Article
Cell Biology
Peng Zhao, Jianhua Cheng, Bin Li, Ding Nie, Chuzhong Li, Songbai Gui, Hongyun Wang, Yazhuo Zhang
Summary: This study demonstrated that miR-149 and miR-99a-3p induced by exosomes could suppress the progression of IPA. The miRNAs were significantly inhibited in pituitary adenoma cells and tissues, and played inhibitory roles in cell proliferation, metastasis, and angiogenesis.
CELL BIOLOGY AND TOXICOLOGY
(2021)
Article
Genetics & Heredity
Elena N. Voropaeva, Tatjana Pospelova, Yuriy L. Orlov, Maria Churkina, Olga Berezina, Anna A. Gurazheva, Tatjana A. Ageeva, Olga B. Seregina, Vladimir N. Maksimov
Summary: This study investigated the methylation status of MIR-203, MIR-129-2, MIR-34A, and MIR-34B/C genes in diffuse large B-cell lymphoma (DLBCL) tumor tissue. The results showed that the methylation of these genes is frequent in DLBCL and associated with prognosis and treatment response.
Article
Genetics & Heredity
Yoshiaki Shinden, Tadahiro Hirashima, Nijiro Nohata, Hiroko Toda, Reona Okada, Shunichi Asai, Takako Tanaka, Yuto Hozaka, Takao Ohtsuka, Yuko Kijima, Naohiko Seki
Summary: Our recent research identified certain passenger strands of miRNAs that function as tumor-suppressive miRNAs in cancer cells, and analyzed the miRNA expression signature of breast cancer (BrCa) to identify oncogenic genes controlled by pre-miR-99a. The study revealed FAM64A as a potential target and highlighted the importance of aberrant expression of FAM64A in the malignant transformation of BrCa.
JOURNAL OF HUMAN GENETICS
(2021)
Article
Medicine, Research & Experimental
Jiabin Deng, Yinqiu Li, Jiaqian Song, Fei Zhu
Summary: TUG1 regulates the migration and invasion of melanoma cells through the miR-145-5p/SOX2 axis.
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2022)
Article
Multidisciplinary Sciences
Pasquale Piccolo, Rosa Ferriero, Anna Barbato, Sergio Attanasio, Marcello Monti, Claudia Perna, Florie Borel, Patrizia Annunziata, Annamaria Carissimo, Rossella De Cegli, Luca Quagliata, Luigi M. Terracciano, Chantal Housset, Jeffrey H. Teckman, Christian Mueller, Nicola Brunetti-Pierri
Summary: AAT deficiency is caused by pathogenic variants in the SERPINA1 gene, with the Z allele encoding for Z alpha 1-antitrypsin leading to hepatotoxic polymers. The up-regulation of miR-34b/c in PiZ mouse livers is correlated to intrahepatic ATZ, and its expression is dependent on JNK phosphorylation on Ser574. Deletion of miR-34b/c in PiZ mice results in early liver fibrosis and increased signaling of platelet-derived growth factor.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Krzysztof Kozniewski, Michal Wasowski, Marta Izabela Jonas, Wojciech Lisik, Maurycy Jonas, Artur Binda, Pawel Jaworski, Wieslaw Tarnowski, Bartlomiej Noszczyk, Monika Puzianowska-Kuznicka, Alina Kurylowicz
Summary: Obesity-related downregulation of ER mRNA levels in adipose tissue might be associated with miRNA interference.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Huangkai Zhu, Xiang Xu, Enkuo Zheng, Junjun Ni, Xu Jiang, Minglei Yang, Guofang Zhao
Summary: This study aimed to elucidate the molecular mechanism of lncRNA RP11-805J14.5 in LUAD development. The study found that RP11-805J14.5 was highly expressed in LUAD tissues and cells and was associated with poor prognosis in LUAD patients. Knockdown of RP11-805J14.5 suppressed LUAD cell growth, invasion, migration, and tumor growth, indicating that RP11-805J14.5 is an important regulator in LUAD.
