DVsc: An Automated Framework for Efficiently Detecting Viral Infection from Single-cell Transcriptomics Data.

Single-cell RNA sequencing (scRNA-seq) has emerged as a valuable tool for studying cellular heterogeneity in various fields, particularly in virological research. By studying the viral and cellular transcriptomes, the dynamics of viral infection can be investigated at a single-cell resolution. However, limited studies have been conducted to investigate whether RNA transcripts from clinical samples contain substantial amounts of viral RNAs, and a specific computational framework for efficiently detecting viral reads based on scRNA-seq data has not been developed. Hence, we introduce DVsc, an open-source framework for precise quantitative analysis of viral infection from single-cell transcriptomics data. When applied to approximately 200 diverse clinical samples that were infected by more than 10 different viruses, DVsc demonstrated high accuracy in systematically detecting viral infection across a wide array of cell types. This innovative bioinformatics pipeline could be crucial for addressing the potential effects of surreptitiously invading viruses on certain illnesses, as well as for designing novel medicines to target viruses in specific host cell subsets and evaluating the efficacy of treatment. DVsc supports the FASTQ format as an input and is compatible with multiple single-cell sequencing platforms. Moreover, it could also be applied to sequences from bulk RNA sequencing data. DVsc is available at http://62.234.32.33:5000/DVsc.

Identification of a Novel MLPH Missense Mutation in a Chinese Griscelli Syndrome 3 Patient.

Melanophilin (MLPH) functions as a linker between RAB27A and myosin Va (MYO5A) in regulating skin pigmentation during the melanosome transport process. The MYO5A-MLPH-RAB27A ternary protein complex is required for anchoring mature melanosomes in the peripheral actin filaments of melanocytes for subsequent transfer to adjacent keratinocytes. Griscelli syndrome type 3 (GS3) is caused by mutations in the MLPH gene. So far, only five variants of MLPH associated with GS3 have been reported. Here, we reported the first patient with GS3 in a Chinese population. The proband carried a novel homozygous missense mutation (c.73G>C; p.D25H), residing in the conserved Slp homology domain of MLPH, and presented with hypopigmentation of the hair, eyebrows, and eyelashes. Light microscopy revealed the presence of abnormal pigment clumping in his hair shaft. In silico tools predicted this MLPH variant to be likely pathogenic. Using immunoblotting and immunofluorescence analysis, we demonstrated that the MLPH (D25H) variant had an inhibitory effect on melanosome transport by exhibiting perinuclear melanosome aggregation in melanocytes, and greatly reduced its binding to RAB27A, although the protein level of MLPH in the patient was not changed. Our findings suggest that MLPH (D25H) is a pathogenic variant that expands the genetic spectrum of the MLPH gene.

New insights into the pathogenesis of Hermansky-Pudlak syndrome.

Hermansky-Pudlak syndrome (HPS) is characterized by defects of multiple tissue-specific lysosome-related organelles (LROs), typically manifesting with oculocutaneous albinism or ocular albinism, bleeding tendency, and in some cases with pulmonary fibrosis, inflammatory bowel disease or immunodeficiency, neuropsychological disorders. Eleven HPS subtypes in humans and at least 15 subtypes in mice have been molecularly identified. Current understanding of the underlying mechanisms of HPS is focusing on the defective biogenesis of LROs. Compelling evidences have shown that HPS protein-associated complexes (HPACs) function in cargo transport, cargo recycling, and cargo removal to maintain LRO homeostasis. Further investigation on the molecular and cellular mechanism of LRO biogenesis and secretion will be helpful for better understanding of its pathogenesis and for the precise intervention of HPS.

A randomized controlled trial to explore the efficacy and safety of transcranial direct current stimulation on patients with post-stroke fatigue.

