Article
Biochemistry & Molecular Biology
Xianhui Ruan, Yue Huang, Lin Geng, Mengran Tian, Yu Liu, Mei Tao, Xiangqian Zheng, Peng Li, Min Zhao
Summary: Single-cell transcriptome sequencing provides higher resolution for cellular differences in papillary thyroid carcinoma. Through integrative analysis of two datasets, we identified 31 consistently differentially expressed genes across multiple cell types, which are related to adaptive immune response and autoimmune thyroid diseases. Experimental validation suggests that KRT7 may be a potential biomarker for PTC epithelial cells.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Developmental Biology
Axel H. Newton, Sarah M. Williams, Andrew T. Major, Craig A. Smith
Summary: This study provides novel insights into the molecular mechanisms underlying the specification and development of the lateral plate mesoderm (LPM) and the initiation of limb development in chicken embryos. The findings reveal the cell-fate decisions, gene activation, and signaling interactions involved in LPM subdivision and early limb initiation. The identification of TWIST1 as a driver of epithelial-to-mesenchymal transition in the somatic LPM and the role of BMP signaling in inducing somatic LPM fate and limb outgrowth contributes to our understanding of LPM development and vertebrate limb initiation.
Article
Oncology
Federico Bocci, Peijie Zhou, Qing Nie
Summary: This study highlights the importance of phenotypic plasticity in cancer progression, emphasizing the roles of intermediate cell states during epithelial-mesenchymal transition (EMT) in driving invasion and metastasis. The research also shows that the increase in EM plasticity correlates with the expression of CSC markers and enhanced cell-cell signaling, shedding light on the interconnected and multi-dimensional landscape of cancer progression.
Article
Cell Biology
Zekai Wu, Yuan Shi, Yueli Cui, Xin Xing, Liya Zhang, Da Liu, Yutian Zhang, Ji Dong, Li Jin, Meijun Pang, Rui-Ping Xiao, Zuoyan Zhu, Jing-Wei Xiong, Xiangjun Tong, Yan Zhang, Shiqiang Wang, Fuchou Tang, Bo Zhang
Summary: Mammals have limited heart regeneration ability, while zebrafish exhibit remarkable cardiac regeneration capacity. In this study, single-cell transcriptome analyses of zebrafish revealed that atrial cardiomyocytes can exhibit a stem-like state and transdifferentiate into ventricular cardiomyocytes during regeneration. Moreover, a regeneration-induced cell population (RIC) in epicardium-derived cells (EPDC) was identified, and Angiopoietin 4 (Angpt4) was identified as a key regulator of heart regeneration. Angpt4 activates RIC through the Tie2-MAPK pathway and induces activation of cathepsin K in cardiomyocytes through RA signaling. It was also discovered that ANGPT4 can enhance proliferation of neonatal rat cardiomyocytes and promote cardiac repair in mice after myocardial infarction.
Article
Immunology
Shahad Iqneibi, Ryosuke Saigusa, Amir Khan, Mohammad Oliaeimotlagh, Sujit Silas Armstrong Suthahar, Sunil Kumar, Ahmad Alimadadi, Christopher P. Durant, Yanal Ghosheh, Coleen A. Mcnamara, Catherine C. Hedrick, Klaus Ley
Summary: Coronary artery disease (CAD) is a leading cause of death worldwide. The role of CD8+ T cells in CAD has not been well understood. Recent studies suggest that there is a breakdown of tolerance in atherosclerosis, leading to the activation of T cell receptors. This study found significant enrichment of T cell receptor signaling pathways in CD8+ T cells from CAD patients, indicating recent T cell receptor activation. There was also significant enrichment of cytotoxic and exhaustion pathways in CAD cases compared to controls.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Zhiliang Zeng, Shouwei Zhao, Yu Peng, Xiang Hu, Zhixiang Yin
Summary: This paper discusses the application of single-cell RNA sequencing technology in the study of cellular dynamics, focusing on the analysis of RNA velocity in single-cell transcriptomics. By developing a cascade forest model, the authors successfully predict the RNA velocity of cells and achieve better results compared to other classifiers. This paper provides guidance for researchers in selecting and applying appropriate classification tools, and suggests possible directions for future improvement of classification tools.
Article
Cell Biology
Congcong Cao, Qian Ma, Shaomei Mo, Ge Shu, Qunlong Liu, Jing Ye, Yaoting Gui
Summary: This study used scRNA-seq data from WT and SCARKO mice testes at p20 to identify four somatic cell populations and two male germ cell populations. The research found that the distribution of Sertoli cells was completely different between WT and SCARKO mice, uncovering cellular heterogeneity and transcriptional changes. Additionally, several DEGs in SCARKO Sertoli cells, implicated in cell cycle, apoptosis, and male infertility, were identified.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Zixun Wang, Linlin Yang, Xiaoye Su, Xiaomei Wu, Rongjia Su
Summary: This study provides insights into the heterogeneity of high-grade serous ovarian carcinoma (HGSC) at the single-cell level and identifies key transcription factors associated with platinum resistance.
