Article
Horticulture
Yaqiong Wu, Tianyu Han, Lianfei Lyu, Weilin Li, Wenlong Wu
Summary: Anthocyanins are important secondary metabolites in plants, which determine the color of flowers and fruits. They have various nutritional and medicinal functions, such as antioxidant, anticancer, and cardiovascular disease prevention. This review discusses the biosynthesis pathway of plant anthocyanins, the key structural genes involved, the impact of transcription factors and microRNAs, the influence of environmental factors, and the effects of six major exogenous hormones on anthocyanin synthesis and metabolism. Future research directions and trends in anthocyanins are also considered to provide a reference for future studies and applications.
SCIENTIA HORTICULTURAE
(2023)
Article
Gastroenterology & Hepatology
Ying Lu, Yangyang Li, Qi Liu, Na Tian, Peng Du, Fangming Zhu, Yichao Han, Xinnan Liu, Xisheng Liu, Xiao Peng, Xiaoxia Wang, Yuchen Wu, Lingfeng Tong, Yakui Li, Yemin Zhu, Lifang Wu, Ping Zhang, Ye Xu, Hanbei Chen, Bin Li, Xuemei Tong
Summary: In colorectal cancer, intratumoral regulatory T cells (Tregs) exhibit low activity of the MondoA-thioredoxin-interacting protein (TXNIP) axis and increased glucose uptake. While MondoA-deficient Tregs promoted Th1 responses in a subcutaneous colorectal cancer model, Treg-specific MondoA knockout mice were more susceptible to colorectal cancer induction.
Article
Gastroenterology & Hepatology
Kelsey Nicole Wiles, Cara Maria Alioto, Nathan Bruce Hodge, Margarette Helen Clevenger, Lia Elyse Tsikretsis, Frederick T. J. Lin, Marie-Pier Tetreault
Summary: This study reveals a novel interaction between IKK beta and STAT3 signaling in the epithelial cells of the esophagus, where IKK beta/IL23/STAT3 signaling regulates neutrophil recruitment during inflammation onset.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Article
Plant Sciences
Maite Colinas, Jacob Pollier, Dries Vaneechoutte, Deniz G. Malat, Fabian Schweizer, Liesbeth De Milde, Rebecca De Clercq, Joana G. Guedes, Teresa Martinez-Cortes, Francisco J. Molina-Hidalgo, Mariana Sottomayor, Klaas Vandepoele, Alain Goossens
Summary: Catharanthus roseus produces a variety of MIA metabolites in a heavily branched pathway, with gene expression being highly specific to cell type, organ, and stress. Further study of ORCA TFs reveals subfunctionalization in terms of regulating target genes and working synergistically with MYC2. Specific amino acid residues within ORCA DNA-binding domains play a role in regulating MIA pathway branches differently.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Reilly A. Sample, Marina F. Nogueira, Robi D. Mitra, Sidharth V. Puram
Summary: Epithelial-to-mesenchymal transition (EMT) is a process in cancer where cells lose their epithelial characteristics and gain mesenchymal phenotypes, driving tumor invasion and metastasis. Recent studies have identified intermediate hybrid E/M states along an epithelial-mesenchymal continuum during EMT. This summary focuses on the involvement of epigenetic regulators, chromatin remodelers, and DNA methylation in hybrid E/M states, while also addressing the challenges of pharmacologically targeting EMT and proposing future research directions.
Article
Biochemical Research Methods
Alba Rubio-Canalejas, Lucas Pedraz, Eduard Torrents
Summary: ReViTA (Reverse in Vitro Transcription Assay) is a novel in vitro transcription-based method used to study gene expression under specific transcription factors. The method was evaluated using two different transcription factors, AlgR and LexA, and demonstrated successful gene expression regulation. ReViTA has the potential to be a rapid and accessible method for studying genes and regulators in various species.
