Article
Medicine, General & Internal
Xin He, Xiaotong Fan, Yongzhi Shan, Xinrui Ji, Lan Su, Yaming Wang
Summary: In this study, next-generation sequencing was used to investigate the genomic profile of primary central nervous system lymphoma (PCNSL). The most common mutation type and mutated genes in PCNSL were identified. Enrichment analysis revealed the involvement of mutated genes in various pathways and functional protein activities. This study provides insights into the molecular mechanisms of PCNSL and potential targets for diagnosis and precision medicine.
Review
Oncology
Kaiyan Tao, Xuefeng Wang, Xin Tian
Summary: Primary Central Nervous System Lymphoma (PCNSL) relapses are often derived from occult lymphoma cells, with treatment options including chemotherapy, radiation therapy, stem cell transplantation, targeted therapy, and immunotherapy. The overall prognosis is very poor, with early and varied clinical symptoms.
FRONTIERS IN ONCOLOGY
(2021)
Review
Hematology
Nicolas Martinez-Calle, Lisa K. Isbell, Kate Cwynarski, Elisabeth Schorb
Summary: Managing primary central nervous system lymphoma in older individuals is a clinical challenge. Optimal therapy and adequate dose intensity are key issues, with high-dose methotrexate-based immunochemotherapy still being the recommended induction treatment. Utilizing geriatric assessment tools and considering individual performance status and comorbidities are important in personalized treatment approaches.
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Review
Oncology
Yan Yuan, Tianling Ding, Shu Wang, Hong Chen, Ying Mao, Tong Chen
Summary: PCNSL is a rare type of lymphoma primarily treated with high-dose methotrexate-based chemotherapy, stem cell transplantation, and whole-brain radiotherapy. Future treatments may focus on targeted therapy and personalized medicine.
BIOMARKER RESEARCH
(2021)
Review
Oncology
Xuefei Sun, Liwei Lv, Yuchen Wu, Qu Cui, Shengjun Sun, Nan Ji, Yuanbo Liu
Summary: Primary central nervous system lymphoma (PCNSL) is a rare type of non-Hodgkin lymphoma. Stereotactic biopsy is the gold standard for diagnosis, but new auxiliary diagnostic methods such as cytokines and tumor circulating DNA show promise. Consolidation treatments, such as whole brain radiotherapy, autologous hematopoietic stem cell transplantation, and non-myeloablative chemotherapy, are being emphasized but there is uncertainty about the optimal strategy. This article reviews the diagnosis and treatment of PCNSL, focusing on research progress in consolidation therapy.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2023)
Review
Hematology
Lauren R. Schaff, Christian Grommes
Summary: Primary central nervous system lymphoma (PCNSL) is a rare malignancy that affects the brain, spinal cord, or eye. Early diagnosis and timely treatment are crucial for optimal outcomes. Advances in high-dose methotrexate chemotherapy have improved prognosis, but relapse is still common. Novel treatments targeting abnormal pathways show promise for relapsed/refractory PCNSL.
Review
Oncology
Jelena Jelicic, Thomas Stauffer Larsen, Zoran Bukumiric, Karen Juul-Jensen, Bosko Andjelic
Summary: Various prognostic models have been proposed for PCNSL in the past decade, but consensus on the optimal model is still lacking. Age and performance status are important prognostic factors, but due to limitations such as small patient numbers and lack of validation, a universally accepted model has not been established. Future multicentre studies are needed to determine the optimal prognostic model for PCNSL.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2021)
Article
Immunology
Zhiguang Lin, Jingjing Ma, Yan Ma, Qing Li, Hui Kang, Mengxue Zhang, Bobin Chen, Rong Xia
Summary: Circulating NK cells have a prognostic impact on primary central nervous system lymphoma (PCNSL). Patients with higher counts and proportions of NK cells have better prognosis, and the changes in NK cell counts before and after chemotherapy are also associated with prognosis. Higher NK cell counts are associated with longer overall survival, while higher fold changes in NK cell proportions and counts are associated with longer progression-free survival.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Oncology
Inka Puhakka, Hanne Kuitunen, Pekka Jakala, Eila Sonkajarvi, Taina Turpeenniemi-Hujanen, Aino Ronka, Tuomas Selander, Miika Korhonen, Outi Kuittinen
Summary: This study provides the first population-based incidence rates and prognosis of primary central nervous system lymphoma (PCNSL) in Finland. The results show that PCNSL incidence in Finland is among the highest reported worldwide, with an annual increase of 2.4%. The prognosis is still poor, especially for elderly patients.
Article
Genetics & Heredity
Linyun Zhang, Fei Sun, Xiaona Lu, Xiaotong Wang, Jie Wang, Jun Li, Yingsong Xu, Daqing Kou, Hongtao Lv, Bin Don
Summary: The tumor microenvironment in PCNSL is closely associated with tumor immune response. Higher ICI scores in PCNSL patients are correlated with a better tumor microenvironment, sensitivity to immunotherapy, and certain small molecule drugs. This study identified genes associated with ICI scores that may serve as important therapeutic and prognostic targets for PCNSL.
