Abstract:Oligonucleotide drugs have experienced accelerated development in the past 10 years, and some of them have been used in clinical treatment. Because of its convenient design, flexible sequence, and high specificity, it is expected to solve the “undruggable” challenge of many targets which are difficult in drug development. Moreover, its clinical transformation period and cost are relatively low, which makes oligonucleotide drug become the frontier of emerging biotechnology drug discovery. Brain diseases include a series of incurable diseases, such as neurodegenerative diseases, glioma, and motor neuron diseases. Many of them are age-related and regarded as aging-associated brain diseases. Due to the complex etiology, many targets are difficult to be drugged. At the same time, the existence of the barrier system “blood-brain barrier” in the brain makes most drugs unable to achieve effective accumulation at brain lesions, and many small molecule drugs have failed in clinical transformation. The specificity and sequence flexibility of oligonucleotide acid drugs provide new possibilities for drug development, but they also face the challenge of brain delivery. Although a variety of oligonucleotide drugs have been used in the medical market, brain-targeted oligonucleotide drugs are still extremely rare. This article reviewed recent advances and discussed key topics and clinical transformation challenges in this field, such as clinical approval cases, bottlenecks of brain-targeted delivery and current strategies, as well as potential targets for aging-related brain diseases.

Abstract:Glioma is the most common malignancy of the central nervous system, originating mainly from glial cells. Because of its highly aggressive nature, glioma has one of the highest rates of death among all types of cancer. Therefore, it is very important to develop new therapeutic approaches and drugs for glioma treatment. Instead of activate the telomerase, approximately 30% of glioma use alternative lenthening of telomere (ALT) to maintain telomere length. The mechanism of ALT development is poorly understood, however, some genetic mutations have been reported to induce the development of ALT glioma, such as ATRX, IDH1, p53, etc. The lack of ALT glioma cell lines and preclinical ALT glioma models has limited the mechanistic studies of ALT glioma. Therefore, this review listed ALT glioma cell lines that derived from primary culture or gene editing in the last decade, as well as the xenografted animal models established by ALT glioma cell lines, and discussed the role and significance these cell and animal models play in preclinical studies.

Abstract:Renal cell carcinoma (RCC) is the primary malignant neoplasm. The ubiquitin-proteasome system (UPS) is crucial to the control of protein level and regulation of physiological and pathological processes. Deubiquitinases (DUBs), key components of UPS, specifically removing ubiquitin chains from the target protein, have showed crucial roles for protein homeostasis and quality control by rigidly regulating the balance between ubiquitination and deubiquitination in normal physiology. Accumulating studies indicate that abnormal function DUBs is associated with the progression and metastasis of RCC. Depending on the substrates, some DUBs may suppress RCC while others promote. Herein, we review recent research advances in RCC-associated DUBs, describe their classification, functional roles, summarize the role and mechanisms of action of DUBs in RCC and discuss the potential of targeting DUBs for cancer treatment.

Abstract:RNA editing, an essential post-transcriptional reaction occurring in double-stranded RNA (dsRNA), generates informational diversity in the transcriptome and proteome. In mammals, the main type of RNA editing is the conversion of adenosine to inosine (A-to-I), processed by adenosine deaminases acting on the RNAs (ADARs) family, and interpreted as guanosine during nucleotide base-pairing. It has been reported that millions of nucleotide sites in human transcriptome undergo A-to-I editing events, catalyzed by the primarily responsible enzyme, ADAR1. In hematological malignancies including myeloid/lymphocytic leukemia and multiple myeloma, dysregulation of ADAR1 directly impacts the A-to-I editing states occurring in coding regions, non-coding regions, and immature miRNA precursors. Subsequently, aberrant A-to-I editing states result in altered molecular events, such as protein-coding sequence changes, intron retention, alternative splicing, and miRNA biogenesis inhibition. As a vital factor of the generation and stemness maintenance in leukemia stem cells (LSCs), disordered RNA editing drives the chaos of molecular regulatory network and ultimately promotes the cell proliferation, apoptosis inhibition and drug resistance. At present, novel drugs designed to target RNA editing (e.g., rebecsinib) are under development and have achieved outstanding results in animal experiments. Compared with traditional antitumor drugs, epigenetic antitumor drugs are expected to overcome the shackle of drug resistance and recurrence in hematological malignancies, and provide new treatment options for patients. This review summarized the recent advances in the regulation mechanism of ADAR1-mediated RNA editing events in hematologic malignancies, and further discussed the medical potential and clinical application of ADAR1.

