Single cell and bulk RNA sequencing identifies tumor microenvironment subtypes and chemoresistance-related IGF1+ cancer-associated fibroblast in gastric cancer.

BACKGROUND: The tumor microenvironment (TME) significantly influences prognosis and drug resistance in various tumors, yet its heterogeneity and the mechanisms affecting therapeutic response remain unclear in gastric cancer (GC). METHODS: The heterogenous TME were explored with single-cell RNA-sequencing (scRNA-seq) data of 50 primary GC samples. We then identified four GC TME subtypes with nonnegative matrix factorization (NMF) and constructed a pearson nearest-centroid classifier based on subtype-specific upregulated genes. Genomic features and clinical significance of four subtypes were comprehensively evaluated. We reclustered fibroblasts to identify cancer-associated fibroblast (CAF) subtype associated with poor clinical outcomes. RT-qPCR and double immunofluorescence staining were applied to validate the findings. Cellchat analysis elucidated potential molecular mechanisms of the CAF subtype in GC disease progression and chemotherapy resistance. FINDINGS: The GC TME exhibited high heterogeneity, influencing chemo-sensitivity. Four TME-based subtypes predicting response to immunotherapy and chemotherapy were identified and validated in 1406 GC patients. Among which, ISG1 subtype displayed higher fibroblasts infiltration and heightened oncogenic pathways, and inferior response to chemotherapy with unfavorable prognosis. Microsatellite instability-high (MSI-H) GCs within four TME subtypes showed immunological heterogeneity. We then reported an IGF1-overexpressing CAF was associated with chemo-resistance and GC recurrence. Cell communication analysis revealed IGF1+ CAF may induce drug-resistant phenotypes in tumor cells through IGF1-α6ß4 integrin ligand-receptor binding and activation of EMT biological process. INTERPRETATION: We identified four TME-based subtypes with different clinical outcomes and IGF1+ CAFs contributing to poor clinical outcomes in GC, which might provide guidance for individualized treatment and facilitate the development of novel therapeutic targets.

Multivariate prognostic index and triplet regimen efficacy predictive index in locally advanced and metastatic gastric cancer: pooled analysis from three clinical trials using individual patient data.

Background: To construct an effective prognostic index to predict overall survival (OS) and triplet regimen efficacy for advanced gastric cancer (AGC) patients treated with platinum-based and fluorouracil-based chemotherapy. Objectives: Between 2011 and 2021, 679 patients from two randomized phase III trials and one phase II trial were enrolled. Designs: We collected 11 baseline clinicopathological and 14 hematological parameters to establish a prognostic index. Methods: Univariate and multivariate Cox analyses were used to screen prognostic factors, and a prognostic index nomogram was conducted. Results: Seven prognostic factors were identified: primary tumor site in the non-proximal gastric area, signet-ring cell carcinoma (SRCC)/mucinous carcinoma, peritoneal metastasis, neutrophil count higher than the upper limit of normal value (ULN), lymphocyte count lower than the lower limit of normal value, lactate dehydrogenase level higher than the ULN, and alkaline phosphatase level higher than the ULN as significant for prognosis. A prognostic nomogram named the Fudan advanced gastric cancer prognostic risk score (FARS) index was constructed, and patients in the high-risk group had significantly shorter OS than those in the low-risk group (median OS, 15.5 versus 8.0 months, p < 0.001). The areas under the curve of the FARS index for 1-, 2-, and 3-year OS were 0.70, 0.72, and 0.77, respectively. A validation and external cohort verified the prognostic value of the FARS index. Moreover, three triplet regimen efficacy parameters were identified: SRCC/mucinous adenocarcinoma, primary tumor location in the non-proximal gastric area, and peripheral neutrophil count higher than the ULN; a TRIS index was subsequently conducted. In patients with any two of the three parameters, the triplet regimen showed significantly longer OS than the doublet regimen (p = 0.018). Conclusion: The constructed FARS index to predict the OS of AGC patients and the TRIS index to screen out the dominant population for triplet regimens can be used to aid clinical decision-making and individual risk stratification.