Article
Biotechnology & Applied Microbiology
Wen Ye, Yachao Cui, Jian Rong, Wenlin Huang, Zhousan Zheng, Anqi Li, Yingchang Li
Summary: The expression of MCPIP1 is reduced in colorectal cancer tissues and is associated with poor prognosis. MCPIP1 exerts its anti-cancer effect by suppressing the NF-κB signaling pathway, making it a potential treatment option.
CANCER GENE THERAPY
(2023)
Article
Biotechnology & Applied Microbiology
Zhenyang Liao, Fei Dong, Juan Liu, Lele Xu, Amy Marshall-Colon, Ray Ming
Summary: This research analyzed the developmental stages of papaya pistil and identified differentially expressed genes related to pistil development and sex differentiation. Transcription factor and hormone-related genes were revealed based on functional and regulatory network analysis. These findings provide new insights into the molecular mechanism of pistil development and sex differentiation in papaya.
Review
Cell Biology
Logan Meurer, Leonard Ferdman, Beau Belcher, Troy Camarata
Summary: The SIX family of transcription factors play crucial roles in embryonic development and tumorigenesis, controlling gene expression, promoting cell self-renewal and differentiation, and disruptions in their function lead to congenital defects and cancer development. Research in developmental biology and cancer have provided extensive understanding of SIX family functions, with common themes emerging when comparing their roles in embryonic and cancer development. The complementary nature of these two fields highlights how knowledge in one area can facilitate new aspects of experimentation in the other.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tiebin Wang, Nathan Tague, Stephen A. Whelan, Mary J. Dunlop
Summary: Transcription factor decoys can effectively regulate gene expression, with tunability through changes in copy number or modifications to the DNA decoy site sequence. Introducing the decoy system can significantly increase arginine production in metabolic flux steering, without affecting growth compared to wild type strains.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Oncology
Gang-Jian Wang, Long-Tao Huangfu, Xiang-Yu Gao, Xue-Jun Gan, Xiao-Fang Xing, Jia-Fu Ji
Summary: Assessment of immune-related transcription factor (IRTF) regulation patterns in gastric cancer patients can enhance our understanding of immune specificities and provide effective strategies for personalized therapy.
FRONTIERS IN ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Mahmoud Ahmed, Trang Huyen Lai, Trang Minh Pham, Sahib Zada, Omar Elashkar, Jin Seok Hwang, Deok Ryong Kim
Summary: This study evaluated the impact of adipogenic transcription factors and co-factors on autophagy gene expression during adipocyte differentiation and established a model to investigate the regulatory mechanisms involved. The findings suggest a hierarchical arrangement between adipogenic transcription factors and co-factors, which collectively regulate autophagy during adipocyte differentiation.
Article
Multidisciplinary Sciences
Yuta Hiraike, Kaede Saito, Misato Oguchi, Takahito Wada, Gotaro Toda, Shuichi Tsutsumi, Kana Bando, Junji Sagawa, Gaku Nagano, Haruya Ohno, Naoto Kubota, Tetsuya Kubota, Hiroyuki Aburatani, Takashi Kadowaki, Hironori Waki, Shintaro Yanagimoto, Toshimasa Yamauchi
Summary: NFIA improves glucose homeostasis and limits weight gain by upregulating oxidative phosphorylation and brown-fat-specific genes, while downregulating inflammatory cytokine genes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Immunology
Lulu Xu, Weiping Hu, Jing Zhang, Jieming Qu
Summary: This study explored the effects of V1 on acute lung inflammation and found that increased expression of V1 may have a protective role in acute inflammation, while interventions targeting V1 might cause a cytokine storm induced by infection.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Audrey R. Q. Lim, Que Kong, Sanjay K. Singh, Liang Guo, Ling Yuan, Wei Ma
Summary: This study identifies and characterizes HaWRI1, a sunflower ortholog of the transcription factor WRI1, which is highly expressed in developing seeds and stimulates oil accumulation. It is demonstrated that HaWRI1 acts as a pivotal transcription factor controlling the expression of genes involved in late glycolysis and fatty acid biosynthesis. The study also highlights the importance of an 80 amino-acid C-terminal domain of HaWRI1 for its transactivation. Additionally, seed-specific overexpression of HaWRI1 in Arabidopsis plants leads to enhanced seed oil content, suggesting its potential for bioengineering sunflower oil yield improvement.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, General & Internal
Rashidah Baharudin, Muhiddin Ishak, Azliana Muhamad Yusof, Sazuita Saidin, Saiful Effendi Syafruddin, Wan Fahmi Wan Mohamad Nazarie, Learn-Han Lee, Nurul-Syakima Ab Mutalib
Summary: This study profiles the DNA methylation in colorectal cancer (CRC) and identifies several potential important methylated genes, which may serve as novel candidate biomarker genes in CRC. Aberrant DNA methylation is significantly involved in CRC pathogenesis and is associated with gene silencing.
