Review
Oncology
Jiro Akimoto
Summary: Gliomatosis cerebri (GC) is a unique glial tumor that has been recognized as a distinct entity of neuroepithelial tumors. However, in the 2016 WHO classification, it was removed as a specific pathological entity and labeled as a growth pattern of diffuse glioma. Many neuro-oncologists have criticized this decision and argued for the continued inclusion of GC in discussions of brain tumors. In Japan, there are ongoing efforts to conduct multicenter research on GC pathology and develop molecular pathological evidence to support future WHO classifications.
BRAIN TUMOR PATHOLOGY
(2023)
Article
Neurosciences
Jon Foss-Skiftesvik, Ulrik Kristoffer Stoltze, Thomas van Overeem Hansen, Lise Barlebo Ahlborn, Erik Sorensen, Sisse Rye Ostrowski, Solvej Margrete Aldringer Kullegaard, Adrian Otamendi Laspiur, Linea Cecilie Melchior, David Scheie, Bjarne Winther Kristensen, Jane Skjoth-Rasmussen, Kjeld Schmiegelow, Karin Wadt, Rene Mathiasen
Summary: Ependymoma, the second most common malignant brain tumor in children, has limited understanding of its genetic predisposition. This study used whole-genome sequencing and DNA methylation profiling to analyze a cohort of Danish children with ependymoma. The results revealed that less than 4% of childhood ependymoma is explained by genetic predisposition, primarily caused by pathogenic variants in NF2 and NF1 genes. Additionally, LZTR1 is suggested as a potential novel ependymoma predisposition gene.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Veronica Barcelona, Yunfeng Huang, Billy A. Caceres, Kevin P. Newhall, Qin Hui, Jessica P. Cerdena, Cindy A. Crusto, Yan Sun, Jacquelyn Y. Taylor
Summary: Potentially traumatic experiences may be related to chronic diseases, and epigenetic mechanisms could explain this association. The study found a significant association between DNAm at a CpG site in the ENOX1 gene and traumatic events in children.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Sandra Ferreyra Vega, Thomas Olsson Bontell, Alba Corell, Anja Smits, Asgeir Store Jakola, Helena Caren
Summary: DNA methylation profiling in adult primary dLGG according to WHO 2016 classification system showed its potential utility in achieving molecular diagnosis and predicting clinical outcomes, demonstrating its reliability and robustness in molecular classification.
CLINICAL EPIGENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Mohammad Shahrokh Esfahani, Emily G. Hamilton, Mahya Mehrmohamadi, Barzin Y. Nabet, Stefan K. Alig, Daniel A. King, Chloe B. Steen, Charles W. Macaulay, Andre Schultz, Monica C. Nesselbush, Joanne Soo, Joseph G. Schroers-Martin, Binbin Chen, Michael S. Binkley, Henning Stehr, Jacob J. Chabon, Brian J. Sworder, Angela B-Y Hui, Matthew J. Frank, Everett J. Moding, Chih Long Liu, Aaron M. Newman, James M. Isbell, Charles M. Rudin, Bob T. Li, David M. Kurtz, Maximilian Diehn, Ash A. Alizadeh
Summary: EPIC-seq is a method that predicts gene expression levels at individual genes from cfDNA. We demonstrate the potential of EPIC-seq in cancer subtype classification and prediction of clinical response.
