USP39 promotes hepatocellular carcinogenesis through regulating alternative splicing in cooperation with SRSF6/HNRNPC.

Abnormal alternative splicing (AS) caused by alterations in spliceosomal factors is implicated in cancers. Standard models posit that splice site selection is mainly determined by early spliceosomal U1 and U2 snRNPs. Whether and how other mid/late-acting spliceosome components such as USP39 modulate tumorigenic splice site choice remains largely elusive. We observed that hepatocyte-specific overexpression of USP39 promoted hepatocarcinogenesis and potently regulated splice site selection in transgenic mice. In human liver cancer cells, USP39 promoted tumor proliferation in a spliceosome-dependent manner. USP39 depletion deregulated hundreds of AS events, including the oncogenic splice-switching of KANK2. Mechanistically, we developed a novel RBP-motif enrichment analysis and found that USP39 modulated exon inclusion/exclusion by interacting with SRSF6/HNRNPC in both humans and mice. Our data represented a paradigm for the control of splice site selection by mid/late-acting spliceosome proteins and their interacting RBPs. USP39 and possibly other mid/late-acting spliceosome proteins may represent potential prognostic biomarkers and targets for cancer therapy.

Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis.

BACKGROUND: In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulated remains largely elusive. RESULT: Here, we analyze Pol II dynamics at 3' ends by combining comprehensive experiments with mathematical modelling. We generate high-resolution serine 2 phosphorylated (Ser2P) Pol II positioning data specifically enriched at 3' ends and define a 3' end pause index (3'PI). The position but not the extent of the 3' end pause correlates with the termination window size. The 3'PI is not decreased but even mildly increased in the termination deficient mutant xrn3, indicating 3' end pause is a regulatory step early during the termination and before XRN3-mediated RNA decay that releases Pol II. Unexpectedly, 3'PI is closely associated with gene exon numbers and co-transcriptional splicing efficiency. Multiple exons genes often display stronger 3' end pauses and more efficient on-chromatin splicing than genes with fewer exons. Chemical inhibition of splicing strongly reduces the 3'PI and disrupts its correlation with exon numbers but does not globally impact 3' end readthrough levels. These results are further confirmed by fitting Pol II positioning data with a mathematical model, which enables the estimation of parameters that define Pol II dynamics. CONCLUSION: Our work highlights that the number of exons via co-transcriptional splicing is a major determinant of Pol II pausing levels at the 3' end of genes in plants.

Amino acid variability, tradeoffs and optimality in human diet.

Studies at the molecular level demonstrate that dietary amino acid intake produces substantial effects on health and disease by modulating metabolism. However, how these effects may manifest in human food consumption and dietary patterns is unknown. Here, we develop a series of algorithms to map, characterize and model the landscape of amino acid content in human food, dietary patterns, and individual consumption including relations to health status, covering over 2,000 foods, ten dietary patterns, and over 30,000 dietary profiles. We find that the type of amino acids contained in foods and human consumption is highly dynamic with variability far exceeding that of fat and carbohydrate. Some amino acids positively associate with conditions such as obesity while others contained in the same food negatively link to disease. Using linear programming and machine learning, we show that these health trade-offs can be accounted for to satisfy biochemical constraints in food and human eating patterns to construct a Pareto front in dietary practice, a means of achieving optimality in the face of trade-offs that are commonly considered in economic and evolutionary theories. Thus this study may enable the design of human protein quality intake guidelines based on a quantitative framework.

MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification.

The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies not only offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way chromatin interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell-cycle-associated genes. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure.

Edaravone Ameliorates Cerebral Ischemia-Reperfusion Injury by Downregulating Ferroptosis via the Nrf2/FPN Pathway in Rats.

