Abstract:《生物化学与生物物理进展》（下简称《进展》）创刊于1974年，始于国家科技发展的艰难阶段。1978年我国迎来了“科学的春天”，在科技春风的吹拂中，《进展》迎来了蓬勃的发展，历经了我国科技发展的不同历史阶段，可以说是我国科技发展的见证者与参与者。
自创刊以来，《进展》一直跟随国家科技进步的步伐，已经成为我国生命科学领域进展状况的一面窗口，反映了50年来中国在生命科学基础研究相关方向上的进步。近年，《进展》在国内外的影响力逐步提升，被SCI、SCOPUS、CA、中国科学引文数据库、中国科技论文与引文数据库、《中文核心期刊要目总览》等国内外重要数据库收录。目前，作为SCI收录的生物学科领域中唯一的一份以中文为主体的刊物，已经成为我国具有较高国际影响力的学术期刊中的一面旗帜。
随着生物学科的发展，《进展》的编审团队也在不断与时俱进。通过借鉴国外优秀期刊编辑部运营模式，编审团队不仅聘请各领域内的资深科学家，近年来也开始邀请青年科研人员组建青年编委会，丰富了编委会的人员结构，力图使《进展》始终保持活力和创新性。《进展》学术内容兼具前沿性和包容性，开设综述与专论、研究快报、研究报告、技术与方法、新技术讲座、科教融合等十几个栏目，论文形式灵活多样，年出版量已经超过3 000页。《进展》始终重视自己的群众基础，始终明白作者和读者群体是自身的根基。所以《进展》的出版形式虽然是以印刷版期刊为核心，但是为了面向更广大的作者和读者群体，近年来也做出了众多改进。开通了期刊微信公众号，实现了移动端论文浏览和稿件查询；创办了生物化学与生物物理进展学术论坛（简称生生论坛）。生生论坛面向的是生命科学领域广大研究生和青年科研人员，这是为青年学者们打造的学术交流平台，是展示其才华的舞台，同时也是刊物联系作者和读者群体的重要纽带。
建设世界科技强国离不开中国特色自主创新道路，要实现科技期刊强国同样如此。《进展》将会坚持以中文为主的办刊理念，重点服务于中文作者和读者的定位，积极报道生物化学与生物物理学领域的前沿进展，加大力度介绍我国科学家的创新成果，努力打造具备国际高水平的学术期刊，为生命科学发展和国家学术文化建设做出更多贡献。

Abstract:From the creation of the universe to the explosion of life, to intelligent evolution, and to artificial intelligence, this is a long river of evolution. The times are asking, where do the brain and mind come from and where will they go? What is the future and destiny of human civilization? How can brain intelligence and artificial intelligence illuminate each other? Can artificial intelligence lead to the “mind” through a completely different path from biological evolution? How does intellectual creativity evolve into New Quality Productivity? The core of these questions is still how the human brain works as a whole? Here, I will outline a dialectical unity of complexity and simplicity at the micro-meso-macro-cosmological scale.

Abstract:Nanozymes, a groundbreaking discovery by Chinese scientists, represent a novel and remarkable property of nanomaterials. They not only exhibit catalytic activity comparable to natural enzymes, but also boast exceptional stability, tunable reactivity, and the ability to catalyze reactions under mild conditions. The identification of nanozymes has unveiled the biocatalytic potential of inorganic nanomaterials. In parallel, inorganic minerals have long been regarded as pivotal catalysts in the origin of life, driving the synthesis of early biomolecules. These minerals not only facilitate redox reactions that convert simple inorganic compounds into organic molecules but also enable chiral selection, the synthesis of biomacromolecules, and radioprotective functions via their surface structures. Recent advances suggest that inorganic nanomaterials can delicately catalyze the formation of biomolecules, aid in macromolecular assembly, and provide radiation shielding. Furthermore, nanominerals are found in abundance across Earth and extraterrestrial environments. This paper seeks to explore the potential of nanozymes as catalytic agents in the processes that gave rise to life, integrating the catalytic roles of inorganic minerals with the unique attributes of nanozymes, which will provide a new perspective for research of origin of life.

Abstract:Life is inseparable from oxygen. The redox state in cells directly regulates the functions of biomacromolecules and mediates cell signal transduction and many physiological and pathological processes such as aging, neurodegenerative diseases, cardiovascular diseases, metabolic diseases, and tumors. In view of The Free Radical Theory of Aging proposed in the 1950s, oxidative stress has long been confused with oxidative damage and is regarded as bad. Antioxidation once became synonymous of “anti-aging”. Here in combination the relevant research work of our laboratory and the frontiers of the redox biology field, we propose three new understandings of “oxidative stress”. (1) Oxidative stress is not equal to oxidative damage and has important physiological functions. (2) Oxidative stress is not related to all physiological and pathological processes without specificity, while redox regulation is specific and redox modification of biomacromolecules is the mechanism. (3) Non-targeting antioxidants do not work well, the redox balance has precise properties, 5R principle should be considered for antioxidant pharmacology and the new era of precision redox medicine has begun. Future challenges are reflected in three major aspects: basic research on redox biology and medicine, the specific molecular mechanisms of oxidative stress in physiological and pathological processes and environmental stress, and precise redox intervention against aging and diseases. Multidisciplinary basic research, in-depth cooperation between basic research and clinical research and international collaboration must be enhanced to achieve breakthroughs in the understanding of redox in life processes, breakthroughs in redox mechanisms, and breakthroughs in precision intervention!

Abstract:Photosynthesis is one of the most important chemical reactions on earth. Oxygenic photosynthetic organisms convert solar energy into chemical energy and release oxygen, thus sustaining almost all life on this planet. Oxygenic phototrophs possess two photosystems, namely photosystem I (PSI) and photosystem II (PSII). Both photosystems are multi-subunit protein complexes embedded in the thylakoid membrane and bind numerous pigment molecules, thereby can efficiently harvest light energy and transfer it to the reaction center. PSI is one of the most efficient nano-photochemical machineries in nature. Its complex structure and sophisticated regulatory mechanisms are crucial for the high photosynthetic efficiency of oxygenic phototrophs. Eukaryotic PSI consists of a core complex where charge separation occurs and a peripheral antenna system that increases the light absorption cross section of the core. The PSI core possesses approximately 12-15 protein subunits, most of them are conserved during evolution, with only several small transmembrane subunits emerging or disappearing. The peripheral antenna system usually contains a number of light-harvesting complexes (LHCs). In contrast to the core, the protein composition and arrangement of LHC antennae vary considerably among different species of photosynthetic organisms. Previous results showed that in angiosperm plants (such as Pisum sativum and Zea mays), the PSI core binds four LHC proteins arranged as an arc-shaped belt, whereas in green algae, the PSI core is associated with more LHCs, presumably a result of adaption to the low-light aquatic environment. In addition, structures of several green algal PSI complexes indicated that green algae can dynamically regulate their light-harvesting capability by adjusting the size of PSI antennae, thereby better adapting to the changing natural environment. In addition to the light harvesting and energy conversion, PSI is also involved in several photosynthetic regulatory processes, including state transitions and cycle electron flow/transfer (CEF/CET). State transitions represent a short-term regulatory mechanism that balances the energy distribution between the two photosystems. During the process of state transitions, when PSII is preferentially excited, a portion of the PSII antenna, the major light-harvesting complex II (LHCII), is phosphorylated, and these phosphorylated LHCIIs bind to the PSI core, forming the PSI-LHCI-LHCII complex. This process is reversible, and when PSI is preferentially excited, LHCII is dephosphorylated, detaches from the PSI and binds to the PSII. Previous reports revealed that although higher plants and green algae possess a similar process of state transitions, their PSI-LHCI-LHCII complexes exhibit specific characteristics in addition to common conserved features. CEF is another important regulatory process in which the PSI participates. In NDH (NAD(P)H dehydrogenase-like complex) dependent CEF, PSI can form supercomplex with NDH to improve the electron transfer efficiency. Previous reports suggested that the PSI bound to NDH and the PSI not bound to NDH possess different LHC compositions, and the exact protein identity and location were recently unraveled based on high-resolution structures. In the past two decades, a number of structures of PSI and PSI-containing complexes have been determined. These structural data provide important information concerning the protein assembly and pigment arrangement of these complexes, allowing for a deeper understanding of the structure and function of green plant PSI. In this review, we summarize the research progresses on the structure of green plant PSIs and PSI-containing complexes involved in photosynthetic regulation, primarily based on the results obtained in our laboratory, and discuss the current state of knowledge concerning the antenna arrangement and the regulatory mechanisms of plant PSI.

