SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function

Deciphering key roles of B cells in prognostication and tailored therapeutic strategies for lung adenocarcinoma: a multi-omics and machine learning approach towards predictive, preventive, and personalized treatment strategies

Background

Lung adenocarcinoma (LUAD) remains a significant global health challenge, with an urgent need for innovative predictive, preventive, and personalized medicine (PPPM) strategies to improve patient outcomes. This study leveraged multi-omics and machine learning approaches to uncover the prognostic roles of B cells in LUAD, thereby reinforcing the PPPM approach.

Methods

We integrated multi-omics data, including bulk RNA, ATAC-seq, single-cell RNA, and spatial transcriptomics sequencing, to characterize the B cell landscape in LUAD within the PPPM framework. Subsequently, we developed an integrative machine learning program that generated the Scissor+ related B cell score (SRBS). This score was validated in the training and validation sets, and its prognostic value was assessed along with clinical features to develop predictive nomograms. This study further assessed the role of SRBS and SRBS genes in response to immunotherapy and identified personalized drug targets for distinct risk subgroups, with gene expression verified experimentally to ensure tailored medical interventions.

Results

Our analysis identified 79 Scissor+ B cell genes linked to LUAD prognosis, supporting the predictive aspect of PPPM. The SRBS model, which utilizes multiple machine learning algorithms, performed excellently in predicting prognosis and clinical transformation, embodying the preventive and personalized aspects of PPPM. Multifactorial analysis confirmed that SRBS was an independent prognostic factor. We observed varying biological functions and immune cell infiltration in the tumor immune microenvironment (TIME) between the high- and low-SRBS groups, underscoring personalized treatment approaches. Notably, patients with elevated SRBS may exhibit resistance to immunotherapy but show increased sensitivity to chemotherapy and targeted therapies. Additionally, we found that LDHA, as an SRBS gene with significant clinical implications, may regulate the sensitivity of LUAD cells to cisplatin.

Conclusion

This study presents a B cell-associated gene signature that serves as a prognostic marker to facilitate personalized treatment for patients with LUAD, adhering to the principles of PPPM.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-024-00390-4.

Carbon-Based Fluorescent Nano-Biosensors for the Detection of Cell-Free Circulating MicroRNAs

Currently, non-communicable diseases (NCDs) have emerged as potential risks for humans due to adopting a sedentary lifestyle and inaccurate diagnoses. The early detection of NCDs using point-of-care technologies significantly decreases the burden and will be poised to transform clinical intervention and healthcare provision. An imbalance in the levels of circulating cell-free microRNAs (ccf-miRNA) has manifested in NCDs, which are passively released into the bloodstream or actively produced from cells, improving the efficacy of disease screening and providing enormous sensing potential. The effective sensing of ccf-miRNA continues to be a significant technical challenge, even though sophisticated equipment is needed to analyze readouts and expression patterns. Nanomaterials have come to light as a potential solution as they provide significant advantages over other widely used diagnostic techniques to measure miRNAs. Particularly, CNDs-based fluorescence nano-biosensors are of great interest. Owing to the excellent fluorescence characteristics of CNDs, developing such sensors for ccf-microRNAs has been much more accessible. Here, we have critically examined recent advancements in fluorescence-based CNDs biosensors, including tools and techniques used for manufacturing these biosensors. Green synthesis methods for scaling up high-quality, fluorescent CNDs from a natural source are discussed. The various surface modifications that help attach biomolecules to CNDs utilizing covalent conjugation techniques for multiple applications, including self-assembly, sensing, and imaging, are analyzed. The current review will be of particular interest to researchers interested in fluorescence-based biosensors, materials chemistry, nanomedicine, and related fields, as we focus on CNDs-based nano-biosensors for ccf-miRNAs detection applications in the medical field.

