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Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again

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A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Causes, Screening and Diagnosis".

Deadline for manuscript submissions: closed (25 November 2022) | Viewed by 31735

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Dr. Alessandra Soriano

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1. Visiting Assistant Professor, Department of Pathology, Case Western Reserve University, Cleveland, OH 44106-1712, USA
2. Gastroenterology Division and Inflammatory Bowel Disease Center, Department of Internal Medicine, IRCCS Azienda Unità Sanitaria Locale di Reggio Emilia, 42122 Reggio Emilia, Italy
Interests: gastrointestinal pathology; inflammatory bowel diseases; gastrointestinal cancer; chronic inflammation; autoimmunity; autoinflammation and innate immunity; microbiome
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Dear Colleagues,

Physicians’ and researchers’ approaches to cancer are dramatically changing. Growing the knowledge of human genetics as well as finding insights into the links between chronic inflammation, immune system, microbiota and cancer development are some of the key steps contributing to moving forward the era of precision oncology, as observed in recent years.

By using the same approach of precision medicine, and with the help of innovative techniques for data analysis including artificial intelligence (i.e., machine learning, deep learning, neural networks), a multidisciplinary team mainly composed of clinicians, surgeons, pathologists, radiologists, biostatisticians, geneticists and biologists surround the cancer patient in order to achieve molecular targeted and immune-based therapeutics across a variety of malignancies.

Gastrointestinal malignancies still have high tumor incidence and mortality rate worldwide, with a significant diversity in terms of prognosis and therapeutic response. There is an urgent need for identification of suitable targets for tailor-made, personalized therapy in such a field.

The aim of this Special Issue is to gather top experts covering all aspects of precision oncology for gastrointestinal cancer in 2021, from bench to bedside, and back again.

Dr. Alessandra Soriano
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 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. Cancers 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 2900 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

gastrointestinal cancer
precision medicine
immunity
gene expression profiling
biomarker
molecular targeted therapy
liquid biopsy
circulating tumor cells (CTCs)
immunotherapy
machine learning
organoids

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Published Papers (11 papers)

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13 pages, 771 KiB

Open AccessArticle

Significant Tumor Regression after Neoadjuvant Chemotherapy in Gastric Cancer, but Poor Survival of the Patient? Role of MHC Class I Alterations

by Theresa Hiltner, Noémi Szörenyi, Meike Kohlruss, Alexander Hapfelmeier, Anna-Lina Herz, Julia Slotta-Huspenina, Moritz Jesinghaus, Alexander Novotny, Sebastian Lange, Katja Ott, Wilko Weichert and Gisela Keller

Cancers 2023, 15(3), 771; https://doi.org/10.3390/cancers15030771 - 26 Jan 2023

Cited by 1 | Viewed by 1838

Abstract

We aimed to determine the clinical and prognostic relevance of allelic imbalance (AI) of the major histocompatibility complex (MHC) class I genes, encompassing the human leukocyte antigen (HLA) class I and beta-2 microglobulin (B2M) genes, in the context of neoadjuvant platinum/fluoropyrimidine chemotherapy (CTx). Biopsies before CTx were studied in 158 patients with adenocarcinoma of the stomach or gastroesophageal junction. The response was histopathologically evaluated. AI was detected by multiplex PCRs analysis of four or five microsatellite markers in HLA and B2M regions, respectively. AI with no marker was significantly associated with response or survival. However, subgroup analysis revealed differences. AI at marker D6S265, close to the HLA-A gene, was associated with an obvious increased risk in responding (HR, 3.62; 95% CI, 0.96–13.68, p = 0.058) but not in non-responding patients (HR, 0.92; 95% CI, 0.51–1.65, p = 0.773). Markers D6S273 and D6S2872 showed similar results. The interaction between AI at D6S265 and response to CTx was significant in a multivariable analysis (p = 0.010). No associations were observed for B2M markers. Our results underline the importance of intact neoantigen presentation specifically for responding patients and may help explain an unexpectedly poor survival of a patient despite significant tumor regression after neoadjuvant platinum/fluoropyrimidine CTx. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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12 pages, 3314 KiB

