1.Research on The Genealogical Inference Efficiency of High-density SNPs
Jing LI ; Yi-Jie SUN ; Wen-Ting ZHAO ; Zi-Chen TANG ; Jing LIU ; Cai-Xia LI
Progress in Biochemistry and Biophysics 2026;53(3):740-753
ObjectiveThis study aims to explore the potential of different orders of magnitude single-nucleotide polymorphism (SNP) locus combinations for predicting distant kinship relationships. A high-density SNP locus set was constructed, and a comprehensive assessment of its inference capability was conducted. MethodsFirstly, we selected three commercial chip panels, CGA (Chinese genotyping array, Illumina), GSA (Global screening array, Illumina), Affy (23MF_V2 high-density SNP array, Affymetrix) and merged them after quality control, forming a high-density SNP locus panel(1 180 k). Secondly, we selected 161 samples and collected their peripheral blood samples by using whole-genome sequencing technology. Within this sample population, the levels of kinship relationships fully covered the range from level 1 to level 9, and the number of kinship pairs at each level was consistently maintained at over 50 pairs. From 161 samples data of whole-genome sequencing, the 1 180 k locus set was extracted, which is referred to as the high-density SNP locus set in the following text. The kinship inference was conducted using the identity-by-descent (IBD) algorithm with the selected optimal parameters. To comprehensively evaluate the performance of the high-density SNP locus set in kinship inference, we compared it with the three commercial chip panels, the intersection of these three chip loci, and the control sets constructed by randomly reducing the number of the high-density SNP locus set. Based on the changes in the IBD lengths, as well as the dynamic trends in prediction accuracy, we conducted a scientific assessment of the kinship inference capability of the high-density SNP locus set. ResultsAfter screening, a set of 1 184 334 autosomal SNPs was obtained. During the process of screening the optimal IBD length threshold, the result revealed that 0 cM, 1 cM, and 2 cM all demonstrated good applicability. However, to avoid the issue of a large amount of redundant information caused by setting a too low IBD length threshold, this study ultimately selected 2 cM as the optimal threshold. Compared with the average results of three chip panels, the high-density SNP locus set increased the total IBD length and the average IBD length across levels 1-9; the accuracy of the confidence interval for level 8 was 70.97%, which represented a 3.50% improvement; the average confidence interval accuracy for levels 1-8 was 91.39%, representing a 1.00% increase; and the false negative rates at levels 8 and 9 were reduced by 2.42% and 6.76%, respectively. The system efficacy of the high-density SNP locus set for kinship inference of first to eighth degree relationships reached 98.91%. Through random reduction of the high-density SNP locus set results, it is found that increasing the number of SNPs with the panel, the detection efficiency of IBD length showed a significant upward trend. At the same time, the overall trend in the accuracy of kinship relationship prediction as well as the confidence interval accuracy also indicated that both metrics steadily increased with the addition of more loci. ConclusionThe results show that the high-density SNPs panel significantly enhances the efficacy of distant kinship inference, accurately covering kinship degrees, with the average confidence interval accuracy for first to eighth degree relationships stably above 90%. The study finds that increasing the number of SNPs panel can improve the ability to predict distant kinship.
2.Research Progress in the Impact of Accelerated Rehabilitation on Bone Tunnel Enlargement After Anterior Cruciate Ligament Reconstruction.
Wen-Bo TANG ; Feng GAO ; Xiao-Han ZHANG ; Bing-Ying ZHANG ; Hao DUAN ; Jing-Bin ZHOU
Acta Academiae Medicinae Sinicae 2025;47(4):634-643
This paper explores the impacts of accelerated rehabilitation protocols following anterior cruciate ligament reconstruction(ACLR)on bone tunnel enlargement(BTE).While accelerated rehabilitation can shorten the recovery time and improve the knee function,it may increase the risk of BTE.In the early rehabilitation phase after ACLR,excessive early weight-bearing and rapid progression of knee flexion angles should be avoided,along with the proper use of braces.Continuous passive motion is not recommended in the early phase post-ACLR to prevent potential effects on BTE.Further research is needed to investigate the mechanisms of BTE and develop more effective rehabilitation strategies.This will help to select appropriate rehabilitation protocols for patients and balance functional recovery with the risk of BTE,thereby reducing the revision rate and improving postoperative outcomes.
