Sub-cellular biochemistry最新文献

Prion diseases are rapidly progressive and fatal neurodegenerative disorders caused by misfolded prion proteins. Accurate and early diagnosis is essential to distinguish these conditions from treatable dementias and to prevent iatrogenic transmission. While definitive confirmation still depends on postmortem neuropathological techniques such as immunohistochemistry and western blot, recent advances have significantly improved antemortem diagnostic capabilities. The antemortem diagnosis combines clinical evaluation, neuroimaging, electroencephalography, and cerebrospinal fluid biomarkers. The development of real-time quaking-induced conversion (RT-QuIC) has enhanced the detection of misfolded prion proteins with high specificity, complementing existing diagnostic methods. Although advancements in biomarkers and diagnostic methodologies have improved the early detection of prion diseases, challenges remain. Continued research is crucial for enhancing early identification, tracking disease progression, optimizing patient management, and further elucidating disease pathogenesis.

Nuclear pores serve as the sole gates mediating nucleocytoplasmic molecular communication. They constantly accept heavy molecular traffic at a rate of ~1000 molecules per second, selected from a vast number of molecules randomly approaching the pores. The central channel of the pores are highly crowded with an intrinsically disordered region of pore-forming subunits and this channel functions as a selective permeability barrier. Recently, the phase separation properties of the hydrophobic subunits of pores have been reported, together with the flexible amphiphilic nature of the transporting molecules. These findings suggest that phase separation is a fundamental mechanism of action in nuclear pores. In this chapter, the entire nucleocytoplasmic transport system and composition of the nuclear pore complex are reviewed, followed by a detailed review of recent studies focusing on the characteristic features of both nuclear pores and transporting molecules. Finally, intrinsic and extrinsic factors that adaptively affect the function of the molecular crowding barrier are introduced.

The inside of a living cell is highly crowded with extremely diverse biomacromolecules, small metabolites and osmolytes. The molecular conditions in cells change dynamically and rapidly depending on the cell cycle and state, organelle, and compartment. Much remains unknown regarding how biomolecular interactions and reactions can proceed in a spatiotemporally specific manner in such crowded, heterogeneous, and dynamic molecular environments. Selective condensation/droplet formation of biomolecules via liquid-liquid phase separation may be critical for interactions and reactions inside cells. In this chapter, we briefly describe the heterogeneity of molecular environments inside cells and the biological roles of liquid-liquid phase separation that allows biomolecular interactions and reactions in such heterogenous molecular environments. Finally, we discuss the mutual relationship between molecular crowding and liquid-liquid phase separation.

Lamins are intermediate filament proteins of the nucleus that are present in nuclear lamina as well as nucleoplasm. They play diverse roles in maintaining the structure and rigidity of the nucleus as well as nuclear homeostasis. Lamins are of two main types-A and B. B-type lamins are expressed from the embryonic stage, whereas A-type lamins are expressed during cell differentiation. Both A- and B-type lamins form distinct but interacting networks that contribute to differential chromosome tethering and distribution within the nucleus. A- and B-type lamins maintain the euchromatin-to-heterochromatin ratio in health and disease. Interestingly, lamin A/B itself varies largely and distinctly in different types of cancer. Likewise, the lamina-associated domains of the chromatin network get significantly altered in the process of carcinogenesis. We have discussed here the differential expression of lamin proteins in different cancers, contributing to distinct genome organization, ultimately precipitating into diverse neoplastic transformation.

The extracellular matrix (ECM) and nuclear lamina are fundamental components of cellular architecture, playing pivotal roles in mechanotransduction and gene regulation. The dynamic interplay between the ECM and lamin proteins profoundly influences chromatin organization, epigenetic modifications, and genomic stability. Variations in ECM stiffness and composition can induce significant alterations in nuclear architecture, including changes in nuclear morphology and lamin A/C expression levels. These structural changes, in turn, modulate histone modifications, DNA methylation patterns, and chromatin compaction, all of which are critical for regulating gene expression. Disruption of this intricate ECM-lamin interaction can lead to aberrant gene expression, increased genomic instability, and the progression of various diseases, particularly cancer. A comprehensive understanding of ECM-lamin dynamics offers valuable insights into the mechanisms underlying epigenetic regulation and genome maintenance, with potential implications in developing novel therapeutic strategies against diseases associated with dysregulation of mechanotransduction.

Prion diseases (PrDs) are devastating and fatal conditions characterized by the accumulation of the misfolded prion protein (PrP^Sc) in the central nervous system (CNS). Definitive diagnosis of PrDs relies on the detection of prions in CNS tissues collected postmortem. The advent of a highly sensitive cell-free amplification technique, named protein misfolding cyclic amplification (PMCA), has revolutionized this field. It has revealed trace amounts of prions in various tissues, including cerebrospinal fluid, urine, blood, and olfactory mucosa of patients with different forms of PrDs. PMCA mirrors in vitro the pathological process of protein misfolding and aggregation, which occurs in vivo but in a significantly accelerated manner. For this reason, this technology is currently used in specialized laboratories to support research and diagnostic activities in human and animal PrDs. This chapter highlights the latest advances and applications of PMCA in the diagnosis of human PrDs.

