Review
Biochemistry & Molecular Biology
Amrutha Menon, Noraini Abd-Aziz, Kanwal Khalid, Chit Laa Poh, Rakesh Naidu
Summary: This review focuses on the role of miRNA in cancer, therapeutic approaches with miRNAs, and effective delivery into the system. Patents and ongoing clinical trials for miRNA therapy are also summarized.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Soudeh Ghafouri-Fard, Mohammadreza Hajiesmaeili, Hamed Shoorei, Zahra Bahroudi, Mohammad Taheri, Guive Sharifi
Summary: Stem cells and cancer stem cells possess the abilities of self-renewal and differentiation, with molecular pathways like Wnt, Notch, and Hedgehog influencing their functions. miRNAs and lncRNAs have been found to regulate the functions of CSCs, particularly in breast cancer and hepatocellular carcinoma.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Medicine, Research & Experimental
Pawan Kumar Raghav, Zoya Mann
Summary: Cancer stem cells play a crucial role in tumorigenesis and present challenges for treatment. Despite multiple treatment options available, the lack of specificity and dose limitation hinders complete efficacy in controlling CSCs.
Article
Oncology
Diego A. Pedroza, Matthew Ramirez, Venkatesh Rajamanickam, Ramadevi Subramani, Victoria Margolis, Tugba Gurbuz, Adriana Estrada, Rajkumar Lakshmanaswamy
Summary: Our study reveals that therapeutic targeting of PGRMC1 in aggressive breast cancers leads to the activation of miRNAs targeting overexpressed genes and deactivation of miRNAs with oncogenic potential.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Milica Jaksic Karisik, Milos Lazarevic, Dijana Mitic, Nadja Nikolic, Maja Milosevic Markovic, Drago Jelovac, Jelena Milasin
Summary: The failure of oral squamous cell carcinoma (OSCC) treatment is often attributed to cancer stem cells (CSCs) which are resistant to therapy. Micro RNA-21 has been found to play a significant role in the development of OSCC. This study aimed to investigate the multipotency of oral CSCs and evaluate the effects of differentiation on stemness, apoptosis, and miRNA expression. The experiments were conducted using a commercially available OSCC cell line (SCC25) and primary OSCC cultures from five patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Azar Shams, Ronak Shabani, Hamidreza Asgari, Mahdi Karimi, Mohammad Najafi, Mohammad Asghari-Jafarabadi, Seyed Mohsen Razavi, Seyed Rouhollah Miri, Mehdi Abbasi, Amirhossein Mohammadi, Morteza Koruji
Summary: The study revealed the remarkable apoptotic induction effects of miRNA-143 and -206 in cancer cells, with miRNA-206 showing stronger apoptotic effects compared to miRNA-143 and mixed miRNAs.
Article
Medicine, Research & Experimental
Soudeh Ghafouri-Fard, Mohammad Hossein Behzad Moghadam, Hamed Shoorei, Zahra Bahroudi, Mohammad Taheri, Afshin Taheriazam
Summary: Self-renewal and differentiation are main characteristics of stem cells, regulated by miRNAs and lncRNAs. Various miRNAs and lncRNAs play important roles in the differentiation of stem cells, impacting tissue regeneration and homeostasis.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Review
Biochemistry & Molecular Biology
Dibyashree Chhetri, Srinivasan Vengadassalapathy, Santhosh Venkadassalapathy, Varadharaju Balachandran, Vidhya Rekha Umapathy, Vishnu Priya Veeraraghavan, Selvaraj Jayaraman, Shankargouda Patil, Ashok Iyaswamy, Kanagaraj Palaniyandi, Dhanavathy Gnanasampanthapandian
Summary: DCLK1, a tumor stem cell marker in various cancers, is closely associated with tumor cell proliferation and metastasis. Targeting the DCLK1 gene and regulating the pathways controlled by DCLK1 may provide potential strategies to inhibit tumor growth and metastasis in gastrointestinal cancer.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Cell Biology
Yuanyuan Ma, Xiaodan Yang, Wei Zhao, Yue Yang, Zhiqian Zhang
Summary: Research has identified a subpopulation of TICs in non-small cell lung carcinoma (NSCLC) that can be specifically defined by the voltage-gated calcium channel alpha 2 delta 1 subunit, demonstrating stem cell-like properties and resistance to conventional chemotherapy. This discovery suggests that targeting alpha 2 delta 1 to prevent calcium influx provides a novel strategy for targeted therapy against TICs in NSCLC.
