Ring domains are essential for GATOR2-dependent mTORC1 activation.

The GATOR2-GATOR1 signaling axis is essential for amino-acid-dependent mTORC1 activation. However, the molecular function of the GATOR2 complex remains unknown. Here, we report that disruption of the Ring domains of Mios, WDR24, or WDR59 completely impedes amino-acid-mediated mTORC1 activation. Mechanistically, via interacting with Ring domains of WDR59 and WDR24, the Ring domain of Mios acts as a hub to maintain GATOR2 integrity, disruption of which leads to self-ubiquitination of WDR24. Physiologically, leucine stimulation dissociates Sestrin2 from the Ring domain of WDR24 and confers its availability to UBE2D3 and subsequent ubiquitination of NPRL2, contributing to GATOR2-mediated GATOR1 inactivation. As such, WDR24 ablation or Ring deletion prevents mTORC1 activation, leading to severe growth defects and embryonic lethality at E10.5 in mice. Hence, our findings demonstrate that Ring domains are essential for GATOR2 to transmit amino acid availability to mTORC1 and further reveal the essentiality of nutrient sensing during embryonic development.

Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses.

We present barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel insitu analyses (BOLORAMIS), a reverse transcription-free method for spatially-resolved, targeted, in situ RNA identification of single or multiple targets. BOLORAMIS was demonstrated on a range of cell types and human cerebral organoids. Singleplex experiments to detect coding and non-coding RNAs in human iPSCs showed a stem-cell signature pattern. Specificity of BOLORAMIS was found to be 92% as illustrated by a clear distinction between human and mouse housekeeping genes in a co-culture system, as well as by recapitulation of subcellular localization of lncRNA MALAT1. Sensitivity of BOLORAMIS was quantified by comparing with single molecule FISH experiments and found to be 11%, 12% and 35% for GAPDH, TFRC and POLR2A, respectively. To demonstrate BOLORAMIS for multiplexed gene analysis, we targeted 96 mRNAs within a co-culture of iNGN neurons and HMC3 human microglial cells. We used fluorescence in situ sequencing to detect error-robust 8-base barcodes associated with each of these genes. We then used this data to uncover the spatial relationship among cells and transcripts by performing single-cell clustering and gene-gene proximity analyses. We anticipate the BOLORAMIS technology for in situ RNA detection to find applications in basic and translational research.

Using protein granularity to extract the protein sequence features.

The feature extraction of protein sequences is a challenging problem. It might need a lot of theoretical and practical knowledge from many fields. The difficulty would increase when investigators extract the features solely from protein sequences. In this paper, we present a method of protein granularity. The concepts of protein granularity, granularity order, granularity bound, granularity limit, and granularity increment are given respectively. The protein granularity can dig out the useful information solely from protein sequences. We provide an approach to construct the feature vectors. The feature vectors include the amino acid composition information, the sequence-order information, the same amino acid 'neighbor' information, and the sequence length information. Hence, the feature vectors can better represent protein sequences. Our feature extraction method does obviously consider the protein sequence length effects. An experiment of the protein structure class prediction was carried out. The prediction achieved 96.6% overall accuracy, and the success rate for each subset is all-α 92.3%, all-ß 100%, α/ß 100%, α+ß 93.5%, respectively. The last three success rates for subsets are equal to the best success rates in the published literatures. The overall accuracy of PG-SVM prediction is the second best result only having one protein prediction error difference with the first best result. The theoretical and experimental results demonstrate the application of protein granularity succeeds in the feature extraction of protein sequences.

Multiplex base editing to convert TAG into TAA codons in the human genome.

Whole-genome recoding has been shown to enable nonstandard amino acids, biocontainment and viral resistance in bacteria. Here we take the first steps to extend this to human cells demonstrating exceptional base editing to convert TAG to TAA for 33 essential genes via a single transfection, and examine base-editing genome-wide (observing ~40 C-to-T off-target events in essential gene exons). We also introduce GRIT, a computational tool for recoding. This demonstrates the feasibility of recoding, and highly multiplex editing in mammalian cells.

Orthogonally induced differentiation of stem cells for the programmatic patterning of vascularized organoids and bioprinted tissues.

