Radiomics Nomogram Based on Dual-Sequence MRI for Assessing Ki-67 Expression in Breast Cancer.

BACKGROUND: Radiomics has been extensively applied in predicting Ki-67 in breast cancer (BC). However, this is often confined to the exploration of a single sequence, without considering the varying sensitivity and specificity among different sequences. PURPOSE: To develop a nomogram based on dual-sequence MRI derived radiomic features combined with clinical characteristics for assessing Ki-67 expression in BC. STUDY TYPE: Retrospective. POPULATION: 227 females (average age, 51 years) with 233 lesions and pathologically confirmed BC, which were divided into the training set (n = 163) and test set (n = 70). FIELD STRENGTH/SEQUENCE: 3.0-T, T1-weighted dynamic contrast-enhanced MRI (DCE-MRI) and apparent diffusion coefficient (ADC) maps from diffusion-weighted MRI (EPI sequence). ASSESSMENT: The regions of interest were manually delineated on ADC and DCE-MRI sequences. Three radiomics models of ADC, DCE-MRI, and dsMRI (combined ADC and DCE-MRI sequences) were constructed by logistic regression and the radiomics score (Radscore) of the best model was calculated. The correlation between Ki-67 expression and clinical characteristics such as receptor status, axillary lymph node (ALN) metastasis status, ADC value, and time signal intensity curve was analyzed, and the clinical model was established. The Radscore was combined with clinical predictors to construct a nomogram. STATISTICAL TESTS: The independent sample t-test, Mann-Whitney U test, Chi-squared test, Interclass correlation coefficients (ICCs), single factor analysis, least absolute shrinkage and selection operator (LASSO), logistic regression, receiver operating characteristics, Delong test, Hosmer_Lemeshow test, calibration curve, decision curve. A P-value <0.05 was considered statistically significant. RESULTS: In the test set, the prediction efficiency of the dsMRI model (AUC = 0.862) was higher than ADC model (AUC = 0.797) and DCE-MRI model (AUC = 0.755). With the inclusion of estrogen receptor (ER) and ALN metastasis, the nomogram displayed quality improvement (AUC = 0.876), which was superior to the clinical model (AUC = 0.787) and radiomics model. DATA CONCLUSION: The nomogram based on dsMRI radiomic features and clinical characteristics may be able to assess Ki-67 expression in BC. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY: Stage 3.

Developing a CT-based radiomics nomogram for predicting post-acute pancreatitis diabetes mellitus incidence.

OBJECTIVE: The present study aimed to develop the utility of a nomogram based on clinical and radiomics as a tool for predicting post-acute pancreatitis diabetes mellitus (PPDM-A). METHODS: This retrospective investigation evaluated 244 patients with acute pancreatitis. Patients were randomized in a 7:3 ratio into training and validation cohorts. Radiomics feature selection was then achieved using the variance threshold, select best K, and least absolute shrinkage and selection operator methods. The area under the curve values, decision, and calibration curves have been used to determine the models' predictive value. RESULTS: The developed nomogram performed superior to the clinical model in the validation (0.815 vs 0.677, p = 0.016) and training cohorts (0.803 vs 0.683, p = 0.002). The calibration curves demonstrated that the expected and actual values were satisfactory. In contrast, decision curve analysis revealed a stronger relationship between the nomogram and net clinical value than with the distinct radiomics or clinical signature effects. CONCLUSION: In summary, the findings of this study demonstrated that establishing a predictive nomogram as a non-invasive technique may be useful in predicting the risk of PPDM-A. ADVANCES IN KNOWLEDGE: This is the first time to use a CT radiomics nomogram to predict PPDM-A. The nomogram is conducive to the personalized prediction of patients. It only needs to input the patient's information, and a simple addition operation can quantitatively obtain its risk. The resultant tool has the potential to provide new opportunities to treat or prevent PPDM-A more effectively.

Efficient synthesis of γ-glutamyl compounds by co-expression of γ-glutamylmethylamide synthetase and polyphosphate kinase in engineered Escherichia coli.

γ-Glutamyl compounds have unveiled their importance as active substances or precursors of pharmaceuticals. In this research, an approach for enzymatic synthesis of γ-glutamyl compounds was developed using γ-glutamylmethylamide synthetase (GMAS) from Methylovorus mays and polyphosphate kinase (PPK) from Corynebacterium glutamicum. GMAS and PPK were co-recombined in pETDuet-1 plasmid and co-expressed in E. coli BL21 (DE3), and the enzymatic properties of GMAS and PPK were investigated, respectively. Under the catalysis of the co-expression system, L-theanine was synthesized with 89.8% conversion when the substrate molar ratio of sodium glutamate and ethylamine (1:1.4) and only 2 mM ATP were used. A total of 14 γ-glutamyl compounds were synthesized by this one-pot method and purified by cation exchange resin and isoelectric point crystallization with a yield range from 22.3 to 72.7%. This study provided an efficient approach for the synthesis of γ-glutamyl compounds by GMAS and PPK co-expression system.

An Infectious Disease-Associated Il12b Polymorphism Regulates IL-12/23 p40 Transcription Involving Poly(ADP-Ribose) Polymerase 1.

