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A supplementary table of a multi-tab excel file including source data (non-NGS) and statistics

Supplementary Datasets Data 1: Sample metadata from AAV-mTSG liver screen. Data 2: Filtered sgRNA-level mutation frequencies Data 3: Gene-level average mutation frequencies Data 4: Gene-level mutation frequencies, averaged by treatment group Data 5: Results of t-tests comparing mutation frequencies: aPD1 vs PBS, or aCTLA4 vs PBS Data 6: Summary of KMT2D mutations in pan-cancer cohort Data 7: Correlation between KMT2D expression and macrophage abundance in TCGA cohorts Data 8: Correlation between KMT2D and GZMB expression in TCGA cohorts Data 9: Correlation between KMT2D and GZMA expression in TCGA cohorts Data 10: Correlation between KMT2D and CD14 expression in TCGA cohorts Data 11: Composite list of genes positively correlated with KMT2D across TCGA cohorts Data 12: Composite list of genes negatively correlated with KMT2D across TCGA cohorts Data 13: Summary of exome sequencing analysis Data 14: Association between KMT2D mutation status and total mutation burden in TCGA cohorts Data 15: Differential accessibility analysis by DESeq, sgKmt2d vs Vector (-IFN-γ) Data 16: Motif analysis of regions more accessible in sgKmt2d vs Vector Data 17: Motif analysis of regions less accessible in sgKmt2d vs Vector Data 18: Differential accessibility analysis by DESeq, sgKmt2d + IFN-γ vs - IFN-γ Data 19: Differential accessibility analysis by DESeq, Vector + IFN-γ vs - IFN-γ Data 20: List of genomic regions in each of the six clusters Data 21: Motif analysis of C1 regions Data 22: Motif analysis of C4 regions Data 23: Motif analysis of C3 regions Data 24: Motif analysis of C5 regions Data 25: Differential expression analysis of RNAseq, sgKmt2d vs Vector Data 26: DAVID gene ontology analysis of genes upregulated in sgKmt2d vs Vector Data 27: DAVID gene ontology analysis of genes downregulated in sgKmt2d vs Vector Data 28: High-confidence predicted neoantigens in sgKmt2d or Vector samples Data 29: Differential expression analysis of transposable elements, sgKmt2d vs Vector

Supplementary data file contains Supplementary Methods and Supplementary Figures S1-S11 and related figure legends

Immune checkpoint blockade (ICB) has shown remarkable clinical efficacy in several cancer types. However, only a fraction of patients will respond to ICB. Here, we performed pooled mutagenic screening with CRISPR-mediated genetically engineered mouse models (CRISPR-GEMM) in ICB settings, and identified KMT2D as a major modulator of ICB response across multiple cancer types. KMT2D encodes a histone H3K4 methyltransferase and is among the most frequently mutated genes in patients with cancer. Kmt2d loss led to increased DNA damage and mutation burden, chromatin remodeling, intron retention, and activation of transposable elements. In addition, Kmt2d-mutant cells exhibited increased protein turnover and IFNγ-stimulated antigen presentation. In turn, Kmt2d-mutant tumors in both mouse and human were characterized by increased immune infiltration. These data demonstrate that Kmt2d deficiency sensitizes tumors to ICB by augmenting tumor immunogenicity, and also highlight the power of CRISPR-GEMMs for interrogating complex molecular landscapes in immunotherapeutic contexts that preserve the native tumor microenvironment.Significance:ICB is ineffective in the majority of patients. Through direct in vivo CRISPR mutagenesis screening in GEMMs of cancer, we find Kmt2d deficiency sensitizes tumors to ICB. Considering the prevalence of KMT2D mutations, this finding potentially has broad implications for patient stratification and clinical decision-making.This article is highlighted in the In This Issue feature, p. 1775

Background Chimeric antigen receptor T cells (CAR-Ts) have demonstrated remarkable efficacy in hematological cancers but have not yet translated in treating solid tumors. The significant hurdles limiting CAR-T therapy were from a paucity of differentially expressed cell surface molecules on solid tumors that can be safely targeted. Here, we present TSH receptor (TSHR) as a putative target for CAR-T therapy of differentiated thyroid cancer (DTC). Methods We undertook a large-scale screen on thyroid cancer tissues and multiple internal organs through bioinformatical analysis and immunohistochemistry to date TSHR expression. Using 3 previously described monoclonal antibodies, we generated 3 third-generation CAR-Ts. We tested anti-TSHR CAR-T in vitro activity by T-cell function and killing assay. Then we tested preclinical therapeutical efficacy in a xenograft mouse model of DTC and analyzed mice’s physical conditions and histological abnormalities to evaluate anti-TSHR CAR-T’s safety. Results TSHR is highly and homogeneously expressed on 90.8% (138/152) of papillary thyroid cancer, 89.2% (33/37) of follicular thyroid cancer, 78.2% (18/23) of cervical lymph node metastases, and 86.7% of radioactive iodine resistance diseases. We developed 3 novel anti-TSHR CAR-Ts from monoclonal antibodies M22, K1-18, and K1-70; all 3 CAR-Ts mediate significant antitumor activity in vitro. Among these, we demonstrate that K1-70 CAR-T can have therapeutical efficacy in vivo, and no apparent toxicity has been observed. Conclusion TSHR is a latent target antigen of CAR-T therapy for DTC. Anti-TSHR CAR-T could represent a therapeutic option for patients with locoregional relapsed or distant metastases of thyroid cancer and should be tested in carefully designed clinical trials.