Abstract:Outer membrane vesicles (OMVs) are nanoscale vesicles secreted by Gram-negative bacteria. As a unique bacterial secretion, OMV secretion can help bacteria maintain the outer membrane stability or remove harmful substances. Studies have shown that local separation of outer membrane and peptidoglycan layers led by abnormalities in outer membrane protein function, abnormal structure or excessive accumulation of LPS, and erroneous accumulation of phospholipids in the outer leaflet, which can all lead to bacterial outer membrane protrusion and eventually bud formation of OMVs. Since OMVs are mainly composed of bacterial outer membrane and periplasmic components, the pathogen associated molecular patterns (PAMPs) on their surface can trigger strong immune responses. For example, OMVs can recruit and activate neutrophils, polarize macrophages to secrete large amounts of inflammatory factors. More importantly, OMVs can act as adjuvants to induce dendritic cell (DC) maturation to enhance adaptive immune response in the body. At the same time, OMVs are derived from bacteria, which make it easy to modify. The methods by genetic engineering and others can improve their tumor targeting, give them new functions, or reduce their immunotoxicity, which is conducive to their application in tumor therapy. OMVs not only induce apoptosis or pyroptosis of tumor cells, but also regulate the host immune system, which makes OMVs themselves have a certain killing effect on tumors. In addition, the tendency of neutrophils to inflammatory tumor sites and the formation of neutrophil extracellular traps enable OMVs to target tumor sites, and the suitable size and the characteristic that they are easily taken up by DCs give OMVs a certain lymphatic targeting ability. Therefore, OMVs are often employed as excellent drug or vaccine carriers in tumor therapy. This review mainly discusses the biological mechanism of OMVs, the regulatory effects of OMVs on immune cells, the functional modification strategies of OMVs, and their research progress in tumor therapy.

Abstract:MXenes is an emerging two-dimensional (2D) material, which was composed of layered transition metal carbides and/or nitrides, have attracted enormous attention in the past decade since their innovative discovery by Gogotsi and Barsoum in 2011. The general formula of MXenes is M_n+1X_nT_x (n=1-4), where M represents transition metal elements (such as Ti, Nb, Ta, etc.), X represents carbon and/or nitrogen, and T_x represents surface terminations (such as —OH, —F, =O, etc.). In recent years, MXenes have been widely applied in the biological field due to their high biocompatibility, abundant surface groups, good conductivity and photothermal properties. Due to the strong absorption of laser in the near infrared region, strong X-ray attenuation ability and surface easily modified by various molecules or nanoparticles, MXenes have been used as photothermal agents and contrast agents in the tumor therapy and tumor diagnosis. This paper reviews the application of MXenes and MXenes-based composites in tumor therapy and active targeting tumor therapy. According to the modal of action on tumor cells, it was divided into monotherapy, bimodal therapy and trimodal therapy. Among them, the monotherapy mainly used the photothermal properties of MXenes for photothermal therapy, studies have found that MXenes QDs can be used for chemodynamic therapy. In addition, sonodynamic therapy can also be achieved by loading the sonosensitizers on the surface of MXenes. Bimodal therapy and trimodal therapy are mainly used to load anticancer drugs, photosensitizers, metal particles and other substances on the surface of MXenes to achieve combination therapy. In contrast to the limited treatment efficacy and possible side effects arising from monotherapy, the development of bimodal therapy and trimodal therapy may harbor the collective merits of respective individual treatments and give rise to much higher anticancer efficacy at lower dosage of therapeutic agents administered, thus avoiding high-dose-induced side effects. The combined use of multiple treatments displayed superior advantages over monotherapy in producing an improved therapy outcome. According to the modal of entry into tumor cells, it was divided into passive targeting and active targeting. Active targeting therapy was mainly divided into homologous targeting therapy and targeting agents targeting therapy. The strategy of homologous targeting therapy was to coat MXenes with tumor cell membrane and increased the uptake of MXenes by tumor cells. Targeting agents targeting therapy used targeting agents to specifically bind to the receptors on the surface of tumor cells, subsequently, the precise uptake of MXenes by tumor cells was achieved. Finally, the current challenges and future development trends of MXenes in preparation technology and tumor therapy are discussed.

