Article
Hematology
Ing S. Tiong, Richard Dillon, Adam Ivey, James A. Kuzich, Nisha Thiagarajah, Kirsty M. Sharplin, Chung Hoow Kok, Aditya Tedjaseputra, James P. Rowland, Carolyn S. Grove, Emad Abro, Jake Shortt, Devendra K. Hiwase, Ashish Bajel, Nicola E. Potter, Matthew L. Smith, Claire J. Hemmaway, Abin Thomas, Amanda F. Gilkes, Nigel H. Russell, Andrew H. Wei
Summary: Monitoring of NPM1 mutant measurable residual disease in AML patients treated with intensive chemotherapy is crucial. Persistence of low copy number MRD post-treatment is associated with disease progression, with preemptive salvage therapy showing significant benefits. Risk factors for disease progression include FLT3-internal tandem duplication at diagnosis and suboptimal MRD response at EOT.
Article
Multidisciplinary Sciences
Brooks A. Benard, Logan B. Leak, Armon Azizi, Daniel Thomas, Andrew J. Gentles, Ravindra Majeti
Summary: This study aggregates multiple AML cohorts to explore the correlation between clonal abundance of somatic mutations and clinical outcomes. High variant allele frequency for certain mutations is associated with poor prognosis, while increased GATA2 variant allele frequency correlates with better outcomes. Clinical features such as white blood cell count and blast percentage are related to the subclonal abundance of mutations like TP53 and IDH1.
NATURE COMMUNICATIONS
(2021)
Review
Oncology
Christian M. Vonk, Adil S. A. Al Hinai, Diana Hanekamp, Peter J. M. Valk
Summary: Although most AML patients achieve CR after initial induction chemotherapy, residual leukemic cells may lead to relapse, with MRD serving as a prognostic marker. Molecular techniques like NGS offer a sensitive assessment of MRD markers, but face challenges such as limited sensitivity/specificity and difficulty in distinguishing mutations. Multiple studies have explored the association between MRD detection by molecular assays and AML relapse, highlighting limitations, challenges, and opportunities.
Article
Oncology
Biao Wang, Bin Yang, Wei Wu, Xuan Liu, Haiqian Li
Summary: This study investigated the correlation between genotypic profiles and clinicopathologic characteristics in AML patients with NPM1 mutation. The co-occurring mutations in signaling pathways and methylation modifiers were found to be associated with the expressions of specific markers, providing mechanistic insights into the immunophenotypic heterogeneity of AML with NPM1 mutation.
Article
Oncology
Biao Wang, Xiaoying Hua, Jihong Zhang, Weiying Gu, Haiqian Li
Summary: This retrospective study aimed to assess the heterogeneity of outcomes in adult patients with NPM1-mutated acute myeloid leukemia (AML) induced with different doses of cytarabine arabinose (Ara-C). The results showed that certain clinical and molecular characteristics, such as TET2 mutation, age, white blood cell count, CD34 expression, and induction with ID-Ara-C, were associated with different outcomes in specific subgroups of patients.
Article
Hematology
Yun-Wei Zhang, Long Su, Ye-Hui Tan, Hai Lin, Xiao-Liang Liu, Qiu-Ju Liu, Jing-Nan Sun, Ming Zhang, Ya-Zhe Du, Fei Song, Wei Han, Su-Jun Gao
Summary: AML with NPM1 mutation is a distinct genetic entity with favorable outcomes. However, this study reveals that it is still a highly heterogeneous disorder. High NPM1 variant allele frequency (VAF) and certain co-mutated genes are associated with poorer outcomes. Additionally, measurable residual disease (MRD) after chemotherapy is an independent predictor. These findings are important for re-stratifying the prognoses of AML patients with NPM1 mutations.
ANNALS OF HEMATOLOGY
(2023)
Article
Oncology
Huirong Mai, Qin Li, Guobing Wang, Ying Wang, Shilin Liu, Xue Tang, Fen Chen, Guichi Zhou, Yi Liu, Tonghui Li, Lulu Wang, Chunyan Wang, Feiqiu Wen, Sixi Liu
Summary: This study explored the feasibility of using Next-generation sequencing (NGS) technology to detect minimal residual disease (MRD) in childhood acute lymphoblastic leukemia (ALL). The results showed that NGS is more sensitive than multiparametric flow cytometry (MFC) and real-time quantitative PCR (RQ-PCR) in detecting MRD. Furthermore, the number of clonal rearrangement sequences detected by NGS before treatment is an independent factor in predicting whether MRD can become negative after chemotherapy.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Oncology
Jong-Mi Lee, Silvia Park, Insik Hwang, Dain Kang, Byung Sik Cho, Hee-Je Kim, Ari Ahn, Myungshin Kim, Yonggoo Kim
Summary: This article presents an ITD-tracing algorithm based on NGS method for monitoring MRD in AML patients. The assay shows high sensitivity and superior performance, and demonstrates prognostic value in AML patients undergoing allogeneic hematopoietic stem cell transplantation.