Edaravone, an antioxidant protective agent, has anti-cerebral ischemic reperfusion injury (CIRI) effects, but its anti-CIRI mechanism is unclear. The aim of this study is to investigate the anti-CIRI mechanism of edaravone based on the nuclear factor-E2-related factor 2 (Nrf2)/ferroportin (FPN) pathway that regulates ferroptosis-mediated cerebral ischemia-reperfusion injury. We evaluated the brain injury by constructing a middle cerebral artery occlusion and reperfusion (MCAO/R) model in rats. The results showed that cerebral infarct volume and neurological impairment scores were increased in cerebral ischemia-reperfusion rats, with impaired sensorimotor ability; furthermore, brain tissue glutathione (GSH) content was decreased, Fe2+, malondialdehyde (MDA) and lipide peroxide (LPO) content were increased, and the expression level of glutathione peroxidase 4 (GPX4), a key protein of ferroptosis, was also decreased. Meanwhile, the Nrf2 expression level was increased and the FPN expression level was decreased after cerebral ischemia-reperfusion, while the levels of interleukin (IL)-6, IL-1ß, tumor necrosis factor (TNF)-α, and myeloperoxidase (MPO) were increased. However, edaravone exhibited a protective effect on cerebral infarct and neurological and sensorimotor function in relevant tests. In addition, we also found that edaravone decreased the contents of Fe2+, MDA, and LPO in the brain tissue of MCAO/R rats and increased GSH content to inhibit ferroptosis. Furthermore, Western blot showed that after treatment with edaravone, the expression of Nrf2, GPX4, and FPN was up-regulated, the nuclear location of Nrf2 was increased, and the levels of inflammation-related indicators IL-6, IL-1ß, TNF-α, and MPO were lower than in the MCAO/R group. Our results demonstrated that edaravone inhibits ferroptosis to attenuate CIRI, probably through the activation of the Nrf2/FPN pathway.

Pinpointing Cancer Sub-Type Specific Metabolic Tasks Facilitates Identification of Anti-cancer Targets.

Metabolic reprogramming is one of the hallmarks of tumorigenesis. Understanding the metabolic changes in cancer cells may provide attractive therapeutic targets and new strategies for cancer therapy. The metabolic states are not the same in different cancer types or subtypes, even within the same sample of solid tumors. In order to understand the heterogeneity of cancer cells, we used the Pareto tasks inference method to analyze the metabolic tasks of different cancers, including breast cancer, lung cancer, digestive organ cancer, digestive tract cancer, and reproductive cancer. We found that cancer subtypes haves different propensities toward metabolic tasks, and the biological significance of these metabolic tasks also varies greatly. Normal cells treat metabolic tasks uniformly, while different cancer cells focus on different pathways. We then integrated the metabolic tasks into the multi-objective genome-scale metabolic network model, which shows higher accuracy in the in silico prediction of cell states after gene knockout than the conventional biomass maximization model. The predicted potential single drug targets could potentially turn into biomarkers or drug design targets. We further implemented the multi-objective genome-scale metabolic network model to predict synthetic lethal target pairs of the Basal and Luminal B subtypes of breast cancer. By analyzing the predicted synthetic lethal targets, we found that mitochondrial enzymes are potential targets for drug combinations. Our study quantitatively analyzes the metabolic tasks of cancer and establishes cancer type-specific metabolic models, which opens a new window for the development of specific anti-cancer drugs and provides promising treatment plans for specific cancer subtypes.

Effects of Interleukin-10 -1082G/A and -592C/A Gene Polymorphisms on the Risk of Human Immunodeficiency Virus-1 Infection: An Updated Meta-analysis.

