differences in terms of embryologic [...] Read more.
Recent research in next-generation sequencing characterized the genomic landscape of urothelial cancer. However, the majority of the studies focused on bladder cancer (BC). Upper urinary tract urothelial carcinomas (UTUC) and BC share some histological characteristics, but, considering the differences in terms of embryologic precursors, epidemiology, genetics, medical and surgical management and response to therapy, UTUC and BC should be considered as two distinct diseases. Our objective is to analyze through a literature search the latest updates and the current knowledge about the genomics of UTUC. We also evaluate genetic differences between BC and UTUC and the potential implications for systemic therapy. Molecular subtyping and variant histology and their correlation with response to chemotherapy were also explored. In summary, the most frequent genomic variations in UTUC included FGFR3, chromatin remodeling genes, TP53/MDM2 and other tumor suppressors/oncogenes. The genomics of UTUC, integrated with clinical data, could drive the selection of patients who could benefit from targeted therapy or off-label treatment. Routine implementation of tumor genomic characterization in UTUC patients should therefore be contemplated and evaluated prospectively. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
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28 pages, 950 KiB  
Review
The Scope of Astrocyte Elevated Gene-1/Metadherin (AEG-1/MTDH) in Cancer Clinicopathology: A Review
by Maheen Khan and Devanand Sarkar
Genes 2021, 12(2), 308; https://doi.org/10.3390/genes12020308 - 22 Feb 2021
Cited by 15 | Viewed by 3233
Abstract
Since its initial cloning in 2002, a plethora of studies in a vast number of cancer indications, has strongly established AEG-1 as a bona fide oncogene. In all types of cancer cells, overexpression and knockdown studies have demonstrated that AEG-1 performs a seminal [...] Read more.
Since its initial cloning in 2002, a plethora of studies in a vast number of cancer indications, has strongly established AEG-1 as a bona fide oncogene. In all types of cancer cells, overexpression and knockdown studies have demonstrated that AEG-1 performs a seminal role in regulating proliferation, invasion, angiogenesis, metastasis and chemoresistance, the defining cancer hallmarks, by a variety of mechanisms, including protein-protein interactions activating diverse oncogenic pathways, RNA-binding promoting translation and regulation of inflammation, lipid metabolism and tumor microenvironment. These findings have been strongly buttressed by demonstration of increased tumorigenesis in tissue-specific AEG-1 transgenic mouse models, and profound resistance of multiple types of cancer development and progression in total and conditional AEG-1 knockout mouse models. Additionally, clinicopathologic correlations of AEG-1 expression in a diverse array of cancers establishing AEG-1 as an independent biomarker for highly aggressive, chemoresistance metastatic disease with poor prognosis have provided a solid foundation to the mechanistic and mouse model studies. In this review a comprehensive analysis of the current and up-to-date literature is provided to delineate the clinical significance of AEG-1 in cancer highlighting the commonality of the findings and the discrepancies and discussing the implications of these observations. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
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23 pages, 418 KiB  
Review
Molecular Biomarkers for Contemporary Therapies in Hormone Receptor-Positive Breast Cancer
by Allegra Freelander, Lauren J. Brown, Andrew Parker, Davendra Segara, Neil Portman, Brandon Lau and Elgene Lim
Genes 2021, 12(2), 285; https://doi.org/10.3390/genes12020285 - 17 Feb 2021
Cited by 20 | Viewed by 4677
Abstract
Systemic treatment of hormone receptor-positive (HR+) breast cancer is undergoing a renaissance, with a number of targeted therapies including CDK4/6, mTOR, and PI3K inhibitors now approved for use in combination with endocrine therapies. The increased use of targeted therapies has changed the natural [...] Read more.
Systemic treatment of hormone receptor-positive (HR+) breast cancer is undergoing a renaissance, with a number of targeted therapies including CDK4/6, mTOR, and PI3K inhibitors now approved for use in combination with endocrine therapies. The increased use of targeted therapies has changed the natural history of HR+ breast cancers, with the emergence of new escape mechanisms leading to the inevitable progression of disease in patients with advanced cancers. The identification of new predictive and pharmacodynamic biomarkers to current standard-of-care therapies and discovery of new therapies is an evolving and urgent clinical challenge in this setting. While traditional, routinely measured biomarkers such as estrogen receptors (ERs), progesterone receptors (PRs), and human epidermal growth factor receptor 2 (HER2) still represent the best prognostic and predictive biomarkers for HR+ breast cancer, a significant proportion of patients either do not respond to endocrine therapy or develop endocrine resistant disease. Genomic tests have emerged as a useful adjunct prognostication tool and guide the addition of chemotherapy to endocrine therapy. In the treatment-resistant setting, mutational profiling has been used to identify ESR1, PIK3CA, and AKT mutations as predictive molecular biomarkers to newer therapies. Additionally, pharmacodynamic biomarkers are being increasingly used and considered in the metastatic setting. In this review, we summarise the current state-of-the-art therapies; prognostic, predictive, and pharmacodynamic molecular biomarkers; and how these are impacted by emerging therapies for HR+ breast cancer. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
16 pages, 813 KiB  
Review
Immune-Based Therapies and the Role of Microsatellite Instability in Pancreatic Cancer
by Michele Ghidini, Andrea Lampis, Milko B. Mirchev, Ali Fuat Okuducu, Margherita Ratti, Nicola Valeri and Jens C. Hahne
Genes 2021, 12(1), 33; https://doi.org/10.3390/genes12010033 - 29 Dec 2020
Cited by 22 | Viewed by 4659
Abstract
Pancreatic cancer is one of the most aggressive malignancies with limited treatment options thus resulting in high morbidity and mortality. Among all cancers, with a five-year survival rates of only 2–9%, pancreatic cancer holds the worst prognostic outcome for patients. To improve the [...] Read more.
