Article
Multidisciplinary Sciences
Matthew Naish, Michael Alonge, Piotr Wlodzimierz, Andrew J. Tock, Bradley W. Abramson, Anna Schmuecker, Terezie Mandakova, Bhagyshree Jamge, Christophe Lambing, Pallas Kuo, Natasha Yelina, Nolan Hartwick, Kelly Colt, Lisa M. Smith, Jurriaan Ton, Tetsuji Kakutani, Robert A. Martienssen, Korbinian Schneeberger, Martin A. Lysak, Frederic Berger, Alexandros Bousios, Todd P. Michael, Michael C. Schatz, Ian R. Henderson
Summary: The study used long-read sequencing to assemble the Arabidopsis genome and resolve all five centromeres. It found that centromeres consist of megabase-scale tandemly repeated satellite arrays and are invaded by retrotransposons. The centromeres are evolving through cycles of satellite homogenization and retrotransposon-driven diversification.
Article
Oncology
Ryosuke Okamura, Razelle Kurzrock, Robert J. Mallory, Paul T. Fanta, Adam M. Burgoyne, Bryan M. Clary, Shumei Kato, Jason K. Sicklick
Summary: Biliary tract cancers have poor prognoses even with cytotoxic chemotherapy, highlighting the need for precision treatment approaches using comprehensive genomic profiling. Analysis of circulating-tumor DNA (ctDNA) and tissue-based tumor DNA is feasible in these cancers. Molecularly matched therapeutic regimens based on genomic profiling show significantly longer progression-free survival and higher disease control rates compared to unmatched regimens.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Oncology
Chia-Chen Hsu, Ying-Hsuan Wang, Yi-Yang Chen, Ying-Ju Chen, Chang-Hsien Lu, Yu-Ying Wu, Yao-Ren Yang, Hsing-Yi Tsou, Chian-Pei Li, Cih-En Huang, Chih-Cheng Chen
Summary: Patients with Philadelphia-chromosome-negative myeloproliferative neoplasms (MPNs) are prone to developing second cancers (SCs), which may be attributed to mutations in genes related to immune pathways and inflammatory networks, as well as increased levels of cytokines. This highlights the importance of inflammation in the pathogenesis of MPN-SC.
Article
Oncology
Peng-Chan Lin, Yu-Min Yeh, Hui-Ping Hsu, Ren-Hao Chan, Bo-Wen Lin, Po-Chuan Chen, Chien-Chang Pan, Keng-Fu Hsu, Jenn-Ren Hsiao, Yan-Shen Shan, Meng-Ru Shen
Summary: This study identified potential genetic markers for hypermutated cancers by investigating driver mutations, mutational signatures, tumor-associated neoantigens, and molecular cancer evolution in cancer patients with six different cancer types. Driver mutations and mutational signatures were found to be associated with sensitivity or resistance to immunotherapy. The order of sequential mutations and coexisting genetic mutations were shown to influence the hypermutation phenotype, serving as important predictors for hypermutated cancers.