Humans
;
Anterior Cruciate Ligament Reconstruction/rehabilitation*
3.Regulatory effect of electroacupuncture on visual cortex plasticity in adult amblyopic mice and its mechanism
Wen LI ; Jing FU ; Chanyuan WANG ; Jing TANG ; Yuting LIU ; Yulin LUO
Chinese Journal of Experimental Ophthalmology 2025;43(2):106-113
Objective:To investigate the regulatory effect of electroacupuncture on visual cortex plasticity in adult amblyopic mice and its mechanism.Methods:Forty-eight SPF male healthy 3-week-old Kunming mice were randomly divided into a normal control group, a monocular form deprivation (MD) group, and an electroacupuncture intervention group by the random number table method, with 16 mice in each group.Except for the normal control group, mice in the other groups had their right eyelids sutured for two weeks to establish an adult MD amblyopia model.The electroacupuncture intervention group received electroacupuncture stimulation at three acupoints, Taiyang (EX-HN5), Jingming (BL1), and Fengchi (GB20) for four weeks at five weeks of age.The subjective visual function (paw probing success rate) of each group of mice was measured at five and nine weeks of age, respectively.At nine weeks of age, the changes in flash-visual evoked potential (F-VEP) of mice in each group was detected.The expression of plasticity related proteins synaptophysin (SYP), synaptic protein 1 (SYN1), neurite overgrowth inhibitor A (Nogo-A), and Nogo receptor (NgR) proteins in the contralateral cortex of the deprived mouse eyes was detected by Western blot.Expression of early growth response gene 1 (Egr-1) in the visual cortex of mice was detected by immunohistochemical staining.This study was approved by the Animal Ethics Committee of Hunan Children's Hospital (No.HCHDWLL-2022-17), and the management and use of animals were in accordance with the Laboratory Animal Management and Use Guide of Hunan Children's Hospital.Results:At nine weeks of age, the success rates of paw probing in the normal control group, MD group, and electroacupuncture intervention group were (71.69±10.60)%, (25.54±10.09)%, and (58.25±8.39)%, respectively, with a statistically significant overall difference ( F=5.987, P=0.006).Among them, the success rate of paw probing was significantly lower in the MD group than in the normal control group, and the electroacupuncture intervention group was significantly higher than in the MD group (both P<0.05).There was a significant overall difference in P2 wave amplitude in F-VEP examination among different groups of mice ( F=63.710, P<0.001), with lower P2 wave amplitude in the deprived eye of the MD group than in the normal control group and the electroacupuncture intervention group, and the differences were statistically significant (both P<0.001).There were significant differences in the expression levels of SYP and SYN1 proteins in the contralateral cortex of the deprived mouse eyes ( F=5.451, 3.871; both P<0.05).The relative expression levels of SYP and SYN1 proteins were significantly lower in the MD group than in the normal control group and electroacupuncture intervention group (all P<0.05).There were significant differences in levels of Nogo-A and NgR proteins in the contralateral cortex of the deprived mouse eyes ( F=4.188, 3.942, both P<0.05).The relative expression levels of Nogo-A and NgR proteins were significantly higher in the MD group than in the normal control group and the electroacupuncture intervention group (all P<0.05).The immunohistochemical staining results showed that compared with the normal control group, the MD group mice had a decrease in the expression of Egr-1 in the contralateral cortical neurons of the deprived eye, and the brown neuron protrusions were indistinguishable.Compared with the MD group, the electroacupuncture intervention group showed significant positive cell expression in the contralateral cortical area of the deprived eye, but the expression intensity was weaker than that of the normal control group. Conclusions:Electroacupuncture treatment of Taiyang (EX-HN5), Jingming (BL1), and Fengchi (GB21) acupoints can reactivate the plasticity of the visual cortex in adult amblyopic mice and improve their visual function.The mechanism may be related to the regulation of Nogo-A/NgR signaling pathway.
4.Influence of Outdoor Light at Night on Early Reproductive Outcomes of In Vitro Fertilization and Its Threshold Effect: Evidence from a Couple-Based Preconception Cohort Study.