Open AccessArticle

Fusobacterium Nucleatum-Induced Tumor Mutation Burden Predicts Poor Survival of Gastric Cancer Patients

by Yung-Yu Hsieh, Wen-Lin Kuo, Wan-Ting Hsu, Shui-Yi Tung and Chin Li

Cancers 2023, 15(1), 269; https://doi.org/10.3390/cancers15010269 - 30 Dec 2022

Cited by 15 | Viewed by 2316

Abstract

Co-infection of Helicobacter pylori and Fusobacterium nucleatum is a microbial biomarker for poor prognosis of gastric cancer patients. Fusobacterium nucleatum is associated with microsatellite instability and the accumulation of mutations in colorectal cancer. Here, we investigated the mutation landscape of Fusobacterium nucleatum-positive resected gastric cancer tissues using Illumina TruSight Oncology 500 comprehensive panel. Sequencing data were processed to identify the small nucleotide variants, small insertions and deletions, and unstable microsatellite sites. The bioinformatic algorithm also calculated copy number gains of preselected genes and tumor mutation burden. The recurrent genetic aberrations were identified in this study cohort. For gene amplification events, ERBB2, cell cycle regulators, and specific FGF ligands and receptors were the most frequently amplified genes. Pathogenic activation mutations of ERBB2, ERBB3, and PIK3CA, as well as loss-of-function of TP53, were identified in multiple patients. Furthermore, Fusobacterium nucleatum infection is positively correlated with a higher tumor mutation burden. Survival analysis showed that the combination of Fusobacterium nucleatum infection and high tumor mutation burden formed an extremely effective biomarker to predict poor prognosis. Our results indicated that the ERBB2-PIK3-AKT-mTOR pathway is frequently activated in gastric cancer and that Fusobacterium nucleatum and high mutation burden are strong biomarkers of poor prognosis for gastric cancer patients. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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17 pages, 1985 KiB

Open AccessArticle

EBV and MSI Status in Gastric Cancer: Does It Matter?

by Catarina Neto do Nascimento, Luís Mascarenhas-Lemos, João Ricardo Silva, Diogo Sousa Marques, Catarina Ferreira Gouveia, Ana Faria, Sónia Velho, Rita Garrido, Rui Maio, Andreia Costa, Patrícia Pontes, Xiaogang Wen, Irene Gullo, Marília Cravo and Fátima Carneiro

Cancers 2023, 15(1), 74; https://doi.org/10.3390/cancers15010074 - 22 Dec 2022

Cited by 7 | Viewed by 2807

Abstract

We investigated the impactof microsatellite instability (MSI) and Epstein–Barr virus (EBV) status in gastric cancer (GC), regarding response to perioperative chemotherapy (POPChT), overall survival (OS), and progression-free survival (PFS). We included 137 cases of operated GC, 51 of which were submitted to POPChT. MSI status was determined by multiplex PCR and EBV status by EBV-encoded RNA in situ hybridization. Thirty-seven (27%) cases presented as MSI-high, and seven (5.1%) were EBV+. Concerning tumor regression after POPChT, no differences were observed between the molecular subtypes, but females were more likely to respond (p = 0.062). No significant differences were found in OS or PFS between different subtypes. In multivariate analysis, age (HR 1.02, IC 95% 1.002–1.056, p = 0.033) and positive lymph nodes (HR 1.82, IC 95% 1.034–3.211, p = 0.038) were the only prognostic factors for OS. However, females with MSI-high tumors treated with POPChT demonstrated a significantly increased OS compared to females with MSS tumors (p = 0.031). In conclusion, we found a high proportion of MSI-high cases. MSI and EBV status did not influence OS or PFS either in patients submitted to POPChT or surgery alone. However, superior survival of females with MSI-high tumors suggests that sex disparities and molecular classification may influence treatment options in GC. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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18 pages, 7305 KiB

Open AccessArticle

Microsatellite Status Detection in Gastrointestinal Cancers: PCR/NGS Is Mandatory in Negative/Patchy MMR Immunohistochemistry

by Federica Zito Marino, Martina Amato, Andrea Ronchi, Iacopo Panarese, Franca Ferraraccio, Ferdinando De Vita, Giuseppe Tirino, Erika Martinelli, Teresa Troiani, Gaetano Facchini, Felice Pirozzi, Michele Perrotta, Pasquale Incoronato, Raffaele Addeo, Francesco Selvaggi, Francesco Saverio Lucido, Michele Caraglia, Giovanni Savarese, Roberto Sirica, Marika Casillo, Eva Lieto, Annamaria Auricchio, Francesca Cardella, Ludovico Docimo, Gennaro Galizia and Renato Franco Show full author list Hide full author list

