Review
Biochemistry & Molecular Biology
Beata Anna Nowakowska, Katarzyna Pankiewicz, Urszula Nowacka, Magdalena Niemiec, Szymon Kozlowski, Tadeusz Issat
Summary: This review presents the current state of knowledge about the genetic disturbances responsible for fetal growth restriction (FGR) diagnosis, and discusses the fetal, placental, and maternal causes, as well as their impact on prenatal diagnostics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Zoe Andrijanic, Nelson Nazzicari, Hrvoje Sarcevic, Aleksandra Sudaric, Paolo Annicchiarico, Ivan Pejic
Summary: This study investigates the genetic diversity and structure of European soybean cultivars and American introductions registered in Europe, supporting optimal exploitation of genetic resources. Results show that the European soybean gene pool still has sufficient diversity due to differences in historical breeding practices and relatively short breeding period in Europe.
Article
Pharmacology & Pharmacy
Chiara Casotti, Claudia Maria Hattinger, Maria Pia Patrizio, Silvia Luppi, Leonardo Fantoni, Michela Pasello, Katia Scotlandi, Toni Ibrahim, Massimo Serra
Summary: In this study, an innovative mmNGS approach was used to investigate SNPs associated with MTX resistance in HGOS cell lines. The results showed that allele changes in TP53, SLC19A1, and MTHFR were functionally involved in the development of MTX resistance. In addition, a fusion transcript of DHFR and MSH3 was identified in the cells with the highest MTX resistance level.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Duo Chen, Wanting Huang, Yun Zhang, Bo Chen, Jie Tan, Quan Yuan, Yanbing Yang
Summary: Mass pathogen screening is crucial in preventing outbreaks and transmission of infectious diseases. A CRISPR-based Amplification-free Viral RNA Electrical Detection platform (CAVRED) is developed for rapid identification of SARS-CoV-2 variants. CAVRED utilizes CRISPR RNA assays to amplify the CRISPR-Cas system's ability to detect single-nucleotide differences between mutant and wild RNA genomes. With highly sensitive field-effect transistor biosensors, CAVRED can detect SARS-CoV-2 virus genome as low as 1 cp mu L-1 within 20 mins without amplification, offering a comparable detection limit to real-time quantitative polymerase chain reaction. An 8-in-1 CAVRED array achieves 95.0% accuracy in rapid identification of 40 simulated throat swab samples of SARS-CoV-2 variants, promising its application in rapid and large-scale epidemic screening.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Plant Sciences
Xi-ou Xiao, Ning Zhang, Hui Jin, Huaijun Si
Summary: This study evaluated the genetic diversity and population structure of 135 autotetraploid potatoes using SLAF-seq methods. Analysis of 3,397,137 high-quality SNPs revealed that the classification of these potatoes based on SNP profiles did not correlate with their geographical origins. Furthermore, 71 PARMS-SNP markers were successfully used to analyze 190 autotetraploid potato varieties. Overall, these novel SNP markers provide a solid foundation for potato genetic diversity analysis, DUS testing, and plant variety protection.
Article
Biochemistry & Molecular Biology
Justyna Basak, Danuta Piotrzkowska, Ireneusz Majsterek, Ewa Kucharska
Summary: Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system with no cure and unclear etiology. This study aimed to identify SNPs associated with an increased risk of developing MS. The findings suggest that the GG AGO1 rs636832 and AA GEMIN4 rs7813 genotypes are associated with an increased risk of MS.
Article
Chemistry, Analytical
Salvatore Petralia, Antonella Vigilanza, Emanuele Sciuto, Michele Maffia, Antonella Romanini, Sabrina Conoci
Summary: The study investigated single nucleotide polymorphisms in the MC1R gene using a miniaturized silicon-based microarray-chip, showing good sensitivity and high confidence level, paving the way for future development of portable genetic assays.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Plant Sciences
Mbali Thembi Gumede, Abe Shegro Gerrano, Assefa Beyene Amelework, Albert Thembinkosi Modi
Summary: This study assessed the genetic diversity and population structure of 90 cowpea accessions using SNP markers. The results showed that cowpea has high tolerance to heat and drought stresses, making it important for improving crop production resilience. The study also revealed low genetic diversity and high homozygosity among cowpea accessions.
Article
Biotechnology & Applied Microbiology
Mozhdeh Moosanezhad Khabisi, Masood Asadi Foozi, Feng-Hua Lv, Ali Esmailizadeh
Summary: Sheep were originally domesticated in the northwest of Iran, where a variety of native sheep breeds with coarse wool characteristics can be found. Iranian sheep exhibit high genetic diversity with low differentiation between populations, and show genetic connections with sheep breeds from other regions.