Breast cancer is one of the most common malignant tumors with a high incidence and leading cancer-related death in women worldwide. MiR-205 plays a crucial role in breast cancer initiation and progression. Here, we identified the relationship between miR-205 and lymphoid specific helicase and confirmed the significance of the miR-205/lymphoid specific helicase (miR-205/HELLS) axis.Data from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database were analyzed to investigate the expression level of miR-205 and HELLS in breast cancer. The TargetScan, Starbase and miRWalk databases were used to predict the candidate target genes of miR-205. Proliferation and migration abilities were examined using cell counting kit-8 assay, colony formation assays, transwell assay and wound-healing assay. Dual-luciferase reporter assay was utilized to confirm the binding of miR-205 and HELLS. Quantitative RT-PCR, western blot assays or immunohistochemistry were conducted to detect the expression level of genes in breast cancer cells or tissues. Mice xenograft models were constructed to explore the function of miR-205 and HELLS in vivo.Overexpressed miR-205 alleviated cancer cell proliferation and migration and influenced patients' prognosis by negatively regulating the HELLS gene. Consistently, animal experiments revealed that both overexpressing miR-205 and knocking down HELLS exhibited significant tumor growth inhibition in vivo.Our study demonstrated that miR-205 targets HELLS to regulate tumor progression. MiR-205 and HELLS could be considered a novel diagnosis and therapeutic molecular marker of breast cancer.

Context Although the incidence of papillary thyroid carcinoma (PTC) is significantly higher in females than in males, the prognosis of male PTC is more unfavorable. However, the cause of higher malignancy of PTC in male patients remains unclear. Objective We conducted our analysis on microarrays datasets, tissue samples from PTC patients and the RNAseq datasets from TCGA with survival data. Methods We searched all publicly available microarray datasets and performed a genome-wide meta-analysis comparing PTC and normal samples. Gene Ontology analysis was then conducted. The candidate genes were tested by quantitative real-time polymerase chain reaction. The analysis of prognostic value of genes was performed with datasets from The Cancer Genome Atlas. Results After meta-analyses, 150 significantly differentially expressed genes (DEGs) were specifically found in male subjects. Gene Ontology analysis of these 150 genes revealed that the viral process was activated. Seven genes involved in the viral process in male patients showed a significantly differential expression between PTC and normal tissue. Survival analysis exhibited that the 7 genes, used in combination, were prognostically valuable and, of them, PSMB1 possessed a conspicuous prognostic value, especially in males. Conclusion In this study, we searched all publicly available microarray datasets and conducted a comprehensive analysis to understand the male propensity for higher malignancy. We found that markers of viral infection showed significantly differential expression only in male patients compared with their female counterparts and had a sex-sensitive prognostic value in PTC.

Anaplastic thyroid carcinoma (ATC) is a rare but extremely lethal malignancy. However, little is known about the pathogenesis of ATC. Given its high mortality, it is critical to improve our understanding of ATC pathogenesis and to find new diagnostic biomarkers. In the present study, two gene microarray profiles (GSE53072 and GSE65144), which included 17 ATC and 17 adjacent non-tumorous tissues, were obtained. Bioinformatic analyses were then performed. Immunohistochemistry (IHC) and receiver operating characteristic (ROC) curves were then used to detect transmembrane protein 158 (TMEM158) expression and to assess diagnostic sensitivity. A total of 372 differentially expressed genes (DEGs) were identified. Through protein-protein interaction (PPI) analysis, we identified a significant module with 37 upregulated genes. Most of the genes in this module were related to cell-cycle processes. After co-expression analysis, 132 hub genes were selected for further study. Nine genes were identified as both DEGs and genes of interest in the weighted gene co-expression network analysis (WGCNA). IHC and ROC curves confirmed that TMEM158 was overexpressed in ATC tissue as compared with other types of thyroid cancer and normal tissue samples. We identified 8 KEGG pathways that were associated with high expression of TMEM158, including aminoacyl-tRNA biosynthesis and DNA replication. Our results suggest that TMEM158 may be a potential oncogene and serve as a diagnostic indicator for ATC.

Chimeric antigen receptor (CAR)-T cell-based immunotherapy for cancer and immunological diseases has made great strides, but it still faces multiple hurdles. Finding the right molecular targets to engineer T cells toward a desired function has broad implications for the armamentarium of T cell-centered therapies. Here, we developed a dead-guide RNA (dgRNA)-based CRISPR activation screen in primary CD8(+) T cells, and identified gain-of-function (GOF) targets for CAR-T engineering. Targeted knock-in or overexpression of a lead target, PRODH2, enhanced CAR-T-based killing and in vivo efficacy in multiple cancer models. Transcriptomics and metabolomics in CAR-T cells revealed that augmenting PRODH2 expression reshaped broad and distinct gene expression and metabolic programs. Mitochondrial, metabolic and immunological analyses showed that PRODH2 engineering enhances the metabolic and immune functions of CAR-T cells against cancer. Together these findings provide a system for identification of GOF immune boosters, and demonstrate PRODH2 as a target to enhance CAR-T efficacy.