Cancers 2022, 14(9), 2204; https://doi.org/10.3390/cancers14092204 - 28 Apr 2022

Cited by 16 | Viewed by 3390

Abstract

Background: Microsatellite instability (MSI) is a predictive biomarker for immune checkpoint inhibitors. The main goal was to investigate the discordance between IHC and PCR/NGS for MSI testing in gastrointestinal cancers. Methods: Two series were analyzed through IHC for mismatch-repair-system proteins (MMRP) and PCR, with one series of 444 colorectal cancers (CRC) and the other of 176 gastric cancers (GC). All cases with discordant results between IHC and PCR were analyzed by NGS. IHC staining was evaluated as follows: proficient MMR (pMMR), with all MMR positive; deficient MMR (dMMR), with the loss of one heterodimer; and cases with the loss/patchy expression of one MMR (lo-paMMR). Cases with instability in at least two markers by PCR were MSI-high (MSI-H) and with instability in one marker, MSI-low (MSI-L). Cases without instability were evaluated as microsatellite-stable (MSS). Results: In the CRC cohort, 15 out of 444 cases were dMMR and 46 lo-paMMR. Among the 15 dMMR, 13 were MSI-H and 2 MSS. Among the 46 lo-paMMR, 13 were MSI-H and 33 were MSS. In the GC cohort, 13 out of 176 cases were dMMR and 6 cases lo-paMMR. Among the 13 dMMR, 12 were MSI-H and only 1 was MSS. All six lo-paMMR cases were MSS. All NGS results were in agreement with PCR. Conclusions: In clinical practice, MMR–IHC could be used as a screening test and additional molecular analysis is mandatory exclusively in cases carrying loss/patchy MMR-IHC. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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Review

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21 pages, 1010 KiB

Open AccessReview

EBV-Driven Lymphoproliferative Disorders and Lymphomas of the Gastrointestinal Tract: A Spectrum of Entities with a Common Denominator (Part 3)

by Magda Zanelli, Francesca Sanguedolce, Andrea Palicelli, Maurizio Zizzo, Giovanni Martino, Cecilia Caprera, Valentina Fragliasso, Alessandra Soriano, Fabrizio Gozzi, Luca Cimino, Francesco Masia, Marina Moretti, Moira Foroni, Loredana De Marco, David Pellegrini, Hendrik De Raeve, Stefano Ricci, Ione Tamagnini, Alessandro Tafuni, Alberto Cavazza, Francesco Merli, Stefano A. Pileri and Stefano Ascani Show full author list Hide full author list

Cancers 2021, 13(23), 6021; https://doi.org/10.3390/cancers13236021 - 30 Nov 2021

Cited by 4 | Viewed by 3083

Abstract

EBV is the first known oncogenic virus involved in the development of several tumors. The majority of the global population are infected with the virus early in life and the virus persists throughout life, in a latent stage, and usually within B lymphocytes. Despite the worldwide diffusion of EBV infection, EBV-associated diseases develop in only in a small subset of individuals often when conditions of immunosuppression disrupt the balance between the infection and host immune system. EBV-driven lymphoid proliferations are either of B-cell or T/NK-cell origin, and range from disorders with an indolent behavior to aggressive lymphomas. In this review, which is divided in three parts, we provide an update of EBV-associated lymphoid disorders developing in the gastrointestinal tract, often representing a challenging diagnostic and therapeutic issue. Our aim is to provide a practical diagnostic approach to clinicians and pathologists who face this complex spectrum of disorders in their daily practice. In this part of the review, the chronic active EBV infection of T-cell and NK-cell type, its systemic form; extranodal NK/T-cell lymphoma, nasal type and post-transplant lymphoproliferative disorders are discussed. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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17 pages, 908 KiB

Open AccessReview

Tetraspanins: Physiology, Colorectal Cancer Development, and Nanomediated Applications

by Stefan Titu, Cristiana Maria Grapa, Teodora Mocan, Ovidiu Balacescu and Alexandru Irimie

Cancers 2021, 13(22), 5662; https://doi.org/10.3390/cancers13225662 - 12 Nov 2021

Cited by 11 | Viewed by 2440

Abstract

Tetraspanins are transmembrane proteins expressed in a multitude of cells throughout the organism. They contribute to many processes that surround cell–cell interactions and are associated with the progress of some diseases, including cancer. Their crucial role in cell physiology is often understated. Furthermore, recent studies have shown their great potential in being used as targeting molecules. Data have suggested the potential of tetraspanins as a targeting vector for nanomediated distribution and delivery for colorectal cancer applications. Our aim is to provide a review on the important part that tetraspanins play in the human organism and highlight their potential use for drug delivery systems using nanotechnology. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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17 pages, 3639 KiB

