Biology subjects

Li, S.

Publications and source records attributed to Li, S..

At least 1,315 records · Page 73Linked to original sources

bioRxiv2018

β-lactam Antibiotics Stimulate the Pathogenicity of Methicillin-resistant Staphylococcus aureus Via SarA-controlled Tandem Lipoprotein Expression

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of nosocomial infections worldwide. MRSA resists nearly all {beta}-lactam antibiotics that have a bactericidal activity and a signal inducer effect. However, studies have yet to clarify whether the inducer effect of empirically used {beta}-lactams stimulates MRSA pathogenicity in vivo. Here, we showed that a new cluster of tandem lipoprotein genes (tlpps) was upregulated in MRSA in response to the subinhibitory concentrations of {beta}-lactam induction. The increased Tlpps significantly altered immune responses by macrophages with high IL-6 and TNF levels. The deletion of the tlpps mutant (N315{Delta}tlpps) significantly decreased the proinflammatory cytokine levels in vitro and in vivo. The bacterial loads of N315{Delta}tlpps in the mouse kidney were also reduced compared with those of the wild type N315. The {beta}-lactam-treated MRSA exacerbated cutaneous infections with increased lesion size, extended illness, and flake-like abscess-formation compared with those of the nontreatment. The {beta}-lactam antibiotics that promoted the MRSA pathogenicity were SarA dependent, and the increasing expression of tlpps after {beta}-lactam treatment was directly controlled by the global regulator SarA. Overall, our findings suggested that {beta}-lactams should be used carefully because it might lead to a worse outcome of MRSA infection than inaction in the treatment.\n\nAuthor summary{beta}-lactams are widely used in practice to treat infectious diseases, however, {beta}-lactams worsening the outcome of a certain disease is poorly understood. In this study, we have identified a new cluster of tandem lipoprotein genes (tlpps) that is upregulated in the major clinically prevalent MRSA clones in response to the subinhibitory concentrations of {beta}-lactams induction. The major highlight in this work is that {beta}-lactams induce SarA expression, and then SarA directly binds to the tlpp cluster promoter region and upregulates the tlpp expression in MRSA. Moreover, the {beta}-lactam stimulated Tlpps are important virulence factors that enhance MRSA pathogenicity. The deletion of the tlpps mutant significantly decreases the proinflammatory cytokine levels in vitro and in vivo. The {beta}-lactam induced Tlpps enhance the host inflammatory responses by triggering the expression of IL-6 and TNF, thereby promoting bacterial colonization and abscess formation. These data elucidate that {beta}-lactams can worsen the outcome of MRSA infection through the induction of tlpps that are controlled by the global regulator SarA.

pathology↗

bioRxiv2018

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology.

systems biology↗

bioRxiv2018

Nrf1D is the first candidate secretory transcription factor in the blood plasma, with its precursor existing as a unique redox-sensitive transmembrane CNC-bZIP protein in somatic tissues

Amongst multiple distinct isoforms, Nrf1D is synthesized from translation of an alternatively-spliced transcript of Nrf1 mRNA, with a naturally-occurring deletion of its stop codon-flanking 1466 nucleotides. This molecular event leads to the reading frameshift mutation, which results in a constitutive substitution of the intact Nrf1s C-terminal 72 amino acids (aa, covering the second half of the leucine zipper motif to C-terminal Neh3L domain) by an additional extended 80-aa stretch to generate a unique variant Nrf1D. The C-terminal extra 80-aa region of Nrf1D was identified to fold into a redox-sensitive transmembrane domain that enables it to be tightly integrated within the endoplasmic reticulum (ER) membranes. Notably, the salient feature of Nrf1D confers it to be distinguishable from prototypic Nrf1, such that Nrf1D is endowed with only a less ability than wild-type Nrf1 at mediating target gene expression. Further evidence has been presented revealing that both mRNA and protein levels of Nrf1D were detected to varying extents in somatic tissues. Surprisingly, we also found the existence of Nrf1D-derived isoforms in the blood plasma, implying that it is a candidate secretory transcription factor, although its precursor acts as an integral transmembrane-bound CNC-bZIP protein that entails dynamic topologies, before being unleashed from the ER to enter the blood plasma.

cell biology↗

bioRxiv2018

PI(4,5)P2 Binding Sites in the Ebola Virus Matrix Protein Modulate Assembly and Budding

