Review
Medicine, General & Internal
Valentina Angerilli, Francesca Galuppini, Fabio Pagni, Nicola Fusco, Umberto Malapelle, Matteo Fassan
Summary: The current practice of pathology is influenced by the increasing complexity of modern medicine, especially precision oncology, as well as major technological advancements. In the era of next-generation technologies, pathologists are responsible for integrating and interpreting morphologic and molecular information, delivering critical answers to diagnostic, prognostic, and predictive queries, and playing a prominent role in molecular tumor boards.
Review
Oncology
Albrecht Stenzinger, Arndt Vogel, Ulrich Lehmann, Angela Lamarca, Paul Hofman, Luigi Terracciano, Nicola Normanno
Summary: Cholangiocarcinomas are a heterogeneous group of tumors with distinct genomic alterations. Next-generation sequencing is a powerful tool for identifying gene variants and guiding personalized treatment for patients with cholangiocarcinomas. Understanding the use of NGS in molecular profiling is crucial for healthcare professionals to optimize treatment outcomes.
CANCER TREATMENT REVIEWS
(2024)
Review
Oncology
Yuchen Jin, Beibei Liu, Muhsin H. Younis, Gang Huang, Jianjun Liu, Weibo Cai, Weijun Wei
Summary: Molecular imaging utilizes radionuclides or artificially modified molecules to image specific disease targets, with newly developed probes enabling target-specific diagnosis and treatment of diseases. Advances in molecular imaging have led to the development of novel tracers based on aptamer, peptide, antibody, nanobody, antibody fragment, and nanoparticle platforms, supporting the management of diseases such as thyroid cancer.
Review
Chemistry, Analytical
Louis Kreitmann, Luca Miglietta, Ke Xu, Kenny Malpartida-Cardenas, Giselle D'Souza, Myrsini Kaforou, Karen Brengel-Pesce, Laurent Drazek, Alison Holmes, Jesus Rodriguez-Manzano
Summary: qPCR is a powerful tool for accurate nucleic acid detection and quantification, but current methods for multiplexing are limited to a small number of targets or require expensive instrumentation. This review discusses the use of machine learning algorithms and data-driven solutions to enhance multiplexing in qPCR. The review also explores the use of computer simulation to optimize the design of mPCR assays. The integration of knowledge-based and data-driven software solutions could streamline assay design and improve target detection and quantification in the multiplex setting.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Oncology
Wencke Walter, Nicole Pfarr, Manja Meggendorfer, Philipp Jost, Torsten Haferlach, Wilko Weichert
Summary: Molecular diagnostics has played a crucial role in precision oncology and has undergone revolutionary developments in recent years. In most cases, it is no longer possible to select treatments for cancer patients without molecular characterization. However, there has been limited scientific research on preanalytical and analytical requirements, and standardization and quality assessment have played a marginal role in the field.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Norman J. Beauchamp, R. Nick Bryan, Marilyn M. Bui, Gabriel P. Krestin, Geraldine B. McGinty, Carolyn C. Meltzer, Michael Neumaier
Summary: Enormous progress in diagnostic testing allows for more accurate diagnosis and improved clinical outcomes. However, the increasing volume and diversity of test results can overwhelm clinicians, leading to incorrect or delayed diagnoses. Integrative diagnostics, combining diagnostic and clinical data through informatics tools, has the potential to enhance treatment selection, modification, and termination, ultimately improving patient outcomes and reducing costs.
INSIGHTS INTO IMAGING
(2023)
Article
Clinical Neurology
Stephen Crosier, Debbie Hicks, Edward C. Schwalbe, Daniel Williamson, Sarah Leigh Nicholson, Amanda Smith, Janet C. Lindsey, Antony Michalski, Barry Pizer, Simon Bailey, Nick Bown, Gavin Cuthbert, Stephen B. Wharton, Thomas S. Jacques, Abhijit Joshi, Steven C. Clifford
Summary: The application of advanced molecular pathology in rare tumors faces challenges such as low sample numbers and accessibility to specialized expertise. A nationwide trial on medulloblastoma demonstrated the feasibility and effectiveness of coordinated real-time centralised pathology review (CPR) in providing robust diagnostics and altering clinical management. It was found that engagement of a specialist pathologist panel was essential for achieving consensus in histological assessments.
