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Genomic Approach for Diagnosis, Prognosis and Therapy Prediction in Cancer...
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Genomic Approach for Diagnosis, Prognosis and Therapy Prediction in Cancer Research

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Pathology and Molecular Diagnostics".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 12633

Special Issue Editors

Dr. Andrea De Giglio

E-Mail Website
Guest Editor
1. Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
2. Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
Interests: non-small cell lung cancer; immunotherapy; thymic epithelial cancers
Dr. Alessandro Di Federico

E-Mail Website
Guest Editor
Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
Interests: clinical and translational oncology; immunotherapy; cancer genomics

Special Issue Information

Dear Colleagues,

In the last decade, we assisted in a remarkable shift from a histology-based to a molecular-based paradigm of diagnosing and treating several cancers.

In particular, the genomic characterization of tumors routinely entered the clinical practice of several solid malignancies such as lung, genitourinary tract, gastrointestinal, skin, or head and neck cancers. This personalized approach improved survival outcomes and quality of life of cancer patients, determining an increasing rate of long survivors.

Molecular characterization is usually performed on tissue sample analysis, even if the possible applications of liquid biopsy techniques constitute an expanding scenario.

In this context, a comprehensive genomic report is pivotal to predict targeted therapies or immunotherapy efficacy. Thus, the international societies for the cure and research of cancer, such as the European Society of medical oncology (ESMO) and the American association of clinical oncology (ASCO), recommend molecular testing at diagnosis or progression to select the best treatment strategy. Notably, a series of novel drugs have been approved with a tumor-agnostic indication based on peculiar genomic alterations unrelated to histology or line of treatment.

Moreover, the presence of molecular alteration may be associated with altered prognosis in relation or not to specific treatments.

This special issue is aimed to expand the current knowledge about the genomic approach to cancer research across several malignancies.

Dr. Andrea De Giglio
Dr. Alessandro Di Federico
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. Diagnostics 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 2600 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

  • genomic characterization
  • agnostic drugs
  • liquid biopsy
  • molecular profile
  • personalized medicine
  • solid tumors

Published Papers (6 papers)