This paper has aimed to review the available evidence on the association between Interleukin (IL) -10 -1082G/A, -592C/A gene polymorphisms and the risk of human immunodeficiency virus-1(HIV-1) infection. The data of PubMed updated in May 2021 were retrieved. The HIV infection risks were estimated in allelic, recessive, dominant, homozygous, heterozygous, over-dominant models of IL-10-1082G/A and-592C/A gene locus as odds ratio (OR) with the corresponding 95% confidence interval (95% CI). The correlation was not significant between -1082G/A polymorphism and HIV-1 susceptibility (allelic model (G vs. A: OR (95% CI)=0.968 (0.878-1.067)); recessive model (GG vs. AA+AG: OR (95% CI)=0.940, (0.771-1.146)); dominant model (GG+AG vs. AA: OR (95% CI)=0.967(0.846-1.106)); homozygous model (GG vs. AA: OR (95% CI)=0.971(0.780-1.209)); heterozygous model (AG vs. AA: OR (95% CI)=0.988(0.797-1.224)) and over-dominant model (GG+AA vs. AG: OR (95% CI)=0.969(0.781-1.201)). IL-10-592C/A polymorphism might be related to HIV-1 in allelic model, dominant model, homozygous model and heterozygous model (OR (95% CI)(0.796-0.965); OR (95% CI)=0.793(0.664-0.948); OR (95% CI)=0.755,(0.612-0.930); OR (95% CI)=0.820(0.679-0.991), respectively), but not to recessive model and over-dominant model (OR (95% CI)=0.882(0.770-1.010) and OR (95% CI)=1.009(0.897-1.148)).

Serum 14-3-3η is a Marker that Complements Current Biomarkers for the Diagnosis of RA: Evidence from a Meta-analysis.

OBJECTIVE: To systematically evaluate the diagnostic value of 14-3-3η protein for rheumatoid arthritis (RA). METHOD: Searched PubMed, Web of Science, Embase and China Biology Medicine (CBM) databases comprehensively from inception to May 2020. The evaluation index were the pooled sensitivity, specificity, diagnosis odds ratio (DOR), positive likelihood ratio (PLR), negative likelihood ratio (NLR), as well as the area under the summary receiver operating characteristic (SROC) curves. Meta-Disc 1.4 and RevMan 5.3 were used to analyze all statistics. QUADAS-2 tool was applied to evaluate the quality of eligible studies. Subgroup analysis and meta-regression were used to explore the sources of heterogeneity. RESULTS: Nine articles containing eleven records were eligible for this meta-analysis. The pooled sensitivity of 14-3-3η was 0.63 (95% CI: 0.60 to 0.66), the pooled specificity was 0.90 (95% CI: 0.88 to 0.91). The pooled PLR and NLR was 6.10 (95% CI: 4.67 to 7.96) and 0.40 (95% CI: 0.33 to 0.48), respectively. The pooled DOR was 15.90 (95% CI: 11.15 to 22.68), and the area under the curve (AUC) was 0.8696. Compared with a single indicator (rheumatoid factor or anti-citrullinated protein antibodies), adding 14-3-3η can bring incremental benefits to the diagnosis of RA. The results of subgroup analysis and meta-regression suggested that the two factors (ethnicity, early vs established RA) we analyzed might not be the source of heterogeneity (P value were 0.0979 and 0.4298, respectively) and there was no publication bias among these articles (P = .42). CONCLUSION: Serum 14-3-3η protein is a supplementary biomarker in the diagnosis of RA.

Jiangzhi Ligan Decoction Inhibits GSDMD-Mediated Canonical/Noncanonical Pyroptosis Pathways and Alleviates High-Fat Diet-Induced Nonalcoholic Fatty Liver Disease.

Increasing evidence suggests that gasdermin D (GSDMD) mediated pyroptosis signaling pathways play a vital role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Jiangzhi Ligan Decoction (JZLGD) has been verified to prevent NAFLD, but its specific mechanism has not been determined. In this study, an NAFLD model was established in Sprague-Dawley rats by a high-fat diet (HFD). After 12 weeks, JZLGD was orally administered once a day for 6 additional weeks. We investigated the effects of JZLGD on NAFLD rats and determined the GSDMD pathway-associated proteins to explore whether such effects were associated with pyroptosis. Our data show that JZLGD significantly reduced the liver index; improved serum lipid levels, liver function parameters, and lipid droplet content; and relieved NAFLD. We further found that the serum levels of the proinflammatory factors interleukin-1ß (IL-1ß), IL-18, tumor necrosis factor-α, and IL-6 were obviously decreased in the JZLGD group. HFD rats treated with GSDMD exhibited NLRP3, caspase-1, lipopolysaccharide (LPS), and caspase-11 activation; however, these effects were blunted by JZLGD treatment. Taken together, JZLGD may exert hepatoprotective effects against NAFLD in a rat HFD model by regulating GSDMD-mediated canonical/noncanonical pyroptosis pathways.

