Article
Oncology
Jiapei Yuan, Kathleen E. Houlahan, Susmita G. Ramanand, Sora Lee, GuemHee Baek, Yang Yang, Yong Chen, Douglas W. Strand, Michael Q. Zhang, Paul C. Boutros, Ram S. Mani
Summary: Prostate cancer is highly heritable and researchers have identified multiple risk alleles associated with the disease. This study used three-dimensional spatial genomics to identify the target genes regulated by these risk alleles in prostate tumors. The findings revealed the complex regulation of these genes and their interactions with different tumor types.
Article
Oncology
Sophie Bartsch, Kimia Mirzakhani, Laura Neubert, Alexander Stenzel, Marzieh Ehsani, Mohsen Esmaeili, Thanakorn Pungsrinont, Merve Kacal, Seyed Mohammad Mahdi Rasa, Julia Kallenbach, Divya Damodaran, Federico Ribaudo, Marc-Oliver Grimm, Francesco Neri, Aria Baniahmad
Summary: The expression of human telomerase reverse transcriptase subunit (hTERT) is hormonally controlled, with androgen treatment suppressing hTERT expression in prostate cancer cells. This inhibition and activation of hTERT by androgens is mediated by androgen receptor (AR) co-repressors ING1 and ING2. This reveals a dual role of AR in controlling hTERT expression during prostate cancer tumorigenesis.
Article
Oncology
Kelsie Raspin, Liesel M. FitzGerald, James R. Marthick, Matt A. Field, Roslyn C. Malley, Annette Banks, Shaun Donovan, Russell J. Thomson, Georgea R. Foley, Janet L. Stanford, Joanne L. Dickinson
Summary: A rare variant (rs78589034) was identified as significantly associated with increased prostate cancer risk, potentially affecting EZH2 function in prostate tissue. This provides evidence for the variant as a potential therapeutic target.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Genetics & Heredity
Heidi Hautakangas, Bendik S. Winsvold, Sanni E. Ruotsalainen, Gyda Bjornsdottir, Aster V. E. Harder, Lisette J. A. Kogelman, Laurent F. Thomas, Raymond Noordam, Christian Benner, Padhraig Gormley, Ville Artto, Karina Banasik, Anna Bjornsdottir, Dorret Boomsma, Ben M. Brumpton, Kristoffer Solvsten Burgdorf, Julie E. Buring, Mona Ameri Chalmer, Irene de Boer, Martin Dichgans, Christian Erikstrup, Markus Farkkila, Maiken Elvestad Garbrielsen, Mohsen Ghanbari, Knut Hagen, Paavo Happola, Jouke-Jan Hottenga, Maria G. Hrafnsdottir, Kristian Hveem, Marianne Bakke Johnsen, Mika Kahonen, Espen S. Kristoffersen, Tobias Kurth, Terho Lehtimaki, Lannie Lighart, Sigurdur H. Magnusson, Rainer Malik, Ole Birger Pedersen, Nadine Pelzer, Brenda W. J. H. Penninx, Caroline Ran, Paul M. Ridker, Frits R. Rosendaal, Gudrun R. Sigurdardottir, Anne Heidi Skogholt, Olafur A. Sveinsson, Thorgeir E. Thorgeirsson, Henrik Ullum, Lisanne S. Vijfhuizen, Elisabeth Widen, Ko Willems van Dijk, Arpo Aromaa, Andrea Carmine Belin, Tobias Freilinger, M. Arfan Ikram, Marjo-Riitta Jarvelin, Olli T. Raitakari, Gisela M. Terwindt, Mikko Kallela, Maija Wessman, Jes Olesen, Daniel Chasman, Dale R. Nyholt, Hreinn Stefansson, Kari Stefansson, Arn M. J. M. van den Maagdenberg, Thomas Folkmann Hansen, Samuli Ripatti, John-Anker Zwart, Aarno Palotie, Matti Pirinen
Summary: This study identified 123 susceptibility loci for migraine through genome-wide association analyses and implicated neurovascular mechanisms in its pathophysiology. Subtype analyses revealed risk loci specific for migraine with or without aura, as well as shared risk variants. The findings highlight the importance of both vascular and central nervous system tissue/cell types in the genetic underpinning of migraine.
Article
Neurosciences
Claudio Toma, Alex D. Shaw, Anna Heath, Kerrie D. Pierce, Philip B. Mitchell, Peter R. Schofield, Janice M. Fullerton
Summary: Combining family-based linkage analysis with next-generation sequencing data is effective in identifying potential disease genes and specific risk variants in complex disorders. Rare missense variants in ANK3, PCDH15, and NRBF2 were identified as potentially contributing to disease risk, providing valuable targets for functional characterization.
