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
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
Biology
Praveen Kumar Guttula, Pedro T. Monteiro, Mukesh Kumar Gupta
Summary: This study predicted and modeled synergistic microRNA regulatory networks, identifying the crucial roles of miR-200/429/141 family in controlling pluripotency and reprogramming, and the essential functions of miR-20/106/17 family in maintaining unipotent cells. The logical modeling demonstrated that synergistic miRNAs regulate MET gene dynamics during reprogramming, which was confirmed by perturbation analysis.
Article
Chemistry, Medicinal
Massimo Moro, Orazio Fortunato, Giulia Bertolini, Mavis Mensah, Cristina Borzi, Giovanni Centonze, Francesca Andriani, Daniela Di Paolo, Patrizia Perri, Mirco Ponzoni, Ugo Pastorino, Gabriella Sozzi, Mattia Boeri
Summary: Despite improvements in therapies and screening strategies, lung cancer prognosis remains poor, especially for patients with metastatic tumors. Cancer stem cells (CSCs) are a major cause of the low survival rate, and microRNA miR-486-5p has been identified as a potential therapeutic target for lung cancer.
Letter
Cell Biology
Jakob V. Kanne, Masaki Ishikawa, Simon Bressendorff, Jeppe Ansbol, Mitsuyasu Hasebe, Eleazar Rodriguez, Morten Petersen
Summary: Animal and plant somatic cells have the ability to switch states or reprogram into stem cells to adapt to stress and injury, a process that requires macroautophagy/autophagy. Overexpression of ATG8/LC3 in the moss Physcomitrium patens enhances the ability of somatic cells to reprogram into stem cells when subjected to severe wounding, indicating that autophagy not only facilitates cell dedifferentiation but also increases their competence to do so.
Review
Immunology
Yan Dong, Zhuo Wan, Xiaotong Gao, Guodong Yang, Li Liu
Summary: This article summarizes the central roles of immune cells in tumor progression and regression, as well as existing and emerging strategies for immune cell-based immunotherapies for different types of cancer. Furthermore, it discusses current challenges and potential solutions in translating these immunotherapies into clinical practice.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Kenji Ito, Kohei Nagata, Sho Ohta, Yutaka Matsuda, Tomoyo Ukai, Ichiro Yasuda, Akira Ota, Ryota Kobayashi, Mio Kabata, Nao Sankoda, Tatsuya Maeda, Knut Woltjen, Liying Yang, Reo Maruyama, Ryohei Katayama, Takuya Yamamoto, Yasuhiro Yamada
Summary: Resistance to transcription factor-mediated reprogramming into pluripotent stem cells is a distinctive feature of cancer cells, but studying the profiles of reprogramming factor binding and transcriptional response can reveal underlying mechanisms and potential therapeutic targets. In cancer cells, oncogenes like EWS/ATF1 can misdirect reprogramming factors to specific enhancers, inhibiting the transcriptional response towards pluripotency. Pharmacological inhibition of corresponding oncogenic signals can sensitize cancer cells to reprogramming cues, while targeting downstream signaling pathways like mTOR can attenuate cancer cell propagation. This highlights the potential for early transcriptional responses to guide the identification of effective therapeutics targets in cancer cells.
Article
Oncology
Narjes Jafari, Saeid Abediankenari, Hadi Hossein-Nataj
Summary: The study revealed that the effect of miR mimic in target gene repression may depend on its concentration and cell type, while pre-miRNAs may have a regulatory function in target repression. These findings will help to develop effective therapeutic strategies in cancer treatment.
CANCER CELL INTERNATIONAL
(2021)
Article
Biochemistry & Molecular Biology
Rahaba Marima, Flavia Zita Francies, Rodney Hull, Thulo Molefi, Meryl Oyomno, Richard Khanyile, Sikhumbuzo Mbatha, Mzubanzi Mabongo, David Owen Bates, Zodwa Dlamini
Summary: Cancer is a complex disease involving alterations in gene expression, with key roles played by miRNA dysregulation and alternative splicing events. Dysregulation of miRNA and splicing events can promote carcinogenesis and drug resistance in various cancers. The interplay between miRNA and alternative splicing, particularly in altering target mRNA binding sites, can impact protein production and drug resistance mechanisms. Understanding these molecular alterations is crucial for developing effective strategies to combat drug resistance in cancer treatment.
