A mitochondrial EglN1-AMPKα axis drives breast cancer progression by enhancing metabolic adaptation to hypoxic stress.

Mitochondria play essential roles in cancer cell adaptation to hypoxia, but the underlying mechanisms remain elusive. Through mitochondrial proteomic profiling, we here find that the prolyl hydroxylase EglN1 (PHD2) accumulates on mitochondria under hypoxia. EglN1 substrate-binding region in the ß2ß3 loop is responsible for its mitochondrial translocation and contributes to breast tumor growth. Furthermore, we identify AMP-activated protein kinase alpha (AMPKα) as an EglN1 substrate on mitochondria. The EglN1-AMPKα interaction is essential for their mutual mitochondrial translocation. After EglN1 prolyl-hydroxylates AMPKα under normoxia, they rapidly dissociate following prolyl-hydroxylation, leading to their immediate release from mitochondria. In contrast, hypoxia results in constant EglN1-AMPKα interaction and their accumulation on mitochondria, leading to the formation of a Ca2+ /calmodulin-dependent protein kinase 2 (CaMKK2)-EglN1-AMPKα complex to activate AMPKα phosphorylation, ensuring metabolic homeostasis and breast tumor growth. Our findings identify EglN1 as an oxygen-sensitive metabolic checkpoint signaling hypoxic stress to mitochondria through its ß2ß3 loop region, suggesting a potential therapeutic target for breast cancer.

An Ultrasmall Ordered High-Entropy Intermetallic with Multiple Active Sites for the Oxygen Reduction Reaction.

Controlling multimetallic ensembles at the atomic level is significantly challenging, particularly for high-entropy alloys with more than five elements. Herein, we report an innovative ultrasmall (∼2 nm) PtFeCoNiCuZn high-entropy intermetallic (PFCNCZ-HEI) with a well-ordered structure synthesized by using the space-confined strategy. By exploiting these combined metals, the PFCNCZ-HEI nanoparticles achieve an ultrahigh mass activity of 2.403 A mgPt-1 at 0.90 V vs reversible hydrogen electrode for the oxygen reduction reaction, which is up to 19-fold higher than that of state-of-the-art commercial Pt/C. A proton exchange membrane fuel cell assembled with PFCNCZ-HEI as the cathode (0.03 mgPt cm-2) exhibits a power density of 1.4 W cm-2 and a high mass-normalized rated power of 45 W mgPt-1. Furthermore, theoretical calculations reveal that the outer electrons of the non-noble-metal atoms on the surface of the PFCNCZ-HEI nanoparticle are modulated to show characteristics of multiple active centers. This work offers a promising catalyst design direction for developing highly ordered HEI nanoparticles for electrocatalysis.

Deep learning in pulmonary nodule detection and segmentation: a systematic review.

OBJECTIVES: The accurate detection and precise segmentation of lung nodules on computed tomography are key prerequisites for early diagnosis and appropriate treatment of lung cancer. This study was designed to compare detection and segmentation methods for pulmonary nodules using deep-learning techniques to fill methodological gaps and biases in the existing literature. METHODS: This study utilized a systematic review with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, searching PubMed, Embase, Web of Science Core Collection, and the Cochrane Library databases up to May 10, 2023. The Quality Assessment of Diagnostic Accuracy Studies 2 criteria was used to assess the risk of bias and was adjusted with the Checklist for Artificial Intelligence in Medical Imaging. The study analyzed and extracted model performance, data sources, and task-focus information. RESULTS: After screening, we included nine studies meeting our inclusion criteria. These studies were published between 2019 and 2023 and predominantly used public datasets, with the Lung Image Database Consortium Image Collection and Image Database Resource Initiative and Lung Nodule Analysis 2016 being the most common. The studies focused on detection, segmentation, and other tasks, primarily utilizing Convolutional Neural Networks for model development. Performance evaluation covered multiple metrics, including sensitivity and the Dice coefficient. CONCLUSIONS: This study highlights the potential power of deep learning in lung nodule detection and segmentation. It underscores the importance of standardized data processing, code and data sharing, the value of external test datasets, and the need to balance model complexity and efficiency in future research. CLINICAL RELEVANCE STATEMENT: Deep learning demonstrates significant promise in autonomously detecting and segmenting pulmonary nodules. Future research should address methodological shortcomings and variability to enhance its clinical utility. KEY POINTS: Deep learning shows potential in the detection and segmentation of pulmonary nodules. There are methodological gaps and biases present in the existing literature. Factors such as external validation and transparency affect the clinical application.