Article
Genetics & Heredity
Chunrong Zhu, Liangjun Zhu, Yanhong Gu, Ping Liu, Xiaoling Tong, Guozhong Wu, Wenyu Zhu, Wenxiang Shen, Hua Bao, Xiangyuan Ma, Ruoying Yu, Xue Wu, Dongqin Zhu, Yongqian Shu, Jifeng Feng
Summary: Gastrointestinal tract cancers in China have high incidence and mortality rates, with colorectal and gastric cancers showing the highest tumor mutation burden. Mutations in polymerase and mismatch repair genes are enriched in high-mutation tumors, with chromosomal instability predominantly in colorectal and gastric cancers. The study provides insights into the molecular landscape and genetic differences between tumor locations in Chinese gastrointestinal cancers.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Andrey A. Yurchenko, Fatemeh Rajabi, Tirzah Braz-Petta, Hiva Fassihi, Alan Lehmann, Chikako Nishigori, Jinxin Wang, Ismael Padioleau, Konstantin Gunbin, Leonardo Panunzi, Fanny Morice-Picard, Pierre Laplante, Caroline Robert, Patricia L. Kannouche, Carlos F. M. Menck, Alain Sarasin, Sergey I. Nikolaev
Summary: Xeroderma pigmentosum (XP) is a rare genetic disorder associated with an increased risk of skin cancer. In this study, the authors analyze skin cancer genomes from five different XP groups, revealing genetic and molecular factors related to the mutational profile and UV-induced mutagenesis in XP.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Dong-Joo Choi, Georgina Armstrong, Brittney Lozzi, Prashanth Vijayaraghavan, Sharon E. Plon, Terence C. Wong, Eric Boerwinkle, Donna M. Muzny, Hsiao-Chi Chen, Richard A. Gibbs, Quinn T. Ostrom, Beatrice Melin, Benjamin Deneen, Melissa L. Bondy, Matthew N. Bainbridge
Summary: This study conducted comprehensive surveillance of the genomic landscape of familial glioma and identified significant enrichment of rare deleterious variants in seven genes, with HERC2 being the most significantly enriched gene. Rare noncoding variants that may affect transcription factor binding sites or cause cryptic splicing were also found. Additionally, validation experiments revealed the significant impacts of DMBT1, HP1BP3, and ZCH7B3 genes on proliferation.
Article
Oncology
Denis L. Jardim, Sherri Z. Millis, Jeffrey S. Ross, Michelle Sue-Ann Woo, Siraj M. Ali, Razelle Kurzrock
Summary: This study found that 9.7% of prostate cancer samples exhibited genomic abnormalities in the cyclin sensitizing pathway, with frequent alterations including CCND1 amplification and CDKN2A and B loss. Additionally, alterations in possible resistance genes RB1 and CCNE1 were detected in a smaller percentage of cases. Furthermore, cyclin sensitizing alterations were often associated with concomitant AR alterations.
Article
Oncology
Jessica K. Lee, Smruthy Sivakumar, Alexa B. Schrock, Russell Madison, David Fabrizio, Ole Gjoerup, Jeffrey S. Ross, Garrett M. Frampton, Pavel Napalkov, Meagan Montesion, Jennifer L. Schutzman, Xin Ye, Priti S. Hegde, Misako Nagasaka, Geoffrey R. Oxnard, Ethan S. Sokol, Sai-Hong Ignatius Ou, Zhen Shi
Summary: Recent clinical development of KRAS inhibitors has increased interest in the genomic landscape of KRAS-altered cancers. Comprehensive genomic profiling revealed the prevalence of KRAS alterations and identified co-alterations and biomarkers associated with KRAS mutations.
NPJ PRECISION ONCOLOGY
(2022)
Article
Oncology
Cen Jiang, Yiyi Lu, Hua Liu, Gang Cai, Zhao Peng, Weiwei Feng, Lin Lin
Summary: This study evaluated the diversity of mutations in different types of gynecological cancers and found similarities and differences in clinical characteristics and genomic mutations. The results provide important information for understanding the molecular mechanisms of gynecological cancers and the development of targeted drugs and precision medicine.
FRONTIERS IN ONCOLOGY
(2023)
Article
Oncology
Bo-Fang Chen, Yi-Fang Tsai, Pei-Ju Lien, Yen-Shu Lin, Chin-Jung Feng, Yen-Jen Chen, Han-Fang Cheng, Chun-Yu Liu, Ta-Chung Chao, Jiun-I. Lai, Ling-Ming Tseng, Chi-Cheng Huang
Summary: This study investigated the molecular alterations and potential therapeutic targets in luminal B1 breast cancer in Taiwan. The most prevalent actionable alterations were found to be PIK3CA, FGFR1, and BRCA1/2. Additionally, PTEN and BRCA1/2 were significantly associated with disease relapse in this subtype of breast cancer.