A prognostic index in locally advanced and metastatic gastric cancer To date, no recognized systematic prognostic score has been established for advanced gastric cancer (AGC). Our research aims to construct an effective prognostic index to predict overall survival (OS) for AGC patients to aid clinical decision-making and individual risk stratification. In our research, seven prognostic factors were identified: primary tumor site in the non-proximal gastric area, signet-ring cell carcinoma (SRCC)/mucinous carcinoma, peritoneal metastasis, neutrophil count higher than the upper limit of normal value (ULN), lymphocyte count lower than the lower limit of normal value, lactate dehydrogenase level higher than the ULN, and alkaline phosphatase level higher than the ULN as significant for prognosis. A prognostic index named the Fudan advanced gastric cancer prognostic risk score (FARS) index was constructed, and patients in the high-risk group had significantly shorter OS than those in low-risk group (median OS, 15.5 months vs. 8.0 months, P < 0.001). Moreover, three triplet regimen efficacy parameters were identified: SRCC/mucinous adenocarcinoma, primary tumor location in the non-proximal gastric area, and peripheral neutrophil count higher than the ULN; a TRIS index was subsequently conducted. In patients with any two of the three parameters, the triplet regimen showed significantly longer OS than the doublet regimen (P = 0.018).

Multi-dimension metabolic prognostic model for gastric cancer.

Background: Metabolic reprogramming is involved in different stages of tumorigenesis. There are six widely recognized tumor-associated metabolic pathways, including cholesterol catabolism process, fatty acid metabolism, glutamine metabolic process, glycolysis, one carbon metabolic process, and pentose phosphate process. This study aimed to classify gastric cancer patients into different metabolic bio-similar clusters. Method: We analyzed six tumor-associated metabolic pathways and calculated the metabolic pathway score through RNA-seq data using single sample gene set enrichment analysis. The consensus clustering analysis was performed to classify patients into different bio-similar clusters by multi-dimensional scaling. Kaplan-Meier curves were presented between different metabolic bio-similar groups for OS analysis. Results: A training set of 370 patients from the Cancer Genome Atlas database with primary gastric cancer was chosen. Patients were classified into four metabolic bio-similar clusters, which were identified as metabolic non-specificity, metabolic-active, cholesterol-silence, and metabolic-silence clusters. Survival analysis showed that patients in metabolic-active cluster and metabolic-silence cluster have significantly poor prognosis than other patients (p=0.031). Patients in metabolic-active cluster and metabolic-silence cluster had significantly higher intra-tumor heterogeneity than other patients (p=0.032). Further analysis was performed in metabolic-active cluster and cholesterol-silence cluster. Three cell-cycle-related pathways, including G2M checkpoints, E2F targets, and MYC targets, were significantly upregulated in metabolic-active cluster than in cholesterol-silence cluster. A validation set of 192 gastric cancer patients from the Gene Expression Omnibus data portal verified that metabolic bio-similar cluster can predict prognosis in gastric cancer. Conclusion: Our study established a multi-dimension metabolic prognostic model in gastric cancer, which may be feasible for predicting clinical outcome.

GepLiver: an integrative liver expression atlas spanning developmental stages and liver disease phases.

Chronic liver diseases usually developed through stepwise pathological transitions under the persistent risk factors. The molecular changes during liver transitions are pivotal to improve liver diagnostics and therapeutics yet still remain elusive. Cumulative large-scale liver transcriptomic studies have been revealing molecular landscape of various liver conditions at bulk and single-cell resolution, however, neither single experiment nor databases enabled thorough investigations of transcriptomic dynamics along the progression of liver diseases. Here we establish GepLiver, a longitudinal and multidimensional liver expression atlas integrating expression profiles of 2469 human bulk tissues, 492 mouse samples, 409,775 single cells from 347 human samples and 27 liver cell lines spanning 16 liver phenotypes with uniformed processing and annotating methods. Using GepLiver, we have demonstrated dynamic changes of gene expression, cell abundance and crosstalk harboring meaningful biological associations. GepLiver can be applied to explore the evolving expression patterns and transcriptomic features for genes and cell types respectively among liver phenotypes, assisting the investigation of liver transcriptomic dynamics and informing biomarkers and targets for liver diseases.

