2.Aberrant fragmentomic features of circulating cell-free mitochondrial DNA enable early detection and prognosis prediction of hepatocellular carcinoma
Yang LIU ; Fan PENG ; Siyuan WANG ; Huanmin JIAO ; Kaixiang ZHOU ; Wenjie GUO ; Shanshan GUO ; Miao DANG ; Huanqin ZHANG ; Weizheng ZHOU ; Xu GUO ; Jinliang XING
Clinical and Molecular Hepatology 2025;31(1):196-212
Background/Aims:
Early detection and effective prognosis prediction in patients with hepatocellular carcinoma (HCC) provide an avenue for survival improvement, yet more effective approaches are greatly needed. We sought to develop the detection and prognosis models with ultra-sensitivity and low cost based on fragmentomic features of circulating cell free mtDNA (ccf-mtDNA).
Methods:
Capture-based mtDNA sequencing was carried out in plasma cell-free DNA samples from 1168 participants, including 571 patients with HCC, 301 patients with chronic hepatitis B or liver cirrhosis (CHB/LC) and 296 healthy controls (HC).
Results:
The systematic analysis revealed significantly aberrant fragmentomic features of ccf-mtDNA in HCC group when compared with CHB/LC and HC groups. Moreover, we constructed a random forest algorithm-based HCC detection model by utilizing ccf-mtDNA fragmentomic features. Both internal and two external validation cohorts demonstrated the excellent capacity of our model in distinguishing early HCC patients from HC and highrisk population with CHB/LC, with AUC exceeding 0.983 and 0.981, sensitivity over 89.6% and 89.61%, and specificity over 98.20% and 95.00%, respectively, greatly surpassing the performance of alpha-fetoprotein (AFP) and mtDNA copy number. We also developed an HCC prognosis prediction model by LASSO-Cox regression to select 20 fragmentomic features, which exhibited exceptional ability in predicting 1-year, 2-year and 3-year survival (AUC=0.8333, 0.8145 and 0.7958 for validation cohort, respectively).
Conclusions
We have developed and validated a high-performing and low-cost approach in a large clinical cohort based on aberrant ccf-mtDNA fragmentomic features with promising clinical translational application for the early detection and prognosis prediction of HCC patients.
4.Aberrant fragmentomic features of circulating cell-free mitochondrial DNA enable early detection and prognosis prediction of hepatocellular carcinoma
Yang LIU ; Fan PENG ; Siyuan WANG ; Huanmin JIAO ; Kaixiang ZHOU ; Wenjie GUO ; Shanshan GUO ; Miao DANG ; Huanqin ZHANG ; Weizheng ZHOU ; Xu GUO ; Jinliang XING
Clinical and Molecular Hepatology 2025;31(1):196-212
Background/Aims:
Early detection and effective prognosis prediction in patients with hepatocellular carcinoma (HCC) provide an avenue for survival improvement, yet more effective approaches are greatly needed. We sought to develop the detection and prognosis models with ultra-sensitivity and low cost based on fragmentomic features of circulating cell free mtDNA (ccf-mtDNA).
Methods:
Capture-based mtDNA sequencing was carried out in plasma cell-free DNA samples from 1168 participants, including 571 patients with HCC, 301 patients with chronic hepatitis B or liver cirrhosis (CHB/LC) and 296 healthy controls (HC).
Results:
The systematic analysis revealed significantly aberrant fragmentomic features of ccf-mtDNA in HCC group when compared with CHB/LC and HC groups. Moreover, we constructed a random forest algorithm-based HCC detection model by utilizing ccf-mtDNA fragmentomic features. Both internal and two external validation cohorts demonstrated the excellent capacity of our model in distinguishing early HCC patients from HC and highrisk population with CHB/LC, with AUC exceeding 0.983 and 0.981, sensitivity over 89.6% and 89.61%, and specificity over 98.20% and 95.00%, respectively, greatly surpassing the performance of alpha-fetoprotein (AFP) and mtDNA copy number. We also developed an HCC prognosis prediction model by LASSO-Cox regression to select 20 fragmentomic features, which exhibited exceptional ability in predicting 1-year, 2-year and 3-year survival (AUC=0.8333, 0.8145 and 0.7958 for validation cohort, respectively).