Article
Dermatology
Jason Thomson, Findlay Bewicke-Copley, Chinedu Anthony Anene, Abha Gulati, Ai Nagano, Karin Purdie, Gareth J. Inman, Charlotte M. Proby, Irene M. Leigh, Catherine A. Harwood, Jun Wang
Summary: This study conducted the largest AK whole exome sequencing study to date and found significant similarities between AK and cSCC in terms of genetic mutations, copy number alterations, driver gene mutations, and mutational signatures. The research identified 44 significantly mutated AK driver genes and suggested that dysregulated TGFf3 signaling may play an important role in AK-cSCC progression.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2021)
Article
Genetics & Heredity
Samuel W. Brady, Kathryn G. Roberts, Zhaohui Gu, Lei Shi, Stanley Pounds, Deqing Pei, Cheng Cheng, Yunfeng Dai, Meenakshi Devidas, Chunxu Qu, Ashley N. Hill, Debbie Payne-Turner, Xiaotu Ma, Ilaria Iacobucci, Pradyuamna Baviskar, Lei Wei, Sasi Arunachalam, Kohei Hagiwara, Yanling Liu, Diane A. Flasch, Yu Liu, Matthew Parker, Xiaolong Chen, Abdelrahman H. Elsayed, Omkar Pathak, Yongjin Li, Yiping Fan, J. Robert Michael, Michael Rusch, Mark R. Wilkinson, Scott Foy, Dale J. Hedges, Scott Newman, Xin Zhou, Jian Wang, Colleen Reilly, Edgar Sioson, Stephen Rice, Victor Pastor Loyola, Gang Wu, Evadnie Rampersaud, Shalini C. Reshmi, Julie Gastier-Foster, Jaime M. Guidry Auvil, Patee Gesuwan, Malcolm A. Smith, Naomi Winick, Andrew J. Carroll, Nyla A. Heerema, Richard C. Harvey, Cheryl L. Willman, Eric Larsen, Elizabeth A. Raetz, Michael J. Borowitz, Brent L. Wood, William L. Carroll, Patrick A. Zweidler-McKay, Karen R. Rabin, Leonard A. Mattano, Kelly W. Maloney, Stuart S. Winter, Michael J. Burke, Wanda Salzer, Kimberly P. Dunsmore, Anne L. Angiolillo, Kristine R. Crews, James R. Downing, Sima Jeha, Ching-Hon Pui, William E. Evans, Jun J. Yang, Mary Relling, Daniela S. Gerhard, Mignon L. Loh, Stephen P. Hunger, Jinghui Zhang, Charles G. Mullighan
Summary: A comprehensive analysis of genomic and transcriptomic data from 2,754 childhood acute lymphoblastic leukemias revealed 376 putative driver genes, as well as associations between disease subtypes and prognosis.
Article
Medicine, Research & Experimental
Emanuele Panza, Benjamin B. Ozenberger, Krystal M. Straessler, Jared J. Barrott, Li Li, Yanliang Wang, Mingchao Xie, Anne Boulet, Simon W. A. Titen, Clinton C. Mason, Alexander J. Lazar, Li Ding, Mario R. Capecchi, Kevin B. Jones
Summary: Clear cell sarcoma is a deadly malignancy affecting adolescents and young adults, characterized by frequent amplifications of the MITF locus and chromosomes 7 and 8. Few alterations are shared with other EWSR1-rearranged tumors.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Biochemistry & Molecular Biology
Lara R. Arauna, Jacob Bergstedt, Jeremy Choin, Javier Mendoza-Revilla, Christine Harmant, Maguelonne Roux, Alex Mas-Sandoval, Laure Lemee, Heidi Colleran, Alexandre Francois, Frederique Valentin, Olivier Cassar, Antoine Gessain, Lluis Quintana-Murci, Etienne Patin
Summary: This study provides insights into the genetic history of ni-Vanuatu populations and how sociocultural processes have shaped the diversity of their genomes. The findings suggest that ni-Vanuatu derive their East Asian and Papuan-related ancestry from the same source populations and that there was a major population turnover around 1700-2300 years ago. The study also reveals the arrival of Polynesian ancestry to Central and South Vanuatu around 600-1000 years ago.
