Harnessing developmental dynamics of spinal cord extracellular matrix improves regenerative potential of spinal cord organoids.

Neonatal spinal cord tissues exhibit remarkable regenerative capabilities as compared to adult spinal cord tissues after injury, but the role of extracellular matrix (ECM) in this process has remained elusive. Here, we found that early developmental spinal cord had higher levels of ECM proteins associated with neural development and axon growth, but fewer inhibitory proteoglycans, compared to those of adult spinal cord. Decellularized spinal cord ECM from neonatal (DNSCM) and adult (DASCM) rabbits preserved these differences. DNSCM promoted proliferation, migration, and neuronal differentiation of neural progenitor cells (NPCs) and facilitated axonal outgrowth and regeneration of spinal cord organoids more effectively than DASCM. Pleiotrophin (PTN) and Tenascin (TNC) in DNSCM were identified as contributors to these abilities. Furthermore, DNSCM demonstrated superior performance as a delivery vehicle for NPCs and organoids in spinal cord injury (SCI) models. This suggests that ECM cues from early development stages might significantly contribute to the prominent regeneration ability in spinal cord.

Complex interplay between FMRP and DHX9 during DNA replication stress.

Mutations in, or deficiency of, fragile X messenger ribonucleoprotein (FMRP) is responsible for the Fragile X syndrome (FXS), the most common cause for inherited intellectual disability. FMRP is a nucleocytoplasmic protein, primarily characterized as a translation repressor with poorly understood nuclear function(s). We recently reported that FXS patient cells lacking FMRP sustain higher level of DNA double-strand breaks (DSBs) than normal cells, specifically at sequences prone to forming R-loops, a phenotype further exacerbated by DNA replication stress. Moreover, expression of FMRP, and not an FMRPI304N mutant known to cause FXS, reduced R-loop-associated DSBs. We subsequently reported that recombinant FMRP directly binds R-loops, primarily through the carboxyl terminal intrinsically disordered region. Here, we show that FMRP directly interacts with an RNA helicase, DHX9. This interaction, which is mediated by the amino terminal structured domain of FMRP, is reduced with FMRPI304N. We also show that FMRP inhibits DHX9 helicase activity on RNA:DNA hybrids and the inhibition is also dependent on the amino terminus. Furthermore, the FMRPI304N mutation causes both FMRP and DHX9 to persist on the chromatin in replication stress. These results suggest an antagonistic relationship between FMRP and DHX9 at the chromatin, where their proper interaction leads to dissociation of both proteins from the fully resolved R-loop. We propose that the absence or the loss of function of FMRP leads to persistent presence of DHX9 or both proteins, respectively, on the unresolved R-loop, ultimately leading to DSBs. Our study sheds new light on our understanding of the genome functions of FMRP.

The role of the symbiotic microecosystem in cancer: gut microbiota, metabolome, and host immunome.

The gut microbiota is not just a simple nutritional symbiosis that parasitizes the host; it is a complex and dynamic ecosystem that coevolves actively with the host and is involved in a variety of biological activities such as circadian rhythm regulation, energy metabolism, and immune response. The development of the immune system and immunological functions are significantly influenced by the interaction between the host and the microbiota. The interactions between gut microbiota and cancer are of a complex nature. The critical role that the gut microbiota plays in tumor occurrence, progression, and treatment is not clear despite the already done research. The development of precision medicine and cancer immunotherapy further emphasizes the importance and significance of the question of how the microbiota takes part in cancer development, progression, and treatment. This review summarizes recent literature on the relationship between the gut microbiome and cancer immunology. The findings suggest the existence of a "symbiotic microecosystem" formed by gut microbiota, metabolome, and host immunome that is fundamental for the pathogenesis analysis and the development of therapeutic strategies for cancer.

Single-cell analysis reveals region-heterogeneous responses in rhesus monkey spinal cord with complete injury.

Spinal cord injury (SCI) leads to severe sensory and motor dysfunction below the lesion. However, the cellular dynamic responses and heterogeneity across different regions below the lesion remain to be elusive. Here, we used single-cell transcriptomics to investigate the region-related cellular responses in female rhesus monkeys with complete thoracic SCI from acute to chronic phases. We found that distal lumbar tissue cells were severely impacted, leading to degenerative microenvironments characterized by disease-associated microglia and oligodendrocytes activation alongside increased inhibitory interneurons proportion following SCI. By implanting scaffold into the injury sites, we could improve the injury microenvironment through glial cells and fibroblast regulation while remodeling spared lumbar tissues via reduced inhibitory neurons proportion and improved phagocytosis and myelination. Our findings offer crucial pathological insights into the spared distal tissues and proximal tissues after SCI, emphasizing the importance of scaffold-based treatment approaches targeting heterogeneous microenvironments.

