Article
Biochemistry & Molecular Biology
Andressa G. Amaral, Camille C. C. da Silva, Julian D. C. Serna, Kinulpe Honorato-Sampaio, Jessica A. Freitas, Amaro N. Duarte-Neto, Antonio C. Bloise, Laura Cassina, Marcos Y. Yoshinaga, Adriano B. Chaves-Filho, Feng Qian, Sayuri Miyamoto, Alessandra Boletta, Silvana Bordin, Alicia J. Kowaltowski, Luiz F. Onuchic
Summary: The disruption of polycystin-1 cleavage leads to cardiac metabolic rewiring in mice, further expanding the understanding of heart dysfunction associated with Pkd1 deficiency.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
Article
Biochemistry & Molecular Biology
Ming-Yang Chang, Shen-Hsing Hsu, Li-Yi Ma, Li-Feng Chou, Cheng-Chieh Hung, Ya-Chung Tian, Chih-Wei Yang
Summary: The study suggests that suramin may reduce renal cyst growth and inflammation by inhibiting the purinergic signaling pathway. However, treatment with suramin could cause tubular cell injuries, limiting its therapeutic potential. Further research on other purinergic receptor antagonists with less nephrotoxicity is needed for the treatment of ADPKD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Urology & Nephrology
Matteus Krappitz, Rishi Bhardwaj, Ke Dong, Tobias Staudner, Duygu Elif Yilmaz, Carlotta Pioppini, Parisa Westergerling, David Ruemmele, Till Hollmann, Thuy Anh Nguyen, Yiqiang Cai, Anna-Rachel Gallagher, Stefan Somlo, Sorin Fedeles
Summary: The study found that the expression of active XBP1 in a murine model with missense Pkd1 mutations can increase the levels of mutant PC1 and improve its trafficking in cells. Transgenic expression of spliced XBP1 can reduce cell proliferation and improve ADPKD progression in tubule segments destined to form cysts.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2023)
Review
Biochemical Research Methods
Jiashu Liu, Cui-Xiang Lin, Xiaoqi Zhang, Zongxuan Li, Wenkui Huang, Jin Liu, Yuanfang Guan, Hong-Dong Li
Summary: Alternative splicing (AS), a key pathway for transcriptional regulation, has been shown to be associated with complex diseases. Computational approaches for detecting disease-associated AS events have been developed. This review discusses the metrics used for characterizing AS events quantitatively. It also reviews and discusses three types of methods for detecting disease-associated splicing events: differential splicing analysis, aberrant splicing detection, and splicing-related network analysis. Additionally, methods for detecting genetic variants that potentially regulate splicing are described. Experimental comparisons are conducted to illustrate the performance of each method. The limitations of these methods are discussed, as well as potential ways to address them. This review aims to provide a systematic understanding of computational approaches for analyzing disease-associated splicing.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Cell Biology
Hyun Jun Jung, Eryn E. Dixon, Richard Coleman, Terry Watnick, Jeremy F. Reiter, Patricia Outeda, Valeriu Cebotaru, Owen M. Woodward, Paul A. Welling
Summary: This study identified genes and pathways associated with autosomal dominant polycystic kidney disease (ADPKD) using a comprehensive gene expression database. The data suggests a potential signaling axis between PC2, cilia, Wnt and MAPK signaling, and dysregulation of Gli-similar transcription factors in the initiation of cyst formation in ADPKD.
PHYSIOLOGICAL GENOMICS
(2023)
Article
Multidisciplinary Sciences
Laura Onuchic, Valeria Padovano, Giorgia Schena, Vanathy Rajendran, Ke Dong, Xiaojian Shi, Raj Pandya, Victoria Rai, Nikolay P. Gresko, Omair Ahmed, TuKiet T. Lam, Weiwei Wang, Hongying Shen, Stefan Somlo, Michael J. Caplan
Summary: In this study, the researchers found that the C-terminal 200 amino acids of PC1 can interact with the mitochondrial enzyme NNT, suppressing cystic disease and preserving renal function. This finding opens up new possibilities for gene therapy strategies for autosomal dominant polycystic kidney disease.