BACKGROUND: Post-stroke fatigue seriously affects the quality of life for stroke patients. There is no effective treatment at present. transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation which may have therapeutic effect on post-stroke fatigue. This study will explore about this. METHOD: A total of 60 patients with post-stroke fatigue were randomly divided into the control group and the treatment group with 30 patients each by minimization randomization. Both groups received basic treatment and conventional rehabilitation. In the treatment group, patients were treated with active tDCS, while in the control group, sham tDCS. Both active and sham tDCS were administered 6 times a week for 4 weeks. Before and after the trial, the Fatigue Severity Scale (FSS), Fugl-Meyer Assessment (FMA) and Modified Barthel Index (MBI) were evaluated and analyzed. And comparisons were made among groups. And there were an 8-week follow-up after the intervention. RESULT: Before the intervention, there were no significant differences in baseline data and assessment scores between the groups (P > 0.05). After 4 weeks of intervention, FSS scores in the treatment group were significantly lower than those in the control group (P = 0.012), and FMA and BMI scores were significantly higher than those in the control group (P < 0.05). There was no significant change in FSS scores after 8 months of follow-up (P > 0.05). DISCUSSION: TDCS is a safe treatment that can effectively reduce the degree of fatigue after stroke, improve the motor function and daily activity ability of patients after stroke, and the efficacy is better than only routine rehabilitation training. TRIAL REGISTRATION NUMBER: Chinese Clinical Trial Registry, ChiCTR2000031120. Registered on March 22, 2020.

Transcranial direct current stimulation in patients after decompressive craniectomy: a finite element model to investigate factors affecting the cortical electric field.

OBJECTIVE: To simulate the process of transcranial direct current stimulation (tDCS) on patients after decompressive craniectomy (DC), and to model cortical electric field distributions under different electrode montages, we constructed a finite element model that represented the human head at high resolution. METHODS: Using computed tomography images, we constructed a human head model with high geometrical similarity. The removed bone flap was simplified to be circular with a diameter of 12 cm. We then constructed finite element models according to bioelectrical parameters. Finally, we simulated tDCS on the finite element models under different electrode montages. RESULTS: Inward current had a linear relationship with peak electric field value, but almost no effect on electric field distribution. If the anode was not over the skull hole (configuration 2), there was almost no difference in electric field magnitude and focality between the circular and square electrodes. However, if the anode was right over the hole (configuration 1), the circular electrodes led to higher peak electric field values and worse focality. In addition, configuration 1 significantly decreased focality compared with configuration 2. CONCLUSION: Our results might serve as guidelines for selecting current and electrode montage settings when performing tDCS on patients after DC.

The first Hermansky-Pudlak syndrome type 9 patient with two novel variants in Chinese population.

Hermansky-Pudlak syndrome 9 (HPS-9) is a recessive disorder caused by BLOC1S6 gene. There are only four variants identified from four HPS-9 patients so far. Here, we reported the first HPS-9 patient in a Chinese population. He had brownish-yellow hair, white skin, brown irises with visual acuity, photophobia and nystagmus. Two novel variants, c.148G>T (p.Glu50*) and c.351dupT (p.Ile118Tyrfs*10) in BLOC1S6 gene were identified by whole-exome sequencing (WES). Absence of platelet dense granules was found by whole-mount platelet electron microscopy and Western blotting assays showed the destabilized BLOC-1 subunits. He had recurrent bruising and was found to have abnormal brain waves by electroencephalogram, but did not develop thrombopenia, immunodeficiency or other symptoms reported in other HPS-9 patients. This is the first case report of BLOC-1 mutation in a Chinese population and our findings expand the mutational spectrum of HPS genes.

A zinc transporter, transmembrane protein 163, is critical for the biogenesis of platelet dense granules.

Lysosome-related organelles (LROs) are a category of secretory organelles enriched with ions such as calcium, which are maintained by ion transporters or channels. Homeostasis of these ions is important for LRO biogenesis and secretion. Hermansky-Pudlak syndrome (HPS) is a recessive disorder with defects in multiple LROs, typically platelet dense granules (DGs) and melanosomes. However, the underlying mechanism of DG deficiency is largely unknown. Using quantitative proteomics, we identified a previously unreported platelet zinc transporter, transmembrane protein 163 (TMEM163), which was significantly reduced in BLOC-1 (Dtnbp1sdy and Pldnpa)-, BLOC-2 (Hps6ru)-, or AP-3 (Ap3b1pe)-deficient mice and HPS patients (HPS2, HPS3, HPS5, HPS6, or HPS9). We observed similar platelet DG defects and higher intracellular zinc accumulation in platelets of mice deficient in either TMEM163 or dysbindin (a BLOC-1 subunit). In addition, we discovered that BLOC-1 was required for the trafficking of TMEM163 to perinuclear DG and late endosome marker-positive compartments (likely DG precursors) in MEG-01 cells. Our results suggest that TMEM163 is critical for DG biogenesis and that BLOC-1 is required for the trafficking of TMEM163 to putative DG precursors. These new findings suggest that loss of TMEM163 function results in disruption of intracellular zinc homeostasis and provide insights into the pathogenesis of HPS or platelet storage pool deficiency.