Review
Biochemistry & Molecular Biology
Pey Yee Lee, Yeelon Yeoh, Teck Yew Low
Summary: Kinases play important roles in regulating biological processes and are associated with cancer. Small-molecule kinase inhibitors have revolutionized cancer treatment, but their selectivity and effectiveness are still challenging. This review provides an overview of the role of kinases in carcinogenesis, the progress of approved small-molecule kinase inhibitors, and the application of mass spectrometry-based proteomics strategies in kinase inhibitor design. It also discusses the challenges and outlook of mass spectrometry-based proteomics techniques for kinase drug research.
Article
Cell Biology
Asmaa Y. Abuhamad, Nurul Nadia Mohamad Zamberi, Ling Sheen, Safaa M. Naes, Siti Nur Hasanah Mohd Yusuf, Asilah Ahmad Tajudin, M. Aiman Mohtar, Amir Syahir Amir Hamzah, Saiful Effendi Syafruddin
Summary: Breast cancer is often caused by genetic alterations, particularly missense mutations, in the TP53 gene. This study used CRISPR-based gene editing technology, specifically the prime editing tool, to revert and introduce a specific TP53 mutation in breast cancer cell lines. Sanger sequencing was initially used but proved to be less sensitive than amplicon target sequencing, which detected the expected substitutions. The overall editing efficiency was low, suggesting the need for workflow and efficiency improvements in future experiments.
Review
Biochemistry & Molecular Biology
Nisa Syakila A. Rahman, Syazalina Zahari, Saiful Effendi Syafruddin, Mohd Firdaus-Raih, Teck Yew Low, M. Aiman Mohtar
Summary: The endoplasmic reticulum (ER) is essential for protein synthesis, folding, and maturation. The protein disulfide isomerase (PDI) family, which plays crucial roles in the ER, has been found to be elevated in cancer and supports cancer growth and metastasis.
CELL AND BIOSCIENCE
(2022)
Article
Biochemical Research Methods
Teck Yew Low, Yu-Ju Chen, Yasushi Ishihama, Max Ching Ming Chung, Stuart Cordwell, Terence Chuen Wai Poon, Ho Jeong Kwon
Summary: The AOHUPO Online Education Series aims to promote scientific education and collaboration among young scientists in the Asia-Oceania region. The second series focused on the renaissance of clinical proteomics and attracted over 300 participants from 29 countries/regions.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Medicine, General & Internal
Muhammad Irfan Abdul Jalal, Kai Shen Ooi, Kai Cheong Foo, Azrul Azlan Hamzah, Chee Seong Goh, Chang Fu Dee, Poh Choon Ooi, Muhamad Ramdzan Buyong, Teck Yew Low, Xin Yun Chua, Doris Sie Chong Lau, Zarina Abdul Latiff, Fook Choe Cheah
Summary: This study aims to find a method to reduce pain in children during intravenous cannulation by using dissolvable maltose microneedles to enhance the absorption of EMLA(R). A randomized trial will compare the effects of four interventions on pain scores and skin conductance algesimeter index, with data collected using VAS rulers and a PainMonitor (TM) machine.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Asmaa Y. Abuhamad, Nurul Nadia Mohamad Zamberi, Sakari Vanharanta, Siti Nur Hasanah Mohd Yusuf, M. Aiman Mohtar, Saiful Effendi Syafruddin
Summary: This study found that clear cell renal cell carcinoma (ccRCC) cells are able to secrete PDGFB, which can activate the mTORC1 signaling pathway and promote the development of ccRCC. The level of PDGFB secretion was positively correlated with the expression of intracellular KLF6 and PDGFB. Reintroduction of either KLF6 or PDGFB sustained mTORC1 signaling activity in KLF6-targeted ccRCC cells. Conditioned media of PDGFB-overexpressing ccRCC cells was able to re-activate mTORC1 activity in KLF6-targeted cells. Cancer cell-derived PDGFB can mediate mTORC1 signaling pathway activation in ccRCC, further solidifying the association between the KLF6-PDGFB axis and mTORC1 signaling pathway activity in ccRCC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Syazalina Zahari, Saiful Effendi Syafruddin, M. Aiman Mohtar
