Next Generation Sequencing samples from mouse liver tumor
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE179352 | GEO | 2021/07/06
REPOSITORIES: GEO
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Project description:Background: Parkinson’s disease (PD) is a multisystem and multifactorial disorder. Therefore, the application of modern genetic techniques may assist in unraveling its complex pathophysiology. Methods: We conducted a clinical-demographic evaluation of 126 patients with PD, all of whom were Caucasian and of Sicilian ancestry. DNA was extracted from peripheral blood for each patient, followed by sequencing using a Next-Generation Sequencing system. This system was based on a custom gene panel comprising 162 genes. The sample underwent further filtering, taking into account allele frequencies of genetic variants, their presence in the Human Gene Mutation Database, and their association in the literature with PD or other movement/neurodegenerative disorders. Results: The largest number of variants was identified in the leucine-rich repeat kinase 2 (LRRK2) gene. However, variants in other genes, such as acid beta-glucosidase (GBA), DNA polymerase gamma, catalytic subunit (POLG), and parkin RBR E3 ubiquitin protein ligase (PRKN), were also discovered. Interestingly, some of these variants had not been previously associated with PD. Conclusions: Enhancing our understanding of the genetic basis of PD and identifying new variants possibly linked to the disease will contribute to improved diagnostic accuracy, therapeutic developments, and prognostic insights for affected individuals.
2024-10-14 | E-MTAB-13523 | biostudies-arrayexpress
Project description:To study the safety and efficacy of clinical application of autologous tumor infiltrating lymphocytes (TIL) after in vitro amplification，in combination with anti-PD-1 monoclonal antibody for the treatment of advanced hepatocellular carcinoma (HCC)
2023-02-01 | GSE220670 | GEO
Project description:Background and Aims: Chronic hepatitis B virus (HBV) infection is the leading cause of hepatocellular carcinoma (HCC) and is a serious health problem in China, East Asia, and North African countries. Effective treatment of HBV-related HCC is currently unavailable. This study evaluated the therapeutic potential of TIGIT blockade in HBV-related HCC. Approach and Results: A mouse model of spontaneous HBV-related HCC was generated by replacing wild-type hepatocytes with HBsAg+ hepatocytes (namely HBs-HepR mice). The tumors in HBs-HepR mice were inflammation-associated HCC, similar to HBV-related HCC in patients, which was distinguished from other HCC mouse models, such as diethylnitrosamine (DEN)-induced HCC, Tak1-knockout-induced HCC, HCC in stelic animal model (STAM), or nonalcoholic steatohepatitis (NASH)-induced HCC. HCC in HBs-HepR mice was characterized by an increased number of CD8+T cells whereas the production of IL-2, TNF-α, and IFN-γ by intrahepatic CD8+T cells was decreased. Increased expression of TIGIT on CD8+T cells was responsible for functional exhaustion. The therapeutic effect of TIGIT blockade was investigated at the early and middle stages of HCC progression in HBs-HepR mice. TIGIT blockade reinvigorated intrahepatic CD8+T cells with increased TNF-α and IFN-γ production and an increased number of CD8+T cells in tumors, thereby slowing the development of HCC in HBs-HepR mice. Blocking PD-L1 did not show direct therapeutic effects or synergize with TIGIT blockade. Conclusions: Blockade of TIGIT alone enhanced the anti-tumor activity of CD8+T cells during the progression of HBV-related HCC in a spontaneous HCC mouse model.
2022-12-31 | GSE209856 | GEO
Project description:Anti-PD-L1-based combination immunotherapy has become the first-line treatment for unresectable hepatocellular carcinoma (HCC). However, the objective response rate is lower than 40%, highlighting the need to identify mechanisms of tolerance to immune checkpoint inhibitors and accurate biomarkers of response. Here, we employed next-generation sequencing to analyze HCC samples from 10 patients receiving anti-PD-L1 therapy. Activation of the renin-angiotensin system was elevated in nonresponders compared with responders, and ACE2 expression was significantly downregulated in nonresponders. ACE2 deficiency promoted HCC development and anti-PD-L1 resistance, whereas ACE2 overexpression inhibited HCC progression in immune competent mice. Mass cytometry by time of flight (CyTOF) revealed that ACE2 deficient murine orthotopic tumor tissues featured elevated M2-like tumor-associated macrophages (TAMs), displayed a CCR5+PD-L1+ immunosuppressive phenotype, and exhibited high VEGFα expression. ACE2 downregulated tumor intrinsic CCL5 expression by suppressing NF-κB signaling through the ACE2/angiotensin-(1–7)/Mas receptor axis. The lower CCL5 levels led to reduced activation of the JAK-STAT3 pathway and suppressed PD-L1 and VEGFα expression in macrophages, blocking macrophage infiltration and M2-like polarization. Pharmacological targeting of CCR5 using maraviroc enhanced the tumor suppressive effect of anti-PD-L1 therapy. Together, these findings suggest that activation of the ACE2 axis overcomes the immunosuppressive microenvironment of HCC and may serve as an immunotherapeutic target and predictive biomarker of response to PD-L1 blockade.