Clinicopathological Analysis and Treatment of Adult Patients with Inflammatory Myofibroblastic Tumor: A 15-Year Single- Center Study.

PURPOSE: Inflammatory myofibroblastic tumor (IMT) is a rare mesenchymal malignancy that occurs primarily in children and adolescents. The clinical and pathological features of IMT in adult patients are not well understood. Materials and Methods: We retrospectively searched for records of adult patients with IMT at Fudan University Shanghai Cancer Center from 2006 to 2021. Clinicopathological data, treatments, and outcomes were collected and analyzed. RESULTS: Thirty adult patients with IMT, mostly women (60.0%), were included. The median age of the patients was 38 (21-77). The most common primary site was abdominopelvic region (53.3%), followed by lungs (20.0%). Seven patients had an abdominal epithelioid inflammatory myofibroblast sarcoma (EIMS). The positivity rate of anaplastic lymphoma kinase (ALK) was 81.5% (22/27). Sixteen patients with advanced ALK-positive disease received crizotinib, with an objective response rate (ORR) of 81.3% and a disease control rate of 87.5%. The median progression-free survival was 20.8 months. EIMS was associated with more aggressive behavior; however, the prognosis was similar to that of non-EIMS patients after treatment with an ALK inhibitor. At a median follow-up time of 30 months (95% confidence interval [CI], 13.6 to 46.4), the 5-year overall survival was 77% (95% CI, 66 to 88) in all patients. CONCLUSION: Adult IMTs appeared more aggressive, with a higher incidence of recurrence and metastases, and patients with EIMS had more aggressive cases. Treatment with ALK inhibitors resulted in a high ORR and a durable response, which suggested that ALK inhibitors could be used as a first-line treatment option in adult patients with ALK-positive advanced IMT.

Randomized phase II study of TX followed by XELOX versus the reverse sequence for chemo-naive patients with metastatic gastric cancer.

This research found that the clinical outcomes (PFS, ORR, OS) of the non-platinum-based doublet regimen (docetaxel capecitabine combination) were similar to those of the platinum-based (oxaliplatin capecitabine combination) when used as first line therapy for MGC patients. Background: Docetaxel, platinum and fluorouracil are the three most important drugs in the treatment of MGC. This study was to compare clinical outcomes of the docetaxel capecitabine combination and the oxaliplatin capecitabine combination as first-line therapy in MGC patients. Methods: In this phase II trial, MGC patients were randomly assigned and treated with either TX (capecitabine 1000 mg/m2/twice daily/1-14 days and docetaxel 60/75 mg/m2 on the 1st day) (because of toxicity, the dose of docetaxel was reduced to 60 mg/m2) or XELOX (capecitabine the same dose with TX and oxaliplatin 130 mg/m2 on the 1st day) as first-line therapy. After progression, patients were crossover to the other group as second-line treatment. Results: Total 134 MGC patients were randomized (69 in TX, 65 in XELOX). There was no significant difference between the PFS of the two groups (TX vs XELOX, 4.6 months vs 5.1 months, p=0.359), and the SFS (9.3 months vs 7.5 months, p=0.705), OS (13.1 months vs 9.6 months, p=0.261), and ORR (46.4% vs 46.2%) were also similar. Among patients with ascites, the TX group had significantly longer PFS and OS than the XELOX group. A total of 85 patients (48 in TX, 37 in XELOX) received second-line treatment, with overall survival of second-line chemotherapy (OS2) of 8.0 m and 5.3 m (p=0.046), respectively. Grade 3 to 4 treatment-related adverse events of first line treatment occurred more in TX group than that in XELOX group(60.6% vs 55.4%). Conclusion: TX regimen is an alternative choice of first-line treatment for MGC patients. We still need to explore the large number of cohort to confirm this results.

XELOX doublet regimen versus EOX triplet regimen as first-line treatment for advanced gastric cancer: An open-labeled, multicenter, randomized, prospective phase III trial (EXELOX).