JOURNAL OF GENE MEDICINE
(2023)
Article
Multidisciplinary Sciences
Eliza Duvall, Cecil M. Benitez, Krissie Tellez, Martin Enge, Philip T. Pauerstein, Lingyu Li, Songjoon Baek, Stephen R. Quake, Jason P. Smith, Nathan C. Sheffield, Seung K. Kim, H. Efsun Arda
Summary: This paper describes the molecular analysis of mouse pancreatic endocrine cell differentiation using single-cell transcriptomics, chromatin accessibility assays, and cytometry-based cell purification. The researchers uncover transcription factor networks that regulate pancreatic cell development and suggest the transcription factor Neurog3 may be important for specifying the pancreatic endocrine lineage. These findings have implications for improving diabetes therapy through replacement endocrine cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Neurosciences
Anzhelika Koldaeva, Cary Zhang, Yu-Pei Huang, Janine Kristin Reinert, Seiya Mizuno, Fumihiro Sugiyama, Satoru Takahashi, Taha Soliman, Hiroaki Matsunami, Izumi Fukunaga
Summary: This study aimed to identify differentially expressed genes between MCs and TCs in the mouse olfactory system and ultimately generate a cell type-specific Cre-driver line. After validating potential markers, Pkib and Lbdh2 remained promising candidates. Using gene editing technology, a new inducible Cre-driver line was established and shown to effectively genetically label MCs.
JOURNAL OF NEUROSCIENCE
(2021)
Article
Oncology
Zhihui Gao, Xiaojian Ni, Bohao Zheng, Wentao Sun, Wenze Wan, Han Liu, Xiaoling Ni, Tao Suo, Na Li, Houbao Liu, Sheng Shen
Summary: This study investigated the biological functions and molecular mechanisms of Biliverdin reductase B (BLVRB) in human cholangiocarcinoma (CCA). The results showed that BLVRB depletion accelerated epithelial-mesenchymal transition (EMT), cell migration, and invasion, while BLVRB overexpression reduced EMT and cell migration and invasion in CCA. Furthermore, BLVRB suppression activated Notch signaling, which enhanced EMT and increased cell migration and invasion in CCA.
Article
Biochemistry & Molecular Biology
Michael Powers, Liu Liu, Dane Deemer, Selina Chen, Aaron Scholl, Masafumi Yoshinaga, Zijuan Liu
Summary: Selenium is an essential micronutrient in mammals and selenite is used to alleviate deficiency symptoms and potentially serve as a chemotherapeutic agent. This study identified selenite as a novel inhibitor of Delta-Notch signaling, showing potential in treating diseases like cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Lisha Zhou, Meiling Wang, Hanrui Guo, Jun Hou, Yingna Zhang, Man Li, Xiangwei Wu, Xueling Chen, Lianghai Wang
Summary: The role of TREM2 signaling in the tumor microenvironment of hepatocellular carcinoma (HCC) was investigated. TREM2 was predominantly expressed by a macrophage subpopulation enriched in tumor tissues and correlated with high infiltrating macrophage abundance and poor prognosis. TREM2(+) LAM-like cells recruited suppressive Treg cells, facilitating microenvironment remodeling.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Yang-Yang Wang, En-Qiang Chang, Rui-Lou Zhu, Xiao-Zhuan Liu, Guang-Zhi Wang, Ning-Tao Li, Wei Zhang, Jun Zhou, Xiang-Dong Wang, Ming-Yang Sun, Jia-Qiang Zhang
Summary: This study aimed to investigate the impact of general anesthesia on the patient's immune system at a single-cell level. Results showed changes in CD56(+) NK cells and monocytes at different time points after anesthesia, as well as differences in immune cell communication between females and males. Additionally, the severity of surgery and type of anesthesia were found to affect communication between immune cells.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Jiangpeng Wu, Xiuping Sun, Chunyi Wu, Xiaoping Hong, Lulin Xie, Zixu Shi, Liang Zhao, Qingfeng Du, Wei Xiao, Jichao Sun, Jigang Wang
Summary: This study used single-cell RNA sequencing to analyze the liver tissues of mice exposed to GLY, the active ingredient of a widely used herbicide. The results showed that GLY can induce changes in cell composition, upregulate oxidative stress and inflammatory response, and affect the functionality of macrophages and hepatic stellate cells.
