Article
Cell Biology
Lu Lu, Yujing Liu, Guangtao Zhang, Yangxian Xu, Dan Hu, Guang Ji, Hanchen Xu
Summary: This study investigated the relationship between circRNA and the malignant transformation from colorectal adenoma to colorectal cancer, and identified potential biomarkers for the early diagnosis of colorectal cancer.
Article
Biochemistry & Molecular Biology
Danique J. I. Heuvelings, Anne G. W. E. Wintjens, Laura Moonen, Sanne M. E. Engelen, Ignace H. J. T. de Hingh, Liselot B. Valkenburg-van Iersel, Marcel den Dulk, Jan Beckervordersandforth, Sharon G. M. Thijssen, Daphne J. G. Leunissen, Laurents P. S. Stassen, Daniel Keszthelyi, Zlatan Mujagic, Ernst-Jan M. Speel, Nicole D. Bouvy
Summary: Metastatic colorectal cancer (CRC) is a common cause of cancer-related mortality, particularly peritoneal metastases (PM) with poor prognosis. This pilot study aimed to explore the genetic alterations in primary CRC tumors that may predict the development of PM. The study found unique BRAF mutations in microsatellite-stable (MSS) PM tumors and emphasized the importance of BRAF-mutated tumors in relation to the development of metachronous PM.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
Cecilia Villegas, Rebeca Perez, Olov Sterner, Ivan Gonzalez-Chavarria, Cristian Paz
Summary: Colorectal cancer is the second leading cause of cancer death worldwide, mainly affecting men, with about 20% of cases due to hereditary syndromes. Curcumin, the main polyphenol pigment in turmeric, has antioxidant properties and synergistic effects with both anticancer and anti-inflammatory drugs in inhibiting the progression of CRC through multiple signaling pathways.
Article
Oncology
Nana Jin, Chau-Ming Kan, Xiao Meng Pei, Wing Lam Cheung, Simon Siu Man Ng, Heong Ting Wong, Hennie Yuk-Lin Cheng, Wing Wa Leung, Yee Ni Wong, Hin Fung Tsang, Amanda Kit Ching Chan, Yin Kwan Evelyn Wong, William Chi Shing Cho, John Kwok Cheung Chan, William Chi Shing Tai, Ting-Fung Chan, Sze Chuen Cesar Wong, Aldrin Kay-Yuen Yim, Allen Chi-Shing Yu
Summary: This study found that the transcriptomic component from intestinal secretory cells was significantly decreased in cfRNA obtained from plasma of colorectal cancer patients. The expression of three genes remained consistent across cfRNA and tissue samples. The identified biomarkers in this study need further validation in a larger sample size to determine their potential use in early diagnosis of colorectal cancer.
FRONTIERS IN ONCOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Xiao-Jing Luo, Qi Zhao, Jia Liu, Jia-Bo Zheng, Miao-Zhen Qiu, Huai-Qiang Ju, Rui-Hua Xu
Summary: The therapeutic strategies for stage II/III colorectal cancer patients post-surgery are still debated, with the need for better biomarkers to stratify patients for adjuvant chemotherapy. Recent advances in sequencing and high-throughput technologies have led to the discovery of novel genetic and epigenetic biomarkers that could aid in prognosis and treatment responses in CRC.
Article
Oncology
Li Yang, Jinlin Yang, Andreas Kleppe, Havard E. Danielsen, David J. Kerr
Summary: The current standard-of-care adjuvant treatment for patients with colorectal cancer is chemotherapy selected on the basis of conventional histopathological staging criteria; however, the clinical benefit from these regimens is limited. The authors of this Perspective discuss strategies to minimize toxicity and monitor efficacy of these regimens, and propose new tools for disease staging that could enable more personalized treatment decisions.