Genetic variants and mutational spectrum of Chinese Hermansky-Pudlak syndrome patients.

Hermansky-Pudlak syndrome (HPS) is a rare recessive disorder characterized by oculocutaneous albinism or ocular albinism, bleeding diathesis, and other symptoms such as colitis and pulmonary fibrosis. Eleven causative genes have been identified for HPS-1-HPS-11 subtypes in humans. We have identified 16 newly reported patients including the first HPS-2 case in the Chinese population. In a total of 40 HPS patients, hypopigmentation was milder in HPS-3, HPS-5, and HPS-6 patients than in HPS-1 and HPS-4 patients. HPS-1 accounted for 47.5% (19 of 40) of HPS cases which is the most common subtype. Exons 11 and 19 were the hotspots of the HPS1 gene mutations. In total, 55 allelic variants were identified in HPS1-HPS6 gene, of which 17 variants were previously unreported. These results will be useful for the evaluation of the relationship between HPS genotypes and phenotypes, and for the precise intervention of HPS patients in the Chinese population.

HPS1 Regulates the Maturation of Large Dense Core Vesicles and Lysozyme Secretion in Paneth Cells.

HPS1, a BLOC-3 subunit that acts as a guanine nucleotide exchange factor of Rab32/38, may play a role in the removal of VAMP7 during the maturation of large dense core vesicles of Paneth cells. Loss of HPS1 impairs lysozyme secretion and alters the composition of intestinal microbiota, which may explain the susceptibility of HPS-associated inflammatory bowel disease. Hermansky-Pudlak syndrome (HPS) is characterized by oculocutaneous albinism, bleeding tendency, and other chronic organ lesions due to defects in tissue-specific lysosome-related organelles (LROs). For some HPS subtypes, such as HPS-1, it is common to have symptoms of HPS-associated inflammatory bowel disease (IBD). However, its underlying mechanism is largely unknown. HPS1 is a subunit of the BLOC-3 complex which functions in the biogenesis of LROs. Large dense core vesicles (LDCVs) in Paneth cells of the intestine are a type of LROs. We here first report the abnormal LDCV morphology (increased number and enlarged size) in HPS1-deficient pale ear (ep) mice. Similar to its role in melanosome maturation, HPS1 plays an important function in the removal of VAMP7 from LDCVs to promote the maturation of LDCVs. The immature LDCVs in ep mice are defective in regulated secretion of lysozyme, a key anti-microbial peptide in the intestine. We observed changes in the composition of intestinal microbiota in both HPS-1 patients and ep mice. These findings provide insights into the underlying mechanism of HPS-associated IBD development, which may be implicated in possible therapeutic intervention of this devastating condition.

The role and mechanism of gastrodin in the medial prefrontal cortex autophagy of PTSD rats.

BACKGROUND: This study provided a reliable experimental basis for exploring the pathogenesis of PTSD-induced memory impairment, fear abnormalities, and affective disorders, aiming to facilitate new thinking for the prevention, treatment, and drug development of clinical PTSD. MATERIAL AND METHODS: A rat model of PTSD was established by continuous single stress stimulation method. The Morris water maze was used to detect the learning and spatial memory exploration abilities of rats. The autonomic motion behavior, fear, and anxiety of rats in each group was detected by the elevated plus maze test and the open field test. The immunofluorescence method was employed to observe and detect the changes of autophagy in mPFC neurons of PTSD rats. Western blotting was used to detect the expressions of autophagy-related genes Beclin-1 and LC3, autophagy substrate p62 protein, and apoptosis-related factors Bcl-2 and Bax. RESULT: Gastrodin could improve the learning and spatial memory abilities of PTSD-SPS rats, the reduction of active movement and inquiry behavior, and the autophagy of mPFC neurons, and also increase the expressions of Beclin-1, LC3-I, LC3-II, and Bax proteins, as well as decrease the expressions of Bcl-2 and p62. CONCLUSIONS: Gastrodin is effective in the treatment of PTSD-induced memory impairment, fear abnormalities, and affective disorders. The mechanism is related to autophagy in mPFC neurons.