Influence of Oxygen Vacancy-Induced Coordination Change on Pd/CeO2 for NO Reduction.

The byproduct formation in environmental catalysis is strongly influenced by the chemical state and coordination of catalysts. Herein, two Pd/CeO2 catalysts (PdCe-350 and PdCe-800) with varying oxygen vacancies (Ov) and coordination numbers (CN) of Pd were prepared to investigate the mechanism of N2O and NH3 formation during NO reduction by CO. PdCe-350 exhibits a higher density of Ov and Pd sites with higher CN, leading to an enhanced metal-support interaction by electron transformation from the support to Pd. Consequently, PdCe-350 displayed increased levels of byproduct formation. In situ spectroscopies under dry and wet conditions revealed that at low temperatures, the N2O formation strongly correlated with the Ov density through the decomposition of chelating nitro species on PdCe-350. Conversely, at high temperatures, it was linked to the reactivity of Pd species, primarily facilitated by monodentate nitrates on PdCe-800. In terms of NH3 formation, its occurrence was closely associated with the activation of H2O and C3H6, since a water-gas shift or hydrocarbon reforming could provide hydrogen. Both bridging and monodentate nitrates showed activity in NH3 formation, while hyponitrites were identified as key intermediates for both catalysts. The insights provide a fundamental understanding of the intricate relationship among the local coordination of Pd, surface Ov, and byproduct distribution.

Genome-wide association analysis of serum alanine and aspartate aminotransferase, and the modifying effects of BMI in 388k European individuals.

Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) are biomarkers for liver health. Here we report the largest genome-wide association analysis to date of serum ALT and AST levels in over 388k people of European ancestry from UK biobank and DiscovEHR. Eleven million imputed markers with a minor allele frequency (MAF) ≥ 0.5% were analyzed. Overall, 300 ALT and 336 AST independent genome-wide significant associations were identified. Among them, 81 ALT and 61 AST associations are reported for the first time. Genome-wide interaction study identified 9 ALT and 12 AST independent associations significantly modified by body mass index (BMI), including several previously reported potential liver disease therapeutic targets, for example, PNPLA3, HSD17B13, and MARC1. While further work is necessary to understand the effect of ALT and AST-associated variants on liver disease, the weighted burden of significant BMI-modified signals is significantly associated with liver disease outcomes. In summary, this study identifies genetic associations which offer an important step forward in understanding the genetic architecture of serum ALT and AST levels. Significant interactions between BMI and genetic loci not only highlight the important role of adiposity in liver damage but also shed light on the genetic etiology of liver disease in obese individuals.

Light-Driven Molecular Whirligig.

A unidirectional light-driven rotary motor was looped in a figure-of-eight molecule by linking two polymer chains between its stator and rotor parts. By properly tuning the size of these linkers, clockwise rotation of the motor under UV light was shown to create conformationally strained twists between the polymer chains, and in this tensed conformation, the energy stored in the molecular object was sufficient to trigger the reverse rotation of the motor back to its fully relaxed state. The functioning principle of this motorized molecular device appears very similar to that of macroscopic whirligig crafts used by children for fun. In addition, we found that in its out-of-equilibrium tensed state, the fluorescence emission of the molecular motor increased by 500% due to the mechanical constraints imposed by the polymer chains on its conjugated core. Finally, by calculating the apparent thermal energies of activation for the backward rotations at different levels of twisting, we quantitatively determined a lower estimate of the work generated by this rotary motor, from which a torque and a force were extracted, thus answering a long-term open question in this field of research.

Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci.