Conclusions
We have developed and validated a high-performing and low-cost approach in a large clinical cohort based on aberrant ccf-mtDNA fragmentomic features with promising clinical translational application for the early detection and prognosis prediction of HCC patients.
6.Aberrant fragmentomic features of circulating cell-free mitochondrial DNA enable early detection and prognosis prediction of hepatocellular carcinoma
Yang LIU ; Fan PENG ; Siyuan WANG ; Huanmin JIAO ; Kaixiang ZHOU ; Wenjie GUO ; Shanshan GUO ; Miao DANG ; Huanqin ZHANG ; Weizheng ZHOU ; Xu GUO ; Jinliang XING
Clinical and Molecular Hepatology 2025;31(1):196-212
Background/Aims:
Early detection and effective prognosis prediction in patients with hepatocellular carcinoma (HCC) provide an avenue for survival improvement, yet more effective approaches are greatly needed. We sought to develop the detection and prognosis models with ultra-sensitivity and low cost based on fragmentomic features of circulating cell free mtDNA (ccf-mtDNA).
Methods:
Capture-based mtDNA sequencing was carried out in plasma cell-free DNA samples from 1168 participants, including 571 patients with HCC, 301 patients with chronic hepatitis B or liver cirrhosis (CHB/LC) and 296 healthy controls (HC).
Results:
The systematic analysis revealed significantly aberrant fragmentomic features of ccf-mtDNA in HCC group when compared with CHB/LC and HC groups. Moreover, we constructed a random forest algorithm-based HCC detection model by utilizing ccf-mtDNA fragmentomic features. Both internal and two external validation cohorts demonstrated the excellent capacity of our model in distinguishing early HCC patients from HC and highrisk population with CHB/LC, with AUC exceeding 0.983 and 0.981, sensitivity over 89.6% and 89.61%, and specificity over 98.20% and 95.00%, respectively, greatly surpassing the performance of alpha-fetoprotein (AFP) and mtDNA copy number. We also developed an HCC prognosis prediction model by LASSO-Cox regression to select 20 fragmentomic features, which exhibited exceptional ability in predicting 1-year, 2-year and 3-year survival (AUC=0.8333, 0.8145 and 0.7958 for validation cohort, respectively).
Conclusions
We have developed and validated a high-performing and low-cost approach in a large clinical cohort based on aberrant ccf-mtDNA fragmentomic features with promising clinical translational application for the early detection and prognosis prediction of HCC patients.
7.Neck Seven-Line Method Combined with Periauricular Acupuncture for 33 Patients with Sudden Hearing Loss in Non-Acute Stage: A Randomized Controlled Trial
Chongyang ZHANG ; Junjie LIANG ; Yang LI ; Xinru WANG ; Yu XING ; Xueshi DI ; Wenting SUN ; Peng BAI
Journal of Traditional Chinese Medicine 2024;65(15):1571-1577
ObjectiveTo evaluate the effectiveness and safety of neck seven-line method combined with periauricular acupuncture as salvage treatment for sudden hearing loss in non-acute stage. MethodsSixty-six patients with non-acute stage of sudden hearing loss with a disease duration of 15-90 days were randomly divided into 33 cases each in treatment group and control group. The treatment group was given neck seven-line method combined with acupuncture at periauricular points; the control group used sham acupuncture and sham electroacupuncture at the same points. Both groups were treated 3 times a week for 6 weeks. The pure tone average hearing threshold of impaired frequencies were examined before treatment, after treatment finish and at follow-up (week 10), and the difference between pure tone average hearing threshold of impaired frequencies before and after treatment was calculated; calculate the proportion of patients with ≥10 dB improvement in pure tone average hearing threshold of impaired frequency after treatment and at follow-up; compare the patients' Tinnitus Evaluation Scale (TEQ) scores, Chinese Medicine Quality of Life Assessment Scale (CQ-11D) health utility values and