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2021)
Article
Hematology
Come Bommier, Claire Mauduit, Juliette Fontaine, Estelle Bourbon, Pierre Sujobert, Sarah Huet, Lucile Baseggio, Sandrine Hayette, Camille Laurent, Emmanuel Bachy, Herve Ghesquieres, Catherine Thieblemont, Gilles Salles, Alexandra Traverse-Glehen
Summary: The study showed that TNGS can lead to a more accurate diagnosis in challenging lymphoma cases, thus improving clinical management in routine practice.
BRITISH JOURNAL OF HAEMATOLOGY
(2021)
Article
Veterinary Sciences
Rebecca P. Wilkes
Summary: Although still mainly used for research purposes, NGS has been adopted by some veterinary diagnostic laboratories. Metagenomics approaches offer the widest detection range for infectious disease diagnostics, but at a higher cost. tNGS maintains the ability to detect a broad range of pathogens at a lower cost compared to mNGS, making it a viable option for syndromic testing in veterinary diagnostic laboratories.
VETERINARY CLINICS OF NORTH AMERICA-FOOD ANIMAL PRACTICE
(2023)
Review
Biology
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo, Gulnaz Zaidi, Shravani Rawool, Ritesh P. Thakare, Shahid Banday, Alok K. Mishra, Gautam Das, Sunil K. Malonia
Summary: Next-generation sequencing (NGS) is a powerful tool that can sequence millions of DNA fragments simultaneously, providing detailed information about genomes, genetic variations, gene activity, and changes in gene behavior. Recent advancements have focused on improving sequencing speed and accuracy, reducing costs, and enhancing data analysis. These advancements have great potential for advancing genomics research and improving our understanding of diseases and personalized healthcare.
Article
Pathology
Jack K. Tung, Kelly A. Devereaux, Archana Lal Erdmann, Iris Schrijver, James Zehnder, Carlos J. Suarez
Summary: This report illustrates three potential pitfalls related to amplicon-based NGS assays and highlights strategies to minimize such risks.
JOURNAL OF CLINICAL PATHOLOGY
(2023)
Article
Multidisciplinary Sciences
Jeffrey M. Conroy, Sarabjot Pabla, Sean T. Glenn, R. J. Seager, Erik Van Roey, Shuang Gao, Blake Burgher, Jonathan Andreas, Vincent Giamo, Melissa Mallon, Yong Hee Lee, Paul DePietro, Mary Nesline, Yirong Wang, Felicia L. Lenzo, Roger Klein, Shengle Zhang
Summary: The study assessed the analytical performance of the TruSight Oncology 500 High-Throughput assay for detection of molecular alterations in solid tumors. Supporting software and automated sample preparation systems were developed to process up to 70 clinical samples in a single sequencing run within 7 days. Results showed that the scalable assay accurately detects various molecular alterations and gene fusions, demonstrating high analytical performance for precision therapeutics in oncology.