Serological Responses after a Fourth Dose of SARS-CoV-2 Vaccine in Solid Organ Transplant Recipients: A Systematic Review and Meta-Analysis.

The humoral immune response and safety of the fourth dose of the coronavirus disease 2019 (COVID-19) vaccine in solid organ transplant (SOT) recipients need to be fully elucidated. We conducted a systematic review and meta-analysis to assess the efficacy and safety associated with this additional dose of the COVID-19 vaccine in the SOT recipients. A comprehensive search was conducted to identify studies on SOT patients without prior natural SARS-CoV-2 infection who received the fourth dose of the COVID-19 vaccine. Serological antibody responses following vaccination were synthesized by a meta-analysis of proportions. The proportions for each outcome were integrated by using a random-effects model. Approximately 56-92% of the SOT patients developed a humoral immune response, and the pooled seroprevalence rate was 75% (95% confidence interval [CI], 62-82%) after administering the third vaccine dose. Following the fourth dose of vaccination, approximately 76-95% of the patients developed a humoral immune response. The pooled seroprevalence rate after the fourth dose was 85% (95% CI, 79-91%). Of the patients who initially tested seronegative after the second dose, approximately 22-76% of patients subsequently became seropositive after the third dose. The pooled seroconversion rate for the third dose was 47% (95% CI, 31-64%). Among the patients who were seronegative after the third dose, approximately 25-76% turned seropositive after the fourth dose. The pooled seroconversion rate after the fourth dose was 51% (95% CI, 40-63%). Safety data were reported in three studies, demonstrating that adverse effects following the fourth dose were generally mild, and patients with these adverse effects did not require hospitalization. No transplant rejection or serious adverse events were observed. A fourth dose of the COVID-19 vaccine in SOT recipients was associated with an improved humoral immune response, and the vaccine was considered relatively safe.

Relationship between homologous recombination deficiency and clinical features of breast cancer based on genomic scar score.

BACKGROUND: Homologous recombination deficiency (HRD) phenotype will sensitize tumors to poly (ADP-ribose) polymerases inhibitors and platinum. However, previous studies did not focus on the prevalence of HRD among Chinese breast cancer (BC) patients. METHODS: One hundred and forty-seven BC patients were included in this study. Their HRD status was assessed by Genomic Scar Score (GSS), which was determined according to the length, site, and type of copy number. HRD was defined as positive when a harmful BRCA1/2 mutation was detected or GSS ≥50. RESULTS: Our data revealed that 9.5% of the 147 patients tested positive for BRCA1/2 mutation, while approximately 34.7% were HRD-positive. For triple negative BC (TNBC), HRD positivity rate (60.5%) was higher than Luminal A (5.3%), Luminal B (HER2-) (28.8%), and Luminal B (HER2+) (31.6%) subgroups. HRD-positive tumors were more likely to be ER/PR-negative and exhibited higher Ki-67 expression. 50.0% of the HRD-positive patients achieved pathologic complete remission (pCR) after neoadjuvant therapy. HRD-positive patients tended to have a higher risk for cancer recurrence or metastasis compared to HRD-negative patients (29.4% vs. 13.5%). CONCLUSION: We investigated the HRD status among Chinese BC patients using an HRD detection tool developed based on the Chinese population. The clinical characteristics, pathological profile, family history pattern, neoadjuvant efficacy, and disease progression events of HRD-positive and negative patients were described and compared. Thus, our data provided an evidence-based basis for applying the original HRD assay in Chinese BC.

Taugt17b1 Overexpression in Trichoderma atroviride Enhances Its Ability to Colonize Roots and Induce Systemic Defense of Plants.

Trichoderma atroviride, a soil fungus, has important applications in the biocontrol of plant diseases. Glycosyltransferases enhance the root colonization ability of Trichoderma spp. This study aimed to functionally characterize glycosyltransferase Taugt17b1 in T. atroviride. We investigated the effect of Taugt17b1 overexpression in T. atroviride H18-1-1 on its biocontrol properties, especially its ability to colonize roots. Our results demonstrated that the overexpression of the Taugt17b1 increases the T. atroviride colony growth rate, improves its root colonization ability, promotes the growth and activity of the defensive enzymatic system of plants, and prevents plant diseases. This study put forth a new role of T. atroviride glycosyltransferase and furthered the understanding of the mechanisms by which fungal biocontrol agents exert their effect.

DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops.