NATURE BIOTECHNOLOGY
(2022)
Review
Oncology
Liliana Montella, Mariella Cuomo, Nunzio Del Gaudio, Michela Buonaiuto, Davide Costabile, Roberta Visconti, Teodolinda Di Risi, Roberta Vinciguerra, Federica Trio, Sara Ferraro, Guglielmo Bove, Gaetano Facchini, Lucia Altucci, Lorenzo Chiariotti, Rosa Della Monica
Summary: This article reviews the druggable epigenetic features of glioblastomas and discusses the corresponding targeted therapies and their potential efficacy. It emphasizes the recent technological improvements that allow routine investigation of many glioblastoma epigenetic biomarkers in clinical practice.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Psychology, Multidisciplinary
Laurel Raffington, Peter T. Tanksley, Aditi Sabhlok, Liza Vinnik, Travis Mallard, Lucy S. King, Bridget Goosby, K. Paige Harden, Elliot M. Tucker-Drob
Summary: Social inequality may impact children's cognitive development through epigenetic mechanisms. Research suggests that children from socioeconomically disadvantaged families and marginalized racial/ethnic groups exhibit DNA methylation profiles associated with chronic inflammation, lower cognitive functioning, and accelerated biological aging. Furthermore, children's salivary DNA methylation profiles are related to their performance in cognitive and academic tests.
PSYCHOLOGICAL SCIENCE
(2023)
Article
Biochemical Research Methods
Joung Min Choi, Chaelin Park, Heejoon Chae
Summary: This paper presents meth-SemiCancer, a semi-supervised cancer subtype classification method based on DNA methylation profiles. The proposed model is pre-trained on methylation datasets with cancer subtype labels, generates pseudo-subtypes for datasets without subtype information, and performs fine-tuning using both labeled and unlabeled datasets. Compared to other methods, meth-SemiCancer achieves higher F1-score and Matthews correlation coefficient.
BMC BIOINFORMATICS
(2023)
Review
Clinical Neurology
Catena Kresbach, Sina Neyazi, Ulrich Schueller
Summary: Ependymal neoplasms are a heterogeneous group of tumors that occur in different parts of the central nervous system. Recent advances in understanding the genetic and molecular characteristics of ependymal tumors have led to an improved classification system. New classification schemes based on global DNA methylation profiling have enhanced the prediction of patients' outcomes.
Article
Environmental Sciences
Arce Domingo-Relloso, Anne Bozack, Samara Kiihl, Zulema Rodriguez-Hernandez, Pilar Rentero-Garrido, J. Antonio Casasnovas, Montserrat Leon-Latre, Tamara Garcia-Barrera, J. Luis Gomez-Ariza, Belen Moreno, Ana Cenarro, Griselda de Marco, Faruque Parvez, Abu B. Siddique, Hasan Shahriar, Mohammad N. Uddin, Tariqul Islam, Ana Navas-Acien, Mary Gamble, Maria Tellez-Plaza
Summary: The study identified common 5-hmC and 5-mC signatures in two populations exposed to varying levels of inorganic As, but differences in As-related epigenetic sites across the study populations may also reflect low and high As-specific associations. This work contributes to a deeper understanding of potential epigenetic dysregulations of As, with further research needed to confirm biological consequences associated with DIP2C epigenetic regulation and investigate the role of 5-hmC and 5-mC separately in As-induced health disorders at different exposure levels.
ENVIRONMENTAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Kwanghoon Lee, Seong-Ik Kim, Eric Eunshik Kim, Yu-Mi Shim, Jae-Kyung Won, Chul-Kee Park, Seung Hong Choi, Hongseok Yun, Hyunju Lee, Sung-Hye Park
Summary: This study aimed to identify ambiguous genetic outliers for O_IDH_mut and A_IDH_mut and redefine the genetic landscape and prognostic factors of IDH-mutant gliomas. NGS, methylation profiles, and clinicopathological features were analyzed for O_IDH_mut (n=74) and A_IDH_mut (n=95). The majority of O_IDH_mut (93.2%) and A_IDH_mut (88.4%) exhibited classic genomic landscapes.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Dai Shimizu, Kenzui Taniue, Yusuke Matsui, Hiroshi Haeno, Hiromitsu Araki, Fumihito Miura, Mitsuko Fukunaga, Kenji Shiraishi, Yuji Miyamoto, Seiichi Tsukamoto, Aya Komine, Yuta Kobayashi, Akihiro Kitagawa, Yukihiro Yoshikawa, Kuniaki Sato, Tomoko Saito, Shuhei Ito, Takaaki Masuda, Atsushi Niida, Makoto Suzuki, Hideo Baba, Takashi Ito, Nobuyoshi Akimitsu, Yasuhiro Kodera, Koshi Mimori
Summary: The study established the CACO methylation panel for accurate cancer diagnosis and origin classification, showing high diagnostic potential and specificity in identifying cancer cell type based on methylation profile from liquid or tissue biopsy. This panel can be a powerful tool for cancer classification and diagnosis.