BACKGROUND: There is no consensus on whether triplet regimen is better than doublet regimen in the first-line treatment of advanced gastric cancer (AGC). We aimed to compare the efficacy and safety of oxaliplatin plus capecitabine (XELOX) and epirubicin, oxaliplatin, plus capecitabine (EOX) regimens in treating AGC. METHODS: This phase III trial enrolled previously untreated patients with AGC who were randomly assigned to receive the XELOX or EOX regimen. The primary endpoint was non-inferiority in progression-free survival (PFS) for XELOX as compared with EOX on an intention-to-treat basis. RESULTS: Between April 10, 2015 and August 20, 2020, 448 AGC patients were randomized to receive XELOX (n = 222) or EOX (n = 226). The median PFS (mPFS) was 5.0 months (95% confidence interval [CI] = 4.5-6.0 months) in the XELOX arm and 5.5 months (95% CI = 5.0-6.0 months) in the EOX arm (hazard ratio [HR] = 0.989, 95% CI = 0.812-1.203; Pnon-inferiority = 0.003). There was no significant difference in median overall survival (mOS) (12.0 vs. 12.0 months, P = 0.384) or objective response rate (37.4% vs. 45.1%, P = 0.291) between the two groups. In patients with poorly differentiated adenocarcinoma and liver metastasis, the EOX arm had a significantly longer mOS (P = 0.021) and a trend of longer mPFS (P = 0.073) than the XELOX arm. The rate of grade 3/4 adverse events (AEs) was 42.2% (90/213) in the XELOX arm and 72.5% (156/215) in the EOX arm (P = 0.001). The global health-related quality of life (QoL) score was significantly higher in the XELOX arm than in the EOX arm during chemotherapy. CONCLUSIONS: This non-inferiority trial demonstrated that the doublet regimen was as effective as the triplet regimen and had a better safety profile and QoL as a first-line treatment for AGC patients. However, the triplet regimen might have a survival advantage in patients with poorly differentiated adenocarcinoma and liver metastasis.

Three-Tier Prognostic Index in Young Adults With Advanced Gastric Cancer.

PURPOSE: To characterize clinical features and identify baseline prognostic factors for survival in young adults with advanced gastric cancer (YAAGC). MATERIALS AND METHODS: A total of 220 young inpatients (age less than or equal to 40 years) with an initial diagnosis of advanced gastric cancer were retrospectively enrolled in this study. RESULTS: Of a consecutive cohort of 220 patients with YAAGC, the median overall survival (OS) time was 16.3 months. One-year survival rate was 43.6% (95% CI: 36.5 to 50.7). In this cohort, a female (71.4%, n = 157) predominance and a number of patients with poorly differentiated tumors (95.9%, n = 211) were observed. In the univariate analysis, OS was significantly associated with neutrophil-lymphocyte ratio (NLR) (≥3.12), hypoproteinemia (<40 g/L), presence of peritoneal or bone metastases, and previous gastrectomy of primary tumor or radical gastrectomy. In multivariate Cox regression analysis, hypoproteinemia [hazard ratio (HR) 1.522, 95% CI 1.085 to 2.137, p = 0.015] and high NLR level (HR 1.446, 95% CI 1.022 to 2.047, p = 0.021) were two independent poor prognostic factors, while previous radical gastrectomy was associated with a favorable OS (HR 0.345, 95% CI 0.205 to 0.583, p = 0.000). A three-tier prognostic index was constructed dividing patients into good-, intermediate-, or poor-risk groups. Median OS for good-, intermediate-, and poor-risk groups was 36.43, 17.87, and 11.27 months, respectively. CONCLUSIONS: Three prognostic factors were identified, and a three-tier prognostic index was devised. The reported prognostic index may aid clinical decision-making, patient risk stratification, and planning of future clinical studies on YAAGC.

A STING-related prognostic score predicts high-risk patients of colorectal cancer and provides insights into immunotherapy.