The generation of organoids and tissues with programmable cellular complexity, architecture and function would benefit from the simultaneous differentiation of human induced pluripotent stem cells (hiPSCs) into divergent cell types. Yet differentiation protocols for the overexpression of specific transcription factors typically produce a single cell type. Here we show that patterned organoids and bioprinted tissues with controlled composition and organization can be generated by simultaneously co-differentiating hiPSCs into distinct cell types via the forced overexpression of transcription factors, independently of culture-media composition. Specifically, we used such orthogonally induced differentiation to generate endothelial cells and neurons from hiPSCs in a one-pot system containing either neural or endothelial stem-cell-specifying media, and to produce vascularized and patterned cortical organoids within days by aggregating inducible-transcription-factor and wild-type hiPSCs into randomly pooled or multicore-shell embryoid bodies. Moreover, by leveraging multimaterial bioprinting of hiPSC inks without extracellular matrix, we generated patterned neural tissues with layered regions composed of neural stem cells, endothelium and neurons. Orthogonally induced differentiation of stem cells may facilitate the fabrication of engineered tissues for biomedical applications.

Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder.

Cerebral organoids can be used to gain insights into cell type specific processes perturbed by genetic variants associated with neuropsychiatric disorders. However, robust and scalable phenotyping of organoids remains challenging. Here, we perform RNA sequencing on 71 samples comprising 1,420 cerebral organoids from 25 donors, and describe a framework (Orgo-Seq) to integrate bulk RNA and single-cell RNA sequence data. We apply Orgo-Seq to 16p11.2 deletions and 15q11-13 duplications, two loci associated with autism spectrum disorder, to identify immature neurons and intermediate progenitor cells as critical cell types for 16p11.2 deletions. We further applied Orgo-Seq to identify cell type-specific driver genes. Our work presents a quantitative phenotyping framework to integrate multi-transcriptomic datasets for the identification of cell types and cell type-specific co-expressed driver genes associated with neuropsychiatric disorders.

Neuronal Cell-type Engineering by Transcriptional Activation.

Gene activation with the CRISPR-Cas system has great implications in studying gene function, controlling cellular behavior, and modulating disease progression. In this review, we survey recent studies on targeted gene activation and multiplexed screening for inducing neuronal differentiation using CRISPR-Cas transcriptional activation (CRISPRa) and open reading frame (ORF) expression. Critical technical parameters of CRISPRa and ORF-based strategies for neuronal programming are presented and discussed. In addition, recent progress on in vivo applications of CRISPRa to the nervous system are highlighted. Overall, CRISPRa represents a valuable addition to the experimental toolbox for neuronal cell-type programming.

Cell therapy strategies for COVID-19: Current approaches and potential applications.

Coronavirus disease 2019 (COVID-19) continues to burden society worldwide. Despite most patients having a mild course, severe presentations have limited treatment options. COVID-19 manifestations extend beyond the lungs and may affect the cardiovascular, nervous, and other organ systems. Current treatments are nonspecific and do not address potential long-term consequences such as pulmonary fibrosis, demyelination, and ischemic organ damage. Cell therapies offer great potential in treating severe COVID-19 presentations due to their customizability and regenerative function. This review summarizes COVID-19 pathogenesis, respective areas where cell therapies have potential, and the ongoing 89 cell therapy trials in COVID-19 as of 1 January 2021.

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.

Methods for highly multiplexed RNA imaging are limited in spatial resolution and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to the mouse brain, which yielded the readout of thousands of genes, including splice variants. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in the neurons of the mouse hippocampus, revealing patterns across multiple cell types, layer-specific cell types across the mouse visual cortex, and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus, ExSeq enables highly multiplexed mapping of RNAs from nanoscale to system scale.

Supraorbital Nerve Radiofrequency for Severe Neuralgia Caused by Herpes Zoster Ophthalmicus.

Background: Radiofrequency of the Gasserian ganglion can be used for ophthalmic herpetic neuralgia (OHN), but it is associated with complications. This study aimed to use the supraorbital nerve for computed tomography- (CT-) guided radiofrequency thermocoagulation to treat refractory OHN. Methods: This was a retrospective case series study of patients with simple or combined OHN treated at our hospital between 06/2012 and 06/2018. The numerical rating score (NRS), spontaneous pain, allodynia, gabapentin dosage, paracetamol/oxycodone dosage, patient global impression of change (PGIC) score, Barrow numbness score, postoperative 360-day recurrence rate, and complications were recorded before the operation and at 1, 30, 90, 180, and 360 days after the operation. Results: Compared with baseline, the NRS was decreased, and PGIC was increased at postoperative 1, 30, 90, 180, and 360 days, and the gabapentin and paracetamol oxycodone doses at postoperative 30, 90, 180, and 360 days were decreased (all P < 0.001). Compared with 1 day after the operation, numbness was decreased at 30, 90, 180, and 360 days after the operation (P < 0.001). Compared with baseline, the number of patients with allodynia at each time point after the operation was decreased (P < 0.001), but without a difference for spontaneous pain (P=0.407). No subjects showed drooping eyelid, corneal ulcers, eyeball damage, decreased vision, and other severe complications. Conclusion: CT-guided supraorbital nerve radiofrequency thermocoagulation for the treatment of OHN can effectively relieve pain and reduce the dose of analgesics, without any serious complication. This study suggests that this technique is feasible and applicable to clinical practice.