CANCER GENE THERAPY
(2022)
Article
Pathology
Daniel R. Rissi, Taryn A. Donovan, Brian F. Porter, Chad Frank, Andrew D. Miller
Summary: Gliomatosis cerebri is a subtype of glioma characterized by diffuse infiltration within the brain parenchyma, rather than specific architectural distortion. Clinical cases in canines have shown variable morphological and immunohistochemical features, suggesting a need for further research to confirm its classification as a distinct infiltrative growth pattern of canine glioma.
VETERINARY PATHOLOGY
(2021)
Article
Gastroenterology & Hepatology
Adriana C. Vidal, Shivram A. Chandramouli, Joddy Marchesoni, Nia Brown, Yukun Liu, Susan K. Murphy, Rachel Maguire, Yaxu Wang, Manal F. Abdelmalek, Alisha M. Mavis, Mustafa R. Bashir, Dereje Jima, David A. Skaar, Cathrine Hoyo, Cynthia A. Moylan
Summary: This study found that hypomethylation of the AHRR gene mediates the association between prenatal tobacco smoke exposure and childhood metabolic dysfunction. The results suggest that the effects of smoking during pregnancy on the fetus may be mediated by alterations in gene methylation.
HEPATOLOGY COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Yared Beyene Yohannes, Shouta M. M. Nakayama, John Yabe, Haruya Toyomaki, Andrew Kataba, Hokuto Nakata, Kaampwe Muzandu, Chihiro Miyashita, Yoshinori Ikenaka, Kennedy Choongo, Mayumi Ishizuka
Summary: Lead exposure has adverse health effects and may lead to changes in DNA methylation. This study found a negative correlation between blood lead levels and LINE-1 DNA methylation, suggesting that higher lead levels are associated with global DNA hypomethylation. However, GSTP1 DNA methylation levels were not significantly associated with lead exposure or health risk, implying that it may not be a reliable biomarker for lead exposure in healthy individuals.
Editorial Material
Radiology, Nuclear Medicine & Medical Imaging
Scott N. Hwang
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Clinical Neurology
Anthony P. Y. Liu, Sandeep K. Dhanda, Tong Lin, Edgar Sioson, Aksana Vasilyeva, Brian Gudenas, Ruth G. Tatevossian, Sujuan Jia, Geoffrey Neale, Daniel C. Bowers, Tim Hassall, Sonia Partap, John R. Crawford, Murali Chintagumpala, Eric Bouffet, Geoff McCowage, Alberto Broniscer, Ibrahim Qaddoumi, Greg Armstrong, Karen D. Wright, Santhosh A. Upadhyaya, Anna Vinitsky, Christopher L. Tinkle, John Lucas, Jason Chiang, Daniel J. Indelicato, Robert Sanders, Paul Klimo, Frederick A. Boop, Thomas E. Merchant, David W. Ellison, Paul A. Northcott, Brent A. Orr, Xin Zhou, Arzu Onar-Thomas, Amar Gajjar, Giles W. Robinson
Summary: Methylation profiling has important implications for the classification and treatment of CNS-PNET. This study provides insights for clinical decision-making by analyzing the clinical and molecular features of pediatric CNS-PNET patients. Significant differences in treatment response and survival rates were observed among different molecular subgroups identified by DNA methylation profiling.