Background/aims The effects of microRNA-423 on proliferation and drug resistance of breast cancer cells were explored, the downstream target genes of miR-423 and the targeted regulatory relationship between them were studied. Methods RT-qPCR was used to detect the expression of miR-423 in breast cancer tissues and cell lines, and the transfection efficiency of miR-423 inhibitory vector miR-423-inhibitor was constructed and verified. CCK-8 and colony formation assays were used to examine the effect of miR-423 on tumor cell proliferation. Target gene prediction and screening and luciferase reporter assay were used to verify downstream target genes of miR-432. The mRNA and protein expression of miR-423target gene ZFP36 was detected by RT-qPCR and Western blotting. Results The expression of miR-423 was significantly higher than that in normal tissues. Compared to the non-malignant mammary epithelial cell line MCF-10A, the expression of miR-423 was significantly raised in MCR-7 and MCF-7/ADR cells. ZFP36 was a downstream target gene of miR-423 and negatively correlated with the expression of miR-423 in breast cancer. The knockdown of miR-423 can significantly enhance the cytotoxicity of the drug, increase the apoptotic rate of MCF-7/ADR cells. miR-423 was capable of activating the Wnt/β-catenin signaling pathway leading to chemoresistance and proliferation, whereas overexpression of ZFP36 reduced drug resistance and proliferation. Conclusion miR-423 acted as an oncogene to promote tumor cell proliferation and migration. ZFP36 was a downstream target gene of miR-423, and miR-423 inhibited the expression of ZFP36 via Wnt/β-catenin signaling pathway of breast cancer cells.

Immunotherapy is the most promising treatment in triple-negative breast cancer (TNBC), and its efficiency is largely dependent on the intra-tumoral immune cells infiltrations. Thus, novel ways to assist immunotherapy by increasing immune cell infiltrations were highly desirable.To find key immune-related genes and discover novel immune-evoking molecules, gene expression profiles of TNBC were downloaded from Gene Expression Omnibus (GEO). Single-sample gene set enrichment analysis (ssGSEA) and Weighted Gene Co-expression Network Analysis (WGCNA) were conducted to identified hub genes. The CMap database was used subsequently to predicate potential drugs that can modulate the overall hub gene expression network.Gene expression profiles of 198 TNBC patients were downloaded from GEO dataset GSE76124, and ssGSEA was used to divide them into Immune Cell Proficiency (ICP) group and Immune Cell Deficiency (ICD) group. Hub differential expressed gene modules between two groups were identified by WGCNA and then annotated by Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. A cyclin-dependent kinase (CDK) 2 inhibitor, GW-8510 was then identified by the CMap database and further investigated. Treatment with GW-8510 resulted in potent inhibition of TNBC cell lines. More importantly,GW-8510, as well as other CDK inhibitors, might serve as potential immune regulators and pyroptosis promotors in TNBC.

Background Papillary thyroid cancer (PTC) is the most common endocrine malignancy, despite marked achieves in recent decades, the mechanisms underlying the pathogenesis and progression for PTC are incomplete. Accumulating evidence shows that γ-glutamylcyclotransferase (GGCT), an enzyme participated in glutathione homeostasis that is elevated in multiple types of tumors, represents an attractive therapeutic target. Methods Bioinformatics, immunohistochemistry (IHC), qRT-PCR and western blot (WB) assays were used to determine the elevation of GGCT in PTC. The biological functions of GGCT were examined using CCK8, wound healing and transwell assays. Subcutaneous xenograft and tail vein pulmonary metastatic mouse models were constructed to determine the effect of GGCT on tumorigenicity and metastasis in vivo. The effect of miR-205-5p on GGCT and the relationship between these two molecules were examined by dual luciferase reporter assay, RNA-RNA pull down assay as well as the rescue experiments both in vitro and in vivo. The interaction between GGCT and CD44 was assessed by co-immunoprecipitation (Co-IP) and IHC assays. Results Our results showed that GGCT expression is upregulated in PTC, correlates with more aggressive clinicopathological characteristics and worse prognosis. GGCT knockdown inhibited the cell proliferation, migratory and invasion ability of PTC cells and reduced the expression of mesenchymal markers (N-cadherin, CD44, MMP-2 and MMP9) while increased epithelial marker (E-cadherin) in PTC cells. We confirmed binding of miR-205-5p on the 3’-UTR regions of GGCT and delivery of miR-205-5p reversed the pro-malignant capacity of GGCT both in vitro and in vivo. Lastly, we found GGCT interacted with and stabilized CD44 in PTC cells. Conclusions Our findings illustrate a novel signaling pathway, miR-205-5p/GGCT/CD44, that involves in the carcinogenesis and progression of PTC. Development of miR-205-mimics or GGCT inhibitors as potential therapeutics for PTC may have remarkable applications.