FRONTIERS IN GENETICS
(2022)
Review
Cell Biology
Di Wu, Dahai Liu, Kensuke Tateishi, Fei Qi, Fang Yang, Chao Ke, Hua You
Summary: This review article presents the phenotypic and genotypic features of primary central nervous system lymphoma (PCNSL) tumor cells, and compiles the preclinical animal models of PCNSL. Researchers hope that these animal models will enhance the understanding of the molecular pathogenesis of PCNSL and accelerate the development of novel therapeutic strategies.
JOURNAL OF CELLULAR PHYSIOLOGY
(2023)
Review
Oncology
Xiaohong Zheng, Parker Li, Qianqian Dong, Yihong Duan, Shoubo Yang, Zehao Cai, Feng Chen, Wenbin Li
Summary: The meta-analysis showed that miRNAs can serve as high-accuracy noninvasive biomarkers for the diagnosis of PCNSL. Two subgroups analyses were introduced, indicating the clinical application of cerebrospinal fluid-based and blood-based miRNAs assays for PCNSL detection. Further high-quality studies with large samples are needed to confirm the results.
FRONTIERS IN ONCOLOGY
(2021)
Editorial Material
Radiology, Nuclear Medicine & Medical Imaging
Betty Salgues, Elsa Kaphan, Elicia Molines, Gilles Brun, Eric Guedj
Summary: The study presented a 42-year-old female patient with primary central nervous system lymphoma (PCNSL) and strong uptake on F-18-FDOPA PET, similar to previous findings with C-11-MET PET. Therefore, PCNSL should be considered as a possible differential neoplastic diagnosis in cases of F-18-FDOPA uptake.
CLINICAL NUCLEAR MEDICINE
(2021)
Review
Oncology
Tong Chen, Yuanbo Liu, Yang Wang, Qing Chang, Jinsong Wu, Zhiliang Wang, Daoying Geng, Jin-Tai Yu, Yuan Li, Xiao-Qiu Li, Hong Chen, Dongxiao Zhuang, Jianyong Li, Bin Wang, Tao Jiang, Lanting Lyu, Yuqin Song, Xiaoguang Qiu, Wenbin Li, Song Lin, Xinghu Zhang, Dehong Lu, Junqiang Lei, Yaolong Chen, Ying Mao
Summary: This consensus provides specific and evidence-based recommendations for the histopathological diagnosis, imaging examinations, treatment regimens, and management of complications in PCNSL patients.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Lenhard Pennig, Ulrike Cornelia Isabel Hoyer, Lukas Goertz, Rahil Shahzad, Thorsten Persigehl, Frank Thiele, Michael Perkuhn, Maximilian Ruge, Christoph Kabbasch, Jan Borggrefe, Liliana Caldeira, Kai Roman Laukamp
Summary: This study investigated the performance of a deep-learning model in automatically detecting and segmenting primary central nervous system lymphoma on clinical MRI. The results showed that the automated segmentations had good spatial overlap with manual segmentations for total tumor volume and tumor core, and the performance was comparable between initial and follow-up scans.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2021)
Article
Biotechnology & Applied Microbiology
Yanmei Dou, Minseok Kwon, Rachel E. Rodin, Isidro Cortes-Ciriano, Ryan Doan, Lovelace J. Luquette, Alon Galor, Craig Bohrson, Christopher A. Walsh, Peter J. Park
NATURE BIOTECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Sandrine Ettou, Youngsook L. Jung, Tomoya Miyoshi, Dhawal Jain, Ken Hiratsuka, Valerie Schumacher, Mary E. Taglienti, Ryuji Morizane, Peter J. Park, Jordan A. Kreidberg
Article
Biochemical Research Methods
Minseok Kwon, Soohyun Lee, Michele Berselli, Chong Chu, Peter J. Park
Summary: Visual inspection of read-level data remains crucial for accurate variant identification despite improvements in algorithms. BamSnap, an efficient BAM file viewer, can rapidly generate high-quality snapshots with customized tracks and layout, serving as a valuable tool in genome analysis.
Article
Neurosciences
Maxwell A. Sherman, Rachel E. Rodin, Giulio Genovese, Caroline Dias, Alison R. Barton, Ronen E. Mukamel, Bonnie Berger, Peter J. Park, Christopher A. Walsh, Po-Ru Loh
Summary: The contribution of mosaic copy number variants (mCNVs) to the risk of autism spectrum disorder (ASD) was investigated in a study, revealing that probands with ASD carry a significant burden of mCNVs compared to their unaffected siblings, particularly large mCNVs. Additionally, the severity of ASD symptoms correlated positively with the size of mCNVs, and no mosaic analogues of common short de novo CNVs associated with ASD were observed.
