Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues.

Spatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into the intricate RNA biology in complex tissues. Human disease-relevant tissues are commonly preserved as formalin-fixed and paraffin-embedded (FFPE) blocks, representing an important resource for human tissue specimens. The capability to spatially explore RNA biology in FFPE tissues holds transformative potential for human biology research and clinical histopathology. Here, we present Patho-DBiT combining in situ polyadenylation and deterministic barcoding for spatial full coverage transcriptome sequencing, tailored for probing the diverse landscape of RNA species even in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish different malignant clones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA-mRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis trajectory. High resolution Patho-DBiT at the cellular level reveals a spatial neighborhood and traces the spatiotemporal kinetics driving tumor progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to study human tissue biology and aid in clinical pathology evaluation.

Cell surface RNAs control neutrophil recruitment.

RNAs localizing to the outer cell surface have been recently identified in mammalian cells, including RNAs with glycan modifications known as glycoRNAs. However, the functional significance of cell surface RNAs and their production are poorly known. We report that cell surface RNAs are critical for neutrophil recruitment and that the mammalian homologs of the sid-1 RNA transporter are required for glycoRNA expression. Cell surface RNAs can be readily detected in murine neutrophils, the elimination of which substantially impairs neutrophil recruitment to inflammatory sites in vivo and reduces neutrophils' adhesion to and migration through endothelial cells. Neutrophil glycoRNAs are predominantly on cell surface, important for neutrophil-endothelial interactions, and can be recognized by P-selectin (Selp). Knockdown of the murine Sidt genes abolishes neutrophil glycoRNAs and functionally mimics the loss of cell surface RNAs. Our data demonstrate the biological importance of cell surface glycoRNAs and highlight a noncanonical dimension of RNA-mediated cellular functions.

Selection of indicators reporting response rate in pharmaceutical trials for systemic lupus erythematosus: preference and relative sensitivity.

OBJECTIVE: SLE is a common multisystem autoimmune disease with chronic inflammation. Many efficacy evaluation indicators of randomised clinical trials (RCTs) for SLE have been proposed but the comparability remains unknown. We aim to explore the preference and comparability of indicators reporting response rate and provide basis for primary outcome selection when evaluating the efficacy of SLE pharmaceutical treatment. METHODS: We systematically searched three databases and three registries to identify pharmacological intervention-controlled SLE RCTs. Relative discriminations between indicators were assessed by the Bayesian hierarchical linear mixed model. RESULTS: 33 RCTs met our inclusion criteria and we compared eight of the most commonly used indicators reporting response rate. SLE Disease Activity Index 4 (SLEDAI-4) and SLE Responder Index 4 were considered the best recommended indicators reporting response rate to discriminate the pharmacological efficacy. Indicator preference was altered by disease severity, classification of drugs and outcome of trials, but SLEDAI-4 had robust efficacy in discriminating ability for most interventions. Of note, BILAG Index-based Combined Lupus Assessment showed efficacy in trials covering all-severity patients, as well as non-biologics RCTs. The British Isles Lupus Assessment Group response and Physician's Global Assessment response were more cautious in evaluating disease changes. Serious adverse event was often applied to evaluate the safety and tolerability of treatments rather than efficacy. CONCLUSIONS: The impressionable efficacy discrimination ability of indicators highlights the importance of flexibility and comprehensiveness when choosing primary outcome(s). As for trials that are only evaluated by SLEDAI-4, attention should be paid to outcome interpretation to avoid the exaggeration of treatment efficacy. Further subgroup analyses are limited by the number of included RCTs. PROSPERO REGISTRATION NUMBER: CRD42022334517.

Global epidemiology of atopic dermatitis: a comprehensive systematic analysis and modelling study.

