Article
Medicine, Research & Experimental
Aussara Panya, Chutamas Thepmalee, Nunghathai Sawasdee, Sasithorn Saengmuang, Piriya Luangwattananun, Pa-thai Yenchitsomanus
Summary: Precision immunotherapy, utilizing genomic and bioinformatic advancements, shows promise in combating cancer. This study demonstrates that adoptive T cells activated by HLArestricted neoantigen peptides can effectively target and destroy cholangiocarcinoma cells, offering valuable insights for developing immunotherapeutic strategies and peptide-vaccines for CCA treatment.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Review
Immunology
Nupur Biswas, Shweta Chakrabarti, Vijay Padul, Lawrence D. Jones, Shashaanka Ashili
Summary: Neoantigen vaccines are being developed to target specific mutated proteins in cancer cells and stimulate the immune system to fight against them. Advances in sequencing technology and computational tools have facilitated the design of these vaccines and several clinical trials have been conducted. This review examines the design criteria, processes, and challenges associated with neoantigens, as well as the outcomes of ongoing clinical trials. The review concludes that neoantigen vaccines have shown promising efficacy in boosting the immune response against cancer cells and have the potential to be used in the treatment of various types of cancers.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biology
Jason Yongsheng Chan, Jing Quan Lim, Choon Kiat Ong
Summary: NKTCL is an aggressive non-Hodgkin lymphoma associated with the Epstein-Barr virus, with some patients still experiencing relapse or treatment resistance despite the incorporation of novel agents like immune checkpoint inhibitors. Recent advancements in molecular biomarkers from multi-omic profiling have the potential to enhance diagnosis, prognosis, and treatment of NKTCL. Emerging biomarkers, such as a 3' UTR structural variant in the PD-L1 gene, show promise for clinical implementation in improving outcomes for patients with NKTCL.
Review
Oncology
Alec J. Redwood, Ian M. Dick, Jenette Creaney, Bruce W. S. Robinson
Summary: The process of tumorigenesis results in genetic changes in tumor cells that have potential to serve as tumor-specific immune targets when expressed. Neoantigen vaccines, harnessing this immunogenicity, have shown efficacy in preclinical models and are now in clinical trials. The challenges in the personalized neoantigen vaccine field include identifying targetable antigens and addressing preexisting immunosuppression, particularly T-cell exhaustion, for the development of effective cancer vaccines.
Article
Biotechnology & Applied Microbiology
Nida Anwar, Faheem Ahmed Memon, Saba Shahid, Muhammad Shakeel, Muhammad Irfan, Aisha Arshad, Arshi Naz, Ikram Din Ujjan, Tahir Shamsi
Summary: Sequencing studies on MDS patients in Pakistan revealed various genetic mutations associated with myeloid malignancies, including mutations not previously observed in MDS or AML. These findings highlight the importance of molecular profiling in diagnosis and treatment of MDS patients in countries with limited resources like Pakistan. Further research with larger sample sizes is necessary to compare molecular characteristics between Asian and global populations.
Article
Oncology
Xiao-Bo Wu, Shu-Ling Hou, Qiao-Hua Zhang, Ning Jia, Min Hou, Wen Shui
Summary: This study investigated the features of ctDNA mutated genes in lymphoma subtypes and found significant correlation between genetic alterations in ctDNA and clinical indices. The genetic heterogeneity across lymphoma subtypes was observed, indicating potential implications for therapeutic targets and risk-adaptive therapies.
FRONTIERS IN ONCOLOGY
(2022)
Review
Oncology
Lifen Zhu, Shufang Xie, Chen Yang, Nanni Hua, Yi Wu, Lei Wang, Wanmao Ni, Xiangmin Tong, Min Fei, Shibing Wang
Summary: This paper reviews the advances in gene mutations related to NKTCL, with a focus on the use of next generation sequencing technology and targeted therapy. These advancements have made genetic mutation a new research hotspot in lymphoma studies.