Educational attainment is widely used as a surrogate for socioeconomic status (SES). Low SES is a risk factor for hypertension and high blood pressure (BP). To identify novel BP loci, we performed multi-ancestry meta-analyses accounting for gene-educational attainment interactions using two variables, "Some College" (yes/no) and "Graduated College" (yes/no). Interactions were evaluated using both a 1 degree of freedom (DF) interaction term and a 2DF joint test of genetic and interaction effects. Analyses were performed for systolic BP, diastolic BP, mean arterial pressure, and pulse pressure. We pursued genome-wide interrogation in Stage 1 studies (N = 117 438) and follow-up on promising variants in Stage 2 studies (N = 293 787) in five ancestry groups. Through combined meta-analyses of Stages 1 and 2, we identified 84 known and 18 novel BP loci at genome-wide significance level (P < 5 × 10-8). Two novel loci were identified based on the 1DF test of interaction with educational attainment, while the remaining 16 loci were identified through the 2DF joint test of genetic and interaction effects. Ten novel loci were identified in individuals of African ancestry. Several novel loci show strong biological plausibility since they involve physiologic systems implicated in BP regulation. They include genes involved in the central nervous system-adrenal signaling axis (ZDHHC17, CADPS, PIK3C2G), vascular structure and function (GNB3, CDON), and renal function (HAS2 and HAS2-AS1, SLIT3). Collectively, these findings suggest a role of educational attainment or SES in further dissection of the genetic architecture of BP.

A highly sensitive electrochemiluminescence method for abrin detection by a portable biosensor based on a screen-printed electrode with a phage display affibody as specific labeled probe.

Abrin is a highly toxic ribosome-inactivating protein, which could be used as a biological warfare agent and terrorist weapon, and thus needs to be detected efficiently and accurately. Affibodies are a new class of engineered affinity proteins with small size, high affinity, high stability, favorable folding and good robustness, but they have rarely played a role in biological detection. In this work, we establish a novel electrochemiluminescence (ECL) method for abrin detection with a phage display affibody as the specific probe for the first time, to our knowledge, and a portable biosensor based on a screen-printed electrode (SPE) as the testing platform. On the basis of the double antibody sandwich structure in our previous work, we used a phage display affibody instead of monoclonal antibody as a new specific labeled probe. Due to numerous signal molecules labeled on M13 phages, significant signal amplification was achieved in this experiment. Under optimized conditions, a linear dependence was observed from 0.005 to 100 ng/mL with a limit of detection (LOD) of 5 pg/mL. This assay also showed good reproducibility and specificity, and performed well in the detection of simulated samples. Considering its high sensitivity, interference resistance and convenience, this new biosensing system based on phage display affibodies and a portable ECL biosensor holds promise for in situ detection of toxins and pollutants in different environments.

A multi-ancestry genome-wide study incorporating gene-smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure.

Elevated blood pressure (BP), a leading cause of global morbidity and mortality, is influenced by both genetic and lifestyle factors. Cigarette smoking is one such lifestyle factor. Across five ancestries, we performed a genome-wide gene-smoking interaction study of mean arterial pressure (MAP) and pulse pressure (PP) in 129 913 individuals in stage 1 and follow-up analysis in 480 178 additional individuals in stage 2. We report here 136 loci significantly associated with MAP and/or PP. Of these, 61 were previously published through main-effect analysis of BP traits, 37 were recently reported by us for systolic BP and/or diastolic BP through gene-smoking interaction analysis and 38 were newly identified (P < 5 × 10-8, false discovery rate < 0.05). We also identified nine new signals near known loci. Of the 136 loci, 8 showed significant interaction with smoking status. They include CSMD1 previously reported for insulin resistance and BP in the spontaneously hypertensive rats. Many of the 38 new loci show biologic plausibility for a role in BP regulation. SLC26A7 encodes a chloride/bicarbonate exchanger expressed in the renal outer medullary collecting duct. AVPR1A is widely expressed, including in vascular smooth muscle cells, kidney, myocardium and brain. FHAD1 is a long non-coding RNA overexpressed in heart failure. TMEM51 was associated with contractile function in cardiomyocytes. CASP9 plays a central role in cardiomyocyte apoptosis. Identified only in African ancestry were 30 novel loci. Our findings highlight the value of multi-ancestry investigations, particularly in studies of interaction with lifestyle factors, where genomic and lifestyle differences may contribute to novel findings.