Article
Nanoscience & Nanotechnology
Lip Ket Chin, Huiyan Li, Jae-Hyeok Choi, Yoshiko Iwamoto, Juhyun Oh, Jouha Min, Suk Kyung Beak, Dahyeon Yoo, Cesar M. Castro, Dongyoung Lee, Hyungsoon Im
Summary: In the era of precision oncology, multicolor fluorescence imaging has become a core technology for molecular analysis of cellular and tissue specimens. Conventional staining methods are labor-intensive and time-consuming, hindering their use in resource-limited settings. This study introduces a new immunostaining method based on hydrogel stamping, which is simple, fast, and reproducible. The hydrogel stamp effectively transfers fluorescent antibodies to targets and eliminates the need for extra washing steps. This method enables high-quality immunostaining in a shorter time and with reduced antibody consumption, and has the potential for use in compact point-of-care systems for cancer diagnosis.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Medicine, General & Internal
Alessio Buonavoglia, Gianvito Lanave, Michele Camero, Marialaura Corrente, Antonio Parisi, Vito Martella, Carlo Prati
Summary: NGS was used to assess endodontic microbiota in a patient with endo-periodontal lesion, revealing different microbial populations in different canals of the same tooth, potentially leading to varying clinical manifestations and prognoses.
Article
Genetics & Heredity
Jing Ma, Xiuli Ma, Ken Lin, Rui Huang, Xianyun Bi, Cheng Ming, Li Li, Xia Li, Guo Li, Liping Zhao, Tao Yang, Yingqin Gao, Tiesong Zhang
Summary: This study conducted genetic sequencing analysis on 879 deaf Chinese children in Yunnan, and identified 428 deafness gene variants, with GJB2 and SLC26A4 being the most common genes. The study also found that the genetic characteristics of deafness in this region differ from other regions and ethnic groups, suggesting the need for customized genetic screening programs.
Article
Oncology
Maria Vittoria Dieci, Luisa Carbognin, Federica Miglietta, Fabio Canino, Carlo Alberto Giorgi, Enrico Cumerlato, Ottavia Amato, Davide Massa, Gaia Griguolo, Elisa Genovesi, Giovanna Garufi, Diana Giannarelli, Antonio Tornincasa, Lucia Trudu, Silvia Michieletto, Tania Saibene, Marcello Lo Mele, Matteo Fassan, Giovanni Zarrilli, Federico Piacentini, Emilio Bria, Valentina Guarneri
Summary: This study demonstrates that incorporating carboplatin into neoadjuvant chemotherapy significantly improves pathological complete response (pCR) in triple-negative breast cancer (TNBC) patients. Additionally, the combination of anthracycline-taxane chemotherapy with carboplatin enhances immune infiltration. Finally, the increase in tumor-infiltrating lymphocytes (TILs) after neoadjuvant chemotherapy exposure is independently associated with distant disease-free survival.
BRITISH JOURNAL OF CANCER
(2023)
Correction
Multidisciplinary Sciences
Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vazquez-Garcia, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D. Morris, Paul T. Spellman, David C. Wedge, Peter Van Loo
Correction
Multidisciplinary Sciences
Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshoj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andres Lanzos, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, Andre Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uuskuela-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jueri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Nuria Lopez-Bigas, Joachim Weischenfeldt, Rameen Beroukhim, Inigo Martincorena, Jakob Skou Pedersen, Gad Getz
Article
Pathology
Federica Miglietta, Valentina Carraro, Ottavia Amato, Gaia Griguolo, Michele Bottosso, Giada Munari, Giovanni Zarrilli, Marcello Lo Mele, Caterina Barbieri, Angelo Paolo Dei Tos, Valentina Guarneri, Maria Vittoria Dieci, Matteo Fassan
Summary: This study aims to track the dynamics of the PI3K/PTEN/mTOR pathway in HR+/HER2- breast cancer patients receiving neoadjuvant chemotherapy. The results show that this pathway is highly dynamic and may play a crucial role in shaping the molecular landscape of breast cancer with residual disease after chemotherapy.
JOURNAL OF CLINICAL PATHOLOGY
(2023)
Article
Pathology
Valentina Angerilli, Paola Parente, Michela Campora, Clara Ugolini, Serena Battista, Paola Cassoni, Alessandro Gambella, Francesco Cavallin, Giuseppe De Lisi, Alessandro Vanoli, Federica Grillo, Luca Mastracci, Matteo Fassan
Summary: In this study, the clinicopathological and molecular features of HER2-low gastric/gastro-oesophageal junction cancers were investigated. It was found that HER2-low expression was more common in biopsy specimens and varied among different institutions. If further research confirms the effectiveness of novel anti-HER2 agents in HER2-low gastro-oesophageal cancers, the interpretation of HER2 status may need to be revised.
