{"title":"Leucine-rich repeat kinase 2 biomarkers for Parkinson's disease.","authors":"Nicolas Dzamko","doi":"10.1042/BCJ20253099","DOIUrl":"https://doi.org/10.1042/BCJ20253099","url":null,"abstract":"<p><p>Leucine-rich repeat kinase 2 (LRRK2) has emerged as a promising therapeutic target for the treatment of neurodegenerative Parkinson's disease (PD). Data from a multitude of pre-clinical models are supportive of a potential role for LRRK2 therapies to ameliorate cellular dysfunctions found in PD, and small molecules to inhibit LRRK2 kinase activity, as well as antisense oligonucleotides to target the protein itself, are in clinical trials. Despite this, exactly how LRRK2 contributes to PD pathogenesis remains to be determined, and definitive biomarkers to track LRRK2 function are still required. Such biomarkers can be useful for monitoring the pharmacodynamic response of LRRK2 therapeutics and/or understanding the relationship between LRRK2 and the clinical progression of PD. Moreover, biomarkers that can identify increased LRRK2 levels or activity beyond just carriers of pathogenic LRRK2 mutations will be important for expanding LRRK2 therapeutics to other PD populations. This review summarizes recent findings regarding biomarkers of LRRK2.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 11","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"LRRK2-mediated mitochondrial dysfunction in Parkinson's disease.","authors":"Silas A Buck, Laurie H Sanders","doi":"10.1042/BCJ20253062","DOIUrl":"https://doi.org/10.1042/BCJ20253062","url":null,"abstract":"<p><p>Parkinson's disease (PD) is a neurodegenerative disorder characterized by motor symptoms including tremor, rigidity, and bradykinesia as well as degeneration of dopamine (DA) neurons in the substantia nigra pars compacta (SNc). A minority of PD cases are familial and are caused by a single genetic mutation. One of the most common PD-causing genes is leucine-rich repeat kinase 2 (LRRK2), which causes an autosomal dominant PD that presents very similarly to sporadic PD. Pathogenic mutations in LRRK2 increase its kinase activity, indicated by both LRRK2 autophosphorylation and phosphorylation of its substrates. To date, the mechanism(s) by which elevated LRRK2 kinase activity induces DA neuron degeneration and PD has not been fully elucidated. One potential mechanism may involve the role of LRRK2 on mitochondria, as mitochondrial dysfunction has been linked to PD pathogenesis, and exciting recent evidence has connected PD pathogenic mutations in LRRK2 to multiple aspects of mitochondrial dysfunction associated with the disease. In this review, we discuss the current knowledge implicating LRRK2 in mitochondrial energetics, oxidative stress, genome integrity, fission/fusion, mitophagy, and ion/protein transport in PD, as well as examine the potential role LRRK2 may play in mediating the effects of mitochondrial therapeutics being investigated for treatment of PD.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 11","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Molecular basis and therapeutic implications of binary YAPOn/YAPOff cancer classes.","authors":"Pinky Sharma, Yale S Michaels, Joel D Pearson","doi":"10.1042/BCJ20253077","DOIUrl":"https://doi.org/10.1042/BCJ20253077","url":null,"abstract":"<p><p>Cancers have traditionally been classified based on their tissue of origin. However, with advances in sophisticated genome sequencing techniques and progression toward an era of precision medicine, it has become increasingly clear that classifying tumors based on unifying molecular features instead of tissue of origin may hold the key to improving patient outcomes. Various efforts have been undertaken to address this critical aspect of cancer biology, but it is still unclear as to the best approach to stratify tumors into different molecular classes. One approach is to define many small subclasses based on complex molecular signatures, while another option is to divide cancers into larger groups based on higher-order features of cancer behavior. This latter approach holds appeal as it may provide opportunities to identify broadly relevant therapeutics. However, our understanding of these fundamental 'rules' of cancer biology and how they can be used to better classify and treat cancers is in its infancy. We recently demonstrated that cancers can be functionally stratified into binary YAPon and YAPoff super-classes with unique therapeutic vulnerabilities based on distinct expression and function of the transcriptional coactivators, YAP and TAZ. In YAPon cancers, YAP and TAZ drive oncogenesis, whereas in YAPoff cancers, YAP and TAZ are instead tumor suppressors. In this review, we discuss our understanding of these distinct cancer classes with a focus on the mechanisms that underlie the opposite function of YAP/TAZ in YAPon and YAPoff cancers, as well as the potential therapeutic implications of these findings.