Nutritional risk index (NRI) is an index based on ideal body weight that aims to present body weight and serum albumin levels. It has been utilized to discriminate patients at risk of postoperative complications and predict the postoperative outcome of major surgeries. However, this index remains limited for breast cancer patients treated with neoadjuvant chemotherapy (NACT). The research explores the clinical and prognostic significance of NRI in breast cancer patients. This study included 785 breast cancer patients (477 cases received NACT and 308 cases did not) were enrolled in this retrospective study. The optimal NRI cutoff value was evaluated by receiver operating characteristic (ROC) curve, then reclassified as low NRI group (P = 0.019, hazard ratio (HR): 1.521, 95% CI: 1.071–2.161 and P = 0.004, HR: 1.415, 95% CI: 1.119–1.789; and P = 0.026, HR:1.500, 95% CI: 1.051–2.143 and P < 0.001, HR: 1.547, 95% CI: 1.221–1.959]. According to the optimal cutoff value of NRI, the high NRI value patients had longer mean DFS and OS time in contrast to those with low NRI value patients (63.47 vs. 40.50 months; 71.50 vs. 56.39 months). Furthermore, the results demonstrated that the high NRI score patients had significantly longer mean DFS and OS time than those with low NRI score patients in early-stage breast cancer (χ2 = 9.0510, P = 0.0026 and χ2 = 9.2140, P = 0.0024) and advanced breast cancer (χ2 = 6.2500, P = 0.0124 and χ2 = 5.8880, P = 0.0152). The mean DFS and OS values in patients with high NRI scores were significantly longer in contrast to those with low NRI scores in different molecular subtypes. The common toxicities after NACT were hematologic and gastrointestinal reactions, and the NRI had no statistically significant effects on toxicities, except in nausea (χ2 = 9.2413, P = 0.0024), mouth ulcers (χ2 = 4.8133, P = 0.0282), anemia (χ2 = 8.5441, P = 0.0140), and leukopenia (χ2 = 11.0951, P = 0.0039). NRI serves as a minimally invasive, easily accessible and convenient prognostic tool for evaluating breast cancer prognoses and treatment efficacy, and may help doctors in terms of selecting measures of greater efficiency or appropriateness to better treat breast cancer.

Targeting membrane proteins could improve the efficacy of T cell-based immunotherapies. To facilitate the identification of T cell targets, we developed a hybrid genetic screening system where the Sleeping Beauty (SB) transposon and single guide RNA cassette are nested in an adeno-associated virus (AAV). SB-mediated genomic integration of the single guide RNA cassette enables efficient gene editing in primary murine T cells as well as a screen readout. We performed in vivo AAV-SB-CRISPR screens for membrane protein targets in CD8+ T cells in mouse models of glioblastoma (GBM). We validated screen hits by demonstrating that adoptive transfer of CD8+ T cells with Pdia3, Mgat5, Emp1 or Lag3 gene editing enhances the survival of GBM-bearing mice in both syngeneic and T-cell receptor transgenic models. Transcriptome profiling, single cell sequencing, cytokine assays and T cell signaling analysis showed that Pdia3 editing in T cells enhances effector functions. Engineered PDIA3 mutant EGFRvIII chimeric antigen T cells are more potent in antigen-specific killing of human GBM cells.

Immune-cell engineering opens new capabilities for fundamental immunology research and immunotherapy. We developed a system for efficient generation of chimeric antigen receptor (CAR)-engineered T cells (CAR-T cells) with considerably enhanced features by streamlined genome engineering. By leveraging trans-activating CRISPR (clustered regularly interspaced short palindromic repeats) RNA (tracrRNA)-independent CRISPR-Cpf1 systems with adeno-associated virus (AAV), we were able to build a stable CAR-T cell with homology-directed-repair knock-in and immune-checkpoint knockout (KIKO CAR-T cell) at high efficiency in one step. The modularity of the AAV-Cpf1 KIKO system enables flexible and highly efficient generation of double knock-in of two different CARs in the same T cell. Compared with Cas9-based methods, the AAV-Cpf1 system generates double-knock-in CAR-T cells more efficiently. CD22-specific AAV-Cpf1 KIKO CAR-T cells have potency comparable to that of Cas9 CAR-T cells in cytokine production and cancer cell killing, while expressing lower levels of exhaustion markers. This versatile system opens new capabilities of T-cell engineering with simplicity and precision.

BackgroundDifferentiated thyroid cancer (DTC) is usually very treatable and is often cured with surgery and, if indicated, follow with radioactive iodine (RAI) and long-term thyroid-stimulating hormone (TSH) suppression with levothyroxine. Unfortunately, locoregional relapse and distant metastases occur in up to 20% at ten years; those relapsed or distant metastatic thyroid cancer is relatively uncommon compare to other cancers, cytotoxic chemotherapies provided low response rates, and two-thirds of cases became RAI refractory (RAI-R). New therapy options for local-regional relapsed or distant metastases thyroid cancer are desperately needed. Chimeric antigen receptor T cells (CAR-T) have been demonstrated remarkable efficacy in hematological cancers but have not yet translated in treating solid tumors. The significant hurdles limiting CAR-T therapy were due to a paucity of differentially expressed cell surface molecules on solid tumors that can be safely targeted. Here, we present thyroid-stimulating hormone receptor (TSHR) as a putative target for CAR-T therapy of DTC.MethodsWe undertook a large-scale screen on thyroid cancer tissues and multiple internal organs through bioinformatical analysis and immunohistochemistry to date TSHR expression. Using three previously described mAb, we generate three third-generation CAR-Ts. We tested anti-TSHR CAR-T in vitro activity by T-cell function assay and killing assay. Then we tested pre-clinical therapeutical efficacy in a xenograft mouse model of DTC and analyzed mice’s physical conditions and histological abnormalities to evaluate anti-TSHR CAR-T’s safety.ResultsTSHR is highly and homogeneously expressed on 90.8%(138/152) of papillary thyroid cancer, 89.2% (33/37) of follicular thyroid cancer, 78.2% (18/23) of the cervical lymph node metastases, and 86.7% of locally recurrent or metastasis lesions with RAI-R disease. We develop three novel anti-TSHR CAR-T from mAb M22, K1-18, and K1-70, all three CAR-Ts mediate significant anti-tumor activity in vitro. Among these, we demonstrate that K1-70 CAR-T can have therapeutical efficacy in vivo, and no apparent toxicity has been observed.ConclusionTSHR is a latent target antigen of CAR-T therapy for DTC. Anti-TSHR CAR-T has strong therapeutical efficacy in vivo while without prominent adverse events. Anti-TSHR CAR-T could represent an exciting therapeutic option for patients with specific local-regional relapsed or distant metastases thyroid cancer and should be tested in carefully designed clinical trials.