CELL DEATH & DISEASE
(2021)
Review
Oncology
Wen Jess Li, Xiaozhuo Liu, Emily M. Dougherty, Dean G. Tang
Summary: The article reviews the tumor suppressive role of miRNA-34a in prostate cancer and discusses therapeutic development strategies for advanced prostate cancer patients.
Review
Oncology
Tong Niu, Weiwei Zhang, Wei Xiao
Summary: Breast cancer stem cells (BCSCs) play critical roles in modulating breast tumor behaviors and drug resistance, while miRNAs in breast cancer exhibit multifaceted roles as suppressors or oncogenes in regulating cancer progression. The review highlights the importance of miRNAs in regulating key signaling pathways that are essential for BCSC maintenance.
CANCER CELL INTERNATIONAL
(2021)
Article
Oncology
Mohith Manjunath, Jialu Yan, Yeoan Youn, Kristen L. Drucker, Thomas M. Kollmeyer, Andrew M. McKinney, Valter Zazubovich, Yi Zhang, Joseph F. Costello, Jeanette Eckel-Passow, Paul R. Selvin, Robert B. Jenkins, Jun S. Song
Summary: The study identified potential causal SNPs within LGG GWAS loci and their regulatory effects on target genes and transcription factors through integrative genomic and epigenomic analysis. The findings provide valuable insights into the molecular mechanisms underlying genetic risk factors for gliomas, facilitating further computational and experimental investigations.
Article
Biochemistry & Molecular Biology
Jacek R. Wilczynski, Milosz Wilczynski, Edyta Paradowska
Summary: This review provides an overview of the biology of ovarian cancer stem cells (OCSCs) and their impact on chemo-resistance and prognosis in ovarian cancer patients. It discusses the role of OCSCs in cancer progression and recurrence, as well as potential treatment options targeted specifically at OCSCs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Elsa N. Garza Trevino, Adriana G. Quiroz Reyes, Juan Antonio Rojas Murillo, David A. de la Garza Kalife, Paulina Delgado Gonzalez, Jose F. Islas, Ana Esther Estrada Rodriguez, Carlos A. Gonzalez Villarreal
Summary: Cancer stem cells (CSCs) have unique properties and are responsible for tumor recurrence, metastasis, and therapy resistance. Recent research shows that immune cells play a crucial role in regulating CSCs. Cellular immunotherapy using T cells, natural killer (NK) cells, macrophages, or stem cells has shown promising results in targeting CSCs in colorectal cancer (CRC). This review summarizes CRC molecular profiles that may benefit from this therapy and discusses the challenges and advantages of combining conventional and targeted treatments in the late stages of CRC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Shunhao Zhang, Yanji Gong, Chunjie Li, Wenbin Yang, Longjiang Li
Summary: Recent studies have shown the crucial role of cancer stem cells (CSCs) in various cancer processes, with their cellular plasticity not entirely explained by genetic mutations. The research on epigenetic modifications as a complementary explanation has been increasing in recent years, leading to the development of therapeutic strategies targeting CSCs. This review summarizes the understanding of CSCs and their role in cancer progression, focusing on epigenetic alterations and specific chemical inhibitors as primary cancer therapies.
CELL PROLIFERATION
(2021)
Article
Neurosciences
Linjing Shen, Changliang Wang, Liang Chen, Garry Wong
Summary: MicroRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) were found to be dysregulated in Parkinson's disease (PD) tissues. When comparing miRNA and piRNA dysregulation in transgenic C. elegans nematodes overexpressing human alpha-synuclein wild-type (WT) or mutant A53T, genetic crosses with tdp-1 null mutants improved behavioral deficits and altered the number of dysregulated miRNAs and piRNAs. Prediction of target genes by specific miRNAs shed light on the molecular landscape of small non-coding RNA dysregulation in PD-associated neurodegenerative disorders.
