1.Gene expression-based machine learning model for diagnosis, prognosis, and treatment response prediction in hepatocellular carcinoma: a retrospective study
Tan Thinh NGUYEN ; Thanh Dat NGUYEN ; Phu Qui Le NGUYEN ; Phuong Thi BUI ; Minh Nam NGUYEN
Journal of Yeungnam Medical Science 2026;43(1):21-
Background:
Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide, largely because of challenges in early diagnosis and the limited sensitivity of conventional biomarkers. Therefore, reliable molecular tools for early detection, prognostic stratification, and individualized treatment predictions are urgently required.
Methods:
This retrospective study analyzed publicly available gene expression datasets. Candidate biomarkers were identified from the GSE14520 cohort using a multistep screening workflow that integrated differential expression analysis, diagnostic performance, and prognostic relevance. A 10-gene diagnostic model was constructed using least absolute shrinkage and selection operator logistic regression and subsequently validated across multiple independent cohorts. Survival outcomes were evaluated using the Kaplan-Meier analysis and treatment responses to sorafenib and transarterial chemoembolization (TACE) were assessed using receiver operating characteristic analysis.
Results:
A 10-gene signature (TOP2A, CDK1, CYP3A4, MASP2, EPHX2, HAO1, RACGAP1, GLYAT, ADH1B, and CYP4A11) was established. The model demonstrated robust internal performance and consistent accuracy across external validation cohorts (area under the curve [AUC], >0.9). This signature effectively identified early-stage HCC and distinguished malignancy from cirrhosis. High-risk scores were significantly associated with poor overall survival and recurrence-free survival (p<0.05). Furthermore, the model could predict treatment sensitivity, with higher risk scores associated with better outcomes for sorafenib (AUC, 0.791), whereas lower risk scores correlated with an improved response to TACE (AUC, 0.768).
Conclusion
Our gene expression-based machine learning model provides a robust tool for HCC diagnosis, prognosis, and treatment response prediction, with potential as a supportive system for personalized clinical decision-making.
2.Differential Peripheral NLRP3 Inflammasome Expression in Patients With Parkinson’s Disease and Patients With Multiple System Atrophy
Jeongjae LEE ; Han-Joon KIM ; Huu Dat NGUYEN ; Suk Jun SONG ; Trung Nguyen THANH ; In Hee KWAK ; Hye Joung CHOI ; Hyeo-il MA ; Young Eun KIM
Journal of Movement Disorders 2026;19(1):31-38
Objective:
The NOD-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome has been proposed to be a downstream mediator of neuroinflammation in individuals with Parkinson’s disease (PD). However, its involvement across disease stages and related synucleinopathies, such as multiple system atrophy (MSA), remains unclear. We aimed to analyze the peripheral mRNA expression of NLRP3-related genes and cytokines across individuals with isolated REM sleep behavior disorder (iRBD), early-stage PD, late-stage PD, and MSA.
Methods:
Peripheral blood mononuclear cells (PBMCs) were collected from 151 participants: 35 healthy controls (HCs), 31 patients with iRBD, 41 patients with early-stage PD, 21 patients with late-stage PD, and 23 patients with MSA. mRNA expression was measured using quantitative real-time polymerase chain reaction. Statistical comparisons were performed using analysis of variance (ANOVA) or Welch’s ANOVA, and associations with clinical variables were analyzed through stepwise multiple linear regression.
Results:
NLRP3 expression was significantly lower in patients with iRBD (p=0.0263) and patients with early-stage PD (p= 0.0101) than in HCs. NIMA-related kinase 7 (NEK7) expression progressively decreased across the disease spectrum (HCs vs. patients with early-stage PD, p=0.0008; vs. patients with late-stage PD, p<0.0001). In contrast, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) and caspase-1 were elevated in patients with PD, especially those in the late stages. Levels of patients with MSA resembled those of HCs but differed from those of patients with PD. Interleukin (IL)-1β and IL-18 levels were not significantly different. In patients with early-stage PD, NLRP3 expression was negatively correlated with disease duration, the Movement Disorder Society-Unified Parkinson’s Disease Rating Scale Part II score, and the cognitive score.
Conclusion
Our findings challenge the prevailing hypothesis that NLRP3 inflammasome activation directly contributes to PD pathogenesis. Instead, the observed increase in ASC and caspase-1 expression suggests the potential involvement of alternative inflammasome pathways during disease progression.