Nix-mediated mitophagy regulates platelet activation and life span.

Platelet activation requires fully functional mitochondria, which provide a vital energy source and control the life span of platelets. Previous reports have shown that both general autophagy and selective mitophagy are critical for platelet function. However, the underlying mechanisms remain incompletely understood. Here, we show that Nix, a previously characterized mitophagy receptor that plays a role in red blood cell maturation, also mediates mitophagy in platelets. Genetic ablation of Nix impairs mitochondrial quality, platelet activation, and FeCl3-induced carotid arterial thrombosis without affecting the expression of platelet glycoproteins (GPs) such as GPIb, GPVI, and αIIbß3 Metabolic analysis revealed decreased mitochondrial membrane potential, enhanced mitochondrial reactive oxygen species level, diminished oxygen consumption rate, and compromised adenosine triphosphate production in Nix -/- platelets. Transplantation of wild-type (WT) bone marrow cells or transfusion of WT platelets into Nix-deficient mice rescued defects in platelet function and thrombosis, suggesting a platelet-autonomous role (acting on platelets, but not other cells) of Nix in platelet activation. Interestingly, loss of Nix increases the life span of platelets in vivo, likely through preventing autophagic degradation of the mitochondrial protein Bcl-xL. Collectively, our findings reveal a novel mechanistic link between Nix-mediated mitophagy, platelet life span, and platelet physiopathology. Our work suggests that targeting platelet mitophagy Nix might provide new antithrombotic strategies.

Instability of BLOC-2 and BLOC-3 in Chinese patients with Hermansky-Pudlak syndrome.

Hermansky-Pudlak syndrome (HPS) is a rare recessive disorder characterized by oculocutaneous albinism (OCA) or ocular albinism (OA), bleeding tendency, and other symptoms due to multiple defects in tissue-specific lysosome-related organelles. Ten HPS subtypes have been characterized with mutations in HPS1 to HPS10, which encode the subunits of BLOC-1, -2, -3, and AP-3. Using next-generation sequencing (NGS), we have screened 100 hypopigmentation genes in OCA or OA patients and identified four HPS-1, one HPS-3, one HPS-4, one HPS-5, and three HPS-6. The HPS-4 case is the first report in the Chinese population. Among these 20 mutational alleles, 16 were previously unreported alleles (6 in HPS1, 1 in HPS3, 2 in HPS4, 2 in HPS5, and 5 in HPS6). BLOC-2 and BLOC-3 were destabilized due to the mutation of these HPS genes which are so far the only reported causative genes in Chinese HPS patients, in which HPS-1 and HPS-6 are the most common subtypes. The mutational spectrum of Chinese HPS is population specific.

Sorting machineries: how platelet-dense granules differ from α-granules.

Platelets respond to vascular injury via surface receptor stimulation and signaling events to trigger aggregation, procoagulant activation, and granule secretion during hemostasis, thrombosis, and vascular remodeling. Platelets contain three major types of secretory granules including dense granules (or δ-granules, DGs), α-granules (AGs), and lysosomes. The contents of platelet granules are specific. Platelet DGs store polyphosphate and small molecules such as ADP, ATP, Ca2+, and serotonin, while AGs package most of the proteins that platelets release. The platelet DGs and AGs are regarded as being budded from the endosomes and the trans-Golgi network (TGN), respectively, and then matured from multivesicular bodies (MVBs). However, the sorting machineries between DGs and AGs are different. Inherited platelet disorders are associated with deficiency of DGs and AGs, leading to bleeding diathesis in patients with Hermansky-Pudlak syndrome (HPS), gray platelet syndrome (GPS), and arthrogryposis, renal dysfunction, and cholestasis syndrome (ARC). Here, we reviewed the current understanding about how DGs differ from AGs in structure, biogenesis, and function. In particular, we focus on the sorting machineries that are involved in the formation of these two types of granules to provide insights into their diverse biological functions.