FRONTIERS IN NEUROSCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Ernest T. Chivero, Raghubendra Singh Dagur, Eric S. Peeples, Susmita Sil, Ke Liao, Rong Ma, Liang Chen, Channabasavaiah B. Gurumurthy, Shilpa Buch, Guoku Hu
Summary: Substance use disorder (SUD) is a growing health problem affecting millions worldwide, with extracellular vesicles (EVs) playing a crucial role in its pathogenesis. EVs have the potential to serve as biomarkers or therapeutic targets in SUD.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Review
Environmental Sciences
Mei Zhuang, Yigal Achmon, Yuping Cao, Xiaomin Liang, Liang Chen, Hui Wang, Bupe A. Siame, Ka Yin Leung
Summary: The presence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the microbiome poses a significant global public health concern. Different habitats are at risk due to excessive antibiotic use and evolutionary changes in the resistome. China leads in the number of papers related to ARGs compared to other countries, with varied distributions of ARG subtypes across different environments.
ENVIRONMENTAL POLLUTION
(2021)
Article
Computer Science, Hardware & Architecture
Wei Du, Yu Sun, Hui-Min Bao, Liang Chen, Ying Li, Yan-Chun Liang
Summary: This study introduces a novel deep learning model for accurate identification of blood-secretory proteins using amino acid sequence information. The model combines a binary classification network and a ranking network, applying descriptive loss and compactness loss to improve prediction accuracy. Transfer learning is utilized to train a highly accurate generalized model with limited samples.
JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xiaobing Huang, Changliang Wang, Liang Chen, Tianjiao Zhang, Ka Lai Leung, Garry Wong
Summary: The study found that the co-expression of A beta and alpha-synuclein in the brains of patients with Lewy body dementia may exacerbate the pathogenic process. The experimental results showed that co-expression of A beta and alpha-syn (A53T) in C. elegans further aggravated movement, egg laying, signaling deficits, and dopaminergic neuron damage. These findings suggest a potential mechanism by which A beta may enhance alpha-syn pathogenesis in Lewy body dementia.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2021)
Article
Ecology
Anna-Lotta Hiillos, Anne Thonig, Karelyn Emily Knott
Summary: Interactions between symbiotic organisms and hosts play a key role in ecological and evolutionary processes. This study developed a ddPCR assay to detect an undescribed agamococcidian symbiont, providing precise and reproducible results for detecting cryptic symbionts in low target concentrations. The assay was used to investigate symbiont infection dynamics in naturally occurring host populations, revealing spatial differences in prevalence, stable seasonal patterns, and varying infection loads among populations. Additionally, symbiont prevalence was influenced by host length and population density, with larger hosts more likely to be infected and high host densities associated with lower infection probabilities.
ECOLOGY AND EVOLUTION
(2021)
Review
Biochemical Research Methods
Tianjiao Zhang, Liang Chen, Rongzhen Li, Ning Liu, Xiaobing Huang, Garry Wong
Summary: PIWI-interacting RNAs (piRNAs) are short molecules found in various species, with the main function of monitoring and protecting the genome from transposons. They have limited bioinformatics resources compared to microRNAs (miRNAs). This review provides an overview of piRNA-specific and non-specific databases, computational models, and their role in disease associations, particularly in cancer and neurodegenerative conditions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Marine & Freshwater Biology
H. Cecilie Petersen, K. Emily Knott, Gary T. Banta, Benni W. Hansen
Summary: The Baltic Sea is a marginal ecosystem between marine and freshwater extremes, and the differences in invasion history and dispersal capabilities of Baltic species have resulted in large variations in species distributions, genetic structure, and edge populations. Through a phylogenomic approach, we found that there is little relation between populations of P. elegans and C. volutator, but a higher degree of resemblance among populations of M. arenaria. Each species exhibited unique phylogenetic patterns.
ESTUARINE COASTAL AND SHELF SCIENCE
(2022)
Article
Microbiology
Anna-Lotta Hiillos, Irin Rony, Sonja Rueckert, K. Emily Knott
Summary: Coinfections of two marine apicomplexans, Rhytidocystis sp. and Selenidium pygospionis, in the polychaete Pygospio elegans, were investigated in relation to host genetic diversity. The results showed that factors other than host genetic diversity might be more influential in the infection patterns of marine apicomplexans.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Sergio Carracedo, Lisa Lirussi, Lene Alsoe, Filip Segers, Changliang Wang, Zdenka Bartosova, Pavol Bohov, Nuriye B. Tekin, Xiang Yi Kong, Q. Ying Esbensen, Liang Chen, Anna Wennerstrom, Penelope Kroustallaki, Deborah Ceolotto, Anke Tonjes, Rolf Kristian Berge, Per Bruheim, Garry Wong, Yvonne Bottcher, Bente Halvorsen, Hilde Nilsen
Summary: The knockout of SMUG1 gene can lead to the development of a fatty liver phenotype, increasing hepatocyte senescence and DNA damage. Changes in the expression of lipid metabolic genes can already be observed in mice as young as three months old.