Effects of Supraorbital Foramen Variations on the Treatment Efficacy of Radiofrequency Therapy for V1 Trigeminal Neuralgia: A Retrospective Study.

Background: Primary V1 trigeminal neuralgia is a common refractory neuralgia in clinical practice, lacking effective treatments. Radiofrequency therapy has certain treatment efficacy, but its long-term efficacy remained poor and the disease might relapse. Objective: To compare the effects of different types of supraorbital foramen variations on the treatment efficacy of radiofrequency therapy for V1 trigeminal neuralgia. Methods: Data of 54 patients with V1 trigeminal neuralgia who underwent treatment in the First Hospital of Jiaxing, Zhejiang, were retrospectively analyzed. All these patients received CT-guided radiofrequency thermocoagulation of supraorbital nerve. According to the CT images, the supraorbital foramen of the patients was categorized as holes (hole group) or notches (notch group). The patient characteristics, including Numerical Rating Scale (NRS) score and effective treatment rates before and 1 d, 0.5 y, 1 y, and 2 y after operation, and numbness degree at day 1 and 2 y after the operation were compared. The short- and long-term complications during postoperative follow-up period were also recorded. Results: Among the 54 patients, 25 patients were grouped into the hole group and 29 into the notch group. The NRS scores before and at 1 d, 0.5 y, 1 y, and 2 y after operation showed no significant differences between the two groups. However, the NRS scores at the remaining time points after operation were significantly decreased when compared with scores before operation (P < 0.05). The numbness and numbness degree after operation showed no significant differences between the two groups. The numbness degree at 2 y after operation was significantly lower than 1 d after operation (P < 0.05). The numbness and numbness degree after operation showed no significant differences between the two groups. The numbness degree at 2 y after operation was significantly lower than 1 d after operation (P < 0.05). The numbness and numbness degree after operation showed no significant differences between the two groups. The numbness degree at 2 y after operation was significantly lower than 1 d after operation (. Conclusion: The short- and long-term effective rates of radiofrequency therapy during V1 trigeminal neuralgia treatment are relatively high in patients with different types of supraorbital foramen variations. However, the effective rate is even higher in patients with hole-type supraorbital foramen. No other severe complications, except numbness, were found, and the acceptability rate remained high in patients.

Quantitative proteomic analysis of human plasma using tandem mass tags to identify novel biomarkers for herpes zoster.