Review
Cell Biology
Vera A. van der Weijden, Aydan Bulut-Karslioglu
Summary: Mammalian embryos have the ability to enter a state of diapause, where development is paused in adverse conditions. Studying diapause can provide insights into principles of stem cell potency and dormancy. Diapause is established and maintained through active rewiring of the embryonic metabolome, epigenome, and gene expression.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cell Biology
Jinxin Liu, Guanning Shang
Summary: This review article describes the role of noncoding RNAs in regulating the development of cancer stem cells (CSCs) in osteosarcoma. The study found that miRNAs, lncRNAs, and circRNAs play crucial roles in the regulation of CSCs development and potential mechanisms.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Larischa de Wet, Anthony Williams, Marc Gillard, Steven Kregel, Sophia Lamperis, Lisa C. Gutgesell, Jordan E. Vellky, Ryan Brown, Kelly Conger, Gladell P. Paner, Heng Wang, Elizabeth E. Platz, Angelo M. De Marzo, Ping Mu, Jonathan L. Coloff, Russell Z. Szmulewitz, Donald J. Vander Griend
Summary: This study investigated the impact of SOX2 expression on patient outcomes and its function within prostate cancer cells. The results revealed that SOX2 expression promotes metastatic progression and therapy resistance in prostate cancer, and affects the metabolic pathways and metabolites of cancer cells. These findings contribute to a better understanding of the role of SOX2 in prostate cancer and suggest its potential as a biomarker and pharmacologic target in clinical settings.
Review
Biochemistry & Molecular Biology
Yazan Al Salhi, Manfredi Bruno Sequi, Fabio Maria Valenzi, Andrea Fuschi, Alessia Martoccia, Paolo Pietro Suraci, Antonio Carbone, Giorgia Tema, Riccardo Lombardo, Antonio Cicione, Antonio Luigi Pastore, Cosimo De Nunzio
Summary: Cancer stem cells (CSCs) are a small and elusive subpopulation of self-renewing cancer cells that have the remarkable ability to initiate, propagate, and spread malignant disease. Previous studies have focused on the role of CSCs in the development and progression of PCa. PCa CSCs typically originate from luminal prostate cells, and the Wnt, Sonic Hedgehog, and Notch signaling pathways are involved in their development. Epithelial mesenchymal transition and specific miRNAs also play important roles in this process. Targeting these pathways has shown promise in improving the management of PCa development and progression. CSCs in prostate cancer represent a significant and promising area of research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Olga A. Krasnova, Karina A. Kulakova, Julia V. Sopova, Evgenyi Y. Smirnov, Sergey A. Silonov, Ekaterina V. Lomert, Olga A. Bystrova, Marina G. Martynova, Irina E. Neganova
Summary: G-protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and play important roles in diverse developmental processes. However, their role in pluripotency maintenance and acquisition during reprogramming towards hiPSCs has been overlooked. Through RNA interference screening, adhesion GPCR GPR123 was identified as a potential reprogramming effector. Suppression of GPR123 leads to loss of pluripotency and differentiation in hPSCs, suggesting its essential role in maintaining and acquiring pluripotency.
Article
Materials Science, Multidisciplinary
Anish Hiresha Verma, Swarna Ganesh, Krishnan Venkatakrishnan, Bo Tan
Summary: This study used ultra-small gold nanoparticles as a nanoscale probe to demethylate the genomic DNA of cancer stem cells, leading to their reprogramming into cancer cells. The results showed a significant decrease in genetic and phenotypic stemness as well as cell cycle quiescence of lung cancer stem cells. This research opens up new avenues for effective anti-cancer treatments and precision nanomedicine.
APPLIED MATERIALS TODAY
(2023)
Article
Genetics & Heredity
Neha Jain, Basudeb Das, Bibekanand Mallick
Summary: In this study, researchers aimed to investigate the combined application of miR-197-5p and Doxorubicin (Dox) in enhancing the sensitivity of fibrosarcoma cells to Dox and improving its anti-tumor effects. Through a series of experiments, they found that miR-197-5p increased the sensitivity of HT1080 fibrosarcoma cells to Dox by promoting apoptosis and G2/M cell cycle arrest, and by suppressing MDR genes to increase drug influx. Additionally, they observed that the target protein of miR-197-5p, KIAA0101, was inhibited by Dox and further repressed when treated in combination with the miRNA. The combination treatment also led to an upregulation of p53, which is negatively correlated with KIAA0101, compared to Dox alone.
Article
Genetics & Heredity
Basudeb Das, Neha Jain, Bibekanand Mallick
Summary: A potential oncogene RRM2 associated with soft tissue sarcoma prognosis was identified, with high RRM2 expression linked to lower survival rates in patients.
Article
Biochemistry & Molecular Biology
Garima Singh, Bibekanand Mallick
Summary: This study analyzed piRNA-target CLIP-Seq datasets to uncover additional characteristic features of piRNA targets, which may enhance the accuracy of target site predictions.