CANCER MANAGEMENT AND RESEARCH
(2021)
Article
Oncology
Margherita Rimini, Eleonora Loi, Carles Fabregat-Franco, Valentina Burgio, Sara Lonardi, Monica Niger, Mario Scartozzi, Ilario G. Raposelli, Giuseppe Aprile, Francesca Ratti, Federica Pedica, Helena Verdaguer, Mario Rizzato, Federico Nichetti, Eleonora Lai, Alessandro Cappetta, Teresa Macarulla, Matteo Fassan, Filippo De Braud, Andrea Pretta, Francesca Simionato, Francesco De Cobelli, Luca Aldrighetti, Lorenzo Fornaro, Stefano Cascinu, Zavattari Patrizia, Andrea Casadei-Gardini
Summary: This study identified three mutation-based clusters in IDH1-mutated intrahepatic cholangiocarcinomas (IDH1m iCCAs) and demonstrated their prognostic significance.
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Genetics & Heredity
Jingcheng Wu, Wenfan Chen, Yuxuan Zhou, Ying Chi, Xiansheng Hua, Jian Wu, Xun Gu, Shuqing Chen, Zhan Zhou
Summary: In this study, the authors present an updated version, TSNAdb v2.0, of the tumor-specific neoantigen database (TSNAdb). This version offers new features, including stricter criteria for neoantigen identification, predicted neoantigens derived from three types of somatic mutations, and the collection of experimentally validated neoantigens categorized according to experimental level.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Hematology
Come Bommier, Claire Mauduit, Juliette Fontaine, Estelle Bourbon, Pierre Sujobert, Sarah Huet, Lucile Baseggio, Sandrine Hayette, Camille Laurent, Emmanuel Bachy, Herve Ghesquieres, Catherine Thieblemont, Gilles Salles, Alexandra Traverse-Glehen
Summary: The study showed that TNGS can lead to a more accurate diagnosis in challenging lymphoma cases, thus improving clinical management in routine practice.
BRITISH JOURNAL OF HAEMATOLOGY
(2021)
Review
Immunology
Xin Zhang, Zheng Xu, Xiangpeng Dai, Xiaoling Zhang, Xueju Wang
Summary: The mutation of crucial genes is important in tumor initiation and development. Non-synonymous mutations in tumor cell genomes produce neoantigens that activate the immune system and show promising therapeutic effects in various cancers. Antigen-loaded dendritic cell vaccines are more effective in inducing immune responses. This review summarizes the recent research on neoantigens, neoantigen-based vaccines, and dendritic cell-based vaccines in pancreatic cancers, highlighting the combination of neoantigens and dendritic cell-based vaccines. This work provides evidence and novel insights for the development of personalized neoantigen-based dendritic cell vaccines.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Jianzhen Lin, Songhui Zhao, Dongxu Wang, Yang Song, Yue Che, Xu Yang, Jinzhu Mao, Fucun Xie, Junyu Long, Yi Bai, Xiaobo Yang, Lei Zhang, Jin Bian, Xin Lu, Xinting Sang, Jie Pan, Kai Wang, Haitao Zhao
Summary: The study revealed widespread intertumoral heterogeneity in multifocal HCC, with TP53 and TERT being the most common truncal drivers and TSC2 being the most frequently mutated branchy driver. Patients with higher levels of intertumoral heterogeneity had shorter recurrence-free survival after surgical resection. Genomic profiling of cfDNA could effectively capture tumor-derived driver mutations in patients with resected multifocal HCC, serving as a non-invasive strategy to decipher genomic alterations.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Songbai Zheng, Xiaodan Wang, Ying Fu, Beibei Li, Jianhua Xu, Haifang Wang, Zhen Huang, Hui Xu, Yurong Qiu, Yaozhou Shi, Kui Li
Summary: This study investigated genetic variations in Chinese NSCLC patients using next-generation sequencing, identifying common mutated genes and genes with copy number variation. GO and KEGG analyses revealed that these genes were mainly involved in tumor-related signaling pathways such as PI3K-Akt, FoxO, and Ras.