the difference between before and after treatment, and record the occurrence of adverse events. ResultsThe pure tone average of impaired frequency in the treatment group were (50.57±18.07) dB and (47.70±17.42) dB at post-treatment and follow-up respectively, and (54.38±21.77) dB and (53.36±20.99) dB in the control group at post-treatment and follow-up. Compared with the pre-treatment period, the pure tone average hearing threshold of impaired frequency in the two groups significantly decreased (P<0.05) at post-treatment and follow-up. The difference of pure tone average hearing threshold of impaired frequency in the treatment group after treatment and at the follow-up visit compared to that before treatment was lower than those in the control group (P<0.05). After treatment, 13 patients (39.39%) in the treatment group and 10 patients (30.30%) in the control group showed improvement of ≥10 dB in pure tone average hearing threshold of impaired frequency; at the follow-up visit, 18 patients (54.55%) in the treatment group and 10 patients (30.30%) in the control group showed improvement of ≥10 dB in the pure tone average hearing threshold of impaired frequency, and there was no statistical significance for comparison between groups at the time of post-treatment and follow-up (P>0.05). The TEQ score of the treatment group significantly lower than that before treatment (P<0.05); the TEQ score of the treatment group and the difference between before and after treatment significantly lower than that of the control group (P<0.05). The difference in CQ-11D health utility values and the difference between before and after treatment were not statistically significant between the two groups (P>0.05). Eight cases of acupuncture-related adverse events occurred among 66 patients, including subcutaneous haematomas after needling, severe pain during needling and needle fainting, which disappeared after symptomatic treatment and did not affect the following treatment. ConclusionNeck seven-line method combined with periauricular acupuncture could be used as salvage treatment for sudden hearing loss in non-acute stage to improve the pure tone average hearing threshold of impaired frequency, alleviate tinnitus, with safety.
8. Optimization and identification of a low density and high purity method for primary hippocampal neuron culture from fetal rats
Peng SU ; Xing-Yi WANG ; Jing-Yan LIANG ; Tian-Qing XIONG ; Jing-Yan LIANG ; Tian-Qing XIONG
Acta Anatomica Sinica 2024;55(1):113-119
Objective To establish a low density, high purity and high stability in vitro culture method of primary hippocampal neurons of fetal rats by co-culturing hippocampal and cortical cells, so as to obtain higher purity and better vitality of primary hippocampal neurons disease. Methods The fetal rat hippocampal tissue was isolated from 16-18 days pregnant SD rats, then cut and digested by 0.125% trypsin. The obtained cell suspension was filtered by 200 mesh cell sieve, and then the obtained cell suspensions were then inoculated into the inner layer and outer ring of the culture plate in a surrounding form. They were co-cultured in DMEM/F12 medium containing 10% horse serum. After 4-6 hours of cell adhesion, the culture medium was changed to maintenance medium (Neurobasal+2% B27+0.5 mmol/L glutamine). Then the cell viability was detected with CCK-8 kit and the purity of hippocampal neurons was detected by immunofluorescent staining. Results Hippocampal neurons grew well and formed crisscross neural networks after 5 days. And it could survive for 3 weeks. The purity of hippocampal neurons was up to 98%. Conclusion The method of co-culturing hippocampal and cortical cells can obtain high-purity, high activity, high survival rate, and high stability primary hippocampal neurons from fetal rats, which can provide certain experimental conditions for the study of hippocampal neuron related diseases in the nervous system and is worthy of promotion and application.