Abstract:Pyroptosis is a form of lytic programmed cell death executed by a family of pore-forming proteins named gasdermin (GSDM). Pyroptosis plays crucial roles in host defense against pathogen infection and eliminating abnormal and harmful cells, while excessive pyroptosis causes inflammatory diseases including cytokine storm and septic shock. Mammalian GSDMs, except for pejvakin (PJVK), adopt an autoinhibited two-domain architecture, in which the N-terminal cytotoxic domain (GSDM-N) is restrained in an inactive state by the intramolecular interaction with the C-terminal inhibitory domain (GSDM-C). These two-domain proteins are activated by upstream protease cleavage within the interdomain linkers. The unleashed GSDM-N binds to acidic phospholipids in the cytoplasmic leaf of plasma membranes and undergoes dramatic conformational changes and oligomerization, then assembling into transmembrane pores for pyroptosis induction. GSDM pores lead to membrane rupture, cell swelling, and cytosol release, thereby mobilizing proinflammatory responses. GSDMs are evolutionarily conserved and have been discovered across all kingdoms of life, including bacteria, fungi, invertebrates such as cnidarians and mollusks, and all vertebrates. Proteolytic cleavage to liberate the pore-forming activity of GSDM-N appears to be a universal mechanism for most GSDMs activation, despite low sequence homology among the GSDMs from diverse species. However, recent studies discover that there exist noncanonical GSDMs lack of functional C-terminal inhibitory domains in some lower eukaryotic species. These noncanonical GSDMs are activated by unprecedent mechanisms independent of proteolytic cleavage. TrichoGSDM, present in the basal metazoan Trichoplax adhaerens, is a pore-forming domain-only protein and exists as a disulfides-linked autoinhibited dimer. Reduction of the disulfides by the conserved cytoplasmic antioxidant system, including glutathione (GSH) and thioredoxin (Trx), generates pore-forming active monomers capable of inducing lytic cell death. In filamentous fungus Neurospora crassa, polymorphic regulator of cell death-1 (rcd-1) encodes two GSDM-like proteins RCD-1-1 and RCD-1-2 in incompatible haplostrains, which trigger pyroptosis-like cell death in nonself discrimination (allorecognition) upon encountering during somatic cell fusion. RCD-1-1 and RCD-1-2 are both monomers and structurally similar to mammalian GSDM-N domains, lacking autoinhibitory fragments. They alone could bind acidic phospholipids, and associate with cell membrane in a resting state. Coexistence of RCD-1-1 and RCD-1-2 leads to formation of RCD-1-1/RCD-1-2 heterodimers through molecular mating, which further oligomerize into membrane-inserted pores, causing rapid lytic cell death. These findings reveal mechanistic diversities in GSDM activation and indicate versatile functions of GSDMs. Due to the highly proinflammatory nature of pyroptosis, the pore-forming activities of GSDMs have been illustrated to be precisely regulated at multiple levels. GSDMD transcription and expression is characterized to be induced by interferon regulatory factors 2 (IRF2). mRNA alternative splicing of GSDMB generates various isoforms, some of which exhibit potent pore-forming activity whereas the others bear none. Additionally, different types of post-translational modifications have been identified on GSDMs, playing distinct regulatory roles. For examples, itaconation of GSDMD, succinylation of GSDMD and GSDME, and phosphorylation of GSDMA, GSDMD and GSDME, negatively regulate GSDM pore formation, thereby inhibiting pyroptosis. Conversely, palmitoylation of GSDMD and GSDME, and ubiquitination of GSDMD promote the pore-forming activities and pyroptosis. Moreover, some proteases can cleave within the GSDM-N domains to block their pore-forming activities. On the other hand, bacterial pathogens evolve specific effectors to hijack host pyroptotic defense pathway through targeting upstream caspases, GSDMs or plasma membrane phospholipids. Given the crucial roles of GSDMD in immune defense and pathological inflammation, a few small-molecule inhibitors have been found to directly inhibit GSDMD activity. Since the identification of GSDMs as the executioners of pyroptosis, the GSDM family has attracted broad attention in immunology researches. Significant progress has been made to greatly advance our knowledge about how GSDMs action, and what are the immunological functions of pyroptosis. Investigations of GSDM-targeting therapies are emerging as a promising translational direction. In this paper, we review recent progress in the field of pyroptosis researches, with focus on various molecular mechanisms underlying GSDMs activation and regulation. The biological implication and future direction of pyroptosis research are also discussed.

Abstract:Cardiovascular diseases are a group of disorders of the heart and blood vessels, primarily including coronary heart disease, stroke, and other diseases. It is the world’s leading cause of death, and its incidence is increasing yearly. Hypertension is a major risk factor for cardiovascular disease. Wnt signaling comprises a series of highly conservative cascading events controlling fundamental biological processes. Wnt signaling pathways include the canonical Wnt pathway (or Wnt/β-catenin pathway), the non-canonical planar cell-polarity pathway, and the non-canonical calcium-dependent pathways. Abnormal Wnt signaling promotes cell proliferation and differentiation, cardiac malformations, various malignancies, so drugs targeting Wnt signaling play a great therapeutic potential. Wnt/β-catenin pathway is involved in the occurrence and development of cardiovascular diseases such as atherosclerosis and stroke by regulating cell proliferation, migration, apoptosis, blood-brain barrier permeability, inflammation, oxidative stress, and immune response. Based on the latest research progress, this review summarizes the role of Wnt/β-catenin signaling in cardiovascular diseases, in order to provide new ideas for the prevention and treatment of cardiovascular diseases.

Abstract:Protein palmitoylation, a prevalent and dynamic form of S-acylation modification, plays a critical role in maintaining the functionality of the nervous system. This reversible process involves the attachment of palmitic acid to cysteine residues in proteins, anchoring them to cellular membranes and regulating their spatial distribution. The functioning of palmitoylation is crucial for normal neuronal activities, influencing key processes such as signal transduction, synaptic function, and protein trafficking. Recent research has increasingly underscored the significance of specific zinc finger Asp-His-His-Cys motif-containing (ZDHHC) S-acyltransferases in neuronal development and synaptic plasticity. These enzymes, which catalyze the palmitoylation of proteins, have emerged as pivotal regulators of brain function. Dysregulation of palmitoylation by these enzymes is now recognized as a potential contributor to the pathogenesis of various neurodegenerative diseases. This review provides an in-depth analysis of the expression patterns and functional diversity of ZDHHC enzymes across different brain regions and cell types. ZDHHC enzymes exhibit significant sequence variability and demonstrate region-specific and cell type-dependent expression. Such heterogeneity suggests that these enzymes may have specialized roles in different areas of the nervous system, making them crucial modulators of neuronal function and synaptic transmission. The review also explores the regulatory mechanisms of protein palmitoylation and their implications in neurodegenerative disease onset and progression. Altered palmitoylation can lead to the destabilization and subsequent aggregation of these proteins, exacerbating neurodegenerative processes. Abnormal palmitoylation of α-synuclein can either promote or inhibit its aggregation in Parkinson’s disease pathology. Proteins related to these key pathological factors, including amyloid precursor protein (APP) and beta-secretase 1 (BACE1), are also influenced by palmitoylation, contributing to the formation of amyloid plaques through the aggregation of Aβ. Additionally, ZDHHC13 and ZDHHC17, which are abundantly and widely expressed in the brain, play crucial roles in this process. For instance, reduced interaction between ZDHHC17 and huntingtin could significantly contribute to the pathogenesis of Huntington’s disease. Thus, modulating the palmitoylation status of these proteins presents a promising therapeutic strategy to prevent their toxic aggregation and mitigate neuronal damage. Actually, regulating palmitoylation has shown potential for therapeutic interventions in neurodegenerative diseases, with studies demonstrating that modulation of palmitoylation can restore neuronal function and improve disease symptoms. Regulating palmitoylation holds significant promise for therapeutic strategies in neurodegenerative diseases, as modulation of this process can restore neuronal function and ameliorate disease symptoms. However, progress is hindered by the lack of high-resolution structural data and comprehensive targeting maps for specific ZDHHC enzymes. Additionally, current detection methods for palmitoylation, which focus on labeling and analyzing palmitic acid and cysteine residues, are often complex and time-consuming, and may produce inconsistent palmitoyl-proteomic profiles. These methodological challenges underscore the need for more robust and efficient detection technologies. A deeper understanding of palmitoylation’s role in neurological diseases, coupled with the development of improved detection methods, is essential for advancing our knowledge of the molecular underpinnings of these conditions and for the creation of innovative therapeutic strategies aimed at combating neurodegenerative diseases.