Article
Marine & Freshwater Biology
Jason T. Magnuson, Rachel R. Leads, Victoria McGruer, Le Qian, Philip Tanabe, Aaron P. Roberts, Daniel Schlenk
Summary: The global sequencing of microRNA (miRNA) and mRNA expression profiles in fish exposed to crude oil revealed consistently dysregulated miRNAs with predicted roles in cardiovascular, neurological, and visually-mediated pathways. Two miRNAs, miR-203a and miR-34b, were found to be primary targets of crude oil. Inhibition of miR-203a and overexpression of miR-34b resulted in neurological and eye toxicity responses similar to those caused by oil exposure.
AQUATIC TOXICOLOGY
(2023)
Article
Cell Biology
Zheng Peng, Yi Zhang, Dazun Shi, Yanyan Jia, Huirong Shi, Huining Liu
Summary: SALL4 interacts with miR-497-5p, affecting the survival period and stem cell properties of choriocarcinoma patients, and subsequently influences the malignant phenotype of cancer cells through regulating DNMT-mediated epigenetic regulation. SALL4 plays a key role in choriocarcinoma, while silencing miR-497-5p and SALL4 promotes the progression of choriocarcinoma.
CELL DEATH & DISEASE
(2021)
Article
Biotechnology & Applied Microbiology
Jun-Hong Hu, Hong-Na Tang, Yu-Hang Wang
Summary: This study reveals that CAFs-exo promotes EMT progression and chemoresistance in CRC cells by secreting LINC00355. Further investigation demonstrates that CAFs-exo-derived LINC00355 enhances the expression of CRKL by inhibiting miR-34b-5p, thereby enhancing chemoresistance and promoting EMT in CRC cells.
CANCER GENE THERAPY
(2023)
Review
Cell Biology
Emilio Francesco Giunta, Gianluca Arrichiello, Marcello Curvietto, Annalisa Pappalardo, Davide Bosso, Mario Rosanova, Anna Diana, Pasqualina Giordano, Angelica Petrillo, Piera Federico, Teresa Fabozzi, Sara Parola, Vittorio Riccio, Brigitta Mucci, Vito Vanella, Lucia Festino, Bruno Daniele, Paolo Antonio Ascierto, Margaret Ottaviano
Summary: Cutaneous melanoma is a deadly disease, but recent progress has improved survival rates, necessitating the need for new therapeutic approaches. Epigenetics plays a crucial role in melanoma and may serve as new targets for future treatments.
Article
Oncology
Yun-Yao Deng, Yu-Juan Min, Kun Zhou, Qing-Song Yang, Mei Peng, Zhao-Rui Cui, Xiang-Lian Zhu, Hao Liu, Min Wang, Xie Zhang, Li-Xin Liu
Summary: This study demonstrated that circ-FOXO3 inhibits CRC metastasis and progression by increasing LATS1 expression via sponging miR-543.
Article
Medicine, Research & Experimental
Katerina-Marina Pilala, Maria-Alexandra Papadimitriou, Konstantina Panoutsopoulou, Petros Barbarigos, Panagiotis Levis, Georgios Kotronopoulos, Konstantinos Stravodimos, Andreas Scorilas, Margaritis Avgeris
Summary: Bladder cancer (BlCa) is characterized by heterogeneous molecular landscape and lacks personalized treatment. In this study, we investigated the epigenetic regulation of the miR-143/145 cluster in BlCa. We found that the methylation of MIR145 core promoter was associated with disease progression and poor survival in BlCa patients. Combining MIR145 core promoter methylation with established disease markers improved risk stratification and prediction of treatment outcome. Our findings highlight the importance of personalized risk stratification and management in BlCa.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Oncology
Vittorio Castaldo, Michele Minopoli, Francesca Di Modugno, Andrea Sacconi, Domenico Liguoro, Rachele Frigerio, Arianna Ortolano, Marta Di Martile, Luisa Gesualdi, Gabriele Madonna, Mariaelena Capone, Roberto Cirombella, Angiolina Catizone, Donatella Del Bufalo, Andrea Vecchione, Maria Vincenza Carriero, Paolo Antonio Ascierto, Rita Mancini, Luigi Fattore, Gennaro Ciliberto
Summary: The study demonstrates that miR-4443 and miR-4488 promote enhanced migratory and invasive phenotypes in drug-resistant melanoma cells. Mechanistically, the intermediate filament nestin has been identified as a molecular target of both oncomiRs. Finally, nestin levels have been shown to predict the response to treatment in melanoma patients, suggesting potential for developing miRNA-targeted therapies and identifying novel biomarkers for guiding clinical decisions.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2023)