Wen Bin FANG ; Ying TANG ; Ya Ning SUN ; Yan Lan TANG ; Yin Yin CHEN ; Ya Wen CAO ; Ji Qi FANG ; Kun Jing HE ; Yu Shan LI ; Ya Ning DAI ; Shuang Shuang BAO ; Peng ZHU ; Shan Shan SHAO ; Fang Biao TAO ; Gui Xia PAN
Biomedical and Environmental Sciences 2025;38(8):1009-1015
5.Construction of CD8+T cell-associated Risk Model in Hepatocellular Carcinoma Based on Bulk and Single-cell RNA-seq Data
Xin-Tong ZHANG ; Jian-Jun ZHU ; Jin WU ; Hao WU ; Fan LU ; Wen-Tao ZHANG ; Jing-Jia CHANG ; Ting TANG ; Zhi-Gao OU ; Feng-Feng JIA ; Li LI ; Peng-Fei YU ; Ming LIU
Chinese Journal of Biochemistry and Molecular Biology 2025;41(10):1511-1528
Hepatocellular carcinoma(HCC),which is essentially primary liver cancer,is closely related to CD8+T cell immune infiltration and immune suppression.We constructed a CD8+T cells related risk score model to pre-dict the prognosis of HCC patients and provided therapeutic guidance based on the risk score.Using integrated bulk RNA sequencing(RNA-seq)and single-cell RNA sequencing(scRNA-seq)datasets,we identified stable CD8+T cell signatures.Based on these signatures,a 3-gene risk score model,comprised of KLRB1,RGS2,and TN-FRSF1B was constructed.The risk score model was well validated through an independent external validation co-hort.We divided patients into high-risk and low-risk groups according to the risk score and compared the differ-ences in immune microenvironment between these two groups.Compared with low-risk patients,high-risk patients have higher M2-type macrophage content(P<0.0001)and lower CD8+T cells infiltration(P<0.0001).High-risk patients predict worse response to immunotherapy treatment than low-risk patients(P<0.01).Drug sensitivity a-nalysis shows that PI3K-β inhibitor AZD6482 and TGFβRII inhibitor SB505124 may be suitable therapies for high-risk patients,while the IGF-1R inhibitor BMS-754807 or the novel pyrimidine-based anti-tumor metabolic drug Gemcitabine could be potential therapeutic choices for low-risk patients.Moreover,expression of these 3-gene mod-el was verified by immunohistochemistry.In summary,the establishment and validation of a CD8+T cell-derived risk model can more accurately predict the prognosis of HCC patients and guide the construction of personalized treatment plans.
6.Multimodal MRI features of cerebral small vessel disease combined with type 2 diabetes mellitus
Jing WANG ; Hang PAN ; Yan-ling ZHENG ; Zi-wen LIANG ; Yu-lin WANG ; Qiu-guo OU ; Fan-ying GUAN ; Hai-yan TAO ; Lei SONG ; Rui TANG
Journal of Regional Anatomy and Operative Surgery 2025;34(8):689-692
Objective To analyze the imaging features of cerebral small vessel disease in patients with type 2 diabetes mellitus by multimodal MRI.Methods The clinical data of 160 patients with cerebral small vessel disease admitted to our hospital from January to December 2020 were retrospectively analyzed.According to whether they were complicated with type 2 diabetes mellitus,they were divided into the diabetic group and the non-diabetic group,with 80 cases in each group.Both groups underwent multimodal MRI scans.And the severity of lacunar infarction,the severity of subcortical and periventricular white matter lesions,white matter integral and cerebral microbleeds of patients in the two groups were compared.Results The severity of lacunar infarction(χ2=34.076,P=0.001),subcortical white matter lesions(χ2=25.000,P=0.001),periventricular white matter lesions(χ2=22.895,P=0.001)and white matter integral(t=12.370,P=0.001)of patients in the diabetic group were significantly higher than those in the non-diabetic group.No cerebral microbleeds were detected in either group of patients.Conclusion Patients with cerebral small vessel disease and type 2 diabetes mellitus show characteristic multimodal MRI changes.The increase in the number of lacunar infarction lesions and the aggravation of white matter lesions can be used as the characteristic imaging basis for the diagnosis of type 2 diabetes mellitus related cerebral small vessel disease.