Abstract:Circulating tumor DNA (ctDNA) comes from tumor, reflecting the genetic information of the tumor well, and will change with the progress of tumor. In recent years, the unique capabilities of ctDNA have attracted much attention and been widely studied. In this paper, based on the summary of the source, properties and sample processing of ctDNA, its detection technology and application in cancer diagnosis and treatment are reviewed. The roles and importance of ctDNA reference material in second-generation sequencing are described. The urgency of establishing uniform standards and specifications of ctDNA in various processes, such as samples collection, storage, quantitative testing and data analysis, has been pointed out.

Abstract:Immunoassays are widely used in medicine, food, environment and other fields due to having the advantages of simpleness, rapidness and accuracy. Combining immunoassays with nanomaterials can improve the performance of immunoassays. Compared with traditional nanomaterials, upconversion nanoparticles (UCNPs) have excellent optical properties such as good photostability, long luminescence lifetime and narrow and tunable emission bands, which can significantly reduce background noise and improve analytical sensitivity when combined with immunoassay. This paper briefly introduces the luminescence mechanism of UCNPs, summarizes the synthesis and surface modification methods of UCNPs. And then 5 UCNPs-based immunoassay techniques, namely, fluorescence resonance energy transfer, inner filter effect, magnetic separation technique, upconversion-linked immunosorbent assay and upconversion immunochromatography, are discussed in detail. These sensing protocols of UCNPs-based immunoassays have been successfully utilized to detect various targets, including small molecules, macromolecules, and pathogens, all of which closely related to food safety, human health, and environmental pollution. Finally, the challenges and prospects of this technique are summarized and prospected. Although the UCNPs immunoassays based on antibodies and antigens have made great progress, most of the research is still in the stage of laboratory, and there is a long way to go to realize its social applications. There is a series of challenges need to be overcome. (1) Designing excellent water soluble and dispersive upconversion nanomaterials is needed. Hydrophilic ligands are bound to smaller upconversion nanoparticles and removing hydrophobic surface ligands are the most widely used methods to improve solubility and dispersity. (2) Multi-detection technology platforms and multi-mode simultaneous detection platforms have great potential, which will improve the efficiency of point of care detection. (3) The researchers also need to focus on some important problems. For examples, the upconversion luminescence efficiency of UCNPs is difficult to maintain, the synthesis method is complex, and the surface modification degree and functionalization are difficult to control.

Abstract:The brain’s neural circuits consist of a large number of highly unstable networks. Despite the existence of many internal and external factors that continuously disturb the balance, our brains employ an array of homeostatic mechanisms that allow neurons or neural circuits to sense how active they are, and when they deviate from a target value, whereby a force must be generated to move neuronal activity back toward this target. Sleep is one of the well-known physiological states in the regulation of homeostasis. Sleep pressure increases during wakefulness and decreases during sleep. When sleep is lost (e.g., sleep deprivation), this loss is compensated by extending or strengthening subsequent sleep. These phenomena are known as sleep homeostasis. The dysregulation of sleep homeostasis accompanies brain-related diseases such as schizophrenia, bipolar disorder, major depressive disorder, and autism spectrum disorder. More importantly, it can significantly undermine the basis of traditional sleep hygiene practices for these diseases. Therefore, clarifying the mechanisms of sleep homeostasis is important for therapy, but it remains an unsolved mystery. In addition to pharmacological treatment, non-invasive brain stimulation has become one of the most promising tools for clinical treatment in recent years due to its low cost, portability and low incidence of side effects. In order to promote relevant technologies, this review will focus on the electrophysiological mechanisms of sleep homeostasis. We first discuss the electrophysiological marker of sleep homeostasis, slow-wave activity, then move to the neuronal firing rates, finally discuss more aspects of sleep homeostasis, including differences in brain area, sleep stages, learning and individual differences.