Article
Oncology
Li-Cheng Tan, Wan-Lin Liu, Xiao-Li Zhu, Peng-Cheng Yu, Xiao Shi, Pei-Zhen Han, Ling Zhang, Liang-Yu Lin, Arseny Semenov, Yu Wang, Qing-Hai Ji, Dong-Mei Ji, Yu-Long Wang, Ning Qu
Summary: By combining cytology and genetic background, the accuracy of diagnosis in thyroid nodules can be enhanced. Next-generation sequencing technology can improve preoperative diagnosis sensitivity and guide medication direction in thyroid nodules. Clinicians can use cytology along with genetic alterations for a more precise diagnosis strategy.
FRONTIERS IN ONCOLOGY
(2021)
Article
Obstetrics & Gynecology
Serdar E. Bulun, Sule Yildiz, Mazhar Adli, Jian-Jun Wei
Summary: Adenomyosis is a challenging uterine disorder with unclear origins, involving contributions from abnormal endometrial tissue and smooth muscle cells. Recent studies suggest a link between adenomyosis and endometriosis in terms of cell origins, indicating both diseases arise from endometrial cell populations carrying specific driver mutations.
HUMAN REPRODUCTION UPDATE
(2021)
Retraction
Neurosciences
Alexandra Garancher, Hiromichi Suzuki, Svasti Haricharan, Lianne Q. Chau, Meher Beigi Masihi, Jessica M. Rusert, Paula S. Norris, Florent Carrette, Megan M. Romero, Sorana A. Morrissy, Patryk Skowron, Florence M. G. Cavalli, Hamza Farooq, Vijay Ramaswamy, Steven J. M. Jones, Richard A. Moore, Andrew J. Mungall, Yussanne Ma, Nina Thiessen, Yisu Li, Alaide Morcavallo, Lin Qi, Mari Kogiso, Yuchen Du, Patricia Baxter, Jacob J. Henderson, John R. Crawford, Michael L. Levy, James M. Olson, Yoon-Jae Cho, Aniruddha J. Deshpande, Xiao-Nan Li, Louis Chesler, Marco A. Marra, Harald Wajant, Oren J. Becher, Linda M. Bradley, Carl F. Ware, Michael D. Taylor, Robert J. Wechsler-Reya
NATURE NEUROSCIENCE
(2022)
Article
Oncology
Dean A. Regier, Brandon Chan, Sarah Costa, David W. Scott, Christian Steidl, Joseph M. Connors, Aly Karsan, Marco A. Marra, Robert Kridel, Ian Cromwell, Samantha Pollard
Summary: This study examined the cost-effectiveness of adding ibrutinib to the treatment of patients under the age of 60 with ABC-DLBCL. The analysis found that genetic testing to diagnose ABC-DLBCL and providing ibrutinib along with standard care treatment had a low to moderate probability of being cost-effective, depending on decision maker willingness to pay and the cost of the genetic test.
Article
Hematology
Kai Zhu, Andrew Jamroz, Steven Huang, Diego Villa, Ciara L. Freeman, David W. Scott, Graham Slack, Laurie H. Sehn, Joseph M. Connors, Cynthia L. Toze, Kerry J. Savage, Alina S. Gerrie
Summary: Hodgkin variant Richter transformation (HvRT) is a rare and challenging complication of chronic lymphocytic leukaemia (CLL) with limited information on prognostic factors and treatment approaches. In a population-based cohort from British Columbia, poor clinical outcomes were observed in the majority of HvRT patients, although those who received curative-intent therapy had similar survival rates to older patients with de novo Hodgkin lymphoma.
