Article
Oncology
Zixiang Yu, Haixing Wang, Qi Song, Jie Huang, Jianfang Xu, Jieakesu Su, Hao Wang, Lijie Tan, Xin Wang, Zhengzeng Jiang, Weijie Chen, Dongxian Jiang, Yingyong Hou
Summary: NTRK1 rearrangement is rare in ESCC, but increased copy number of NTRK1 may serve as a prognostic indicator for DFS and OS in patients with ESCC.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2021)
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Sijia Cui, Nicholas McGranahan, Jing Gao, Peng Chen, Wei Jiang, Lingrong Yang, Li Ma, Junfang Liao, Tian Xie, Congying Xie, Tariq Enver, Shixiu Wu
Summary: This study uses multi-omics analysis to investigate heterogeneity and evolution in oesophageal squamous cell carcinoma (ESCC). The study reveals ongoing chromosomal instability underlying genomic, epigenomic, and transcriptomic heterogeneity. It also shows that immune infiltration acts as a selective force in shaping the clonal evolution of ESCC.
NATURE COMMUNICATIONS
(2023)
Review
Oncology
Noortje Verschoor, Teoman Deger, Agnes Jager, Stefan Sleijfer, Saskia M. Wilting, John W. M. Martens
Summary: Liquid biopsies have the potential to provide valuable information for HER2 assessment, but there is currently a lack of well-designed studies to determine their accuracy and clinical utility in HER2 evaluation.
CANCER TREATMENT REVIEWS
(2022)
Article
Cell Biology
Kyukwang Kim, Mooyoung Kim, Andrew J. Lee, Sang-Hyun Song, Jun-Kyu Kang, Junghyun Eom, Young-Joon Kim, Gyeong Hoon Kang, Jeong Mo Bae, Sunwoo Min, Yeonsoo Kim, Yoojoo Lim, Han Sang Kim, Tae -You Kim, Inkyung Jung
Summary: This study investigates the regulatory effect of non-coding large-scale structural variations (SVs) on proto-oncogene activation by profiling 3D cancer genome maps. The analysis reveals the establishment of de novo chromatin contacts that span multiple topologically associating domains (TADs) and the occurrence of super-enhancer (SE) hijacking and its clonal characteristics. The activation of oncogenes and increased drug resistance due to SE hijacking are validated using CRISPR-Cas9. This research provides insights into the regulatory principles of large-scale SVs in oncogene activation and their clinical implications.
Article
Medicine, Research & Experimental
Yang Li, Riyue Feng, Xiao Yu, Lei Li, Yuhao Liu, Ruixiang Zhang, Xiankai Chen, Yahui Zhao, Zhihua Liu
Summary: SLC35E2 promotes ESCC cell proliferation, and KLF4 acts as a transcriptional repressor by regulating the expression of SLC35E2 to affect the malignant characteristics of ESCC.
Article
Oncology
Hidenari Hirata, Atsushi Niida, Nobuyuki Kakiuchi, Ryutaro Uchi, Keishi Sugimachi, Takaaki Masuda, Tomoko Saito, Shun-Ichiro Kageyama, Yushi Motomura, Shuhei Ito, Tadamasa Yoshitake, Daisuke Tsurumaru, Yusuke Nishimuta, Akira Yokoyama, Takanori Hasegawa, Kenichi Chiba, Yuichi Shiraishi, Junyan Du, Fumihito Miura, Masaru Morita, Yasushi Toh, Masakazu Hirakawa, Yoshiyuki Shioyama, Takashi Ito, Tetsuo Akimoto, Satoru Miyano, Tatsuhiro Shibata, Masaki Mori, Yutaka Suzuki, Seishi Ogawa, Kousei Ishigami, Koshi Mimori
Summary: A study sequencing 52 tumor samples from 33 ESCC patients who received radiotherapy combined with 5-fluorouracil/platinum revealed the impact of chemoradiotherapy on clonal evolution, with MYC gain potentially serving as a marker for therapy resistance. The findings enhance understanding of therapeutic resistance and support the rationale for precision chemoradiotherapy.