NATURE REVIEWS CLINICAL ONCOLOGY
(2023)
Article
Medicine, Research & Experimental
Florian Uhlitz, Philip Bischoff, Stefan Peidli, Anja Sieber, Alexandra Trinks, Mareen Luethen, Benedikt Obermayer, Eric Blanc, Yana Ruchiy, Thomas Sell, Soulafa Mamlouk, Roberto Arsie, Tzu-Ting Wei, Kathleen Klotz-Noack, Roland F. Schwarz, Birgit Sawitzki, Carsten Kamphues, Dieter Beule, Markus Landthaler, Christine Sers, David Horst, Nils Bluethgen, Markus Morkel
Summary: In colorectal cancer, single-cell transcriptome analysis revealed patient-overarching cell clusters with differential oncogenic signaling activities, defining developmental trajectories of cancer cells along a mitogen-activated protein kinase gradient. Experimental targeting of EGFR-BRAF-MEK affected signaling and gene expression in patient-derived organoids, overriding default developmental trajectories and highlighting the importance of directional cancer cell development in response to targeted therapy.
EMBO MOLECULAR MEDICINE
(2021)
Review
Biochemistry & Molecular Biology
Chau-Ming Kan, Xiao Meng Pei, Martin Ho Yin Yeung, Nana Jin, Simon Siu Man Ng, Hin Fung Tsang, William Chi Shing Cho, Aldrin Kay-Yuen Yim, Allen Chi-Shing Yu, Sze Chuen Cesar Wong
Summary: Circulating tumor RNA (ctRNA) is a novel and attractive liquid biomarker that can provide important information about the expression of target genes noninvasively through circulating RNA sequencing. It overcomes limitations of low quantities of circulating tumor DNA (ctDNA) by increasing the tumor-derived RNA signal through overexpression of cancer-specific transcripts. This article presents an up-to-date review of ctRNAs as biomarkers for the diagnosis, prognosis, prediction, and drug resistance of colorectal cancer, and discusses practical aspects of analyzing plasma ctRNA, including storage and isolation, detection technologies, and limitations in clinical applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
De-Shen Wang, Hui Yang, Xiao-Yun Liu, Zhi-Gang Chen, Yun Wang, William Pat Fong, Ming-Tao Hu, Yuan-Chao Zheng, Yun Zheng, Bin-Kui Li, Yun-Fei Yuan, Gong Chen, Zhi-Zhong Pan, Lele Song, Yu-Hong Li, Rui-Hua Xu
Summary: This study found that ctDNA analysis can be used to predict the prognosis of patients undergoing resection of CRLM. Patients with a higher baseline ctDNA variant allele frequency represent a higher tumor burden, while decreased ctDNA during pre-operative chemotherapy predicted better tumor response. Patients with detectable ctDNA post-operatively and after adjuvant chemotherapy were associated with significantly shorter recurrence-free survival.
Article
Oncology
Yuchong Yang, Yao Lu, Hui Tan, Ming Bai, Xia Wang, Shaohua Ge, Tao Ning, Le Zhang, Jingjing Duan, Yansha Sun, Rui Liu, Hongli Li, Yi Ba, Ting Deng
Summary: The timing of postoperative adjuvant chemotherapy has significant effects on the survival rate of colorectal cancer patients. Starting chemotherapy within 8 weeks after surgery leads to better outcomes. There is no noticeable difference in survival benefits between starting chemotherapy within 5-8 weeks and within <= 4 weeks. Delaying chemotherapy for approximately 5-6 months after surgery is still beneficial in improving prognosis compared to patients not receiving chemotherapy.
Review
Oncology
Laura Masfarre, Joana Vidal, Concepcion Fernandez-Rodriguez, Clara Montagut
Summary: Detection of minimal residual disease (MRD) through circulating tumor DNA (ctDNA) has emerged as a powerful prognostic biomarker for identifying patients at higher risk of recurrence following surgery for localized colorectal cancer (CRC). Clinical trials are ongoing to evaluate the impact of ctDNA-guided treatment on improving clinical outcomes for CRC patients.