The circular RNA Edis regulates neurodevelopment and innate immunity

Circular RNAs (circRNAs) are widely expressed in eukaryotes. However, only a subset has been functionally characterized. We identify and validate a collection of circRNAs in Drosophila, and show that depletion of the brain-enriched circRNA Edis (circ_Ect4) causes hyperactivation of antibacterial innate immunity both in cultured cells and in vivo. Notably, Edis depleted flies display heightened resistance to bacterial infection and enhanced pathogen clearance. Conversely, ectopic Edis expression blocks innate immunity signaling. In addition, inactivation of Edis in vivo leads to impaired locomotor activity and shortened lifespan. Remarkably, these phenotypes can be recapitulated with neuron-specific depletion of Edis, accompanied by defective neurodevelopment. Furthermore, inactivation of Relish suppresses the innate immunity hyperactivation phenotype in the fly brain. Moreover, we provide evidence that Edis encodes a functional protein that associates with and compromises the processing and activation of the immune transcription factor Relish. Importantly, restoring Edis expression or ectopic expression of Edis-encoded protein suppresses both innate immunity and neurodevelopment phenotypes elicited by Edis depletion. Thus, our study establishes Edis as a key regulator of neurodevelopment and innate immunity.

Correlation Between Single Nucleotide Polymorphisms at the 3'-UTR of the NFKB1 Gene and Acute Kidney Injury in Sepsis

Objective: We aimed to study the relationship between single nucleotide polymorphisms (SNPs) in the 3'-untranslated region of the nuclear factor-kappaB (NF-κB) gene NFKB1 and the risk of acute kidney injury (AKI) in sepsis. Methods: The genotypes of the NFKB1 gene loci rs41275743 and rs4648143 were obtained by Sanger sequencing from 235 AKI patients and 235 non-AKI patients (No AKI). The plasma levels of Homo sapiens (human) microRNAs (hsa-miR)-580, hsa-miR-671-3p, hsa-miR-886-5p, hsa-miR-299-5p, hsa-miR-557, and hsa-miR-9 were determined by quantitative real-time polymerase chain reaction. The P50 protein in lymphocytes and the levels of tumor necrosis factor alpha (TNF-α), serum creatinine (SCr), cystatin (Cys)-C, and kidney injury molecule (KIM)-1 in plasma were detected by enzyme-linked immunosorbent assays. Results: The risk of AKI in patients with sepsis in A-allele carriers of the NFKB1 gene rs41275743 locus was 1.46 times higher than that of the G-allele carriers. The risk of AKI in patients with sepsis in A-allele carriers of the NFKB1 gene rs4648143 locus was 1.56 times higher than that of the G-allele carriers. Acute Physiology and Chronic Health Evaluation (APACHE) III score, Simplified Acute Physiological Score (SAPS) II, Sequential Organ Failure Assessment (SOFA), rs41275743, and rs4648143 were all independent risk factors for AKI. The plasma levels of P50 protein, TNF-α, SCr, Cys-C, and KIM-1 from patients with sepsis carrying the rs11475743 GG and rs4648143 GG genotypes were significantly lower than in those carrying the A-alleles (GA/AA). The levels of hsa-miR-580, hsa-miR-671-3p, and hsa-miR-886-5p in the plasma of patients carrying the rs41275743 GA/AA genotypes were significantly lower than in those with the GG genotype, whereas the levels of hsa-miR-299-5p, hsa-miR-557, and hsa-miR-9 showed no significant difference in patients with different genotypes of the rs41275743 locus. The levels of hsa-miR-299-5p, hsa-miR-557, and hsa-miR-9 in the plasma of patients carrying the GA/AA genotype of the rs4648143 locus were significantly lower than in those with the GG genotype, whereas the levels of hsa-miR-580, hsa-miR-671-3p, and hsa-miR-886-5p did not change significantly in patients carrying different genotypes at the rs4648143 locus. Conclusion: SNPs in the NFKB1 gene loci rs41275743 and rs4648143 are associated with the risk of AKI in patients with sepsis.

