A blueprint for tumor-infiltrating B cells across human cancers.

B lymphocytes are essential mediators of humoral immunity and play multiple roles in human cancer. To decode the functions of tumor-infiltrating B cells, we generated a B cell blueprint encompassing single-cell transcriptome, B cell-receptor repertoire, and chromatin accessibility data across 20 different cancer types (477 samples, 269 patients). B cells harbored extraordinary heterogeneity and comprised 15 subsets, which could be grouped into two independent developmental paths (extrafollicular versus germinal center). Tumor types grouped into the extrafollicular pathway were linked with worse clinical outcomes and resistance to immunotherapy. The dysfunctional extrafollicular program was associated with glutamine-derived metabolites through epigenetic-metabolic cross-talk, which promoted a T cell-driven immunosuppressive program. These data suggest an intratumor B cell balance between extrafollicular and germinal-center responses and suggest that humoral immunity could possibly be harnessed for B cell-targeting immunotherapy.

Neutrophil profiling illuminates anti-tumor antigen-presenting potency.

Neutrophils, the most abundant and efficient defenders against pathogens, exert opposing functions across cancer types. However, given their short half-life, it remains challenging to explore how neutrophils adopt specific fates in cancer. Here, we generated and integrated single-cell neutrophil transcriptomes from 17 cancer types (225 samples from 143 patients). Neutrophils exhibited extraordinary complexity, with 10 distinct states including inflammation, angiogenesis, and antigen presentation. Notably, the antigen-presenting program was associated with favorable survival in most cancers and could be evoked by leucine metabolism and subsequent histone H3K27ac modification. These neutrophils could further invoke both (neo)antigen-specific and antigen-independent T cell responses. Neutrophil delivery or a leucine diet fine-tuned the immune balance to enhance anti-PD-1 therapy in various murine cancer models. In summary, these data not only indicate the neutrophil divergence across cancers but also suggest therapeutic opportunities such as antigen-presenting neutrophil delivery.

An Inflammatory Checkpoint Generated by IL1RN Splicing Offers Therapeutic Opportunity for KRAS-Mutant Intrahepatic Cholangiocarcinoma.

KRAS mutations are causally linked to protumor inflammation and are identified as driving factors in tumorigenesis. Here, using multiomics data gathered from a large set of patients, we showed that KRAS mutation was associated with a specific landscape of alternative mRNA splicing that connected to myeloid inflammation in intrahepatic cholangiocarcinoma (iCCA). Then, we identified a negative feedback mechanism in which the upregulation of interleukin 1 receptor antagonist (IL1RN)-201/203 due to alternative splicing confers vital anti-inflammatory effects in KRAS-mutant iCCA. In KRAS-mutant iCCA mice, both IL1RN-201/203 upregulation and anakinra treatment ignited a significant antitumor immune response by altering neutrophil recruitment and phenotypes. Furthermore, anakinra treatment synergistically enhanced anti-PD-1 therapy to activate intratumoral GZMB+ CD8+ T cells in KRAS-mutant iCCA mice. Clinically, we found that high IL1RN-201/203 levels in patients with KRAS-mutant iCCA were significantly associated with superior response to anti-PD-1 immunotherapy. SIGNIFICANCE: This work describes a novel inflammatory checkpoint mediated by IL1RN alternative splicing variants that may serve as a promising basis to develop therapeutic options for KRAS-mutant iCCA and other cancers. This article is featured in Selected Articles from This Issue, p. 2109.

Gene-based cancer-testis antigens as prognostic indicators in hepatocellular carcinoma.

Cancer/testis antigens (CTAs) are reproductive tissue-restricted genes, frequently ectopic expressed in tumors. CTA genes associate with a poor prognosis in some solid tumors, due to their potential roles in the tumorigenesis and progression. However, whether CTAs relate with hepatocellular carcinoma (HCC) remains unclear. In this study, the prognostic signatures based on CTA genes were investigated and validated in three cohorts including Chinese HCC patients with hepatitis B virus infection (CHCC-HBV), International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) cohorts. Univariate, LASSO, and multivariate Cox regression analyses were used to screen prognostic genes and develop the prognostic gene signature. A prognosis model was established with six CTA genes (SSX1, CTCFL, OIP5, CEP55, NOL4, and TPPP2) in CHCC-HBV cohort, and further validated in the ICGC and TCGA cohorts. The CTA signature was an essential prognostic predictor independent of other clinical pathological factors. High-risk group exhibited up-regulated cell cycle-related and tumor-related pathways and more M0 macrophage, activated mast cell, activated memory CD4+ T cell, and memory B cell infiltration. Furthermore, CTA signature correlated with the sensitivity to multiple chemotherapy drugs. Our results highlighted that the CTA gene profiling was a prognostic assessment tool for HCC patients.