CELLULAR & MOLECULAR BIOLOGY LETTERS
(2023)
Article
Anatomy & Morphology
Ayalur R. Subbalakshmi, Sarthak Sahoo, Kuheli Biswas, Mohit Kumar Jolly
Summary: Epithelial-mesenchymal plasticity plays a crucial role in aggressive tumor progression, and cells in hybrid epithelial/mesenchymal phenotype exhibit greater aggressiveness. The study reveals that SLUG can stabilize cells in the hybrid epithelial/mesenchymal phenotype, functioning as a phenotypic stability factor. This finding has important implications for understanding metastasis mechanisms.
CELLS TISSUES ORGANS
(2023)
Article
Biochemistry & Molecular Biology
Samuel A. Vilchez Mercedes, Federico Bocci, Mona Ahmed, Ian Eder, Ninghao Zhu, Herbert Levine, Jose N. Onuchic, Mohit Kumar Jolly, Pak Kin Wong
Summary: In this study, the researchers used a combination of immunocytochemistry, single cell biosensors, and computational modeling to show that the transcription factor Nrf2 functions as a phenotypic stability factor for hybrid epithelial/mesenchymal cells during collective cancer migration. They also demonstrated that Nrf2 and EMT signaling are spatially coordinated near the leading edge, and that the Nrf2-EMT-Notch network enhances the expression of certain genes associated with the formation of leader cells and protruding tips.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Oncology
Abdullah A. Osman, Emre Arslan, Mason Bartels, Chieko Michikawa, Antje Lindemann, Katarzyna Tomczak, Wangjie Yu, Vlad Sandulache, Wencai Ma, Li Shen, Jing Wang, Anand K. Singh, Mitchell J. Frederick, Nakia D. Spencer, Jeffery Kovacs, Timothy Heffernan, William F. Symmans, Kunal Rai, Jeffrey N. Myers
Summary: This study aimed to investigate the mechanisms of cisplatin (CDDP) resistance and metastasis in head and neck squamous cell carcinomas (HNSCC). Activation of the NRF2 pathway was found to be a key event in tumor progression and metastasis. In vitro and in vivo experiments showed that NRF2 activation led to increased CDDP resistance and distant metastasis. Inhibiting NRF2 or restoring wild-type KEAP1 genes could overcome the resistance and reduce metastasis. Targeting the KEAP1/NRF2 pathway or glutamine metabolism may be a promising strategy for CDDP-resistant head and neck tumors.
CLINICAL CANCER RESEARCH
(2023)
Article
Cardiac & Cardiovascular Systems
Nicolas Zhou, Cynthia S. Bell, Hope A. Feldman, Cara L. Haymaker, Wayne L. Hofstetter, Anne S. Tsao, Reza J. Mehran, David C. Rice, Boris Sepesi, Mesothelioma Immune Genomic Grp
Summary: This study aimed to evaluate tumor thickness as a predictor and prognostic marker in neoadjuvant therapy for resectable malignant pleural mesothelioma. The results showed that baseline tumor thickness was associated with different tumor response and survival rates. Further studies are needed to validate the value of tumor thickness as a prognostic and predictive biomarker.
JOURNAL OF THORACIC AND CARDIOVASCULAR SURGERY
(2023)
Article
Anatomy & Morphology
Burhanuddin Sabuwala, Kishore Hari, Abhishek Shanmuga Vengatasalam, Mohit Kumar Jolly
Summary: Multistability is important in biological systems and can be achieved through positive feedback loops. This study investigates the bistability characteristics of mutual inhibition, mutual activation, and self-activation loops. The results show that mutual inhibition-based architecture provides discrete and robust control, multistability, and coordinated expression among multiple genes compared to mutual activation-based architecture. A combination of mutual inhibition and mutual activation architectures is proposed to improve coordination and multistability. This research improves our understanding of control structures in cell-fate decisions and provides insights for controlled decision-making in synthetic systems.
CELLS TISSUES ORGANS
(2023)
Article
Multidisciplinary Sciences
Sharaj Kunjar, Ariana Strandburg-Peshkin, Helge Giese, Pranav Minasandra, Sumantra Sarkar, Mohit Kumar Jolly, Nico Gradwohl
Summary: Consensus decision-making in social groups is influenced by communication links that determine information exchange. This study shows that strategically adjusting communication links can bias group-level outcomes and help achieve consensus, but strong preferences can lead to non-consensus outcomes.
ROYAL SOCIETY OPEN SCIENCE
(2023)
Article
Oncology
Viola Hedrich, Kristina Breitenecker, Gregor Ortmayr, Franziska Pupp, Heidemarie Huber, Doris Chen, Sarthak Sahoo, Mohit Kumar Jolly, Wolfgang Mikulits
Summary: This study identified PRAME as a target gene of the Gas6/Axl signaling pathway in hepatocellular carcinoma. PRAME promotes dedifferentiation, epithelial-to-mesenchymal transition, and invasion in liver cancer cells. The expression of PRAME is associated with an unfavorable prognosis in HCC patients.