Ebola virus (EBOV) causes sever hemorrhagic fever in humans, can cause death in a large percentage of those infected, and still lacks FDA approved treatment options. In this study, we investigated how the essential EBOV protein, VP40, forms stable oligomers to mediate budding and assembly from the host cell plasma membrane. An array of in vitro and cellular assays identified and characterized two lysine rich regions that bind to PI(4,5)P2 and serve distinct functions through the lipid binding and assembly of the viral matrix layer. We found that when VP40 binds PI(4,5)P2, VP40 oligomers become extremely stable and long lived. Together, this work characterizes the molecular basis of PI(4,5)P2 binding by VP40, which stabilizes formation of VP40 oligomers necessary for viral assembly and budding. Quercetin, a natural product that lowers PI(4,5)P2 in the plasma membrane, inhibited budding of VP40 VLPs and may inform future treatment strategies against EBOV.

microbiology↗

bioRxiv2018

Heteromeric GABAA receptor structures in positively-modulated active states

Type-A {gamma}-aminobutyric acid (GABAA) receptors are pentameric ligand-gated ion channels (pLGICs), typically consisting of /{beta}/{gamma} subunit combinations. They are the principal mediators of inhibitory neurotransmission throughout the central nervous system and targets of major clinical drugs, such as benzodiazepines (BZDs) used to treat epilepsy, insomnia, anxiety, panic disorder and muscle spasm. However, the structures of heteromeric receptors and the molecular basis of BZD operation remain unknown. Here we report the cryo-EM structure of a human 1{beta}3{gamma}2 GABAAR in complex with GABA and a nanobody that acts as a novel positive allosteric modulator (PAM). The receptor subunits assume a unified quaternary activated conformation around an open pore. We also present crystal structures of engineered 5 and 5{gamma}2 GABAAR constructs, revealing the interfacial site for allosteric modulation by BZDs, including the binding modes and the conformational impact of the potent anxiolytic and partial PAM, bretazenil, and the BZD antagonist, flumazenil. These findings provide the foundation for understanding the mechanistic basis of GABAAR activation.

biophysics↗

bioRxiv2018

Pan-cancer machine learning predictors of tissue of origin and molecular subtype

BackgroundIt is estimated by the American Cancer Society that approximately 5% of all metastatic tumors have no defined primary site (tissue) of origin and are classified as cancers of unknown primary (CUPs). The current standard of care for CUP patients depends on immunohistochemistry (IHC) based approaches to identify the primary site. The addition of post-mortem evaluation to IHC based tests helps to reveal the identity of the primary site for only 25% of the CUPs, emphasizing the acute need for better methods of determination of the site of origin. CUP patients are therefore given generic chemotherapeutic agents resulting in poor prognosis. When the tissue of origin is known, patients can be given site specific therapy with significant improvement in clinical outcome. Similarly, identifying the primary site of origin of metastatic cancer is of great importance for designing treatment.\n\nIdentification of the primary site of origin is an import first step but may not be sufficient information for optimal treatment of the patient. Recent studies, primarily from The Cancer Genome Atlas (TCGA) project, and others, have revealed molecular subtypes in several cancer types with distinct clinical outcome. The molecular subtype captures the fundamental mechanisms driving the cancer and provides information that is essential for the optimal treatment of a cancer. Thus, along with primary site of origin, molecular subtype of a tumor is emerging as a criterion for personalized medicine and patient entry into clinical trials.\n\nHowever, there is no comprehensive toolset available for precise identification of tissue of origin or molecular subtype for precision medicine and translational research.\n\nMethods and FindingsWe posited that metastatic tumors will harbor the gene expression profiles of the primary site of origin of the cancer. Therefore, we decided to learn the molecular characteristics of the primary tumors using the large number of cancer genome profiles available from the TCGA project. Our predictors were trained for 33 cancer types and for the 11 cancers where there are established molecular subtypes. We estimated the accuracy of several machine learning models using cross-validation methods. The extensive testing using independent test sets revealed that the predictors had a median sensitivity and specificity of 97.2% and 99.9% respectively without losing classification of any tumor. Subtype classifiers achieved median sensitivity of 87.7% and specificity of 94.5% via cross validation and presented median sensitivity of 79.6% and specificity of 94.6% in two external datasets of 1,999 total samples. Importantly, these external data shows that our classifiers can robustly predict the primary site of origin from external microarray data, metastatic cancer data, and patient-derived xenograft (PDX) data.\n\nConclusionWe have demonstrated the utility of gene expression profiles to solve the important clinical challenge of identifying the primary site of origin and the molecular subtype of cancers based on machine learning algorithms. We show, for the first time to our knowledge, that our pan-cancer classifiers can predict multiple cancers primary site of origin from metastatic samples. The predictors will be made available as open source software, freely available for academic non-commercial use.