Quantitative proteomic analysis of the association between decreasing O‑GlcNAcylation and metastasis in MCF‑7 breast cancer cells

Breast cancer is the most common type of cancer and leading cause of cancer-associated mortality in women worldwide. O-linked N-acetyl glucosaminylation (O-GlcNAcylation) is a dynamic post-translational modification of nuclear, cytoplasmic and mitochondrial proteins. Mounting evidence suggests that abnormal O-GlcNAcylation status is associated with cancer malignancy. In our previous study, it was reported that O-GlcNAc and O-GlcNAc transferase (OGT; an enzyme responsible for the addition of O-GlcNAc) were upregulated in breast cancer tissues and cells. Moreover, O-GlcNAcylation was required for resistance to anoikis and the anchorage-independent growth of breast cancer cells. However, the precise roles of this modification on the development of malignancy are yet to be elucidated. Therefore, in the present study, the effects of inhibiting O-GlcNAc on the malignant transformation of MCF-7 breast cancer cells under different culture conditions were determined, using monolayer (primary growth), anoikis resistance (spheroid growth) and reseeding (secondary growth) to mimic the metastatic process. Decreasing O-GlcNAc levels using small interfering (si)RNA targeting OGT resulted in a reduction in cell viability and invasiveness in anoikis resistant and reseeding conditions. Furthermore, gel-free quantitative proteomics was performed to identify the proteins affected by a reduction of O-GlcNAc. A total of 317 proteins were identified and compared, and the expression of 162 proteins was altered >1.5 fold in the siOGT treated cells compared with the siScamble (siSC) treated cells. Notably, 100 proteins involved in cellular metabolism, cellular localization, stress responses and gene expression were significantly altered in the reseeding condition. Among these differentially expressed proteins, the levels of small nuclear ribonucleoprotein Sm D1 exhibited the largest decrease in expression following knockdown of OGT, and this reduction in expression was associated with a significant decrease in the levels of mTOR expression, a protein which promotes tumor growth and progression. Taken together, the results of the present study demonstrate that decreasing O-GlcNAcylation altered protein expression, and ultimately influenced the metastatic processes, particulary regarding the invasion and reattached growth of MCF-7 breast cancer cells.

N6-Adenosine Methylation in RNA and a Reduced m3G/TMG Level in Non-Coding RNAs Appear at Microirradiation-Induced DNA Lesions

The DNA damage response is mediated by both DNA repair proteins and epigenetic markers. Here, we observe that N6-methyladenosine (m6A), a mark of the epitranscriptome, was common in RNAs accumulated at UV-damaged chromatin; however, inhibitors of RNA polymerases I and II did not affect the m6A RNA level at the irradiated genomic regions. After genome injury, m6A RNAs either diffused to the damaged chromatin or appeared at the lesions enzymatically. DNA damage did not change the levels of METTL3 and METTL14 methyltransferases. In a subset of irradiated cells, only the METTL16 enzyme, responsible for m6A in non-coding RNAs as well as for splicing regulation, was recruited to microirradiated sites. Importantly, the levels of the studied splicing factors were not changed by UVA light. Overall, if the appearance of m6A RNAs at DNA lesions is regulated enzymatically, this process must be mediated via the coregulatory function of METTL-like enzymes. This event is additionally accompanied by radiation-induced depletion of 2,2,7-methylguanosine (m3G/TMG) in RNA. Moreover, UV-irradiation also decreases the global cellular level of N1-methyladenosine (m1A) in RNAs. Based on these results, we prefer a model in which m6A RNAs rapidly respond to radiation-induced stress and diffuse to the damaged sites. The level of both (m1A) RNAs and m3G/TMG in RNAs is reduced as a consequence of DNA damage, recognized by the nucleotide excision repair mechanism.

MicroRNAs Dysregulation and Metabolism in Multiple System Atrophy

Multiple system atrophy (MSA) is an adult onset, fatal disease, characterized by an accumulation of alpha-synuclein (α-syn) in oligodendroglial cells. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-translational regulation and several biological processes. Disruption of miRNA-related pathways in the central nervous system (CNS) plays an important role in the pathogenesis of neurodegenerative diseases, including MSA. While the exact mechanisms underlying miRNAs in the pathogenesis of MSA remain unclear, it is known that miRNAs can repress the translation of messenger RNAs (mRNAs) that regulate the following pathogenesis associated with MSA: autophagy, neuroinflammation, α-syn accumulation, synaptic transmission, oxidative stress, and apoptosis. In this review, the metabolism of miRNAs and their functional roles in the pathogenesis of MSA are discussed, thereby highlighting miRNAs as potential new biomarkers for the diagnosis of MSA and in increasing our understanding of the disease process.

