Article
Oncology
Cecilia Yeung, Xiaoyu Qu, Olga Sala-Torra, David Woolston, Jerry Radich, Min Fang
Summary: The study proposed a rapid method for detecting gene fusions using FusionPlex RNA NGS and CGAT in B-acute lymphoblastic leukemia patients. Results showed that RNA NGS had 100% sensitivity and specificity in detecting fusions, indicating its robustness and reliability for fusion detection.
Article
Hematology
Zhenhua Li, Ti-Cheng Chang, Jacob J. Junco, Meenakshi Devidas, Yizhen Li, Wenjian Yang, Xin Huang, Dale J. Hedges, Zhongshan Cheng, Mary Shago, Andrew J. Carroll, Nyla A. Heerema, Julie Gastier-Foster, Brent L. Wood, Michael J. Borowitz, Lauren Sanclemente, Elizabeth A. Raetz, Stephen P. Hunger, Eleanor Feingold, Tracie C. Rosser, Stephanie L. Sherman, Mignon L. Loh, Charles G. Mullighan, Jiyang Yu, Gang Wu, Philip J. Lupo, Karen R. Rabin, Jun J. Yang
Summary: This study investigates the genomics of Down syndrome-related acute lymphoblastic leukemia (DS-ALL) and identifies 15 molecular subtypes, as well as abnormal activation of key genes. It also reveals the common occurrence of somatic genomic abnormalities mediated by gene rearrangements in DS-ALL and the association between subtype heterogeneity and prognosis. These findings provide important insights into the biology of DS-ALL and offer opportunities for individualized treatment.
Review
Medicine, General & Internal
Ilaria Iacobucci, Shunsuke Kimura, Charles G. Mullighan
Summary: Acute lymphoblastic leukemia (ALL) has achieved cure rates exceeding 90% in children, but remains a leading cause of cancer-related death in the young. Next generation sequencing has led to significant advances in understanding leukemogenesis and the development of novel therapeutic approaches, including mutation-specific and mutation-agnostic treatments.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Medicine, General & Internal
Owen D. Mitchell, Katie Gilliam, Daniela del Gaudio, Kelsey E. McNeely, Shaili Smith, Maria Acevedo, Meghana Gaduraju, Rachel Hodge, Aubrianna S. S. Ramsland, Jeremy Segal, Soma Das, Feighanne Hathaway, Darren S. Bryan, Sanjukta Tawde, Shelly Galasinski, Peng Wang, Melissa Y. Tjota, Aliya N. Husain, Samuel G. Armato, Jessica Donington, Mark K. Ferguson, Kiran Turaga, Jane E. Churpek, Hedy L. Kindler, Michael W. Drazer
Summary: This study aims to determine the prevalence of incidental germline P/LP variants in patients with mesothelioma through tumor-only next-generation sequencing (NGS), which is not designed for this purpose.
Article
Oncology
Qiong Shi, Lin Liu, Jianru Chen, Weigang Zhang, Weinan Guo, Xiao Wang, Huina Wang, Sen Guo, Qiao Yue, Jingjing Ma, Yu Liu, Guannan Zhu, Tao Zhao, Jianhong Zhao, Ying Liu, Tianwen Gao, Chunying Li
Summary: This study conducted genomic research on acral melanoma in Asian populations, identifying mutated genes associated with the disease and analyzing its pathogenesis and therapeutic targets. Additionally, it reconstructed the mutational processes of the samples and identified early mutational events. This study provides a foundation for the development of personalized strategies for treating acral melanoma in Asian populations.