A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure.

Genome-wide association analysis advanced understanding of blood pressure (BP), a major risk factor for vascular conditions such as coronary heart disease and stroke. Accounting for smoking behavior may help identify BP loci and extend our knowledge of its genetic architecture. We performed genome-wide association meta-analyses of systolic and diastolic BP incorporating gene-smoking interactions in 610,091 individuals. Stage 1 analysis examined ∼18.8 million SNPs and small insertion/deletion variants in 129,913 individuals from four ancestries (European, African, Asian, and Hispanic) with follow-up analysis of promising variants in 480,178 additional individuals from five ancestries. We identified 15 loci that were genome-wide significant (p < 5 × 10-8) in stage 1 and formally replicated in stage 2. A combined stage 1 and 2 meta-analysis identified 66 additional genome-wide significant loci (13, 35, and 18 loci in European, African, and trans-ancestry, respectively). A total of 56 known BP loci were also identified by our results (p < 5 × 10-8). Of the newly identified loci, ten showed significant interaction with smoking status, but none of them were replicated in stage 2. Several loci were identified in African ancestry, highlighting the importance of genetic studies in diverse populations. The identified loci show strong evidence for regulatory features and support shared pathophysiology with cardiometabolic and addiction traits. They also highlight a role in BP regulation for biological candidates such as modulators of vascular structure and function (CDKN1B, BCAR1-CFDP1, PXDN, EEA1), ciliopathies (SDCCAG8, RPGRIP1L), telomere maintenance (TNKS, PINX1, AKTIP), and central dopaminergic signaling (MSRA, EBF2).

A CT-based radiomics nomogram for differentiation of lympho-associated benign and malignant lesions of the parotid gland.

OBJECTIVES: Preoperative differentiation between benign lymphoepithelial lesion (BLEL) and mucosa-associated lymphoid tissue lymphoma (MALToma) in the parotid gland is important for treatment decisions. The purpose of this study was to develop and validate a CT-based radiomics nomogram combining radiomics signature and clinical factors for the preoperative differentiation of BLEL from MALToma in the parotid gland. METHODS: A total of 101 patients with BLEL (n = 46) or MALToma (n = 55) were divided into a training set (n = 70) and validation set (n = 31). Radiomics features were extracted from non-contrast CT images, a radiomics signature was constructed, and a radiomics score (Rad-score) was calculated. Demographics and CT findings were assessed to build a clinical factor model. A radiomics nomogram combining the Rad-score and independent clinical factors was constructed using multivariate logistic regression analysis. The performance levels of the nomogram, radiomics signature, and clinical model were evaluated and validated on the training and validation datasets, and then compared among the three models. RESULTS: Seven features were used to build the radiomics signature. The radiomics nomogram incorporating the clinical factors and radiomics signature showed favorable predictive value for differentiating parotid BLEL from MALToma, with AUCs of 0.983 and 0.950 for the training set and validation set, respectively. Decision curve analysis showed that the nomogram outperformed the clinical factor model in terms of clinical usefulness. CONCLUSIONS: The CT-based radiomics nomogram incorporating the Rad-score and clinical factors showed favorable predictive efficacy for differentiating BLEL from MALToma in the parotid gland, and may help in the clinical decision-making process. KEY POINTS: • Differential diagnosis between BLEL and MALToma in parotid gland is rather difficult by conventional imaging modalities. • A radiomics nomogram integrated with the radiomics signature, demographics, and CT findings facilitates differentiation of BLEL from MALToma with improved diagnostic efficacy.

Multipollutant Control (MPC) of Flue Gas from Stationary Sources Using SCR Technology: A Critical Review.