Article
Oncology
Fu-Jia Liu, Wen-Yan Cheng, Xiao-Jing Lin, Shi-Yang Wang, Tian-Yi Jiang, Ting-Ting Ma, Yong-Mei Zhu, Yang Shen
Summary: This study demonstrated that the combination of MFC MRD and molecular MRD can establish prognostic value in AML patients with specific genetic lesions. After two cycles of consolidation, MFC MRD showed independent predictive significance for clinical outcomes, highlighting the importance of integrating different MRD assessment methods based on genetic characteristics of AML.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Yan Hui, Yi Li, Xiwen Tong, Lifang Huang, Xia Mao, Liang Huang, Donghua Zhang
Summary: R/R-AML is characterized by high incidence, short survival, and poor prognosis. Factors influencing prognosis include bone marrow blast proportion and achieving complete remission after reinduction chemotherapy. Hematopoietic stem cell transplantation following complete remission can improve prognosis. The DCIA/DCHA regimen shows good efficacy and tolerable adverse reactions, making it a potential bridging regimen for allo-HSCT in R/R-AML.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Oncology
Hong Wang, Xue-Qian Li, Tian-Tian Chu, Shi-Yu Han, Jia-Qian Qi, Ya-Qiong Tang, Hui-Ying Qiu, Cheng-Cheng Fu, Xiao-Wen Tang, Chang-Geng Ruan, De-Pei Wu, Yue Han
Summary: Genetic changes play a prognostic role in CN-AML, with FLT3-ITD mutation and CEBPA(wt) being identified as independent risk factors associated with poor OS and DFS. HSCT significantly improves the prognosis of standard/high risk CN-AML patients, especially in those with combined CEBPA and FLT3-ITD mutations. Integration of molecular marker analyses and MRD assessment before transplantation can help predict patient outcomes in HSCT-treated patients.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2021)
Article
Oncology
Jun Kong, Meng-Ge Gao, Ya-Zhen Qin, Yu Wang, Chen-Hua Yan, Yu-Qian Sun, Ying-Jun Chang, Lan-Ping Xu, Xiao-Hui Zhang, Kai-Yan Liu, Xiao-Jun Huang, Xiao-Su Zhao
Summary: This study aimed to analyze the dynamic changes of MLL-PTD peri-transplantation and determine the best threshold for predicting relapse after transplantation. The study included 48 patients with MLL-PTD AML or MDS-EB who underwent allo-HSCT. The results showed that MLL-PTD after transplantation can serve as an effective indicator for predicting relapse. The expression level of MLL-PTD >= 1.0% was identified as the optimal cut-off value for predicting hematological relapse after allo-HSCT.
Article
Oncology
Hannah J. Uckelmann, Elena L. Haarer, Reina Takeda, Eric M. Wong, Charlie Hatton, Christian Marinaccio, Florian Perner, Masooma Rajput, Noa J. C. Antonissen, Yanhe Wen, Lu Yang, Lorenzo Brunetti, Chun -Wei Chen, Scott A. Armstrong
Summary: The dysregulation of developmental and stem cell-associated genes is a common phenomenon during cancer development. Most patients with acute myeloid leukemia (AML) express high levels of HOXA cluster genes and MEIS1, with an NPM1 mutation (NPM1c) being common in these cases. This study reveals that NPM1c directly binds to specific chromatin targets, collaborates with the MLL1 complex, and directly regulates oncogenic gene expression in AML.
Article
Medicine, General & Internal
Jinghan Wang, Jiajia Pan, Shujuan Huang, Fenglin Li, Jiansong Huang, Xia Li, Qing Ling, Wenle Ye, Yungui Wang, Wenjuan Yu, Jie Jin
Summary: Through circRNA sequencing and cellular metabolomic analysis, we identified that the expression of hsa_circ_0075451 may independently contribute to the poor prognosis of AML, presenting a novel therapeutic target.