Herpes zoster (HZ), commonly called shingles, it is a distinctive syndrome caused by reactivation of varicella zoster virus (VZV). A better understanding of the biological characteristics of HZ patients can help develop new targeted therapies to improve the prognosis. High-throughput proteomics technology can deeply study the molecular changes in the development and progression of HZ disease and integrate different levels of information, this is important to help make clinical decisions. Circulating blood contains a lot of biological information, we conducted a proteomics study of patient plasma, hoping to identify key proteins that could indicate the development of HZ. Compared to healthy human plasma, we found 44 differentially expressed proteins in the plasma of HZ patients, the main pathways involved in these molecules are MAPK signaling pathway, Neuroactive ligand-receptor interaction, Acute myeloid leukemia, Transcriptional misregulation in cancer. We found that 27 proteins have direct protein-protein interactions. Based on the comprehensive score, we identified six key molecules as candidate molecules for further study, and then validated another 80 plasma samples (40 HZ patient plasma and 40 healthy human plasma) using enzyme-linked immunosorbent assay (ELISA), immunoblot assay and receiver operating characteristic (ROC) curve analysis. Finally, we found that the expression levels of these three proteins (PLG, F2, VTN) were significantly lower than those of healthy controls (P < .05). To the best of our knowledge, we first used tandem mass tag (TMT) combined with liquid chromatography-mass spectrometry (LC-MS/MS) to screen for differentially expressed proteins in plasma between HZ patients and healthy individuals. It is preliminarily proved that the plasma protein expression profile of HZ patients is different from that of uninfected patients, it has also been found that these three altered key proteins may be used as biomarkers to test early HZ infection. This study reveals new insights into HZ that help to more accurately identify early HZ patients and to find new therapeutic targets. SIGNIFICANCE: Varicella-zoster virus (VZV; termed human alphaherpesvirus 3 by the International Committee on Taxonomy of Viruses) is a herpesvirus that is ubiquitous in humans and can cause chickenpox and herpes zoster (HZ). After the initial infection of varicella, the VZV goes into a dormant state in the sensory ganglia and cranial nerves. As age or immunosuppression increases, the cellular immunity to VZV decreases, and the virus reactivates and spreads along the sensory nerves to the skin, causing a unique prodromal pain followed by a rash. About one in five people around the world may be infected with VZV at some point in their lives. According to statistics, about one-third of infected people will develop HZ in their lifetime, and an estimated 1 million cases of herpes zoster occur in the United States each year. Herpes zoster can occur at any age and is usually less severe in children and young adults, but the greatest morbidity and mortality are observed in elderly and immunocompromised patients. 20% of patients with HZ have complications including vasculitis, increased risk of myocardial infarction, or postherpetic neuralgia, the overall mortality rate of patients with HZ in the United States is close to 5%. Considering the wide clinical severity and complications of this disease, there is a great need for biomarkers that contribute to early diagnosis, classification of risks, and prediction of outcomes, which will help elucidate the mechanisms underlying their clinical development. As a useful tool in biology, quantitative proteomics can repeatedly identify and accurately quantify proteins in a variety of biological samples. Proteomic analysis focuses on translational proteins, which play a direct role in most biological processes. Although a small number of proteins can be studied simultaneously with traditional methods, such as ELISA and Western blotting, typical proteomics studies can simultaneously analyze thousands of proteins for a more comprehensive identification. Proteomics has been successfully applied to human-based disease research, Analysis of exposed and unexposed subjects based on mass spectrometry (MS) has been found to reveal altered expression of proteins that can be identified as intermediate biomarkers of early disease effects. Tandem mass tags (TMTs) are chemical labels used for MS-based identification and quantification of biological molecules. TMTs play an important role in proteomic analysis in a variety of samples such as cells, tissues, and body fluids. The body fluids that are often detected clinically are blood, which are easy to obtain and contain abundant biological information related to physiological and pathological processes, we hope to develop protein biomarkers from these blood. Therefore, in order to better characterize the pathological process of HZ patients, we performed proteomic analysis of HZ patients and healthy human plasma using the TMT method. This comparison aims to identify specific processes in the development of HZ disease through protein profiling, which may help to improve our biological understanding of HZ.

Liquiritin Alleviates Pain Through Inhibiting CXCL1/CXCR2 Signaling Pathway in Bone Cancer Pain Rat.

Bone cancer pain (BCP) is an intractable clinical problem, and lacked effective drugs for treating it. Recent research showed that several chemokines in the spinal cord are involved in the pathogenesis of BCP. In this study, the antinociceptive effects of liquiritin, which is an active component extracted from Glycyrrhizae Radix, were tested and the underlying mechanisms targeting spinal dorsal horn (SDH) were investigated. The BCP group displayed a significant decrease in the mechanical withdrawal threshold on days 6, 12, and 18 when compared with sham groups. Intrathecal administration of different doses of liquiritin alleviated mechanical allodynia in BCP rats. The results of immunofluorescent staining and western blotting showed that liquiritin inhibited BCP-induced activation of astrocytes in the spinal cord. Moreover, intrathecal administration of liquiritin effectively inhibited the activation of CXCL1/CXCR2 signaling pathway and production of IL-1ß and IL-17 in BCP rats. In astroglial-enriched cultures, Lipopolysaccharides (LPS) elicited the release of chemokine CXCL1, and the release was decreased in a dose-dependent manner by liquiritin. In primary neurons, liquiritin indirectly reduced the increase of CXCR2 by astroglial-enriched-conditioned medium but not directly on the CXCR2 target site. These results suggested that liquiritin effectively attenuated BCP in rats by inhibiting the activation of spinal astrocytic CXCL1 and neuronal CXCR2 pathway. These findings provided evidence regarding the the antinociceptive effect of liquiritin on BCP.