Pharmacotranscriptomic profiles, which capture drug-induced changes in gene expression, offer vast potential for computational drug discovery and are widely used in modern medicine. However, current computational approaches neglected the associations within gene‒gene functional networks and unrevealed the systematic relationship between drug efficacy and the reversal effect. Here, we developed a new genome-scale functional module (GSFM) transformation framework to quantitatively evaluate drug efficacy for in silico drug discovery. GSFM employs four biologically interpretable quantifiers: GSFM_Up, GSFM_Down, GSFM_ssGSEA, and GSFM_TF to comprehensively evaluate the multi-dimension activities of each functional module (FM) at gene-level, pathway-level, and transcriptional regulatory network-level. Through a data transformation strategy, GSFM effectively converts noisy and potentially unreliable gene expression data into a more dependable FM active matrix, significantly outperforming other methods in terms of both robustness and accuracy. Besides, we found a positive correlation between RS_GSFM and drug efficacy, suggesting that RS_GSFM could serve as representative measure of drug efficacy. Furthermore, we identified WYE-354, perhexiline, and NTNCB as candidate therapeutic agents for the treatment of breast-invasive carcinoma, lung adenocarcinoma, and castration-resistant prostate cancer, respectively. The results from in vitro and in vivo experiments have validated that all identified compounds exhibit potent anti-tumor effects, providing proof-of-concept for our computational approach.

Objective:To investigate the clinical characteristics and prognosis of fetuses with HNF1B gene variants. Methods:Fifty-two fetuses with HNF1B gene variants diagnosed by chromosomal copy number variation sequencing and/or whole exome sequencing at the First Affiliated Hospital of Zhengzhou University from January 2018 to June 2024 were retrospectively enrolled in this study, including 47 cases of 17q12 microdeletion and five cases of HNF1B point mutations. Prenatal ultrasound features, pregnancy outcomes, and postnatal manifestations were summarized and analyzed using descriptive statistics. Results:The prenatal ultrasound features of the 52 fetuses included enhanced renal parenchymal echo in 43 cases (82.7%), renal cysts in 15 cases (28.8%), enlarged kidney volume in 14 cases (26.9%), and pyelectasis in 13 cases (25.0%). Parental verification was completed for 35 cases, with 71.4% (25/35) being de novo mutations and 28.6% (10/35) inherited from either parent. Apart from eight cases with unknown pregnancy outcome (six cases were lost to follow-up, two cases refused to be followed up), the other 44 cases were successfully followed up, among which 68.2% (30/44) terminated the pregnancies and 31.8% (14/44) continued, resulting in live births. Prenatal ultrasound indicated renal abnormalities in all 14 live births, while postnatal follow-up showed seven cases with normal kidneys, one with reduced bilateral renal cysts, one with alleviated bilateral pyelectasis, four with unimproved renal structural abnormalities, and one who did not undergo a re-examination. Conclusion:The rate of renal abnormalities diagnosed by prenatal ultrasound in fetuses with HNF1B gene variants is high, and most of the pregnancies are terminated, although the renal sturctural abnormalities may improve after birth.

Objective:To investigate the clinical characteristics and genetic etiology of fetal Dandy-Walker spectrum (DWS) anomalies.Methods:This retrospective cohort study analyzed 28 fetuses with ultrasonographically confirmed DWS (ten classic Dandy-Walker malformations and 18 Dandy-Walker variants) at the First Affiliated Hospital, Zhengzhou University from January 2019 to June 2024. All cases underwent systematic ultrasonographic evaluation. Genetic analyses included chromosomal karyotyping alone ( n=4) or combined with copy number variation sequencing (CNV-seq) ( n=10). Descriptive statistics and Chi-square tests (or Fisher's exact test) with Bonferroni correction were applied. Results:(1) Among 28 fetuses, seven (25.0%) had isolated DWS and 21 (75.0%) non-isolated DWS. Central nervous system anomalies were most common (53.6%, 15/28). (2) Karyotyping identified abnormalities in four cases (4/14), including two triploidies, one case of mosaicism for a derivative chromosome der(1;10), and one 17p deletion. CNV-seq detected anomalies in six cases (25.0%, 6/24), four of which were missed by karyotyping: 3q23 deletion (encompassing ZIC1/ ZIC4), 13q11 duplication, and other critical variants. (3) Combined testing yielded a higher detection rate (28.6%, 8/28) than karyotyping alone (4/14, χ2=4.62, P=0.032) or CNV-seq alone (25.0%, 6/24, χ2=4.83, P=0.028) ( P=0.048 and 0.044 after Bonferroni correction). Conclusions:DWS demonstrates significant genetic heterogeneity, primarily involving chromosomal numerical anomalies (e.g., triploidy) and copy number variations (e.g., 3q23 deletion). Combined karyotyping and CNV-seq improves detection rates of genetic abnormalities.