BACKGROUND: Atopic dermatitis (AD) is the leading cause of the global burden from skin disease; no study has provided global and country-specific epidemiological estimates of AD. OBJECTIVES: To quantify global, regional and country-specific estimates of the epidemiology of AD. METHODS: A comprehensive search for epidemiological studies in AD was conducted in four electronic databases (PubMed, Embase, Web of Science and China National Knowledge Infrastructure). A Bayesian hierarchical linear mixed model was constructed to calculate epidemiological estimates of AD considering the heterogeneity of regions, countries, type of diagnoses and age strata. RESULTS: In total, 344 studies met the inclusion criteria. Incidence varied substantially with the location and age of the surveyed participants. The global prevalence of AD and the population affected by AD were estimated to be 2.6% [95% uncertainty interval (UI) 1.9-3.5] and 204.05 million people, respectively. Around 101.27 million adults and 102.78 million children worldwide have AD, corresponding to prevalence rates of 2.0% (95% UI 1.4-2.6) and 4.0% (95% UI 2.8-5.3), respectively. Females were more likely to suffer from AD than males: the global prevalence of AD in females was 2.8% (95% UI 2.0-3.7%) and affected 108.29 million people, while in males the corresponding estimates were 2.4% (95% UI 1.7-3.3%) and 95.76 million people. CONCLUSIONS: Epidemiological AD data are lacking in 41.5% of countries worldwide. The epidemiology of AD varies substantially with age and sex and is distributed unequally across geographical regions.

Compression drives diverse transcriptomic and phenotypic adaptations in melanoma.

Physical forces are prominent during tumor progression. However, it is still unclear how they impact and drive the diverse phenotypes found in cancer. Here, we apply an integrative approach to investigate the impact of compression on melanoma cells. We apply bioinformatics to screen for the most significant compression-induced transcriptomic changes and investigate phenotypic responses. We show that compression-induced transcriptomic changes are associated with both improvement and worsening of patient prognoses. Phenotypically, volumetric compression inhibits cell proliferation and cell migration. It also induces organelle stress and intracellular oxidative stress and increases pigmentation in malignant melanoma cells and normal human melanocytes. Finally, cells that have undergone compression become more resistant to cisplatin treatment. Our findings indicate that volumetric compression is a double-edged sword for melanoma progression and drives tumor evolution.

Global, regional, and national incidence and prevalence of systemic sclerosis.

OBJECTIVES: To estimate the global and country-specific unbiased epidemiological data of SSc. METHODS: Epidemiological studies were systematically searched in four databases. A Bayesian hierarchical linear mixed model was constructed to estimate epidemiological data. RESULTS: 82 studies were included and epidemiological data on SSc were missing for 83.9% of countries worldwide. The global SSc incidence and newly diagnosed population were estimated to be 8.64 per 100,000 person-years (1.78-23.57) and 0.67 million (0.14-1.84) people annually, respectively. Regarding prevalence, the global SSc prevalence and affected population were 18.87 per 100,000 persons (1.55-25.28) and 1.47 million (0.12-1.97) people, respectively. Relatively higher incidence and prevalence were observed in females, adults, and high-income level countries. CONCLUSIONS: We provide a comprehensive synthesis of SSc epidemiology and fill data gaps in most countries. Especially in low- and middle-income countries, epidemiological studies of SSc are insufficient. Further large-scale and standardized reported epidemiological investigations of SSc are imperative.

Global epidemiology of systemic lupus erythematosus: a comprehensive systematic analysis and modelling study.

OBJECTIVES: To quantify global, regional and country-specific estimates of epidemiology of systemic lupus erythematosus (SLE). METHODS: Four databases were systematically searched, and a Bayesian hierarchical linear mixed model was constructed to estimate the global, regional, and country-specific incidence and prevalence of SLE. RESULTS: 112 studies met the inclusion criteria. The global SLE incidence and newly diagnosed population were estimated to be 5.14 (1.4 to 15.13) per 100 000 person-years and 0.40 million people annually, respectively. In women, the values were 8.82 (2.4 to 25.99) per 100 000 person-years and 0.34 million people annually, while in men, the estimates were 1.53 (0.41 to 4.46) per 100 000 person-years and 0.06 million people annually, respectively. Poland, the USA and Barbados had the highest estimates of SLE incidence. Regarding prevalence, the global SLE prevalence and affected population were estimated to be 43.7 (15.87 to 108.92) per 100 000 persons and 3.41 million people, respectively. In women, the values were 78.73 (28.61 to 196.33) per 100 000 persons and 3.04 million people, while in men the estimates were 9.26 (3.36 to 22.97) per 100 000 persons and 0.36 million people, respectively. The United Arab Emirates, Barbados and Brazil had the highest SLE prevalence. In addition to regional and sex differences, age and prevalence estimation method (period or point prevalence) differences could also lead to variations in epidemiological SLE findings. CONCLUSIONS: Epidemiological data on SLE are lacking for 79.8% of countries worldwide. The epidemiology of SLE varies substantially between different sex and age groups and is distributed unequally among geographical regions; specifically, SLE occurs more frequently in high-income countries.