Abstract:Pain is an unpleasant sensory and emotional experience involving multi-level neural processing, with a highly complex neural activity pattern. Recent advancements in non-invasive brain functional imaging techniques have enhanced our understanding of the neural mechanisms underlying pain processing in humans at the whole-brain level. Functional magnetic resonance imaging (fMRI), in particular, plays an important role due to its high spatial resolution and has driven significant advancements in this field. This review focused on fMRI studies of pain in humans. We first summarized research that explored brain responses to pain and showing that pain processing involves neural activities across multiple brain regions, constituting the pain matrix, which includes the somatosensory cortex, thalamus, insula, anterior cingulate cortex, and other areas. However, modulating the activity of a single brain region has limited effects on pain experiences, suggesting that pain processing entails communications among multiple brain regions. Thus, we reviewed research investigating interactions between brain regions, finding that multiple neural pathways spanning the whole brain are involved in pain processing. Beyond interactions between pairs of regions, understanding how these interactions construct a pain-related network is crucial for fully comprehending the neural representation of pain. Two main approaches are used to describe neural networks across the whole brain. The first one is theory-driven, such as graph theory. Using this method, researchers explored how network properties evolve during pain processing and identified a tightly connected network that emerges during pain, encompassing the somatosensory, salience, and fronto-parietal networks, forming a pain-related super-system. As pain is modulated or diminishes, this system becomes less connected. The second approach relies on data-driven methods, such as methods based on independent component analysis or principal component analysis, and machine learning. These methods are not constrained by pre-defined brain networks. Advancements in machine learning have provided valuable insights, enabling researchers to develop pain biomarkers with promising clinical potential. Theory-driven and data-driven approaches provide complementary insights into our understanding of the neural mechanisms of pain. In recent years, two rapidly advancing and promising techniques have further enhanced the precision and comprehensiveness of pain neural network. One is ultra-high-field magnetic resonance imaging, and the other is simultaneous brain-spinal imaging. Ultra-high-field magnetic resonance imaging has overcome previous spatial resolution limitations in fMRI. In subcortical regions, it helps distinguish neural activities of different nuclei. In cortical regions, high resolution enables the differentiation of neural activities across cortical layers, thereby providing a more in-depth and detailed understanding of the neural mechanisms of pain. Simultaneous brain-spinal imaging technology enables the exploration of brain-spinal networks involved in pain processing, making it possible to construct a comprehensive neural network representation of pain throughout the entire central nervous system. Based on current findings, we suggested that in the clinical treatment of pain using neuromodulation techniques, the selection of stimulation targets could be guided by the pain neural network. Targeting hubs within the pain network could significantly impact the network and may efficiently influence pain experiences. Finally, we discussed the limitations of current research on the neural representation of pain and proposed future directions, including exploring pain-specific representation, systematically comparing experimental and clinical pain, and examining individualized neural representations.

Abstract:Connectomics, a research field in neuroscience studying the synaptic connectivity patterns between neurons across different brain regions, is crucial for understanding neural computations underlying complex functions such as emotion, learning, and cognition. Specifically, micrometer-resolution mesoscale connectomics has become the most widely used technology in rodent neuroscience due to its unique advantages, and it also has the potential to transform brain research in non-human primates. Traditional mesoscale connectome techniques typically use fluorescence labeling and optical imaging to perform anterograde or retrograde tracing of neural circuits. To achieve single-cell resolution, methods for sparse labeling of neurons have been developed. However, it remains challenging to trace neurons in high throughput in individual animals and integrate multi-omics data across modalities. In the past decade, high-throughput mesoscale connectome technologies based on DNA barcoding have made significant progress. These technologies have provided novel tools to map single cell connectome, with higher throughput, lower cost, and multi-omics compatibility. Here we review several mature mesoscale connectome technologies based on DNA barcoding, discussing their principles, applications, advantages and disadvantages. We also propose future directions for barcoding-based connectomics.

Abstract:Optical-neural stimulation, which encompasses cutting-edge techniques such as optogenetics and infrared neurostimulation, employs distinct mechanisms to modulate brain function and behavior. These advanced neuromodulation techniques offer accurate manipulation of targeted areas, even selectively modulating specific neurons, in the brain. This makes it possible to investigate the cause-and-effect connections between neural activity and behavior, allowing for a better comprehension of the intricate brain dynamics towards complex environments. Non-human primates serve as an essential animal model for investigating these complex functions in brain research, bridging the gap between the basic research and clinical applications. One of the earliest optical studies utilizing optogenetic neuromodulation in monkeys was conducted in 2009. Since then, the optical-neural stimulations have been effectively applied in non-human primates. This review summarises recent research that employed optogenetics or infrared neurostimulation techniques to regulate brain function and behavior in non-human primates. The current state of optical-neural stimulations discussed here demonstrates their efficacy in advancing the understanding of brain systems. Nevertheless, there are still challenges that need to be addressed before they can fully achieve their potential.

Abstract:Laminar organization is a hallmark of the mammalian neocortex, where the orderly arrangement of diverse neurons stereotypically forms into six distinct layers. The laminar structure provides a basis for the formation of precise neural circuits responsible for high-level cognitive functions. A deeper understanding of the mechanisms underlying neocortical layer formation and cell assembly in the brain will provide a more comprehensive insight into mammalian and even human physiology and behavior. It will also enable the development of novel diagnostic and therapeutic strategies for neurological disorders. To achieve this, it is imperative to elucidate the molecular regulatory networks that determine the fate of neurons in the neocortex. MicroRNAs (miRNAs) are small non-coding RNAs of 18-25 nucleotides in length that play important roles in the gene expression network. A large number of studies have reported that miRNAs are involved in various developmental processes within the nervous system. This review summarizes the progress of research on miRNAs that have been identified in recent years with regard to neocortical layer formation. We start with a comparative analysis of different Cre-line mediated conditional knockout mice for Dicer, a gene indispensable for the synthesis of almost all miRNAs. The results indicate that miRNAs are essential for the formation of neocortical layers, including the determination of the fate of projection neurons and the migration of these cells. Next, we summarize the regulatory roles of miRNAs in the coordinated execution of a series of developmental events that contribute to neocortical layer formation. First, the temporal patterning of neocortical neural progenitors is regulated by miRNAs. Two types of temporally opposite expression gradients and functionally antagonistic miRNAs modulate the competence of neural progenitors by changing their relative expression levels during neurogenesis, thereby shifting the progressive generation of neocortical neurons. Second, it is described that miRNAs influence lamination by regulating the fate of intermediate progenitor cells (IPCs). In particular, several miRNAs that are specifically expressed in multiple gyrencephalic species have been identified in recent years and are involved in regulating the generation of IPCs as well as the generation of upper layer neurons. Third, the regulatory roles of miRNAs in the migration of cortical projection neurons, including the multipolar to bipolar transition and other processes, were presented. Fourth, we described miRNAs that are expressed in postmitotic neurons but play roles in the further specification of different cortical projection neuron subtype identities, in particular the role of several miRNAs in the Mirg cluster in establishing different subtype identities of projection neurons in layer V, promoting corticospinal motor neuron (CSMN) identity but inhibiting callosal projection neuron (CPN) identity. Finally, we discussed current challenges in the study of miRNAs in neocortical layer formation and looked forward to future directions that deserve further exploration, such as the functions of a large number of newly discovered miRNAs, or whether miRNAs regulate the layer-dependent pattern of other neuronal cells with layer distribution features; the contribution of miRNAs in the rapid evolution of the neocortex, especially in the formation of characteristic structures in the primate neocortex; and the use of miRNAs as an entry point to explore finer regulatory networks.

Abstract:Alzheimer’s disease (AD), characterized by cognitive decline and neurodegeneration, currently relies on pharmacological treatments that are limited in efficacy and often accompanied by side effects. As the number of AD patients increases, so does the economic burden on both the global healthcare system and families of patients, further worsening the quality of life for patients in their later years. Therefore, it is crucial to find new and more effective therapeutic approaches. This necessity has sparked a growing interest in non-invasive therapies, such as 40 Hz rhythmic stimulation, which aims to modulate brain activity to potentially reverse pathological changes and alleviate symptoms. This review provides an overview of the effects of 40 Hz stimulation on AD pathology and symptoms, its impact on cognitive functions in healthy individuals, the underlying mechanisms of action, and strategies to enhance the treatment’s compliance and effectiveness. Research has demonstrated that 40 Hz rhythmic stimulation, particularly through auditory and visual modalities, can influence core AD pathologies. In mouse models of AD, this stimulation has been shown to reduce amyloid-beta protein (Aβ) plaques and phosphorylated tau protein levels, hallmarks of AD pathology. These effects are thought to stem from enhanced waste clearance mechanisms, facilitated by the stimulation of the glymphatic system and the activation of microglia. Clinical applications in AD patients have shown promising results, with improvements noted in cognitive functions and behavioral symptoms. These findings suggest that 40 Hz rhythmic stimulation could offer a non-pharmacological option to mitigate the pathological progression and symptomatic expression of AD. In healthy individuals, the cognitive outcomes of 40 Hz stimulation appear more variable. Some studies indicate potential enhancements in memory and attention, proposing that 40 Hz stimulation may bolster cognitive resilience and processing efficiency in a non-diseased brain. However, these effects are not consistently replicated across studies, indicating that individual differences and specific stimulation parameters may significantly influence outcomes. The beneficial effects of 40 Hz rhythmic stimulation are believed to be primarily due to neural entrainment, where neural circuits synchronize their activity to the external frequency. This entrainment may restore the balance between excitatory and inhibitory neural activity, which is often disrupted in AD mice and AD patients. By reinforcing natural brain rhythms, 40 Hz stimulation may enhance neural connectivity and function, facilitating cognitive and memory processes that are deteriorated in AD. Neural entrainment at 40 Hz has been demonstrated to aid in restoring neural network function, enhancing the glymphatic system, improving cerebral blood flow, and providing neuroprotection. These mechanisms are thought to work synergistically to regulate brain activity, potentially leading to a reduction in lesions and an improvement in cognitive performance. To optimize the therapeutic benefits of 40 Hz stimulation, several factors need to be considered. Treatment protocols should be tailored to individual needs, accounting for variability in disease progression and personal health status. Enhancing patient compliance involves simplifying treatment regimens and using portable, user-friendly devices that can be easily incorporated into daily routines. Ongoing research should focus on refining stimulation parameters and delivery methods to maximize efficacy and minimize potential side effects. In conclusion, while 40 Hz rhythmic stimulation represents a promising avenue for treating AD and enhancing cognitive functions, further research is required to fully elucidate its mechanisms, refine its application, and ensure its practicality and efficacy in broad clinical and everyday settings.