JOURNAL OF PSYCHIATRY & NEUROSCIENCE
(2021)
Article
Genetics & Heredity
Anamay Shetty, Ji-Heui Seo, Connor A. Bell, Edward P. O'Connor, Mark M. Pomerantz, Matthew L. Freedman, Alexander Gusev
Summary: Integration of epigenomic data from tumor and normal tissues has identified risk-harboring regulatory elements for prostate cancer, with some risk variants showing significant allele specificity in tumors. These findings suggest a role for tumor-specific regulation in cancer risk and highlight potential causal regulatory elements at GWAS loci.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Plant Sciences
Tong Li, Liangwei Yin, Claire E. Stoll, Damon Lisch, Meixia Zhao
Summary: Genomic imprinting is a parent-of-origin-dependent epigenetic phenomenon. This study reveals the importance of transposable elements and conserved noncoding sequences in genomic imprinting in maize.
Article
Chemistry, Multidisciplinary
Jianbang Chen, Jie Zhang, Aixin Zhu, Xuchu Huang
Summary: Two new quaternary rare-earth borates were synthesized and characterized, showing the potential for applications in the deep UV region.
NEW JOURNAL OF CHEMISTRY
(2022)
Article
Medicine, Research & Experimental
Maike Stentenbach, Judith A. Ermer, Danielle L. Rudler, Kara L. Perks, Samuel A. Raven, Richard G. Lee, Tim McCubbin, Esteban Marcellin, Stefan J. Siira, Oliver Rackham, Aleksandra Filipovska
Summary: Prostate cancer is a common and deadly malignancy. Using CRISPR-Cas9 genome editing, researchers introduced a missense variant in the ELAC2 gene into mice, causing prostate enlargement, inflammation, and nodule formation. The study also showed that Elac2 mutation exacerbated the onset and progression of prostate cancer in transgenic mice models.
EMBO MOLECULAR MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
So-Young Seol, Gi-Eun Yang, Yoon Cho, Min Chan Kim, Hong-Jo Choi, Yung Hyun Choi, Sun-Hee Leem
Summary: This study found a significant association between rare alleles of MUC2-MS8 and the occurrence of rectal cancer, especially increasing the risk in the younger population. Additionally, the study showed that the repeat region of MUC2-MS8 is related to genomic instability, further emphasizing its potential role in cancer susceptibility.
Article
Oncology
Benjamin L. Lampson, Aditi Gupta, Svitlana Tyekucheva, Kiyomi Mashima, Anna Petrackova, Zixu Wang, Natalia Wojciechowska, Conner J. Shaughnessy, Peter O. Baker, Stacey M. Fernandes, Samantha Shupe, John-Hanson Machado, Rayan Fardoun, Annette S. Kim, Jennifer R. Brown
Summary: Germline missense variants of unknown significance in the ATM gene are more frequent in CLL patients and influence the clinical characteristics of CLL, such as 11q deletion. These variants cluster within CLL, affect its phenotype, and have functional significance.
JOURNAL OF CLINICAL ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Yuyan Qian, Jianhu Wang, Wenbin wANG, Peng li, Zhenhao Zhao, Yuan Jiang, Dandan Huang, He Ren, Yang Yang, Zhongfan Zhao, Lei Zhang, Jiandan Shi, Mulin Jun, Wangee Li
Summary: Using fine-mapping analysis and functional annotation, we identified likely causal variants and their target genes in prostate cancer. We found 3,395 potential disease-causing variants and linked them to 487 target genes through functional annotation. The top-ranked SNP, rs10486567, was predicted to regulate the HOTTIP gene. Deletion of the enhancer associated with rs10486567 reduced invasive migration in prostate cancer cells, which was rescued by HOTTIP overexpression in enhancer-deficient cells. Furthermore, rs10486567 was found to regulate HOTTIP through allele-specific long-range chromatin interaction.