JOURNAL OF CLINICAL PATHOLOGY
(2023)
Article
Oncology
Sibilla Molon, Paola Brun, Melania Scarpa, Dario Bizzotto, Gaia Zuccolotto, Marco Scarpa, Matteo Fassan, Imerio Angriman, Antonio Rosato, Paola Braghetta, Ignazio Castagliuolo, Paolo Bonaldo
Summary: The study investigates the role of collagen VI in the development of intestinal inflammation and finds that it plays an important role in lymphatic vessel development and intestinal inflammation. The study also reveals that high collagen VI expression in the colon biopsies of CD patients is associated with increased surgical risk and disease recurrence.
JOURNAL OF PATHOLOGY
(2023)
Correction
Biotechnology & Applied Microbiology
Sergei Yakneen, Sebastian M. Waszak, Michael Gertz, Jan O. Korbel
NATURE BIOTECHNOLOGY
(2023)
Article
Genetics & Heredity
Andrea Remo, Federica Grillo, Luca Mastracci, Michele Simbolo, Matteo Fassan, Maria Paola Cecchini, Giuseppe Miscio, Antonio Sassano, Paola Parente, Alessandro Vanoli, Giovanna Sabella, Guido Giordano, Emanuele Damiano Urso, Luigi Cerulo, Aldo Scarpa, Francesco Fiorica, Massimo Pancione
Summary: A recent study explores the genetic and immunophenotypic characteristics of rhabdoid colorectal tumors (RCTs). The findings reveal that RCTs exhibit mismatch repair-deficient phenotypes, CK7-/CK20-/CDX2- marker phenotype, and aberrant activation of the MAPK pathway, particularly with BRAF V600E mutations. While SMARCB1/INI1 expression is normal, the ciliogenic markers CROCC and β-tubulin are globally altered in RCTs. Overall, these results indicate that primary ciliogenesis and MAPK pathway activation contribute to the aggressiveness of RCTs, suggesting a potential therapeutic target.
Article
Medicine, General & Internal
Anna Caterina Milanetto, Anna-Lea Gais Zurcher, Alina David, Matteo Fassan, Claudio Pasquali
Summary: This retrospective study evaluated the possible prognostic role of clinic-pathological features and surgery in pancreatic neuroendocrine neoplasms (pNENs). The results showed that about 20% of pNENs had a size > 4 cm, 78% were nonfunctioning, and 55% had distant metastases at diagnosis. However, long-term survival of more than five years can be achieved after surgery.
JOURNAL OF CLINICAL MEDICINE
(2023)
Review
Oncology
Astghik Stepanyan, Matteo Fassan, Gaya Spolverato, Ignazio Castagliuolo, Melania Scarpa, Marco Scarpa, IMMUNOREACT Study Grp
Summary: Neoadjuvant therapy (NT) followed by surgery is the main treatment for rectal cancer patients. Immune biomarkers are being recognized as potential predictors of NT response. A meta-analysis was performed to estimate their predictive significance.
Article
Oncology
Ottavia De Simoni, Luca Dal Santo, Marco Scarpa, Giada Munari, Ylenia Camilla Spolverato, Antonio Scapinello, Sara Lonardi, Caterina Solda, Francesca Bergamo, Alberto Fantin, Romeo Bardini, Pierluigi Pilati, Matteo Fassan, Mario Gruppo
Summary: The aim of this study is to determine the potential significant tumor microenvironment (TME) immune markers of long-term survival in pancreatic ductal adenocarcinoma (PDAC) patients. Immunohistochemical staining was performed to characterize the TME using tissue microarray. The results showed that high density of CD8+ lymphocytes and low density of FOXP3+ and iNOS+ tumor-associated macrophages (TAMs) are predictors of good prognosis in PDAC patients.