Review
Chemistry, Multidisciplinary
Seemadri Subhadarshini, Joel Markus, Sarthak Sahoo, Mohit Kumar Jolly
Summary: Epithelial-mesenchymal plasticity (EMP) is a crucial factor in cancer metastasis and therapeutic resistance, allowing cancer cells to alter their characteristics along the epithelial-mesenchymal spectrum. Single-cell studies have provided valuable insights into the dynamics of EMP, showing the heterogeneity of hybrid epithelial/mesenchymal phenotypes and their impact on patient survival.
Article
Cell Biology
Shinjinee Sengupta, Namrata Singh, Ajoy Paul, Debalina Datta, Debdeep Chatterjee, Semanti Mukherjee, Laxmikant Gadhe, Jyoti Devi, Yeshwanth Mahesh, Mohit Kumar Jolly, Samir K. Maji
Summary: The study found a strong correlation between p53 amyloid load and cancer grades. Both mutant and wild-type p53 were capable of forming amyloids in cancer tissues. Furthermore, the p53 amyloids sequestered higher amounts of related proteins, suggesting a potential mechanism for loss of tumor-suppressive function and gain of oncogenic function in cancer progression.
JOURNAL OF CELL SCIENCE
(2023)
Review
Physics, Multidisciplinary
Federico Bocci, Dongya Jia, Qing Nie, Mohit Kumar Jolly, Jose Onuchic
Summary: The last decade has seen a rise in theoretical and computational models used to describe complex gene regulatory networks and their dynamics, which can result in multistable and heterogeneous cell populations. The application of theoretical modeling in genetic and biochemical circuits has become more widespread, with theoreticians incorporating concepts from statistical physics, non-linear dynamics, and network theory. This review provides an overview of important methodologies in the field, discusses current and future challenges, offers hands-on tutorials for solving and simulating biological system models, and presents concrete examples for theoreticians interested in this fast-developing field.
REPORTS ON PROGRESS IN PHYSICS
(2023)
Article
Mathematical & Computational Biology
Kishore Hari, William Duncan, Mohammed Adil Ibrahim, Mohit Kumar Jolly, Breschine Cummins, Tomas Gedeon
Summary: Mathematical modeling of gene regulatory networks (GRN) is challenging due to parameter dependence and lack of reliable experimental parameters. This study compares two approaches, RACIPE and DSGRN, for describing GRN dynamics across unknown parameters and finds agreement in simulation and predictions for cellular decision making. The observation is important as DSGRN parameter domains accurately predict ODE model dynamics within a biologically reasonable range of parameters.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Review
Computer Science, Interdisciplinary Applications
Maalavika Pillai, Emilia Hojel, Mohit Kumar Jolly, Yogesh Goyal
Summary: Computational models and tools have been used to understand the origins and nature of non-genetic heterogeneity in cancer, which has significant clinical implications. Non-genetic heterogeneity is increasingly associated with therapy resistance and metastasis in cancer. Identifying the origins of non-genetic heterogeneity is crucial for making clinical breakthroughs.
NATURE COMPUTATIONAL SCIENCE
(2023)
Article
Multidisciplinary Sciences
Paras Jain, Sophia Corbo, Kulsoom Mohammad, Sarthak Sahoo, Santhalakshmi Ranganathan, Jason T. George, Herbert Levine, Joseph Taube, Michael Toneff, Mohit Kumar Jolly
Summary: Epithelial-mesenchymal transition (EMT) and its reverse mesenchymal-epithelial transition (MET) play crucial roles in embryonic development, wound healing, and cancer metastasis. While short-term EMT induction can lead to reversible phenotypic changes, long-term EMT induction is often associated with irreversibility. In this study, we demonstrate that the phenotypic changes observed in MCF10A cells during long-term EMT induction by TGF-beta can in fact have longer timescales of reversibility. We also propose a mathematical model that explains how the epigenetic memory gained during long-term EMT induction can slow down the recovery to the epithelial state after TGF-beta withdrawal.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Oncology
Manas Sehgal, Soundharya Ramu, Joel Markus Vaz, Yogheshwer Raja Ganapathy, Srinath Muralidharan, Sankalpa Venkatraghavan, Mohit Kumar Jolly
Summary: This study investigates the relationship between gene expression patterns and phenotypic plasticity and heterogeneity in colorectal cancer (CRC). The results demonstrate the interconnectedness between different Consensus Molecular Subtypes (CMS) of CRC and specific phenotypes such as epithelial and mesenchymal characteristics. Additionally, the study reveals correlations between metabolic pathways and phenotypic scores, as well as between PD-L1 activity and mesenchymal phenotype. Single-cell RNA sequencing analysis further confirms the heterogeneity of different CMS subtypes. These findings have important implications for understanding CRC heterogeneity and developing targeted therapies.
TRANSLATIONAL ONCOLOGY
(2024)