Dynamic changes in gene expression and alternative splicing mediate the response to acute alcohol exposure in Drosophila melanogaster

Environmental changes typically cause rapid gene expression responses in the exposed organisms, including changes in the representation of gene isoforms with different functions or properties. Identifying the genes that respond to environmental change, including in genotype-specific ways, is an important step in treating the undesirable physiological effects of stress, such as exposure to toxins or ethanol. Ethanol is a unique environmental stress in that chronic exposure results in permanent physiological changes and the development of alcohol use disorders. Drosophila is a classic model for deciphering the mechanisms of the response to alcohol exposure, as it meets the criteria for the development of alcohol use disorders, and has similar physiological underpinnings with vertebrates. Because many studies on the response to ethanol have relied on a priori candidate genes, broad surveys of gene expression and splicing are required and have been investigated here. Further, we expose Drosophila to ethanol in an environment that is genetically, socially, and ecologically relevant. Both expression and splicing differences, inasmuch as they can be decomposed, contribute to the response to ethanol in Drosophila melanogaster. However, we find that while D. melanogaster responds to ethanol, there is very little genetic variation in how it responds to ethanol. In addition, the response to alcohol over time is dynamic, suggesting that incorporating time into studies on the response to the environment is important.

Neurochondrin interacts with the SMN protein suggesting a novel mechanism for spinal muscular atrophy pathology

Spinal muscular atrophy (SMA) is an inherited neurodegenerative condition caused by a reduction in the amount of functional survival motor neuron (SMN) protein. SMN has been implicated in transport of mRNA in neural cells for local translation. We previously identified microtubule-dependent mobile vesicles rich in SMN and SNRPB, a member of the Sm family of small nuclear ribonucleoprotein (snRNP)-associated proteins, in neural cells. By comparing the interactomes of SNRPB and SNRPN, a neural-specific Sm protein, we now show that the essential neural protein neurochondrin (NCDN) interacts with Sm proteins and SMN in the context of mobile vesicles in neurites. NCDN has roles in protein localisation in neural cells and in maintenance of cell polarity. NCDN is required for the correct localisation of SMN, suggesting they may both be required for formation and transport of trafficking vesicles. NCDN may have potential as a therapeutic target for SMA together with, or in place of the targeting of SMN expression.

This article has an associated First Person interview with the first author of the paper.

Highlighted Article: The essential neural protein neurochondrin interacts with the spinal muscular atrophy (SMA) protein SMN in cell lines and in mice. This might be relevant to the molecular pathology of SMA.

miRNA targeting and alternative splicing in the stress response - events hosted by membrane-less compartments

Stress can be temporary or chronic, and mild or acute. Depending on its extent and severity, cells either alter their metabolism, and adopt a new state, or die. Fluctuations in environmental conditions occur frequently, and such stress disturbs cellular homeostasis, but in general, stresses are reversible and last only a short time. There is increasing evidence that regulation of gene expression in response to temporal stress happens post-transcriptionally in specialized subcellular membrane-less compartments called ribonucleoprotein (RNP) granules. RNP granules assemble through a concentration-dependent liquid-liquid phase separation of RNA-binding proteins that contain low-complexity sequence domains (LCDs). Interestingly, many factors that regulate microRNA (miRNA) biogenesis and alternative splicing are RNA-binding proteins that contain LCDs and localize to stress-induced liquid-like compartments. Consequently, gene silencing through miRNAs and alternative splicing of pre-mRNAs are emerging as crucial post-transcriptional mechanisms that function on a genome-wide scale to regulate the cellular stress response. In this Review, we describe the interplay between these two post-transcriptional processes that occur in liquid-like compartments as an adaptive cellular response to stress.