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Pathology
Samar Samir Youssef, Rady Eid El-Araby, Eman Abd El-Razek Abbas, Mohamed Hassany, Tamer Elbaz
Summary: This study used cfDNA to investigate the CNV in BCL9 and RPS6KB1 genes and its impact on prognosis in HCC. The results showed that gain in CNV of BCL9 and RPS6KB1 genes was detected in 14% and 24% of HCC patients, respectively. CNV gain in these genes was associated with different risk factors and showed higher mortality rates and reduced survival times.
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
(2023)
Article
Medical Laboratory Technology
L. Y. Lois Choy, Wenlei Peng, Peiyong Jiang, Suk Hang Cheng, Stephanie C. Y. Yu, Huimin Shang, O. Y. Olivia Tse, John Wong, Vincent Wai Sun Wong, Grace L. H. Wong, W. K. Jacky Lam, Stephen L. Chan, Rossa W. K. Chiu, K. C. Allen Chan, Y. M. Dennis Lo
Summary: Background analysis of circulating tumor DNA is crucial for cancer care, but previous studies focused on short DNA fragments. Bisulfite sequencing, a traditional method for methylation analysis, causes DNA degradation. This study overcame these limitations using single-molecule sequencing and discovered a previously unknown long cfDNA population.
CLINICAL CHEMISTRY
(2022)
Article
Oncology
Hongyi Li, Yongjia Weng, Shaojie Wang, Fang Wang, Yanqiang Wang, Pengzhou Kong, Ling Zhang, Caixia Cheng, Heyang Cui, Enwei Xu, Shuqing Wei, Dinghe Guo, Fei Chen, Yanghui Bi, Yongsheng Meng, Xiaolong Cheng, Yongping Cui
Summary: The study revealed that CDCA7 may act as an oncogene by directly upregulating CCNA2 to facilitate tumor progression in ESCC.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Retno Ningsi, Maha Elazezy, Luisa Stegat, Elena Laakmann, Sven Peine, Sabine Riethdorf, Volkmar Mueller, Klaus Pantel, Simon A. Joosse
Summary: CTCs have been found to be associated with metastasis and survival in breast cancer patients. Evaluating the expression of estrogen receptors (ER) in CTCs may help with personalized treatment. Some patients have both ER-positive and ER-negative CTCs at the time of metastasis, which may lead to resistance to hormonal therapy. Therefore, monitoring the status of CTC-ER in breast cancer patients can provide prognostic and predictive value.
Article
Immunology
Manuela Moraru, Adriana Perez-Portilla, Karima Al-Akioui Sanz, Alfonso Blazquez-Moreno, Antonio Arnaiz-Villena, Hugh T. Reyburn, Carlos Vilches
Summary: Fc gamma receptors (FcγR) are cell-surface glycoproteins that play a role in immune responses. The CNR5 deletion on the FCGR locus can lead to loss and recombination of FCGR genes, potentially affecting immune function. The distribution of FCGR polymorphism shows significant variation in the highlands of Ecuador, with CNR5 deletion being relatively common.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Clinical Neurology
Aurelien Perrin, Raul Juntas Morales, Francoise Chapon, Corinne Theze, Delphine Lacourt, Henri Pegeot, Emmanuelle Uro-Coste, Diane Giovannini, Nicolas Leboucq, Martial Mallaret, Emmeline Lagrange, Valerie Rigau, Karen Gaudon, Pascale Richard, Michel Koenig, Corinne Metay, Mireille Cossee
Summary: This study analyzed patients from two distinct families with a novel distal titinopathy phenotype associated with the same CNV in the TTN gene. The CNV reported in this study is the most proximal out-of-frame TTN variant and leads to aberrant splicing transcripts, resulting in frameshift and possibly dominant effects. This data represents a novel phenotype-genotype association and provides hypotheses for its dominant effects.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2021)
Editorial Material
Hematology
Immacolata Andolfo, Seth L. Alper, Achille Iolascon
AMERICAN JOURNAL OF HEMATOLOGY
(2022)
Letter
Medical Laboratory Technology
Francesco Broccolo, Marta Giovanetti, Alessio Colombo, Nicola Perrelli, Adelaide Bussini, Silvia Cavalli, Massimo Ciccozzi, Massimo Zollo
CLINICAL CHEMISTRY AND LABORATORY MEDICINE
(2022)
Article
Genetics & Heredity
Stefania Mantovani, Sergio Daga, Chiara Fallerini, Margherita Baldassarri, Elisa Benetti, Nicola Picchiotti, Francesca Fava, Anna Galli, Silvia Zibellini, Mirella Bruttini, Maria Palmieri, Susanna Croci, Sara Amitrano, Diana Alaverdian, Katia Capitani, Simone Furini, Francesca Mari, Ilaria Meloni, Elisa Frullanti, Mario U. Mondelli, Alessandra Renieri
Summary: TLR7 variants in male patients lead to impaired immune response to viruses like SARS-CoV-2, resulting in severe COVID-19. These variants cause significant damage to the TLR7 signaling pathway and hinder the type I and II interferon responses.