Article
Computer Science, Artificial Intelligence
Xuan Wu, Jizong Han, Di Wang, Pengyue Gao, Quanlong Cui, Liang Chen, Yanchun Liang, Han Huang, Heow Pueh Lee, Chunyan Miao, You Zhou, Chunguo Wu
Summary: In this work, we use Surprisingly Popular Algorithm (SPA) as an additional metric to evaluate particle performance in addition to fitness. This allows particles that are not widely known to be selected as learning exemplars. We also propose a Euclidean distance-based adaptive topology where each particle only connects to a limited number of particles with the shortest Euclidean distance. Moreover, we apply the adaptive topology to heterogeneous populations to solve large-scale problems more effectively.
SWARM AND EVOLUTIONARY COMPUTATION
(2023)
Article
Ecology
H. Cecilie Petersen, Rumakanta Sapkota, Anna-Lotta Hiillos, Benni W. Hansen, Gary T. Banta, K. Emily Knott
Summary: This study used amplicon sequencing to analyze the microbial sediment communities in the coastal areas of the Baltic Sea and North Sea, and found that salinity affects the alpha diversity of bacteria but not eukaryotes. Additionally, the community network structure and beta diversity are also influenced by other environmental factors.
AQUATIC MICROBIAL ECOLOGY
(2023)
Article
Multidisciplinary Sciences
Xiaobing Huang, Changliang Wang, Tianjiao Zhang, Rongzhen Li, Liang Chen, Ka Lai Leung, Merja Lakso, Qinghua Zhou, Hongjie Zhang, Garry Wong
Summary: PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that play important roles in regulating gene expression and neurodegeneration. This study found dysregulated expression of piRNAs in disease models and brain samples of Parkinson's disease patients, suggesting their involvement in the pathogenesis of Lewy body diseases. The results provide insights into the molecular mechanisms underlying neurodegenerative disorders.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
H. Cecilie Petersen, Benni W. Hansen, K. Emily Knott, Gary T. Banta
Summary: This study evaluated the species-genetic diversity correlation (SGDC) in benthic macrofauna communities in the Baltic Sea. The results showed no significant correlation between species diversity and genetic diversity for any focal species. Both positive and negative trends of SGDC were observed for individual species, and no common environmental factors driving the SGDC relationships were found among species. The study highlights the importance of assessing SGDC using multiple species and considering the ecology and life history of focal species.
BMC ECOLOGY AND EVOLUTION
(2022)
Review
Biochemical Research Methods
Liang Chen, Changliang Wang, Huiyan Sun, Juexin Wang, Yanchun Liang, Yan Wang, Garry Wong
Summary: Circular RNAs (circRNAs) are a unique class of RNA molecules produced by back-splicing of linear RNA, and recent advances in sequencing technologies and bioinformatics tools have greatly expanded our understanding of their biological functions and practical applications. There are now numerous bioinformatics tools available for circRNA annotation, identification, and network analysis, which continue to evolve to support various research projects in this field.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Diana Medina-Felix, Francisco Vargas-Albores, Estefania Garibay-Valdez, Luis Rafael Martinez-Cordova, Marcel Martinez-Porchas
Summary: In this research, the effects of Nocardia infection on fish gastrointestinal microbiota were analyzed. It was found that the infection led to decreased survival rate, severe damage to the stomach microbiota, and a significant increase in Proteobacteria. A negative correlation network between Proteobacteria and other important phyla was observed. Therefore, Nocardia sp. is an emerging pathogen capable of inducing dysbiosis and causing significant mortalities.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Lele Wu, Wen Sun, Jiale Zhou, Yaolin Li, Jun Li, Zongcheng Song, Changbin Song, Shihong Xu, Xinlu Yue, Xian Li
Summary: The study finds that red light induces dichromatic skin pigmentation in turbot juveniles, with some individuals displaying black coloration and others displaying lighter skin. The upregulated gene expressions related to melanin synthesis and the involvement of the nervous system in spectral environment-driven color regulation are both crucial factors.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2024)