Unscheduled R loops can be a source of genome instability, a hallmark of cancer cells. Although targeted proteomic approaches and cellular analysis of specific mutants have uncovered factors potentially involved in R-loop homeostasis, we report a more open screening of factors whose depletion causes R loops based on the ability of activation-induced cytidine deaminase (AID) to target R loops. Immunofluorescence analysis of γH2AX caused by small interfering RNAs (siRNAs) covering 3,205 protein-coding genes identifies 59 potential candidates, from which 13 are analyzed further and show a significant increase of R loops. Such candidates are enriched in factors involved in chromatin, transcription, and RNA biogenesis and other processes. A more focused study shows that the DDX47 helicase is an R-loop resolvase, whereas the MeCP2 methyl-CpG-binding protein uncovers a link between DNA methylation and R loops. Thus, our results suggest that a plethora of gene dysfunctions can alter cell physiology via affecting R-loop homeostasis by different mechanisms.

Machine Learning-Enabled Framework for High-Throughput Screening of MOFs: Application in Radon/Indoor Air Separation.

Radon and its progeny may cause severe health hazards, especially for people working in underground spaces. Therefore, in this study, a hybrid artificial intelligence machine learning-enabled framework is proposed for high-throughput screening of metal-organic frameworks (MOFs) as adsorbents for radon separation from indoor air. MOFs from a specific database were initially screened using a pore-limiting diameter filter. Subsequently, random forest classification and grand canonical Monte Carlo simulations were implemented to identify MOFs with a high adsorbent performance score (APS) and high regenerability (R %). Interpretability and trustworthiness were determined by variable importance analysis , and adsorption mechanisms were elucidated by calculating the adsorption sites using Materials Studio. Notably, two MOF candidates were discovered with higher APS values in both the radon/N2 and radon/O2 systems compared with that of ZrSQU which is the best-performing MOF thus far, with R % values exceeding 85%. Furthermore, the proposed framework can be flexibly applied to multiple data sets due to good performance in model transfer. Therefore, the proposed framework has the potential to provide guidelines for the strategic design of MOFs for radon separation.

A model based on meta-analysis to evaluate poor prognosis of patients with severe fever with thrombocytopenia syndrome.

Background: Early identification of risk factors associated with poor prognosis in Severe fever with thrombocytopenia syndrome (SFTS) patients is crucial to improving patient survival. Method: Retrieve literature related to fatal risk factors in SFTS patients in the database, extract the risk factors and corresponding RRs and 95% CIs, and merge them. Statistically significant factors were included in the model, and stratified and assigned a corresponding score. Finally, a validation cohort from Yantai Qishan Hospital in 2021 was used to verify its predictive ability. Result: A total of 24 articles were included in the meta-analysis. The model includes six risk factors: age, hemorrhagic manifestations, encephalopathy, Scr and BUN. The analysis of lasso regression and multivariate logistic regression shows that model score is an independent risk factor (OR = 1.032, 95% CI 1.002-1.063, p = 0.034). The model had an area under the curve (AUC) of 0.779 (95% CI 0.669-0.889, P<0.001). The validation cohort was divided into four risk groups with cut-off values. Compared with the low-medium risk group, the mortality rate of high-risk and very high-risk patients was more significant (RR =5.677, 95% CI 4.961-6.496, P<0.001). Conclusion: The prediction model for the fatal outcome of SFTS patients has shown positive outcomes.Systematic review registration:https://www.crd.york.ac.uk/prospero/ (CRD42023453157).

Multifaceted regulation of the sumoylation of the Sgs1 DNA helicase.

Homologous recombination repairs DNA breaks and sequence gaps via the production of joint DNA intermediates such as Holliday junctions. Dissolving Holliday junctions into linear DNA repair products requires the activity of the Sgs1 helicase in yeast and of its homologs in other organisms. Recent studies suggest that the functions of these conserved helicases are regulated by sumoylation; however, the mechanisms that promote their sumoylation are not well understood. Here, we employed in vitro sumoylation systems and cellular assays to determine the roles of DNA and the scaffold protein Esc2 in Sgs1 sumoylation. We show that DNA binding enhances Sgs1 sumoylation in vitro. In addition, we demonstrate the Esc2's midregion (MR) with DNA-binding activity is required for Sgs1 sumoylation. Unexpectedly, we found that the sumoylation-promoting effect of Esc2-MR is DNA independent, suggesting a second function for this domain. In agreement with our biochemical data, we found the Esc2-MR domain, like its SUMO E2-binding C-terminal domain characterized in previous studies, is required for proficient sumoylation of Sgs1 and its cofactors, Top3 and Rmi1, in cells. Taken together, these findings provide evidence that while DNA binding enhances Sgs1 sumoylation, Esc2-based stimulation of this modification is mediated by two distinct domains.