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Research

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21 pages, 13832 KiB  
Article
A Comprehensive Pan-Cancer Analysis Identifies CEP55 as a Potential Oncogene and Novel Therapeutic Target
by Mohamed Samir A. Zaki, Muhammad Alaa Eldeen, Waleed K. Abdulsahib, Ayed A. Shati, Youssef A. Alqahtani, Saleh M. Al-Qahtani, Hassan M. Otifi, Ashwag Asiri, Hesham M. Hassan, Hebatallah Emam Mohammed Ahmed, Samy A. Dawood, Amr Negm and Refaat A. Eid
Diagnostics 2023, 13(9), 1613; https://doi.org/10.3390/diagnostics13091613 - 02 May 2023
Cited by 1 | Viewed by 2088
Abstract
Emerging research findings have shown that a centrosomal protein (CEP55) is a potential oncogene in numerous human malignancies. Nevertheless, no pan-cancer analysis has been conducted to investigate the various aspects and behavior of this oncogene in different human cancerous tissues. Numerous [...] Read more.
Emerging research findings have shown that a centrosomal protein (CEP55) is a potential oncogene in numerous human malignancies. Nevertheless, no pan-cancer analysis has been conducted to investigate the various aspects and behavior of this oncogene in different human cancerous tissues. Numerous databases were investigated to conduct a detailed analysis of CEP55. Initially, we evaluated the expression of CEP55 in several types of cancers and attempted to find the correlation between that and the stage of the examined malignancies. Then, we conducted a survival analysis to determine the relationship between CEP55 overexpression in malignancies and the patient’s survival. Furthermore, we examined the genetic alteration forms and the methylation status of this oncogene. Additionally, the interference of CEP55 expression with immune cell infiltration, the response to various chemotherapeutic agents, and the putative molecular mechanism of CEP55 in tumorigenesis were investigated. The current study found that CEP55 was upregulated in cancerous tissues versus normal controls where this upregulation was correlated with a poor prognosis in multiple forms of human cancers. Additionally, it influenced the level of different immune cell infiltration and several chemokines levels in the tumor microenvironment in addition to the response to several antitumor drugs. Herein, we provide an in-depth understanding of the oncogenic activities of CEP55, identifying it as a possible predictive marker as well as a specific target for developing anticancer therapies. Full article
(This article belongs to the Special Issue Genomic Approach for Diagnosis, Prognosis and Therapy Prediction in Cancer Research)
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12 pages, 2247 KiB  
Article
Targeted Genomic Profiling and Chemotherapy Outcomes in Grade 3 Gastro-Entero-Pancreatic Neuroendocrine Tumors (G3 GEP-NET)
by Giuseppe Lamberti, Natalie Prinzi, Alberto Bongiovanni, Mariangela Torniai, Elisa Andrini, Dario de Biase, Deborah Malvi, Mirta Mosca, Rossana Berardi, Toni Ibrahim, Sara Pusceddu and Davide Campana
Diagnostics 2023, 13(9), 1595; https://doi.org/10.3390/diagnostics13091595 - 29 Apr 2023
Cited by 1 | Viewed by 1604
Abstract
Background: Grade 3 gastro-entero-pancreatic neuroendocrine tumors (G3 GEP-NET) are poorly characterized in terms of molecular features and response to treatments. Methods: Patients with G3 GEP-NET were included if they received capecitabine and temozolomide (CAPTEM) or oxaliplatin with either 5-fluorouracile (FOLFOX) or capecitabine (XELOX) [...] Read more.
Background: Grade 3 gastro-entero-pancreatic neuroendocrine tumors (G3 GEP-NET) are poorly characterized in terms of molecular features and response to treatments. Methods: Patients with G3 GEP-NET were included if they received capecitabine and temozolomide (CAPTEM) or oxaliplatin with either 5-fluorouracile (FOLFOX) or capecitabine (XELOX) as first-line treatment (chemotherapy cohort). G3 NET which successfully undergone next-generation sequencing (NGS) were included in the NGS cohort. Results: In total, 49 patients were included in the chemotherapy cohort: 15 received CAPTEM and 34 received FOLFOX/XELOX. Objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) were 42.9%, 9.0 months, and 33.6 months, respectively. Calculating a Ki67 cutoff using ROC curve analysis, tumors with Ki67 ≥ 40% had lower ORR (51.2% vs. 0%; p = 0.007) and shorter PFS (10.6 months vs. 4.4 months; p < 0.001) and OS (49.4 months vs. 10.0 months; p = 0.023). In patients who received FOLFOX/XELOX as a first-line treatment, ORR, PFS, and OS were 38.2%, 7.9 months, and 30.0 months, respectively. In the NGS cohort (N = 13), the most mutated genes were DAXX/ATRX (N = 5, 38%), MEN1 (N = 4, 31%), TP53 (N = 4, 31%), AKT1 (N = 2, 15%), and PIK3CA (N = 1, 8%). Conclusions: FOLFOX/XELOX chemotherapy is active as the first-line treatment of patients with G3 GEP-NET. The mutational landscape of G3 NET is more similar to well-differentiated NETs than NECs. Full article
(This article belongs to the Special Issue Genomic Approach for Diagnosis, Prognosis and Therapy Prediction in Cancer Research)
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12 pages, 830 KiB  
Article
Analytical Performance of a Highly Sensitive System to Detect Gene Variants Using Next-Generation Sequencing for Lung Cancer Companion Diagnostics
by Kikuya Kato, Jiro Okami, Harumi Nakamura, Keiichiro Honma, Yoshiharu Sato, Seiji Nakamura, Yoji Kukita, Shin-ichi Nakatsuka and Masahiko Higashiyama
Diagnostics 2023, 13(8), 1476; https://doi.org/10.3390/diagnostics13081476 - 19 Apr 2023
Cited by 3 | Viewed by 2213
Abstract
The recent increase in the number of molecular targeted agents for lung cancer has led to the demand for the simultaneous testing of multiple genes. Although gene panels using next-generation sequencing (NGS) are ideal, conventional panels require a high tumor content, and biopsy [...] Read more.
The recent increase in the number of molecular targeted agents for lung cancer has led to the demand for the simultaneous testing of multiple genes. Although gene panels using next-generation sequencing (NGS) are ideal, conventional panels require a high tumor content, and biopsy samples often do not meet this requirement. We developed a new NGS panel, called compact panel, characterized by high sensitivity, with detection limits for mutations of 0.14%, 0.20%, 0.48%, 0.24%, and 0.20% for EGFR exon 19 deletion, L858R, T790M, BRAF V600E, and KRAS G12C, respectively. Mutation detection also had a high quantitative ability, with correlation coefficients ranging from 0.966 to 0.992. The threshold for fusion detection was 1%. The panel exhibited good concordance with the approved tests. The identity rates were as follows: EGFR positive, 100% (95% confidence interval, 95.5–100); EGFR negative, 90.9 (82.2–96.3); BRAF positive, 100 (59.0–100); BRAF negative, 100 (94.9–100); KRAS G12C positive, 100 (92.7–100); KRAS G12C negative, 100 (93.0–100); ALK positive, 96.7 (83.8–99.9); ALK negative, 98.4 (97.2–99.2); ROS1 positive, 100 (66.4–100); ROS1 negative, 99.0 (94.6–100); MET positive, 98.0 (89.0–99.9); MET negative 100 (92.8–100); RET positive, 93.8 (69.8–100); RET negative, 100 (94.9–100). The analytical performance showed that the panel could handle various types of biopsy samples obtained by routine clinical practice without requiring strict pathological monitoring, as in the case of conventional NGS panels. Full article
(This article belongs to the Special Issue Genomic Approach for Diagnosis, Prognosis and Therapy Prediction in Cancer Research)
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13 pages, 1960 KiB  
Article
Genomic Characterization of Rare Primary Cardiac Sarcoma Entities
by Livia Gozzellino, Margherita Nannini, Carmine Pizzi, Ornella Leone, Barbara Corti, Valentina Indio, Chiara Baldovini, Pasquale Paolisso, Alberto Foà, Davide Pacini, Gianluca Folesani, Angela Schipani, Alice Costa, Gianandrea Pasquinelli, Maria Abbondanza Pantaleo and Annalisa Astolfi
Diagnostics 2023, 13(2), 214; https://doi.org/10.3390/diagnostics13020214 - 06 Jan 2023
Cited by 2 | Viewed by 1533
Abstract
Primary cardiac sarcomas are considered rare malignant entities associated with poor prognosis. In fact, knowledge regarding their gene signature and possible treatments is still limited. In our study, whole-transcriptome sequencing on formalin-fixed paraffin-embedded (FFPE) samples from one cardiac osteosarcoma and one cardiac leiomyosarcoma [...] Read more.
Primary cardiac sarcomas are considered rare malignant entities associated with poor prognosis. In fact, knowledge regarding their gene signature and possible treatments is still limited. In our study, whole-transcriptome sequencing on formalin-fixed paraffin-embedded (FFPE) samples from one cardiac osteosarcoma and one cardiac leiomyosarcoma was performed, to investigate their mutational profiles and to highlight differences and/or similarities to other cardiac histotypes. Both cases have been deeply detailed from a pathological point of view. The osteosarcoma sample presented mutations involving ATRX, ERCC5, and COL1A1, while the leiomyosarcoma case showed EXT2, DNM2, and PSIP1 alterations. Altered genes, along with the most differentially expressed genes in the leiomyosarcoma or osteosarcoma sample versus the cardiac angiosarcomas and intimal sarcomas (e.g., YAF2, PAK5, and CRABP1), appeared to be associated with cell growth, proliferation, apoptosis, and the repair of DNA damage, which are key mechanisms involved in tumorigenesis. Moreover, a distinct gene expression profile was detected in the osteosarcoma sample when compared to other cardiac sarcomas. For instance, WIF1, a marker of osteoblastic differentiation, was upregulated in our bone tumor. These findings pave the way for further studies on these entities, in order to identify targeted therapies and, therefore, improve patients’ prognoses. Full article
(This article belongs to the Special Issue Genomic Approach for Diagnosis, Prognosis and Therapy Prediction in Cancer Research)
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Review