7.Correlation between total cholesterol/high-density lipoprotein cholesterol ratio and onset of gestational metabolic syndrome and its association with pregnancy outcomes
Wen TAI ; Hong WU ; Qiuqin TANG ; Jing WANG
Journal of Chinese Physician 2025;27(8):1167-1173
Objective:To explore the correlation between the total cholesterol/high-density lipoprotein cholesterol (TC/HDL-C) ratio during pregnancy and the onset of gestational metabolic syndrome (GMS), as well as its association with pregnancy outcomes.Methods:Clinical data of 153 pregnant women diagnosed with GMS in the third trimester admitted to Women′s Hospital of Nanjing Medical University from January 2020 to December 2022 (observation group) were collected, and data of 153 healthy pregnant women (control group) were randomly selected for a comparative study. Indicators of the two groups were observed and compared. Multiple linear regression and restricted cubic spline analysis were used to analyze the correlation between TC/HDL-C in the first and second trimesters and metabolic indicators in the third trimester and GMS risk, respectively. According to the pregnancy outcomes of GMS pregnant women with different TC/HDL-C ratios, the association between TC/HDL-C ratio and preterm birth subtypes was analyzed.Results:There were statistically significant differences between the two groups in age, gestational week, pre-pregnancy body mass index (BMI), weight gain during pregnancy, abdominal circumference in the third trimester, whether to deliver vaginally, history of preterm birth, history of cesarean section, history of abortion, neonatal birth weight, and neonatal length (all P<0.05). There were statistically significant differences in blood pressure and BMI between the two groups in the second and third trimesters (all P<0.01). In the first trimester (gestational week <14 weeks), there were statistically significant differences in fasting plasma glucose (FPG), HDL-C, and TC/HDL-C ratio between the two groups (all P<0.05). In the second trimester (gestational weeks 14-27) and third trimester (gestational week ≥28 weeks), the levels of FPG, fasting insulin (FINS), triglyceride (TG), TC, low-density lipoprotein cholesterol (LDL-C), and TC/HDL-C ratio in the observation group were higher than those in the control group, while HDL-C was lower (all P<0.05). There were statistically significant differences between the two groups in postpartum abnormal blood pressure, abnormal BMI, abnormal glucose metabolism, and abnormal lipid metabolism (all P<0.05). After adjusting for age, gestational week, and BMI, first-trimester TC/HDL-C ratio was correlated with third-trimester FPG, systolic blood pressure, diastolic blood pressure, TG, TC, and HDL-C (all P<0.05); second-trimester TC/HDL-C ratio was correlated with third-trimester FPG, FINS, systolic blood pressure, diastolic blood pressure, TG, TC, HDL-C, and LDL-C (all P<0.05), and both were linearly related to third-trimester GMS risk ( Pfor trend<0.01). The TC/HDL-C ratio was positively correlated with the preterm birth rate ( RR>1). Conclusions:An increased TC/HDL-C ratio is closely related to the occurrence of GMS, which is prone to cause preterm birth and affect fetal growth and development.
8.Regulatory effect of electroacupuncture on visual cortex plasticity in adult amblyopic mice and its mechanism
Wen LI ; Jing FU ; Chanyuan WANG ; Jing TANG ; Yuting LIU ; Yulin LUO
Chinese Journal of Experimental Ophthalmology 2025;43(2):106-113
Objective:To investigate the regulatory effect of electroacupuncture on visual cortex plasticity in adult amblyopic mice and its mechanism.Methods:Forty-eight SPF male healthy 3-week-old Kunming mice were randomly divided into a normal control group, a monocular form deprivation (MD) group, and an electroacupuncture intervention group by the random number table method, with 16 mice in each group.Except for the normal control group, mice in the other groups had their right eyelids sutured for two weeks to establish an adult MD amblyopia model.The electroacupuncture intervention group received electroacupuncture stimulation at three acupoints, Taiyang (EX-HN5), Jingming (BL1), and Fengchi (GB20) for four weeks at five weeks of age.The subjective visual function (paw probing success rate) of each group of mice was measured at five and nine weeks of age, respectively.At nine weeks of age, the changes in flash-visual evoked potential (F-VEP) of mice in each group was detected.The expression of plasticity related proteins synaptophysin (SYP), synaptic protein 1 (SYN1), neurite overgrowth inhibitor A (Nogo-A), and Nogo receptor (NgR) proteins in the contralateral cortex of the deprived mouse eyes was detected by