Article
Genetics & Heredity
Misteru Tesfaye, Tileye Feyissa, Teklehaimanot Hailesilassie, Selvaraju Kanagarajan, Li-Hua Zhu
Summary: This study investigated the genetic diversity and population structure of Ethiopian mustard (Brassica carinata) genotypes of different origins using high-throughput single nucleotide polymorphism (SNP) markers. The results revealed two distinct subpopulations, with the majority of accessions clustered in one subpopulation mainly obtained from specific regions. The analysis showed high genetic variation within populations and low genetic differentiation between populations, indicating the presence of gene flow and weak geographical structure. The study provides important information for future breeding and conservation efforts of B. carinata.
Article
Biochemistry & Molecular Biology
Danial Jahantigh, Saeedeh Ghazaey Zidanloo, Seyedeh Zahra Moossavi, Forough Forghani
Summary: Functional single nucleotide polymorphisms (SNPs) in the IL-12B gene can significantly affect protein expression or modify its functions, potentially leading to immune disorders. The relationship between common IL-12B SNPs and the risk of preeclampsia (PE) has been unclear. A case-control study genotyped 253 PE patients and 250 healthy subjects for IL-12B rs3212227 and IL-12B rs6887695 SNPs. In-silico analysis was also conducted to assess the potential functions of these polymorphisms. The results showed an association between the rs3212227 variation in the IL-12B gene and susceptibility to PE. The rs6887695 SNP correlated negatively with PE development and had a protective effect on PE risk. The study also found certain haplotypes of IL-12B to be more prevalent in PE patients.
Article
Medicine, General & Internal
Shaowei Jiang, Yang Wang, Liang Chen, Honghua Mu, Connor Meaney, Yiwen Fan, Janesh Pillay, Hairong Wang, Jincheng Zhang, Shuming Pan, Chengjin Gao
Summary: This study investigates the associations among serum levels of PAI-1, PAI-1 gene polymorphisms, immunological indicators, and clinical outcomes in septic patients. The results suggest that genetic polymorphisms of PAI-1 can affect serum levels of PAI-1, which in turn may influence mortality by affecting neutrophil activity.
CHINESE MEDICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Claudia Maria Hattinger, Chiara Casotti, Maria Pia Patrizio, Silvia Luppi, Leonardo Fantoni, Katia Scotlandi, Toni Ibrahim, Massimo Serra
Summary: This study investigated the relationship between SNPs and CDDP resistance in high-grade osteosarcoma cells, providing a basis for further research on the topic.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Lovepreet Singh, Yanqi Wu, James D. McCurdy, Barry R. Stewart, Marilyn L. Warburton, Brian S. Baldwin, Hongxu Dong
Summary: This study investigated the genetic diversity of 206 bermudagrass accessions using genetic markers. Four subpopulations were identified, indicating a high level of genetic variation in bermudagrass. These findings provide valuable resources for further breeding programs and cultivar development.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Oncology
Huitong Chen, Qian Guan, Huiqin Guo, Lei Miao, Zhenjian Zhuo
Summary: Hepatoblastoma, the most common malignant liver cancer in childhood, is believed to have genetic predisposition, although specific exposures or genetic events related to its occurrence are still unclear. Recent advances in understanding the genetic changes underlying hepatoblastoma may lead to improved patient outcomes. Single nucleotide polymorphisms (SNPs) have been widely used in researching etiology, disease treatment, and prognosis assessment for hepatoblastoma.
FRONTIERS IN ONCOLOGY
(2021)
Article
Hematology
Maximilian Stahl, Andriy Derkach, Noushin Farnoud, Jan Philipp Bewersdorf, Troy Robinson, Christopher Famulare, Christina Cho, Sean Devlin, Kamal Menghrajani, Minal A. Patel, Sheng F. Cai, Linde A. Miles, Robert L. Bowman, Mark B. Geyer, Andrew Dunbar, Zachary D. Epstein-Peterson, Erin McGovern, Jessica Schulman, Jacob L. Glass, Justin Taylor, Aaron D. Viny, Eytan M. Stein, Bartlomiej Getta, Maria E. Arcila, Qi Gao, Juliet Barker, Brian C. Shaffer, Esperanza B. Papadopoulos, Boglarka Gyurkocza, Miguel-Angel Perales, Omar Abdel-Wahab, Ross L. Levine, Sergio A. Giralt, Yanming Zhang, Wenbin Xiao, Nidhi Pai, Elli Papaemmanuil, Martin S. Tallman, Mikhail Roshal, Aaron D. Goldberg
Summary: Measurable residual disease (MRD) is a powerful prognostic factor in acute myeloid leukemia (AML). This study aims to identify pre-treatment molecular predictors of immunophenotypic MRD clearance in AML patients. The results showed that induction chemotherapy led to different MRD responses, with 35% achieving MRD- remission, 27% achieving MRD+ remission, and 38% having persistent disease. Subsequent therapy resulted in MRD conversion in 34% of MRD+ patients and 26% of patients with persistent disease. Specific gene mutations and karyotypic abnormalities were found to be associated with high or low rates of MRD- remission. Patients with fewer individual clones were more likely to achieve MRD- remission. Furthermore, the study demonstrated that achieving MRD- prior to allogeneic stem cell transplant (allo-SCT) was associated with favorable outcomes. Therefore, the inclusion of patients with specific baseline mutational patterns and high clone numbers in clinical trials should be considered.
