Phylogenetic inference of inter-population transmission rates for infectious diseases.

Estimating transmission rates is a challenging yet essential aspect of comprehending and controlling the spread of infectious diseases. Various methods exist for estimating transmission rates, each with distinct assumptions, data needs, and constraints. This study introduces a novel phylogenetic approach called transRate, which integrates genetic information with traditional epidemiological approaches to estimate inter-population transmission rates. The phylogenetic method is statistically consistent as the sample size (i.e. the number of pathogen genomes) approaches infinity under the multi-population susceptible-infected-recovered model. Simulation analyses indicate that transRate can accurately estimate the transmission rate with a sample size of 200 ~ 400 pathogen genomes. Using transRate, we analyzed 40,028 high-quality sequences of SARS-CoV-2 in human hosts during the early pandemic. Our analysis uncovered significant transmission between populations even before widespread travel restrictions were implemented. The development of transRate provides valuable insights for scientists and public health officials to enhance their understanding of the pandemic's progression and aiding in preparedness for future viral outbreaks. As public databases for genomic sequences continue to expand, transRate is increasingly vital for tracking and mitigating the spread of infectious diseases.

A developmental validation of the Quick TargSeq 1.0 integrated system for automated DNA genotyping in forensic science for reference samples.

Analysis of short tandem repeats (STRs) is a global standard method for human identification. Insertion/Deletion polymorphisms (DIPs) can be used for biogeographical ancestry inference. Current DNA typing involves a trained forensic worker operating several specialized instruments in a controlled laboratory environment, which takes 6-8 h. We developed the Quick TargSeq 1.0 integrated system (hereinafter abbreviated to Quick TargSeq) for automated generation of STR and DIP profiles from buccal swab samples and blood stains. The system fully integrates the processes of DNA extraction, polymerase chain reaction (PCR) amplification, and electrophoresis separation using microfluidic biochip technology. Internal validation studies were performed using RTyper 21 or DIP 38 chip cartridges with single-source reference samples according to the Scientific Working Group for DNA Analysis Methods guidelines. These results indicated that the Quick TargSeq system can process reference samples and generate STR or DIP profiles in approximately 2 h, and the profiles were concordant with those determined using traditional STR or DIP analysis methods. Thus, reproducible and concordant DNA profiles were obtained from reference samples. Throughout the study, no lane-to-lane or run-to-run contamination was observed. The Quick TargSeq system produced full profiles from buccal swabs with at least eight swipes, dried blood spot cards with two 2-mm disks, or 10 ng of purified DNA. Potential PCR inhibitors (i.e., coffee, smoking tobacco, and chewing tobacco) did not appear to affect the amplification reactions of the instrument. The overall success rate and concordance rate of 153 samples were 94.12% and 93.44%, respectively, which is comparable to other commercially available rapid DNA instruments. A blind test initiated by a DNA expert group showed that the system can correctly produce DNA profiles with 97.29% genotype concordance with standard bench-processing methods, and the profiles can be uploaded into the national DNA database. These results demonstrated that the Quick TargSeq system can rapidly generate reliable DNA profiles in an automated manner and has the potential for use in the field and forensic laboratories.

Testing of two SNP array-based genealogy algorithms using extended Han Chinese pedigrees and recommendations for improved performances in forensic practice.

Distant genetic relatives can be linked to a crime scene sample by computing identity-by-state (IBS) and identity-by-descent (IBD) shared by individuals. To test the methods of genetic genealogy estimation and optimal the parameters for forensic investigation, a family-based genetic genealogy analysis was performed using a dataset of 262 Han Chinese individuals from 11 families. The dataset covered relative pairs from 1st- to 14th degrees. But the 7th-degree relative is the most distant kinship to be fully investigated, and each individual has ∼200 relatives within the 7th degree. The KING algorithm by calculating IBS and IBD statistics can correctly discriminate the first-degree relationships of monozygotic twin, parent-offspring and full sibling. The inferred relationship was reliable within the fifth-degree, false positive rate <1.8%. The IBD segment algorithm, GERMLINE + ERSA, could provide reliable inference result prolonged to eighth degree. Analysis of IBD segments produced obviously false negative estimations (<27.4%) rather than false positives (0%) within the eighth-degree inferences. We studied different minimum IBD segment threshold settings (changed from >0 to 6 cM); the inferred results did not make much difference. In distant relative analysis, genetically undetectable relationships begin to occur from the sixth degree (second cousin once removed), which means the offspring after seven meiotic divisions may share no ancestor IBD segment at all. Application of KING and GERMLINE + ERSA worked complementarily to ensure accurate inference from first degree to eighth degree. Using simulated low call rate data, the KING algorithm shows better tolerance to marker decrease compared with the GERMLINE + ERSA segment algorithm.