Article
Pathology
Remo Alessandris, Federico Moroso, Mauro Michelotto, Matteo Fassan, Valentina Angerilli, Linda Callegari, Mirto Foletto
Summary: The use of preoperative upper gastrointestinal endoscopy and postoperative histopathological examination in bariatric surgery is still controversial. Based on the clinical experience of the authors, both preoperative endoscopic assessment and postoperative histopathological examination of the specimen are recommended to provide optimal treatment for these patients.
Review
Pathology
Valentina Angerilli, Matteo Fassan, Paola Parente, Irene Gullo, Michela Campora, Chiara Rossi, Maria Luisa Sacramento, Gianmaria Pennelli, Alessandro Vanoli, Federica Grillo, Luca Mastracci
Summary: PD-L1 is an established immunohistochemical biomarker for predicting the response to immunotherapy. However, it still has limitations due to changing cut-off values and scoring systems, as well as variability between observers and laboratories. This review focuses on the staining patterns and challenges in evaluating PD-L1 in gastroesophageal adenocarcinoma and esophageal squamous cell carcinoma.
Review
Pathology
Valentina Angerilli, Lorenzo Fornaro, Francesco Pepe, Silvia Maria Rossi, Giuseppe Perrone, Umberto Malapelle, Matteo Fassan
Summary: Cholangiocarcinoma (CCA) is a heterogeneous group of neoplasms with a poor prognosis. FGFR2 fusions/rearrangements are druggable genetic alterations in a subset of CCAs. Standardization of molecular testing for FGFR2 alterations in CCA is necessary with the emergence of FGFR-targeting therapies.
Article
Surgery
Gaya Spolverato, Matteo Fassan, Melania Scarpa, Astghik Stepanyan, Ottavia De Simoni, Federico Scognamiglio, Valentina Chiminazzo, Clarissa De Nardi, Giulia Tamponi, Silvia Negro, Imerio Angriman, Andromachi Kotsafti, Cesare Ruffolo, Chiara Vignotto, Maurizio Zizzo, Francesco Marchegiani, Luca Facci, Francesca Bergamo, Stefano Brignola, Gianluca Businello, Vincenza Guzzardo, Luca Dal Santo, Roberta Salmaso, Carlotta Ceccon, Marco Massani, Anna Pozza, Ivana Cataldo, Tommaso Stecca, Angelo Paolo Dei Tos, Vittorina Zagonel, Pierluigi Pilati, Boris Franzato, Antonio Scapinello, Giovanni Pirozzolo, Alfonso Recordare, Roberto Merenda, Giovanni Bordignon, Licia Laurino, Silvio Guerriero, Chiara Romiti, Giuseppe Portale, Chiara Cipollari, Salvatore Candioli, Laura Gavagna, Giulia Pozza, Mario Godina, Isabella Mondi, Giulia Noaro, Monica Ortenzi, Mario Guerrieri, Giovanni Tagliente, Monica Tomassi, Umberto Tedeschi, Andrea Porzionato, Marco Agostini, Isacco Maretto, Quoc Riccardo Bao, Francesco Cavallin, Barbara Di Camillo, Romeo Bardini, Ignazio Castagliuolo, Salvatore Pucciarelli, Marco Scarpa
Summary: The study found that early-onset rectal cancer is rarely associated with common hereditary syndromes. The tumor microenvironment is characterized by a high frequency of mutations impairing the local immune surveillance mechanisms and low expression of immune editing-related genes. A constitutively low number of CD4 T cells associated with a high number of T regulators indicates an imbalance in the immune surveillance mechanisms.
BRITISH JOURNAL OF SURGERY
(2023)