Abstract:Compared to in vitro purified protein complexes, protein complexes in a working state within cells are often more complete, and their three-dimensional structures are in a fully physiological conformation. This is crucial for understanding the structural basis of important functions that protein complexes play in life activities and can also provide more precise target information for drug design. The direct in situ structural analysis of protein complexes within cells is known as in situ structural analysis of proteins, and cryo-electron tomography (cryo-ET) is the key technology for in situ structural analysis. However, cryo-ET has limitations such as low data acquisition throughput for tilt series, cumbersome data processing, and special sample requirements to achieve near-atomic resolution. These issues have become bottlenecks limiting the resolution and practical application of in situ structural analysis. In recent years, a method based on the analysis of non-tilted images has developed rapidly, allowing high-throughput, high-resolution structural analysis of protein complexes within cells. This review will discuss the principles of this method, compare its advantages and disadvantages with traditional tomography, and provide an outlook on in situ structural analysis of proteins. It is hoped that this review will assist structural biologists in better choosing suitable tools.

Abstract:Volume electron microscopy (vEM) imaging technology was rapidly developed in recent years. It has been the advanced technology to solve high-resolution three-dimensional structures of biological samples. Much wonderful work has revealed the fine structure and interactions of intracellular organelles, the ultrastructure of tissues, and even the three-dimensional structure of entire small biological organisms. With the continuous improvement of resolution, scale and throughput, vEM is becoming more and more widely used in medicine, life sciences, clinical diagnostics and other fields. As a result, this technology has been rated by Nature as one of the seven most noteworthy frontier technologies to watch in 2023. However, the development and application of vEM-related technologies started late in China and need to be further promoted. We write this review to introduce all related vEM technologies, covering the development history of vEM, technology classification, sample preparation, data collection, image processing, etc., which is convenient for people in various fields to understand, learn, apply and further develop this technology.

Abstract:In recent years, with the continuous development of in situ cryo-electron microscopy (cryo-EM) and artificial intelligence (AI) technologies, the research of structural biology has undergone a paradigm shift. Structural analysis is no longer confined to isolated and purified biomolecules, and determination of high-resolution in situ structures directly within cells and tissues becomes feasible. Furthermore, structural analysis of the molecular landscapes of subcellular regions can be performed to gain a deeper understanding of the molecular mechanisms of living activities in the native functional context. Through determining in situ structures of various protein complexes within the cell, it is feasible to visualize the proteome with spatial and quantitative information, which is often referred to as visual proteomics. Emerging in situ structural methods represented by cryo-electron tomography (cryo-ET) hold the promise to elucidate the three-dimensional interaction networks of the intracellular proteome and understand their activities in a systematic manner. To advance in situ cryo-EM/ET and visual proteomics in China, this review summarizes the new research paradigms and technological advances, showcases the superiority of new concepts and technologies with representative examples, and discusses the future prospects in the field.

Abstract:The breakthrough progress of implantable brain-computer interfaces (iBCIs) technology in the field of clinical trials has attracted widespread attention from both academia and industry. The development and advancement of this technology have provided new solutions for the rehabilitation of patients with movement disorders. However, challenges from many aspects make it difficult for iBCIs to further implement and transform technologies. This paper illustrates the key challenges restricting the large-scale development of iBCIs from the perspective of system implementation, then discusses the latest clinical application progress in depth, aiming to provide new ideas for researchers. For the system implementation part, we have elaborated the front-end signal collector, signal processing and decoder, then the effector. The most important part of the front-end module is the neural electrode, which can be divided into two types: piercing and attached. These two types of electrodes are newly classified and described. In the signal processing and decoder section, we have discussed the experimental paradigm together with signal processing and decoder for the first time and believed that the experimental paradigm acts as a learning benchmark for decoders that play a pivotal role in iBCIs systems. In addition, the characteristics and roles of the effectors commonly used in iBCIs systems, including cursors and robotic arms, are analyzed in detail. In the clinical progress section, we have divided the latest clinical progress into two categories: functional rehabilitation and functional replacement from the perspective of the application scenarios of iBCIs. Functional rehabilitation and functional replacement are two different types of application, though the boundary between the two is not absolute. To this end, we have first introduced the corresponding clinical trial progress from the three levels: application field, research team, and clinical timeline, and then conducted an in-depth discussion and analysis of their functional boundaries, in order to provide guidance for future research. Finally, this paper mentions that the key technical challenges in the development of iBCIs technology come from multiple aspects. First of all, from the signal acquisition level, high-throughput and highly bio-compatible neural interface designing is essential to ensure long-term stable signal acquisition. The electrode surface modification method and electrode packaging were discussed. Secondly, in terms of decoding performance, real-time, accurate, and robust algorithms have a decisive impact on improving the reliability of iBCIs systems. The third key technology is from the perspective of practicality, we believe that the signal transmission mode of wireless communication is the trend of the future, but it still needs to overcome challenges such as data transmission rate and battery life. Finally, we believe that issues such as ethics, privacy, and security need to be addressed through legal, policy, and technological innovation. In summary, the development of iBCIs technology requires not only the unremitting efforts of scientific researchers, but also the participation and support of policymakers, medical professionals, technology developers, and all sectors of society. Through interdisciplinary collaboration and innovation, iBCIs technology will achieve wider clinical applications in the future and make important contributions to improving the quality of life of patients.

Abstract:The success of the Human Genome Project has significantly deepened our understanding of genomics and catalyzed a growing focus on proteomics, as researchers aim to decipher the complex relationship between genes and proteins. Given the central role of proteins in regulating physiological processes—including DNA replication, metabolic reactions, signal transduction, pH balance, and cellular structure—developing advanced protein sequencing technologies is critical. Proteins are fundamental to nearly all biological activities, making their detailed study essential for understanding cellular functions and disease mechanisms. The Edman degradation method, developed in the 1950s, was a breakthrough in sequencing short peptides. However, its limitations in read length (fewer than 50 amino acids) and slow cycle time fall short of modern demands. Mass spectrometry has since emerged as the gold standard in protein sequencing due to its high accuracy, throughput, and reproducibility. The method is enhanced by a robust sample preparation workflow and advances in mass spectrometry technology. Despite these strengths, mass spectrometry faces limitations in dynamic range, sensitivity, read length, and sequence coverage, hindering complete de novo protein sequencing. These technological gaps underscore the need for innovative methods to provide more detailed and accurate protein sequence data. In the past decade, new protein sequencing methods, including tunneling current, fluorescence fingerprinting, and real-time dynamic fluorescence, have shown significant developmental potential. However, these methods are not yet ready for widespread application, as each still faces technical hurdles. Meanwhile, advances in nanopore DNA sequencing have sparked interest in applying nanopore technology to protein sequencing, particularly owing to its speed, convenience, and cost-effectiveness. Unlike DNA sequencing, protein sequencing presents greater challenges due to proteins’ complex three-dimensional structures, heterogeneous electrical charges, difficulties in directional movement, and diverse amino acid compositions, further complicated by post-translational modifications. Researchers have made significant strides in addressing these challenges, such as using unfolding enzymes, high temperatures, high voltage, and deformers to unravel protein structures, and employing charged sequences and electroosmotic flow to control peptide translocation. The latest strategies for nanopore protein sequencing can be broadly categorized into three approaches: strand sequencing, enzyme-assisted nanopore sequencing, and nanopore fingerprinting. In strand sequencing, dragging a protein-oligonucleotide conjugate through a nanopore with the aid of protein motors generates stepped current signals produced by the peptide strand. In enzyme-assisted nanopore sequencing, 20 proteinogenic amino acids and various post-translational modifications have been distinguished using nanopores, and sequencing of short peptides has also been demonstrated. In nanopore fingerprinting, polypeptide fragments resulting from protease digestion of a protein can be identified through nanopore sensing. Despite these advances, further improvements in protein engineering, data processing, identification accuracy, and read length are needed to make these strategies practically useful. This review provides an overview of the current major approaches to nanopore protein sequencing, emphasizing the strategies, recent advances, breakthroughs and challenges in nanopore protein sequencing. As nanopore technology continues to evolve, it is expected to offer more efficient and accurate sequencing solutions in proteomics, potentially leading to new technological breakthroughs in biochemistry and biomedicine.