cancer biology↗

bioRxiv2018

WNT signaling memory is required for ACTIVIN to function as a morphogen in human gastruloids

Self-organization of discrete fates in human gastruloids is mediated by a hierarchy of signaling pathways. How these pathways are integrated in time, and whether cells maintain a memory of their signaling history remains obscure. Here, we dissect the temporal integration of two key pathways, WNT and ACTIVIN, which along with BMP control gastrulation. CRISPR/Cas9 live reporters of SMAD1, 2 and 4 demonstrate that in contrast to the stable signaling by SMAD1, signaling and transcriptional response by SMAD2 is transient, and while necessary for pluripotency, it is insufficient for differentiation. Pre-exposure to WNT, however, endows cells with the competence to respond to graded levels of ACTIVIN, which induces differentiation without changing SMAD2 dynamics. This cellular memory of WNT signaling is necessary for ACTIVIN morphogen activity. A re-evaluation of the evidence gathered over decades in model systems, re-enforces our conclusions and points to an evolutionarily conserved mechanism.

developmental biology↗

bioRxiv2018

Necroptosis and apoptosis contribute to cisplatin and aminoglycoside ototoxicity

Ototoxic side effects of cisplatin and aminoglycosides have been extensively studied, but no therapy is available to date. Sensory hair cells, upon exposure to cisplatin or aminoglycosides, undergo apoptotic and necrotic cell death. Blocking these cell death pathways has therapeutic potential in theory, but incomplete protection and lack of therapeutic targets in the case of necrosis, has hampered the development of clinically applicable drugs. Over the past decade, a novel form of necrosis, termed necroptosis, was established as an alternative cell death pathway. Necroptosis is distinguished from passive necrotic cell death, in that it follows a cellular program, involving the receptor-interacting protein kinases 1 and 3 (RIPK1 and 3). In this study, we used pharmacological and genetic intervention to test the relative contributions of necroptosis and caspase-8-mediated apoptosis towards cisplatin and aminoglycoside ototoxicity. We find that ex vivo, only apoptosis contributes to cisplatin and aminoglycoside ototoxicity, while in vivo, both necroptosis and apoptosis are involved. Inhibition of necroptosis and apoptosis using pharmacological compounds is thus a viable strategy to ameliorate aminoglycoside and cisplatin ototoxicity.\n\nSignificance statementThe clinical application of cisplatin and aminoglycosides is limited due to ototoxic side effects. Here, using pharmaceutical and genetic intervention, we present evidence that two types of programmed cell death, apoptosis and necroptosis, contribute to aminoglycoside and cisplatin ototoxicity. Key molecular factors mediating necroptosis are well characterized and druggable, presenting new avenues for pharmaceutical intervention.

neuroscience↗

bioRxiv2018

Analysis of Transcripts and splice isoforms in Red Clover (Trifolium pratense L.) by single-molecule long-read sequencing

Red clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of mRNA transcripts remain unclear, which limit further explore on red clover. In this study, the red clover transcriptome was sequenced using single-molecule long-read sequencing to identify full-length splice isoforms, and 29,730 novel isoforms from known genes and 2,194 novel isoforms from novel genes were identified. A total of 5,492 alternative splicing events was identified and the majority of alter spliced events in red clover was corrected as intron retention. In addition, of the 15,229 genes detected by SMRT, 8,719 including 1,86,517 transcripts have at least one poly(A) site. Furthermore, we identified 4,333 long non-coding RNAs and 3,762 fusion transcripts. Our results show the feasibility of deep sequencing full-length RNA from red clover transcriptome on a single-molecule level.

plant biology↗

bioRxiv2018

Combined use of procalcitonin and C-reactive protein levels can help clinically diagnose bacterial co-infections in children infected with H1N1 influenza