Western blot.Expression of early growth response gene 1 (Egr-1) in the visual cortex of mice was detected by immunohistochemical staining.This study was approved by the Animal Ethics Committee of Hunan Children's Hospital (No.HCHDWLL-2022-17), and the management and use of animals were in accordance with the Laboratory Animal Management and Use Guide of Hunan Children's Hospital.Results:At nine weeks of age, the success rates of paw probing in the normal control group, MD group, and electroacupuncture intervention group were (71.69±10.60)%, (25.54±10.09)%, and (58.25±8.39)%, respectively, with a statistically significant overall difference ( F=5.987, P=0.006).Among them, the success rate of paw probing was significantly lower in the MD group than in the normal control group, and the electroacupuncture intervention group was significantly higher than in the MD group (both P<0.05).There was a significant overall difference in P2 wave amplitude in F-VEP examination among different groups of mice ( F=63.710, P<0.001), with lower P2 wave amplitude in the deprived eye of the MD group than in the normal control group and the electroacupuncture intervention group, and the differences were statistically significant (both P<0.001).There were significant differences in the expression levels of SYP and SYN1 proteins in the contralateral cortex of the deprived mouse eyes ( F=5.451, 3.871; both P<0.05).The relative expression levels of SYP and SYN1 proteins were significantly lower in the MD group than in the normal control group and electroacupuncture intervention group (all P<0.05).There were significant differences in levels of Nogo-A and NgR proteins in the contralateral cortex of the deprived mouse eyes ( F=4.188, 3.942, both P<0.05).The relative expression levels of Nogo-A and NgR proteins were significantly higher in the MD group than in the normal control group and the electroacupuncture intervention group (all P<0.05).The immunohistochemical staining results showed that compared with the normal control group, the MD group mice had a decrease in the expression of Egr-1 in the contralateral cortical neurons of the deprived eye, and the brown neuron protrusions were indistinguishable.Compared with the MD group, the electroacupuncture intervention group showed significant positive cell expression in the contralateral cortical area of the deprived eye, but the expression intensity was weaker than that of the normal control group. Conclusions:Electroacupuncture treatment of Taiyang (EX-HN5), Jingming (BL1), and Fengchi (GB21) acupoints can reactivate the plasticity of the visual cortex in adult amblyopic mice and improve their visual function.The mechanism may be related to the regulation of Nogo-A/NgR signaling pathway.
9.Establishment of different pneumonia mouse models suitable for traditional Chinese medicine screening.
Xing-Nan YUE ; Jia-Yin HAN ; Chen PAN ; Yu-Shi ZHANG ; Su-Yan LIU ; Yong ZHAO ; Xiao-Meng ZHANG ; Jing-Wen WU ; Xuan TANG ; Ai-Hua LIANG
China Journal of Chinese Materia Medica 2025;50(15):4089-4099
In this study, lipopolysaccharide(LPS), ovalbumin(OVA), and compound 48/80(C48/80) were administered to establish non-infectious pneumonia models under simulated clinical conditions, and the correlation between their pathological characteristics and traditional Chinese medicine(TCM) syndromes was compared, providing the basis for the selection of appropriate animal models for TCM efficacy evaluation. An acute pneumonia model was established by nasal instillation of LPS combined with intraperitoneal injection for intensive stimulation. Three doses of OVA mixed with aluminum hydroxide adjuvant were injected intraperitoneally on days one, three, and five and OVA was administered via endotracheal drip for excitation on days 14-18 to establish an OVA-induced allergic pneumonia model. A single intravenous injection of three doses of C48/80 was adopted to establish a C48/80-induced pneumonia model. By detecting the changes in peripheral blood leukocyte classification, lung tissue and plasma cytokines, immunoglobulins(Ig), histamine levels, and arachidonic acid metabolites, the multi-dimensional analysis was carried out based on pathological evaluation. The results showed that the three models could cause pulmonary edema, increased wet weight in the lung, and obvious exudative inflammation in lung tissue pathology, especially for LPS. A number of pyrogenic cytokines, inclading interleukin(IL)-6, interferon(IFN)-γ, IL-1β, and IL-4 were significantly elevated in the LPS pneumonia model. Significantly increased levels of prostacyclin analogs such as prostaglandin E2(PGE2) and PGD2, which cause increased vascular permeability, and