BACKGROUND: Targeted therapeutic strategies for advanced colorectal cancer (CRC) have been limited. STING is crucial to the antitumor immunotherapy, for it stimulates IFN signaling to mediate the crosstalk between innate and adaptive immune responses. Emerging evidence suggests that STING also contributes to the prognosis of CRC. However, prognostic models relating to STING have not yet been explored. METHODS: A total of 431 CRC samples from the TCGA database were analyzed to explore the prognostic value of STING-related genes. We trained prognostic models using the multivariate Cox regression. A STING-related prognostic score (SPS) was calculated as the gene expression multiplied by the corresponding coefficients of the final model. A backward stepAIC strategy was adopted to select the optimal model. A nomogram was used to personalize medical decisions for CRC. RESULTS: The expression level of STING was upregulated in the CMS1 subtype (P=0.036). Among STING-related genes, DHX9 (HR =0.72, P=0.01), IRF2 (HR =1.34, P=0.022), and POLR1D (HR =1.23, P=0.038) showed significant prognostic value. The SPS was proven to be an independent risk factor (training: HR =2.9, P=0.00013; validation: HR =3.02, P=0.01), and outperformed random classifiers in identifying high-risk CRC. The high SPS group was characterized by less genomic aberrations, upregulated IL6-JAK-STAT3 and IL2-STAT5 signaling pathways, increased expression of TIM-3, increased infiltration of regulatory T (Treg) cells and T helper 17 (Th17) cells, and decreased infiltration of M0 macrophages. Finally, the nomogram based on the SPS and clinical factors showed good performance in CRC. CONCLUSIONS: SPS is an independent risk factor that could identify high-risk CRC. While ICBs may benefit patients of the CMS1 subtype, for the CMS2, CMS3, and CMS4 subtypes in the high SPS group, STING agonists and immunotherapies targeting the Th17 axis may be beneficial. Finally, the SPS-based nomogram could help advance personalized medical decisions for CRC.

Identification of a Four-Gene-Based SERM Signature for Prognostic and Drug Sensitivity Prediction in Gastric Cancer.

BACKGROUND: Gastric cancer (GC) is a highly molecular heterogeneous tumor with poor prognosis. Epithelial-mesenchymal transition (EMT) process and cancer stem cells (CSCs) are reported to share common signaling pathways and cause poor prognosis in GC. Considering about the close relationship between these two processes, we aimed to establish a gene signature based on both processes to achieve better prognostic prediction in GC. METHODS: The gene signature was constructed by univariate Cox and the least absolute shrinkage and selection operator (LASSO) Cox regression analyses by using The Cancer Genome Atlas (TCGA) GC cohort. We performed enrichment analyses to explore the potential mechanisms of the gene signature. Kaplan-Meier analysis and time-dependent receiver operating characteristic (ROC) curves were implemented to assess its prognostic value in TCGA cohort. The prognostic value of gene signature on overall survival (OS), disease-free survival (DFS), and drug sensitivity was validated in different cohorts. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) validation of the prognostic value of gene signature for OS and DFS prediction was performed in the Fudan cohort. RESULTS: A prognostic signature including SERPINE1, EDIL3, RGS4, and MATN3 (SERM signature) was constructed to predict OS, DFS, and drug sensitivity in GC. Enrichment analyses illustrated that the gene signature has tight connection with the CSC and EMT processes in GC. Patients were divided into two groups based on the risk score obtained from the formula. The Kaplan-Meier analyses indicated high-risk group yielded significantly poor prognosis compared with low-risk group. Pearson's correlation analysis indicated that the risk score was positively correlated with carboplatin and 5-fluorouracil IC50 of GC cell lines. Multivariate Cox regression analyses showed that the gene signature was an independent prognostic factor for predicting GC patients' OS, DFS, and susceptibility to adjuvant chemotherapy. CONCLUSIONS: Our SERM prognostic signature is of great value for OS, DFS, and drug sensitivity prediction in GC, which may give guidance to the development of targeted therapy for CSC- and EMT-related gene in the future.

Intra-tumoral heterogeneity and immune responses predicts prognosis of gastric cancer.