Lineage tracing reveals the origin of Nestin-positive cells are heterogeneous and rarely from ependymal cells after spinal cord injury.

Nestin is expressed extensively in neural stem/progenitor cells during neural development, but its expression is mainly restricted to the ependymal cells in the adult spinal cord. After spinal cord injury (SCI), Nestin expression is reactivated and Nestin-positive (Nestin+) cells aggregate at the injury site. However, the derivation of Nestin+ cells is not clearly defined. Here, we found that Nestin expression was substantially increased in the lesion edge and lesion core after SCI. Using a tamoxifen inducible CreER(T2)-loxP system, we verified that ependymal cells contribute few Nestin+ cells either to the lesion core or the lesion edge after SCI. In the lesion edge, GFAP+ astrocytes were the main cell type that expressed Nestin; they then formed an astrocyte scar. In the lesion core, Nestin+ cells expressed αSMA or Desmin, indicating that they might be derived from pericytes. Our results reveal that Nestin+ cells in the lesion core and edge came from various cell types and rarely from ependymal cells after complete transected SCI, which may provide new insights into SCI repair.

Single-cell RNA sequencing reveals Nestin+ active neural stem cells outside the central canal after spinal cord injury.

Neural stem cells (NSCs) in the spinal cord hold great potential for repair after spinal cord injury (SCI). The ependyma in the central canal (CC) region has been considered as the NSCs source in the spinal cord. However, the ependyma function as NSCs after SCI is still under debate. We used Nestin as a marker to isolate potential NSCs and their immediate progeny, and characterized the cells before and after SCI by single-cell RNA-sequencing (scRNA-seq). We identified two subgroups of NSCs: the subgroup located within the CC cannot prime to active NSCs after SCI, while the subgroup located outside the CC were activated and exhibited the active NSCs properties after SCI. We demonstrated the comprehensive dynamic transcriptome of NSCs from quiescent to active NSCs after SCI. This study reveals that Nestin+ cells outside CC were NSCs that activated upon SCI and may thus serve as endogenous NSCs for regenerative treatment of SCI in the future.

Study on Crack Development and Micro-Pore Mechanism of Expansive Soil Improved by Coal Gangue under Drying-Wetting Cycles.

Expansive soil is prone to cracks under a drying-wetting cycle environment, which brings many disasters to road engineering. The main purpose of this study is use coal gangue powder to improve expansive soil, in order to reduce its cracks and further explore its micro-pore mechanism. The drying-wetting cycles test is carried out on the soil sample, and the crack parameters of the soil sample are obtained by Matlab and Image J software. The roughness and micro-pore characteristics of the soil samples are revealed by means of the Laser confocal 3D microscope and Mercury intrusion meter. The results show that coal gangue powder reduces the crack area ratio of expansive soil by 48.9%, and the crack initiation time is delayed by at least 60 min. Coal gangue powder can increase the internal roughness of expansive soil. The greater the roughness of the soil, the less cracks in the soil. After six drying-wetting cycles, the porosity and average pore diameter of the improved and expanded soil are reduced by 37% and 30%, respectively, as compared to the plain expansive soil. By analyzing the cumulative pore volume and cumulative pore density parameters of soil samples, it is found that the macro-cracks are caused by the continuous connection and fusion of micro-voids in soil. Coal gangue powder can significantly reduce the proportion of micro-voids, cumulative pore volume, and cumulative pore density in expansive soil, so as to reduce the macro-cracks.

Esc2 orchestrates substrate-specific sumoylation by acting as a SUMO E2 cofactor in genome maintenance.

SUMO modification regulates diverse cellular processes by targeting hundreds of proteins. However, the limited number of sumoylation enzymes raises the question of how such a large number of substrates are efficiently modified. Specifically, how genome maintenance factors are dynamically sumoylated at DNA replication and repair sites to modulate their functions is poorly understood. Here, we demonstrate a role for the conserved yeast Esc2 protein in this process by acting as a SUMO E2 cofactor. Esc2 is required for genome stability and binds to Holliday junctions and replication fork structures. Our targeted screen found that Esc2 promotes the sumoylation of a Holliday junction dissolution complex and specific replisome proteins. Esc2 does not elicit these effects via stable interactions with substrates or their common SUMO E3. Rather, we show that a SUMO-like domain of Esc2 stimulates sumoylation by exploiting a noncovalent SUMO binding site on the E2 enzyme. This role of Esc2 in sumoylation is required for Holliday junction clearance and genome stability. Our findings thus suggest that Esc2 acts as a SUMO E2 cofactor at distinct DNA structures to promote the sumoylation of specific substrates and genome maintenance.