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 11","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The bacterial transcription terminator, Rho, functions as an RNA:DNA hybrid (RDH) helicase in vivo.","authors":"Ankita Bhosale,Ranjan Sen","doi":"10.1042/bcj20253089","DOIUrl":"https://doi.org/10.1042/bcj20253089","url":null,"abstract":"Ribonuclease HI (rnhA) removes the deleterious RNA:DNA hybrids (RDHs) by cleaving its RNA component. The bacterial transcription terminator Rho is an RNA-dependent 5' → 3' helicase capable of unwinding RDH formed on a single-stranded RNA in vitro. We hypothesize that Rho might be directly involved in RDH removal in vivo. Here, we demonstrate that Rho primary RNA-binding site (PBS) mutants defective in RNA binding and helicase activity are synthetically lethal specifically when RNase HI is absent. This lethality was not observed in the absence of RNase HII (rnhB) alone. Rho-PBS mutants in an rnhA- strain exhibited increased plasmid-concatemer and plasmid copy number, altered cell morphology, and were highly susceptible to DNA-damaging agents. These Rho mutants increased the accumulation of RDHs in vivo, suggesting defects in the RDH removal process. Rho was colocalized to RDHs in vivo when RNase HI was absent. Certain catalytically inactive mutants of RNase H that bind to the RDH blocked the entry of Rho to the RDH, inducing cell death, indicating the role of Rho in the removal of deleterious RDHs in the absence of RNase HI. Under in vitro conditions, Rho was capable of binding to the RDHs and unwinding them in a rut-site-dependent manner. Therefore, we concluded that in the absence of RNase HI, Rho, by its RNA-dependent helicase activity, is capable of unwinding RDHs in a rut-site-dependent manner. These results establish the non-transcription terminator role of Rho and its functional synergy with RNase HI in vivo.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"16 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144146099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Reconstituted systems for studying the architecture and dynamics of actin networks.","authors":"Alice Cantat,Alexandra Colin","doi":"10.1042/bcj20253044","DOIUrl":"https://doi.org/10.1042/bcj20253044","url":null,"abstract":"Actin, a ubiquitous protein essential for numerous cellular functions, is found in all eukaryotes. Despite extensive research across molecular to organismal scales, fundamental questions persist regarding the regulation of dynamic actin architectures, their interaction with membranes, and their mechanical properties. Characterizing the factors governing these processes presents significant challenges. This review emphasizes the value of simplified, reconstituted systems in addressing these unresolved questions. We particularly highlight the critical importance of macroscopic, network-level reconstitutions for tackling these issues. We first describe the available methodological toolkit for (1) controlling actin polymerization spatiotemporally and (2) confining actin networks within closed environments to examine boundary constraint effects or the impact of limited component availability on network properties. We then review studies employing these reconstituted systems to investigate how actin architecture influences various processes and how dynamic actin structures are established and maintained. Further, we discuss how network-level reconstitutions have enhanced our understanding of actin networks' mechanical properties and their interaction with the lipid membranes. Throughout the review, we discuss future perspectives for each topic and explain how macroscale reconstitutions can provide deeper mechanistic insights into actin-related processes.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"23 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144133663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohammed Alhadidy,Rebecca Mueller,Jared Lamp,Nicholas Kanaan
{"title":"Polyamination with spermidine enhances pathogenic tau conformations while reducing filamentous aggregate formation in vitro.","authors":"Mohammed Alhadidy,Rebecca Mueller,Jared Lamp,Nicholas Kanaan","doi":"10.1042/bcj20253079","DOIUrl":"https://doi.org/10.1042/bcj20253079","url":null,"abstract":"Tau is subject to a broad range of post-translational modifications (PTMs) that regulate its biological activity in health and disease, including microtubule (MT) dynamics, aggregation, and adoption of pathogenic conformations. The most studied PTMs of tau are phosphorylation and acetylation; however, the salience of other PTMs is not fully explored. Tissue transglutaminase (TG) is an enzyme whose activity is elevated in Alzheimer's disease (AD). TG action on tau may lead to intramolecular and intermolecular cross-linking along with the incorporation of cationic polyamines [e.g. spermidine (SPD)] onto glutamine residues (Q). Even though SPD levels are significantly elevated in AD, the effects of SPD polyamination on tau biology have yet to be examined. In this work, we describe a method to produce recombinant SPD-modified tau where SPD modifications are mainly localized to Q residues within the N-terminus. MT binding and polymerization assays showed that SPD modification does not significantly alter tau's binding to MTs but increases MT polymerization kinetics. In addition, biochemical and biophysical assays showed that SPD polyamination of tau markedly reduces tau polymerization into filamentous and β-sheet containing aggregates. On the other hand, SPD modification promotes the formation of pathogenic conformations (e.g. oligomerization and misfolding) by tau with or without inducing tau polymerization. Taken together, these data suggest that SPD polyamination of tau enhances its ability to polymerize microtubules and favors the adoption of pathogenic tau conformations but not filamentous aggregates in vitro.