Chemotherapy resistance eventually develops in patients with gastric cancer (GC). Intra-tumoral heterogeneity (ITH) refers to the intercellular genetic variations and phenotypic diversity that affect responses to drug therapy. We measured ITH using mutant-allele tumor heterogeneity (MATH) derived from whole-exome sequencing data of patients with GC in The Cancer Genome Atlas (TCGA) database. The study included 385 patients from the TCGA database with available data regarding gastrectomy, survival, and whole-exome sequencing. Further analysis was performed in 171 GC patients with available data regarding adjuvant chemotherapy. Multiple factor analysis showed that MATH was an independent predictor of OS (hazard ratio [HR], 1.432; 95% confidence interval [CI], 1.073-1.913; P = 0.015) in patients with GC. Moreover, MATH was also an independent predictor of OS among the 171 GC patients who received adjuvant chemotherapy (HR, 2.016; 95% CI, 1.236-3.289; P = 0.005). Pathway enrichment and immune cell analyses revealed significantly higher infiltration by 20 types of immune cells in the low/intermediate group, compared to the group with high MATH scores. In conclusion, low/intermediate MATH scores predicted longer OS, when compared to those with high MATH scores. The immune response was obviously upregulated in patients with GC and low/intermediate MATH scores.

A pan-cancer analysis of HER2 index revealed transcriptional pattern for precise selection of HER2-targeted therapy.

BACKGROUND: The prevalence of HER2 alterations in pan-cancer indicates a broader range of application of HER2-targeted therapies; however, biomarkers for such therapies are still insufficient and limited to breast cancer and gastric cancer. METHODS: Using multi-omics data from The Cancer Genome Atlas (TCGA), the landscape of HER2 alterations was exhibited across 33 tumor types. A HER2 index was constructed using one-class logistic regression (OCLR). With the predictive value validated in GEO cohorts and pan-cancer cell lines, the index was then applied to evaluate the HER2-enriched expression pattern across TCGA pan-cancer types. FINDINGS: Increased HER2 somatic copy number alterations (SCNAs) could be divided into two patterns, focal- or arm-level. The expression-based HER2 index successfully distinguished the HER2-enriched subtype from the others and provided a stable and superior performance in predicting the response to HER2-targeted therapies both in breast tumor tissue and pan-cancer cell lines. With frequencies varying from 12.0% to 0.9%, tumors including head and neck squamous tumors, gastrointestinal tumors, bladder cancer, lung cancer and uterine tumors exhibited high HER2 indices together with HER2 amplification or overexpression, which may be more suitable for HER2-targeted therapies. The BLCA.3 and HNSC.Basal were the most distinguishable subtypes within bladder cancer and head and neck cancer respectively by HER2 index, implying their potential benefits from HER2-targeted therapies. INTERPRETATION: As a pan-cancer predictive biomarker of HER2-targeted therapies, the HER2 index could help identify potential candidates for such treatment in multiple tumor types by combining with HER2 multi-omics features. The discoveries of our study highlight the importance of incorporating transcriptional pattern into the assessment of HER2 status for better patient selection. FUNDING: The National Key Research and Development Program of China; Clinical Research and Cultivation Project of Shanghai ShenKang Hospital Development Center.

Severe loss of visceral fat and skeletal muscle after chemotherapy predicts poor prognosis in metastatic gastric cancer patients without gastrectomy.

Background: The influence of body composition parameters in cancer prognosis attracted researchers' attention. This study investigated the role of visceral fat and skeletal muscle in the prognosis and efficacy of chemotherapy in metastatic gastric cancer (MGC). Methods: This study included MGC patients without gastrectomy treated with EOF regimen (epirubicin, oxaliplatin and fluorouracil), who participated in a Phase II clinical trial (NCT00767377) with available PACS image data. The visceral fat area (VFA) and skeletal muscle area (SMA) were measured using standard computed tomography (CT). Results: A total of 46 patients were enrolled in the study. Patients with low baseline VFA and SMA had significantly shorter PFS and OS. In addition, the loss of VFA and SMA also predicts significantly shorter PFS and OS. A prognostic index that included two risk factors, severe loss of VFA and SMA, was used to categorize the patients into two groups: good-risk group (0 risk factors), poor-risk group (1 or 2 risk factors). Compared with the good-risk group, the poor-risk group displayed a 3.562-fold-increased risk of progression [hazard ratio (HR) 3.652, 95 % CI 1.653-7.678; P =0.001] and 2.859-fold-increased risk of death [hazard ratio (HR) 2.859, 95 % CI 1.271-6.434; P =0.011]. Conclusion: Low baseline VFA and SMA, as well as the severe loss of VFA and SMA predict poor prognosis for MGC patients treated by EOF regimen. In patients with severe loss of VFA and/or SMA after 2-cycle chemotherapy, the decision of subsequent chemotherapy should be made after deliberate consideration.