Abstract:Exosome is a kind of extracellular vesicles secreted by cells to the outside. Biogenesis mainly involves two invaginations of the cytoplasmic membrane, the formation of multivesicular bodies, and the release of exosomes. Exosomes have abundant and diverse inclusions—including landmark membrane proteins, soluble proteins, various RNA molecules and DNA fragments, etc. Cells can achieve intercellular signal communication by secreting and receiving exosomes. Through interaction of ligand molecules on the exosome membrane with receptors on the surface of other cytoplasmic membranes, exosomes can activate cell signal transduction or fuse with the cell membrane to release its contents into the cytoplasm to exert regulatory functions. In the central nervous system, exosomes secreted by neurons and various glial cells can mediate wired synaptic signal transmission, but mainly play a role similar to neuromodulator by way of volume transmission. In this paper, the biogenesis of exosomes and important functional components are described in detail, and the characteristics of neural exosomes in the biogenesis, content sorting and controlled release are compared with those of synaptic vesicles. We further review the research progress on the physiological functions of neural exosomes on the central nervous system and their roles in the occurrence and development of neurodegenerative diseases and major depressive disorder. We also prospect the application of exosomes in the early diagnosis and targeted therapy of nervous system diseases.

Abstract:Intestinal organoids are constructed by crypts or stem cells from the intestine under the 3D support of the culture matrix. They contain all mature cells of the intestine, and have become a new and efficient platform for studying the mechanism of intestinal diseases. Compared with 2D cell culture, organoids can not only more effectively simulate the physiological structure and function of the intestine, but also better restore the true ecology of the intestine in different external environments. Therefore, it is more widely used in the study of pathogenesis of different intestinal diseases. This article reviewed the new progress of intestinal organoids culture, and the application and progress of intestinal organoids in the pathogenesis of inflammatory bowel diseases, colorectal cancer and celiac disease in recent years, and also discussed the application of intestinal organoids in drug research and development and screening.

Abstract:Objective The traditional Chinese medicine Strychnos nux-vomica L. (SN) has the clinical effect of reducing swelling and relieving pain; however, SN is toxic due to its alkaloid components. Little is known about the endogenous metabolic changes induced by SN toxicity in rats and their potential effects on the metabolic dysregulation of intestinal microbiota. Therefore, toxicological investigation of SN is of great significance to its safety assessment. In this study, the toxic mechanisms of SN were explored using a combination of metabonomics and 16S rRNA gene sequencing.Methods The toxic dose, intensity, and target organ of SN were determined in rats using acute, cumulative, and subacute toxicity tests. UHPLC-MS was used to analyze the serum, liver, and renal samples of rats after intragastric SN administration. The decision tree and K Nearest Neighbor (KNN) model were established based on the bootstrap aggregation (bagging) algorithm to classify the omics data. After samples were extracted from rat feces, the high-throughput sequencing platform was used to analyze the 16S rRNA V3-V4 region of bacteria.Results The bagging algorithm improved the accuracy of sample classification. Twelve biomarkers were identified, where their metabolic dysregulation may be responsible for SN toxicity in vivo. Several types of bacteria such as Bacteroidetes, Anaerostipes, Oscillospira and Bilophila, were demonstrated to be closely related to physiological indices of renal and liver function, indicating that SN-induced liver and kidney damage may be related to the disturbance of these intestinal bacteria.Conclusion The toxicity mechanism of SN was revealed in vivo, which provides a scientific basis for the safe and rational clinical use of SN.