CLINICAL CANCER RESEARCH
(2022)
Article
Multidisciplinary Sciences
Jennifer L. Kamens, Stephanie Nance, Cary Koss, Beisi Xu, Anitria Cotton, Jeannie W. Lam, Elizabeth A. R. Garfinkle, Pratima Nallagatla, Amelia M. R. Smith, Sharnise Mitchell, Jing Ma, Duane Currier, William C. Wright, Kanisha Kavdia, Vishwajeeth R. Pagala, Wonil Kim, LaShanale M. Wallace, Ji-Hoon Cho, Yiping Fan, Aman Seth, Nathaniel Twarog, John K. Choi, Esther A. Obeng, Mark E. Hatley, Monika L. Metzger, Hiroto Inaba, Sima Jeha, Jeffrey E. Rubnitz, Junmin Peng, Taosheng Chen, Anang A. Shelat, R. Kiplin Guy, Tanja A. Gruber
Summary: Proteasome inhibition is found to be effective in KMT2Ar infant acute lymphoblastic leukemia, leading to the depletion of histone modifications and downregulation of KMT2A gene expression signature. A cohort of relapsed/refractory KMT2Ar patients treated with this approach showed a high overall response rate. This innovative treatment approach is now being evaluated in a multi-institutional upfront trial for infants with newly diagnosed ALL.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Shawn H. R. Lee, Wenjian Yang, Yoshihiro Gocho, August John, Lauren Rowland, Brandon Smart, Hannah Williams, Dylan Maxwell, Jeremy Hunt, Wentao Yang, Kristine R. R. Crews, Kathryn G. G. Roberts, Sima Jeha, Cheng Cheng, Seth E. E. Karol, Mary V. V. Relling, Gary L. L. Rosner, Hiroto Inaba, Charles G. G. Mullighan, Ching-Hon Pui, William E. E. Evans, Jun J. J. Yang
Summary: Contemporary chemotherapy for childhood acute lymphoblastic leukemia is personalized based on clinical features, leukemia genomics, and minimal residual disease. However, the pharmacological basis of these prognostic variables is unclear. A study analyzing samples from 805 children with newly diagnosed leukemia identified variations in drug response and determined that certain subtypes were more sensitive to specific agents. The findings suggest opportunities for individualizing therapy and exploring alternative strategies for childhood acute lymphoblastic leukemia.
Review
Oncology
Sara Ribeiro, Anna M. Eiring, Jamshid S. Khorashad
Summary: AML is a heterogeneous malignancy with various genetic abnormalities, some of which have led to the development of specific inhibitors approved by the FDA for eligible patients. Cytogenetic profiling and gene mutation analysis are essential for the diagnosis, classification, prognosis, and treatment of AML. The review discussed genomic abnormalities in AML, the significance of certain gene mutations as therapeutic targets, and the limitations of current genomic approaches in producing a comprehensive understanding of the disease.
Review
Oncology
Thai Hoa Tran, Stephen P. Hunger
Summary: Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and has shown significant improvement in survival rates through risk-adapted chemotherapy, prevention measures, and molecular analysis. However, challenges remain for older patients and relapsed/refractory cases.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Oncology
Alexandre Andre Balieiro Anastacio da Costa, Glauco Baiocchi
Summary: Ovarian cancer, particularly high-grade serous carcinoma, is highly sensitive to platinum-based treatment but often develops resistance due to alterations in DNA repair pathways. Understanding mechanisms of sensitivity and resistance can guide new therapeutic opportunities. Discovery of synthetic lethality pathways related to DNA repair and cell cycle regulation has opened up new avenues for drug therapy.
SEMINARS IN CANCER BIOLOGY
(2021)
Article
Hematology
Xinjie Xu, Christian N. Paxton, Robert J. Hayashi, Kimberly P. Dunsmore, Stuart S. Winter, Stephen P. Hunger, Naomi J. Winick, William L. Carroll, Mignon L. Loh, Meenakshi Devidas, Thomas G. Gross, Catherine M. Bollard, Sherrie L. Perkins, Rodney R. Miles
Summary: ETP-LLy is a subtype of T-LLy that shares similarities with ETP-ALL but also has distinct genetic features compared to non-ETP T-LLy, indicating it may be a separate entity.
Article
Oncology
Sean M. Hacking, Dean Pavlick, Yihong Wang, Benedito A. Carneiro, Matthew Mullally, Shaolei Lu, Mariana Canepa, Gennady Bratslavsky, Joseph Jacob, Andrea Necchi, Philippe E. Spiess, Li Wang, Evgeny Yakirevich, Jeffrey Ross
Summary: Comprehensive genomic profiling (CGP) was used to evaluate the frequency of NF2 genomic alterations in histologic subtypes of kidney tumors and co-occurring genomic alterations in other genes and biomarkers. The study found that NF2 mutations were more frequent in collecting duct carcinoma, sarcomatoid carcinoma, papillary carcinoma, and unclassified carcinoma, while less frequent in clear cell carcinoma, urothelial carcinoma of renal pelvis, and Wilms tumor. NF2-mutant RCC also exhibited co-occurring genetic alterations in CDKN2A/B, SETD2, and BAP1, which could potentially serve as therapeutic targets. Moreover, the higher level of PD-L1 expression in NF2-mutant tumors suggests that these tumors might be sensitive to immune checkpoint inhibitor therapies.