PAR-CLIP for Discovering Target Sites of RNA-Binding Proteins

RNA-binding proteins (RBPs) establish posttranscriptional gene regulation (PTGR) by coordinating the maturation, editing, transport, stability, and translation of cellular RNAs. A variety of experimental approaches have been developed to characterize the RNAs associated with RBPs in vitro as well as in vivo. Our laboratory developed Photoactivatable-Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP), which in combination with next-generation sequencing enables the identification of RNA targets of RBPs at a nucleotide-level resolution. Here we present an updated and condensed step-by-step PAR-CLIP protocol followed by the description of our RNA-seq data analysis pipeline.

Role of microRNAs in obesity and obesity-related diseases

In recent years, the link between regulatory microRNAs (miRNAs) and diseases has been the object of intensive research. miRNAs have emerged as key mediators of metabolic processes, playing crucial roles in maintaining/altering physiological processes, including energy balance and metabolic homeostasis. Altered miRNAs expression has been reported in association with obesity, both in animal and human studies. Dysregulation of miRNAs may affect the status and functions of different tissues and organs, including the adipose tissue, pancreas, liver, and muscle, possibly contributing to metabolic abnormalities associated with obesity and obesity-related diseases. More recently, the discovery of circulating miRNAs easily detectable in plasma and other body fluids has emphasized their potential as both endocrine signaling molecules and disease indicators. In this review, the status of current research on the role of miRNAs in obesity and related metabolic abnormalities is summarized and discussed.

A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis

During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels. Indeed, a large number of the investigated candidates, including splicing factors and other mRNA processing proteins, have effects on miRNA processing. As an example, we show that TRIM71/LIN41 is a potent regulator of miR-29a processing and its inactivation directly affects miR-29a targets. We provide an extended database of RBPs that interact with pre-miRNAs in extracts of different cell types, highlighting a widespread layer of co- and posttranscriptional regulation of miRNA biogenesis.

Probing Long Non-coding RNA-Protein Interactions

Non-coding RNA sequences outnumber the protein-coding genes in the human genome, however our knowledge of their functions is still limited. RNA-binding proteins follow the transcripts, including non-coding RNAs, throughout their life, regulating not only maturation, nuclear export, stability and eventually translation, but also RNA functions. Therefore, development of sophisticated methods to study RNA-protein interactions are key to the systematic characterization of lncRNAs. Although mostly applicable to RNA-protein interactions in general, many approaches, especially the computational ones, need adjustment to be adapted to the length and complexity of lncRNA transcripts. Here we critically review all the wet lab and computational methods to study lncRNA-protein interactions and their potential to clarify the dark side of the genome.

A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana

To identify regulators of pre-mRNA splicing in plants, we developed a forward genetic screen based on an alternatively spliced GFP reporter gene in Arabidopsis thaliana In wild-type plants, three major splice variants issue from the GFP gene but only one represents a translatable GFP mRNA. Compared to wild-type seedlings, which exhibit an intermediate level of GFP expression, mutants identified in the screen feature either a "GFP-weak" or "Hyper-GFP" phenotype depending on the ratio of the three splice variants. GFP-weak mutants, including previously identified prp8 and rtf2, contain a higher proportion of unspliced transcript or canonically spliced transcript, neither of which is translatable into GFP protein. In contrast, the coilin-deficient hyper-gfp1 (hgf1) mutant displays a higher proportion of translatable GFP mRNA, which arises from enhanced splicing of a U2-type intron with noncanonical AT-AC splice sites. Here we report three new hgf mutants that are defective, respectively, in spliceosome-associated proteins SMU1, SmF, and CWC16, an Yju2/CCDC130-related protein that has not yet been described in plants. The smu1 and cwc16 mutants have substantially increased levels of translatable GFP transcript owing to preferential splicing of the U2-type AT-AC intron, suggesting that SMU1 and CWC16 influence splice site selection in GFP pre-mRNA. Genome-wide analyses of splicing in smu1 and cwc16 mutants revealed a number of introns that were variably spliced from endogenous pre-mRNAs. These results indicate that SMU1 and CWC16, which are predicted to act directly prior to and during the first catalytic step of splicing, respectively, function more generally to modulate splicing patterns in plants.