IL-12 and IL-23 are important host defense factors produced by APCs against certain intracellular and extracellular pathogens. Their dysregulation has also been implicated in several autoimmune diseases. The nucleotide polymorphism in the promoter region of Il12b (rs41292470 consisting of the long or short allele) encoding the shared subunit of IL-12 and IL-23, p40, has been reported to associate with susceptibility to infectious diseases and autoimmune disorders. How these genetic variants impact Il12b expression at the molecular level was unclear. We established an Il12b promoter-luciferase reporter system containing the long or short allele driving the reporter gene expression and found that the long allele (infection-resistant) displayed ∼2-fold higher transcriptional activity than the short allele (infection-susceptible), associated with a selective and differential nuclear binding activity to the two alleles in activated macrophages. DNA pull-down assays coupled with mass spectrometry analyses identified the specific DNA binding activity as poly(ADP-ribose) polymerase 1 (PARP-1). Small hairpin RNA-mediated knockdown of the endogenous PARP-1 expression resulted in reduced p40 mRNA expression and Il12b promoter activity. Bone marrow-derived macrophages from PARP-1-deficient mice had decreased p40 expression at both mRNA and protein levels. Furthermore, selective PARP-1 inhibitors resulted in impaired production of IL-12p40 and IL-23 in bone-marrow derived macrophages and PBMCs. Chromatin immunoprecipitation assay revealed that PARP-1 could bind specifically to Il12b in LPS-stimulated macrophages. Our study opens the way for further elucidating the molecular mechanism whereby allele-specific immune responses to foreign and self-antigens mediated by IL-12/IL-23 are controlled in an individually variable manner.

Mycobacterium Lysine ε-aminotransferase is a novel alarmone metabolism related persister gene via dysregulating the intracellular amino acid level.

Bacterial persisters, usually slow-growing, non-replicating cells highly tolerant to antibiotics, play a crucial role contributing to the recalcitrance of chronic infections and treatment failure. Understanding the molecular mechanism of persister cells formation and maintenance would obviously inspire the discovery of new antibiotics. The significant upregulation of Mycobacterium tuberculosis Rv3290c, a highly conserved mycobacterial lysine ε-aminotransferase (LAT) during hypoxia persistent model, suggested a role of LAT in persistence. To test this, a lat deleted Mycobacterium smegmatis was constructed. The expression of transcriptional regulator leucine-responsive regulatory protein (LrpA) and the amino acids abundance in M. smegmatis lat deletion mutants were lowered. Thus, the persistence capacity of the deletion mutant was impaired upon norfloxacin exposure under nutrient starvation. In summary, our study firstly reported the involvement of mycobacterium LAT in persister formation, and possibly through altering the intracellular amino acid metabolism balance.

Regulation of IL-10 and IL-12 production and function in macrophages and dendritic cells.

Interleukin-10 and Interleukin-12 are produced primarily by pathogen-activated antigen-presenting cells, particularly macrophages and dendritic cells. IL-10 and IL-12 play very important immunoregulatory roles in host defense and immune homeostasis. Being anti- and pro-inflammatory in nature, respectively, their functions are antagonistically opposing. A comprehensive and in-depth understanding of their immunological properties and signaling mechanisms will help develop better clinical intervention strategies in therapy for a wide range of human disorders. Here, we provide an update on some emerging concepts, controversies, unanswered questions, and opinions regarding the immune signaling of IL-10 and IL-12.

Involvement of Holliday junction resolvase in fluoroquinolone-mediated killing of Mycobacterium smegmatis.

The absence of the Holliday-junction Ruv resolvase of Mycobacterium smegmatis increased the bacteriostatic and bactericidal activities of the fluoroquinolone moxifloxacin, an important antituberculosis agent. The treatment of ruvAB-deficient cells with thiourea and 2,2'-bipyridyl lowered moxifloxacin lethality to wild-type levels, indicating that the absence of ruvAB stimulates a lethal pathway involving reactive oxygen species. A hexapeptide that traps the Holliday junction substrate of RuvAB potentiated moxifloxacin-mediated lethality, supporting the development of small-molecule enhancers for moxifloxacin activity against mycobacteria.

Characterization of a novel mutation in the overlap of tlyA and ppnK involved in capreomycin resistance in Mycobacterium.

Capreomycin (CAP) is an important second-line drug for multidrug-resistant tuberculosis. To further define the drug resistance mechanism of CAP, a Mycobacterium smegmatis transposon mutant library was constructed using Tn5 transposon for screening isolates with enhanced CAP resistance. A mutant (named C4) with fourfold increased CAP resistance was isolated and characterized. Tn5 was found to be inserted into MSMEG_0841, an annotated pseudogene. However, knockout demonstrated that MSMEG_0841 was not responsible for CAP resistance. We further sequenced the whole genome of C4 and found an A to G substitution in the overlap region between tlyA and ppnK, which leads a stop codon mutation in upstream tlyA and a T2A mutation in downstream ppnK. Mutation in the overlap might confer the dysfuction of both genes. tlyA is a known gene involved in CAP action. Overexpression of ppnK in both Escherichia coli and M. smegmatis confer subtle susceptible to CAP. Taken together, our study found that a novel mutation involved in CAP resistance.