neutrophils in peripheral blood were significantly elevated. The model could partly reflect the clinical characteristics of phlegm heat accumulating in the lung or dampness toxin obstructing the lung. The OVA model showed that the sensitization mediators IgE and leukotriene E4(LTE4) were increased, and the anti-inflammatory prostacyclin 6-keto-PGF2α was decreased. Immune cells(lymphocytes and monocytes) were decreased, and inflammatory cells(neutrophils and basophils) were increased, reflecting the characteristics of "deficiency", "phlegm", or "dampness". Lymphocytes, monocytes, and basophils were significantly increased in the C48/80 model. The phenotype of the model was that the content of histamine, a large number of prostacyclins(6-keto-PGE1, PGF2α, 15-keto-PGF2α, 6-keto-PGF1α, 13,14-D-15-keto-PGE2, PGD2, PGE2, and PGH2), LTE4, and 5-hydroxyeicosatetraenoic acid(5S-HETE) was significantly increased, and these indicators were associated with vascular expansion and increased vascular permeability. The pyrogenic inflammatory cytokines were not increased. The C48/80 model reflected the characteristics of cold and damp accumulation. In the study, three non-infectious pneumonia models were constructed. The LPS model exhibited neutrophil infiltration and elevated inflammatory factors, which was suitable for the efficacy study of TCM for clearing heat, detoxifying, removing dampness, and eliminating phlegm. The OVA model, which took allergic inflammation as an index, was suitable for the efficacy study of Yiqi Gubiao formulas. The C48/80 model exhibited increased vasoactive substances(histamine, PGs, and LTE4), which was suitable for the efficacy study and evaluation of TCM for warming the lung, dispersing cold, drying dampness, and resolving phlegm. The study provides a theoretical basis for model selection for the efficacy evaluation of TCM in the treatment of pneumonia.
Animals
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Disease Models, Animal
;
Mice
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Pneumonia/genetics*
;
Medicine, Chinese Traditional
;
Male
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Humans
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Cytokines/immunology*
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Female
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Lipopolysaccharides/adverse effects*
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Lung/drug effects*
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Drugs, Chinese Herbal
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Ovalbumin
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Mice, Inbred BALB C
10.Construction of CD8+T cell-associated Risk Model in Hepatocellular Carcinoma Based on Bulk and Single-cell RNA-seq Data
Xin-Tong ZHANG ; Jian-Jun ZHU ; Jin WU ; Hao WU ; Fan LU ; Wen-Tao ZHANG ; Jing-Jia CHANG ; Ting TANG ; Zhi-Gao OU ; Feng-Feng JIA ; Li LI ; Peng-Fei YU ; Ming LIU
Chinese Journal of Biochemistry and Molecular Biology 2025;41(10):1511-1528
Hepatocellular carcinoma(HCC),which is essentially primary liver cancer,is closely related to CD8+T cell immune infiltration and immune suppression.We constructed a CD8+T cells related risk score model to pre-dict the prognosis of HCC patients and provided therapeutic guidance based on the risk score.Using integrated bulk RNA sequencing(RNA-seq)and single-cell RNA sequencing(scRNA-seq)datasets,we identified stable CD8+T cell signatures.Based on these signatures,a 3-gene risk score model,comprised of KLRB1,RGS2,and TN-FRSF1B was constructed.The risk score model was well validated through an independent external validation co-hort.We divided patients into high-risk and low-risk groups according to the risk score and compared the differ-ences in immune microenvironment between these two groups.Compared with low-risk patients,high-risk patients have higher M2-type macrophage content(P<0.0001)and lower CD8+T cells infiltration(P<0.0001).High-risk patients predict worse response to immunotherapy treatment than low-risk patients(P<0.01).Drug sensitivity a-nalysis shows that PI3K-β inhibitor AZD6482 and TGFβRII inhibitor SB505124 may be suitable therapies for high-risk patients,while the IGF-1R inhibitor BMS-754807 or the novel pyrimidine-based anti-tumor metabolic drug Gemcitabine could be potential therapeutic choices for low-risk patients.Moreover,expression of these 3-gene mod-el was verified by immunohistochemistry.In summary,the establishment and validation of a CD8+T cell-derived risk model can more accurately predict the prognosis of HCC patients and guide the construction of personalized treatment plans.

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