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"31 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144114168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cas11 augments Cascade functions in type I-E CRISPR system but is redundant for gene silencing and plasmid interference.","authors":"Neha Pandey,Chitra Misra,Devashish Rath","doi":"10.1042/bcj20253056","DOIUrl":"https://doi.org/10.1042/bcj20253056","url":null,"abstract":"The structural and mechanistic complexity of Escherichia coli's type I CRISPR-Cas system compared to the multidomain, single effector protein-based type II systems, limits its application in genome editing and silencing. Despite higher prevalence of the type I endogenous systems in bacteria, significant research has focused on improving the type II systems. While the type-I CRISPR system possesses several advantages over others, it may benefit from further studies to simplify the system for ease of use. To enable this, the dispensability of the type-I Cascade components (Cas8, Cas11, Cas7, Cas5, Cas6) for genome editing and silencing applications was evaluated in vivo. We created deletion variants of each of the Cascade components and investigated their effects on gene silencing and plasmid interference in two genetically distinct Escherichia coli lineages, BW25113, a K-12 strain that bears an endogenous, albeit repressed type I-E CRISPR system and BL21, a natural mutant lacking the type I-E CRISPR-Cascade system. Cas8, Cas7 and Cas5 were found to be indispensable for gene silencing and plasmid interference. Dispensability of Cas6, which is involved in crRNA maturation, was strain-dependent. Notably, Cas11 which has no definitive function assigned to it, was found to be dispensable for gene silencing and plasmid interference.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"14 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144114173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Danielle M Pascual, Delaram Jebreili Rizi, Harsimran Kaur, Paul C Marcogliese
{"title":"Excess Wnt in neurological disease.","authors":"Danielle M Pascual, Delaram Jebreili Rizi, Harsimran Kaur, Paul C Marcogliese","doi":"10.1042/BCJ20240265","DOIUrl":"10.1042/BCJ20240265","url":null,"abstract":"<p><p>Wnt pathways are critical developmental signaling cascades that are conserved across multicellular life. A clear role for Wnt signaling in proper neural development has been well-established, yet less is known about its sustained expression and signaling in the mature nervous system. The precise role for Wnt pathways, canonical or otherwise, and individual Wnt components (ligands, receptors, transducers, effectors, and regulators) in the mature brain are poorly understood. However, genetic evidence implicating Wnt-related components in both neurodevelopmental and neurodegenerative disorders suggests that fine-tuned regulation of Wnt signaling is required for proper nervous system development and long-term homeostasis. Much has been documented about down-regulated Wnt signaling and its association with neurological conditions. Hence, the focus of this review is to consolidate and highlight the evidence for up-regulated Wnt transcription and/or signaling in neurodevelopmental and neurodegenerative disorders with a brief discussion on the role of deregulated Wnt in cancer. Finally, we touch upon the therapeutic prospect of Wnt inhibition in the nervous system.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 10","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Multifaceted roles of Epac signaling in renal functions.","authors":"Oleh Pochynyuk,Kyrylo Pyrshev,Xiaodong Cheng","doi":"10.1042/bcj20253103","DOIUrl":"https://doi.org/10.1042/bcj20253103","url":null,"abstract":"3',5'-cyclic adenosine monophosphate (cAMP) is a fundamental secondary messenger capable of rapidly amplifying and propagating cellular signals in response to various extracellular stimuli. cAMP plays a significant role in hormone-mediated regulation of renal fluid and electrolyte balance. Impaired signaling of cAMP has been linked to a variety of pathological ramifications in the kidneys. This review explores the physiological functions of exchange proteins directly activated by cAMP (Epac) in renal water balance and the regulation of solute transport in the renal tubule. Additionally, the involvement of Epac signaling in renal pathologies such as acute kidney injury, chronic kidney disease, and polycystic kidney disease is discussed.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"57 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"GPCR signaling via cAMP nanodomains.","authors":"Rahul Yadav, Manuela Zaccolo","doi":"10.1042/BCJ20253088","DOIUrl":"10.1042/BCJ20253088","url":null,"abstract":"<p><p>G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors, mediating essential physiological responses through diverse intracellular signaling pathways. When coupled to Gs or Gi proteins, GPCR modulates the synthesis of 3'-5'-cyclic adenosine monophosphate (cAMP), which governs a wide array of processes, ranging from cellular growth and survival to metabolic regulation. Studies have highlighted that cAMP is not uniformly distributed within cells but instead is compartmentalized into highly localized nanodomains. These nanodomains, mostly regulated by phosphodiesterases (PDEs), play a critical role in enabling signal precision and functional effects that are specific to individual stimuli. GPCRs can initiate distinct cAMP responses based on their localization within the cell, with evidence showing that both receptors resident at the plasma membrane and intracellular receptors-including endosomal, Golgi, and nuclear GPCRs-elicit unique cAMP signaling profiles. This review examines the mechanisms underlying GPCR signaling through cAMP nanodomains. We focus on the role of PDE-mediated cAMP degradation in shaping local cAMP signals, the emerging views on mechanisms that may contribute to signal compartmentalization, and the role of intracellular membrane compartments. By exploring these aspects, we aim to highlight the complexity of GPCR signaling networks and illustrate some of the implications for the regulation of cellular function.</p>","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"482 10","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}