Abstract:Objective To investigate the genetic polymorphism and structure of 47 autosomal microhaplotypes in the Han population in Changshu City, Jiangsu Province, and to evaluate the forensic efficiencies and forensic parameters.Methods The DNA library of unrelated individual samples was prepared according to MHSeqTyper47 kit manual and sequenced on the MiSeq FGx platform. Microhaplotype genotyping and sequencing depth statistics were processed using MHTyper. The genetic information of samples was then evaluated. The fixation index and genetic distance between the Jiangsu Changshu population and the reference populations in the 1000 Genomes Project phase 3 (1KG) were calculated, and forensic parameters were evaluated.Results The fixation index and genetic distance between the Han population in Changshu, Jiangsu, and the CHB (Han Chinese in Beijing, China) reference population in 1KG were the lowest. The effective allele number (A_e) of each locus is also the closest between the two populations. The combined matching probability (CMP) of the Changshu Han population is close to the 5 populations of the East Asian reference super-population in 1KG, which is 1.25×10^-36, and the combined probability of exclusion reached 0.999 999 999 964 1.Conclusion This study reported the genetic polymorphism and allele frequency of 47 microhaplotypes in a Han population in Changshu City, Jiangsu Province. This information provides a data basis for 47 microhaplotypes in forensic applications. In addition, the polymorphism differences between the 1KG reference population and the Han population in Changshu, Jiangsu were compared, and the genetic structure of 47 microhaplotypes in the Han population in Changshu, Jiangsu was revealed. In general, the reference data of the East Asian super-population in 1KG is more in line with the genetic characteristics of Han population in Changshu, Jiangsu.

Abstract:Objective A growing body of research suggests a strong link between metabolic imbalance and Alzheimer’s disease (AD). In recent years, the development of metabolomics makes it possible to study the characteristic changes of peripheral metabolism in AD. Serum levels of tryptophan and tyrosine were associated with mild cognitive impairment (MCI) and AD. The purpose of this study is to further characterize tryptophan and tyrosine levels in MCI and AD.Methods We stratified 765 participants from the Alzheimer’s Disease Neuroimaging Initiative-1 (ADNI-1) cohort into cognitively normal (CN; n=207), stable mild cognitive impairment (sMCI; n=201), progressive mild cognitive impairment (pMCI; n=171), and dementia due to AD (n=186). Serum tryptophan and tyrosine were analyzed for diagnostic value of MCI and AD. To evaluate the relationships between serum tryptophan and tyrosine and cerebrospinal fluid (CSF) biomarkers, brain structure (magnetic resonance imaging, MRI), cerebral glucose metabolism (¹⁸F-fluorodeoxyglucose-positron emission tomography, FDG-PET), and cognitive declines, through different cognitive subgroups.Results Serum tryptophan was decreased in patients with AD, pMCI or sMCI compared with CN. Serum tyrosine was decreased in patients with AD or pMCI compared with CN. Serum tryptophan has diagnostic value for pMCI and AD. Serum tyrosine has diagnostic value for AD.Conclusion Serum tryptophan and tyrosine contribute to the early diagnosis of AD. The detection of tryptophan and tyrosine can contribute to the pathogenesis of AD. Serum tryptophan and tyrosine were not significantly associated with core AD markers, cognitive function, brain structure and brain metabolism, so serum tryptophan and tyrosine may not be good peripheral AD biomarkers.

Abstract:Objective Direct continuous monitoring of arterial blood pressure is invasive and continuous monitoring cannot be achieved by traditional cuffed indirect blood pressure measurement methods. Previously, continuous non-invasive arterial blood pressure monitoring was achieved by using photoplethysmography (PPG), but it is discrete values of systolic and diastolic blood pressures rather than continuous values constructing arterial blood pressure waves. This study aimed to reconstruct arterial blood pressure wave signal based on CNN-LSTM using PPG to achieve continuous non-invasive arterial blood pressure monitoring.Methods A CNN-LSTM hybrid neural network model was constructed, and the PPG and arterial blood pressure wave synchronized recorded signal data from the Medical Information Mart for Intensive Care (MIMIC) were used. The PPG signals were input to this model after noise reduction, normalization, and sliding window segmentation. The corresponding arterial blood pressure waves were reconstructed from PPG by using the CNN-LSTM hybrid model.Results When using the CNN-LSTM neural network with a window length of 312, the error between the reconstructed arterial blood pressure values and the actual arterial blood pressure values was minimal: the values of mean absolute error (MAE) and root mean square error (RMSE) were 2.79 mmHg and 4.24 mmHg, respectively, and the cosine similarity is the optimal. The reconstructed arterial blood pressure values were highly correlated with the actual arterial blood pressure values, which met the Association for the Advancement of Medical Instrumentation (AAMI) standards.Conclusion CNN-LSTM hybrid neural network can reconstruct arterial blood pressure wave signal using PPG to achieve continuous non-invasive arterial blood pressure monitoring.