Review
Medicine, General & Internal
Emmanouil Georgilis, Maria Gavriatopoulou, Diamantis I. Tsilimigras, Panagiotis Malandrakis, Theodosios Theodosopoulos, Ioannis Ntanasis-Stathopoulos
Summary: Although surgical resection is the gold standard for resectable colorectal cancer liver metastases (CRLMs), the management after surgery remains controversial. This systematic review aimed to evaluate the efficacy, tolerability, and safety profile of different chemotherapeutic agents used as adjuvant treatment after surgical resection of CRLMs. The results showed that adjuvant therapy improved regression-free survival (RFS) and disease-free survival (DFS), but did not significantly prolong overall survival (OS), and the choice of therapeutic strategy did not have a differential impact on patient outcomes. More high-quality clinical trials are needed to determine which patients would benefit the most from adjuvant therapy after surgery for CRLMs.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Olivia M. Marx, Marc M. Mankarious, Melanie A. Eshelman, Wei Ding, Walter A. Koltun, Gregory S. Yochum
Summary: Despite a global decrease in colorectal cancer (CRC) incidence, the prevalence of early-onset colorectal cancer (EOCRC) has steadily increased. The understanding of genetic and molecular basis of EOCRC is limited. This study identified increased expression of c-MYC proto-oncogene (MYC) and its downstream targets in tumor samples. Elevated expression of the PVT1 long-non-coding RNA (lncRNA) was also detected. The findings suggest that deregulated MYC contributes to CRCs in younger patients.
Article
Cell Biology
Na Li, Qin Guo, Qiao Zhang, Bai-Jun Chen, Xiao-An Li, Yan Zhou
Summary: This study identified numerous differentially m(6)A methylated sites and genes in CRC, suggesting potential mechanisms of m(6)A-mediated gene expression regulation in colorectal cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Oncology
Navid Sobhani, Richard Chahwan, Raheleh Roudi, Rachel Morris, Stefano Volinia, Dafei Chai, Alberto D'Angelo, Daniele Generali
Summary: Non-coding RNA plays a crucial role in breast cancer and has predictive and prognostic value. It can be used as biomarkers and therapies. This class of RNA molecules includes both oncogenic and tumor suppressive molecules.
Article
Biochemistry & Molecular Biology
Filippo Martignano, Uday Munagala, Stefania Crucitta, Alessandra Mingrino, Roberto Semeraro, Marzia Del Re, Iacopo Petrini, Alberto Magi, Silvestro G. Conticello
Summary: Liquid biopsy, particularly analyzing cell-free DNA, is crucial in precision oncology. Nanopore sequencing provides a cost-effective and rapid alternative for detecting copy number variations in plasma DNA, making it accessible for both research and clinical purposes.
Article
Genetics & Heredity
Davide Bolognini, Alberto Magi
Summary: This research evaluates the performance of five long-read SV callers across four long-read aligners using both real and synthetic nanopore datasets. It focuses on the effects of read alignment, sequencing coverage, and variant allele depth on the detection and genotyping of SVs of different types and size ranges. Insights into precision and recall of SV callsets generated by integrating various long-read aligners and SV callers are provided.
FRONTIERS IN GENETICS
(2021)
Article
Pathology
Pamela Magini, Alessandra Mingrino, Barbara Gega, Gianluca Mattei, Roberto Semeraro, Davide Bolognini, Patrizia Mongelli, Laura Desiderio, Maria Carla Pittalis, Tommaso Pippucci, Alberto Magi
Summary: Copy number variants (CNVs) play important roles in genetic syndromes. Traditional and molecular karyotyping are time-consuming diagnostic tests. Nanopore sequencing offers a faster alternative with the same resolution for detecting CNVs.