Abstract:Fluorescence microscopy is a vital tool in life science research, but the diffraction nature of light limits further observation of cells. Super-resolution imaging techniques provide deeper insights into cellular structures, including stimulated emission depletion microscopy (STED), structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM). Each of these methods offers unique advantages and principles that push the boundaries of spatial resolution beyond conventional diffraction limits. Among these techniques, SMLM stands out for its exceptional resolution, offering nanometer resolution and becoming a powerful tool for obtaining high-resolution images. SMLM is particularly valuable for studying the spatial distribution and interactions of organelles and macromolecular complexes. Following the award of the Nobel Prize in Chemistry in 2014, super-duper resolution imaging techniques were listed as one of Nature’s seven technologies to watch in 2024. The development of these techniques remains an important area of research. We introduce the development of multi-color SMLM, three-dimensional (3D) SMLM, and nanoscale resolution microscopes. We describe several methods to achieve multi-color SMLM. Sequential imaging and Exchange-PAINT require image targets in sequence, excitation or emission spectral demixing can obtain multi-color images simultaneously based on spectral difference between fluorescent dyes, dual-channel spectroscopic SMLM to achieve simultaneous imaging and spectral analysis of each molecule, and techniques based on binding kinetics of PAINT achieve multi-color by designing the blinking behavior of targets with engineered binding frequency and duration in DNA-PAINT. We then discuss various approaches for 3D imaging. Point spread function (PSF) engineering techniques manipulate the shape and properties of the PSF to improve 3D localization accuracy. Multi-plane imaging methods capture images from different focal planes and reconstruct them to obtain 3D information. Interferometry methods use single molecule interference to achieve high precision in axial localization, providing another way for high resolution 3D nanoscopy. Finally, we highlight advances in new nanoscale resolution microscopes based on modulated illumination patterns, including minimal photon fluxes (MINFLUX), repetitive optical selective exposure (ROSE), ROSE-Z, SIMFLUX, SIMPLE, and ModLoc. MINFLUX is known for its ability to achieve ultra-high resolution by detecting minimal photon fluxes from single molecules using a doughnut-shaped excitation spot to spatially modulate excitation intensities. Typically, we focus on ROSE and ROSE-Z, which outperform other techniques, using a resonant mirror to eliminate localization errors caused by fluorescence blinking. Recently, resolution enhancement by sequential imaging (RESI) and one nanometre expansion (ONE) was introduced to achieve resolution down to the ?ngstr?m scale. Nanoscopy serves as a new role between super resolution microscopy and structural biology and will lead to more discoveries in complex biological systems. Overall, this article provides a comprehensive overview of current advances in super-resolution imaging techniques, highlighting their contributions to overcoming the diffraction limit and enabling detailed observation of nanoscale biological structures, and provides an outlook on promising new techniques and applications. Through detailed descriptions of the principles, benefits, and applications of multi-color and 3D techniques, the article highlights new nanoscale imaging techniques that are expanding our ability to visualize and understand the intricate details of molecular and cellular processes. We hope that this article can be a primer resource for both newcomers and seasoned practitioners of SMLM.

Abstract:Adaptive immunity is a critical component of the human immune system, playing an essential role in identifying antigens and orchestrating a tailored immune response. This review delves into the significant strides made in the development of epitope prediction tools, their integration into vaccine design, and their pivotal role in enhancing immunotherapy strategies. The review emphasizes the transformative potential of these tools in refining our understanding and application of immune responses. Adaptive immunity distinguishes itself from innate immunity by its ability to recognize specific antigens and remember past infections, leading to quicker and more effective responses upon subsequent exposures. This facet of immunity involves complex interactions between various cell types, primarily B cells and T cells, which recognize distinct epitopes presented by antigens. Epitopes are small sequences or configurations on antigens that are recognized by the immune receptors on B cells and T cells, acting as the focal points of immune recognition and response. Epitopes can be broadly classified into two types: linear (or sequential) epitopes and conformational (or discontinuous) epitopes. Linear epitopes consist of a sequence of amino acids in a protein that are recognized by B cells and T cells in their primary structure form. Conformational epitopes, on the other hand, are formed by spatially distinct amino acids that come together in the tertiary structure of the protein, often recognized by the immune system only when the protein folds into its native conformation. The role of epitopes in the immune response is critical as they are the primary triggers for the activation of B cells and T cells. When an epitope is recognized, it can stimulate B cells to produce antibodies, mobilize helper T cells to secrete cytokines, or prompt cytotoxic T cells to kill infected cells. These actions form the basis of the adaptive immune response, tailored to eliminate specific pathogens or infected cells effectively. The prediction of B cell and T cell epitopes has evolved with advances in computational biology, leading to the development of several sophisticated tools that utilize a variety of algorithms to predict the likelihood of epitope regions on antigens. Tools employing machine learning methods, such as support vector machines (SVMs), XGBoost, random forest, analyze large datasets of known epitopes to classify new sequences as potential epitopes based on their similarity to known data. Moreover, deep learning has emerged as a powerful method in epitope prediction, leveraging neural networks capable of learning high-dimensional data from vast amounts of immunological inputs to identify patterns that may not be evident to other predictive models. Deep learning models, such as convolutional neural networks (CNNs), recurrent neural networks (RNNs) and ESM protein language model have demonstrated superior accuracy in mapping the nonlinear relationships inherent in protein structures and epitope interactions. The application of epitope prediction tools in vaccine design is transformative, enabling the development of epitope-based vaccines that can elicit targeted immune responses against specific parts of the pathogen. These vaccines, by focusing the immune response on highly specific regions of the pathogen, can offer high efficacy and reduced side effects. Similarly, in cancer immunotherapy, epitope prediction tools help identify tumor-specific antigens that can be targeted to develop personalized immunotherapeutic strategies, thereby enhancing the precision of cancer treatments. The future of epitope prediction technology appears promising, with ongoing advancements anticipated to enhance the precision and efficiency of these tools further. The integration of broader immunological data, such as patient-specific immune profiles and pathogen variability, along with advances in AI and machine learning, will likely drive the development of more adaptive, robust, and clinically relevant prediction models. This will not only improve the effectiveness of vaccines and immunotherapies but also contribute to our broader understanding of immune mechanisms, potentially leading to breakthroughs in the treatment and prevention of multiple diseases. In conclusion, the development and refinement of epitope prediction tools stand as a cornerstone in the advancement of immunological research and therapeutic design, highlighting a path toward more precise and personalized medicine. The ongoing integration of computational models with experimental immunology holds the promise of revolutionizing our approach to combating infectious diseases and cancer.

Abstract:Cancer stem cells (CSCs), a small subset of cells in the tumor bulk with the ability of self-renewal and differentiation, are the key to tumor occurrence, metastasis, drug resistance and relapse. CSCs are resided in a specific microenvironment, and their number maintenance, self-renewal and differentiation are precisely regulated by the microenvironment, and the immune microenvironment is one of the most critical microenvironments for CSCs. In recent years, tumor immunotherapy has achieved great success, but drug resistance and recurrence are frequently occurred after immunotherapy. Compared with non-CSC tumor cells, CSCs harbor stronger immune escape ability, and their roles in tumor immune escape are increasingly followed. In this review, we described the discovery history and lineage sources of CSCs, focused on immune cells in the CSC microenvironment, such as tumor-infiltrating lymphocytes, tumor-associated macrophages, and tumor-associated dendritic cells, and analyzed the mechanism of CSC-immune cell interaction. Intervention strategies targeting CSCs and their immune microenvironment are also described. With the development and application of advanced technologies such as CSC-immune cell co-culture, single-cell sequencing and lineage tracing, the immune escape of CSCs can be suppressed by targeting the interaction between CSCs and immune cells or reversing the immunosuppressive microenvironment, which is expected to provide potential solutions to the problems of drug resistance and relapse in tumor immunotherapy.

Abstract:Tumor immune microenvironment is an important microecology for tumor development, where tumor-associated macrophages are the most abundant immune cells in the tumor immune microenvironment, with high plasticity and heterogeneity. Under the regulation of various environmental factors, tumor-associated macrophages can differentiate into different subgroups. Though complex and variable, all these environmental factors ultimately regulate tumor-associated macrophages by influencing the temporal and spatial heterogeneity of these cells’ internal components, structure, and functions. Mitochondrion are important organelles, responsible for energy production, metabolism, and centers of multiple signal transduction. More and more studies have found that mitochondria can regulate cell functions through various mechanisms such as morphological change, metabolic reprogramming, intermediate metabolites or mitochondrial genetic material. Mitochondrial disorders are involved in many diseases and pathological processes. Here, we review the mechanisms by which mitochondria regulate the polarization of macrophages and thus reshape the tumor immune microenvironment. Further, we discuss and prospect the current status of macrophage mitochondria-related tumor immunotherapy.