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Letter
Oncology
Andrea C. Lo, Caroline L. Holloway, Kerry J. Savage, Laurie H. Sehn, Daniel F. Worsley, Joseph M. Connors, Tom Pickles
LEUKEMIA & LYMPHOMA
(2022)
Article
Pathology
Basile Tessier-Cloutier, Jasleen K. Grewal, Martin R. Jones, Erin Pleasance, Yaoqing Shen, Ellen Cai, Chris Dunham, Lynn Hoang, Basil Horst, David G. Huntsman, Diana Ionescu, Anthony N. Karnezis, Anna F. Lee, Cheng Han Lee, Tae Hoon Lee, David D. W. Twa, Andrew J. Mungall, Karen Mungall, Julia R. Naso, Tony Ng, David F. Schaeffer, Brandon S. Sheffield, Brian Skinnider, Tyler Smith, Laura Williamson, Ellia Zhong, Dean A. Regier, Janessa Laskin, Marco A. Marra, C. Blake Gilks, Steven J. M. Jones, Stephen Yip
Summary: The study evaluates the impact of whole genome and transcriptome analysis on predictive molecular profiling and histologic diagnosis. The results show that WGTA provides reports with molecular alterations and site/tissue of origin prediction, which can accurately determine the origin and tissue type of tumors.
JOURNAL OF PATHOLOGY CLINICAL RESEARCH
(2022)
Article
Oncology
E. Pleasance, A. Bohm, L. M. Williamson, J. M. T. Nelson, Y. Shen, M. Bonakdar, E. Titmuss, V Csizmok, K. Wee, S. Hosseinzadeh, C. J. Grisdale, C. Reisle, G. A. Taylor, E. Lewis, M. R. Jones, D. Bleile, S. Sadeghi, W. Zhang, A. Davies, B. Pellegrini, T. Wong, R. Bowlby, S. K. Chan, K. L. Mungall, E. Chuah, A. J. Mungall, R. A. Moore, Y. Zhao, B. Deol, A. Fisic, A. Fok, D. A. Regier, D. Weymann, D. F. Schaeffer, S. Young, S. Yip, K. Schrader, N. Levasseur, S. K. Taylor, X. Feng, A. Tinker, K. J. Savage, S. Chia, K. Gelmon, S. Sun, H. Lim, D. J. Renouf, S. J. M. Jones, M. A. Marra, J. Laskin
Summary: This study demonstrates the importance of comprehensive whole-genome and transcriptome sequencing and analysis in guiding personalized cancer therapy, resulting in positive clinical benefits for a significant proportion of patients.
ANNALS OF ONCOLOGY
(2022)
Letter
Hematology
Christopher K. Rushton, Kostiantyn Dreval, Ryan D. Morin
Article
Multidisciplinary Sciences
Tyler Funnell, Ciara H. O'Flanagan, Marc J. Williams, Andrew McPherson, Steven McKinney, Farhia Kabeer, Hakwoo Lee, Sohrab Salehi, Ignacio Vazquez-Garcia, Hongyu Shi, Emily Leventhal, Tehmina Masud, Peter Eirew, Damian Yap, Allen W. Zhang, Jamie L. P. Lim, Beixi Wang, Jazmine Brimhall, Justina Biele, Jerome Ting, Vinci Au, Michael Van Vliet, Yi Fei Liu, Sean Beatty, Daniel Lai, Jenifer Pham, Diljot Grewal, Douglas Abrams, Eliyahu Havasov, Samantha Leung, Viktoria Bojilova, Richard A. Moore, Nicole Rusk, Florian Uhlitz, Nicholas Ceglia, Adam C. Weiner, Elena Zaikova, J. Maxwell Douglas, Dmitriy Zamarin, Britta Weigelt, Sarah H. Kim, Arnaud Da Cruz Paula, Jorge S. Reis-Filho, Spencer D. Martin, Yangguang Li, Hong Xu, Teresa Ruiz de Algara, So Ra Lee, Viviana Cerda Llanos, David G. Huntsman, Jessica N. McAlpine, Sohrab P. Shah, Samuel Aparicio
Summary: This study reveals the contribution of cell-to-cell structural variation to the phenotypic and evolutionary diversity in human breast cancer and ovarian cancer, and provides insights into the genomic and mutational states of individual cancer cells.
