Interpretable machine learning for predicting the response duration to Sintilimab plus chemotherapy in patients with advanced gastric or gastroesophageal junction cancer.

Background: Sintilimab plus chemotherapy has proven effective as a combination immunotherapy for patients with advanced gastric and gastroesophageal junction adenocarcinoma (GC/GEJC). A multi-center study conducted in China revealed a median progression-free survival (PFS) of 7.1 months. However, the prediction of response duration to this immunotherapy has not been thoroughly investigated. Additionally, the potential of baseline laboratory features in predicting PFS remains largely unexplored. Therefore, we developed an interpretable machine learning (ML) framework, iPFS-SC, aimed at predicting PFS using baseline (pre-treatment) laboratory features and providing interpretations of the predictions. Materials and methods: A cohort of 146 patients with advanced GC/GEJC, along with their baseline laboratory features, was included in the iPFS-SC framework. Through a forward feature selection process, predictive baseline features were identified, and four ML algorithms were developed to categorize PFS duration based on a threshold of 7.1 months. Furthermore, we employed explainable artificial intelligence (XAI) methodologies to elucidate the relationship between features and model predictions. Results: The findings demonstrated that LightGBM achieved an accuracy of 0.70 in predicting PFS for advanced GC/GEJC patients. Furthermore, an F1-score of 0.77 was attained for identifying patients with PFS durations shorter than 7.1 months. Through the feature selection process, we identified 11 predictive features. Additionally, our framework facilitated the discovery of relationships between laboratory features and PFS. Conclusion: A ML-based framework was developed to predict Sintilimab plus chemotherapy response duration with high accuracy. The suggested predictive features are easily accessible through routine laboratory tests. Furthermore, XAI techniques offer comprehensive explanations, both at the global and individual level, regarding PFS predictions. This framework enables patients to better understand their treatment plans, while clinicians can customize therapeutic approaches based on the explanations provided by the model.

Clinical correlation of B7-H3 and B3GALT4 with the prognosis of colorectal cancer.

AIM: To investigate the expression and clinical significance of B7 homolog 3 (B7-H3) and ß-1,3-galactosyltransferase-4 (B3GALT4) in colorectal cancer (CRC) patients. METHODS: Using tissue microarray, we identified the expression of B7-H3 and B3GALT4 in 223 CRC patient samples by immunohistochemistry and evaluated the possible correlation between B7-H3 and B3GALT4 and clinical outcomes. Further, the mRNA and protein expression were identified to establish the regulatory relationship of B7-H3 with B3GALT4 in vitro. RESULTS: A significant positive correlation between B7-H3 and B3GALT4 was observed in CRC specimens (r = 0.219, P = 0.001). High expression of B7-H3 was identified as a significant independent predictor of poor overall survival (OS) [hazard ratio (HR) = 1.781; 95%CI: 1.027-3.089; P = 0.040]. Moreover, high expression of B3GALT4 was also recognized as an independent predictor of inferior OS (HR = 1.597; 95%CI: 1.007-2.533; P = 0.047). Additionally, CRC patients expressing both high B7-H3 and high B3GALT4 contributed to a significant decrease in OS (HR = 2.283; 95%CI: 1.289-4.042; P = 0.005). In CRC cell lines with stable expression of high B7-H3, the mRNA and protein expressions of B3GALT4 were significantly upregulated. Similarly, the expression of B3GALT4 was significantly reduced when expression of B7-H3 was knocked down. CONCLUSION: The expression of B3GALT4 in CRC is positively correlated with B7-H3 expression in vitro. B7-H3/B3GLAT4 may be used as dual prognostic biomarkers for CRC.

Lower serum CA125 level, negative vascular invasion, and wild BRAF were strongly associated with better 2-year disease-free survival in patients with stage III colorectal cancer who received adjuvant chemotherapy.

BACKGROUND: Adjuvant chemotherapy plays important role in the comprehensive treatment of patients with stage III colorectal cancer. However, there is few molecular markers for predicting the therapeutic effect. OBJECTIVE: To identify factors that could predict adjuvant chemotherapy benefits in patients with stage III colorectal cancer. METHODS: The medical records of 294 patients were reviewed and analyzed using the Kaplan-Meier method and Cox analysis. RESULTS: Lower CA125 (⩽ 35 u/ml, P= 0.0015) serum levels, stage IIIa (P= 0.0027), 1-3 positive lymph nodes (P= 0.0256), negative vascular invasion (P= 0.0215), lower CA199 (⩽ 27 u/ml, P= 0.0038) serum levels, and wild-type BRAF status (P= 0.0125) were significantly associated with a higher 2-year DFS rate in patients with stage III colorectal cancer. However, in multivariate COX analysis, the association remained significant only for CA125 levels (vs. ⩽ 35 u/ml group, HR 3.341; 95% CI, 1.198-9.316; P= 0.0212), vascular invasion (vs. negative vascular invasion, HR, 2.349; 95% CI, 1.227-4.499; P= 0.01), and BRAF (V600E) (vs. wild Braf, HR, 7.794; 95% CI, 1.867-32.531; P= 0.0049). CONCLUSION: Lower CA125 serum levels, negative vascular invasion, and wild-type BRAF status were significantly associated with improved 2-year DFS rates among patient with stage III disease who received adjuvant chemotherapy.