Genotype-immunophenotype analysis reveals the immunogenomic subtype and prognosis of multiple myeloma.

Immune dysfunction plays an important role in tumour development, recurrence, therapeutic responses and overall survival (OS). Multiple myeloma (MM) is a clonal B-cell malignancy which characterized by anti-tumoural immune dysfunction. In this study, we analysed 28 tumour-immune-related pathways and calculated the immune pathway score through published microarray data from the Gene Expression Omnibus (GEO) data portal. A training set of 345 patients and a validation set of 214 patients with primary MM were chosen. We performed least absolute shrinkage and selection operator (LASSO) analysis to identify prognostic factors. Then, we used cluster analysis to divide patients into three immunogenomic subtypes, which named abnormal immune activated type, common type and anti-myeloma immune activated type. Log­rank tests showed that anti-myeloma immune activated type had the best prognosis and abnormal immune activated type had the shortest OS (P = 0.000) and event-free survival (EFS) (P = 0.000). Multivariate Cox also indicated that the immunogenomic subtype was an independent predictor of OS (P = 0.001) and EFS (P = 0.000). We also analysed the characteristics and the immune-response patterns of different subtypes. Then, we established a mathematical model to classify patients in the validation set. In the validation set, patients with different immunogenomic subtypes also had a significantly different OS (P = 0.001) and EFS (P = 0.005). Our study explored tumour-immune-related pathways at a multi-dimensional level and found the immunogenomic subtype of MM. Potential mechanisms on the genetic level of how tumour-immunity influences the prognosis and therapeutic responses are provided. The immunogenomic subtype may be feasible for deciding clinical treatment in the future.

Genomic pattern of intratumor heterogeneity predicts the risk of progression in early stage diffuse large B-cell lymphoma.

Intratumor heterogeneity (ITH) plays an important role in tumor development, metastases, recurrence and has impact on clinical diagnosis, therapeutic responses. In this study, we used mutant-allele tumor heterogeneity (MATH) through whole-exome sequencing data to evaluate ITH in early stage diffuse large B-cell lymphoma (DLBCL). A discovery set of 22 patients and a validation set of 35 patients with primary DLBCL which staged I or II were chosen from The Cancer Genome Atlas database and The Gene Index Project database, respectively. Then patients were divided into low and high MATH score groups according to the median expression level. As a result, higher MATH score displayed an increasing risk of progression compared with lower MATH score both in the discovery set (P = 0.045) and the validation set (P = 0.025). Further, the genomic pattern according to MATH demonstrated that mutation rates of immunoglobulin lambda locus, B-cell translocation gene and membrane-associated guanylate kinase were the sites with the highest mutation rate. Moreover, Gene enrichment analysis showed that immunoglobulin lambda constant 2 (IGLC2) which belongs to immunoglobulin lambda locus was only enriched in high MATH group. Besides, BTG2 and Caspase recruitment domain-containing protein 11 were cancer driver genes which listed on the top three high rate of mutation. Our study revealed the prognostic value of MATH and relevant genomic pattern in early stage DLBCL. Potential mechanisms on genetic level of how genomic aberration influence the ITH of DLBCL are provided. MATH based on whole genome sequencing may be feasible for deciding clinical treatment of DLBCL patients in the future researches.

Baseline serum lactate dehydrogenase level predicts survival benefit in patients with metastatic colorectal cancer receiving bevacizumab as first-line chemotherapy: a systematic review and meta-analysis of 7 studies and 1,219 patients.