Letter
Pathology
Spencer D. Martin, Simon Cheung, Andrew Churg
Article
Virology
Anna Appah, Charlotte J. Beelen, Don Kirkby, Winnie Dong, Aniqa Shahid, Brian Foley, Miriam Mensah, Vincent Ganu, Peter Puplampu, Linda E. Amoah, Nicholas I. Nii-Trebi, Chanson J. Brumme, Zabrina L. Brumme
Summary: The study focused on HIV-1 subtype diversity, drug resistance, and coreceptor usage in Ghana. The dominant subtype in the region was confirmed as CRF02_AG, with a significant presence of recombinant forms as well. The study found a high prevalence of NNRTI resistance but a low prevalence of INSTI resistance, supporting the use of INSTI-based first-line regimens in Ghana.
Review
Oncology
Celine M. Laumont, Brad H. Nelson
Summary: Our understanding of tumor-infiltrating lymphocytes (TILs) is expanding to include B cells and plasma cells, collectively known as TIL-Bs. TIL-Bs have prognostic significance and predict response to immune checkpoint inhibitors in many cancers. They can perform multiple functions, including antigen presentation and antibody production, and play a crucial role in supporting immune responses and innate mechanisms. TIL-Bs are prominent in tertiary lymphoid structures and interact dynamically with the tumor stroma. Therapeutic opportunities arise from their unique tumor recognition and effector mechanisms.
Article
Biochemistry & Molecular Biology
E. Titmuss, K. Milne, M. R. Jones, T. Ng, J. T. Topham, S. D. Brown, D. F. Schaeffer, S. Kalloger, D. Wilson, R. D. Corbett, L. M. Williamson, K. Mungall, A. J. Mungall, R. A. Holt, B. H. Nelson, S. J. M. Jones, J. Laskin, H. J. Lim, M. A. Marra
Summary: The POG program at BC Cancer identified specific alterations in colorectal cancer using whole genome and transcriptome analysis, and successfully treated a patient with irbesartan, an antihypertensive drug, resulting in a profound and durable response. Analysis showed an increase in immune signaling and infiltrating immune cells, particularly CD8+ T cells, in the relapsed tumor, suggesting an activated immune response contributed to the anti-tumor effect.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Virology
Yulia Alexandrova, Alexis Yero, Ralph-Sydney Mboumba Bouassa, Eve Comeau, Suzanne Samarani, Zabrina L. Brumme, Mark Hull, Angela M. Crawley, Marc-Andre Langlois, Jonathan B. Angel, Curtis L. Cooper, Judy Needham, Terry Lee, Joel Singer, Aslam H. Anis, Cecilia T. Costiniuk, Mohammad-Ali Jenabian
Summary: In this study, the T-cell immunogenicity following three doses of SARS-CoV-2 vaccine in people living with HIV (PLWH) was assessed. The results showed that two doses of the vaccine induced a strong T-cell immune response in PLWH, and there were no significant differences in the immune response between PLWH and uninfected controls after the third dose.
Article
Virology
Riley M. Horvath, Zabrina L. Brumme, Ivan Sadowski
Summary: Mediator kinases CDK8 and CDK19 play a significant role in regulating HIV-1 transcription, and inhibitors of these enzymes may contribute to therapies for latent HIV-1 infection.
JOURNAL OF VIROLOGY
(2023)
Review
Medicine, General & Internal
Spencer D. D. Martin, Ishmam Bhuiyan, Maryam Soleimani, Gang Wang
Summary: Immune checkpoint inhibitor therapy has revolutionized renal cell carcinoma treatment, but it can lead to adverse autoimmunity and some patients receive no benefit. Traditional biomarkers do not predict response to ICI in renal cell carcinoma, but emerging biomarkers such as gene expression profiles and loss of pro-angiogenic proteins show promise. This review discusses the effectiveness of different biomarkers and introduces novel biomarkers that have demonstrated promise in clinical trials.
JOURNAL OF CLINICAL MEDICINE
(2023)