Cellular stress signaling activates type-I IFN response through FOXO3-regulated lamin posttranslational modification.

Neural stem/progenitor cells (NSPCs) persist over the lifespan while encountering constant challenges from age or injury related brain environmental changes like elevated oxidative stress. But how oxidative stress regulates NSPC and its neurogenic differentiation is less clear. Here we report that acutely elevated cellular oxidative stress in NSPCs modulates neurogenic differentiation through induction of Forkhead box protein O3 (FOXO3)-mediated cGAS/STING and type I interferon (IFN-I) responses. We show that oxidative stress activates FOXO3 and its transcriptional target glycine-N-methyltransferase (GNMT) whose upregulation triggers depletion of s-adenosylmethionine (SAM), a key co-substrate involved in methyl group transfer reactions. Mechanistically, we demonstrate that reduced intracellular SAM availability disrupts carboxymethylation and maturation of nuclear lamin, which induce cytosolic release of chromatin fragments and subsequent activation of the cGAS/STING-IFN-I cascade to suppress neurogenic differentiation. Together, our findings suggest the FOXO3-GNMT/SAM-lamin-cGAS/STING-IFN-I signaling cascade as a critical stress response program that regulates long-term regenerative potential.

Urinary Tumor Necrosis Factor-Like Weak Inducer of Apoptosis as a Biomarker for Diagnosis and Evaluating Activity in Lupus Nephritis: A Meta-analysis.

OBJECTIVE: Urinary tumor necrosis factor-like weak inducer of apoptosis (uTWEAK) has been identified as a candidate biomarker for lupus nephritis (LN). However, its diagnostic value remains unclear. This meta-analysis was conducted to comprehensively evaluate the value of uTWEAK for diagnosis and evaluating activity in LN. METHODS: Medline, Web of Science, Chinese Biomedical Medical, and Chinese National Knowledge Infrastructure databases were searched to acquire eligible studies published before September 30, 2019. The quality of the studies was evaluated by Quality Assessment of Diagnostic Accuracy Studies-2. Summary receiver operating characteristic curve and area under the curve were applied to summarize the overall diagnostic performances. The pooled sensitivity, specificity, and diagnostic odds ratio (DOR) were calculated with the fixed-effects model. RevMan 5.3, Stata 12.0, and Meta-disc 1.4 software were used. RESULTS: A total of 7 studies were included. Of these, 4 studies were available for comparison between SLE with and without LN, and 3 studies were for active and inactive LN. The total area under the curve was 0.8640, and DOR was 14.89 (95% confidence interval [CI], 7.95-27.86). For LN diagnosis, the pooled sensitivity, specificity, and DOR were 0.55 (95% CI, 0.47-0.63), 0.92 (95% CI, 0.86-0.96), and 16.54 (95% CI, 7.57-36.15), respectively. For assessing LN activity, the pooled sensitivity, specificity, and DOR were 0.91 (95% CI, 0.82-0.96), 0.70 (95% CI, 0.58-0.81), and 18.45 (95% CI, 7.45-45.87), respectively. CONCLUSIONS: This meta-analysis indicated that uTWEAK has relatively moderate sensitivity and specificity for diagnosis and evaluating activity in LN, suggesting that uTWEAK can serve as a helpful biomarker for LN.

Astragaloside IV Alleviates Cerebral Ischemia-Reperfusion Injury through NLRP3 Inflammasome-Mediated Pyroptosis Inhibition via Activating Nrf2.