MALAT1 is a prognostic factor in glioblastoma multiforme and induces chemoresistance to temozolomide through suppressing miR-203 and promoting thymidylate synthase expression.

Glioblastoma multiforme (GBM) is the most malignant brain tumor with limited therapeutic options. Temozolomide (TMZ) is a novel cytotoxic agent used as first-line chemotherapy for GBM, however, some individual cells can't be isolated for surgical resection and show treatment-resistance, thus inducing poor prognosis. By using the HiSeq sequencing and bioinformatics methods, we identified lncRNAs showing different expression levels in TMZ-resistant and non-resistant patients. RT-qPCR was then performed in tissues and serum samples, and lncRNA MALAT1 was finally identified to show considerable discriminating potential to identify responding patients from non-responding patients. Moreover, high serum MALAT1 expression was associated with poor chemoresponse and survival in GBM patients receiving TMZ treatment. Subsequently, the TMZ resistant cell lines were established, and the CCK8 assay showed that lncRNA MALAT1 knockdown significantly reversed TMZ resistance in GBM cells. The gain and loss-function experiments revealed that miR-203 was down-regulated by MALAT1 and this interaction has reciprocal effects. Besides, thymidylate synthase (TS) mRNA was identified as a direct target of miR-203. LncRNA MALAT1 inhibition re-sensitized TMZ resistant cells through up-regulating miR-203 and down-regulating TS expression. On the other hand, MALAT1 overexpression promoted resistance by suppressing miR-203 and promoting TS expression. In conclusion, our integrated approach demonstrates that enhanced expression of lncRNA MALAT1 confers a potent poor therapeutic efficacy and inhibition of MALAT1 levels could be a future direction to develop a novel therapeutic strategy to overcome TMZ resistance in GBM patients.

Genomic Characterization of Esophageal Squamous Cell Carcinoma Reveals Critical Genes Underlying Tumorigenesis and Poor Prognosis.

The genetic mechanisms underlying the poor prognosis of esophageal squamous cell carcinoma (ESCC) are not well understood. Here, we report somatic mutations found in ESCC from sequencing 10 whole-genome and 57 whole-exome matched tumor-normal sample pairs. Among the identified genes, we characterized mutations in VANGL1 and showed that they accelerated cell growth in vitro. We also found that five other genes, including three coding genes (SHANK2, MYBL2, FADD) and two non-coding genes (miR-4707-5p, PCAT1), were involved in somatic copy-number alterations (SCNAs) or structural variants (SVs). A survival analysis based on the expression profiles of 321 individuals with ESCC indicated that these genes were significantly associated with poorer survival. Subsequently, we performed functional studies, which showed that miR-4707-5p and MYBL2 promoted proliferation and metastasis. Together, our results shed light on somatic mutations and genomic events that contribute to ESCC tumorigenesis and prognosis and might suggest therapeutic targets.

[Advances in Raman Spectroscopy for Nasopharyngeal Carcinoma Tissue].

Nasopharyngeal carcinoma is a unique malignant tumor that has a distinct geographic and racial distribution, with a high incidence in southeast Asia and southern China. High degree of malignancy, poor prognosis and difficulty in early diagnosis remain a problem in nasopharyngeal carcinoma. Raman spectroscopy technique based on inelastic scattering is a rapid and nonivasive detection method, which is capable of providing the information of biochemical components at molecular vibration level.This article reviewed the recent research progress of nasopharyngeal carcinoma based on Raman spectroscopy. It mainly introduces the study of detecting nasopharyngeal carcinoma tissue by using Raman spectroscopy as well as surface-enhanced Raman scattering spectroscopy (SERS). The emphasis is put on the latest works by our research group, including high wavenumber Raman spectroscopy of tissue, Raman spectroscopy of tissue smears, and a specially designed endoscopic device combined with Raman spectroscopy for in vivo nasopharyngeal cancerous tissue detection, which was firstly developed by our group. Finally, the prospects of the development of Raman spectroscopy for nasopharyngeal carcinoma were discussed.