3.Immunohistochemical expression of anaplastic lymphoma kinase in neuroblastoma and its relations with some clinical and histopathological features
Thu Dang Anh PHAN ; Thao Quyen NGUYEN ; Nhi Thuy TO ; Thien Ly THANH ; Dat Quoc NGO
Journal of Pathology and Translational Medicine 2024;58(1):29-34
Background:
Anaplastic lymphoma kinase (ALK) mutations have been identified as a prominent cause of some familial and sporadic neuroblastoma (NB). ALK expression in NB and its relationship with clinical and histopathological features remains controversial. This study investigated ALK expression and its potential relations with these features in NB.
Methods:
Ninety cases of NB at the Department of Pathology, University of Medicine and Pharmacy at Ho Chi Minh City, Viet Nam from 01/01/2018 to 12/31/2021, were immunohistochemically stained with ALK (D5F3) antibody. The ALK expression and its relations with some clinical and histopathological features were investigated.
Results:
The rate of ALK expression in NB was 91.1%. High ALK expression (over 50% of tumor cells were positive with moderate-strong intensity) accounted for 65.6%, and low ALK expression accounted for 34.4%. All the MYCN-amplified NB patients had ALK immunohistochemistry positivity, most cases had high ALK protein expression. The undifferentiated subtype of NB had a lower ALK-positive rate than the poorly differentiated and differentiated subtype. The percentages of ALK positivity were significantly higher in more differentiated histological types of NB (p = .024). There was no relation between ALK expression and: age group, sex, primary tumor location, tumor stage, MYCN status, clinical risk, Mitotic-Karyorrhectic Index, prognostic group, necrosis, and calcification.
Conclusions
ALK was highly expressed in NB. ALK expression was not related to several clinical and histopathological features. More studies are needed to elucidate the association between ALK expression and ALK gene status and to investigate disease progression, especially the oncogenesis of ALK-positive NB.
4.Immunohistochemical expression in idiopathic inflammatory myopathies at a single center in Vietnam
Dat Quoc NGO ; Si Tri LE ; Khanh Hoang Phuong PHAN ; Thao Thi Phuong DOAN ; Linh Ngoc Khanh NGUYEN ; Minh Hoang DANG ; Thien Thanh LY ; Thu Dang Anh PHAN
Journal of Pathology and Translational Medicine 2024;58(4):174-181
Background:
The identification of idiopathic inflammatory myopathies (IIMs) requires a comprehensive analysis involving clinical manifestations and histological findings. This study aims to provide insights into the histopathological and immunohistochemical aspects of IIMs.
Methods:
This retrospective case series involved 56 patients diagnosed with IIMs at the Department of Pathology, University of Medicine and Pharmacy at Ho Chi Minh City, from 2019 to 2023. The histology and immunohistochemical expression of HLA-ABC, HLA-DR, C5b-9, Mx1/2/3, and p62 were detected.
Results:
We examined six categories of inflammatory myopathy, including immunemediated necrotizing myopathy (58.9%), dermatomyositis (DM; 23.2%), overlap myositis (8.9%), antisynthetase syndrome (5.4%), inclusion body myositis (IBM; 1.8%), and polymyositis (1.8%). The average age of the patients was 49.7 ± 16.1 years, with a female-to-male ratio of 3:1. Inflammatory cell infiltration in the endomysium was present in 62.5% of cases, perifascicular atrophy was found in 17.8%, and fiber necrosis was observed in 42 cases (75.0%). Rimmed vacuoles were present in 100% of cases in the IBM group. Immunohistochemistry showed the following positivity rates: HLA-ABC (89.2%), HLA-DR (19.6%), C5b-9 (57.1%), and Mx1/2/3 (10.7%). Mx1/2/3 expression was high in DM cases. p62 vacuole deposits were noted in the IBM case. The combination of membrane attack complex and major histocompatibility complex I helped detect IIMs in 96% of cases.
Conclusions
The diagnosis of IIMs and their subtypes should be based on clinical features and histopathological characteristics. Immunohistochemistry plays a crucial role in the diagnosis and differentiation of these subgroups.
5.A study of pathological characteristics and BRAF V600E status in Langerhans cell histiocytosis of Vietnamese children
Thu Dang Anh PHAN ; Bao Gia PHUNG ; Tu Thanh DUONG ; Vu Anh HOANG ; Dat Quoc NGO ; Nguyen Dinh The TRINH ; Tung Thanh TRAN
Journal of Pathology and Translational Medicine 2021;55(2):112-117
Background:
Langerhans cell histiocytosis (LCH) is more common in children than adults and involves many organs. In children, the BRAF V600E mutation is associated with recurrent and high-risk LCH.