ObjectiveThis study evaluated the diagnostic value of measuring the levels of procalcitonin (PCT) and C-reactive protein (CRP) to differentiate children co-infected with H1N1 influenza and bacteria from children infected with H1N1 influenza alone and to provide a reliable clinical diagnostic support system with improved accuracy and precision control.\n\nMethodsConsecutive patients (children aged <5 years) with laboratory-confirmed H1N1 influenza who were hospitalized or received outpatient care from a tertiary-care hospital in Canton, China between 1 January 2012 and 1 September 2017 were included in the present study. Laboratory results, including serum PCT and CRP levels, white blood cell (WBC) counts, and blood and sputum cultures, were analyzed. The predictive value of the combination of biomarkers versus either biomarker alone for diagnosing bacterial co-infections was evaluated using logistic regression analyses.\n\nResultsOf 3180 children infected with H1N1 influenza, 226 (7.1%) met the bacterial co-infection criteria, with Staphylococcus pneumoniae being the most commonly identified bacteria (36.28%). Significantly higher PCT (1.46 vs 0.21 ng/ml, p<0.001) and CRP (19.20 vs 5.10 mg/dl, p<0.001) levels were detected in the bacterial co-infection group than in the H1N1 infection only group. Multivariate logistic regression analysis showed independent associations between PCT (odds ratio [OR]: 1.73, 95% confidence interval [CI],1.34-2.42, p<0.001) and CRP levels (OR:1.09, 95% CI, 1.06-1.13, p<0.001) with bacterial co-infections. Using PCT or CRP levels alone, the areas under the curves (AUCs) for predicting bacterial co-infections were 0.801 (95%CI, 0.772-0.855) and 0.762 (95%CI, 0.722-0.803), respectively. Using a combination of PCT and CRP, the logistic regression-based model, Logit(P)=-1.912+0.546 PCT+0.087 CRP, showed significantly greater accuracy (AUC: 0.893, 95%CI: 0.842-0.934) than did the other three biomarkers.\n\nConclusionsThe combination of PCT and CRP levels could provide a useful method of distinguishing bacterial co-infections from an H1N1 influenza infection alone in children during the early disease phase. After further validation, the flexible model derived here could assist clinicians in decision-making processes.

microbiology↗

bioRxiv2018

SPLASH: fast tandem mass spectra clustering using locality sensitive hashing

Large-scale proteomics projects often generate massive and highly redundant tandem mass (MS/MS) spectra. Spectra clustering algorithms can reduce the redundancy in these datasets, and thus speed up the database searching for peptide identification, a major bottleneck for proteomic data analysis. Furthermore, the consensus spectra derived from highly similar MS/MS spectra in the same cluster may enhance the signal peaks while reduce the noise peaks, and thus will improve the sensitivity of peptide identification. In this paper, we present the software msCRUSH, which implemented a novel spectra clustering algorithm based on the locality sensitive hashing (LSH) technique. When tested on a large-scale proteomic dataset consisting of 18.4 million spectra (including 11.5 million spectra of charge 2+), msCRUSH runs 7.6-12.1x faster than the state-of-the-art spectra clustering software, PRIDE Cluster, while achieves higher clustering sensitivity and comparable accuracy. Using the consensus spectra reported by msCRUSH, commonly used spectra search engines MSGF+ and Mascot can identify 5% and 4% more unique peptides, respectively, comparing to the identification results from the raw MS/MS spectra at the same false discovery rate (1% FDR) of peptides. msCRUSH is implemented in C++, and is released as open source software.

bioinformatics↗

bioRxiv2018

An optimal kernel-based method for gene set association analysis

Single-variant based genome-wide association studies have successfully detected many genetic variants that are associated with many complex traits. However, their power is limited due to weak marginal signals and ignoring potential complex interactions among genetic variants. Set-based strategy was proposed to provide a remedy where multiple genetic variants in a given set (e.g., gene or pathway) are jointly evaluated, so that the systematic effect of the set is considered. Among many, the kernel-based testing (KBT) framework is one of the most popular and powerful methods in set-based association studies. Given a set of candidate kernels, method has been proposed to choose the one with the smallest p-value. Such a method, however, can yield inflated type I error, especially when the number of variants in a set is large. Alternatively one can get p-values by permutations which, however, could be very time consuming. In this work, we proposed an efficient testing procedure that can not only control type I error rate but also generate power close to the one obtained under the optimal kernel. Our method is built upon the KBT framework and is based on asymptotic results under a high-dimensional setting. Hence it can efficiently deal with the case where the number of variants in a set is much larger than the sample size. Both simulation and real data analysis demonstrate the advantages of the method compared with its counterparts.