9.Application of CRISPR/Cas System-integrated Paper-based Analytical Devices for Rapid Detection of Foodborne Pathogens
Peng-Ru LI ; Xing SHEN ; Jing-Nan MENG ; Lin LUO ; Juan WANG ; Zhen-Lin XU
Progress in Biochemistry and Biophysics 2024;51(5):1147-1160
Foods can be contaminated with foodborne pathogens through a variety of pathways, including water, air and soil. Food safety events caused by foodborne pathogens show a serious impact on human health. However, due to the diversity of foodborne pathogens and the complexity of food matrices, the rapid detection of foodborne pathogens was difficult. The conventional microbial culture and physiological and biochemical identification can hardly meet the need of rapid detection of foodborne pathogens in the field. It is necessary to develop rapid detection technologies for foodborne pathogens. Clustered regularly interspaced short palindromic repeats (CRISPR) and associated protein (Cas) are an adaptive immune systems of prokaryotes with specific recognition and cleavage of nucleic acid sequences, which shows good potential for development of nucleic acid detection and biosensing in the field. According to different forms of application, paper-based analytical devices can be categorized into test paper, lateral flow assay and microfluidic paper-based chips, etc. As a good simplicity and low-cost analytical testing tools, they show good prospects in the field of rapid testing. Therefore, the rapid and sensitive detection of foodborne pathogens can be realized by combining the efficient recognition ability of CRISPR/Cas system and the simplicity of paper-based analytical devices. In this paper, we briefly introduce an overview of the CRISPR/Cas system for nucleic acid detection, and this section focuses on an overview of the features and principles of the class 2 system, including types II, V and VI, which uses a single effector. The application of CRISPR/Cas system based test paper analysis, lateral flow assay and microfluidic paper-based chips for the detection of foodborne pathogens are highlighted in the paper, and finally the advantages, current challenges and future prospects of CRISPR/Cas system in combination with paper-based analytical devices to establish detection methods are discussed.
10.Effects of berberine on renal tubular epithelial cell injury in diabetic
Peng-Fei ZHANG ; Qiong-Xing BU ; Yan-Yan HENG ; Fei-Fei WANG ; Wei WEI
The Chinese Journal of Clinical Pharmacology 2024;40(3):358-362
Objective To study the effect of berberine on the damage of renal tubular epithelial cells(RETC)in diabetic in vitro.Methods RTEC were divided into control group,model group(high glucose),low dose experimental group(2 mg·L-1 berberine and high glucose),medium dose experimental group(4 mg·L-1 berberine and high glucose),high dose experimental group(8 mg·L-1 berberine and high glucose),BBM-H+miR-NC(transfected with mimics control group,8 mg·L-1 berberine and high glucose),BBM-H+miR-135b group(transfected with miR-135b mimics,8 mg·L-1 berberine and high glucose).Methyl thiazolyl tetrazolium(MTT)method was used to detect cell proliferation activity,flow cytometry was used to detect cell apoptosis rate,Western blot was used to detect the expression of B-cell lymphoma-2(Bcl-2)and Bel-associated X(Bax)proteins in cells,and reactive oxygen species(ROS)level were detected by chemical fluorescence method,thiobarbituric acid method was used to detect malondialdehyde(MDA)level,and xanthine oxidation method was used to detect superoxide dismutase(SOD)level,the levels of tumor necrosis factor-α(TNF-α),interleukin-8(IL-8)and interleukin-1β(IL-1 β)were detected by enzyme-linked immunosorbent assay(ELISA).Results The proliferative activity(OD value)of RTEC in control group,model group and low,medium,high dose experimental groups were 0.66±0.04,0.36±0.02,0.43±0.03,0.54±0.03,0.63±0.05;the apoptosis rates were(3.62±0.31)%,(29.41±2.33)%,(20.10±1.65)%,(15.02±1.25)%,(9.58±1.43)%;MDA were(1.04±0.12),(5.24±0.29),(3.45±0.22),(2.16±0.13),(1.60±0.11)nmol·mL-1;SOD were(240.22±12.06),(130.56±10.84),(169.62±12.50),(201.97±12.78),(236.74±14.52)U·mL-1;TNF-α were(31.25±2.51),(51.84±4.20),(44.52±2.61),(38.25±1.50),(32.10±1.78)mg·L-1;IL-8 were(10.59±1.14),(19.95±1.74),(16.10±1.03),(13.52±1.25),(11.17±0.92)mg·L-1;IL-1β were(23.01±1.45),(56.92±2.51),(43.20±1.96),(32.05±1.23),(26.37±2.48)mg·L-1.There were statistically significant differences between model group and control group(all P<0.05).Compared with the model group,the above indexes in low,medium and high dose experimental group were statistically significant(all P<0.05).The above indexes of BBM-H+miR-NC group were statistically significant compared with those of BBM-H+miR-135b group(all P<0.05).Conclusion Berberine can reduce diabetic renal tubular epithelial cell damage by down-regulating miR-135b.

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