Genome-Scale CRISPR screen identifies LAPTM5 driving lenvatinib resistance in hepatocellular carcinoma.

ABBREVIATIONS: cld-CASP3: cleaved caspase 3; cld-PARP: cleaved PARP; DTP: drug tolerant persister; GO: Gene Ontology; GTEx: The Genotype-Tissue Expression; HCC: hepatocellular carcinoma; HCQ: hydroxychloroquine; IC50: half maximal inhibitory concentration value; KEGG: Kyoto Encyclopedia of Genes and Genomes; LAPTM5: lysosomal protein transmembrane 5; NT: non-targeting; PDC: patient-derived primary cell lines; PDO: patient-derived primary organoid; TCGA: The Cancer Genome Atlas.

LncRNA UCA1 promotes cisplatin resistance in gastric cancer via recruiting EZH2 and activating PI3K/AKT pathway.

Background: Drug resistance of cancer cells is one of the major causes of chemotherapy failure. Recently research demonstrated that long non-coding RNA Urothelial cancer associated 1 (UCA1) could promote tumor cisplatin resistance. In this study, we aim to investigate the role of UCA1 in the cisplatin treatment of gastric cancer and its underlying mechanism. Methods: Cell counting kit-8 (CCK-8) assay and apoptosis assay were used to detect the effects of different doses of cisplatin on the proliferation and apoptosis of gastric cancer. We examined the expression relationship between the Enhancer of Zeste Homologue 2 (EZH2) and UCA1 by quantitative Real-time polymerase chain reaction (qRT-PCR) and western blot analysis. Western blot analysis was also performed to detect the expression levels of apoptosis-related proteins, EZH2 and key genes in PI3K/AKT signaling pathway, RIP and RNA pull down assays were performed to explore the interaction between UCA1 and EZH2. Results: We demonstrated that higher the UCA1 expression levels in GC tissues correlated with the poorer the prognosis of patients according to the TCGA database, the GEO database. Moreover, overexpression of UCA1 promotes GC cell proliferation and inhibits cisplatin-induced apoptosis. Knockdown of UCA1 showed the opposite results. Besides, UCA1 exerted its function through interacting with EZH2 and regulates EZH2 expression, knockdown of EZH2 decreased cisplatin resistance of GC cells. Hence, UCA1 promotes cisplatin resistance of GC via recruiting EZH2 and activating PI3K/AKT pathway. Conclusion: Our research revealed the lncRNA UCA1 promoted the cisplatin resistance of GC by recruiting EZH2 and activating PI3K/AKT pathway to modulate cell apoptosis, indicating treatments targeting UCA1 or EZH2 might provide meaningful therapeutic strategies for cisplatin-resistance GC patients.

Three Biomarkers Predict Gastric Cancer Patients' Susceptibility To Fluorouracil-based Chemotherapy.

Background: Fluorouracil-based chemotherapy is recommended by the main clinical guidelines for post-operative gastric cancer (GC) patient's chemotherapy treatment, this study aim to establish relate model to predict patients' susceptibility to fluorouracil-based chemotherapy to prevent patients' unnecessary exposure to chemotherapy treatments and improve patients' treatment. Methods: Data from Gene Expression Omnibus (GEO) database, Cancer Cell Line Encyclopedia (CCLE) database, Cancer Therapeutics Response Portal (CTRP) and The Cancer Genome Atlas (TCGA) were used. A predictive model was built based on univariate and multivariate Cox analysis and visualized by nomogram. Survival analysis was performed using Kaplan-Meier and log-rank test. Results: A total of 514 differentially expressed genes (DEGs) were identified between fluorouracil-resistant cell lines and fluorouracil-sensitive cell lines based on CCLE database. A total of 300 patients who had radical gastrectomy were recruited, of which 144 received fluorouracil-based chemotherapy and 156 were untreated. Three biomarkers (CTF1, BTN3A3, ADAD2) were finally selected by univariate and multivariate Cox regression analysis to establish the predictive models visualized by nomogram. This model could precisely predict both the Disease free survival (DFS) and Overall survival (OS) of patients treated with fluorouracil-based chemotherapy after surgery compared to untreated GC patients validated by both GEO database and TCGA database. Conclusion: Our data established three genes-based predictive model which might predict GC patients' susceptibility to fluorouracil and help clinicians develop personalized treatment.