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29 pages, 2693 KiB  
Review
From Development to Place in Therapy of Lorlatinib for the Treatment of ALK and ROS1 Rearranged Non-Small Cell Lung Cancer (NSCLC)
by Laura Fabbri, Alessandro Di Federico, Martina Astore, Virginia Marchiori, Agnese Rejtano, Renata Seminerio, Francesco Gelsomino and Andrea De Giglio
Diagnostics 2024, 14(1), 48; https://doi.org/10.3390/diagnostics14010048 - 25 Dec 2023
Cited by 1 | Viewed by 1596
Abstract
Following the results of the CROWN phase III trial, the third-generation macrocyclic ALK inhibitor lorlatinib has been introduced as a salvage option after the failure of a first-line TKI in ALK-rearranged NSCLC, while its precise role in the therapeutic algorithm of ROS1 positive [...] Read more.
Following the results of the CROWN phase III trial, the third-generation macrocyclic ALK inhibitor lorlatinib has been introduced as a salvage option after the failure of a first-line TKI in ALK-rearranged NSCLC, while its precise role in the therapeutic algorithm of ROS1 positive disease is still to be completely defined. The ability to overcome acquired resistance to prior generation TKIs (alectinib, brigatinib, ceritinib, and crizotinib) and the high intracranial activity in brain metastatic disease thanks to increased blood–brain barrier penetration are the reasons for the growing popularity and interest in this molecule. Nevertheless, the major vulnerability of this drug resides in a peculiar profile of related collateral events, with neurological impairment being the most conflicting and debated clinical issue. The cognitive safety concern, the susceptibility to heterogeneous resistance pathways, and the absence of a valid alternative in the second line are strongly jeopardizing a potential paradigm shift in this oncogene-addicted disease. So, when prescribing lorlatinib, clinicians must face two diametrically opposed characteristics: a great therapeutic potential without the intrinsic limitations of its precursor TKIs, a cytotoxic activity threatened by suboptimal tolerability, and the unavoidable onset of resistance mechanisms we cannot properly manage yet. In this paper, we give a critical point of view on the stepwise introduction of this promising drug into clinical practice, starting from its innovative molecular and biochemical properties to intriguing future developments, without forgetting its weaknesses. Full article
(This article belongs to the Special Issue Genomic Approach for Diagnosis, Prognosis and Therapy Prediction in Cancer Research)
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Other