Machine learning-enhanced echocardiography for screening coronary artery disease.

BACKGROUND: Since myocardial work (MW) and left atrial strain are valuable for screening coronary artery disease (CAD), this study aimed to develop a novel CAD screening approach based on machine learning-enhanced echocardiography. METHODS: This prospective study used data from patients undergoing coronary angiography, in which the novel echocardiography features were extracted by a machine learning algorithm. A total of 818 patients were enrolled and randomly divided into training (80%) and testing (20%) groups. An additional 115 patients were also enrolled in the validation group. RESULTS: The superior diagnosis model of CAD was optimized using 59 echocardiographic features in a gradient-boosting classifier. This model showed that the value of the receiver operating characteristic area under the curve (AUC) was 0.852 in the test group and 0.834 in the validation group, with high sensitivity (0.952) and low specificity (0.691), suggesting that this model is very sensitive for detecting CAD, but its low specificity may increase the high false-positive rate. We also determined that the false-positive cases were more susceptible to suffering cardiac events than the true-negative cases. CONCLUSIONS: Machine learning-enhanced echocardiography can improve CAD detection based on the MW and left atrial strain features. Our developed model is valuable for estimating the pre-test probability of CAD and screening CAD patients in clinical practice. TRIAL REGISTRATION: Registered as NCT03905200 at ClinicalTrials.gov. Registered on 5 April 2019.

In situ embedding of glucose oxidase in amorphous ZIF-7 with high catalytic activity and stability and mechanism investigation.

Glucose oxidase (GOx) has a great application potential in the determination of glucose concentration. However, its sensitivity to the environment and poor recyclability limited its broader application. Herein, with the assistance of DA-PEG-DA, a novel immobilized GOx based on amorphous Zn-MOFs (DA-PEG-DA/GOx@aZIF-7/PDA) was developed to impart excellent properties to the enzyme. SEM, TEM, XRD, and BET analyses confirmed that GOx was embedded in amorphous ZIF-7 with ∼5 wt% loading. Compared with free GOx, DA-PEG-DA/GOx@aZIF-7/PDA exhibited enhanced stability, excellent reusability, and promising potential for glucose detection. After 10 repetitions, the catalytic activity of DA-PEG-DA/GOx@aZIF-7/PDA can maintain 95.53 % ± 3.16 %. In understanding the in situ embedding of GOx in ZIF-7, the interaction of zinc ion and benzimidazole with GOx was studied by using molecular docking and multi-spectral methods. Results showed that zinc ions and benzimidazole had multiple binding sites on the enzyme, which induced the accelerated synthesis of ZIF-7 around the enzyme. During binding, the structure of the enzyme changes, but such changes hardly affect the activity of the enzyme. This study provides not only a preparation strategy of immobilized enzyme with high activity, high stability, and low enzyme leakage rate for glucose detection, but also a more comprehensive understanding of the formation of immobilized enzymes using the in situ embedding strategy.

Optimization scheme of machine learning model for genetic division between northern Han, southern Han, Korean and Japanese.

Han Chinese, Korean and Japanese are the main populations of East Asia, and Han Chinese presents a gradient admixture from north to south. There are differences among the East Asian populations in genetic structure. To achieve fine-scale genetic classification of southern (S-) and northern (N-) Han Chinese, Korean and Japanese individuals in this study, we collected and analyzed 1185 ancestry informative SNPs (AISNPs) from previous literature reports and our laboratory findings. First, two machine learning algorithms, softmax and randomForest, were used to build genetic classification models. Then, phylogenetic tree, STRUCTURE and principal component analysis were used to evaluate the performance of classification for different AISNP panels. The 234-AISNP panel achieved a fine-scale differentiation among the target populations in four classification schemes. The accuracy of the softmax model was 92%, which realized the accurate classification of the S-Han, N-Han, Korean and Japanese individuals. The two machine learning models tested in this study provided important references for the high-resolution discrimination of close-range populations and will be useful tools to optimize marker panels for developing forensic DNA ancestry inference systems.

Forecasting Slope Displacement of the Agricultural Mountainous Area Based on the ACO-SVM Model.