Splicing stimulates siRNA formation at Drosophila DNA double-strand breaks

DNA double-strand breaks trigger the production of locus-derived siRNAs in fruit flies, human cells and plants. At least in flies, their biogenesis depends on active transcription running towards the break. Since siRNAs derive from a double-stranded RNA precursor, a major question is how broken DNA ends can generate matching sense and antisense transcripts. We performed a genome-wide RNAi-screen in cultured Drosophila cells, which revealed that in addition to DNA repair factors, many spliceosome components are required for efficient siRNA generation. We validated this observation through site-specific DNA cleavage with CRISPR-cas9 followed by deep sequencing of small RNAs. DNA breaks in intron-less genes or upstream of a gene's first intron did not efficiently trigger siRNA production. When DNA double-strand breaks were induced downstream of an intron, however, this led to robust siRNA generation. Furthermore, a downstream break slowed down splicing of the upstream intron and a detailed analysis of siRNA coverage at the targeted locus revealed that unspliced pre-mRNA contributes the sense strand to the siRNA precursor. Since splicing factors are stimulating the response but unspliced transcripts are entering the siRNA biogenesis, the spliceosome is apparently stalled in a pre-catalytic state and serves as a signaling hub. We conclude that convergent transcription at DNA breaks is stimulated by a splicing dependent control process. The resulting double-stranded RNA is converted into siRNAs that instruct the degradation of cognate mRNAs. In addition to a potential role in DNA repair, the break-induced transcription may thus be a means to cull improper RNAs from the transcriptome of Drosophila melanogaster. Since the splicing factors identified in our screen also stimulated siRNA production from high copy transgenes, it is possible that this surveillance mechanism serves in genome defense beyond DNA double-strand breaks.

[Predictive value of miRNA-29a and miRNA-10a-5p for 28-day mortality in patients with sepsis-induced acute kidney injury]

OBJECTIVE

To investigate the value of miR-29a and miR-10a-5p in predicting 28-day mortality in patients with sepsis-induced acute kidney injury.

METHODS

Seventy-four patients with sepsis-induced acute kidney injury (AKI) and 41 patients with sepsis but without AKI (control) were examined for serum levels of miR-29a and miR-10a-5p using RT-PCR. The patients were followed up for 28 days to record their survival. Pearson correlation analysis was used to test the correlations of miR-29a and miR-10a-5p with serum creatinine (Scr), cystatin C (Cys-C), and KIM-1 in patients with AKI. Multivariate logistic regression analysis was used to analyze the correlations of miR-29a, miR-10a-5p, Scr, Cys-C, KIM-1 and other risk factors with the 28-day mortality in patients with sepsis. The predictive value of these indicators for evaluating the prognosis of patients with sepsis was analyzed using ROC curve, and miR-29a combined with miR-10a-5p was assessed for their value in predicting the prognosis of the patients.

RESULT

During the follow-up for 28 days, 21 of the 74 (35.53%) AKI patients died. Compared with the survivors, the patients died within 28 days showed significantly increased serum levels of Scr , Cys-C, KIM-1, miR-29a, and miR-10a-5p (P<0.05). Pearson correlation analysis showed that miR-29a and miR-10a-5p were positively correlated with serum Scr, Cys-C, and KIM-1 levels; multivariate regression analysis identified miR-29a and miR-10a-5p as the independent risk factors for mortality in the septic patients. The ROC curve analysis showed that the area under the curve (AUC) of miR-29a and miR-10a-5p was 0.82 (95%CI: 0.71-0.89) and 0.75 (95%CI: 0.64-0.85), and that of Scr, Cys-C and KIM-1 was 0.72 (95%CI: 0.66-0.86) , 0.71 (95% CI: 0.63-0.84) and 0.81 (95% CI: 0.72-0.81), respectively. The AUC of miR-29a combined with miR-10a-5p was significantly greater than that of miR-29a, miR-10a-5p, Scr, Cys-C and KIM-1 alone (P<0.05).