The emission of gaseous pollutants from the combustion of fossil fuels is believed to be one of the most serious environmental challenges in the 21st century. Given the increasing demands of multipollutant control (MPC) via adsorption or catalysis technologies, such as NOx, volatile organic compounds (VOCs), heavy metals (Hg etc.), and ammonia, and considering investment costs and site space, the use of existing equipment, especially the selective catalytic reduction (SCR) system to convert pollutants into harmless or readily adsorbed substances, is one of the most practical approaches. Consequently, many efforts have been directed at achieving the simultaneous elimination of multipollutants in a SCR convertor, and this method has been widely used to mitigate the stationary emission of NOx. However, the development of active, selective, stable, and multifunctional catalysts/adsorbents suitable for large-scale commercialization remains challenging. Herein, we summarize recent works on the applications of SCR in MPC, describing the approaches of (i) SCR + VOCs oxidation, (ii) SCR + heavy metal control, and (iii) SCR + NH3 reduction to reveal that the efficiency of simultaneous elimination depends on catalyst composition and flue gas parameters. Furthermore, the synergistic promotional/inhibitory effects between SCR and VOCs/ammonia/heavy metal oxidations are shown to be the key to the feasibility of the reactions.

Improved production of ß-glucan by a T-DNA-based mutant of Aureobasidium pullulans.

To improve ß-1,3-1,6-D-glucan (ß-glucan) production by Aureobasidium pullulans, an Agrobacterium tumefaciens-mediated transformation method was developed to screen a mutant A. pullulans CGMCC 19650. Based on thermal asymmetric-interlaced PCR detection, DNA sequencing, BLAST analysis, and quantitative real-time PCR assay, the T-DNA was identified to be inserted in the coding region of mal31 gene, which encodes a sugar transporter involved in pullulan biosynthesis in the mutant. The maximal biomass and ß-glucan production under batch fermentation were significantly increased by 47.6% and 78.6%, respectively, while pullulan production was decreased by 41.7% in the mutant, as compared to the parental strain A. pullulans CCTCC M 2012259. Analysis of the physiological mechanism of these changes revealed that mal31 gene disruption increased the transcriptional levels of pgm2, ugp, fks1, and kre6 genes; increased the amounts of key enzymes associated with UDPG and ß-glucan biosynthesis; and improved intracellular UDPG contents and energy supply, all of which favored ß-glucan production. However, the T-DNA insertion decreased the transcriptional levels of ags2 genes, and reduced the biosynthetic capability to form pullulan, resulting in the decrease in pullulan production. This study not only provides an effective approach for improved ß-glucan production by A. pullulans, but also presents an accurate and useful gene for metabolic engineering of the producer for efficient polysaccharide production. KEY POINTS: • A mutant A. pullulans CGMCC 19650 was screened by using the ATMT method. • The mal31 gene encoding a sugar transporter was disrupted in the mutant. • ß-Glucan produced by the mutant was significantly improved.

Effects of different drying methods on the chemical constituents of Lilium lancifolium Thunb. based on UHPLC-MS analysis and antidepressant activity of the main chemical component regaloside A.

The Lilium lancifolium Thunb. is a herb with multiple functions in both medicine and food in China, and its extracts have shown antidepressant effects. In this study, fresh bulbs of Lilium lancifolium Thunb. were processed to study the effects of different drying processes on changes in its main chemical components. We found that different drying methods can affect the chemical constituents of the herb. Among these components, Regaloside A has been found as the characteristic component. Here, Cell Counting Kit-8 assay, and Western blotting were used to evaluate the neuroprotective antidepressant effects of Regaloside A. The results showed the cell survival rate was improved, the phosphorylation levels of brain-derived neurotrophic factor, tyrosine kinase receptor B, phosphatidylinositol 3 kinase, protein kinase B, and mammalian target of rapamycin were increased after Regaloside A treatment. In general, different drying methods have a significant influence on the chemical composition of the herb, and Regaloside A may be the main chemical component of the herb. It can alleviate the damage of corticosterone in SH-SY5Y cells, and phosphatidylinositol-3-kinase/protein kinase B/mammalian target of rapamycin signaling mediated by brain-derived neurotrophic factor/tyrosine kinase receptor B may play an important role in the neuroprotective antidepressant effects of Regaloside A.