Effect of route of preoperative biopsy on endoscopic submucosal dissection for patients with early gastric cancer.

OBJECTIVE: To observe and compare the effects of multi-patch biopsy under conventional white light imaging endoscopy (C-WLI) and precise targeted biopsy under magnifying narrow-band imaging endoscopy (M-NBI) on the endoscopic submucosal dissection (ESD) of early gastric cancers and intraepithelial neoplasias. METHODS: According to the way of selecting biopsy specimens, patients were divided into C-WLI and M-NBI groups, 20 cases. The ESD operations of the 2 groups were compared quantitively. RESULTS: The mean frequency of biopsy in M-NBI group was (1.00±0.00), obviously lower than in the C-WLI group (4.78±1.02) (P<0.01).The average total number of selected biopsy specimens was also fewer (1.45±0.12 and 7.82±2.22, respectively, P<0.01). There was no significant difference in the time of determining excision extension, marking time and the time of specimen excision of 2 groups during the ESD (P>0.05), whereas submucosal injection time, mucosal dissection time, stopping bleeding time, wound processing time in the M-NBI group were significantly shorter than in the C-WLI group (P<0.01). CONCLUSION: Precise targeted biopsy under M-NBI can obviously shorten the time of ESD operation, with small quantity of tissues but high pathological positive rate.

HOTAIR, a prognostic factor in esophageal squamous cell carcinoma, inhibits WIF-1 expression and activates Wnt pathway.

Long non-coding RNAs (LncRNAs) have been recently found to be pervasively transcribed in the genome and critical regulators of the epigenome. HOTAIR, as a well-known LncRNA, has been found to play important roles in several tumors. Herein, the clinical application value and biological functions of HOTAIR were focused and explored in esophageal squamous cell carcinoma (ESCC). It was found that there was a great upregulation of HOTAIR in ESCC compared to their adjacent normal esophageal tissues. Meanwhile, patients with high HOTAIR expression have a significantly poorer prognosis than those with low expression. Moreover, HOTAIR was further validated to promote migration and invasion of ESCC cells in vitro. Then some specific molecules with great significance were investigated after HOTAIR overexpression using microarray and quantitative real time-polymerase chain reaction (qPCR). WIF-1 playing an important role in Wnt/ß-catenin signaling pathway was selected and further tested by immunehistochemistry. Generally, inverse correlation between HOTAIR and WIF-1 expression was demonstrated both in ESCC cells and tissues. Mechanistically, HOTAIR directly decreased WIF-1 expression by promoting its histone H3K27 methylation in the promoter region and then activated the Wnt/ß-catenin signaling pathway. This newly identified HOTAIR/WIF-1 axis clarified the molecular mechanism of ESCC cell metastasis and represented a novel therapeutic target in patients with ESCC.

[Role of transcription factor T-bet and Eomes in IFN-gamma secretion of different human T cell subsets].

AIM: To investigate the effect of siRNAs specific for T-bet and Eomesodermin (Eomes) in interferon-gamma (IFN-gamma) production of different human T cell subsets. METHODS: Double-stranded small interfering RNA (siRNA) sequences specific for genes of T-bet and Eomes were chemically synthesized and transfected into anti-CD3 mAb activated alphabeta T cells and Mtb-Ag activated gammadelta T cells. CD4(+), CD8(+) T and gammadelta T cells were sorted by flow cytometry and the expressions of T-bet and Eomes gene mRNA were detected by RT-PCR technique. The changes of IFN-gamma production were determined by flow cytometry. RESULTS: After two series of transfection, the siRNA-FAM(+) cells were about 50% in the transfected cells. The IFN-gamma(+) cells in CD4(+) T cells (50.20%) decreased in the cells transfected with T-bet siRNA (18.46%) but no obvious decrease was observed in the cells transfected with Eomes siRNA, whereas the IFN-gamma(+) cells in CD8(+) T cells (76.51%) decreased in the cells transfected with Eomes siRNA (25.37%) and no obvious decrease was observed in the cells transfected with T-bet siRNA. However, the IFN-gamma producing cells in gammadelta T cells (76.52%) decreased in the cells transfected with T-bet siRNA (56.57%) or with Eomes siRNA (42.53%). CONCLUSION: At the level of transcription factors, T-bet and Eomes are important transcription factors for the regulation of IFN-gamma production in CD4(+) and CD8(+) T cells, respectively. Both T-bet and Eomes may simultaneously be involved in the regulation of the IFN-gamma production of gammadeltaT cells.