Article
Oncology
Sean M. Hacking, Dean Pavlick, Yihong Wang, Benedito A. Carneiro, Matthew Mullally, Shaolei Lu, Mariana Canepa, Gennady Bratslavsky, Joseph Jacob, Andrea Necchi, Philippe E. Spiess, Li Wang, Evgeny Yakirevich, Jeffrey Ross
Summary: Genomic alterations in NF2 tumor-suppressor gene are associated with aggressive behavior in kidney tumors. NF2 mutations are more frequent in certain histologic subtypes, such as cdRCC, sRCC, uRCC, and pRCC. These tumors also harbor co-occurring genomic alterations in other genes, and have higher expression of PD-L1, suggesting potential sensitivity to immune checkpoint inhibitors.
Article
Multidisciplinary Sciences
Leonard M. Quinn, Sam Haldenby, Philip Antzcak, Anna Fowler, Katie Bullock, John Kenny, Timothy Gilbert, Timothy Andrews, Rafael Diaz-Nieto, Stephen Fenwick, Robert Jones, Eithne Costello-Goldring, Graeme Poston, William Greenhalf, Daniel Palmer, Hassan Malik, Chris Goldring
Summary: By sequencing the DNA of 42 resected pCCA tumors and normal bile ducts, we found high frequency mutations in genes associated with immunological pathways, such as Dectin-2 and PD-1. Most patients had cancer-associated mutations, many of which are not typically associated with cholangiocarcinoma but may increase eligibility for targeted trials.
SCIENTIFIC REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Agnieszka Kaczmarska, Patrycja Sliwa, Joanna Zawitkowska, Monika Lejman
Summary: Pediatric acute lymphoblastic leukemia (ALL) with t(9;22)(q34;q11.2) is a rare malignancy in children, with approximately 3-5% of patients having the Philadelphia chromosome. Treatment outcomes have improved significantly in recent years, with tyrosine kinase inhibitor (TKI)-imatinib playing a key role in increasing overall survival for ALL Ph+ patients. Genetic analyses, particularly focusing on the IKZF1 gene, provide important prognostic information for pediatric ALL Ph+ cases, highlighting the need for targeted therapies and immunotherapy to enhance patient outcomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
James B. Studd, Minjun Yang, Zhenhua Li, Jayaram Vijayakrishnan, Yi Lu, Allen Eng-Juh Yeoh, Kajsa Paulsson, Richard S. Houlston
Article
Oncology
Linda Olsson, Kristina B. Lundin-Stroem, Anders Castor, Mikael Behrendtz, Andrea Biloglav, Ulrika Noren-Nystroem, Kajsa Paulsson, Bertil Johansson
GENES CHROMOSOMES & CANCER
(2018)
Article
Oncology
Ching-Hon Pui, Paola Rebora, Martin Schrappe, Andishe Attarbaschi, Andre Baruchel, Giuseppe Basso, Helene Cave, Sarah Elitzur, Katsuyoshi Koh, Hsi-Che Liu, Kajsa Paulsson, Rob Pieters, Lewis B. Silverman, Jan Stary, Ajay Vora, Allen Yeoh, Christine J. Harrison, Maria Grazia Valsecchi
JOURNAL OF CLINICAL ONCOLOGY
(2019)
Article
Oncology
Ola Forslund, Natsuki Sugiyama, Chengjun Wu, Naveen Ravi, Yuesheng Jin, Sabine Swoboda, Fredrik Andersson, Davit Bzhalava, Emilie Hultin, Kajsa Paulsson, Joakim Dillner, Stefan Schwartz, Johan Wennerberg, Lars Ekblad
Article
Oncology