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Article
Hematology
Hideki Makishima, Ryunosuke Saiki, Yasuhito Nannya, Sophia Korotev, Carmelo Gurnari, June Takeda, Yukihide Momozawa, Steve Best, Pramila Krishnamurthy, Tetsuichi Yoshizato, Yoshiko Atsuta, Yusuke Shiozawa, Yuka Iijima-Yamashita, Kenichi Yoshida, Yuichi Shiraishi, Yasunobu Nagata, Nobuyuki Kakiuchi, Makoto Onizuka, Kenichi Chiba, Hiroko Tanaka, Ayana Kon, Yotaro Ochi, Masahiro M. Nakagawa, Rurika Okuda, Takuto Mori, Akinori Yoda, Hidehiro Itonaga, Yasushi Miyazaki, Masashi Sanada, Takayuki Ishikawa, Shigeru Chiba, Hisashi Tsurumi, Senji Kasahara, Carsten Mueller-Tidow, Akifumi Takaori-Kondo, Kazuma Ohyashiki, Toru Kiguchi, Fumihiko Matsuda, Joop H. Jansen, Chantana Polprasert, Piers Blombery, Yoichiro Kamatani, Sator Miyano, Luca Malcovati, Torsten Haferlach, Michiaki Kubo, Mario Cazzola, Austin G. Kulasekararaj, Lucy A. Godley, Jaroslaw P. Maclejewski, Seishi Ogawa
Summary: DDX41 gene mutations play an important role in late-onset myeloid neoplasms, but many crucial features of DDX41-mutated neoplasms still need to be elucidated. This study comprehensively characterized DDX41-mutated neoplasms and found that DDX41 risk variants accounted for 80% of known genetic predispositions to myeloid neoplasms in adults. Additionally, DDX41 risk alleles were significantly enriched in Japanese cases and more prominent in males compared to females.
Review
Oncology
Takahiko Yasuda, Masashi Sanada, Shinobu Tsuzuki, Fumihiko Hayakawa
Summary: B-cell acute lymphoblastic leukemia (B-ALL) is a genetically heterogeneous disease that can be classified into different molecular subtypes based on genetic alterations. Recent advances in sequencing technology have uncovered B-ALL molecular subtypes prevalent in adolescents and adults. These findings provide more precise prognostic estimations and personalized treatment options, as well as a deeper understanding of the genetic basis of B-ALL in these age groups.
Letter
Oncology
Kentaro Ohki, Ellie R. Butler, Nobutaka Kiyokawa, Shinsuke Hirabayashi, Anke K. Bergmann, Anja Moericke, Judith M. Boer, Helene Cave, Giovanni Cazzaniga, Allen Eng Juh Yeoh, Masashi Sanada, Toshihiko Imamura, Hiroto Inaba, Charles G. Mullighan, Mignon L. Loh, Ulrika Noren-Nystrom, Lee-Yung Shih, Marketa Zaliova, Ching-Hon Pui, Oskar A. Haas, Christine J. Harrison, Anthony V. Moorman, Atsushi Manabe
Article
Oncology
Koya Odaira, Takahiko Yasuda, Kentaro Okada, Takuya Shimooka, Yukino Kojima, Mina Noura, Shogo Tamura, Shingo Kurahashi, Eisuke Iwamoto, Masashi Sanada, Itaru Matsumura, Yasushi Miyazaki, Tetsuhito Kojima, Hitoshi Kiyoi, Shinobu Tsuzuki, Fumihiko Hayakawa
Summary: This study found that the fusion gene CEBPA-IGH suppresses the target genes of MEF2s, promoting the development of CEBPA-IGH-positive B-ALL.