Spatiotemporal dynamic changes, proliferation, and differentiation characteristics of Sox9-positive cells after severe complete transection spinal cord injury.

Studying the spatiotemporal dynamic changes of various cells following spinal cord injury (SCI) is of great significance for understanding the pathological processes of SCI. Changes in the characteristics of Sox9-positive cells, which are widely present in the spinal cord, have rarely been studied following SCI. We found that Sox9-positive cells were widely distributed in the central canal and parenchyma of the uninjured adult spinal cord, with the greatest distribution in the central spinal cord and relatively few cells in the dorsal and ventral sides. Ranging between 14.20% ± 1.61% and 15.60% ± 0.36% of total cells in the spinal cord, almost all Sox9-positive cells were in a quiescent state. However, Sox9-positive cells activated following SCI exhibited different characteristics according to their distance from the lesion area. In the reactive region, Sox9-positive cells highly expressed nestin and exhibited a single-branching structure, whereas in the non-reactive region, cells showed low nestin expression and a multi-branching structure. In response to SCI, a large number of Sox9-positive cells in the spinal cord parenchyma proliferated to participate in the formation of glial scars, whereas Sox9-positive cells in the central canal located near the lesion site accumulated at its broken ends through proliferation. Finally, we found that approximately 6.30% ± 0.35% of Sox9-positive cells differentiated into oligodendrocytes within two weeks after SCI. By examining the spatiotemporal dynamic changes, proliferation and differentiation characteristics of Sox9-positive cells after SCI, our findings provide a theoretical basis for understanding the pathological process of SCI.

Small molecules combined with collagen hydrogel direct neurogenesis and migration of neural stem cells after spinal cord injury.

Complete spinal cord injury (SCI) leads to cell death, interruption of axonal connections and permanent functional impairments. In the development of SCI treatments, cell transplantation combined with biomaterial-growth factor-based therapies have been widely studied. Another avenue worth exploring is the generation of neurons from endogenous neural stem cells (NSCs) or reactive astrocytes activated by SCI. Here, we screened a combination of four small molecules, LDN193189, SB431542, CHIR99021 and P7C3-A20, that can increase neuronal differentiation of mouse and rat spinal cord NSCs. Moreover, the small molecules loaded in an injectable collagen hydrogel induced neurogenesis and inhibited astrogliogenesis of endogenous NSCs in the injury site, which usually differentiate into astrocytes under pathological conditions. Meanwhile, induced neurons migrated into the non-neural lesion core, and genetic fate mapping showed that neurons mainly originated from NSCs in the parenchyma, but not from the central canal of the spinal cord. The neuronal regeneration in the lesion sites resulted in some recovery of locomotion. Our findings indicate that the combined treatment of small molecules and collagen hydrogel is a potential therapeutic strategy for SCI by inducing in situ endogenous NSCs to form neurons and restore damaged functions.

Network temporality can promote and suppress information spreading.

Temporality is an essential characteristic of many real-world networks and dramatically affects the spreading dynamics on networks. In this paper, we propose an information spreading model on temporal networks with heterogeneous populations. Individuals are divided into activists and bigots to describe the willingness to accept the information. Through a developed discrete Markov chain approach and extensive numerical simulations, we discuss the phase diagram of the model and the effects of network temporality. From the phase diagram, we find that the outbreak phase transition is continuous when bigots are relatively rare, and a hysteresis loop emerges when there are a sufficient number of bigots. The network temporality does not qualitatively alter the phase diagram. However, we find that the network temporality affects the spreading outbreak size by either promoting or suppressing, which relies on the heterogeneities of population and of degree distribution. Specifically, in networks with homogeneous and weak heterogeneous degree distribution, the network temporality suppresses (promotes) the information spreading for small (large) values of information transmission probability. In networks with strong heterogeneous degree distribution, the network temporality always promotes the information spreading when activists dominate the population, or there are relatively fewer activists. Finally, we also find the optimal network evolution scale, under which the network information spreading is maximized.

Protocol for Purification of Human ZGRF1 and Its Regulatory Function on RAD51-Mediated D-Loop Formation.

Human ZGRF1 is one of the many helicases that play important roles in the repair of damaged chromosomes by homologous recombination. However, the lack of biochemical characterization of the ZGRF1 protein has hindered the understanding of its function. We have developed a facile protocol to express human ZGRF1 in insect cells and for its purification. We have also tuned biochemical assays by lowering the protein and DNA concentrations to analyze its functions in RAD51-mediated D-loop formation and dissociation. For complete details on the use and execution of this protocol, please refer to Brannvoll et al. (2020).