Gender differences in the protective effects of green tea against amnestic mild cognitive impairment in the elderly Han population.

BACKGROUND: Gender differences may contribute to variances in the potential protective effects of tea against cognitive impairment in the elderly. OBJECTIVE: To examine the association between different types of tea consumption and the risk of amnestic mild cognitive impairment (aMCI) along gender lines. METHODS: A cross-sectional study was conducted with reference to 20 communities in China. The sample population included elderly participants aged 60 years or older. A standardized questionnaire was used to collect each participant's general demographic information. Trained psychologists administrated the Mini-Mental State Examination (MMSE) and the Montreal Cognitive Assessment (MoCA) to assess participants' cognitive function. An attending psychiatrist evaluated each participant's cognitive function. Finally, data from 2,131 participants were analyzed to assess the association. RESULTS: With regard to male participants, the percentage of green tea consumption was higher in the normal control group than in the aMCI group (X2=4.64, P=0.031). Logistic regression analysis showed that green tea consumption reduced the risk of aMCI in male participants (OR=0.657, P=0.019), and this finding was highly significant in males aged under 70 years (OR=0.376, P=0.002). Regarding female participants across every age group, the results indicated that tea consumption failed to significantly decrease the risk of aMCI (P>0.05). Unlike green tea, black tea and oolong tea were not correlated with a reduced risk of aMCI in terms of gender or age group. Multiple linear regression analysis also revealed that age, years of education, and green tea consumption (B=0.996, P=0.000) were associated with MoCA and MMSE scores, though only in male participants. CONCLUSION: Green tea consumption showed a protective effect against aMCI in males but not in females, particularly in males aged <70 years. However, black tea and oolong tea failed to show any protective effect in either males or females.

Effects of tandospirone augmentation in major depressive disorder patients with high anxiety: A multicenter, randomized, parallel-controlled, open-label study.

BACKGROUND: High levels of anxiety symptoms are common in individuals with major depressive disorder (MDD). Adjunctive anxiolytics are widely used in such patients; however, only a few studies have examined the strategy using tandospirone. This study aimed to evaluate the efficacy and safety of adjunctive tandospirone in individuals with MDD and high level of anxiety symptoms. METHODS: A multicenter, randomized, parallel-controlled, open-label study was conducted to evaluate the efficacy and safety of tandospirone coupled with selective serotonin reuptake inhibitors (SSRIs) in patients with MDD and high level of anxiety symptoms. Two hundred and forty-five patients fulfilling the DSM-IV-TR criteria for MDD were randomly assigned to 6 weeks of either SSRIs and tandospirone or SSRIs alone treatment. The efficacy was measured by HAMA total scores, HAMD-17 total scores, and Clinical Global Impressions severity subscale (CGI-S) score. RESULTS: After a 6-week follow-up, two hundred and thirty patients completed this study. Tandospirone coupled with SSRIs significantly improved depressive and anxiety symptoms compared to monotherapy with SSRIs as assessed by HAMD-17 total score (P = 0.003), HAMA total score (P = 0.010), and CGI-S score at week 6 (P = 0.003). The incidence rate of treatment-emergent adverse events (TEAEs) was similar in both groups; the therapy was well-tolerated. CONCLUSIONS: Short-term tandospirone augmentation was effective and well-tolerated in this study. Addition of tandospirone may improve outcomes in MDD patients with high anxiety.

Study on Lentivirus-Mediated ABCA7 Improves Neurocognitive Function and Related Mechanisms in the C57BL/6 Mouse Model of Alzheimer's Disease.