Open AccessReview

EBV-Driven Lymphoproliferative Disorders and Lymphomas of the Gastrointestinal Tract: A Spectrum of Entities with a Common Denominator (Part 1)

by Magda Zanelli, Francesca Sanguedolce, Andrea Palicelli, Maurizio Zizzo, Giovanni Martino, Cecilia Caprera, Valentina Fragliasso, Alessandra Soriano, Luca Valle, Stefano Ricci, Alberto Cavazza, Francesco Merli, Stefano A. Pileri and Stefano Ascani

Cancers 2021, 13(18), 4578; https://doi.org/10.3390/cancers13184578 - 12 Sep 2021

Cited by 18 | Viewed by 3327

Abstract

EBV is the most common persistent virus in humans. The interaction of EBV with B lymphocytes, which are considered the virus reservoir, is at the base of the life-long latent infection. Under circumstances of immunosuppression, the balance between virus and host immune system is altered and hence, EBV-associated lymphoid proliferations may originate. These disorders encompass several entities, ranging from self-limited diseases with indolent behavior to aggressive lymphomas. The virus may infect not only B-cells, but even T- and NK-cells. The occurrence of different types of lymphoid disorders depends on both the type of infected cells and the state of host immunity. EBV-driven lymphoproliferative lesions can rarely occur in the gastrointestinal tract and may be missed even by expert pathologists due to both the uncommon site of presentation and the frequent overlapping morphology and immunophenotypic features shared by different entities. The aim of this review is to provide a comprehensive overview of the current knowledge of EBV-associated lymphoproliferative disorders, arising within the gastrointestinal tract. The review is divided in three parts. In this part, the available data on EBV biology, EBV-positive mucocutaneous ulcer, EBV-positive diffuse large B-cell lymphoma, not otherwise specified and classic Hodgkin lymphoma are discussed. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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20 pages, 18966 KiB

Open AccessReview

EBV-Driven Lymphoproliferative Disorders and Lymphomas of the Gastrointestinal Tract: A Spectrum of Entities with a Common Denominator (Part 2)

by Magda Zanelli, Francesca Sanguedolce, Andrea Palicelli, Maurizio Zizzo, Giovanni Martino, Cecilia Caprera, Valentina Fragliasso, Alessandra Soriano, Luca Valle, Stefano Ricci, Fabrizio Gozzi, Luca Cimino, Alberto Cavazza, Francesco Merli, Stefano A. Pileri and Stefano Ascani

Cancers 2021, 13(18), 4527; https://doi.org/10.3390/cancers13184527 - 8 Sep 2021

Cited by 15 | Viewed by 2724

Abstract

Epstein–Barr virus (EBV) is a common pathogen infecting people primarily early in life. The virus has the ability to persist throughout a person’s life, usually in B lymphocytes. Conditions of immunodeficiency as well as the introduction of immunosuppressive therapies and the advent of transplant technologies has brought immunodeficiency-associated lymphoproliferative disorders into view, which are often driven by EBV. The group of EBV-associated lymphoproliferative disorders includes different entities, with distinct biological features, ranging from indolent disorders, which may even spontaneously regress, to aggressive lymphomas requiring prompt and adequate treatment. These disorders are often diagnostically challenging due to their overlapping morphology and immunophenotype. Both nodal and extra-nodal sites, including the gastrointestinal tract, may be involved. This review, divided in three parts, summarizes the clinical, pathological, molecular features and treatment strategies of EBV-related lymphoproliferative disorders occurring in the gastrointestinal tract and critically analyzes the major issues in the differential diagnosis. In this part of the review, we discuss plasmablastic lymphoma, extra-cavitary primary effusion lymphoma and Burkitt lymphoma. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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13 pages, 713 KiB

Open AccessReview

Gastrointestinal Manifestations in Systemic Mastocytosis: The Need of a Multidisciplinary Approach

by Magda Zanelli, Marco Pizzi, Francesca Sanguedolce, Maurizio Zizzo, Andrea Palicelli, Alessandra Soriano, Alessandra Bisagni, Giovanni Martino, Cecilia Caprera, Marina Moretti, Francesco Masia, Loredana De Marco, Elisabetta Froio, Moira Foroni, Giuditta Bernardelli, Maria Isabel Alvarez de Celis, Alessandro Giunta, Francesco Merli and Stefano Ascani