Review
Oncology
Hossein Mahmudi, Mohammad Amin Adili-Aghdam, Mohammad Shahpouri, Mehdi Jaymand, Zohreh Amoozgar, Rana Jahanban-Esfahlan
Summary: Chitosan and its derivatives have diverse medical applications, particularly in cancer treatment. They have the ability to take on various shapes and cross biological barriers. Combined with other biomaterials, they can be used for controlled drug release, targeted delivery, and combination therapy. This article provides an overview of different forms and properties of chitosan, discusses its use as an efficient drug delivery system to overcome therapeutic barriers in solid tumors, and explores the clinical translation and future prospects of chitosan nanoparticles in treating recurrent cancer.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Philipp Rentzsch, Daniela Witten, Gregory M. Cooper, Jay Shendure, Martin Kircher
NUCLEIC ACIDS RESEARCH
(2019)
Article
Genetics & Heredity
Jose L. McFaline-Figueroa, Andrew J. Hill, Xiaojie Qiu, Dana Jackson, Jay Shendure, Cole Trapnell
Article
Biochemical Research Methods
Hannah A. Pliner, Jay Shendure, Cole Trapnell
Article
Biology
Jes Alexander, Gregory M. Findlay, Martin Kircher, Jay Shendure
Review
Genetics & Heredity
Molly Gasperini, Jacob M. Tome, Jay Shendure
NATURE REVIEWS GENETICS
(2020)
Article
Biochemistry & Molecular Biology
Adebola Enikanolaiye, Julie Ruston, Rong Zeng, Christine Taylor, Marijke Schrock, Christie M. Buchovecky, Jay Shendure, Elif Acar, Monica J. Justice
Article
Biotechnology & Applied Microbiology
Junyue Cao, Wei Zhou, Frank Steemers, Cole Trapnell, Jay Shendure
NATURE BIOTECHNOLOGY
(2020)
Article
Biochemical Research Methods
Jason C. Klein, Vikram Agarwal, Fumitaka Inoue, Aidan Keith, Beth Martin, Martin Kircher, Nadav Ahituv, Jay Shendure
Article
Multidisciplinary Sciences
He Fang, Giancarlo Bonora, Jordan P. Lewandowski, Jitendra Thakur, Galina N. Filippova, Steven Henikoff, Jay Shendure, Zhijun Duan, John L. Rinn, Xinxian Deng, William S. Noble, Christine M. Disteche
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Timothy J. Durham, Riza M. Daza, Louis Gevirtzman, Darren A. Cusanovich, Olubusayo Bolonduro, William Stafford Noble, Jay Shendure, Robert H. Waterston
Summary: Recent developments in single-cell technologies have allowed researchers to study cell states in Caenorhabditis elegans at a higher resolution, including gene expression patterns and chromatin accessibility. A novel implementation of the latent Dirichlet allocation algorithm has identified 37 clusters of cells corresponding to different cell types in the worm, providing new insights into cellular differentiation and gene regulation.
Article
Multidisciplinary Sciences
Vikram Agarwal, Sereno Lopez-Darwin, David R. Kelley, Jay Shendure
Summary: This study quantifies the differential usage of 3' UTR isoforms among cell types during mouse embryonic development, showing a global lengthening of 3' UTRs across all cell types with specific RNA-binding proteins (RBPs) regulating this process.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Junhong Choi, Wei Chen, Chase C. Suiter, Choli Lee, Florence M. Chardon, Wei Yang, Anh Leith, Riza M. Daza, Beth Martin, Jay Shendure
Summary: The PRIME-Del method induces deletions with high precision using a pair of prime editing sgRNAs, outperforming CRISPR-Cas9 and sgRNA pairs in programming deletions up to 10 kb. This method can be broadly useful for precise, flexible programming of genomic deletions and potentially other rearrangements.
NATURE BIOTECHNOLOGY
(2022)
Letter
Biochemistry & Molecular Biology
Michael Boeckh, Helen Y. Chu, Janet A. Englund, Christina M. Lockwood, Deborah A. Nickerson, Jay Shendure, Lea Starita
Article
Hematology
Jill M. Johnsen, Shelley N. Fletcher, Angela Dove, Haley McCracken, Beth K. Martin, Martin Kircher, Neil C. Josephson, Jay Shendure, Sarah E. Ruuska, Leonard A. Valentino, Glenn F. Pierce, Crystal Watson, Dunlei Cheng, Michael Recht, Barbara A. Konkle
Summary: The findings of this study report the results of the largest hemophilia genotyping project performed to date. The results support the importance of comprehensive genetic approaches in hemophilia and contribute to a better understanding of variation in the F8 and F9 genes and the risks of inhibitor formation.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2022)
Article
Multidisciplinary Sciences
Bailey A. T. Weatherbee, Carlos W. Gantner, Lisa K. Iwamoto-Stohl, Riza M. Daza, Nobuhiko Hamazaki, Jay Shendure, Magdalena Zernicka-Goetz
Summary: By inducing stem cells, we have established a model of the human post-implantation embryo that mimics key aspects of human development and allows us to study tissue-tissue interactions. This model is important for investigating critical questions related to human post-implantation development and understanding the causes of pregnancy failure during this stage.