Article
Biochemistry & Molecular Biology
Saadat Hussain, Nori Sadouni, Dominic van Essen, Lan T. M. Dao, Quentin Ferre, Guillaume Charbonnier, Magali Torres, Frederic Gallardo, Charles-Henri Lecellier, Tom Sexton, Simona Saccani, Salvatore Spicuglia
Summary: This study uses the STARR-seq method to identify and characterize silencer elements in mammals. The identified silencers are associated with chromatin marks and known transcriptional repressors, and are involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Additionally, the study reveals the role of short tandem repeats in silencer activity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Amber A. DeVries, Joe Dennis, Jonathan P. Tyrer, Pei-Chen Peng, Simon G. Coetzee, Alberto L. Reyes, Jasmine T. Plummer, Brian D. Davis, Stephanie S. Chen, Felipe Segato Dezem, Katja K. H. Aben, Hoda Anton-Culver, Natalia N. Antonenkova, Matthias W. Beckmann, Alicia Beeghly-Fadiel, Andrew Berchuck, Natalia Bogdanova, Nadja Bogdanova-Markov, James D. Brenton, Ralf Butzow, Ian Campbell, Jenny Chang-Claude, Georgia Chenevix-Trench, Linda S. Cook, Anna DeFazio, Jennifer A. Doherty, Thilo Dork, Diana M. Eccles, A. Heather Eliassen, Peter A. Fasching, Renee T. Fortner, Graham G. Giles, Ellen L. Goode, Marc T. Goodman, Jacek Gronwald, Niclas Hakansson, Michelle A. T. Hildebrandt, Chad Huff, David G. Huntsman, Allan Jensen, Siddhartha Kar, Beth Y. Karlan, Elza K. Khusnutdinova, Lambertus A. Kiemeney, Susanne K. Kjaer, Jolanta Kupryjanczyk, Marilyne Labrie, Diether Lambrechts, Nhu D. Le, Jan Lubinski, Taymaa May, Usha Menon, Roger L. Milne, Francesmary Modugno, Alvaro N. Monteiro, Kirsten B. Moysich, Kunle Odunsi, Hakan Olsson, Celeste L. Pearce, Tanja Pejovic, Susan J. Ramus, Elio Riboli, Marjorie J. Riggan, Isabelle Romieu, Dale P. Sandler, Joellen M. Schildkraut, V. Wendy Setiawan, Weiva Sieh, Honglin Song, Rebecca Sutphen, Kathryn L. Terry, Pamela J. Thompson, Linda Titus, Shelley S. Tworoger, Els Van Nieuwenhuysen, Digna Velez Edwards, Penelope M. Webb, Nicolas Wentzensen, Alice S. Whittemore, Alicja Wolk, Anna H. Wu, Argyrios Ziogas, Matthew L. Freedman, Kate Lawrenson, Paul D. P. Pharoah, Douglas F. Easton, Simon A. Gayther, Michelle R. Jones
Summary: This study identified risk associations between copy number variants (CNVs) and epithelial ovarian cancer (EOC), particularly for the BRCA1, BRCA2, and RAD51C genes. The study also found enrichment of CNVs at known EOC risk loci and functional biofeatures in EOC-related cell types. These findings suggest that CNVs may play a potentially pathogenic role in the development of EOC.
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2022)
Article
Multidisciplinary Sciences
Mengyi Song, Xuefei Yuan, Claudia Racioppi, Meaghan Leslie, Nathan Stutt, Anastasiia Aleksandrova, Lionel Christiaen, Michael D. Wilson, Ian C. Scott
Summary: GATA4/5/6 transcription factors are crucial for heart development and regulate the transition from mesoderm to cardiac fate. Loss of Gata5/6 alters the population structure of mesendoderm-derived cells and leads to extensive changes in chromatin accessibility near cardiac and pharyngeal genes.
Article
Microbiology
Sung Ho Yun, Sang-Yeop Lee, Chi-Won Choi, Hayoung Lee, Hyun-Joo Ro, Sangmi Jun, Yong Min Kwon, Kae Kyoung Kwon, Sang-Jin Kim, Gun-Hwa Kim, Seung Il Kim
JOURNAL OF MICROBIOLOGY
(2017)
Correction
Multidisciplinary Sciences
Sang-Yeop Lee, Gun-Hwa Kim, Sung Ho Yun, Chi-Won Choi, Yoon-Sun Yi, Jonghyun Kim, Young-Ho Chung, Edmond Changkyun Park, Seung Il Kim
Article
Immunology
Chi-Won Choi, Edmond Changkyun Park, Sung Ho Yun, Sang-Yeop Lee, Seung Il Kim, Gun-Hwa Kim
JOURNAL OF IMMUNOLOGY RESEARCH
(2017)
Article
Biochemical Research Methods
Edmond Changkyun Park, Jae Sung Lim, Seung Il Kim, Sang-Yeop Lee, Yu-Kyung Tak, Chi-Won Choi, Sungho Yun, Joohyun Park, Minji Lee, Hyo Kyun Chung, Koon Soon Kim, Yong Gil Na, Ju Hyun Shin, Gun-Hwa Kim