GENES AND IMMUNITY
(2022)
Article
Biochemistry & Molecular Biology
Veronica Ferrucci, Pasqualino de Antonellis, Fabrizio Quarantelli, Fatemeh Asadzadeh, Francesca Bibbo, Roberto Siciliano, Carmen Sorice, Ida Pisano, Barbara Izzo, Carmela Di Domenico, Angelo Boccia, Maria Vargas, Biancamaria Pierri, Maurizio Viscardi, Sergio Brandi, Giovanna Fusco, Pellegrino Cerino, Livia De Pietro, Ciro Furfaro, Leonardo Antonio Napolitano, Giovanni Paolella, Lidia Festa, Stefania Marzinotto, Maria Concetta Conte, Ivan Gentile, Giuseppe Servillo, Francesco Curcio, Tiziana de Cristofaro, Francesco Broccolo, Ettore Capoluongo, Massimo Zollo
Summary: The study found that subgenomic RNA transcripts (particularly sgN) can serve as markers of active SARS-CoV-2 virus replication and are correlated with high viral loads. The loss of sgN indicates the negativization of patient condition. A new detection kit has been developed to detect sgN, gene E, gene ORF1ab, and gene RNAse P. In addition, in vitro experiments showed that 2'-O-methyl antisense RNA related to the sgN sequence can inhibit SARS-CoV-2 N protein synthesis, viral replication, and syncytia formation in human cells, suggesting potential therapeutic applications against SARS-CoV-2.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Materials Science, Multidisciplinary
Werner E. G. Mueller, Hadrian Schepler, Meik Neufurth, Shunfeng Wang, Veronica Ferrucci, Massimo Zollo, Rongwei Tan, Heinz C. Schroeder, Xiaohong Wang
Summary: The polyP hydrogel formulation can accelerate the healing of chronic wounds and provide more metabolic energy by encapsulating and killing bacteria.
JOURNAL OF MATERIALS SCIENCE & TECHNOLOGY
(2023)
Article
Hematology
Enrica Federti, Francesca Vinchi, Iana Iatcenko, Alessandra Ghigo, Alessandro Matte, Serge Cedrick Mbiandjeu Toya, Angela Siciliano, Deborah Chiabrando, Emanuela Tolosano, Steven Zebulon Vance, Veronica Riccardi, Immacolata Andolfo, Manuela Iezzi, Alessia Lamolinara, Achille Iolascon, Lucia De Franceschi
Summary: Cardiomyopathy greatly affects the well-being and survival of patients with 13-thalassemia or transfusion-dependent myelodysplastic syndromes. Recent research has found a connection between Nrf2 activity and iron metabolism. In this study, Nrf2-/- mice developed age-dependent cardiomyopathy characterized by oxidation, degradation of SERCA2A, and iron accumulation. The absence of Nrf2 paradoxically protected against heart iron accumulation when exposed to an iron overload diet. The activation of the unfolded protein response system and cardiac fibrosis were observed in a model of 13-thalassemia independent of heart iron content. These findings provide insights into potential early treatment for cardiomyopathy in patients with 13-thalassemia.
Article
Genetics & Heredity
Alessandro De Falco, Daniele De Brasi, Matteo Della Monica, Claudia Cesario, Stefano Petrocchi, Antonio Novelli, Giuseppe D'Alterio, Achille Iolascon, Mario Capasso, Carmelo Piscopo
Summary: Cornelia de Lange Syndrome (CdLS) is a rare genetic disorder that affects multiple organs. This study presents clinical and genetic findings of a patient with CdLS type 4, a syndrome that has been rarely described before. The patient exhibited previously reported clinical features of CdLS type 4 as well as additional symptoms not mentioned previously. The novel genetic variant found in this patient suggests its pathogenicity. This report provides valuable insights for counseling future CdLS type 4 cases.