Abstract:Improving the prognosis of patients with colorectal cancer (CRC) holds important clinical and social significance. Immunotherapy is an emerging therapy approach for cancers, which mainly include immune checkpoint inhibitors (ICI), immune vaccine and adoptive cell therapy. ICI have achieved good clinical translation in treatment of metastatic CRC with deficient DNA mismatch repair/high microsatellite instability (dMMR/MSI-H) status. The application of some ICI, such as PD-1 inhibitors pembrolizumab and nivolumab, in this type patients have been approved by the FDA. In addition,numerous positive results are acquired in clinical trials of neoadjuvant therapy for resectable dMMR/MSI-H CRC. These results greatly bolstered the exploration enthusiasm of CRC immunotherapy. However, the proficient DNA mismatch repair/microsatellite stability (pMMR/MSS) CRC, which accounting for the vast majority in related patients, hardly benefit from ICI therapy. Various combination strategies, mainly including ICI combined with traditional chemotherapy, radiotherapy, or targeted therapy, have been attempted to alter the “cold tumors” microenvironment characteristics of pMMR/MSS CRC in clinical trials, whereas no breakthrough results were reached. Theoretically, tumor vaccines are ideal choice to break down the barrier of insufficient immune infiltration in solid tumors. However, the outcomes of related clinical trials in CRC patents are not satisfactory, and partially due to the weak specificity of the applied tumor-associated antigens. Clinical studies of adoptive cell therapy in CRC are also actively underway. The favorable efficacy of tumor-infiltrating lymphocyte, cytokine-induced killer (CIK) and dendritic cell-CIK in CRC have been confirmed, while the CAR-T and TCR-T therapies need more exploration based on screening more suitable antigens and optimizing engineering design. In this review, we made a summary based on the mainline of clinical studies related to diverse immunotherapies, so as to clarify the progress of CRC immunotherapy and provide bases for exploration of better treatment options.

Abstract:Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the digestive tract system, which is induced by multiple factors, involving multiple genes and complicated mechanism. Its incidence and mortality rank fourth and second respectively in China, and accounting for more than 85% of primary liver cancers. Tumor immune microenvironment (TIME), plays a critical role in determining the tumor progression and treatment outcomes, making it become a hotspot in current studies. Summarising the previous studies, it is found that the progression of HCC is significantly influenced by the TIME and its complex interactions. TIME consists of various cellular and non-cellular components, such as myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages (TAMs), tumor-associated neutrophils (TANs), regulatory T cells (Tregs), innate lymphoid cells (ILCs), as well as growth factors, proteolytic enzymes, and extracellular matrix proteins. Due to long-term exposure to bacterial components carried by the portal vein, food-derived antigens, and a large amount of foreign antigenic substances, the microenvironment of liver exhibits a certain degree of immune suppression to resist excessive inflammation caused by the non-pathogenic intestinal environment. Besides, the inhibitory immune microenvironment shaped by tumor cells which induces changes in the phenotype and function of immune cells, and attenuates the cytotoxic capabilities of immune system. Meanwhile, the regulation of immune cell metabolism is crucial for anti-tumor immune response. Abnormal metabolites of liver cancer microenvironment and intestinal flora metabolites regulate the remodeling of immune microenvironment and the progression in liver cancer. Normally, the cancer immune cycle functions effectively to remove tumor cells, while the immunosuppressive, exhausted T cells and metabolic disorders of the TIME leads to defects in the cancer immunity cycle and promotes to tumor progression. Furthermore, during the processes of rapid proliferation and differentiation, tumor cells alter their metabolic status through “metabolic reprogramming”, allowing them to compete with anti-tumor immune cells for vital nutrients including glucose, lipids, and nucleotides. At the same time, the abnormal consumption of metabolites leads to local hypoxia, lower pH levels, and the accumulation of metabolic products, which in turn suppress the proliferation and effector functions of immune cells, ultimately facilitating immune evasion and tumor progression. According to the above, local immune imbalance and metabolic disorders in the liver collectively shape the unique microenvironment of HCC, resulting in the accumulation of immunosuppressive cytokines, extracellular matrix and abnormal metabolites. These factors induce abnormal tumor angiogenesis, recruitment of immunosuppressive cells, reduce T-cell infiltration, and diminish anti-tumor function, which accelerates the progression of HCC and immune escape. Currently, there are still remarkable limitations in the clinical treatment methods and outcomes for HCC, while immunotherapy offers a new strategy. The advantages of immunotherapy demonstrate relatively higher specificity and fewer side effects compared to traditional treatment methods such as surgery, radiotherapy, and chemotherapy. Up to now, more and more evidence has been uncovered that liver cancer immunotherapy is closely related to TIME. Targeting the TIME of HCC provides a new perspective into a deeper understanding of the mechanisms of immunotherapy resistance and the development of new immunotherapy approaches. However, single immunotherapy has not shown satisfactory results in improving the prognosis of HCC patients. At present, dual immune checkpoint inhibitors or their combination with existing therapies are being widely explored in clinical studies, hoping to overcome the limitations of HCC therapy. Therefore, this review summarizes the composition of immunosuppressive microenvironment in liver cancer and metabolic regulation, and further discusses clinical therapeutic strategies by targeting microenvironment remodeling for the treatment of liver cancer, which provides new avenues for tumor immunotherapy.

Abstract:Gene editing technology utilizes artificial nucleases to insert, replace, or delete specific sequences in desired genomic regions. The discovery of CRISPR/Cas9 nucleases was a milestone in the development of advanced gene editing tools, which revolutionized the field due to their simplicity and versatility. However, the limited precision of Cas9 nucleases remains a notable obstacle. Recently, derivative technologies such as prime editing have earned considerable attention for their enhanced efficiency and precision. The prime editing system consists of two components: the SpCas9 nickase (H840A) fused with reverse transcriptase (MLV-RT) and an engineered prime editing guide RNA (pegRNA). This system can irreversibly introduce various types of genetic changes into the genome, including 12 possible types of point mutations, as well as insertions, deletions and their combinations, without the need for DNA double-strand breaks (DSBs) or donor DNA templates. Prime editing offers several advantages in terms of editing accuracy, versatility, PAM constraints, and off-target effects. The editing results of prime editing system is highly accurate and can be tailored to specific needs. In addition, the system can be edited near or far from PAM sites, making it less constrained by PAM site restrictions. Moreover, it demonstrates high genome-wide specificity. The system also supports a variety of edits, demonstrating immense potential, especially in large DNA fragment editing—an area that relied heavily on CRISPR/Cas9 nucleases before. The development of prime editing, especially bi-direction prime editor, shed new light on large DNA fragment manipulations, including deletions, insertions, replacements, gene integration, as well as chromosomal translocations, inversions, and tandem duplications. Despite the significant progress made with prime editing technology, its application still faces challenges, especially low editing efficiency, which limits its potential in broader research and clinical settings. Consequently, researchers are exploring strategies to enhance the efficiency of prime editing. This review highlights several approaches to improving prime editing efficiency. These include optimizing pegRNA by refining PBS and RT parameters, increasing pegRNA stability and expression levels, and developing automated pegRNA design software. Additionally, efforts are being made to optimize the prime editing system proteins, such as screening for Cas9 and reverse transcriptase variants and performing codon optimization. The final aspect is the regulation of endogenous factors, including the inhibition of mismatch repair mechanisms and the modulation of chromatin environment. These approaches significantly enhance the practicality of prime editing in research and clinical contexts. In conclusion, prime editing represents a major advancement in the field of gene editing, offering powerful tools and methods for both basic research and clinical applications. This review will introduce the discovery, improvement and applications of prime editors, with a focus on prime editing mediated large DNA fragment manipulations. Hopefully, these insights will serve as valuable references for future research and applications of prime editing technology.

Abstract:The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is widely used for targeted genomic and epigenomic modifications, transcriptional regulation and real-time cell imaging, and has already demonstrated great potential for applications in agriculture, industry and medicine. The promise of the technology depends upon the five intrinsic properties of CRISPR/Cas: targeting, target unwinding, target cutting, target residence, and collateral cleavage. Here, mainly using Streptococcus pyogenes CRISPR/Cas9 as example, we will focus on the target residence of CRISPR/Cas in applications of the CRISPR/Cas technology, summarize the recent progress, and discuss the effect of CRISPR/Cas target binding and residence on DNA double strand break repair pathway choices and the opportunities that CRISPR/Cas target residence presents to optimize the CRISPR/Cas technology.