Histone demethylase KDM3A is required for enhancer activation of hippo target genes in colorectal cancer.

Hippo pathway is involved in tumorigenesis, and its regulation in cytosol has been extensively studied, but its regulatory mechanisms in the nuclear are not clear. In the current study, using a FBS-inducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes. KDM3A promotes gene expression through two mechanisms, one is to upregulate YAP1 expression, and the other is to facilitate H3K27ac on the enhancers of hippo target genes. H3K27ac upregulation is more relevant with gene activation, but not H3K4me3; and KDM3A depletion caused H3K9me2 upregulation mainly on TEAD1-binding enhancers rather than gene bodies, further resulting in H3K27ac decrease, less TEAD1 binding on enhancers and impaired transcription. Moreover, KDM3A is associated with p300 and required for p300 recruitment to enhancers. KDM3A deficiency delayed cancer cell growth and migration, which was rescued by YAP1 expression. KDM3A expression is correlated with YAP1 and hippo target genes in colorectal cancer patient tissues, and may serve as a potential prognosis mark. Taken together, our study reveals novel mechanisms for hippo signaling and enhancer activation, which is critical for tumorigenesis of colorectal cancer.

Giant cell tumors of the mobile spine with invasion of adjacent vertebrae: an unusual imaging finding.

BACKGROUND: Giant cell tumors of the mobile spine invasion of the adjacent vertebrae are an ignored imaging finding. METHODS: Nine patients with giant cell tumors of the mobile spine with invasion of the adjacent vertebrae confirmed by pathology were enrolled. Eight patients had pure giant cell tumors (GCTs), while one patient also had an aneurysmal bone cyst. All patients underwent conventional computed tomography, three-dimensional reconstruction, and conventional magnetic resonance imaging, while seven patients also underwent post-contrast magnetic resonance imaging. RESULTS: All patients showed GCTs of the mobile spine that arose from the vertebral body and extended to the vertebral arch. The tumors showed soft-tissue attenuation with no evidence of a mineralized matrix. Pathological fracture was seen in five patients. The margin of the original tumor showed partial sclerosis in four patients and involved an adjacent vertebral body with a sclerotic rim in two patients. The tumors showed a homogeneous and similar signal intensity to the normal spinal cord on T1WI (T1-weighted image) in five patients. The cystic area of the tumors was hyperintense on T2WI in the remaining four patients, while one patient showed hemorrhage that was hyperintense on T1WI. The solid components of the GCTs show marked enhancement in all cases, while the cystic area of the tumors was observed without enhancement on contrast-enhanced images in four patients. Bone destruction of the adjacent vertebral body showed a homogeneous signal on T1WI and T2WI and marked enhancement on contrast-enhanced images. CONCLUSIONS: Giant cell tumors of the mobile spine with invasion into adjacent vertebrae are an unusual imaging finding. Radiologists should be familiar with this imaging characteristic.

Hybrid molecules with potential in vitro antiplasmodial and in vivo antimalarial activity against drug-resistant Plasmodium falciparum.

Malaria is a tropical disease, leading to around half a million deaths annually. Antimalarials such as quinolines are crucial to fight against malaria, but malaria control is extremely challenged by the limited pipeline of effective pharmaceuticals against drug-resistant strains of Plasmodium falciparum which are resistant toward almost all currently accessible antimalarials. To tackle the growing resistance, new antimalarial drugs are needed urgently. Hybrid molecules which contain two or more pharmacophores have the potential to overcome the drug resistance, and hybridization of quinoline privileged antimalarial building block with other antimalarial pharmacophores may provide novel molecules with enhanced in vitro and in vivo activity against drug-resistant (including multidrug-resistant) P falciparum. In recent years, numerous of quinoline hybrids were developed, and their activities against a panel of drug-resistant P falciparum strains were screened. Some of quinoline hybrids were found to possess promising in vitro and in vivo potency. This review emphasized quinoline hybrid molecules with potential in vitro antiplasmodial and in vivo antimalarial activity against drug-resistant P falciparum, covering articles published between 2010 and 2019.

NUDT21 suppresses the growth of small cell lung cancer by modulating GLS1 splicing.