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16 pages, 1730 KiB  
Systematic Review
A Systematic Review of Diagnostic and Prognostic Biomarkers for Head and Neck Cancer of Unknown Primary: An Unmet Clinical Need
by Daria Maria Filippini, Elisabetta Broseghini, Francesca Carosi, Davide Dal Molin, Mattia Riefolo, Laura Fabbri, Andi Abeshi, Ignacio Javier Fernandez and Manuela Ferracin
Diagnostics 2023, 13(8), 1492; https://doi.org/10.3390/diagnostics13081492 - 20 Apr 2023
Cited by 2 | Viewed by 3042
Abstract
Head and neck cancer of unknown primary (HNCUP) is defined as cervical lymph node metastases without a detectable primary tumor. The management of these patients presents a challenge to clinicians since guidelines in the diagnosis and treatment of HNCUP remain controversial. An accurate [...] Read more.
Head and neck cancer of unknown primary (HNCUP) is defined as cervical lymph node metastases without a detectable primary tumor. The management of these patients presents a challenge to clinicians since guidelines in the diagnosis and treatment of HNCUP remain controversial. An accurate diagnostic workup is fundamental for the search for the hidden primary tumor to allow the best adequate treatment strategy. The purpose of this systematic review is to present the currently available data about the diagnostic and prognostic molecular biomarkers for HNCUP. Systematic research in an electronic database was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol and identified 704 articles, of which 23 studies were selected and included in the analysis. Fourteen studies investigated HNCUP diagnostic biomarkers and focused on the human papilloma virus (HPV) and the Epstein–Barr virus (EBV) due to the strong associations with oropharyngeal cancer and nasopharyngeal cancer, respectively. HPV status was shown to possess prognostic value, correlating with longer disease-free survival and overall survival. HPV and EBV are the only available HNCUP biomarkers, and they are already used in clinical practice. A better characterization of the molecular profiling and the development of tissue-of-origin classifiers are necessary to improve the diagnosis, staging, and therapeutic management of patients with HNCUP. Full article
(This article belongs to the Special Issue Genomic Approach for Diagnosis, Prognosis and Therapy Prediction in Cancer Research)
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