Cancers 2021, 13(13), 3316; https://doi.org/10.3390/cancers13133316 - 1 Jul 2021

Cited by 24 | Viewed by 3764

Abstract

Mastocytosis represents a heterogeneous group of neoplastic mast cell disorders. The basic classification into a skin-limited disease and a systemic form with multi-organ involvement remains valid. Systemic mastocytosis is a disease often hard to diagnose, characterized by different symptoms originating from either the release of mast cell mediators or organ damage due to mast cell infiltration. Gastrointestinal symptoms represent one of the major causes of morbidity, being present in 60–80% of patients. A high index of suspicion by clinicians and pathologists is required to reach the diagnosis. Gastrointestinal mastocytosis can be a challenging diagnosis, as symptoms simulate other more common gastrointestinal diseases. The endoscopic appearance is generally unremarkable or nonspecific and gastrointestinal mast cell infiltration can be focal and subtle, requiring an adequate sampling with multiple biopsies by the endoscopists. Special stains, such as CD117, tryptase, and CD25, should be performed in order not to miss the gastrointestinal mast cell infiltrate. A proper patient’s workup requires a multidisciplinary approach including gastroenterologists, endoscopists, hematologists, oncologists, and pathologists. The aim of this review is to analyze the clinicopathological features of gastrointestinal involvement in systemic mastocytosis, focusing on the relevance of a multidisciplinary approach. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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12 pages, 1117 KiB

Open AccessReview

Indolent T-Cell Lymphoproliferative Disorders of the Gastrointestinal Tract (iTLPD-GI): A Review

by Francesca Sanguedolce, Magda Zanelli, Maurizio Zizzo, Stefano Luminari, Giovanni Martino, Alessandra Soriano, Linda Ricci, Cecilia Caprera and Stefano Ascani

Cancers 2021, 13(11), 2790; https://doi.org/10.3390/cancers13112790 - 3 Jun 2021

Cited by 21 | Viewed by 2633

Abstract

iTLPD-GI is a low-grade clonal T-cell lymphoproliferative disease arising in GI organs. It is an uncommon disease, and only recently has it been enlisted as a distinct provisional entity in the current WHO Classification. Data from the literature disclose high heterogeneity in terms of pathological and molecular features; on the other hand, establishing an accurate diagnosis of iTLPD-GI is of pivotal importance, since treatment options are different from that of other, more frequent lymphomas that arise in the gastrointestinal tract. In this review, we aimed to better define this novel entity, and to identify useful diagnostic biomarkers; moreover, we provide a biomarker-based approach to the diagnosis and describe the most common issues in differentiating iTLPD-GI from other neoplastic and non-neoplastic disorders. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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19 pages, 1327 KiB

Open AccessSystematic Review

Tissue vs. Fecal-Derived Bacterial Dysbiosis in Precancerous Colorectal Lesions: A Systematic Review

by Jurate Valciukiene, Kestutis Strupas and Tomas Poskus

Cancers 2023, 15(5), 1602; https://doi.org/10.3390/cancers15051602 - 4 Mar 2023

Cited by 3 | Viewed by 2014

Abstract

Alterations in gut microbiota play a pivotal role in the adenoma-carcinoma sequence. However, there is still a notable lack of the correct implementation of tissue and fecal sampling in the setting of human gut microbiota examination. This study aimed to review the literature and to consolidate the current evidence on the use of mucosa and a stool-based matrix investigating human gut microbiota changes in precancerous colorectal lesions. A systematic review of papers from 2012 until November 2022 published on the PubMed and Web of Science databases was conducted. The majority of the included studies have significantly associated gut microbial dysbiosis with premalignant polyps in the colorectum. Although methodological differences hampered the precise fecal and tissue-derived dysbiosis comparison, the analysis revealed several common characteristics in stool-based and fecal-derived gut microbiota structures in patients with colorectal polyps: simple or advanced adenomas, serrated lesions, and carcinomas in situ. The mucosal samples considered were more relevant for the evaluation of microbiota’s pathophysiological involvement in CR carcinogenesis, while non-invasive stool sampling could be beneficial for early CRC detection strategies in the future. Further studies are required to identify and validate mucosa-associated and luminal colorectal microbial patterns and their role in CRC carcinogenesis, as well as in the clinical setting of human microbiota studies. Full article

(This article belongs to the Special Issue Gastrointestinal Malignancies in the Era of Precision Oncology: From Bench to Bedside and Back Again)

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