Article
Oncology
Lindsay M. Gurska, Rachel Okabe, Alexandra Schurer, Meng Maxine Tong, Mark Soto, Daniel Choi, Kristina Ames, Shira Glushakow-Smith, Allison Montoya, Ellen Tein, Linde A. Miles, Haiying Cheng, Pamela Hankey-Giblin, Ross L. Levine, Swati Goel, Balazs Halmos, Kira Gritsman
Summary: The study found that crizotinib could suppress the activation of the JAK/STAT signaling pathway and decrease the disease burden of MPN. Additionally, crizotinib could overcome the persistence of JAK inhibitors by disrupting the interaction between RON kinase and JAK2. This research suggests that crizotinib should be further explored as a potential treatment for patients with MPN.
CLINICAL CANCER RESEARCH
(2023)
Article
Pharmacology & Pharmacy
Thao Thu Thi Nguyen, Yoichi Tanaka, Masashi Sanada, Masumi Hosaka, Minori Tamai, Keiko Kagami, Chiaki Komatsu, Shinpei Somazu, Daisuke Harama, Shin Kasai, Atsushi Watanabe, Koushi Akahane, Kumiko Goi, Takeshi Inukai
Summary: 6-mercaptopurine is an essential component in the maintenance therapy for childhood acute lymphoblastic leukemia. Recent sequencing analysis has identified relapse-specific mutations in the NT5C2 and PRPS1 genes, which are involved in thiopurine metabolism. The development of human leukemia models with these mutations is urgently needed to establish new therapeutic strategies for overcoming 6-mercaptopurine resistance in relapsed ALL.
MOLECULAR PHARMACOLOGY
(2023)
Article
Multidisciplinary Sciences
Jerome Fortin, Ming-Feng Chiang, Cem Meydan, Jonathan Foox, Parameswaran Ramachandran, Julie Leca, Francois Lemonnier, Wanda Y. Li, Miki S. Gams, Takashi Sakamoto, Mandy Chu, Chantal Tobin, Eric Laugesen, Troy M. Robinson, Annick You-Ten, Daniel J. Butler, Thorsten Berger, Mark D. Minden, Ross L. Levine, Cynthia J. Guidos, Ari M. Melnick, Christopher E. Mason, Tak W. Maka
Summary: Mutations in IDH1, IDH2, and TET2 genes are commonly observed in myeloid neoplasms. These mutations have unexpected, distinct effects on hematopoietic stem and progenitor cells, contrary to previous expectations. Understanding these molecular alterations could lead to the development of more effective, genotype-specific therapies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Editorial Material
Oncology
Troy M. Robinson, Ross L. Levine
Summary: In this study, the researchers used mass spectrometry metabolomics, stable isotope labeling, and functional studies to investigate metabolic vulnerabilities in cancers with mutations in isocitrate dehydrogenase (IDH). They provide compelling evidence that dysregulated lipid synthesis is a synthetic lethal target in cancers with IDH1 mutations, but not IDH2 mutations.
Article
Hematology
Andrew J. Dunbar, Dongjoo Kim, Min Lu, Mirko Farina, Robert L. Bowman, Julie L. Yang, Young Park, Abdul Karzai, Wenbin Xiao, Zach Zaroogian, Kavi O'Connor, Shoron Mowla, Francesca Gobbo, Paola Verachi, Fabrizio Martelli, Giuseppe Sarli, Lijuan Xia, Nada Elmansy, Maria Kleppe, Zhuo Chen, Yang Xiao, Erin McGovern, Jenna Snyder, Aishwarya Krishnan, Corrine Hill, Keith Cordner, Anouar Zouak, Mohamed E. Salama, Jayden Yohai, Eric Tucker, Jonathan Chen, Jing Zhou, Timothy McConnell, Anna R. Migliaccio, Richard Koche, Raajit Rampal, Rong Fan, Ross L. Levine, Ronald Hoffman
Summary: Inflammatory signaling is crucial in the development of myelofibrosis (MF), a type of cancer. Recent studies have identified the involvement of JAK/STAT and NF-kappa B signaling in MF progression. This study further explores the role of CXCL8/CXCR2 signaling in MF pathogenesis, and highlights its potential as a therapeutic target.