JOURNAL OF MOLECULAR DIAGNOSTICS
(2022)
Article
Biochemistry & Molecular Biology
Romina D'Aurizio, Orazio Catona, Mattia Pitasi, Yang Eric Li, Bing Ren, Silvia Kirsten Nicolis
Summary: Non-coding variation in complex human disease has been confirmed to be important, especially variations in regulatory elements that affect the expression of disease-related genes. Enhancers connect to their target gene promoters through long-range physical interactions, and human regions syntenic with mouse DNA regions involved in these interactions have been identified. These findings provide a valuable resource for further exploration of neural diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Maria Elena Melica, Giulia Antonelli, Roberto Semeraro, Maria Lucia Angelotti, Gianmarco Lugli, Samuela Landini, Fiammetta Ravaglia, Gilda La Regina, Carolina Conte, Letizia De Chiara, Anna Julie Peired, Benedetta Mazzinghi, Marta Donati, Alice Molli, Stefanie Steiger, Alberto Magi, Niccolo Bartalucci, Valentina Raglianti, Francesco Guzzi, Laura Maggi, Francesco Annunziato, Alexa Burger, Elena Lazzeri, Hans-Joachim Anders, Laura Lasagni, Paola Romagnani
Summary: Crescentic glomerulonephritis is a disease characterized by vascular necrosis and hyperplasia of epithelial cells, resulting in the formation of crescents. Little is known about the molecular mechanisms driving this process. Research on mouse models showed that crescents are derived from the clonal expansion of immature parietal epithelial cells. Treatment with panobinostat, a histone deacetylase inhibitor, attenuated crescentic glomerulonephritis and restored kidney function by inducing differentiation of immature hyperplastic parietal epithelial cells into podocytes.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Letizia De Chiara, Carolina Conte, Roberto Semeraro, Paula Diaz-Bulnes, Maria Lucia Angelotti, Benedetta Mazzinghi, Alice Molli, Giulia Antonelli, Samuela Landini, Maria Elena Melica, Anna Julie Peired, Laura Maggi, Marta Donati, Gilda La Regina, Marco Allinovi, Fiammetta Ravaglia, Daniele Guasti, Daniele Bani, Luigi Cirillo, Francesca Becherucci, Francesco Guzzi, Alberto Magi, Francesco Annunziato, Laura Lasagni, Hans-Joachim Anders, Elena Lazzeri, Paola Romagnani
Summary: In this study, the distribution of polyploid tubular cells (TC) during acute kidney injury (AKI) was characterized using DNA content analysis and single cell RNA-sequencing. It was found that YAP1-driven TC polyploidization outside the site of injury is a mechanism to sustain residual kidney function during early AKI. However, polyploid TC senescence promotes interstitial fibrosis and CKD in AKI survivors. Targeting TC polyploidization after the early AKI phase prevents AKI-CKD transition without affecting AKI lethality. Senolytic treatment blocks repeated TC polyploidization cycles and prevents CKD.
NATURE COMMUNICATIONS
(2022)
Review
Genetics & Heredity
Giulia Carangelo, Alberto Magi, Roberto Semeraro
Summary: Single cell RNA sequencing (scRNA-seq) is a common and powerful technology in biomedical research, allowing for the analysis of the entire transcriptome of individual cells and revealing the heterogeneity of complex clinical samples. With advancements in technology and computation, scRNA-seq has become an important tool in biomedical research.
FRONTIERS IN GENETICS
(2022)
Review
Oncology
Valentina Russo, Eleonora Lallo, Armelle Munnia, Miriana Spedicato, Luca Messerini, Romina D'Aurizio, Elia Giuseppe Ceroni, Giulia Brunelli, Antonio Galvano, Antonio Russo, Ida Landini, Stefania Nobili, Marcello Ceppi, Marco Bruzzone, Fabio Cianchi, Fabio Staderini, Mario Roselli, Silvia Riondino, Patrizia Ferroni, Fiorella Guadagni, Enrico Mini, Marco Peluso
Summary: Metastatic colorectal cancer (mCRC) has a high incidence and mortality rate. Innovative biomarkers have been developed for predicting treatment response. By analyzing specific narrative publications, this study examines the ability of learning methods to build predictive models for mCRC patients, either for chemotherapy alone or combined with targeted therapy. The results show promising outcomes in predicting treatment response or toxic side-effects. Radiomics and molecular biomarkers are able to accurately identify responders and non-responders in the majority of patients.