Review
Immunology
Cen Chang, Lingxia Xu, Runrun Zhang, Yehua Jin, Ping Jiang, Kai Wei, Linshuai Xu, Yiming Shi, Jianan Zhao, Momiao Xiong, Shicheng Guo, Dongyi He
Summary: MicroRNAs (miRNAs) play crucial roles in the pathogenesis, diagnosis, and therapeutic intervention of rheumatoid arthritis (RA). They regulate gene expression, immune system differentiation, and serve as potential biomarkers and therapeutic targets.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Dermatology
Bongyong Lee, Anupama Sahoo, Junko Sawada, John Marchica, Sanjay Sahoo, Fabiana I. A. L. Layng, Darren Finlay, Joseph Mazar, Piyush Joshi, Masanobu Komatsu, Kristiina Vuori, Petrus R. de Jong, Animesh Ray, Ranjan J. Perera
Summary: miR-211 promotes aggressive growth of BRAF(V600E)-mutant melanoma xenografts by activating ERK5 signaling pathway, leading to increased resistance of melanoma cells to BRAF and MAPK/ERK kinase inhibitors. This indicates a potential mechanism for developing drug-resistant tumors and a target for overcoming resistance.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2021)
Article
Genetics & Heredity
Ardalan Naseri, Junjie Shi, Xihong Lin, Shaojie Zhang, Degui Zhi
Summary: Inferring familial relationships from whole-genome genetic data is crucial for genome-wide association studies, but current leading methods may not be efficient for very large cohorts. RAFFI is a fast and accurate relationship inference method that leverages IBD segments, showing robustness against errors and significantly faster performance compared to KING, especially for distant relatives in large cohorts.
Article
Biochemical Research Methods
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Summary: The static PBWT has been generalized to a dynamic data structure, d-PBWT, allowing for dynamic updates of the haplotype panel. Efficient algorithms for insertion and deletion of individual haplotypes have been developed, with d-PBWT shown to support all PBWT algorithms. Variations in set maximal match and long match query algorithms were systematically investigated, revealing differences in worst case complexities and dependencies on additional data structures.
Article
Biochemistry & Molecular Biology
Shahidul Islam, Md Mahfuzur Rahaman, Shaojie Zhang
Summary: Understanding the 3D structural properties of RNAs is crucial for identifying functional characteristics and designing new RNAs; a new method RNAMotifContrast focuses on analyzing the similarities and variations of RNA structural motif characteristics; analyzing structural features among motifs has led to the discovery and generalization of motif subfamilies.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Oncology
Animesh Ray, Haritha Kunhiraman, Ranjan J. Perera
Summary: This article summarizes the impact and regulatory mechanisms of regulatory non-coding RNA MIR211 on various cancer types, discussing its complex role in tumorigenesis and potential research directions.
FRONTIERS IN ONCOLOGY
(2021)
Article
Computer Science, Artificial Intelligence
Animesh Ray
Summary: Machine learning is revolutionizing biology by enabling the analysis of massive biological datasets and solving biological problems. It is distinct from classical statistical methods and has the potential to transform medicine, public health, and agricultural technology while providing valuable gene-based guidance for complex environmental management.
WILEY INTERDISCIPLINARY REVIEWS-DATA MINING AND KNOWLEDGE DISCOVERY
(2022)
Article
Virology
Kritika Kedarinath, Candace R. Fox, Erin Crowgey, Joseph Mazar, Peter Phelan, Tamarah J. Westmoreland, Kenneth A. Alexander, Griffith D. Parks
Summary: The study found that CD24 expression in neuroblastoma cells suppresses intracellular antiviral pathways, suggesting that CD24 may represent a novel biomarker in cancer cells for susceptibility to oncolytic viruses.