Bioinformatics identifies predictors of arteriovenous fistula maturation.

BACKGROUND: Arteriovenous fistulae (AVF) are the preferred access for hemodialysis but still have poor rates of maturation and patency limiting their clinical use. The underlying mechanisms of venous remodeling remain poorly understood, and only limited numbers of unbiased approaches have been reported. METHODS: Biological Gene Ontology (GO) term enrichment analysis and differentially expressed genes (DEG) analysis were performed for three AVF datasets. A microRNA enrichment analysis and L1000CDS2 query were performed to identify factors predicting AVF patency. RESULTS: The inflammatory and immune responses were activated during both early and late phases of AVF maturation, with upregulation of neutrophil and leukocyte regulation, cytokine production, and cytokine-mediated signaling. In men with failed AVF, negative regulation of myeloid-leukocyte differentiation and regulation of macrophage activation were significantly upregulated. Compared to non-diabetic patients, diabetic patients had significantly reduced immune response-related enrichment such as cell activation in immune response, regulation of immune-effector process, and positive regulation of defense response; in addition, diabetic patients showed no enrichment of the immune response-regulating signaling pathway. CONCLUSIONS: These data show coordinated, and differential regulation of genes associated with AVF maturation, and different patterns of several pathways are associated with sex differences in AVF failure. Inflammatory and immune responses are activated during AVF maturation and diabetes may impair AVF maturation by altering these responses. These findings suggest several novel molecular targets to improve sex specific AVF maturation.

Evitar: designing anti-viral RNA therapies against future RNA viruses.

MOTIVATION: The coronavirus disease 2019 (COVID-19) pandemic has highlighted the threat of emerging respiratory viruses and has exposed the lack of availability of off-the-shelf therapeutics against new RNA viruses. Previous research has established the potential that siRNAs and RNA-targeting CRISPR have in combating known RNA viruses. However, the feasibility and tools for designing anti-viral RNA therapeutics against future RNA viruses have not yet been established. RESULTS: We develop the Emerging-Virus-Targeting RNA (Evitar) pipeline for designing anti-viral siRNAs and CRISPR Cas13a guide RNA (gRNA) sequences. Within Evitar, we develop Greedy Algorithm with Redundancy and Similarity-weighted Greedy Algorithm with Redundancy to enhance the performance. Time simulations using known coronavirus genomes deposited as early as 10 years prior to the COVID-19 outbreak show that at least three SARS-CoV-2-targeting siRNAs are among the top 30 pre-designed siRNAs. In addition, among the top 19 pre-designed gRNAs, there are three SARS-CoV-2-targeting Cas13a gRNAs that could be predicted using information from 2011. Before-the-outbreak design is also possible against the MERS-CoV virus and the 2009-H1N1 swine flu virus. Designed siRNAs are further shown to suppress SARS-CoV-2 viral sequences using in vitro reporter assays. Our results support the utility of Evitar to pre-design anti-viral siRNAs/gRNAs against future viruses. Therefore, we propose the development of a collection consisting of roughly 30 pre-designed, safety-tested and off-the-shelf siRNA/CRISPR therapeutics that could accelerate responses to future RNA virus outbreaks. AVAILABILITY AND IMPLEMENTATION: Codes are available at GitHub (https://github.com/dingyaozhang/Evitar). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

5-Fluorouracil efficacy requires anti-tumor immunity triggered by cancer-cell-intrinsic STING.