ACTA NEUROPATHOLOGICA
(2022)
Editorial Material
Oncology
Anthony P. Y. Liu, Paul A. Northcott
Summary: This study summarizes the high expression of FOXR2 in various cancers, uncovers a previously unknown mechanism of epigenetic activation, and expands the transcriptional targets of FOXR2. It enhances the understanding of FOXR2-driven malignancy and has the potential to discover new therapeutic opportunities.
Editorial Material
Radiology, Nuclear Medicine & Medical Imaging
Scott N. Hwang
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Multidisciplinary Sciences
Kyle S. Smith, Laure Bihannic, Brian L. Gudenas, Parthiv Haldipur, Ran Tao, Qingsong Gao, Yiran Li, Kimberly A. Aldinger, Igor Y. Iskusnykh, Victor V. Chizhikov, Matthew Scoggins, Silu Zhang, Angela Edwards, Mei Deng, Ian A. Glass, Lynne M. Overman, Jake Millman, Alexandria H. Sjoboen, Jennifer Hadley, Joseph Golser, Kshitij Mankad, Heather Sheppard, Arzu Onar-Thomas, Amar Gajjar, Giles W. Robinson, Volker Hovestadt, Brent A. Orr, Zoltan Patay, Kathleen J. Millen, Paul A. Northcott
Summary: Medulloblastoma, a malignant childhood cerebellar tumour, has different subgroups with distinct developmental origins. Multi-omics analysis connects the molecular features of medulloblastoma subgroups to their origins during early development.
Meeting Abstract
Hematology
Nam H. K. Nguyen, Abderrahmane Tagmount, Jeffrey E. Rubnitz, Raul C. Ribeiro, Xueyuan Cao, Stanley B. Pounds, Chris D. Vulpe, Jatinder K. Lamba
Meeting Abstract
Hematology
Jatinder K. Lamba, Richard J. Marrero, Abdelrahman H. Elsayed, Xueyuan Cao, Huiyun Wu, Hiroto Inaba, Susana C. Raimondi, Ching-Hon Pui, Raul C. Ribeiro, Jeffrey E. Rubnitz, Stanley B. Pounds
Article
Oncology
Audrey Lasry, Bettina Nadorp, Maarten Fornerod, Deedra Nicolet, Huiyun Wu, Christopher J. Walker, Zhengxi Sun, Matthew T. Witkowski, Anastasia N. Tikhonova, Maria Guillamot-Ruano, Geraldine Cayanan, Anna Yeaton, Gabriel Robbins, Esther A. Obeng, Aristotelis Tsirigos, Richard M. Stone, John C. Byrd, Stanley Pounds, William L. Carroll, Tanja A. Gruber, Ann-Kathrin Eisfeld, Iannis Aifantis
Summary: This study provides a comprehensive analysis of the bone marrow immune microenvironment in adult and pediatric AML patients. Unique inflammation signatures were identified in a subset of AML patients, which were associated with poor outcomes. Dysfunctional B-cell subtype, atypical B cells, were found to be enriched in high-inflammation AML patients, along with an increase in CD8(+)GZMK(+) and regulatory T cells, and a reduction in T-cell clonal expansion. An inflammation-associated gene score (iScore) was developed which predicts survival outcomes and refines current risk stratifications in AML patients. The study highlights the importance of considering the inflammatory state in clinical settings.
Article
Oncology
Georgios E. Christakopoulos, Kendra N. Walker, Jesse Smith, Clifford M. Takemoto, Yan Zheng, Ching-Hon Pui, Raul C. Ribeiro, Lei Wang, Stanley B. Pounds, Jeffrey E. Rubnitz, Hiroto Inaba
Summary: This study investigated the clinical management strategies and effects of cytoreduction in pediatric patients with acute myeloid leukemia (AML) and hyperleukocytosis. The results showed that LD-cytarabine treatment was safe and effective in reducing leukocyte counts in children with AML and hyperleukocytosis.