Article
Pathology
Juliana Mota Siqueira, Yoshitsugu Mitani, Camilla Oliveira Hoff, Flavia Bonini, Luana Guimaraes de Sousa, Mario L. Marques-Piubelli, Anurag Purushothaman, Mutsumi Mitani, Hui Dai, Shiaw-Yih Lin, Michael T. Spiotto, Ehab Y. Hanna, Daniel J. McGrail, Adel K. El-Naggar, Renata Ferrarotto
Summary: B7-H4 expression pattern varies among different types of salivary gland carcinomas, and high B7-H4 expression is associated with poor prognosis in adenoid cystic carcinoma.
Article
Pathology
Basile Tessier-Cloutier, Felix K. F. Kommoss, David L. Kolin, Kristyna Nemejcova, Dupreez Smith, Jennifer Pors, Colin J. R. Stewart, W. Glenn Mccluggage, William D. Foulkes, Andreas von Deimling, Martin Kobel, Cheng-Han Lee
Summary: This study provides a detailed analysis of the clinical, pathological, immunohistochemical, and molecular features of DDOC/UDOC. The majority of patients presented with extraovarian disease and had rapid disease progression resulting in high mortality rate.
Review
Pathology
Sophia J. Wagner, Christian Matek, Sayedali Shetab Boushehri, Melanie Boxberg, Lorenz Lamm, Ario Sada, Dominik J. E. Winter, Carsten Marr, Tingying Peng
Summary: Computational pathology research driven by deep learning faces challenges in reproducibility and reusability. Codebase with good documentation and robustness and generalizability of models are crucial. The reuse of computational pathology algorithms is limited, and their application in clinical settings is even rarer. This study evaluates 160 peer-reviewed articles, providing criteria for data and code availability and statistical analysis of results.
Article
Pathology
Andres M. Acosta, Lynette M. Sholl, Fiona Maclean, Chia-Sui Kao, Thomas M. Ulbright
Summary: This study assessed the clinicopathologic and genomic features of 14 cases of testicular sex cord-stromal tumors. The results showed that CTNNB1 mutations are rare in these tumors, and most of them have genomic alterations similar to testicular sex cord-stromal tumors with pure or predominant spindle cell components.
Article
Pathology
Toru Odate, Kaishi Satomi, Takashi Kubo, Yuko Matsushita, Toshihide Ueno, Akira Kurose, Kohei Shomori, Tokiko Nakai, Reiko Watanabe, Keiko Segawa, Shusa Ohshika, Naritomo Miyake, Sayaka Kudo, Tatsunori Shimoi, Eisuke Kobayashi, Motokiyo Komiyama, Seiichi Yoshimoto, Fumihiko Nakatani, Akira Kawai, Yasushi Yatabe, Shinji Kohsaka, Koichi Ichimura, Hitoshi Ichikawa, Akihiko Yoshida
Summary: Inflammatory rhabdomyoblastic tumors (IRMTs) are newly recognized skeletal muscle tumors with uncertain malignant potential. This study investigated 13 IRMTs using clinicopathologic, genetic, and epigenetic methods. The results showed specific histologic features and genetic mutations in these tumors, and most of them exhibited benign behavior.
Article
Pathology
Dale L. Davis, Adam C. Lechner, David B. Chapel, Jonathan C. Slack, Chrystalle Katte Carreon, Bradley J. Quade, Carlos Parra-Herran
Summary: The Amsterdam Consensus Statement introduced the term maternal vascular malperfusion (MVM) to classify a group of findings related to impaired maternal-placental circulation. The study found that features such as low placental weight, accelerated villous maturation, decidual arteriopathy, and infarcts are associated with adverse obstetrical outcomes, while the role of other features like distal villous hypoplasia, excess multinucleated trophoblast, and retroplacental hemorrhage needs further research.
Review
Pathology
Alain C. Borczuk
Summary: COVID-19 is an acute respiratory illness that can progress to acute respiratory distress syndrome. While most patients recover completely, some may experience persistent respiratory dysfunction, known as long COVID. The pathogenesis involves immune and cellular disturbances.
Article
Pathology
Annikka Weissferdt, Cheuk H. Leung, Heather Lin, Boris Sepesi, William N. William, Stephen G. Swisher, Tina Cascone, J. Jack Lee, Abujiang Pataer
Summary: Neoadjuvant treatment of non-small cell lung cancer challenges traditional processing of pathology specimens, and accurate evaluation of residual tumor is crucial for assessing treatment efficacy.