NATURE COMMUNICATIONS
(2023)
Article
Peripheral Vascular Disease
Mouad Hamzaoui, Deborah Groussard, Dorian Nezam, Zoubir Djerada, Gaspard Lamy, Virginie Tardif, Anais Dumesnil, Sylvanie Renet, Valery Brunel, Dorien J. M. Peters, Laurence Chevalier, Melanie Hanoy, Paul Mulder, Vincent Richard, Jeremy Bellien, Dominique Guerrot
Summary: This study provides the first in vivo demonstration that specific deletion of Pkd1 in endothelial cells promotes endothelial dysfunction and hypertension, impairs arteriovenous fistula development, and potentiates the cardiovascular alterations associated with chronic kidney disease.
Article
Genetics & Heredity
Qianying Zhao, Yu Tan, Xiao Xiao, Qinqin Xiang, Mei Yang, He Wang, Shanling Liu
Summary: In this study, trio exome sequencing was used to discover a novel PKD1 variant as the cause of ADPKD in a Chinese family. The variant at the exon-intron boundary induced alternative splicing and resulted in the formation of abnormal transcription products. Validating the variant on the cDNA level provided more comprehensive genetic information and expanded the spectrum of PKD1 variants in ADPKD.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2023)
Article
Medicine, General & Internal
Huixia Li, Chunli Wang, Ruochen Che, Bixia Zheng, Wei Zhou, Songming Huang, Zhanjun Jia, Aihua Zhang, Fei Zhao, Guixia Ding
Summary: Autosomal recessive polycystic kidney disease (ARPKD) is a rare ciliopathy characterized by enlarged kidneys and collecting duct dilatation. There is currently no efficient treatment for ARPKD. We designed antisense oligonucleotides (ASOs) to correct splicing defects and investigated their potential as a treatment option for ARPKD.
JOURNAL OF CLINICAL MEDICINE
(2023)
Review
Immunology
Jianli Zhou, Qiao Zhang, Yuzhen Zhao, Yuchen Song, Yanan Leng, Moxian Chen, Shaoming Zhou, Zhaoxia Wang
Summary: Inflammatory bowel disease (IBD) is a group of chronic diseases including Crohn's disease and ulcerative colitis, which have a global impact on both children and adults. The burden of IBD is increasing worldwide, and the costs associated with it are high. The pathogenesis of IBD is still unclear, but is believed to be related to environmental factors, gut microbiota, immune imbalance, and genetic susceptibility. This article reviews the research progress on alternative splicing events, splicing factors, and splicing mutations associated with IBD.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Cheng-Chao Lin, Luis F. Menezes, Jiahe Qiu, Elisabeth Pearson, Fang G. Zhou, Yu Ishimoto, D. Eric Anderson, Gregory G. Germino
Summary: This study reports a new mouse model in which HA epitopes and eGFP are inserted into the endogenous mouse Pkd1 gene using CRISPR/Cas9. The researchers were able to visualize endogenous PC1-eGFP and performed affinity-purification mass spectrometry (AP-MS) and network analyses. The findings suggest that this mouse model and interactome data will be valuable for understanding the function of PC1, but new methods and brighter tags are needed to track endogenous PC1.
Review
Biochemistry & Molecular Biology
Robin L. Maser, James P. Calvet, Stephen C. Parnell
Summary: This article reviews the GPCR-like functions of Polycystin-1 (PC1) and their relevance to cystic disease. PC1 has a GPCR-like ability to bind to the cell membrane and regulate G protein signaling, which is crucial for preventing kidney cyst development. However, the specific mechanisms by which PC1 regulates G protein activity still need to be further investigated.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Urology & Nephrology
Biswajit Padhy, Jian Xie, Runping Wang, Fang Lin, Chou-Long Huang
Summary: Polycystin-2 in the endoplasmic reticulum plays a critical role in the pathogenesis of autosomal dominant polycystic kidney disease (ADPKD) by acting as a potassium ion channel and facilitating the exchange of potassium and calcium ions. This study provides a deeper understanding of ADPKD and suggests that TRIC-B activators could be used as a potential pharmacotherapy.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2022)
Review
Biochemistry & Molecular Biology
Lingfei Luo, Sudipto Roy, Li Li, Ming Ma
Summary: Autosomal dominant polycystic kidney disease (ADPKD) is a monogenic disease caused by mutations in PKD1 and PKD2. The proteins encoded by these genes, polycystin 1 (PC1) and polycystin 2 (PC2), are located in the cilia of renal epithelial cells and play a role in inhibiting cyst activation. However, PC deficiency leads to cyst growth. Re-expression of PCs in established cysts has been shown to reverse PKD, suggesting potential therapeutic implications. Overall, this review highlights novel avenues for future research on PCs and their therapeutic potential for ADPKD.