Editorial Material
Radiology, Nuclear Medicine & Medical Imaging
Scott N. Hwang
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Clinical Neurology
Quynh T. Tran, Santhosh A. Upadhyaya, Catherine A. Billups, Arzu Onar-Thomas, Md. Zahangir Alom, Steven S. Carey, Giles W. Robinson, David W. Ellison, Amar Gajjar, Brent A. Orr
ACTA NEUROPATHOLOGICA
(2023)
Article
Oncology
Zahangir Alom, Quynh T. Tran, Asim K. Bag, John T. Lucas, Brent A. Orr
Summary: This study demonstrates that MRI-based machine learning models can effectively predict the methylation class of brain tumors, expanding the range of tumor types that can be used for radiomic or radiogenomic modeling.
NEURO-ONCOLOGY ADVANCES
(2023)
Meeting Abstract
Oncology
Nicole Michmerhuizen, Bappaditya Chandra, Hazheen Shirnekhi, Swarnendu Tripathi, Brittany Pioso, David Baggett, Diana Mitrea, Ilaria Iacobucci, Michael White, Jingjing Chen, Cheon-Gil Park, Huiyun Wu, Stanley Pounds, Anna Medyukhina, Khaled Khairy, Qingsong Gao, Chunxu Qu, Scott Gorman, Simran Bawa, Carolyn Maslanka, Swati Kinger, Priyanka Dogra, Danika Di Giacomo, Cristina Mecucci, Jeffery Klco, Charles Mullighan, Richard Kriwacki
CLINICAL LYMPHOMA MYELOMA & LEUKEMIA
(2022)
Article
Medicine, Research & Experimental
Sherif Abdelhamed, Melvin E. Thomas III, Tamara Westover, Masayuki Umeda, Emily Xiong, Chandra Rolle, Michael P. Walsh, Huiyun Wu, Jason R. Schwartz, Virginia Valentine, Marcus Valentine, Stanley Pounds, Jing Ma, Laura J. Janke, Jeffery M. Klco
Summary: SAMD9 and SAMD9L germline mutations are newly identified genetic predispositions to pediatric myeloid neoplasms. These mutations impair hematopoiesis and increase the risk of clonal chromosome 7 deletions leading to MDS and AML. In a mouse model, expressing mutant Samd9l in hematopoietic cells further disrupts stemness and leads to bone marrow hypocellularity, which resembles the phenotypes observed in patients. The study also identifies TGF-beta as a potential therapeutic target and observes genetic deletion of the mutant Samd9l locus on mouse chromosome 6, mimicking patients' chromosome 7 deletions.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Article
Oncology
Masayuki Umeda, Jing Ma, Benjamin J. Huang, Kohei Hagiwara, Tamara Westover, Sherif Abdelhamed, Juan M. Barajas, Melvin E. Thomas, Michael P. Walsh, Guangchun Song, Liqing Tian, Yanling Liu, Xiaolong Chen, Pandurang Kolekar, Quang Tran, Scott G. Foy, Jamie L. Maciaszek, Andrew B. Kleist, Amanda R. Leonti, Bengsheng Ju, John Easton, Huiyun Wu, Virginia Valentine, Marcus B. Valentine, Yen-Chun Liu, Rhonda E. Ries, Jenny L. Smith, Evan Parganas, Ilaria Iacobucci, Ryan Hiltenbrand, Jonathan Miller, Jason R. Myers, Evadnie Rampersaud, Delaram Rahbarinia, Michael Rusch, Gang Wu, Hiroto Inaba, Yi-Cheng Wang, Todd A. Alonzo, James R. Downing, Charles G. Mullighan, Stanley Pounds, M. Madan Babu, Jinghui Zhang, Jeffrey E. Rubnitz, Soheil Meshinchi, Xiaotu Ma, Jeffery M. Klco
Summary: The study reveals UBTF-TD as a new recurrent genetic alteration in relapsed pediatric AML, which is more common in children and associated with poor outcomes.
BLOOD CANCER DISCOVERY
(2022)