CONCLUSION

miR-29a and miR-10a-5p have good predictive value in assessing the 28-day mortality of patients with sepsis.

[Predictive value of miRNA-29a and miRNA-10a-5p for 28-day mortality in patients with sepsis-induced acute kidney injury]

OBJECTIVE

To investigate the value of miR-29a and miR-10a-5p in predicting 28-day mortality in patients with sepsis-induced acute kidney injury.

METHODS

Seventy-four patients with sepsis-induced acute kidney injury (AKI) and 41 patients with sepsis but without AKI (control) were examined for serum levels of miR-29a and miR-10a-5p using RT-PCR. The patients were followed up for 28 days to record their survival. Pearson correlation analysis was used to test the correlations of miR-29a and miR-10a-5p with serum creatinine (Scr), cystatin C (Cys-C), and KIM-1 in patients with AKI. Multivariate logistic regression analysis was used to analyze the correlations of miR-29a, miR-10a-5p, Scr, Cys-C, KIM-1 and other risk factors with the 28-day mortality in patients with sepsis. The predictive value of these indicators for evaluating the prognosis of patients with sepsis was analyzed using ROC curve, and miR-29a combined with miR-10a-5p was assessed for their value in predicting the prognosis of the patients.

RESULT

During the follow-up for 28 days, 21 of the 74 (35.53%) AKI patients died. Compared with the survivors, the patients died within 28 days showed significantly increased serum levels of Scr , Cys-C, KIM-1, miR-29a, and miR-10a-5p (P<0.05). Pearson correlation analysis showed that miR-29a and miR-10a-5p were positively correlated with serum Scr, Cys-C, and KIM-1 levels; multivariate regression analysis identified miR-29a and miR-10a-5p as the independent risk factors for mortality in the septic patients. The ROC curve analysis showed that the area under the curve (AUC) of miR-29a and miR-10a-5p was 0.82 (95%CI: 0.71-0.89) and 0.75 (95%CI: 0.64-0.85), and that of Scr, Cys-C and KIM-1 was 0.72 (95%CI: 0.66-0.86) , 0.71 (95% CI: 0.63-0.84) and 0.81 (95% CI: 0.72-0.81), respectively. The AUC of miR-29a combined with miR-10a-5p was significantly greater than that of miR-29a, miR-10a-5p, Scr, Cys-C and KIM-1 alone (P<0.05).

CONCLUSION

miR-29a and miR-10a-5p have good predictive value in assessing the 28-day mortality of patients with sepsis.

Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins

Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in combination with next-generation sequencing is a powerful method for identifying endogenous targets of RNA-binding proteins (RBPs). Depending on the characteristics of each RBP, key steps in the PAR-CLIP procedure must be optimized. Here we present a comprehensive step-by-step PAR-CLIP protocol with detailed explanations of the critical steps. Furthermore, we report the application of a new PAR-CLIP data analysis pipeline to three distinct RBPs targeting different annotation categories of cellular RNAs.

miR-34 Modulates Innate Immunity and Ecdysone Signaling in Drosophila

microRNAs are endogenous small regulatory RNAs that modulate myriad biological processes by repressing target gene expression in a sequence-specific manner. Here we show that the conserved miRNA miR-34 regulates innate immunity and ecdysone signaling in Drosophila. miR-34 over-expression activates antibacterial innate immunity signaling both in cultured cells and in vivo, and flies over-expressing miR-34 display improved survival and pathogen clearance upon Gram-negative bacterial infection; whereas miR-34 knockout animals are defective in antibacterial defense. In particular, miR-34 achieves its immune-stimulatory function, at least in part, by repressing the two novel target genes Dlg1 and Eip75B. In addition, our study reveals a mutual repression between miR-34 expression and ecdysone signaling, and identifies miR-34 as a node in the intricate interplay between ecdysone signaling and innate immunity. Lastly, we identify cis-regulatory genomic elements and trans-acting transcription factors required for optimal ecdysone-mediated repression of miR-34. Taken together, our study enriches the repertoire of immune-modulating miRNAs in animals, and provides new insights into the interplay between steroid hormone signaling and innate immunity.