Methods:
We collected paraffin blocks of 94 pediatric LCH patients to detect BRAF V600E mutation by sequencing. The relationship between BRAF V600E status and clinicopathological parameters were also critically analyzed.
Results:
BRAF V600E mutation exon 15 was detected in 45 cases (47.9%). Multiple systems LCH showed a significantly higher BRAF V600E mutation rate than a single system (p=.001). No statistical significance was evident for other clinical characteristics such as age, sex, location, risk organs involvement, and CD1a expression.
Conclusions
In Vietnamese LCH children, the proportion of BRAF V600E mutational status was relatively high and related to multiple systems.
6. Anti-inflammatory effects of alkaloid enriched extract from roots of Eurycoma longifolia Jack
Dao Thi Thanh HIEN ; Tran Phi LONG ; Tran Phuong THAO ; Jeong-Hyung LEE ; Duong Thu TRANG ; Nguyen Thi Thu MINH ; Pham VAN CUONG ; Nguyen Hai DANG ; Do Thi Ngoc LAN ; Nguyen Tien DAT
Asian Pacific Journal of Tropical Biomedicine 2019;9(1):18-23
Objective: To examine the in vitro and in vivo anti-inflammatory effects of the alkaloid enriched extract (ELA) from the roots of Eurycoma longifolia. Methods: The in vitro antiinflammatory effects of ELA were evaluated by examining its inhibitory activities against nitric oxide (NO) production and inducible nitric oxide synthase (iNOS) and cyclooxygenase 2 (COX-2) expressions in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. The level of NO produced in the culture media was determined by Griess method. The iNOS and COX-2 protein expressions were analyzed by Western blot. The in vivo effect of ELA was evaluated on LPS-induced septic shock in mice model. Mice mortality was monitored for 5 days after injection of LPS. The chemical contents of the ELA were determined by using various chromatographic and spectroscopic techniques. Results: The ELA was found to exhibit a significant anti-inflammatory effect in both in vitro and in vivo models. The results demonstrated that ELA dose-dependently inhibited LPS-induced NO production as well as the protein iNOS and COX-2 expressions. In the septic shock model, ELA dose-dependently protected mice from LPS-induced mortality. Further study on the isolated components of ELA indicated that 9,10-dimethoxycanthin-6-one may contribute significantly to the anti-inflammatory effects of the extract. Conclusions: These results suggest that ELA exhibits the anti-inflammatory activity via suppression of pro-inflammatory mediators such as NO, iNOS, and COX-2 and protects mice from LPS-induced mortality in septic shock model.
7.HER2 Status and Its Heterogeneity in Gastric Carcinoma of Vietnamese Patient.
Dang Anh Thu PHAN ; Vu Thien NGUYEN ; Thi Ngoc Ha HUA ; Quoc Dat NGO ; Thi Phuong Thao DOAN ; Sao Trung NGUYEN ; Anh Tu THAI ; Van Thanh NGUYEN
Journal of Pathology and Translational Medicine 2017;51(4):396-402
BACKGROUND: Human epidermal growth factor receptor 2 (HER2) is related to the pathogenesis and poor outcome of numerous types of carcinomas, including gastric carcinoma. Gastric cancer patients with HER2 positivity have become potential candidates for targeted therapy with trastuzumab. METHODS: We investigated 208 gastric cancer specimens using immunohistochemistry (IHC), fluorescence in situ hybridization and dual in situ hybridization (ISH). We also investigated the concordance between IHC and ISH. The correlation between HER2 status and various clinicopathological findings was also investigated. RESULTS: In total, 15.9% (33/208) and 24.5% (51/208) of gastric cancers showed HER2 gene amplification and protein overexpression, respectively. A high level of concordance between ISH and IHC analyses (91.3%, κ = 0.76) was found. A significant correlation between HER2 status and intestinal-type (p < .05) and differentiated carcinomas (p < .05) was also noted. The HER2 heterogeneity was high in gastric cancers; we found 68.8% phenotypic heterogeneity and 57.6% genotypic heterogeneity. Heterogeneity in HER2 protein expression and gene amplification showed a close association with diffuse histologic type and IHC 2+. CONCLUSIONS: HER2 protein overexpression and gene amplification were detected in 24.5% and 15.9% of gastric cancer specimens, respectively. Intestinal-type showed a higher level of HER2 protein overexpression and gene amplification than diffuse type. HER2 status also showed a significant relationship with well- and moderately-differentiated carcinomas. The ratio of phenotypic and genotypic heterogeneity of HER2 was high in gastric carcinomas and was associated with HER2 IHC 2+ and diffuse histologic type.