Due to the combined influence of complex engineering geological conditions and environmental factors from agricultural mountainous areas, the evolution of slope deformation is complicated and nonlinear. Support vector machine (SVM) technology could effectively solve the technical problems of small sample, high dimension, and nonlinear, so it is applied to data mining of the measured slope displacement and the prediction and analysis of the slope deformation trend. In order to avoid blindness of human choice of SVM parameters and to improve the prediction accuracy and generalization ability of the model, an ACO-SVM model is built by adopting an improved ant colony algorithm (ACO) to optimize parameters in association with the rolling forecasting method of displacement time series. The model was applied to two engineering examples. The research results showed that the ACO-SVM model was correct with high accuracy. The ACO-SVM model had higher accuracy of prediction and stronger generalization ability than optimizing SVM based on the genetic algorithm or particle swarm optimization. The forecasting results were more reasonable. It has certain engineering application values for slope deformation prediction.

Endogenous DOPA inhibits melanoma through suppression of CHRM1 signaling.

Melanoma risk is 30 times higher in people with lightly pigmented skin versus darkly pigmented skin. Using primary human melanocytes representing the full human skin pigment continuum and preclinical melanoma models, we show that cell-intrinsic differences between dark and light melanocytes regulate melanocyte proliferative capacity and susceptibility to malignant transformation, independent of melanin and ultraviolet exposure. These differences result from dihydroxyphenylalanine (DOPA), a melanin precursor synthesized at higher levels in melanocytes from darkly pigmented skin. We used both high-throughput pharmacologic and genetic in vivo CRISPR screens to determine that DOPA limits melanocyte and melanoma cell proliferation by inhibiting the muscarinic acetylcholine receptor M1 (CHRM1) signaling. Pharmacologic CHRM1 antagonism in melanoma leads to depletion of c-Myc and FOXM1, both of which are proliferation drivers associated with aggressive melanoma. In preclinical mouse melanoma models, pharmacologic inhibition of CHRM1 or FOXM1 inhibited tumor growth. CHRM1 and FOXM1 may be new therapeutic targets for melanoma.

Interleukin-17D promotes lung cancer progression by inducing tumor-associated macrophage infiltration via the p38 MAPK signaling pathway.

Cancer immunoediting is defined as the integration of the immune system's dual host-protective and tumor-promoting roles, including three phases: elimination, equilibrium, and escape. Immune selective pressure causes tumor cells to lose major histocompatibility complex expression or acquire immunosuppressive gene expression, which promotes tumor immune evasion and tumor progression. Interleukin-17D (IL-17D), a member of the IL-17 family of cytokines, plays an important role in the host defense against infection and inflammation. However, the role of IL-17D in the progression of lung cancer remains unclear. In this study, we found that IL-17D was highly expressed in human lung cancer, and increased IL-17D expression was associated with tumor stage and short overall survival. IL-17D overexpression significantly promoted tumor growth in subcutaneous xenograft mouse models but only slightly affected cell proliferation in vitro. Using flow cytometry, we found that IL-17D overexpression enhances the recruitment of tumor-associated macrophages to the tumor microenvironment. Based on the expression profile of IL17D-overexpressing A549 cells, we found that IL-17D increased the expression levels of macrophage polarization- and recruitment-related genes through the MAPK signaling pathway. Moreover, inhibition of the p38 pathway blocked macrophage infiltration induced by IL-17D. These results suggest that IL-17D regulates the tumor immune microenvironment via the p38 MAPK signaling pathway, highlighting IL-17D as a potential therapeutic target for lung cancer.

Comparative Analysis of Salt Responsive MicroRNAs in Two Sweetpotato [Ipomoea batatas (L.) Lam.] Cultivars With Different Salt Stress Resistance.

Sweetpotato [Ipomoea batatas (L.) Lam.] is an important food, vegetable and economic crop, but its productivity is remarkably affected by soil salinity. MiRNAs are a class of endogenous non-coding small RNAs that play an important role in plant resistance to salt stress. However, the function of miRNAs still remains largely unknown in sweetpotato under salt stress. Previously, we identified salt-responsive miRNAs in one salt-sensitive sweetpotato cultivar "Xushu 32." In this study, we identified miRNAs in another salt-tolerant cultivar "Xushu 22" by high-throughput deep sequencing and compared the salt-responsive miRNAs between these two cultivars with different salt sensitivity. We identified 687 miRNAs in "Xushu 22," including 514 known miRNAs and 173 novel miRNAs. Among the 759 miRNAs from the two cultivars, 72 and 109 miRNAs were specifically expressed in "Xushu 32" and "Xushu 22," respectively, and 578 miRNAs were co-expressed. The comparison of "Xushu 32" and "Xushu 22" genotypes showed a total of 235 miRNAs with obvious differential expression and 177 salt-responsive miRNAs that were obviously differently expressed between "Xushu 32" and "Xushu 22" under salt stress. The target genes of the miRNAs were predicted and identified using the Target Finder tool and degradome sequencing. The results showed that most of the targets were transcription factors and proteins related to metabolism and stress response. Gene Ontology analysis revealed that these target genes are involved in key pathways related to salt stress response and secondary redox metabolism. The comparative analysis of salt-responsive miRNAs in sweetpotato cultivars with different salt sensitivity is helpful for understanding the regulatory pattern of miRNA in different sweetpotato genotypes and improving the agronomic traits of sweetpotato by miRNA manipulation in the future.