BACKGROUND: Bevacizumab, a humanized monoclonal antibody against vascular epithelial growth factor, plays a significant role in first-line, second-line, beyond-progression, and maintenance treatment of patients with metastatic colorectal carcinoma (mCRC). Nevertheless, there are currently no biomarkers available to predict patient response or resistance to bevacizumab, which would be useful in clinical trials. METHODS: Using PRISMA guidelines, we conducted a systematic review and meta-analysis of the association between serum lactate dehydrogenase (LDH) level and progression-free survival (PFS), overall survival (OS), and objective response rate in mCRC patients treated with bevacizumab-based first-line chemotherapy. A comprehensive, computerized literature search of PubMed, the Web of Science, Scopus, Ovid, and the gray literature was performed. Only studies conforming to specific eligibility criteria were included. Pooled hazard ratios (HRs) were estimated using random-effects or fixed-effects models according to heterogeneity between studies. Sensitivity analysis was conducted to evaluate the stability of the results by removing each individual study from the meta-analysis. RESULTS: Seven eligible studies of 1,219 total patients were included in the analysis. Meta-analysis of all studies revealed that high serum LDH level is associated with shorter PFS (HR: 1.43, 95% CI: 1.05-1.94; P=0.023) and OS (HR: 1.667, 95% CI: 1.230-2.259; P=0.001) times in mCRC patients treated with bevacizumab-based first-line chemotherapy. However, there was no significant association between serum LDH and objective response rate. CONCLUSIONS: High serum LDH level is significantly associated with shorter PFS and OS time and may have utility as a prognostic factor for mCRC patients receiving bevacizumab as first-line chemotherapy and as a predictive factor for those receiving bevacizumab-based therapy at other times.

Influence of SLCO1B1 in gastric cancer patients treated with EOF chemotherapy.

Cytochrome-P450 enzymes, ATP-binding cassette transporters, and solute carriers mediate drug metabolism as metabolic enzymes and membrane transporters, respectively. The present study investigated whether single nucleotide polymorphisms (SNPs) in genes encoding these proteins were predictive or prognostic factors in patients with metastatic gastric cancer (MGC) undergoing chemotherapy. A retrospective study of 108 MGC patients who received epirubicin, oxaliplatin, and 5-fluorouracil (EOF) as first-line treatment was performed. A total of 13 SNPs were genotyped, including SLCO1B1 (rs4149056), SLC2A9 (rs16890979, rs6449213, rs734553), ABCG2 (rs2231142), CYP2C9 (rs1057910, rs1799853), CYP2C19 (rs72552267, rs28399504, rs56337013, rs41291556) and CYP1A2 (rs12720461, rs56107638). The associations between these genotypes and disease-control rate (DCR), progression-free survival (PFS) and overall survival (OS) were analyzed. Patients with SLCO1B1 rs4149056 TT genotype had a significantly shorter OS compared with those with a C allele (CC + CT; 312 vs. 565 days, P=0.039). Multivariate analysis revealed that the rs4149056 TT homozygous genotype was an independent prognostic factor for shorter OS (hazard ratio: 2.565, 95% confidence interval: 1.215-5.415, P=0.014). However, no significant associations between SLCO1B1 rs4149056 and PFS were observed, between the other 12 SNPs and PFS or OS, or between any of the 13 SNPs and DCR. In conclusion, SLCO1B1 rs4149056 TT may be an independent predictor of survival in patients with MCG treated with EOF chemotherapy.

Efficacy prediction of targeted therapy for gastric cancer: The current status (Review).

Despite significant progress in the treatment of gastric cancer (GC), the prognosis remains poor and the mortality is high. Targeted drugs have been incorporated into routine treatment to improve treatment efficacy. However, the therapy response is still below 50%. Therefore, there is a need to identify predictive factors for patient response to a specific drug in order to improve the efficacy of drug therapy. The present article reviewed the predictive factors for target therapy in GC, including epidermal growth factor receptor, human epidermal receptor 2, vascular endothelial growth factor family, molecules in the mesenchymal­epithelial transition pathway and the mammalian target of rapamycin. Additionally, the present review described the interactions between these molecules and signaling pathways.