genetics↗

bioRxiv2018

RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome

Nuclear speckles are interchromatin structures enriched in RNA splicing factors. Determining their relative positions with respect to the folded nuclear genome could provide critical information on co-and post-transcriptional regulation of gene expression. However, it remains challenging to identify which parts of the nuclear genome are in proximity to nuclear speckles, due to physical separation between nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNAs, 7SK and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA, nuclear speckle associated RNA), may extend to sufficient proximity to the nuclear genome. Leveraging a transcriptome-genome interaction assay (MARGI), we identified nsaRNA-interacting genomic sequences, which exhibited clustering patterns (nsaPeaks) in the genome, suggesting existence of relatively stable interaction sites for nsaRNAs in nuclear genome. Posttranscriptional pre-mRNAs, which are known to be clustered to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Furthermore, CDK9 proteins that localize to the vicinity of nuclear speckles produced ChIP-seq peaks that overlapped with nsaPeaks. Our combined DNA FISH and immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs locate in sufficient proximity to nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles.

bioinformatics↗

bioRxiv2018

A simple and robust procedure for preparing graphene-oxide cryo-EM grids

Graphene oxide (GO) sheets have been used successfully as a supporting substrate film in several recent cryogenic electron-microscopy (cryo-EM) studies of challenging biological macromolecules. However, difficulties in preparing GO-covered holey carbon EM grids have limited its widespread use. Here, we report a simple and robust method for covering holey carbon EM grids with GO sheets and demonstrate that these grids are suitable for high-resolution single particle cryo-EM. GO substrates adhere macromolecules, allowing cryo-EM grid preparation with lower specimen concentrations and providing partial protection from the air-water interface. Additionally, the signal from images of the GO lattice beneath the frozen-hydrated specimen can be discerned in many motion-corrected micrographs, providing a high-resolution fiducial for evaluating beam-induced motion correction.

biophysics↗

bioRxiv2018

Linear-double-stranded DNA (ldsDNA) based AND logic computation in mammalian cells

Synthetic biology employs engineering principles to redesign biological system for clinical or industrial purposes. The development and application of novel genetic devices for genetic circuits construction will facilitate the rapid development of synthetic biology. Here we demonstrate that mammalian cells could perform two- and three-input linear-double-stranded DNA (ldsDNA) based Boolean AND logic computation. Through hydrodynamic ldsDNA delivery, two-input ldsDNA-base AND-gate computation could be achieved in vivo. Inhibition of DNA-PKcs expression, a key enzyme in non-homologous end joining (NHEJ), could significantly downregulate the intensity of output signals from ldsDNA-based AND-gate. We further reveal that in mammalian cells ldsDNAs could undergo end processing and then perform AND-gate calculation to generate in-frame output proteins. Moreover, we show that ldsDNAs or plasmids with identical overlapping sequences could also serve as inputs of AND-gate computation. Our work establishes novel genetic devices and principles for genetic circuits construction, thus may open a new gate for the development of new disease targeting strategies and new protein genesis methodologies.

synthetic biology↗

bioRxiv2018

Preclinical Study: Sunitinib-suppressed MiR-452-5p Facilitates Renal Cancer Cell Invasion and Metastasis Through Modulating SMAD4/SMAD7/EMT Signals