A high-performance SNP panel developed by machine-learning approaches for characterizing genetic differences of Southern and Northern Han Chinese, Korean, and Japanese individuals.

Population stratification analyses targeting genetically closely related East Asians have revealed that distinguishable differentiation exists between Han Chinese, Korean, and Japanese individuals, as well as between southern (S-) and northern (N-) Han Chinese. Previous studies offer a number of choices for ancestry informative single nucleotide polymorphisms (AISNPs) to discriminate East-Asian populations. In this study, we collected and examined the efficiency of 1185 AISNPs using frequency and genotype data from various publicly available databases. With the aim to perform fine-scale classification of S-Han, N-Han, Korean, and Japanese subjects, machine-learning methods (Softmax and Random Forest) were used to screen a panel of highly informative AISNPs and to develop a superior classification model. Stepwise classification was implemented to increase and balance the discrimination in the process of AISNP selection, first discriminating Han, Korean, and Japanese individuals, and then characterizing stratification between S-Han and N-Han. The final 272-AISNP panel is an alternative optimization of various previous works, which promises reliable and >90% accuracy in classification of the four East-Asian groups. This AISNP panel and the machine-learning model could be a useful and superior choice in medical genome-wide association studies and in forensic investigations for unknown suspect identity.

SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia.

Acute myeloid leukemia (AML) cells rely on phospho-signaling pathways to gain unlimited proliferation potential. Here, we use domain-focused CRISPR screening and identify the nuclear phosphatase SCP4 as a dependency in AML, yet this enzyme is dispensable in normal hematopoietic progenitor cells. Using CRISPR exon scanning and gene complementation assays, we show that the catalytic function of SCP4 is essential in AML. Through mass spectrometry analysis of affinity-purified complexes, we identify the kinase paralogs STK35 and PDIK1L as binding partners and substrates of the SCP4 phosphatase domain. We show that STK35 and PDIK1L function catalytically and redundantly in the same pathway as SCP4 to maintain AML proliferation and to support amino acid biosynthesis and transport. We provide evidence that SCP4 regulates STK35/PDIK1L through two distinct mechanisms: catalytic removal of inhibitory phosphorylation and by promoting kinase stability. Our findings reveal a phosphatase-kinase signaling complex that supports the pathogenesis of AML.

SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia.

An enhanced requirement for nutrients is a hallmark property of cancer cells. Here, we optimized an in vivo genetic screening strategy in acute myeloid leukemia (AML), which led to the identification of the myo-inositol transporter SLC5A3 as a dependency in this disease. We demonstrate that SLC5A3 is essential to support a myo-inositol auxotrophy in AML. The commonality among SLC5A3-dependent AML lines is the transcriptional silencing of ISYNA1, which encodes the rate-limiting enzyme for myo-inositol biosynthesis, inositol-3-phosphate synthase 1. We use gain- and loss-of-function experiments to reveal a synthetic lethal genetic interaction between ISYNA1 and SLC5A3 in AML, which function redundantly to sustain intracellular myo-inositol. Transcriptional silencing and DNA hypermethylation of ISYNA1 occur in a recurrent manner in human AML patient samples, in association with IDH1/IDH2 and CEBPA mutations. Our findings reveal myo-inositol as a nutrient dependency in AML caused by the aberrant silencing of a biosynthetic enzyme. SIGNIFICANCE: We show how epigenetic silencing can provoke a nutrient dependency in AML by exploiting a synthetic lethality relationship between biosynthesis and transport of myo-inositol. Blocking the function of this solute carrier may have therapeutic potential in an epigenetically defined subset of AML.This article is highlighted in the In This Issue feature, p. 275.

Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops.