Article
Oncology
Amanda Cox, Daniel Nierenberg, Oscar Camargo, Eunkyung Lee, Amr S. S. Khaled, Joseph Mazar, Rebecca J. J. Boohaker, Tamarah J. J. Westmoreland, Annette R. R. Khaled
Summary: The study reveals that CCT2 is highly expressed in pediatric cancers, playing a crucial role in promoting the invasive capacity of neuroblastoma cells, and serving as a potential molecular target for novel therapeutics and diagnostics.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Qiuying Liu, Mariah K. Novak, Rachel M. Pepin, Katharine R. Maschhoff, Kailey Worner, Xiaoli Chen, Shaojie Zhang, Wenqian Hu
Summary: Mutations in Trim71 gene cause congenital hydrocephalus by altering its mRNA substrate specificity and regulatory function on Lsd1 mRNA, leading to accelerated stem-cell differentiation and neural lineage commitment. Inhibition of the repression or an increase of Lsd1 levels can alleviate the defects associated with the mutant cells, suggesting potential therapeutic targets for treating hydrocephalus and providing insights into the disease mechanisms.
Article
Biochemistry & Molecular Biology
Xiaoli Chen, Shaojie Zhang
Summary: The functions of non-coding RNAs are dependent on their 3D structures, making it critical to compare RNA 3D structures in order to analyze their functions. In this study, we identified a phenomenon where two non-coding RNAs may have similar substructures when their sequence order is rotated. To address this, we developed a software tool called CircularSTAR3D to detect circular matched substructures in RNA 3D structures. Our computational experiments on a non-redundant RNA structure dataset revealed the ubiquity of circular matching. We also demonstrated the usefulness of CircularSTAR3D in detecting conserved substructures missed by regular alignment tools.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Nabila Shahnaz Khan, Md Mahfuzur Rahaman, Shahidul Islam, Shaojie Zhang
Summary: The significance of RNA functions and their role in evolution and disease control have expanded the research scope in RNA science. The challenge lies in maintaining the quality and integrity of the growing RNA structure data in PDB.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Victor Wang, Ardalan Naseri, Shaojie Zhang, Degui Zhi
Summary: This study proposes a variation of PBWT called Syllable-PBWT, which achieves efficient long match query algorithm while saving space. The results demonstrate that Syllable-Query reduces memory usage and has faster runtime compared to existing solutions.
Article
Biochemical Research Methods
Yuan Wei, Ardalan Naseri, Degui Zhi, Shaojie Zhang
Summary: Due to the rapid growth of the genetic database size, genealogical search has become a viable approach to help individuals finding missing family members or law enforcement agencies locating suspects. A new method, RaPID-Query, is introduced to make fast genealogical search possible by identifying IBD segments between a query haplotype and a panel of haplotypes.
Article
Oncology
Bongyong Lee, Keisuke Katsushima, Rudramani Pokhrel, Menglang Yuan, Stacie Stapleton, George Jallo, Robert J. Wechsler-Reya, Charles G. Eberhart, Animesh Ray, Ranjan J. Perera
Summary: SPRIGHTLY lncRNA is upregulated in group 4 medulloblastoma (G4 MB) and regulates cell proliferation, invasion, and apoptosis through interaction with SMYD3 and PTPB1 protein. Deletion of SPRIGHTLY lncRNA results in smaller G4 MB tumors.
NEURO-ONCOLOGY ADVANCES
(2022)
Proceedings Paper
Computer Science, Theory & Methods
Maria-Florina Balcan, Dan DeBlasio, Travis Dick, Carl Kingsford, Tuomas Sandholm, Ellen Vitercik
Summary: Algorithms often have tunable parameters that impact performance metrics, but worst-case instances may be rare. Data-driven algorithm design can lead to performance improvements by returning parameter settings based on a training set. The challenge lies in the volatile nature of performance based on parameter changes.
STOC '21: PROCEEDINGS OF THE 53RD ANNUAL ACM SIGACT SYMPOSIUM ON THEORY OF COMPUTING
(2021)