Background Long non-coding RNAs (lncRNAs) are novel regulatory molecules in breast cancer development. LncRNA LUCAT1 is a potential tumor promoter in human cancers. In this study, we aimed to explore the role of LUCAT1 in human breast cancer tissues and cells. Methods A total of 31 breast cancer patients who underwent tumor resection, but without chemo- or radiotherapy or acute lung/heart/kidney diseases, provided tumor and adjacent normal tissues. Bioinformatic analysis, qRT-PCR, and luciferase reporter assay were carried out during the study. Results qRT-PCR analysis indicated that, compared with the adjacent tissues and MCF-10A normal breast epithelial cells, LUCAT1 was markedly up-regulated in the breast cancer tissues and five BC cell lines, including MDA-MB-231, MDA-MB-468, MDA-MB-435, SKBR3, and MCF-7. The knockdown of LUCAT1, through the transfection of small interfering RNA (siRNA) specific to LUCAT1, resulted in inhibition of proliferation in breast cancer cells. The expression levels of miR-181a-5p were decreased in the breast cancer tissues and five BC cell lines. Bioinformatic analysis and luciferase reporter assay suggested the interaction between miR-181a-5p and LUCAT1. In addition, the effects of LUCAT1 on promoting cell proliferation were attenuated by overexpression of miR-181a-5p through the transfection of miR-181a-5p mimic. Moreover, bioinformatics and luciferase reporter assay confirmed that miR-181a-5p targeted the 3′-UTR region of KLF6 and KLF15 mRNA, which were two tumor suppressor genes. LUCAT1/miR-181a-5p axis regulated the expression of KLF6 and KLF15 both in vitro and in vivo. Conclusions Our data indicate that LUCAT1/miR-181a-5p axis can serve as a novel therapeutic target in breast cancer.

Immune checkpoint blockade (ICB) has shown remarkable clinical efficacy in several cancer types. However, only a fraction of patients will respond to ICB. Here, we performed pooled mutagenic screening with CRISPR-mediated genetically engineered mouse models (CRISPR-GEMM) in ICB settings, and identified KMT2D as a major modulator of ICB response across multiple cancer types. KMT2D encodes a histone H3K4 methyltransferase and is among the most frequently mutated genes in patients with cancer. Kmt2d loss led to increased DNA damage and mutation burden, chromatin remodeling, intron retention, and activation of transposable elements. In addition, Kmt2d-mutant cells exhibited increased protein turnover and IFNγ-stimulated antigen presentation. In turn, Kmt2d-mutant tumors in both mouse and human were characterized by increased immune infiltration. These data demonstrate that Kmt2d deficiency sensitizes tumors to ICB by augmenting tumor immunogenicity, and also highlight the power of CRISPR-GEMMs for interrogating complex molecular landscapes in immunotherapeutic contexts that preserve the native tumor microenvironment.Significance:ICB is ineffective in the majority of patients. Through direct in vivo CRISPR mutagenesis screening in GEMMs of cancer, we find Kmt2d deficiency sensitizes tumors to ICB. Considering the prevalence of KMT2D mutations, this finding potentially has broad implications for patient stratification and clinical decision-making.This article is highlighted in the In This Issue feature, p. 1775

Purpose: This systematic review and meta-analysis was carried out with the aim of investigating the relationship between Foxp3 polymorphisms (rs3761547, r3761548, and rs3761549) and the risk of Graves' disease (GD). Methods: Four online database including PubMed, EMBASE, ISI Web of Science, and CNKI were searched to identify observational studies that evaluated the association between Foxp3 polymorphisms and risk of GD. The strength of associations was indicated as odds ratio (OR) and corresponding 95% confidence interval (95%CI) under the allelic model. The Newcastle-Ottawa Scale was used to assess the methodological quality. Pre-specified subgroup analysis and sensitivity analysis were performed using RevMan 5.3 software. Publication bias was detected by Egger's and Begg's tests. Results: Eight case control studies involving 3,104 GD patients and 3,599 healthy controls were included. The methodological quality of included studies was considered to be moderate to high. The results of our meta-analysis supported no association of rs3761547 and risk of GD in Asians (OR: 1.07, 95%CI 0.97, 1.19, P = 0.18). Evidence for rs3761547 and GD risk among Caucasians was still limited because only one study reported marginally increased risk of GD with the minor allele of rs3761547 (P = 0.04). The variant allele of both rs3761548 (OR: 1.31, 95%CI 1.04, 1.64; P = 0.02) and rs3761549 (OR: 1.30, 95%CI 1.03, 1.64; P = 0.03) was associated with increased risk of GD among Asians, but neither polymorphism turned out to be related with GD among Caucasians. Conclusion: Rs3761548 and rs3761549 polymorphisms in Foxp3 were associated with risk of GD among Asians, possibly due to suppressed function of regulatory T cells and augmented autoimmune response. Their genetic effect among Caucasians remained to be confirmed by future large-scale and well-designed studies.