Summary: Breast cancer is a complex and challenging disease. The secretome, which includes proteins, lipids, and nucleic acids secreted by breast cancer cells, plays a crucial role in the development, progression, and drug resistance of breast cancer. Understanding the role of the secretome is essential for developing innovative therapies. This review explores the impact of the secretome on breast cancer progression and its interactions with the tumor microenvironment, and identifies potential therapeutic opportunities.
Review
Biology
Marjanu Hikmah Elias, Nurunnajah Lazim, Zulazmi Sutaji, Mohammad Azrai Abu, Abdul Kadir Abdul Karim, Azizah Ugusman, Saiful Effendi Syafruddin, Mohd Helmy Mokhtar, Mohd Faizal Ahmad
Summary: Endometriosis is an inflammatory chronic systemic disease causing pelvic pain and infertility. The identification of the disease is insufficient, leading to a high misdiagnosis rate. Our focus is on the abnormal hypermethylation of HOXA10 in endometriosis. A comprehensive literature search was conducted to determine the DNA methylation level of HOXA10 in endometriosis patients across different populations. The gathered evidence demonstrated a higher HOXA10 DNA methylation level in the endometrium tissue of women with endometriosis in all included studies.
Article
Biology
Nur Syakirah Othman, Amilia Aminuddin, Shahidee Zainal Abidin, Saiful Effendi Syafruddin, Mohd Faizal Ahmad, Norfilza Mohd Mokhtar, Jaya Kumar, Adila A. Hamid, Azizah Ugusman
Summary: Hyperglycemia in diabetes mellitus leads to oxidative stress, apoptosis, and dysfunction of vascular endothelial cells. This study aimed to analyze the miRNA profile of human umbilical-vein endothelial cells (HUVECs) exposed to hyperglycemia. RNA sequencing revealed 17 differentially expressed miRNAs between control and hyperglycemia groups, with 4 upregulated and 13 downregulated miRNAs. Validation with qPCR confirmed the differential expression of two miRNAs. These findings suggest a role for miRNAs in diabetic vascular endothelial dysfunction and provide potential targets for therapy.
Review
Biochemistry & Molecular Biology
Duangnapa Kovanich, Teck Yew Low, Manuela Zaccolo
Summary: cAMP is a second messenger that plays a crucial role in regulating cellular functions. The compartmentalization of cAMP signaling is essential for its specificity, and the formation of dynamic signaling domains is responsible for precise spatiotemporal regulation. Proteomics can be used to identify the components of these domains and define the dynamic landscape of cellular cAMP signaling. Understanding compartmentalized cAMP signaling in physiological and pathological conditions can provide insights into disease mechanisms and guide the development of precision medicine interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Alyssa Zi-Xin Leong, Pey Yee Lee, M. Aiman Mohtar, Saiful Effendi Syafruddin, Yuh-Fen Pung, Teck Yew Low
Summary: This review discusses the history, development, and strategies used for identifying, validating, and characterizing sORFs and microproteins. Methods such as ribosome profiling, mass spectrometry-based proteomics, CRISPR/Cas9 screening, and protein-protein interaction studies are employed for detection and functional characterization. The review also highlights the challenges and potential solutions in identifying and validating these novel entities.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