As one of the fundamental components of Astragalus membranaceus, astragaloside IV (AST IV) exerts protective effects against cerebral ischemia-reperfusion injury (CIRI). Nevertheless, the underlying mechanisms have not yet been conclusively elucidated. To do so, here, we report on the regulatory effects of Nrf2 on NLRP3 inflammasome-mediated pyroptosis. CIRI was induced by middle cerebral artery occlusion-reperfusion (MCAO/R) in Sprague Dawley rats and modeled by oxygen and glucose deprivation/reoxygenation (OGD/R) in SH-SY5Y cells. Cerebral infarct volume and neurological deficit score served as indices to evaluate MCAO/R injury. In addition, the CCK-8 assay was used to assess cell viability, the LDH leakage rate was used as a quantitative index, and propidium iodide (PI) staining was used to visualize cells after OGD/R injury. The NLRP3/Caspase-1/GSDMD pathway, which produces the pores in the cell membrane that are central to the pyroptosis process, was assessed to investigate pyroptosis. Nrf2 activation was assessed by detecting Nrf2 protein levels and immunofluorescence analysis. We show that after MCAO/R of rats, the infarct volume and neurological deficit score of rats were strongly increased, and after OGD/R of cell cultures, cell viability was strongly decreased, and the LDH leakage rate and the proportion of PI-positive cells were strongly increased. In turn, MCAO/R and OGD/R enhanced the protein levels of NLRP3, Caspase-1, IL-1ß, GSDMD, and GSDMD-N. Moreover, Nrf2 protein levels increased, and Nrf2 translocation was promoted after CIRI. Interestingly, AST IV (i) reduced the cerebral infarct volume and the neurological deficit score in vivo and (ii) increased the cell viability and reduced the LDH leakage rate and the proportion of PI-positive cells in vitro. AST IV reduced the protein levels of NLRP3, Caspase-1, IL-1ß, GSDMD, and GSDMD-N, inhibiting NLRP3 inflammasome-mediated pyroptosis. AST IV also increased the protein levels of Nrf2 and promoted the transfer of Nrf2 to the nucleus, accelerating Nrf2 activation. Particularly revealing was that the Nrf2 inhibitor ML385 partly blocked the above effects of AST IV. Taken together, these results demonstrate that AST IV alleviates CIRI through inhibiting NLRP3 inflammasome-mediated pyroptosis via activating Nrf2.

Erratum: Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin.

[This corrects the article DOI: 10.1016/j.isci.2020.100855.].

Author Correction: The evolving metabolic landscape of chromatin biology and epigenetics.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The evolving metabolic landscape of chromatin biology and epigenetics.

Molecular inputs to chromatin via cellular metabolism are modifiers of the epigenome. These inputs - which include both nutrient availability as a result of diet and growth factor signalling - are implicated in linking the environment to the maintenance of cellular homeostasis and cell identity. Recent studies have demonstrated that these inputs are much broader than had previously been known, encompassing metabolism from a wide variety of sources, including alcohol and microbiotal metabolism. These factors modify DNA and histones and exert specific effects on cell biology, systemic physiology and pathology. In this Review, we discuss the nature of these molecular networks, highlight their role in mediating cellular responses and explore their modifiability through dietary and pharmacological interventions.

Quantitative Analysis of the Physiological Contributions of Glucose to the TCA Cycle.

The nutritional source for catabolism in the tricarboxylic acid (TCA) cycle is a fundamental question in metabolic physiology. Limited by data and mathematical analysis, controversy exists. Using isotope-labeling data in vivo across several experimental conditions, we construct multiple models of central carbon metabolism and develop methods based on metabolic flux analysis (MFA) to solve for the preferences of glucose, lactate, and other nutrients used in the TCA cycle. We show that in nearly all circumstances, glucose contributes more than lactate as a substrate to the TCA cycle. This conclusion is verified in different animal strains from different studies and different administrations of 13C glucose, and is extended to multiple tissue types. Thus, this quantitative analysis of organismal metabolism defines the relative contributions of nutrient fluxes in physiology, provides a resource for analysis of in vivo isotope tracing data, and concludes that glucose is the major nutrient used in mammals.