5-Fluorouracil (5-FU) is a widely used chemotherapeutic drug, but the mechanisms underlying 5-FU efficacy in immunocompetent hosts in vivo remain largely elusive. Through modeling 5-FU response of murine colon and melanoma tumors, we report that effective reduction of tumor burden by 5-FU is dependent on anti-tumor immunity triggered by the activation of cancer-cell-intrinsic STING. While the loss of STING does not induce 5-FU resistance in vitro, effective 5-FU responsiveness in vivo requires cancer-cell-intrinsic cGAS, STING, and subsequent type I interferon (IFN) production, as well as IFN-sensing by bone-marrow-derived cells. In the absence of cancer-cell-intrinsic STING, a much higher dose of 5-FU is needed to reduce tumor burden. 5-FU treatment leads to increased intratumoral T cells, and T-cell depletion significantly reduces the efficacy of 5-FU in vivo. In human colorectal specimens, higher STING expression is associated with better survival and responsiveness to chemotherapy. Our results support a model in which 5-FU triggers cancer-cell-initiated anti-tumor immunity to reduce tumor burden, and our findings could be harnessed to improve therapeutic effectiveness and toxicity for colon and other cancers.

In Silico Design of siRNAs Targeting Existing and Future Respiratory Viruses with VirusSi.

The COVID-19 pandemic has exposed global inadequacies in therapeutic options against both the COVID-19-causing SARS-CoV-2 virus and other newly emerged respiratory viruses. In this study, we present the VirusSi computational pipeline, which facilitates the rational design of siRNAs to target existing and future respiratory viruses. Mode A of VirusSi designs siRNAs against an existing virus, incorporating considerations on siRNA properties, off-target effects, viral RNA structure and viral mutations. It designs multiple siRNAs out of which the top candidate targets >99% of SARS-CoV-2 strains, and the combination of the top four siRNAs is predicted to target all SARS-CoV-2 strains. Additionally, we develop Greedy Algorithm with Redundancy (GAR) and Similarity-weighted Greedy Algorithm with Redundancy (SGAR) to support the Mode B of VirusSi, which pre-designs siRNAs against future emerging viruses based on existing viral sequences. Time-simulations using known coronavirus genomes as early as 10 years prior to the COVID-19 outbreak show that at least three SARS-CoV-2-targeting siRNAs are among the top 30 pre-designed siRNAs. Before-the-outbreak pre-design is also possible against the MERS-CoV virus and the 2009-H1N1 swine flu virus. Our data support the feasibility of pre-designing anti-viral siRNA therapeutics prior to viral outbreaks. We propose the development of a collection of pre-designed, safety-tested, and off-the-shelf siRNAs that could accelerate responses toward future viral diseases.

dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease.

Although thousands of pseudogenes have been annotated in the human genome, their transcriptional regulation, expression profiles and functional mechanisms are largely unknown. In this study, we developed dreamBase (http://rna.sysu.edu.cn/dreamBase) to facilitate the investigation of DNA modification, RNA regulation and protein binding of potential expressed pseudogenes from multidimensional high-throughput sequencing data. Based on ∼5500 ChIP-seq and DNase-seq datasets, we identified genome-wide binding profiles of various transcription-associated factors around pseudogene loci. By integrating ∼18 000 RNA-seq data, we analysed the expression profiles of pseudogenes and explored their co-expression patterns with their parent genes in 32 cancers and 31 normal tissues. By combining microRNA binding sites, we demonstrated complex post-transcriptional regulation networks involving 275 microRNAs and 1201 pseudogenes. We generated ceRNA networks to illustrate the crosstalk between pseudogenes and their parent genes through competitive binding of microRNAs. In addition, we studied transcriptome-wide interactions between RNA binding proteins (RBPs) and pseudogenes based on 458 CLIP-seq datasets. In conjunction with epitranscriptome sequencing data, we also mapped 1039 RNA modification sites onto 635 pseudogenes. This database will provide insights into the transcriptional regulation, expression, functions and mechanisms of pseudogenes as well as their roles in biological processes and diseases.