ZW10 interacting kinetochore protein (ZWINT) is an essential component for the mitotic spindle checkpoint and has been reported to be upregulated in numerous types of human cancer. Nonetheless, its role in breast cancer (BC) remains unclear. Herein, it was demonstrated that the expression of ZWINT was significantly higher in BC than in normal breast tissues, on the basis of integrated analysis of bioinformatics studies, cancer database analyses and immunohistochemical detection. Elevated ZWINT levels were associated with a number of clinicopathological characteristics in patients with BC. These characteristics include: i) Positive human epidermal growth factor receptor 2 expression; ii) triple-negative BC; iii) younger age; iv) basal-like subtype; and v) greater Scarff-Bloom-Richardson grades. Additionally, prognostic analysis indicated that shorter relapse-free survival, overall survival and metastatic relapse-free survival may be associated with high ZWINT expression. A total of 16 pathways associated with high ZWINT expression, including Myc targets V1/2, DNA repair and mitotic spindle pathways, were identified using Gene Set Enrichment Analysis. In addition, a positive correlation between cyclin-dependent kinase 1 (CDK1) and ZWINT mRNA expression was identified by co-expression analysis. The present study suggested that ZWINT may serve as an effective prognostic biomarker for BC. In addition, ZWINT may be implicated in the CDK1-mediated initiation and progression of BC. However, further research is required to understand the role of ZWINT in BC.

As a critical member of the Retinal Determination Gene Network (RDGN), SIX1 has been regarded as a tumor promoter in various types of cancer. However, its role in papillary thyroid carcinoma (PTC) has never been investigated. In this study, thyroid carcinoma tissue microarray staining was employed to identify the expression patterns of SIX1 and its co-activator EYA1. Papillary thyroid cancer cell lines, BCPAP, and TPC-1 cells were used to investigate the potential mechanism of SIX1 in vitro and in vivo. Flow cytometry analysis, MTT assay, the growth curve assay, colony formation assay, EdU incorporation and xenograft assay were performed to demonstrate the role of SIX1 in the malignant change of PTC cells. Western blot and Real-time PCR were used to detect the interaction among the SIX1, EYA1, and STAT3 signaling. In comparison with normal tissue, high expressions of SIX1 and EYA1 were associated with a malignant tumor. Importantly, SIX1 strongly correlated with EYA1 in thyroid carcinoma tissue microarray. Functional assays indicated SIX1 increased EYA1 expression by stabilizing EYA1 at the post-transcriptional level. Besides, SIX1 promoted the proliferation and invasion of thyroid carcinoma via activation of STAT3 signaling and its downstream targets in an EYA1-dependent manner. SIX1 can integrate with EYA1 to contribute to PTC development via activation of the classical STAT3 signaling. These data suggested targeting the abnormal activation of the SIX1/EYA1 complex may represent a novel therapeutic strategy for advanced PTC patients.

Recent evidence indicates that long non-coding RNAs play important roles in tumorigenesis and cancer progression. BRAF-activated non-protein coding RNA (BANCR) is a novel and potential regulator of cancer cell proliferation and migration. However, little is known regarding the role of BANCR in papillary thyroid cancer (PTC). The current study used quantitative PCR to demonstrate that BANCR was significantly downregulated in 60 paired PTC tissues compared with normal tissues. In addition, BANCR was significantly correlated with lymph node metastasis (p = 0.02). Furthermore, Cell Counting Kits and Transwell assays were used to demonstrate that knocking down BANCR with short hairpin RNA (shRNA) transfection significantly promoted the proliferation and invasion of PTC cell lines. The flow cytometric analysis of apoptosis and the cell cycle revealed that the overexpression of BANCR inhibited cancer cell proliferation and invasion, which was associated with the induction of cell-cycle G2/M phase arrest and increased apoptosis. Moreover, western blotting was used to show that the MAPK and PI3K-Akt pathways were aberrantly activated during BANCR-mediated PTC cell proliferation and migration. These findings revealed that BANCR functions as a tumor suppressor during thyroid carcinogenesis.