The mRNA precursor 3'-end modification factor NUDT21 is a major regulator of 3'UTR shortening and an important component of pre-mRNA cleavage and polyadenylation. However, its role in pathologic progress of small cell lung cancer (SCLC) remains unclear. In this study, we observed that NUDT21 expression is downregulated in SCLC tissues. Hypoxia-induced down-regulation of NUDT21 through HIF-1α. NUDT21 shRNA transduction promotes proliferation and inhibits apoptosis of A549 cells. NUDT21 inhibition also promotes tumor growth in a mouse xenograft model. Furthermore, we clarified that HIF-1α mediated NUDT21 downregulation which altered the expression patterns of two isoforms of GLS1, GAC and KGA. These results link the hypoxic tumor environments to aberrant glutamine metabolism which is important for cellular energy in SCLC cells. Therefore, NUDT21 could be considered as a potential target for the treatment of SCLC.

Co-expression networks reveal the tissue-specific regulation of transcription and splicing.

Gene co-expression networks capture biologically important patterns in gene expression data, enabling functional analyses of genes, discovery of biomarkers, and interpretation of genetic variants. Most network analyses to date have been limited to assessing correlation between total gene expression levels in a single tissue or small sets of tissues. Here, we built networks that additionally capture the regulation of relative isoform abundance and splicing, along with tissue-specific connections unique to each of a diverse set of tissues. We used the Genotype-Tissue Expression (GTEx) project v6 RNA sequencing data across 50 tissues and 449 individuals. First, we developed a framework called Transcriptome-Wide Networks (TWNs) for combining total expression and relative isoform levels into a single sparse network, capturing the interplay between the regulation of splicing and transcription. We built TWNs for 16 tissues and found that hubs in these networks were strongly enriched for splicing and RNA binding genes, demonstrating their utility in unraveling regulation of splicing in the human transcriptome. Next, we used a Bayesian biclustering model that identifies network edges unique to a single tissue to reconstruct Tissue-Specific Networks (TSNs) for 26 distinct tissues and 10 groups of related tissues. Finally, we found genetic variants associated with pairs of adjacent nodes in our networks, supporting the estimated network structures and identifying 20 genetic variants with distant regulatory impact on transcription and splicing. Our networks provide an improved understanding of the complex relationships of the human transcriptome across tissues.

Genome-wide interaction with the insulin secretion locus MTNR1B reveals CMIP as a novel type 2 diabetes susceptibility gene in African Americans.

Although type 2 diabetes (T2D) results from metabolic defects in insulin secretion and insulin sensitivity, most of the genetic risk loci identified to date relates to insulin secretion. We reported that T2D loci influencing insulin sensitivity may be identified through interactions with insulin secretion loci, thereby leading to T2D. Here, we hypothesize that joint testing of variant main effects and interaction effects with an insulin secretion locus increases power to identify genetic interactions leading to T2D. We tested this hypothesis with an intronic MTNR1B SNP, rs10830963, which is associated with acute insulin response to glucose, a dynamic measure of insulin secretion. rs10830963 was tested for interaction and joint (main + interaction) effects with genome-wide data in African Americans (2,452 cases and 3,772 controls) from five cohorts. Genome-wide genotype data (Affymetrix Human Genome 6.0 array) was imputed to a 1000 Genomes Project reference panel. T2D risk was modeled using logistic regression with rs10830963 dosage, age, sex, and principal component as predictors. Joint effects were captured using the Kraft two degrees of freedom test. Genome-wide significant (P < 5 × 10-8 ) interaction with MTNR1B and joint effects were detected for CMIP intronic SNP rs17197883 (Pinteraction  = 1.43 × 10-8 ; Pjoint  = 4.70 × 10-8 ). CMIP variants have been nominally associated with T2D, fasting glucose, and adiponectin in individuals of East Asian ancestry, with high-density lipoprotein, and with waist-to-hip ratio adjusted for body mass index in Europeans. These data support the hypothesis that additional genetic factors contributing to T2D risk, including insulin sensitivity loci, can be identified through interactions with insulin secretion loci.