Cells are crowded entities, but the intracellular space represents an inhomogeneously crowded environment, where the concentrations of macromolecules (proteins, nucleic acids, etc.) are not uniformly distributed throughout the cell resulting in regions with different levels of crowding. Liquid-liquid phase separation (LLPS)-driven formation of various membrane-less organelles (MLOs) represents a means for the control, regulation, and redistribution of cellular crowded environment. Because MLOs contain the high concentrations of biological macromolecules (proteins and RNAs), often significantly exceeding those of the surrounding cytoplasm or nucleoplasm, their inside represents an overcrowded milieu. It is well-known that the appearance of the stress-induced MLOs represents a reaction to various types of stresses, enabling the protection of the genetic and protein material during hostile conditions. However, stress can also cause structural, functional, and compositional changes in the MLOs, which are constitutively present in the cells, thereby causing the reshuffling of the overcrowded environment. This chapter describes stress-induced changes in several MLOs (nucleolus, Cajal bodies, paraspeckles, nuclear speckles, NELF-Bodies, nucleolar stress bodies, PML-bodies, stress-granules, and Р-bodies) found in the eukaryotic cells.

The role of the nuclear envelope (NE) in skeletal muscle function was first recognized 30 years ago when mutations in NE-associated genes, such as SUN-1, Syne1, Syne2, and LMNA, were linked to muscular dystrophies, also known as nuclear envelopathies. These findings underscored the critical role of NE components in maintaining muscle fiber integrity and function. NE proteins, including lamin A/C, SUN-1/2, nesprins, and LAP1, play a key role in anchoring and positioning nuclei within muscle fibers. In particular, the correct positioning of subsynaptic nuclei (SSNs) beneath the neuromuscular junction (NMJ) is essential for their differentiation and functional specialization, ensuring efficient neuromuscular transmission. The crucial role of the NE in SSNs and NMJ function has been further emphasized by its association with an atypical form of congenital myasthenic syndrome (CMS). Despite significant advances in understanding NMJ formation and motor neuron-myofiber communication, the mechanisms governing gene regulation in SSNs remain largely unexplored.

Healthy brain functioning requires a continuous fine-tuning of gene expression, involving changes in the epigenetic landscape and 3D chromatin organization. Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD) are three multifactorial neurodegenerative diseases (NDDs) that are partially explained by genetics (gene mutations and genetic risk factors) and influenced by non-genetic factors (i.e., aging, lifestyle, and environmental conditions). Examining comprehensive studies of global and locus-specific (epi)genomic and transcriptomic alterations in human and mouse brain samples at the cell-type resolution has uncovered important phenomena associated with AD. First, DNA methylation and histone marks at promoters contribute to transcriptional dysregulation of genes that are directly implicated in AD pathogenesis (i.e., APP), neuroplasticity and cognition (i.e., PSD95), and microglial activation (i.e., TREM2). Second, the presence of AD genetic risk variants in cell-type-specific distal enhancers (i.e., BIN1 in microglia) alters transcription, presumably by disrupting associated enhancer-promoter interactions and chromatin looping. Third, epigenomic erosion is associated with widespread transcriptional disruption and cell identity loss. And fourth, aging, high cholesterol, air pollution, and pesticides have emerged as potential drivers of AD by inducing locus-specific and global epigenetic modifications that impact key AD-related pathways. Epigenetic studies in ALS/FTD also provide evidence that genetic and non-genetic factors alter gene expression profiles in neurons and astrocytes through aberrant epigenetic mechanisms. We additionally overview the recent development of potential new therapeutic strategies involving (epi)genetic editing and the use of small chromatin-modifying molecules (epidrugs).

The filamentous nuclear lamina network is predominantly made up of lamin proteins, which play pivotal roles in maintaining nuclear architecture, chromatin structure, mechanotransduction and various other nuclear processes. Among the lamin proteins, A type is the principal mechanical component of the nucleus and controls gene expression via direct interactions with chromatin and chromatin modulator proteins. Mutations in the LMNA gene cause a plethora of diseases termed laminopathies, including various cardiac and muscular ailments, by disrupting nuclear integrity and mechanotransduction signalling. These mutations also alter chromatin organisation and epigenetic landscape, tantamount to compromised cellular homeostasis. In this chapter, we elaborate on lamin A's molecular structure, assembly dynamics and its role in nuclear mechanotransduction and chromatin maintenance. Additionally, we highlighted the pathological consequences of lamin A dysfunction and discussed emerging approaches aimed at rationalising the cellular- and tissue-specific effects during laminopathies.