Novel molecular-targeted treatments show great prospects for radioiodine-refractory and surgically inoperable thyroid carcinomas. While aberrations in protein-coding genes are a focus in molecular thyroid cancer medicine, the impact of oncogenes on the expression of long noncoding RNAs (lncRNAs) has been largely uncharacterized. We aimed to identify the expression patterns of lncRNAs and mRNAs in high-throughput molecular profiles of 18 papillary thyroid cancer (PTC) patients. We identified 452 mRNAs and 240 unannotated lncRNAs that were differentially expressed in PTC. Significantly enriched GO terms and pathways were identified, many of which were linked to cancer. By integrating the predicted lncRNA target genes with differentially expressed mRNAs, we identified 20 candidate lncRNAs in 45 PTC patients. Five lncRNAs (CTD-3193O13.11, RP5-1024C24.1, AC007255.8, HOXD-AS1, and RP11-402L6.1) were verified to be differentially expressed in PTC and to exhibit specific topological characteristics in the lncRNA-mRNA co-expression network. LncRNA CTD-3193O13.11 was determined to comprise a node of co-regulation with the other lncRNAs in PTC tumorigenesis. LncRNA RP5-1024C24.1, AC007255.8, and HOXD-AS1 expression was significantly related to clinical stage, lncRNA RP11-402L6.1 expression was associated with lymph node metastasis, lncRNA CTD-3193O13.11 expression was proportional to tumor size, and lncRNA AC007255.8 expression was proportional to patient age. Therefore, our study provides a genome-wide screening and analysis of lncRNA expression in PTC, which brings novel insights into the roles of lncRNAs in PTC progression.

Background Breast cancer was dangerous to women health. A growing number of evidences indicate that long non-coding RNAs (lncRNAs) have many functions in the development and progression of breast cancer and may serve as the markers of diagnosis or prognosis. BLACAT1 is one of lncRNA and the roles of it in breast cancer is not clear. In this study, it is aimed to explore the roles and molecular mechanisms of BLACAT1 in breast cancer. Results We found BLACAT1 took part in breast cancer cell aggressive phenotype. The real-time PCR result showed that BLACAT1 was up-regulated in tumor tissues compared to adjacent normal tissues. The molecular mechanism experiments demonstrated that BLACAT1 down-regulation suppressed the proliferation and metastasis of human breast cancer cells by regulating miR-150-5p targeting CCR2. The clinical studies indicated that lack of BLACAT1 was related to tumor size, metastasis. Conclusion: The present study verified the involvement of the BLACAT1 in the mediation of cell survival and metastasis through miR-150-5p targeting CCR2 in breast cancer cells.

CD8 T cells play essential roles in anti-tumor immune responses. Here, we performed genome-scale CRISPR screens in CD8 T cells directly under cancer immunotherapy settings, and identified regulators of tumor infiltration and degranulation. The in vivo screen robustly re-identified canonical immunotherapy targets such as PD-1 and Tim-3, along with genes that have not been characterized in T cells. The infiltration and degranulation screens converged on an RNA helicase Dhx37. Dhx37 knockout enhanced the efficacy of antigen-specific CD8 T cells against triple-negative breast cancer in vivo. Immunological characterization in mouse and human CD8 T cells revealed that DHX37 suppresses effector functions, cytokine production, and T cell activation. Transcriptomic profiling and biochemical interrogation revealed a role for DHX37 in modulating NF-κB. These data demonstrate high-throughput in vivo genetic screens for immunotherapy target discovery and establishes DHX37 as a functional regulator of CD8 T cells.

Background Assembling evidences suggested that aberrant expression of tissue differentiation-inducing non-protein coding RNA (TINCR) intimately associated with variety of human cancer. However, the expression pattern and involvement of TINCR in breast cancer has not been fully investigated. Here we set out to analyze expression of TINCR in breast cancer and elucidate its mechanistic involvement in tumor incidence and progression. Methods The expression of TINCR was determined by q-PCR. SP1 binding sites were analyzed by ChIP-qPCR. The relative transcription activity was measured with luciferase reporter assay. Cell viability was measured with CCK-8 method. Clonogenic capacity was evaluated by soft agar assay. Cell apoptosis was analyzed by Annexin V/7-AAD staining. The migration and invasion were determined by trans-well assay and wound healing. The tumor growth in vivo was evaluated in xenograft mice model. Protein expression was quantified by immunoblotting. Results TINCR was aberrantly up-regulated by SP1, which in turn stimulated cell proliferation, anchorage-independent growth and suppressed cell apoptosis in breast cancer. TINCR silencing significantly suppressed migration and invasion in vitro and xenograft tumor growth in vivo. Mechanistically, TINCR modulated KLF4 expression via competing with miR-7, which consequently contributed to its oncogenic potential. MiR-7 inhibition severely compromised TINCR silencing-elicited tumor repressive effects. Conclusion Our data uncovered a crucial role of TINCR-miR-7-KLF4 axis in human breast cancer. Electronic supplementary material The online version of this article (10.1186/s12885-018-4255-3) contains supplementary material, which is available to authorized users.

ZnS nanoparticles (NPs) were prepared inside nanosized colloidal mesoporous silica (CMS) by in situ generation procedure. The ZnS-containing CMS (ZnS–CMS) was modified with 8-hydroxyquinoline (HQ) by the coordination with zinc atom of ZnS surface (the resulting hybrid named as HQ–ZnS–CMS). The size of the generated ZnS NPs in the channels of CMS was estimated to be about 2.5 nm. The existence of ZnS inside the CMS hosts resulted in the decrease in surface area and pore volume. The HQ–ZnS–CMS exhibited a strong and stable fluorescence emission at about 490 nm in both solid state and polar solvent, while evident quenching phenomenon was observed for bis(8-hydroxyquinoline) zinc(II) (Znq2) complex in polar solvent, such as DMF. The PL decay study indicated that the ZnS–CMS and HQ–ZnS–CMS exhibited similar biexponential decay with the lifetimes in the nanosecond time domain for the emission at about 410 and 490 nm, respectively. The decay behaviors of the containing-ZnS CMS obviously differed from that of Znq2–CMS carrying more long lifetime for the emission at 490 nm. The transparent fluorescent nanocomposites were prepared by in situ bulk polymerization of HQ–ZnS–CMS in the suitable organic monomers. The maximum excitation and emission wavelengths of the polymer nanocomposites had a red-shift with the increasing content of HQ–ZnS–CMS because of the cooperative interaction between the HQ–ZnS–CMS and polymer matrix with blue emission.