Abstract:The advent of gene editing represents one of the most transformative breakthroughs in life science, making genome manipulation more accessible than ever before. While traditional CRISPR/Cas-based gene editing, which involves double-strand DNA breaks (DSBs), excels at gene disruption, it is less effective for accurate gene modification. The limitation arises because DSBs are primarily repaired via non-homologous end joining (NHEJ), which tends to introduce indels at the break site. While homology-directed repair (HDR) can achieve precise editing when a donor DNA template is provided, the reliance on DSBs often results in unintended genome damage. HDR is restricted to specific cell cycle phases, limiting its application. Currently, gene editing has evolved to unprecedented levels of precision without relying on DSB and HDR. The development of innovative systems, such as base editing, prime editing, and CRISPR-associated transposases (CASTs), now allow for precise editing ranging from single nucleotides to large DNA fragments. Base editors (BEs) enable the direct conversion of one nucleotide to another, and prime editors (PEs) further expand gene editing capabilities by allowing for the insertion, deletion, or alteration of small DNA fragments. The CAST system, a recent innovation, allows for the precise insertion of large DNA fragments at specific genomic locations. In recent years, the optimization of these precise gene editing tools has led to significant improvements in editing efficiency, specificity, and versatility, with advancements such as the creation of base editors for nucleotide transversions, enhanced prime editing systems for more efficient and precise modifications, and refined CAST systems for targeted large DNA insertions, expanding the range of applications for these tools. Concurrently, these advances are complemented by significant improvements in in vivo delivery methods, which have paved the way for therapeutic application of precise gene editing tools. Effective delivery systems are critical for the success of gene therapies, and recent developments in both viral and non-viral vectors have improved the efficiency and safety of gene editing. For instance, adeno-associated viruses (AAVs) are widely used due to their high transfection efficiency and low immunogenicity, though challenges such as limited cargo capacity and potential for immune responses remain. Non-viral delivery systems, including lipid nanoparticles (LNPs), offer an alternative with lower immunogenicity and higher payload capacity, although their transfection efficiency can be lower. The therapeutic potential of these precise gene editing technologies is vast, particularly in treating genetic disorders. Preclinical studies have demonstrated the effectiveness of base editing in correcting genetic mutations responsible for diseases such as cardiomyopathy, liver disease, and hereditary hearing loss. These technologies promise to treat symptoms and potentially cure the underlying genetic causes of these conditions. Meanwhile, challenges remain, such as optimizing the safety and specificity of gene editing tools, improving delivery systems, and overcoming off-target effects, all of which are critical for their successful application in clinical settings. In summary, the continuous evolution of precise gene editing technologies, combined with advancements in delivery systems, is driving the field toward new therapeutic applications that can potentially transform the treatment of genetic disorders by targeting their root causes.

Abstract:The mutations in human disease-causing genes are predominantly caused by point mutations, with more than half of them being transitions between guanine (G) and adenine (A). Precise and efficient in situ repair of these mutations is the most ideal approach for the treatment of genetic diseases. Given that most point mutations are transitions between G and A, adenine base editors (ABEs) based on the CRISPR/Cas9 system, which convert A to G, are particularly important for repairing these mutations in the treatment of human genetic diseases. In recent years, ABEs have been continuously optimized, with both activity and fidelity being improved. Here we summarize the progress of ABEs, especially those key mutants developed during the process of ABE optimization. It also reflects on the existing defects in current ABEs. Additionally, the article reviews the clinical applications (including preclinical studies) of ABE. Overall, the article aims to provide references for the discovery and optimization of new ABEs and their applications.

Abstract:Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant solid tumor of the digestive system, characterized by rapid progression and difficulties of early diagnosis. Five-year survival rate of the patients is less than 9%. With the acceleration of global population aging and lifestyle change, the incidence of PDAC has been increasing annually. Currently, surgical treatment and chemotherapy remain the standard treatment options for PDAC patients. Early symptoms of PDAC are so undetectable that most patients miss the optimal opportunity for radical surgical resection. Even among those who undergo surgery, the high recurrence rate remains a major problem. PDAC is known for its unique tumor microenvironment. The cellular and non-cellular components in the tumor microenvironment account for as much as 90% of the tumor stroma, presenting many potential targets for PDAC therapy. Activated pancreatic stellate cells within PDAC tissue express specific proteins and secrete various cytokines and metabolites, which directly contribute to the proliferation, invasion, and metastasis of PDAC cells. These elements are critical in extracellular matrix production, connective tissue hyperplasia, immune tolerance, and drug resistance. Immune cells, such as macrophages and neutrophils, exert immunosuppressive and tumor-promoting roles in PDAC progression. The extracellular matrix, which serve as a natural physical barrier, induces interstitial hypertension and reduces blood supply, thereby hindering the delivery of drugs to the tumor. Additionally, it helps the metastasis and differentiation of PDAC cells, reducing the efficacy of clinical chemotherapy and immunotherapy. Although chemotherapeutic agents like gemcitabine have been used in the clinical treatment of PDAC for more than 20 years, the curative effect is obstructed by their poor stability in the bloodstream, low cellular uptake, and poor targeting. While small-molecule inhibitors targeting mutations such as KRAS^G12C, BRCA, and NTRK fusion have shown great potential for molecular targeted treatments and gene therapies of PDAC, their broader application is limited by side effects and restricted scope of patients. The advancement of nanotechnology brings new strategies for PDAC treatment. By virtue of unique size characteristics and actual versatility, different drug-delivery nanosystems contribute to overcome the dense stromal barrier, prolong the circulation time of therapeutics and realize precise PDAC treatment by targeted drug delivery. Clinical nanodrugs such as albumin-bound paclitaxel (nab-paclitaxel) and irinotecan liposome greatly improve the pharmacokinetics of conventional chemotherapeutics and promote drug accumulation inside the tumor, thereby are applying to the first-line treatment of PDAC. It is noteworthy that none nanodrugs with active targeting design have been approved for clinical treatment yet, though many are in clinical trials. In this review, we discuss promising targeting strategies based on different nanodrug delivery systems for treatment of PDAC. One major nanostrategy focuses on the tumor cell targeting and its applications in chemotherapy, molecular targeting therapy, gene therapy, and immunotherapy of PDAC. Another nanostrategy targets the tumor microenvironment, which highlights the nanosystems specifically regulating pancreatic stellate cells, immune cells and the extracellular matrix. Recent progress of developing new nanotheraputics for breakthrough in the fight of PDAC are elaborated in this review. We also provide our perspectives on the challenges and opportunities in the field.

Abstract:In recent years, nucleic acid therapy, as a revolutionary therapeutic tool, has shown great potential in the treatment of genetic diseases, infectious diseases and cancer. Lipid nanoparticles (LNPs) are currently the most advanced mRNA delivery carriers, and their emergence is an important reason for the rapid approval and use of COVID-19 mRNA vaccines and the development of mRNA therapy. Currently, mRNA therapeutics using LNP as a carrier have been widely used in protein replacement therapy, vaccines and gene editing. Conventional LNP is composed of four components: ionizable lipids, phospholipids, cholesterol, and polyethylene glycol (PEG) lipids, which can effectively load mRNA to improve the stability of mRNA and promote the delivery of mRNA to the cytoplasm. However, in the face of the complexity and diversity of clinical diseases, the structure, properties and functions of existing LNPs are too homogeneous, and the lack of targeted delivery capability may result in the risk of off-targeting. LNPs are flexibly designed and structurally stable vectors, and the adjustment of the types or proportions of their components can give them additional functions without affecting the ability of LNPs to deliver mRNAs. For example, by replacing and optimizing the basic components of LNP, introducing a fifth component, and modifying its surface, LNP can be made to have more precise targeting ability to reduce the side effects caused by treatment, or be given additional functions to synergistically enhance the efficacy of mRNA therapy to respond to the clinical demand for nucleic acid therapy. It is also possible to further improve the efficiency of LNP delivery of mRNA through machine learning-assisted LNP iteration. This review can provide a reference method for the rational design of engineered lipid nanoparticles delivering mRNA to treat diseases.

Abstract:Protein phosphorylation modification is one of the key regulatory mechanisms in cellular signaling transduction and metabolic processes. The phosphorylation state of target proteins is regulated by specific protein kinases and phosphatases, which add or remove phosphate groups. Histidine phosphorylation (pHis) plays a crucial role in both prokaryotes and eukaryotes life activities and is linked to various pathological processes. Unlike the stable phosphorylation of proteins via phosphate ester bonds, histidine phosphorylation is linked through phosphoramide bonds, making it highly sensitive to high temperatures and low pH. This sensitivity has historically impeded progress in identifying and studying histidine phosphorylation. In recent years, the development of new techniques in phosphoproteomics and the emergence of pHis-specific antibodies have promoted the identification and functional research of pHis-modified substrates. For the first time, more than 700 pHis-modified proteins have been identified in mammalian cells, and pHis-modified substrates such as focal adhesion kinase (FAK) and phosphoglycerate mutase 1 (PGAM1) have been found to promote tumor development. This article mainly reviewed the key mechanisms and functions of histidine kinases and histidine phosphatases in regulating the histidine phosphorylation of specific substrates, and highlights their significant roles in human physiological and pathological processes, aiming to provide guidance for further research into the biological functions of histidine phosphorylation.

Abstract:In recent years, the development of single-cell sequencing technology has significantly advanced our understanding of single-cell genomics and transcriptomics. However, the study of proteomics, directly related to single-cell life processes, has been limited by slow technological progress. With advancements in sample preparation techniques and chromatography-mass spectrometry instruments, the analytical sensitivity of single-cell proteomics (SCP) has markedly improved. In this review, we thoroughly examine the development of SCP and its applications in life sciences. Regarding sample preparation, various methods such as gentle acoustic dispensing, microfluidic chips, and laser microdissection have been developed for single-cell sorting, gradually transitioning from multi-step to one-step processing, thereby reducing sample loss. In mass spectrometry, both label-free quantification and methods based on isotopic and isobaric labeling have been extensively explored, each with their own technical strengths and weaknesses. SCP has unveiled new biological insights in early embryonic cell development, stem cell differentiation, and spatial heterogeneity of liver tissues. Finally, we summarize the current challenges facing SCP technology, including detection throughput, cost, and data analysis complexity, while envisioning its future directions and emphasizing its broad potential in basic research and clinical applications.