TRENDS IN MOLECULAR MEDICINE
(2023)
Article
Medicine, General & Internal
Ahsan Alam, Emilie Cornec-Le Gall, Ronald D. Perrone
Summary: This article describes autosomal dominant polycystic kidney disease, its signs and symptoms, diagnosis, and treatment options.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Correction
Multidisciplinary Sciences
Wang Zheng, Xiaoyong Yang, Ruikun Hu, Ruiqi Cai, Laura Hofmann, Zhifei Wang, Qiaolin Hu, Xiong Liu, David Bulkley, Yong Yu, Jingfeng Tang, Veit Flockerzi, Ying Cao, Erhu Cao, Xing-Zhen Chen
NATURE COMMUNICATIONS
(2019)
Correction
Biochemistry & Molecular Biology
P. Kashyap, C. Ng, Z. Wang, B. Li, M. Arif Pavel, H. Martin, Y. Yu
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Zhifei Wang, Courtney Ng, Xiong Liu, Yan Wang, Bin Li, Parul Kashyap, Haroon A. Chaudhry, Alexis Castro, Enessa M. Kalontar, Leah Ilyayev, Rebecca Walker, R. Todd Alexander, Feng Qian, Xing-Zhen Chen, Yong Yu
Article
Multidisciplinary Sciences
Qiang Su, Mengying Chen, Yan Wang, Bin Li, Dan Jing, Xiechao Zhan, Yong Yu, Yigong Shi
Summary: This study investigates the structure of the murine PKD1L3/PKD2L1 heteromeric complex and the mechanism of calcium-induced channel activation, revealing a potential new Ca2+ binding site.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Bin Li, Yan Wang, Alexis Castro, Courtney Ng, Zhifei Wang, Haroon Chaudhry, Zainab Agbaje, Gabriella A. Ulloa, Yong Yu
Summary: This study reveals the importance of two extracellular loops in human Otop1 channel function, with residue H229 critical for proton sensing and the S11-12 loop essential for the channel's structure and function.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xia Yao, Shuai Gao, Jixin Wang, Zhangqiang Li, Jian Huang, Yan Wang, Zhifei Wang, Jiaofeng Chen, Xiao Fan, Weipeng Wang, Xueqin Jin, Xiaojing Pan, Yong Yu, Armando Lagrutta, Nieng Yan
Summary: The study reveals the molecular basis for the physical and pharmacodynamic interaction of sofosbuvir and amiodarone on the scaffold of Cav channels.
Article
Multidisciplinary Sciences
Xia Yao, Yan Wang, Zhifei Wang, Xiao Fan, Di Wu, Jian Huang, Alexander Mueller, Sarah Gao, Miaohui Hu, Carol Robinson, Yong Yu, Shuai Gao, Nieng Yan
Summary: The cryo-EM structures of the R-type voltage-gated Ca2+ channel Ca(v)2.3 and its mutant were determined, revealing the potential drug target for neurological diseases and the importance of intracellular segments in channel conformation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Yan Wang, Zhifei Wang, Mahmud Arif Pavel, Courtney Ng, Parul Kashyap, Bin Li, Tiago D. C. Morais, Gabriella A. Ulloa, Yong Yu
Summary: Autosomal dominant polycystic kidney disease is caused by mutations in PKD1 or PKD2 genes, and this study investigated the effects of 31 point mutations on the ion channel activity of a PC2 mutant expressed in Xenopus oocytes. The results showed that mutations in the transmembrane domains, channel pore region, and extracellular tetragonal opening for polycystins domain were critical for PC2 channel function, while mutations in the tetragonal opening for polycystins domain and C-terminal tail had mild or no effects. The study provided insights into the structure and function of the PC2 ion channel and the molecular mechanism of pathogenesis caused by these mutations.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Shuai Gao, Xia Yao, Jiaofeng Chen, Gaoxingyu Huang, Xiao Fan, Lingfeng Xue, Zhangqiang Li, Tong Wu, Yupeng Zheng, Jian Huang, Xueqin Jin, Yan Wang, Zhifei Wang, Yong Yu, Lei Liu, Xiaojing Pan, Chen Song, Nieng Yan
Summary: Cav1.2 channels have important functions in neuronal and physiological processes. Cryo-EM structures of human Cav1.2 in different states, including its apo form and in complex with drugs or peptides, reveal consistent inactivated conformations. The binding of certain drugs induces structural changes, such as upward movement of VSDII and dilation of the selectivity filter and its surrounding segments.
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)