Cooperative virus propagation in COVID-19 transmission.

The global pandemic due to the emergence of a novel coronavirus (COVID-19) is a threat to humanity. There remains an urgent need to understand its transmission characteristics and design effective interventions to mitigate its spread. In this study, we define a non-linear (known in biochemistry models as allosteric or cooperative) relationship between viral shedding, viral dose and COVID-19 infection propagation. We develop a mathematical model of the dynamics of COVID-19 to link quantitative features of viral shedding, human exposure and transmission in nine countries impacted by the ongoing COVID-19 pandemic, and state-wide transmission in the United States of America (USA). The model was then used to evaluate the efficacy of interventions against virus transmission. We found that cooperativity was important to capture country-specific transmission dynamics and leads to resistance to mitigating transmission in mild or moderate interventions. The behaviors of the model emphasize that strict interventions greatly limiting both virus shedding and human exposure are indispensable to achieving effective containment of COVID-19. Finally, in the USA we find that by the summer of 2021, a difference of about 1.5 million deaths may be observed depending on whether the interventions are to be maintained strictly or lifted in entirety.

Using antagonistic pleiotropy to design a chemotherapy-induced evolutionary trap to target drug resistance in cancer.

Local adaptation directs populations towards environment-specific fitness maxima through acquisition of positively selected traits. However, rapid environmental changes can identify hidden fitness trade-offs that turn adaptation into maladaptation, resulting in evolutionary traps. Cancer, a disease that is prone to drug resistance, is in principle susceptible to such traps. We therefore performed pooled CRISPR-Cas9 knockout screens in acute myeloid leukemia (AML) cells treated with various chemotherapies to map the drug-dependent genetic basis of fitness trade-offs, a concept known as antagonistic pleiotropy (AP). We identified a PRC2-NSD2/3-mediated MYC regulatory axis as a drug-induced AP pathway whose ability to confer resistance to bromodomain inhibition and sensitivity to BCL-2 inhibition templates an evolutionary trap. Across diverse AML cell-line and patient-derived xenograft models, we find that acquisition of resistance to bromodomain inhibition through this pathway exposes coincident hypersensitivity to BCL-2 inhibition. Thus, drug-induced AP can be leveraged to design evolutionary traps that selectively target drug resistance in cancer.

Metabolism in the tumor microenvironment: insights from single-cell analysis.

The metabolism of both cancer and immune cells in the tumor microenvironment (TME) is poorly understood since most studies have focused on analysis in bulk samples and ex vivo cell culture models. Our recent analyses of single-cell RNA sequencing data suggest that the metabolic features of single cells within TME differ greatly from those of the bulk measurements. Here, we discuss some key findings about metabolism in cancer and immune cells and discuss possible relevance to immunotherapy.

Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin.

Cellular metabolism is dynamic, but quantifying non-steady metabolic fluxes by stable isotope tracers presents unique computational challenges. Here, we developed an efficient 13C-tracer dynamic metabolic flux analysis (13C-DMFA) framework for modeling central carbon fluxes that vary over time. We used B-splines to generalize the flux parameterization system and to improve the stability of the optimization algorithm. As proof of concept, we investigated how 3T3-L1 cultured adipocytes acutely metabolize glucose in response to insulin. Insulin rapidly stimulates glucose uptake, but intracellular pathways responded with differing speeds and magnitudes. Fluxes in lower glycolysis increased faster than those in upper glycolysis. Glycolysis fluxes rose disproportionally larger and faster than the tricarboxylic acid cycle, with lactate a primary glucose end product. The uncovered array of flux dynamics suggests that glucose catabolism is additionally regulated beyond uptake to help shunt glucose into appropriate pathways. This work demonstrates the value of using dynamic intracellular fluxes to understand metabolic function and pathway regulation.