Abstract:Objective TePixD (Tll0078) is a blue light-using flavin (BLUF) photoreceptor protein from Thermosynechococcus elongatus BP-1. TePixD protein has a conserved Tyr8-Gln50-Met93 triad around the FAD pocket to mediate the proton-coupled electron transfer (PCET) process. But the detailed light response mechanism needs further study. We aimed to elucidate the structure and biochemical properties of TePixD mutants at key light response sites to analyze the light response process of TePixD.Methods We employed X-ray crystallography to resolve the crystal structure of the TePixD Y8F mutant. The side chain of Tyr8 is involved in PCET while Phe8 in mutation loses the function due to the loss of its hydroxyl group. We compared the structure of TePixD Y8F mutation to TePixD wild type (WT) and its homology protein SyPixD Y8F. Using multi-angle light scattering (MALS), we analyzed the oligomerization of multiple TePixD mutations (Y8F, Q50L, W91F, Y8F/W91F, and Q50L/W91F), focusing specifically on mutational sites that are critical residues for the protein’s photo response to dark and light conditions.Results We resolved the crystal structure of TePixD Y8F mutant at a resolution of 2.54 ? and found that it shares a similar overall structure with the TePixD WT but exhibits significant differences from the SyPixD Y8F structure. Biochemical analysis revealed differences in molecular mass and elution profiles between the TePixD mutants and the WT under dark and light conditions, indicating the perturbation on the light-induced conformational change by the mutants.Conclusion Our structure determination and biochemical analyses will add information to reveal the light response mechanism of BLUF proteins.

Abstract:Objective The advent of atomic force microscope (AFM) provides a powerful tool for the studies of life sciences. Particularly, AFM-based indentation assay has become an important method for the detection of cellular mechanics, yielding numerous novel insights into the physiological and pathological activities from the single-cell level and considerably complementing traditional biochemical ensemble-averaged assays. However, current AFM indentation technology is mainly dependent on manual operation with low efficiency, seriously restricting its practical applications in the field of life sciences. Here, a method based on the combination of deep learning image recognition and AFM is developed for precisely and efficiently detecting the mechanical properties of single isolated cells and clustered cells.Methods The YOLO deep learning algorithm was used to recognize the central region of the cell in the optical image, the dual UNet neural network with an embedded vision transformer (ViT) module was used to recognize the peripheral regions of cell, and the template matching algorithm was used to recognize the tip of spherical probe. Based on the automatic determination of the positional relationships between the microsphere tip and the different parts of cell, the AFM tip was accurately moved to the central and peripheral regions of the target cell for rapid measurements of cell mechanical properties. Two types of cells, including HEK 293 cell (human embryonic kidney cell) and HGC-27 cell (human undifferentiated gastric cancer cell), were used for the experiments. The Hertz model was applied to analyze the force curves obtained on cells to obtain cellular Young’s modulus.Results AFM probe can be precisely moved to the different parts (central areas and peripheral areas) of cells to perform mechanical measurements under the guidance of deep learning-based optical image automatic recognition. The experimental results show that the proposed method is not only suitable for single isolated cells, but also suitable for clustered cells.Conclusion The research demonstrates the great potential of deep learning image recognition to aid AFM in the precise and efficient detection of cellular mechanical properties mechanics, and combining deep learning-based image recognition with AFM will benefit the development of high-throughput AFM-based methodology to measure the mechanical properties of cells.

Abstract:General education in natural sciences is a critical component in higher education. In this article, I introduced the exploration and practice of curriculum construction of “Biological Clock and Health” at Tsinghua University. The course has been open to students for 3 semesters so far. Students who selected the course come from 27 departments of the university. The students provided positive feedbacks after taking this class, including self-report of improved sleep quality and better understanding of the research logic and methods in life sciences. The logic and methods of the construction of “Biological Clock and Health” described in this article provide insights to the construction of other courses in natural sciences of general education.