Characterization of a tuberculosis patient's sera reactive Mycobacterium tuberculosis transcription factor Rv2175c.

The transcriptional factor plays an important role in the regulation of gene expression and crucial to understand the biology of organisms. Mycobacterium tuberculosis, the causative agent of tuberculosis, harbors multiple transcriptional factors. Few transcriptional factors are well-documented antigens. Based on the screening of antigen with TB patients sera, a functional unknown ORF (Rv2175c) annotated as transcriptional factor was heterologously expressed, purified and for serodiagnostic value. E.coli recombinant Rv2175c protein was produced and antibodies were generated in rabbit using the recombinant antigens. ELISA and novel electrochemical immunosensor were employed in a parallel fashion in order to define its serodiagnositic value. Electrochemical immunosensor showed a sharp difference between health and TB sera. The data showed that Rv2715c is antigenic and can be used for TB seradignosis candidate in non BCG vaccinated areas.

Mycobacterium tuberculosis rrs A1401G mutation correlates with high-level resistance to kanamycin, amikacin, and capreomycin in clinical isolates from mainland China.

Mutations correlating phenotypic resistance level with the injectable second-line anti-tuberculosis drugs (SLDs) including kanamycin (KAN), amikacin (AMK), and capreomycin (CAP) remain elusive. A collection of 114 Mycobacterium tuberculosis clinical isolates from mainland China was analyzed. The minimum inhibitory concentration (MIC) of each strain was determined and the sequences of rrs, tlyA, promoter of eis as well as 5' untranslated region (UTR) of whiB7 were amplified and sequenced. No mutation in tlyA, promoter of eis and 5' UTR of whiB7, was found to be associated with resistance among these samples. Sequencing data of 1400 rrs region demonstrated the A1401G mutation in rrs was prevalent, which presented in 84% of the KAN resistant isolates while only in about 50% of the AMK or CAP resistant isolates. Furthermore, most of the resistant isolates with A1401G mutation showed high-level resistance to these injectable SLDs. In conclusion, our results suggest the rrs A1401G mutation was related to high-level resistance to KAN, AMK, and CAP in M. tuberculosis isolates from mainland China.

gyrA/B fluoroquinolone resistance allele profiles amongst Mycobacterium tuberculosis isolates from mainland China.

Fluoroquinolones are important second-line drugs for the treatment of tuberculosis. A comprehensive profile of resistance mutation patterns of DNA gyrase, the major target of fluoroquinolones, is crucial for molecular diagnosis of drug resistance and improvement of treatment efficacy. To investigate the mutation types of the genes encoding the A and B subunits of DNA gyrase (gyrA and gyrB, respectively) in ofloxacin- and levofloxacin-resistant Mycobacterium tuberculosis strains prevalent in mainland China, 177 clinical drug-resistant isolates collected by the National Tuberculosis Reference Laboratory of China were analysed. The GyrB single mutations (Glu498 and Gly551) and double mutation (Thr539Asn-Gly551Arg) as well as a GyrA double mutation (Asp94Asn-Gly112His) were reported to be involved in fluoroquinolone resistance for the first time. To simplify quantification of the contribution of each mutation type and mutation site to overall fluoroquinolone resistance, a mathematical method was established by assigning each resistance allele a numerical score between 5 and 50 (the larger the number, the higher the resistance level). The score of double mutants is the sum of the scores for the two single alleles. The double mutation types, including Asn538Ile(GyrB)-Asp94Ala(GyrA), Ala543Val(GyrB)-Asp94Asn(GyrA) and Ala543Val(GyrB)-Asp94Gly(GyrA) scored relatively high by this methodology.

The biology of Mycobacterium cord factor and roles in pathogen-host interaction.

Mycobacterium cord factor was long held as a virulence factor contributing to the pathogenesis of Mycobacterium tuberculosis. Abundant studies have shed light on its unique chemical structures, metabolism, and receptors on macrophages. The mechanisms underlying cord factor virulence remain elusive. This progress is summarized in this paper, especially the receptors of cord factor, such as Toll-like receptors and Mincle. This might facilitate better use of cord factor as an adjuvant for tuberculosis therapy or selection of drug targets involved in its biosynthesis to combat tuberculosis.

Thiamin (vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets?

Drug resistance of pathogens has necessitated the identification of novel targets for antibiotics. Thiamin (vitamin B1) is an essential cofactor for all organisms in its active form thiamin diphosphate (ThDP). Therefore, its metabolic pathways might be one largely untapped source of antibiotics targets. This review describes bacterial thiamin biosynthetic, salvage, and transport pathways. Essential thiamin synthetic enzymes such as Dxs and ThiE are proposed as promising drug targets. The regulation mechanism of thiamin biosynthesis by ThDP riboswitch is also discussed. As drug targets of existing antimicrobial compound pyrithiamin, the ThDP riboswitch might serves as alternative targets for more antibiotics.