Objective To develop an ultra-sensitive nanoparticle contrast agent for magnetic resonance angiography(MRA),to establish a highly sensitive imaging method for complicated vascular structures,and to provide imaging evidence for precision diagnosis,treatment,prognosis,and individualized treatment of ischemic stroke.Methods A dual-modality MRA contrast agent was prepared through ligand exchange of ultra-small NaGdF4 nanocrystals synthesized via a high temperature method,with biocompatible polyethylene glycol(PEG-dp)ligands.The basic structure,morphology,size distribution,and relaxation rate of the NaGdF4 nano contrast agent were characterized using transmission electron microscopy(TEM),a particle size potential analyzer,and a 7.0 T small-animal MRI scanner.A total of 6 healthy male SPF-grade BALB/c mice were selected and randomly divided into two groups,a NaGdF4 group and a Gd-DTPA group.The mice in the two groups were injected with NaGdF4 nanoparticle contrast agent or clinical Gd-DTPA contrast agent(0.1 mmol Gd3+/kg)via the tail vein.MRA images were obtained using a 7.0 T small animal magnetic resonance imaging system before and after the injection.A total of 6 healthy male SPF-grade Sprague Dawley(SD)rats were selected to establish a right middle cerebral artery occlusion(rMCAO)model to simulate ischemic stroke.The rats were injected with NaGdF4 nano-contrast agent(0.1 mmol Gd3+/kg)via the tail vein.Before and after the injection,brain MRI images of the rats were obtained using a 7.0 T small animal magnetic resonance imaging system.The in vitro and in vivo biological safety of the nano contrast agent was verified through cytotoxicity and hemolysis experiments and HE staining.Results Uniform spherical oil-phase NaGdF4 nanocrystals with an average particle size of approximately(4.43±0.46)nm were successfully prepared.After ligand exchange,biocompatible water-phase nanocrystals were obtained with a hydrodynamic size of 16.1 nm and a surface potential of-1.9 mV.The relaxation performance of this nanocrystal contrast agent was significantly superior to that of the clinical contrast agent Gd-DTPA.The longitudinal molar relaxivity rate(r1)of the NaGdF4 nano contrast agent was 8.84 mM-1s-1,while the transverse molar relaxivity rate(r2)was 27.36 mM-1s-1,which were 1.96 times(4.52 mM-1s-1)and 3.37 times(8.13 mM-1s-1)those of Gd-DTPA,respectively.It also demonstrated excellent biocompatibility.NaGdF4-enhanced MRA achieved high-resolution vascular imaging and effectively enabled the differentiation of the ischemic area,infarct core,and ischemic penumbra in an animal model of ischemic stroke.Conclusion The multi-parameter MRA based on NaGdF4 nanoparticles provides critical imaging evidence for the clinical diagnosis and prognosis of ischemic stroke.

Objective:To investigate the clinical characteristics and prognosis of fetuses with HNF1B gene variants. Methods:Fifty-two fetuses with HNF1B gene variants diagnosed by chromosomal copy number variation sequencing and/or whole exome sequencing at the First Affiliated Hospital of Zhengzhou University from January 2018 to June 2024 were retrospectively enrolled in this study, including 47 cases of 17q12 microdeletion and five cases of HNF1B point mutations. Prenatal ultrasound features, pregnancy outcomes, and postnatal manifestations were summarized and analyzed using descriptive statistics. Results:The prenatal ultrasound features of the 52 fetuses included enhanced renal parenchymal echo in 43 cases (82.7%), renal cysts in 15 cases (28.8%), enlarged kidney volume in 14 cases (26.9%), and pyelectasis in 13 cases (25.0%). Parental verification was completed for 35 cases, with 71.4% (25/35) being de novo mutations and 28.6% (10/35) inherited from either parent. Apart from eight cases with unknown pregnancy outcome (six cases were lost to follow-up, two cases refused to be followed up), the other 44 cases were successfully followed up, among which 68.2% (30/44) terminated the pregnancies and 31.8% (14/44) continued, resulting in live births. Prenatal ultrasound indicated renal abnormalities in all 14 live births, while postnatal follow-up showed seven cases with normal kidneys, one with reduced bilateral renal cysts, one with alleviated bilateral pyelectasis, four with unimproved renal structural abnormalities, and one who did not undergo a re-examination. Conclusion:The rate of renal abnormalities diagnosed by prenatal ultrasound in fetuses with HNF1B gene variants is high, and most of the pregnancies are terminated, although the renal sturctural abnormalities may improve after birth.