Article
Oncology
Fabio Pastorino, Mario Capasso, Chiara Brignole, Vito A. Lasorsa, Veronica Bensa, Patrizia Perri, Sueva Cantalupo, Serena Giglio, Massimo Provenzi, Marco Rabusin, Elvira Pota, Monica Cellini, Annalisa Tondo, Maria A. De Ioris, Angela R. Sementa, Alberto Garaventa, Mirco Ponzoni, Loredana Amoroso
Summary: Approximately 50% of high-risk neuroblastomas (NB) relapse within two years after treatment, and additional therapeutic options are needed for relapsed or refractory patients. The identification of ALK somatic mutations or amplification is crucial for the treatment of these patients. ALK inhibitors may have a significant role in treating high-risk, ALK-mutated NB patients in the era of precision medicine.
Article
Hematology
Immacolata Andolfo, Vittoria Monaco, Flora Cozzolino, Barbara Eleni Rosato, Roberta Marra, Vincenza Cerbone, Valeria Maria Pinto, Gian Luca Forni, Sule Unal, Achille Iolascon, Maria Monti, Roberta Russo
Letter
Hematology
Valeria Maria Pinto, Roberta Russo, Sabrina Quintino, Barbara Eleni Rosato, Roberta Marra, Federica Del Giudice, Massimo Mogni, Massimo Maffei, Achille Iolascon, Gian Luca Forni, Immacolata Andolfo
Summary: This study provides an overview of the workflow and includes some examples of the achieved results.
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Article
Multidisciplinary Sciences
Daniele Pirone, Annalaura Montella, Daniele G. Sirico, Martina Mugnano, Massimiliano M. Villone, Vittorio Bianco, Lisa Miccio, Anna Maria Porcelli, Ivana Kurelac, Mario Capasso, Achille Iolascon, Pier Luca Maffettone, Pasquale Memmolo, Pietro Ferraro
Summary: In this study, we introduce a machine learning-powered tomographic phase imaging flow cytometry system that can provide high-throughput 3D phase-contrast tomograms of individual cells for the identification of circulating tumor cells in microfluidic cytometry condition. We propose a hierarchical machine learning decision-maker that utilizes 3D morphological features calculated from the cells' refractive index to accurately discriminate tumor cells from white blood cells as well as identify the tumor type. Experimental results demonstrate a success rate of over 97% in identifying tumor cells and an accuracy of over 97% in discriminating between different cancer cell types, highlighting the potential of this stain-free liquid biopsy tool for detecting and classifying circulating tumor cells in blood.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Alessandro De Falco, Achille Iolascon, Flora Ascione, Carmelo Piscopo
Summary: The use of array comparative genomic hybridization (array-CGH) has identified new microdeletion/microduplication syndromes, including the 9q21.13 microdeletion syndrome. This syndrome involves the loss of a specific genomic region and is associated with developmental delay, intellectual disability, autistic behavior, seizures, facial dysmorphism, myopia, and previously unreported brain anomalies. A study of 28 patients, including our case, allowed for the classification and analysis of candidate genes, as well as the correlation between genotype and phenotype. These findings provide a better understanding of the syndromic spectrum of 9q21.13 microdeletion syndrome and suggest the need for regular ophthalmological and neurological monitoring.
Review
Genetics & Heredity
Francesca Gorini, Marco Miceli, Pasqualino de Antonellis, Stefano Amente, Massimo Zollo, Veronica Ferrucci
Summary: Medulloblastoma (MB) is a childhood tumor of the cerebellum that has been classified into four molecular subgroups and further divided into biologically distinct subtypes. The brain tumor microenvironment (BTME) plays a crucial role in regulating cancer progression in MB by influencing immune cells. Previously, MB was considered to have a low influx of immune cells, but recent studies have shown the presence of immunosuppressive immune cells in the BTME. This article provides an overview of the epigenetic alterations in MB and explores the potential of new immunotherapeutic approaches to target these immunosuppressive cells.
FRONTIERS IN GENETICS
(2023)