Znq2–functionalized colloidal mesoporous silicas (Znq2–CMS)/polymer transparent nanocomposites were prepared by in situ bulk polymerization. CMS nanoparticles or nanorods with hydroxyl-, mercapto- and sulfonic-functionalized interiors were obtained by different synthetic routes in the nanosize dimensions between 50 and 500 nm. The luminescent Znq2 complex was successfully introduced in the pores of different mesoporous silicas by chemical adsorption as the driving force. The different internal circumstances of mesoporous silicas had an obvious effect on the luminescence and lifetime of Znq2 complex. The transparent fluorescent nanocomposites were fabricated from different Znq2–CMS and suitable monomers. The Znq2–CMS were uniformly dispersed in the polymer matrix without evident aggregation. The photoluminescence properties of Znq2–CMS in the transparent matrix exhibited a dependence on the inner surrounding of CMS due to the interaction between Znq2–CMS and polymers. The maximum emission peak of the nanocomposites had a red-shift of 28 nm as compared to pure Znq2–CMS.

A facile ligand exchange approach for surface-functionalized ZnS nanoparticles (NPs) with 5-(2-methacryloylethyloxymethyl)-8-quinolinol (MQ) is described. The MQ-ZnS NPs, with a cubic crystal structure, have the same diameter as ZnS NPs without MQ about 3.0 nm. The MQ-ZnS NPs exhibit strong fluorescence emission at about 500 nm and a high photoluminescence (PL) quantum yield (QY), up to 40%, with a decreasing ratio of MQ to ZnS NPs. The PL decay study reveals that the lifetimes of the different MQ-ZnS NPs with a single exponential decay are in the nanosecond time domain for emission at about 500 nm, which is obviously different from that of ZnS NPs with a biexponential decay for defect-state emission at 420 nm. The functionalized MQ-ZnS NPs are successfully incorporated into the polymer matrix by in situ bulk polymerization to fabricate transparent bulk nanocomposites with good thermal stability and processability. Transmission electron microscopy results show that the NPs are uniformly dispersed in the polymer matrix without aggregation. The good PL properties of MQ-ZnS NPs are preserved in the bulk nanocomposites. It is observed that the nanocomposites have red-shifted excitation and emission wavelengths compared with those of both the polymer matrix and MQ-ZnS NPs, possibly because of the cooperative interaction between MQ-ZnS NPs and the polymer matrix with blue emission.

5-Amino-1,10-phenanthroline (Aphen) was used as an organic ligand to functionalize CdS nanocrystals (NCs) by a ligand-exchange process. The functional Aphen-CdS NCs have strong luminescent emission at 552 nm and good dispersibility in the polar organic monomers. The Aphen-CdS NCs were dispersed in polymeric monomers to prepare a series of transparent luminescent nanocomposites with excellent thermal stability via in-situ bulk polymerization. The fluorescent properties of the Aphen-CdS NCs were well retained in the polymer matrix. It was found that when the methacrylic acid (MAA) and glycidyl methacrylate (GMA) as the comonomers were introduced into the polymer matrix, the emission peaks of the resultant nanocomposites had a blue shift and the fluorescent intensities also increased due to the interaction between NCs and the polymer matrices. The transparent NCs/polymer nanocomposites with tunable fluorescent emission can be potentially used for the fabrication of optoelectronic devices.

A series of APhen-functionalized ZnS nanoparticles (NPs)–polymer transparent nanocomposites with tunable fluorescent emission were prepared via ligand exchange and in situ bulk polymerization. The APhen-ZnS NPs were synthesized from the mercaptoethanol (ME)-capped ZnS nanoparticles (ME–ZnS NPs) and 5-amino-1,10-phenanthroline (APhen) by a ligand-exchange process. The APhen–ZnS NPs still had a cubic crystal structure and a diameter of about 3.0 nm as before functionalization of ME–ZnS NPs. The fluorescent emission of APhen–ZnS NPs exhibited a red shift at 550 nm as compared to ME–ZnS NPs (423 nm) and APhen (473 nm). The APhen–ZnS NPs were incorporated into different polymer matrix by in situ bulk polymerization. TEM results showed that the NPs were uniformly dispersed in the polymer matrix without aggregation. It was found that the nanocomposites exhibited a dependence of photoluminescence properties on the concentration of NPs in polymer and the composition of polymer. As the methacrylic acid (MAA) and glycidyl methacrylate (GMA) as co-monomers were introduced in polymer matrix, the emission peaks of APhen–ZnS NPs–polymer nanocomposites had a blue shift. These transparent nanocomposites with tunable photoluminescence can be potentially used for the fabrication of optical and optoelectronic devices.