Objective:To investigate the clinical characteristics and genetic etiology of fetal Dandy-Walker spectrum (DWS) anomalies.Methods:This retrospective cohort study analyzed 28 fetuses with ultrasonographically confirmed DWS (ten classic Dandy-Walker malformations and 18 Dandy-Walker variants) at the First Affiliated Hospital, Zhengzhou University from January 2019 to June 2024. All cases underwent systematic ultrasonographic evaluation. Genetic analyses included chromosomal karyotyping alone ( n=4) or combined with copy number variation sequencing (CNV-seq) ( n=10). Descriptive statistics and Chi-square tests (or Fisher's exact test) with Bonferroni correction were applied. Results:(1) Among 28 fetuses, seven (25.0%) had isolated DWS and 21 (75.0%) non-isolated DWS. Central nervous system anomalies were most common (53.6%, 15/28). (2) Karyotyping identified abnormalities in four cases (4/14), including two triploidies, one case of mosaicism for a derivative chromosome der(1;10), and one 17p deletion. CNV-seq detected anomalies in six cases (25.0%, 6/24), four of which were missed by karyotyping: 3q23 deletion (encompassing ZIC1/ ZIC4), 13q11 duplication, and other critical variants. (3) Combined testing yielded a higher detection rate (28.6%, 8/28) than karyotyping alone (4/14, χ2=4.62, P=0.032) or CNV-seq alone (25.0%, 6/24, χ2=4.83, P=0.028) ( P=0.048 and 0.044 after Bonferroni correction). Conclusions:DWS demonstrates significant genetic heterogeneity, primarily involving chromosomal numerical anomalies (e.g., triploidy) and copy number variations (e.g., 3q23 deletion). Combined karyotyping and CNV-seq improves detection rates of genetic abnormalities.

Objective To analyze the application of ADOPT(attitude,definition,open mind,planning,try it out)model in parturients with gestational diabetes.Methods A total of 120 parturients with gestational diabetes admitted to Nantong Maternal and Child Health Hospital from January 2022 to February 2023 were selected as research objects.They were divided into control group and observation group according to the admission order,with 60 cases in each group.The mean age of parturients in the control group was(28.35±5.06)years(range,24-35 years).The mean age of parturients in the observation group was(28.29±5.33)years(range,23-36 years).The control group received conventional care,and the observation group were given ADOPT mode.The psychological resilience scale score,diabetes self-efficacy scale score,and blood glucose level before the intervention and at 7 d of intervention,as well as the incidence of adverse pregnancy outcomes were compared between the two groups.Results Before the intervention,there was no significant difference in the maternal psychological resilience scale score,diabetes self-efficacy scale score or blood glucose level between two groups(all P>0.05).At 7 d of intervention,the scores of maternal health knowledge rating scale and diabetes self-efficacy scale of the observation group were higher than those of the control group,and fasting blood glucose and 2-hour postprandial blood glucose in the observation group were lower than those in the control group(all P<0.05).After the intervention,the incidence of adverse pregnancy outcomes in the observation group(6.67%in parturients,5.00%in newborns)was lower than that in the control group(20.00%in parturients,16.67%in newborns)(P<0.05).Conclusion The ADOPT model can significantly improve the psychological resilience,strengthen self-efficacy,effectively control blood glucose level,and reduce the incidence of adverse pregnancy outcomes in parturients with gestational diabetes.