MOLECULAR & CELLULAR PROTEOMICS
(2018)
Article
Biochemical Research Methods
Edmond Changkyun Park, Sang-Yeop Lee, Sung Ho Yun, Chi-Won Choi, Hayoung Lee, Hyun Seok Song, Sangmi Jun, Gun-Hwa Kim, Chang-Seop Lee, Seung Il Kim
CLINICAL PROTEOMICS
(2018)
Article
Infectious Diseases
Sang-Yeop Lee, Man Hwan Oh, Sung Ho Yun, Chi-Won Choi, Edmond Changkyun Park, Hyun Seok Song, Hayoung Lee, Yoon-Sun Yi, Juhyun Shin, Chaeuk Chung, Jae Young Moong, Je Chul Lee, Gun-Hwa Kim, Seung Il Kim
INFECTION GENETICS AND EVOLUTION
(2018)
Article
Multidisciplinary Sciences
Sang-Yeop Lee, Gun-Hwa Kim, Sung Ho Yun, Chi-Won Choi, Yoon-Sun Yi, Jonghyun Kim, Young-Ho Chung, Edmond Changkyun Park, Seung Il Kim
Article
Biochemical Research Methods
Sung Ho Yun, Edmond Changkyun Park, Sang-Yeop Lee, Hayoung Lee, Chi-Won Choi, Yoon-Sun Yi, Hyun-Joo Ro, Je Chul Lee, Sangmi Jun, Hye-Yeon Kim, Gun-Hwa Kim, Seung Il Kim
CLINICAL PROTEOMICS
(2018)
Article
Chemistry, Multidisciplinary
Sang-Yeop Lee, Sung Ho Yun, Hayoung Lee, Yoon-Sun Yi, Edmond Changkyun Park, Wooyoung Kim, Hye-Yeon Kim, Je Chul Lee, Gun-Hwa Kim, Seung Il Kim
Article
Multidisciplinary Sciences
Sang-Yeop Lee, Hayoung Lee, Sung Ho Yun, Sangmi Jun, Yujeong Lee, Wooyoung Kim, Edmond Changkyun Park, Joonyoung Baek, Yoonna Kwak, Soojin Noh, Giwan Seo, Soojin Jang, Chul Min Park, Seung Il Kim
SCIENTIFIC REPORTS
(2020)
Article
Genetics & Heredity
Min-Hye Kim, Gi-Eun Yang, Mi-So Jeong, Jeong-Yeon Mun, Sang-Yeop Lee, Jong-Kil Nam, Yung Hyun Choi, Tae Nam Kim, Sun-Hee Leem
Summary: The study identified a VNTR in the breakpoint region of the ABL1 gene, named ABL1-MS1, and found a significant association between the rare ABL1-MS1 allele and bladder cancer risk. The VNTR region was shown to inhibit ABL1 expression in non-cancer cells but not in bladder cancer cells, providing insights into the mechanisms of tumor development. Additionally, the accurate transmission of ABL1-MS1 through Mendelian inheritance suggests its potential as a DNA fingerprinting marker for predicting susceptibility to bladder cancer.
BMC MEDICAL GENOMICS
(2021)
Article
Microbiology
Hayoung Lee, Sung Ho Yun, Ju-yong Hyon, Sang-Yeop Lee, Yoon-Sun Yi, Chi-Won Choi, Sangmi Jun, Edmond Changkyun Park, Seung Il Kim
Summary: The study demonstrates the potential of Streptococcus equi-derived extracellular vesicles (EVs) as a vaccine candidate against S. equi infection, showing improved survival rates in mice and containing various immunogenic antigens within the EV proteome.
VETERINARY MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hayoung Lee, Sung Ho Yun, Ju-yong Hyon, Sang-Yeop Lee, Yoon-Sun Yi, Chi-Won Choi, Sangmi Jun, Edmond Changkyun Park, Seung Il Kim
Summary: This study provides a dataset associated with the research publication on Streptococcus equi-derived extracellular vesicles as a vaccine candidate against Streptococcus equi infections, describing genomic differences and proteome information. The proteomics data were analyzed using shotgun proteomics with mass spectrometry, and the acquired data has been deposited in the PRIDE public repository.
Article
Spectroscopy
Sang-Yeop Lee, Sung Ho Yun, Geul Bang, Chang-Seop Lee, Seung Il Kim
Summary: The shotgun proteomic analysis revealed RsmD as a potential biomarker of Orientia tsutsugamushi in the sera of scrub typhus patients.
MASS SPECTROMETRY LETTERS
(2021)
Article
Chemistry, Analytical
Sang-Yeop Lee, Sung Ho Yun, Hayoung Lee, Giwan Seo, Seung Il Kim
Summary: The genome analysis of Delftia sp. K82 was completed, and using multi-omics approaches, complete gene clusters for aniline biodegradation pathways were identified, highlighting the usefulness of these tools for understanding metabolic diversity in soil bacteria.
JOURNAL OF ANALYTICAL SCIENCE AND TECHNOLOGY
(2021)