Article
Virology
Rafael Contreras-Galindo, Mark H. Kaplan, Derek Dube, Marta J. Gonzalez-Hernandez, Susana Chan, Fan Meng, Manhong Dai, Gilbert S. Omenn, Scott D. Gitlin, David M. Markovitz
JOURNAL OF VIROLOGY
(2015)
Article
Biotechnology & Applied Microbiology
Joseph Zahn, Mark H. Kaplan, Sabrina Fischer, Manhong Dai, Fan Meng, Anjan Kumar Saha, Patrick Cervantes, Susana M. Chan, Derek Dube, Gilbert S. Omenn, David M. Markovitz, Rafael Contreras-Galindo
Article
Biochemistry & Molecular Biology
Rafael Contreras-Galindo, Sabrina Fischer, Anjan K. Saha, John D. Lundy, Patrick W. Cervantes, Mohamad Mourad, Claire Wang, Brian Qian, Manhong Dai, Fan Meng, Arul Chinnaiyan, Gilbert S. Omenn, Mark H. Kaplan, David M. Markovitz
Article
Virology
Rafael Contreras-Galindo, Derek Dube, Koh Fujinaga, Mark H. Kaplan, David M. Markovitz
JOURNAL OF VIROLOGY
(2017)
Article
Multidisciplinary Sciences
Susana M. Chan, Tamar Sapir, Sung-Soo Park, Jean-Francois Rual, Rafael Contreras-Galindo, Orly Reiner, David M. Markovitz
Article
Genetics & Heredity
Mark H. Kaplan, Mark Kaminski, Judith M. Estes, Scott D. Gitlin, Joseph Zahn, James T. Elder, Trilokraj Tejasvi, Elizabeth Gensterblum, Amr H. Sawalha, Joseph Patrick McGowan, Michael H. Dosik, Haner Direskeneli, Guher Saruhan Direskeneli, Sally N. Adebamowo, Clement A. Adebamowo, Mohammad Sajadi, Rafael Contreras-Galindo
BMC MEDICAL GENOMICS
(2019)
Article
Medicine, Research & Experimental
Maegan L. Capitano, Nirit Mor-Vaknin, Anjan K. Saha, Scott Cooper, Maureen Legendre, Haihong Guo, Rafael Contreras-Galindo, Ferdinand Kappes, Maureen A. Sartor, Christopher T. Lee, Xinxin Huang, David M. Markovitz, Hal E. Broxmeyer
JOURNAL OF CLINICAL INVESTIGATION
(2019)
Article
Oncology
Mark H. Kaplan, Rafael Contreras-Galindo, Evelyn Jiagge, Sofia D. Merajver, Lisa Newman, Galya Bigman, Michael H. Dosik, Ganesh S. Palapattu, Javed Siddiqui, Arul M. Chinnaiyan, Sally Adebamowo, Clement Adebamowo
INFECTIOUS AGENTS AND CANCER
(2020)
Article
Biochemistry & Molecular Biology
Anjan K. Saha, Rafael Contreras-Galindo, Yashar S. Niknafs, Matthew Iyer, Tingting Qin, Karthik Padmanabhan, Javed Siddiqui, Monica Palande, Claire Wang, Brian Qian, Elizabeth Ward, Tara Tang, Scott A. Tomlins, Scott D. Gitlin, Maureen A. Sartor, Gilbert S. Omenn, Arul M. Chinnaiyan, David M. Markovitz
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Review
Biochemistry & Molecular Biology
Estanislao Peixoto, Asad Khan, Zachary A. Lewis, Rafael Contreras-Galindo, Wioletta Czaja
Summary: Robust and tightly regulated DNA repair is crucial for maintaining genome stability and preventing cancer. HELLS, a chromatin remodeler, plays important roles in DNA repair, genome stability, and cancer-associated pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Souren Paul, Mark H. Kaplan, Dinesh Khanna, Preston M. McCourt, Anjan K. Saha, Pei-Suen Tsou, Mahek Anand, Alexander Radecki, Mohamad Mourad, Amr H. Sawalha, David M. Markovitz, Rafael Contreras-Galindo
Summary: Skin fibrosis plays an important role in scleroderma. This study reveals significant alterations in centromeric DNA and cytoplasmic leaking of centromere proteins in fibroblasts from scleroderma patients. These abnormalities may be linked to genetic and epigenetic abnormalities at the centromere, chromosome instability, and autoimmune reactions.
NATURE COMMUNICATIONS
(2022)