Although microRNAs (miRNAs) have been revealed as crucial modulators in tumor metastasis and target therapy, our understanding of their roles in metastatic renal cell carcinoma (mRCC) and Sunitinib treatment is limited. Here, We focused on 2 published microarray data to select out our anchored miRNA which was downregulated after Sunitinib treatment while upregulated in metastasis RCC tissues. Then we discovered that treating with Sunitinib, the targeted receptor tyrosine kinase inhibitor (TKI), inhibited renal cell migration and invasion via attenuating the expression of miR-452-5p. The novel identified miR-452-5p was upregulated and associated with poor prognosis in RCC. Preclinical studies using multiple RCC cells and xenografts model illustrated that miR-452-5p could promote RCC cell migration and invasion in vitro and in vivo. Mechanistically, P65 could directly bind to the miR-452-5p promoter and thus transcriptionally induce miR-452-5p expression, which led to post-transcriptionally abrogate SMAD4 expression, thus inhibition of its downstream signals including SMAD7 and EMT (Epithelial-Mesenchymal Transition) associated genes. Our study presented a road map for targeting this newly identified miR-452-5p and its SMAD4/SMAD7/EMT signals pathway, which imparted a new potential therapeutic strategy for mRCC treatment.

cancer biology↗

bioRxiv2018

High dimensional analyses of cells dissociated from cryopreserved synovial tissue

BackgroundDetailed molecular analyses of cells from rheumatoid arthritis (RA) synovium hold promise in identifying cellular phenotypes that drive tissue pathology and joint damage. The Accelerating Medicines Partnership (AMP) RA/SLE network aims to deconstruct autoimmune pathology by examining cells within target tissues through multiple high-dimensional assays. Robust standardized protocols need to be developed before cellular phenotypes at a single cell level can be effectively compared across patient samples.\n\nMethodsMultiple clinical sites collected cryopreserved synovial tissue fragments from arthroplasty and synovial biopsy in a 10%-DMSO solution. Mechanical and enzymatic dissociation parameters were optimized for viable cell extraction and surface protein preservation for cell sorting and mass cytometry, as well as for reproducibility in RNA sequencing (RNA-seq). Cryopreserved synovial samples were collectively analyzed at a central processing site by a custom-designed and validated 35-marker mass cytometry panel. In parallel, each sample was flow sorted into fibroblast, T cell, B cell, and macrophage suspensions for bulk population RNA-seq and plate-based single cell CEL-Seq2 RNA-seq.\n\nResultsUpon dissociation, cryopreserved synovial tissue fragments yielded a high frequency of viable cells, comparable to samples undergoing immediate processing. Optimization of synovial tissue dissociation across six clinical collection sites with [~]30 arthroplasty and [~]20 biopsy samples yielded a consensus digestion protocol using 100{micro}g/mL of Liberase TL enzyme. This protocol yielded immune and stromal cell lineages with preserved surface markers and minimized variability across replicate RNA-seq transcriptomes. Mass cytometry analysis of cells from cryopreserved synovium distinguished: 1) diverse fibroblast phenotypes, 2) distinct populations of memory B cells and antibody-secreting cells, and 3) multiple CD4+ and CD8+ T cell activation states. Bulk RNA sequencing of sorted cell populations demonstrated robust separation of synovial lymphocytes, fibroblasts, and macrophages. Single cell RNA-seq produced transcriptomes of over 1000 genes/cell, including transcripts encoding characteristic lineage markers identified.\n\nConclusionWe have established a robust protocol to acquire viable cells from cryopreserved synovial tissue with intact transcriptomes and cell surface phenotypes. A centralized pipeline to generate multiple high-dimensional analyses of synovial tissue samples collected across a collaborative network was developed. Integrated analysis of such datasets from large patient cohorts may help define molecular heterogeneity within RA pathology and identify new therapeutic targets and biomarkers.

immunology↗

bioRxiv2018

Novel role of Lin28 signaling in regulation of mammalian PNS and CNS axon regeneration

Several signaling molecules involved in cellular reprogramming have been shown to regulate mammalian axon regeneration. We hypothesized that reprogramming factors are key regulators of axon regeneration. Here we investigated the role of Lin28, an important reprogramming factor, in the regulation of axon regeneration. We found that Lin28a and Lin28b and their regulatory partners, let-7 microRNAs (miRNAs), were both necessary and sufficient in regulating mature sensory axon regeneration in vivo. More importantly, overexpression of either Lin28a or Lin28b in mature retinal ganglion cells (RGCs) promoted robust and sustained optic nerve regeneration. Additionally, combined overexpression of Lin28a and downregulation of PTEN in RGCs acted additively to promote optic nerve regeneration by reducing the backward turning of regenerating RGC axons. Our findings not only identified a novel molecule promoting optic nerve regeneration but also suggested that reprogramming factors may play vital roles in regulating axon regeneration in mammals.

neuroscience↗