ATP-binding cassette transporter A7 (ABCA7) is expressed in the hippocampus and cortex of the brain and was confirmed to be involved in the development of Alzheimer's disease (AD). Previous studies have demonstrated that ABCA7 regulated Aß production, lipid transport, leading to AD characteristic pathological changes. However, the role and mechanism of ABCA7 in the context of AD needs further research. We augmented the expression of ABCA7 using lentiviral vector carrying ABCA7 gene to investigate the effect of ABCA7 overexpression on AD mice; then, we further explored the underlying mechanism in vitro. In the present study, ABCA7 was expressed successfully in the hippocampus of AD mice through lentiviral vector mediating ABCA7 gene; we showed that ABCA7 overexpression can effectively improve cognitive behavior of AD mice and diminished Aß production; meanwhile, ABCA7 overexpression significantly relieved the neurotoxicity of Aß by promoting cell viability and reducing endoplasmic reticulum stress. In conclusion, our findings showed that ABCA7 had obvious anti-Aß effect and appeared to improve cognitive function of AD mice. Our results provided a new thought and basic scientific data for the clinical treatment of AD.

NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients.

Hermansky-Pudlak syndrome (HPS) is a rare recessive disorder characterized by hypopigmentation, bleeding diathesis, and other symptoms due to multiple defects in lysosome-related organelles. Ten HPS subtypes have been identified with mutations in HPS1 to HPS10. Only four patients with HPS-1 have been reported in Chinese population. Using next-generation sequencing (NGS), we have screened 100 hypopigmentation genes and identified four HPS-1, two HPS-3, one HPS-5, and three HPS-6 in Chinese HPS patients with typical ocular or oculocutaneous albinism and the absence of platelet dense granules together with other variable phenotypes. All these patients except one homozygote were compound heterozygotes. Among these mutations, 14 were previously unreported alleles (four in HPS1, three in HPS3, two in HPS5, five in HPS6). Our results demonstrate the feasibility and utility of NGS-based panel diagnostics for HPS. Genotyping of HPS subtypes is a prerequisite for intervention of subtype-specific symptoms.

SLC35D3 increases autophagic activity in midbrain dopaminergic neurons by enhancing BECN1-ATG14-PIK3C3 complex formation.

Searching for new regulators of autophagy involved in selective dopaminergic (DA) neuron loss is a hallmark in the pathogenesis of Parkinson disease (PD). We here report that an endoplasmic reticulum (ER)-associated transmembrane protein SLC35D3 is selectively expressed in subsets of midbrain DA neurons in about 10% TH (tyrosine hydroxylase)-positive neurons in the substantia nigra pars compacta (SNc) and in about 22% TH-positive neurons in the ventral tegmental area (VTA). Loss of SLC35D3 in ros (roswell mutant) mice showed a reduction of 11.9% DA neurons in the SNc and 15.5% DA neuron loss in the VTA with impaired autophagy. We determined that SLC35D3 enhanced the formation of the BECN1-ATG14-PIK3C3 complex to induce autophagy. These results suggest that SLC35D3 is a new regulator of tissue-specific autophagy and plays an important role in the increased autophagic activity required for the survival of subsets of DA neurons.

Impaired autophagy in hilar mossy cells of the dentate gyrus and its implication in schizophrenia.

Schizophrenia (SCZ) is a complex disease that has been regarded as a neurodevelopmental, synaptic or epigenetic disorder. Here we provide evidence that neurodegeneration is implicated in SCZ. The DTNBP1 (dystrobrevin-binding protein 1) gene encodes dysbindin-1 and is a leading susceptibility gene of SCZ. We previously reported that the dysbindin-1C isoform regulates the survival of the hilar glutamatergic mossy cells in the dentate gyrus, which controls the adult hippocampal neurogenesis. However, the underlying mechanism of hilar mossy cell loss in the dysbindin-1-deficient sandy (sdy) mice (a mouse model of SCZ) is unknown. In this study, we did not observe the apoptotic signals in the hilar mossy cells of the sdy mice by using the TUNEL assay and immunostaining of cleaved caspase-3 or necdin, a dysbindin-1- and p53-interacting protein required for neuronal survival. However, we found that the steady-state level of LC3-II, a marker of autophagosomes, was decreased in the hippocampal formation in the mice lacking dysbindin-1C. Furthermore, we observed a significant reduction of the cytosolic LC3-II puncta in the mossy cells of sdy mice. In addition, overexpression of dysbindin-1C, but not 1A, in cultured cells increased LC3-II level and the LC3 puncta in the transfected cells. These results suggest that dysbindin-1C deficiency causes impaired autophagy, which is likely implicated in the pathogenesis of SCZ.