Abstract:DNA replication is a fundamental DNA metabolism process in living organisms. In human cells, thousands of DNA replication origins are activated simultaneously within the chromatin environment to initiate the replication process and eventually complete genome duplication. This process is regulated by the chromatin environment and coordinated with other chromatin metabolism events, ensuring accurate inheritance of genomic and epigenetic information. With the rapid development of research techniques and the massive accumulation of research data, the systematic understanding of DNA replication in eukaryotic cells, especially in mammals, within complex chromatin environments is a future research trend. Here, we review the multilayered regulatory modes of DNA replication from initiation to termination in the chromatin environment, offering insights for future research.

Abstract:Objective In kinesin-3, the neck coil correlates with the following segments to form an extended neck that contains a characteristic hinge diverse from a proline in KIF13B to a long flexible linker in KIF1A. The function of this neck hinge for controlling processive movement, however, remains unclear.Methods We made a series of modifications to the neck hinges of KIF13B and KIF1A and tested their movement using a single-molecule motility assay.Results In KIF13B, the insertion of flexible residues before or after the proline differentially impacts the processivity or velocity, while the removal of this proline increases the both. In KIF1A, the deletion of entire flexible neck hinge merely enhances the processivity. The engineering of these hinge-truncated necks of kinesin-3 into kinesin-1 similarly boosts the processive movement of kinesin-1.Conclusion The neck hinge in kinesin-3 controls its processive movement and proper modifications tune the motor motility, which provides a novel strategy to reshape the processive movement of kinesin motors.

Abstract:Objective Triple-negative breast cancer (TNBC) is the breast cancer subtype with the worst prognosis, and lacks effective therapeutic targets. Colony stimulating factors (CSFs) are cytokines that can regulate the production of blood cells and stimulate the growth and development of immune cells, playing an important role in the malignant progression of TNBC. This article aims to construct a novel prognostic model based on the expression of colony stimulating factors-related genes (CRGs), and analyze the sensitivity of TNBC patients to immunotherapy and drug therapy.Methods We downloaded CRGs from public databases and screened for differentially expressed CRGs between normal and TNBC tissues in the TCGA-BRCA database. Through LASSO Cox regression analysis, we constructed a prognostic model and stratified TNBC patients into high-risk and low-risk groups based on the colony stimulating factors-related genes risk score (CRRS). We further analyzed the correlation between CRRS and patient prognosis, clinical features, tumor microenvironment (TME) in both high-risk and low-risk groups, and evaluated the relationship between CRRS and sensitivity to immunotherapy and drug therapy.Results We identified 842 differentially expressed CRGs in breast cancer tissues of TNBC patients and selected 13 CRGs for constructing the prognostic model. Kaplan-Meier survival curves, time-dependent receiver operating characteristic curves, and other analyses confirmed that TNBC patients with high CRRS had shorter overall survival, and the predictive ability of CRRS prognostic model was further validated using the GEO dataset. Nomogram combining clinical features confirmed that CRRS was an independent factor for the prognosis of TNBC patients. Moreover, patients in the high-risk group had lower levels of immune infiltration in the TME and were sensitive to chemotherapeutic drugs such as 5-fluorouracil, ipatasertib, and paclitaxel.Conclusion We have developed a CRRS-based prognostic model composed of 13 differentially expressed CRGs, which may serve as a useful tool for predicting the prognosis of TNBC patients and guiding clinical treatment. Moreover, the key genes within this model may represent potential molecular targets for future therapies of TNBC.

Abstract:Objective Alveolar macrophages (AMs) are critical for maintaining the homeostasis of pulmonary microenvironment. They process surfactants to ensure alveoli patency, and also serve as the first line of immune defense against pathogen invasion. Available studies have shown that monocyte-derived AMs continuously release pro-inflammatory cytokines and chemokines, recruiting other immune cells to the damaged area during pulmonary fibrosis. These monocyte-derived AMs maintains and amplifies inflammation, playing a negative role in pulmonary fibrosis progression. Current researches have predominantly focused on the gene expression levels of AMs in pulmonary fibrosis microenvironment, with less emphasis on the function and regulation of proteins. This study aims to investigate the differentially expressed proteins (DEPs) of AMs under normal physiological conditions and after pulmonary fibrosis, in order to gain a more comprehensive understanding of the role of AMs in the progression of pulmonary fibrosis.Methods Firstly, the construction of bleomycin-induced pulmonary fibrosis mouse models was evaluated through using measurements such as body mass, lung coefficient, lung wet-to-dry mass ratio, H&E staining and Masson staining. Subsequently, AMs from both the saline controls and the pulmonary fibrosis models (2.5×10⁵ cells per sample) were collected using FACS sorting, and protein expression profiles of these cells were obtained through label-free proteomics approach. The quality of the proteomic data was assessed by comparing our saline control proteomic data with public proteomic data of physiological AMs. Thirdly, DEPs analysis between the saline controls and the bleomycin groups was carried out using R package Prostar. Functional enrichment analyses of significantly upregulated DEPs were performed using R package Clusterprofiler for GO and KEGG pathways. Finally, the STRING database was used to explore the protein-protein interaction networks related to phagocytosis regulation, inflammatory response regulation, and I-κB/NF-κB signaling pathway. The expression levels of Tlr2 and Pycard were detected respectively by FACS and western blotting.Results Compared to the saline controls, mice in the bleomycin groups exhibited a lower average body mass, extensive infiltration of inflammatory cells, and deposition of collagen in the lungs. This indicates that bleomycin successfully induced pulmonary fibrosis in mouse models. The proteomic data of AMs obtained from these models was of high quality and fulfilled the research requirements. A comprehensive analysis showed that 778 proteins were upregulated in pulmonary fibrosis groups compared with control groups. Moreover, the signal pathways enriched in up-regulated DEPs were related to the I-κB/NF-κB pathway, inflammatory response regulation, phagocytosis regulation, TGF-β signaling, and HIF-1 pathway, indicating that AMs in pulmonary fibrosis microenvironment exerted pro-inflammatory and pro-fibrotic functions. Protein-protein interaction network analysis of the DEPs suggested that the interactions between Tlr2 and Pycard were control nodes for the pro-inflammatory phenotype of AMs, thereby contributing to pulmonary fibrosis progression. Further validation by FACS and Western blotting respectively confirmed that the expression levels of Tlr2 and Pycard in AMs were significantly increased after pulmonary fibrosis.Conclusion This study investigates the changes in the protein expression profile of AMs in the pulmonary fibrosis microenvironment. The results show that AMs notably enhanced the activity of various pathways associated with inflammation and fibrosis, suggesting that the interaction between Tlr2 and Pycard serves as a key control node for the highly pro-inflammatory behavior of AMs.

Abstract:Glycolysis is a fundamental topic in the biochemistry curriculum, pivotal for understanding glucose metabolism, and it stands as a challenging subject in various life science disciplines, including microbiology, marine biology, zoology, cell biology, and bioengineering. The process of glycolysis encompasses 10 successive reactions, involving numerous enzymes and intermediate metabolites, making it a complex pathway that both consumes and generates energy (ATP). Over the past decades, and continuing to the present, the standard pedagogical approach has been to explain glycolysis step by step, a method known as the sequential teaching method, which has not yielded optimal educational outcomes. In this paper, we introduce an innovative teaching strategy that frames the overall reaction of glycolysis as the division of one molecule (6C) of glucose into two molecules (3C) of pyruvate. To achieve the equal division of the hexose molecule, a phosphate group is added to both the head (C1) and tail (C6) of the hexose carbon chain, resulting in the formation of fructose 1,6-bisphosphate. A critical chemical bond breakage at the center of the molecule (C3-C4) then occurs, yielding two molecules of phosphorylated aldose. The subsequent five reactions involve a series of steps, including the transfer of phosphate groups, culminating in the production of pyruvate from phosphorylated aldose. This novel education approach, which begins with the concept of “equal division of the hexose carbon chain”, is termed the “hexose equal division” teaching method. Graduate (n=63) and undergraduate (n=39) students were enrolled in a teaching research study where glycolysis was taught using the “hexose equal division” method, followed by a questionnaire survey. The results showed that before receiving the “hexose equal division” teaching, students found it challenging to grasp and retain the steps of glycolysis, with the reactions being prone to be forgotten after memorization. However, after employing the “hexose equal division” teaching method, the majority of graduate students reported that glycolysis steps became more comprehensible and easier to recall compared to the “sequential teaching method” used during their undergraduate studies. This same approach was applied to undergraduate students, and a statistical analysis revealed no significant difference (P>0.05) in outcome between the two groups. Consequently, the “hexose equal division” teaching method has been shown to enhance students" understanding of the glycolysis mechanism, aid in memorization, and encourage independent thinking, thus leading to improved learning outcomes.