Salinity, as a major environmental stressor, limits plant growth, development, and crop yield remarkably. However, plants evolve their own defense systems in response to salt stress. Recently, microRNA (miRNA) has been broadly studied and considered to be an important regulator of the plant salt-stress response at the post-transcription level. In this review, we have summarized the recent research progress on the identification, functional characterization, and regulatory mechanism of miRNA involved in salt stress, have discussed the emerging manipulation of miRNA to improve crop salt resistance, and have provided future direction for plant miRNA study under salt stress, suggesting that the salinity resistance of crops could be improved by the manipulation of microRNA.

Transcriptional Silencing of ALDH2 Confers a Dependency on Fanconi Anemia Proteins in Acute Myeloid Leukemia.

Hundreds of genes become aberrantly silenced in acute myeloid leukemia (AML), with most of these epigenetic changes being of unknown functional consequence. Here, we demonstrate how gene silencing can lead to an acquired dependency on the DNA repair machinery in AML. We make this observation by profiling the essentiality of the ubiquitination machinery in cancer cell lines using domain-focused CRISPR screening, which revealed Fanconi anemia (FA) proteins UBE2T and FANCL as unique dependencies in AML. We demonstrate that these dependencies are due to a synthetic lethal interaction between FA proteins and aldehyde dehydrogenase 2 (ALDH2), which function in parallel pathways to counteract the genotoxicity of endogenous aldehydes. We show DNA hypermethylation and silencing of ALDH2 occur in a recurrent manner in human AML, which is sufficient to confer FA pathway dependency. Our study suggests that targeting of the ubiquitination reaction catalyzed by FA proteins can eliminate ALDH2-deficient AML. SIGNIFICANCE: Aberrant gene silencing is an epigenetic hallmark of human cancer, but the functional consequences of this process are largely unknown. In this study, we show how an epigenetic alteration leads to an actionable dependency on a DNA repair pathway through the disabling of genetic redundancy.This article is highlighted in the In This Issue feature, p. 2113.

Long-term treatment effect of a modified jailed-balloon technique for de Winter syndrome: a case report.

Timely recognition of the characteristic electrocardiographic pattern of de Winter syndrome is important for providing immediate reperfusion therapy for acute anterior myocardial infarction. In this case, an electrocardiogram showed 1- to 3-mm upsloping ST-segment depression at the J point in leads V1 to V6, with loss of R wave progression in leads V1 to V4. Urgent angiography showed occlusion of the proximal left anterior descending coronary artery and 70% stenosis in the ostial first diagonal branch (Medina type 1.1.1.). For this bifurcation lesion, we successfully performed a modified jailed-balloon technique to protect the side branch during percutaneous coronary intervention stenting. Thereafter, thrombolysis in myocardial infarction 3 flow was restored in both branches. This modified jailed-balloon technique is safe and effective in stent placement for de Winter syndrome without any loss of side branches.

Salt-inducible kinase inhibition suppresses acute myeloid leukemia progression in vivo.

Lineage-defining transcription factors (TFs) are compelling targets for leukemia therapy, yet they are among the most challenging proteins to modulate directly with small molecules. We previously used CRISPR screening to identify a salt-inducible kinase 3 (SIK3) requirement for the growth of acute myeloid leukemia (AML) cell lines that overexpress the lineage TF myocyte enhancer factor (MEF2C). In this context, SIK3 maintains MEF2C function by directly phosphorylating histone deacetylase 4 (HDAC4), a repressive cofactor of MEF2C. In this study, we evaluated whether inhibition of SIK3 with the tool compound YKL-05-099 can suppress MEF2C function and attenuate disease progression in animal models of AML. Genetic targeting of SIK3 or MEF2C selectively suppressed the growth of transformed hematopoietic cells under in vitro and in vivo conditions. Similar phenotypes were obtained when cells were exposed to YKL-05-099, which caused cell-cycle arrest and apoptosis in MEF2C-expressing AML cell lines. An epigenomic analysis revealed that YKL-05-099 rapidly suppressed MEF2C function by altering the phosphorylation state and nuclear localization of HDAC4. Using a gatekeeper allele of SIK3, we found that the antiproliferative effects of YKL-05-099 occurred through on-target inhibition of SIK3 kinase activity. Based on these findings, we treated 2 different mouse models of MLL-AF9 AML with YKL-05-099, which attenuated disease progression in vivo and extended animal survival at well-tolerated doses. These findings validate SIK3 as a therapeutic target in MEF2C-addicted AML and provide a rationale for developing druglike inhibitors of SIK3 for definitive preclinical investigation and for studies in human patients.