Palmitate acid promotes gastric cancer metastasis via FABP5/SP1/UCA1 pathway.

BACKGROUND: Gastric cancer (GC) has a clear predilection for metastasis toward omentum which is primarily composed of adipose tissue, combine with our previous research that long non-coding RNA Urothelial cancer associated 1 (UCA1) could promote the peritoneal metastasis of GC, we put forward the hypothesis that fatty acids (FAs) might contribute to these phenomena and a connection between FAs and UCA1 might exist. METHODS: TCGA database was applied to investigate the expression levels of UCA1 in GC tissues and normal gastric tissues and its correlation with GC patients' survival. Transfection of siRNA was utilized to knockdown cellular levels of FA-binding protein 5 (FABP5), SP1, UCA1. Migration assay and invasion assay were performed to assess the biological effects of palmitate acid (PA), FABP5, SP1 and UCA1 on GC metastasis. The underlying mechanism was investigated via western blot, immunofluorescence (IF), semi-quantitative RT-PCR (sqRT-PCR) and quantitative RT-PCR (qRT-PCR) analysis. RESULTS: Here we demonstrated that PA could promote the nuclear transport of FABP5, which then increased the nuclear protein levels of SP1. Consequently, GC cellular expression levels of UCA1 were increased which promoted the metastatic properties of GC. Besides, the cellular levels of UCA1 in GC tumor tissues were significantly higher than that in normal tissues. Its levels in GC tumor tissues also negatively correlated with the prognosis of GC patients using TCGA database. CONCLUSIONS: Our research revealed the potential tumor-promoting effect of FA transport protein FABP5. We also established a connection between non-coding RNA and FA metabolism, treatment targeted either to patients' diets or FABP5 might improve the prognosis of GC patients.

Prediction of platinum-resistance patients of gastric cancer using bioinformatics.

Lack of guidelines for personalized chemotherapy treatment after surgery has caused gastric cancer (GC) patients' unnecessary exposure to toxicity and the financial burden of chemotherapy treatments. In our study, we aimed to identify potential biomarkers to predict GC patients' susceptibility to platinum-based on Gene Expression Omnibus (GEO) data sets. A total of 603 differentially expressed genes (DEGs) were identified between platinum-resistant cell lines and platinum-sensitive cell lines based on the Cancer Cell Line Encyclopedia (CCLE) data sets. A total of 253 patients who had accepted radical gastrectomy were recruited, of which 97 received platinum-based chemotherapy and 156 were untreated. Three biomarkers (BRMS1, ND6, SRXN1) were then selected by univariate and multivariate Cox regression analysis to establish the predictive models using nomogram. Then this model was further validated through the GEO data set (GSE62254) which showed that this model could precisely predict the disease-free survival and overall survival of patients treated with platinum-based chemotherapy after surgery compared with untreated GC patients (P < 0.0001). This predictive model might provide helpful messages about the patients' susceptibility to platinum to guide personalized chemotherapy.

CD36 mediates palmitate acid-induced metastasis of gastric cancer via AKT/GSK-3ß/ß-catenin pathway.

BACKGROUND: Gastric cancer (GC) has a clear predilection for metastasis toward the omentum which is primarily composed of adipose tissue, indicating that fatty acids may contribute to this phenomenon. However their function remains poorly understood in GC. In this study, we investigated the role of palmitate acid (PA) and its cellular receptor CD36 in the progression of GC. METHODS: Immunohistochemical (IHC) staining was performed to detect CD36 expression in GC tissues and its clinical significance was determined statistically. CD36 over-expression and knock-down expression cell models were developed and tested in vitro. Wound-healing assays, migration assays, and invasion assays were performed and peritoneal implants into nude mice were done to assess the biological effects of PA and CD36. The underlying mechanisms were investigated using western blot, immunofluorescence (IF), quantitative real-time PCR (qRT-PCR) and antibody blocking assays. RESULTS: PA promoted the metastasis of GC by phosphorylation of AKT, which facilitated the nuclear localization of ß-catenin through inactivation of GSK-3ß via phosphorylation. This tumor-promoting effect of PA was mediated by CD36, a cell surface receptor of fatty acids (FAs). The higher the CD36 expression levels in GC tissues correlated with the poorer the prognosis of patients according to the TCGA database, the GEO database and our own clinical data. CONCLUSIONS: Our experiments established CD36 as a key mediator of FA-induced metastasis of GC via the AKT/GSK-3ß/ß-catenin signaling pathway. CD36 might, therefore, constitute a potential therapeutic target for clinical intervention in GC.