Objective To investigate the genetic association between nonalcoholic fatty liver disease(NAFLD)and type 2 diabetes mellitus(T2DM)using bidirectional two-sample Mendelian randomization(MR),as well as the causal relationship between NAFLD and T2DM across different body mass index(BMI)categories.Methods The data were derived from genome-wide association studies conducted in European populations,with a sample size of 32 941 cases for NAFLD,312 646 cases for T2DM,and 681 275 cases for BMI.The univariate and multivariate MR methods were used to assess the bidirectional causal relationship between NAFLD and T2DM in the general population and across different BMI subtypes.The methods of inverse-variance weighting,MR-Egger regression,constrained maximum likelihood and model averaging,and weighted median were used to conduct the MR analysis,and MR-Pleiotropy Residual Sum and Outlier,radial MR,the MR-Egger intercept method,and the Cochrane Q test were used for sensitivity analysis.Results The univariate MR analysis revealed a bidirectional causal relationship between NAFLD and T2DM in the general population(forward analysis:odds ratio[OR]=9.75,95%confidence interval[CI]:2.57-37.00,P＜0.001;reverse analysis:OR=1.01,95%CI:1.00-1.01,P＜0.01).After adjustment for BMI,the multivariate MR analysis showed that the causal relationship between NAFLD and T2DM remained significant in the general population(OR=33.12,95%CI:7.57-144.95,P＜0.000 1).The subgroup analysis showed a causal relationship between NAFLD and T2DM across all BMI subtypes(lean subgroup:OR=12.19,95%CI:3.35-44.40,P＜0.001;overweight subgroup:OR=4.30,95%CI:1.69-10.92,P＜0.01;obese subgroup:OR=1.67,95%CI:1.14-2.44,P＜0.01).Conclusion This study reveals the causal relationship between NAFLD and T2DM in the general population of NAFLD and across different BMI subtypes from a genetic perspective.

Objective:To investigate the diagnostic value of thyroid imaging report and data system (TIRADS) combined with BRAF V600E mutation detection in differentiating uncertain thyroid nodules by using fine needle aspiration cytology (FNAC), and to analyze the role of TIRADS classification in screening the nodules needed to be routinely detected for BRAF V600E mutation.Methods:The clinicopathological data of 337 thyroid nodules patients diagnosed with TIRADS classification, FNAC Bethesda classification, BRAF V600E mutation detection and postoperative histopathology from the Second Hospital of Hebei Medical University between January 2018 and August 2021 were retrospectively analyzed. The role of TIRADS classification, FNAC Bethesda classification and BRAF V600E mutation detection alone and the combined detection in the differentiation of benign and malignant thyroid nodules was also analyzed.Results:The postoperative histopathological result was regarded as the gold standard. The sensitivity of TIRADS classification, FNAC Bethesda classification and BRAF V600E mutation for thyroid cancer diagnosis was 76.0%, 88.1% and 80.4% respectively, and the corresponding specificity was 84.0%, 96.0% and 100.0%, respectively. Histologically, 37 (62.7%) of 59 nodules with FNAC uncertainty were malignant nodules after the surgery. The sensitivity and accuracy of BRAF V600E mutation detection in the diagnosis of FNAC uncertain nodules were 51.4% and 69.5%, respectively, while the sensitivity and accuracy of BRAF V600E mutation detection combined with TIRADS classification were 86.5% and 84.7%, respectively. The sensitivity and accuracy of BRAF V600E mutation detection combined with TIRADS classification were both improved ( P values were 0.002 and 0.049, respectively). The positive rate of BRAF V600E mutation in thyroid nodules increased step by step with the rise of risk degree in TIRADS classification, and the type 3 cases were lower than those in type 4a cases [14.3% (1/7) vs. 68.6% (24/35), P = 0.012], and there were no statistically significant differences among the adjacent groups above 4a (all P > 0.05). Conclusions:TIRADS combined with BRAF V600E mutation detection can improve the sensitivity and accuracy in the diagnosis of FNAC uncertain thyroid nodules. The BRAF V600E mutation rate of TIRADS 4a and above nodules is high, so routine detection is recommended.

OBJECTIVE: To carry out prenatal diagnosis for a fetus with normal ultrasonographic finding at 20 weeks' gestation but a copy number variant(CNV) of 13q indicated by non-invasive prenatal test (NIPT). METHODS: Karyotyping analysis and chromosomal CNV assay were carried out on the amniotic fluid sample. Parental peripheral blood sample was collected for chromosomal analysis. Detailed fetal ultrasound scan was carried out to rule out structural abnormalities of the fetus. RESULTS: The fetus was detected with a heterozygous 10.14 Mb deletion at 13q21.1q21.32, which has originated from the phenotypically normal mother. No apparent karyotypic abnormality was detected in the fetus and its parents. No ultrasonic abnormality was found in the fetus. CONCLUSION Both the fetus and its mother have carried a heterozygous 10.14 Mb deletion at 13q21.1q21.32 and presented normal phenotypes.Combined with literature review, the segmental deletion was judged to be a benign variant.
Female ; Genetic Counseling ; Humans ; Karyotyping ; Pedigree ; Pregnancy ; Prenatal Diagnosis ; Ultrasonography, Prenatal