Article
Biochemistry & Molecular Biology
Sara Mercurio, Giorgia Pozzolini, Roberta Baldi, Sara E. Barila, Mattia Pitasi, Orazio Catona, Romina D'Aurizio, Silvia K. Nicolis
Summary: New sequencing technologies have revealed the regulatory roles of DNA sequence variants in neurodevelopmental disorders. By generating genome-wide long-range interaction maps, it is possible to identify enhancer-gene connections that are far from the nearest promoter and associate these with DNA sequence variants linked to NDD. This approach not only confirms known disease-causing genes, but also identifies new candidate genes that were previously unknown.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Gennaro Bruno, Nicoletta Nastasi, Angela Subbiani, Alessia Boaretto, Sara Ciullini Mannurita, Gianluca Mattei, Patrizia Nardini, Chiara Della Bella, Alberto Magi, Alessandro Pini, Emanuela De Marco, Annalisa Tondo, Claudio Favre, Maura Calvani
Summary: Neuroblastoma is a heterogeneous extracranial tumor that occurs in childhood and has the ability to secrete catecholamines. In a murine model of neuroblastoma, modulation of the beta 3-adrenergic receptor resulted in reactivation of the immune response against the tumor. This modulation affected the PD-1/PD-L1 signaling axis and immune-related pathways.
CANCER GENE THERAPY
(2023)
Article
Biology
Alberto Magi, Gianluca Mattei, Alessandra Mingrino, Chiara Caprioli, Chiara Ronchini, GianMaria Frige, Roberto Semeraro, Davide Bolognini, Alessandro Rambaldi, Anna Candoni, Emanuela Colombo, Luca Mazzarella, Pier Giuseppe Pelicci
Summary: DNA methylation patterns in sparse CpG regions drive chemoresistance in Acute Myeloid Leukemia patients.
COMMUNICATIONS BIOLOGY
(2023)
Article
Psychiatry
Flavia Privitera, Maria A. Trusso, Floriana Valentino, Gabriella Doddato, Chiara Fallerini, Giulia Brunelli, Romina D'Aurizio, Simone Furini, Arianna Goracci, Andrea Fagiolini, Francesca Mari, Alessandra Renieri, Francesca Ariani
Summary: This study focuses on a large family with 12 members affected by bipolar disorder. Through whole-exome sequencing, certain genes, including CLN6 and ZNF92, were identified as having variations associated with the disorder. The findings suggest that heterozygous carriers of CLN6 may develop bipolar disorder later in life if combined with additional variants in ZNF92.
BRAZILIAN JOURNAL OF PSYCHIATRY
(2023)
Meeting Abstract
Immunology
A. Vanni, A. Mazzoni, R. Semeraro, M. Capone, P. Maschmeyer, G. Lamacchia, L. Salvati, A. Carnasciali, P. Farahvachi, T. Giani, G. Simonini, G. Filocamo, M. Romano, F. Liotta, M-F Mashreghi, L. Cosmi, R. Cimaz, A. Magi, L. Maggi, F. Annunziato
EUROPEAN JOURNAL OF IMMUNOLOGY
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Pamela Magini, Alessandra Mingrino, Barbara Gega, Davide Bolognini, Gianluca Mattei, Roberto Semeraro, Patrizia Mongelli, Laura Desiderio, Maria C. Pittalis, Tommaso Pippucci, Alberto Magi
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Roberta Croce, Lucia Corrado, Nadia Barizzone, Alice Di Pierro, Loredana Marialuisa Genovese, Filippo Geraci, Eleonora Mangano, Romina D'Aurizio, Roberta Bordoni, Davide Cora, Francesco Favero, Miriam Zuccala, Cristoforo Comi, Fabiola De Marchi, Luca Magistrelli, Giovanni Manzini, Gianluca De Bellis, Alfredo Brusco, Marco Severgnini, Marco Pellegrini, Letizia Mazzini, Sandra D'Alfonso
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)