Asian Continental Ancestry Group*
;
Fluorescence
;
Gene Amplification
;
Genes, erbB-2
;
Humans
;
Immunohistochemistry
;
In Situ Hybridization
;
Population Characteristics*
;
Receptor, Epidermal Growth Factor
;
Stomach Neoplasms
;
Trastuzumab
8.Anti-inflammatory Triterpenes and Glyceryl Glycosides from Kandelia candel (L.) Druce.
Le Duc DAT ; Nguyen Phuong THAO ; Bui Huu TAI ; Bui Thi Thuy LUYEN ; Seo Young YANG ; Sohyun KIM ; Jung Eun KOO ; Young Sang KOH ; Nguyen The CUONG ; Nguyen Hoai NAM ; Nguyen Van THANH ; Phan Van KIEM ; Chau Van MINH ; Young Ho KIM
Natural Product Sciences 2015;21(3):150-154
Phytochemical investigation of Kandelia candel resulted in the isolation of six triterpenes (1 - 5) and two glyceryl glycosides (6 and 7) and their structures were determined by comparing the spectroscopic data with those of reported values. In present study, we described the inhibitory effects of fractions and isolated compounds from K. candel on pro-inflammatory cytokines (IL-12 p40, IL-6, and TNF-alpha) production in lipopolysaccharide (LPS) stimulated bone marrow-derived dendritic cells (BMDCs). Results indicated that compounds 3, 6, and 7 showed potent inhibition on IL-6 production (IC50 values at less than 0.5 microM, respectively). Meanwhile, compounds 6 and 7 exhibited strong inhibitory effects on the production of TNF-alpha (IC50 values of 1.7 +/- 0.1 and 5.5 +/- 0.2 microM). Compounds 1 and 3 were also showed the inhibitory effects on IL-12 p40 production (IC50 values of 8.9 +/- 0.4 and 3.3 +/- 0.1 microM, respectively).
Cytokines
;
Dendritic Cells
;
Glycosides*
;
Interleukin-12
;
Interleukin-6
;
Rhizophoraceae*
;
Triterpenes*
;
Tumor Necrosis Factor-alpha
9.Emerging a member of reoviridae family associated with acute encephalitis syndrome in Gia Lai province, 2005
Nga Thi Phan ; Thuy Thanh Nguyen ; Trang Minh Bui ; Tuan Thi Nguyen ; Dat Tuan Dang ; Hien Tran Nguyen
Journal of Preventive Medicine 2007;17(2):5-9
Background: In recent years, some arbo viruses which causes acute encephalitis syndrome (AES) have been identified in serveral countries in the world such as Chandipura virus belonging to Rhabdoviridae family in India, Banna virus belonging to Reoviridae family in China. In Vietnam, apart from Japanese Encephalitis Virus which is considered as main cause of AES, there are a few intestinal viruses like Herpes symplex virus type 1 and 4 and Nam Dinh virus considering other causes of AES. Objective: To identify the hyppothesis that one virus strain parasitizing in mosquito in Gia Lai province causes AES in order to provide more information about virus strains which cause AES in Vietnam. Subjects and method: Aedes albopictus cell line clone C6/36 was used for the isolation of virus in 43 cerebrospinal fluid samples of patients who were treated in Gia Lai hospital, from January/2005 to July/2005. Result and Conclusion: One virus strain from a 3-year old girl in Gia Lai province was isolated in 2005. The virus coded 05VN225 has the morphology similar to other viruses belonging to Reoviridea family.The nucleic acid sequence of the virus was checked with specific primers of alphavirus and flavirus groups, Nam Dinh virus and Conti virus group B (reovirus) of the Reoviridae. The positive result was confirmed with reovirus primers. This member of the Reoviridae family was isolated from acute encephalitis syndrome in Vietnam in 2005. Further study on pathology of the virus is very necessary.
Encephalitis
;
Arbovirus/ epidemiology
;
pathology
;
Reoviridae/ growth &
;
development
;
pathogenicity
;

Result Analysis
Print
Save
E-mail