Pancreatic cancer is one of the most aggressive malignancies with limited treatment options thus resulting in high morbidity and mortality. Among all cancers, with a five-year survival rates of only 2–9%, pancreatic cancer holds the worst prognostic outcome for patients. To improve the overall survival, an earlier diagnosis and stratification of cancer patients for personalized treatment options are urgent needs. A minority of pancreatic cancers belong to the spectrum of Lynch syndrome-associated cancers and are characterized by microsatellite instability (MSI). MSI is a consequence of defective mismatch repair protein functions and it has been well characterized in other gastrointestinal tumors such as colorectal and gastric cancer. In the latter, high levels of MSI are linked to a better prognosis and to an increased benefit to immune-based therapies. Therefore, the same therapies could offer an opportunity of treatment for pancreatic cancer patients with MSI. In this review, we summarize the current knowledge about immune-based therapies and MSI in pancreatic cancer. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
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22 pages, 2601 KiB  
Review
Contactin 1: An Important and Emerging Oncogenic Protein Promoting Cancer Progression and Metastasis
by Yan Gu, Taosha Li, Anil Kapoor, Pierre Major and Damu Tang
Genes 2020, 11(8), 874; https://doi.org/10.3390/genes11080874 - 31 Jul 2020
Cited by 12 | Viewed by 3837
Abstract
Even with recent progress, cancer remains the second leading cause of death, outlining a need to widen the current understanding on oncogenic factors. Accumulating evidence from recent years suggest Contactin 1 (CNTN1)’s possession of multiple oncogenic activities in a variety of cancer types. [...] Read more.
Even with recent progress, cancer remains the second leading cause of death, outlining a need to widen the current understanding on oncogenic factors. Accumulating evidence from recent years suggest Contactin 1 (CNTN1)’s possession of multiple oncogenic activities in a variety of cancer types. CNTN1 is a cell adhesion molecule that is dysregulated in many human carcinomas and plays important roles in cancer progression and metastases. Abnormalities in CNTN1 expression associate with cancer progression and poor prognosis. Mechanistically, CNTN1 functions in various signaling pathways frequently altered in cancer, such as the vascular endothelial growth factor C (VEGFC)-VEGF receptor 3 (VEFGR3)/fms-related tyrosine kinase 4 (Flt4) axis, phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT), Notch signaling pathway and epithelial-mesenchymal transition (EMT) process. These oncogenic events are resulted via interactions between tumor and stroma, which can be contributed by CNTN1, an adhesion protein. CNTN1 expression in breast cancer correlates with the expression of genes functioning in cancer-stroma interactions and skeletal system development. Evidence supports that CNTN1 promotes cancer-stromal interaction, resulting in activation of a complex network required for cancer progression and metastasis (bone metastasis for breast cancer). CNTN1 inhibitions has been proven to be effective in experimental models to reduce oncogenesis. In this paper, we will review CNTN1′s alterations in cancer, its main biochemical mechanisms and interactions with its relevant cancer pathways. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
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19 pages, 2462 KiB  
Review
PTEN Alterations and Their Role in Cancer Management: Are We Making Headway on Precision Medicine?
by Nicola Fusco, Elham Sajjadi, Konstantinos Venetis, Gabriella Gaudioso, Gianluca Lopez, Chiara Corti, Elena Guerini Rocco, Carmen Criscitiello, Umberto Malapelle and Marco Invernizzi
Genes 2020, 11(7), 719; https://doi.org/10.3390/genes11070719 - 28 Jun 2020
Cited by 68 | Viewed by 6232
Abstract
Alterations in the tumor suppressor phosphatase and tensin homolog (PTEN) occur in a substantial proportion of solid tumors. These events drive tumorigenesis and tumor progression. Given its central role as a downregulator of the phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) [...] Read more.
Alterations in the tumor suppressor phosphatase and tensin homolog (PTEN) occur in a substantial proportion of solid tumors. These events drive tumorigenesis and tumor progression. Given its central role as a downregulator of the phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway, PTEN is deeply involved in cell growth, proliferation, and survival. This gene is also implicated in the modulation of the DNA damage response and in tumor immune microenvironment modeling. Despite the actionability of PTEN alterations, their role as biomarkers remains controversial in clinical practice. To date, there is still a substantial lack of validated guidelines and/or recommendations for PTEN testing. Here, we provide an update on the current state of knowledge on biologic and genetic alterations of PTEN across the most frequent solid tumors, as well as on their actual and/or possible clinical applications. We focus on possible tailored schemes for cancer patients’ clinical management, including risk assessment, diagnosis, prognostication, and treatment. Full article
(This article belongs to the Special Issue Molecular Biomarkers in Solid Tumors)
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