JOURNAL OF MOLECULAR RECOGNITION
(2022)
Review
Cell Biology
Neha Jain, Pooja Gupta, Swapnil Sahoo, Bibekanand Mallick
Summary: Non-coding RNAs play crucial roles in women's health, impacting normal physiology and reproductive health. Understanding the functions and mode of actions of ncRNAs is vital for developing effective prognostic and therapeutic strategies.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Article
Medicine, Research & Experimental
Basudeb Das, Swapnil Sahoo, Bibekanand Mallick
Summary: This study reveals for the first time that HIWI2 acts as a tumor suppressor in fibrosarcoma by modulating the ROS/DNA damage/p53 pathway.
Article
Biochemistry & Molecular Biology
Rojalin Nayak, Trisha Chattopadhyay, Bibekanand Mallick
Summary: This study identified miRNAs and genes involved in endometriosis progression and infertility, and predicted repurposed drugs to counteract the regulatory effect of these miRNAs. One of the drugs showed promising results for treating infertility. These findings provide a theoretical basis for treating endometriosis and preventing recurrent infertility.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Oncology
Shibjyoti Debnath, Abhisek Sarkar, Dipanwita Das Mukherjee, Subha Ray, Barun Mahata, Tarun Mahata, Pravat K. Parida, Troyee Das, Rupak Mukhopadhyay, Zhumur Ghosh, Kaushik Biswas
Summary: This study reveals the mechanism of selective cytotoxicity of Eriodictyol towards cancer cells by upregulating TNFR1 expression and inducing apoptosis through molecular events. In vivo experiments demonstrate that Eriodictyol not only impedes tumor growth and progression, but also inhibits metastasis. This suggests that Eriodictyol is a promising compound for cancer therapeutics.
TRANSLATIONAL ONCOLOGY
(2022)
Article
Genetics & Heredity
Trisha Chattopadhyay, Pooja Gupta, Rojalin Nayak, Bibekanand Mallick
Summary: This study provides the first evidence of piRNAs in TSCC and reveals differentially expressed piRNAs and target genes that are involved in multiple pathways in the initiation and progression of TSCC, with FDFT1 being a potential drug target.
Editorial Material
Endocrinology & Metabolism
Ahmet Ucar, Baris Binay, Bibekanand Mallick
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Rojalin Nayak, Trisha Chattopadhyay, Pooja Gupta, Bibekanand Mallick
Summary: This study profiled miRNAs, piRNAs, and genes in U-87 MG GBM cells and predicted their roles in malignancy. 335 miRNAs, 665 piRNAs, and 4286 genes were found to be differentially expressed in GBM. Some of the differentially expressed genes were targeted by both miRNAs and piRNAs, while others were targeted solely by miRNAs or piRNAs. These differentially expressed genes were associated with cancer processes and linked to the progression and overall survival of GBM patients.
Article
Biology
Arijita Sarkar, Troyee Das, Gourab Das, Zhumur Ghosh
Summary: Acute Myeloid Leukemia (AML) can be detected by analyzing the miRNome and transcriptome of AML samples, identifying significant miRNA-target mRNA pairs, and developing the machine learning-based prediction tool 'TbAMLPred' for preliminary AML diagnosis. The selected miRNA target features can effectively separate control and disease samples, making 'TbAMLPred' a promising non-invasive tool for AML diagnosis in the future.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Gourab Das, Troyee Das, Sibun Parida, Zhumur Ghosh
Summary: Long non-coding RNAs play a significant role in various biological processes, and it is important to understand their functions in order to comprehend the molecular mechanism of complex biological systems. Existing lncRNA target prediction tools have limitations in execution time and real-time prediction. We have developed a machine learning-based lncRNA-mRNA target prediction model, addressing these issues by generating reliable negative datasets and creating robust ML models.
Article
Medicine, Research & Experimental
Trisha Chattopadhyay, Bibekanand Mallick
Summary: This study investigates the role of piR-39980 and its target FDFT1 in the malignancy of tongue squamous cell carcinoma (TSCC). The results show that overexpression of piR-39980 can inhibit proliferation, migration, and ROS generation in TSCC cells, while increasing DNA damage and chromatin condensation causing cell death. The repression of FDFT1 is believed to induce hypoxia, leading to DNA damage and cell death in TSCC cells.
Article
Biochemistry & Molecular Biology
Pooja Gupta, Gourab Das, Trisha Chattopadhyay, Zhumur Ghosh, Bibekanand Mallick
Summary: Piwi-interacting RNAs (piRNAs) are a class of small non-coding single-stranded RNAs that play important roles in various biological activities, including transposon silencing. They regulate gene expression by binding to mRNAs through interaction with PIWI proteins. However, the targeting mechanism and functions of piRNAs remain unclear. To address this, we developed TarpiD, a comprehensive database that provides information on piRNAs and their targets, including expression, target identification/validation methods, cell/tissue types, diseases, target gene regulation types, target binding regions, and key functions. TarpiD will serve as a valuable resource for understanding the functions and gene-regulatory mechanisms mediated by piRNAs.