NATURE NEUROSCIENCE
(2021)
Article
Multidisciplinary Sciences
Sara Bizzotto, Yanmei Dou, Javier Ganz, Ryan N. Doan, Minseok Kwon, Craig L. Bohrson, Sonia N. Kim, Taejeong Bae, Alexej Abyzov, Peter J. Park, Christopher A. Walsh
Summary: Through high-depth whole-genome sequencing and single-cell analysis, this study reveals the process of early cell division in human embryonic development and explores the asymmetric contributions of early progenitors to the formation of different organs and tissues.
Article
Multidisciplinary Sciences
Joshua H. Cook, Giorgio E. M. Melloni, Doga C. Gulhan, Peter J. Park, Kevin M. Haigis
Summary: Mutational activation of KRAS plays a key role in promoting cancer initiation and progression, with tissue-specific genetic interactions and dependencies driving the clinical consequences of mutant alleles. Genetic analysis reveals distinct signaling properties and comutation networks associated with different mutant KRAS alleles across multiple cancer types, highlighting the complexity underlying the genetic interactions of oncogenic KRAS mutations.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Cell Biology
Lovelace J. Luquette, Peter J. Park
Summary: The researchers have developed a new method to detect somatic mutations present in very few cells on a single molecule of DNA, and applied it to human tissues in different stages.
Article
Multidisciplinary Sciences
Chong Chu, Rebeca Borges-Monroy, Vinayak V. Viswanadham, Soohyun Lee, Heng Li, Eunjung Alice Lee, Peter J. Park
Summary: Identification of transposable element (TE) insertions from whole genome sequencing data remains challenging. However, the xTea tool developed by the authors provides a comprehensive solution for both short-read and long-read sequencing data, outperforming other methods and enabling creation of a catalogue of TE insertions.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Soohyun Lee, Clara Bakker, Carl Vitzthum, Burak H. Alver, Peter J. Park
Summary: With the increasing amount of 3D chromosomal interaction data, efficient storage and access to such data become crucial. Pairs is a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix is an open-source C application for indexing and querying Pairs files. Additionally, PairsQC is a collapsible HTML quality control report generator for Pairs files.
Review
Genetics & Heredity
Isidro Cortes-Ciriano, Doga C. Gulhan, Jake June-Koo Lee, Giorgio E. M. Melloni, Peter J. Park
Summary: This review provides an overview of key algorithmic developments, popular tools, and emerging technologies used in the bioinformatic analysis of cancer genomes. It also describes how such analysis can identify point mutations, copy number alterations, structural variations, and mutational signatures in cancer genomes.
NATURE REVIEWS GENETICS
(2022)
Article
Genetics & Heredity
Rebeca Borges-Monroy, Chong Chu, Caroline Dias, Jaejoon Choi, Soohyun Lee, Yue Gao, Taehwan Shin, Peter J. Park, Christopher A. Walsh, Eunjung Alice Lee
Summary: This study analyzed retrotransposon insertions in a cohort of 2288 ASD families using WGS data, identifying a large number of previously unreported polymorphic retrotransposon insertions and 158 de novo retrotransposition events. While the overall burden of de novo events was similar between ASD individuals and unaffected siblings, ASD cases showed an increased number of de novo L1 insertions compared to expectations in ASD genes.
Article
Multidisciplinary Sciences
Zijie Jin, Wenjian Huang, Ning Shen, Juan Li, Xiaochen Wang, Jigiao Dong, Peter J. Park, Ruibin Xi
Summary: The authors developed a computational tool called scFusion for detecting gene fusions in single-cell RNA sequencing data. Evaluation using simulated and real datasets showed that scFusion efficiently and sensitively detects fusions with low false discovery rate. The method was applied to study cellular heterogeneity and transcriptional impact of gene fusions at the single-cell level.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Dhawal Jain, Chong Chu, Burak Han Alver, Soohyun Lee, Eunjung Alice Lee, Peter J. Park
Summary: Hi-C data is used to detect mobile transposable element insertions across the entire genome. The HiTea pipeline utilizes clipped Hi-C reads and discordant read pairs to effectively detect TE insertions from three major families in humans, showing competitive performance with existing callers based on WGS data.
Article
Biotechnology & Applied Microbiology
Jae Won Yun, Lixing Yang, Hye-Young Park, Chang-Woo Lee, Hongui Cha, Hyun-Tae Shin, Ka-Won Noh, Yoon-La Choi, Woong-Yang Park, Peter J. Park
Article
Biotechnology & Applied Microbiology
Lixing Yang, Su Wang, Jake June-Koo Lee, Semin Lee, Eunjung Lee, Eve Shinbrot, David A. Wheeler, Raju Kucherlapati, Peter J. Park