Naveen Ravi, Minjun Yang, Sigurdur Gretarsson, Caroline Jansson, Nektaria Mylona, Saskia R. Sydow, Eleanor L. Woodward, Lars Ekblad, Johan Wennerberg, Kajsa Paulsson
Article
Multidisciplinary Sciences
Minjun Yang, Mattias Vesterlund, Ioannis Siavelis, Larissa H. Moura-Castro, Anders Castor, Thoas Fioretos, Rozbeh Jafari, Henrik Lilljebjorn, Duncan T. Odom, Linda Olsson, Naveen Ravi, Eleanor L. Woodward, Louise Harewood, Janne Lehtio, Kajsa Paulsson
NATURE COMMUNICATIONS
(2019)
Article
Otorhinolaryngology
Sigurdur Gretarsson, Alexander Nygren, Ann H. Rosendahl, Nektaria Mylona, Elisabeth Kjellen, Yuesheng Jin, Kajsa Paulsson, Ake Borg, Eva Brun, Jan Tennvall, Anders Bergenfelz, Lennart Greiff, Johan Wennerberg, Lars Ekblad
ACTA OTO-LARYNGOLOGICA
(2020)
Article
Hematology
Minjun Yang, Setareh Safavi, Eleanor L. Woodward, Nicolas Duployez, Linda Olsson-Arvidsson, Jonas Ungerback, Mikael Sigvardsson, Marketa Zaliova, Jan Zuna, Thoas Fioretos, Bertil Johansson, Karolin H. Nord, Kajsa Paulsson
Article
Oncology
Naveen Ravi, Minjun Yang, Nektaria Mylona, Johan Wennerberg, Kajsa Paulsson
Article
Oncology
Larissa H. Moura-Castro, Pablo Pena-Martinez, Anders Castor, Roman Galeev, Jonas Larsson, Marcus Jaras, Minjun Yang, Kajsa Paulsson
Summary: High hyperdiploid acute lymphoblastic leukemia (ALL) in children often displays defective sister chromatid cohesion, potentially due to low levels of cohesin or condensin, leading to a range of mild to very severe defects and increased chromosomal copy number heterogeneity. These abnormalities may contribute to clonal evolution in hyperdiploid pediatric ALL.
GENES CHROMOSOMES & CANCER
(2021)
Letter
Oncology
Rebeqa Gunnarsson, Minjun Yang, Linda Olsson-Arvidsson, Andrea Biloglav, Mikael Behrendtz, Anders Castor, Kajsa Paulsson, Bertil Johansson
Article
Oncology
Adam Stenman, Minjun Yang, Johan O. Paulsson, Jan Zedenius, Kajsa Paulsson, C. Christofer Juhlin
Summary: Anaplastic thyroid carcinoma is a deadly tumor with limited treatment options once it spreads. Research found genetic abnormalities in the patients that may respond to CDK inhibitors, as well as a phenomenon called kataegis, which could be therapeutically relevant.
Letter
Hematology
Agatheeswaran Subramaniam, Carl Sanden, Larissa Moura-Castro, Kristijonas Zemaitis, Ludwig Schmiderer, Aurelie Baudet, Alexandra Backstrom, Elin Arvidsson, Simon Hultmark, Natsumi Miharada, Mattias Magnusson, Kajsa Paulsson, Thoas Fioretos, Jonas Larsson
Letter
Oncology
Rebeqa Gunnarsson, Minjun Yang, Andrea Biloglav, Vladimir Lazarevic, Kajsa Paulsson, Bertil Johansson
Article
Multidisciplinary Sciences
Eleanor L. Woodward, Minjun Yang, Larissa H. Moura-Castro, Hilda van den Bos, Rebeqa Gunnarsson, Linda Olsson-Arvidsson, Diana C. J. Spierings, Anders Castor, Nicolas Duployez, Marketa Zaliova, Jan Zuna, Bertil Johansson, Floris Foijer, Kajsa Paulsson
Summary: This study reveals that the aneuploidies in high hyperdiploid acute lymphoblastic leukemia (HeH ALL) may originate early and follow a punctuated evolution process, using single-cell whole genome sequencing and in silico modeling.
NATURE COMMUNICATIONS
(2023)