Article
Oncology
Vu H. Duong, Amy S. Ruppert, Alice S. Mims, Uma Borate, Eytan M. Stein, Maria R. Baer, Wendy Stock, Tibor Kovacsovics, William Blum, Martha L. Arellano, Gary J. Schiller, Rebecca L. Olin, James M. Foran, Mark R. Litzow, Tara L. Lin, Prapti A. Patel, Matthew C. Foster, Robert L. Redner, Zeina Al-Mansour, Christopher R. Cogle, Ronan T. Swords, Robert H. Collins, Jo-Anne Vergilio, Nyla A. Heerema, Leonard Rosenberg, Ashley O. Yocum, Sonja Marcus, Timothy Chen, Franchesca Druggan, Mona Stefanos, Theophilus J. Gana, Abigail B. Shoben, Brian J. Druker, Amy Burd, John C. Byrd, Ross L. Levine, Michael M. Boyiadzis
Summary: This study evaluated the efficacy of entospletinib, an oral inhibitor of spleen tyrosine kinase, combined with decitabine in patients with acute myeloid leukemia (AML) who have poor prognosis. The combination showed some activity and acceptable tolerance, but the complete remission rates were low and overall survival was short.
Article
Endocrinology & Metabolism
Laura Boucai, Ryan N. Ptashkin, Ross L. Levine, James A. Fagin
Summary: In this prospective cohort study, the effects of therapeutic radioactive iodine (RAI) on clonal hematopoiesis (CH) were examined. The results showed no increase in CH in patients treated with RAI over a 2-year follow-up period. It was also found that the presence of CH was associated with worse structural progression in both BRAFV600E-mutant and wild-type thyroid cancers.
CLINICAL ENDOCRINOLOGY
(2023)
Article
Multidisciplinary Sciences
Florian Perner, Eytan M. M. Stein, Daniela V. V. Wenge, Sukrit Singh, Jeonghyeon Kim, Athina Apazidis, Homa Rahnamoun, Disha Anand, Christian Marinaccio, Charlie Hatton, Yanhe Wen, Richard M. M. Stone, David Schaller, Shoron Mowla, Wenbin Xiao, Holly A. A. Gamlen, Aaron J. J. Stonestrom, Sonali Persaud, Elizabeth Ener, Jevon A. A. Cutler, John G. G. Doench, Gerard M. M. McGeehan, Andrea Volkamer, John D. D. Chodera, Radoslaw P. Nowak, Eric S. S. Fischer, Ross L. L. Levine, Scott A. A. Armstrong, Sheng F. F. Cai
Summary: Chromatin-binding proteins are important regulators of cell state in haematopoiesis. Clinical trials have shown that the menin inhibitor revumenib can treat leukaemia with KMT2Ar or NPM1 mutations. However, acquired resistance to menin inhibition may be caused by somatic mutations in the MEN1 gene.
Article
Biochemistry & Molecular Biology
Pablo Sanchez Vela, Jennifer J. J. Trowbridge, Ross L. L. Levine
Summary: New data reveals the surprising association between clonal hematopoiesis and protection from Alzheimer's disease, highlighting the need for future studies to unravel the complex mechanisms underlying the role of clonal hematopoiesis in tissue-disease contexts and aging-associated diseases.
Article
Hematology
Umeshkumar Vekariya, Monika Toma, Margaret Nieborowska-Skorska, Bac Viet Le, Marie-Christine Caron, Anna-Mariya Kukuyan, Katherine Sullivan-Reed, Paulina Podszywalow-Bartnicka, Kumaraswamy N. Chitrala, Jessica Atkins, Malgorzata Drzewiecka, Wanjuan Feng, Joe Chan, Srinivas Chatla, Konstantin Golovine, Jaroslav Jelinek, Tomasz Sliwinski, Jayashri Ghosh, Ksenia Matlawska-Wasowska, Gurushankar Chandramouly, Reza Nejati, Mariusz Wasik, Stephen M. Sykes, Katarzyna Piwocka, Emir Hadzijusufovic, Peter Valent, Richard T. Pomerantz, George Morton, Wayne Childers, Huaqing Zhao, Elisabeth M. Paietta, Ross L. Levine, Martin S. Tallman, Hugo F. Fernandez, Mark R. Litzow, Gaorav P. Gupta, Jean-Yves Masson, Tomasz Skorski
Summary: Leukemia cells accumulate DNA damage, but altered DNA repair mechanisms protect them from apoptosis. Formaldehyde generated by serine/1-carbon cycle metabolism contributes to the accumulation of toxic DNA-protein crosslinks (DPCs) in leukemia cells. Oncogenic tyrosine kinases (OTKs) enhance the expression of DNA polymerase theta (POL theta) to repair DPC-containing DNA double-strand breaks. Inhibition of POL theta can be an effective therapeutic strategy for leukemia.