2024-10-22 | GSE279750 | GEO
Project description:Anti-PD-L1-based combination immunotherapy has become the first-line treatment for unresectable hepatocellular carcinoma (HCC). However, the objective response rate is lower than 40%, highlighting the need to identify mechanisms of tolerance to immune checkpoint inhibitors and accurate biomarkers of response. Here, we employed next-generation sequencing to analyze HCC samples from 10 patients receiving anti-PD-L1 therapy. Activation of the renin-angiotensin system was elevated in nonresponders compared with responders, and ACE2 expression was significantly downregulated in nonresponders. ACE2 deficiency promoted HCC development and anti-PD-L1 resistance, whereas ACE2 overexpression inhibited HCC progression in immune competent mice. Mass cytometry by time of flight (CyTOF) revealed that ACE2 deficient murine orthotopic tumor tissues featured elevated M2-like tumor-associated macrophages (TAMs), displayed a CCR5+PD-L1+ immunosuppressive phenotype, and exhibited high VEGFα expression. ACE2 downregulated tumor intrinsic CCL5 expression by suppressing NF-κB signaling through the ACE2/angiotensin-(1–7)/Mas receptor axis. The lower CCL5 levels led to reduced activation of the JAK-STAT3 pathway and suppressed PD-L1 and VEGFα expression in macrophages, blocking macrophage infiltration and M2-like polarization. Pharmacological targeting of CCR5 using maraviroc enhanced the tumor suppressive effect of anti-PD-L1 therapy. Together, these findings suggest that activation of the ACE2 axis overcomes the immunosuppressive microenvironment of HCC and may serve as an immunotherapeutic target and predictive biomarker of response to PD-L1 blockade.
2024-10-14 | GSE279110 | GEO
Project description:Anti-PD-L1-based combination immunotherapy has become the first-line treatment for unresectable hepatocellular carcinoma (HCC). However, the objective response rate is lower than 40%, highlighting the need to identify mechanisms of tolerance to immune checkpoint inhibitors and accurate biomarkers of response. Here, we employed next-generation sequencing to analyze HCC samples from 10 patients receiving anti-PD-L1 therapy. Activation of the renin-angiotensin system was elevated in nonresponders compared with responders, and ACE2 expression was significantly downregulated in nonresponders. ACE2 deficiency promoted HCC development and anti-PD-L1 resistance, whereas ACE2 overexpression inhibited HCC progression in immune competent mice. Mass cytometry by time of flight (CyTOF) revealed that ACE2 deficient murine orthotopic tumor tissues featured elevated M2-like tumor-associated macrophages (TAMs), displayed a CCR5+PD-L1+ immunosuppressive phenotype, and exhibited high VEGFα expression. ACE2 downregulated tumor intrinsic CCL5 expression by suppressing NF-κB signaling through the ACE2/angiotensin-(1–7)/Mas receptor axis. The lower CCL5 levels led to reduced activation of the JAK-STAT3 pathway and suppressed PD-L1 and VEGFα expression in macrophages, blocking macrophage infiltration and M2-like polarization. Pharmacological targeting of CCR5 using maraviroc enhanced the tumor suppressive effect of anti-PD-L1 therapy. Together, these findings suggest that activation of the ACE2 axis overcomes the immunosuppressive microenvironment of HCC and may serve as an immunotherapeutic target and predictive biomarker of response to PD-L1 blockade.
2024-10-14 | GSE279109 | GEO
Project description:Liver cancer is one of the leading causes of cancer-related deaths worldwide. Hepatocellular carcinoma (HCC) is the most common liver cancer, and limited therapeutic options are available. Here we discovered that urinary dimethylarginine, especially symmetric dimethylarginine (SDMA), was found to be increased in HCC in a MYC-dependent manner. Mechanistically, protein arginine methyltransferase 5 (Prmt5), which was highly induced in HCC, is a direct MYC target gene. Moreover, administration of GSK3326595, a PRMT5 inhibitor, to human MYC-overexpressing transgenic mice that spontaneously develop HCC, suppressed the growth of liver tumors. GSK3326595 exhibited anti-proliferative activity and enhanced anti-tumor immune response. Collectively, this study suggest that PRMT5 could be a new drug target for HCC treatment.
2021-05-10 | GSE154514 | GEO
Project description:Immune checkpoint blockade (ICB), particularly programmed death 1 (PD-1) and its ligand (PD-L1), has shown considerable clinical benefits in patients with various cancers. Many studies show that PD-L1 expression may be biomarkers to help select responders for anti-PD-1 treatment. Therefore, it is necessary to elucidate the molecular mechanisms that control PD-L1 expression. As a potential chemosensitizer and anticancer drug, copper combined with disulfiram (DSF) kills tumor cells by regulating multiple signaling pathways and transcription factors in vitro and in vivo. Here, we showed that DSF increased PD-L1 expression in triple negative breast cancer (TNBC) cells. Through TCGA data analysis, we found that DNMT1 and IRF7 were highly expressed and the hypermethylation states in the IRF7 gene body promoter region in TNBC vs normal breast tissue (NBT). Then, we demonstrated that DSF affected PD-L1 expression via DNMT1-mediated IRF7 hypomethylation in two TNBC cell lines. In vivo experiments, DSF significantly enhanced the response to PD-1 antibody (Ab) in the triple-negative 4T1 BC mouse model. By analyzing the results of the tumor tissue sequencing, the DSF joint anti-PD-1 Ab could be a significant activation of anti-tumor immunity. And the inactive state of immune associated pathways was found to be reversed, such as Th1 and Th2 cell differentiation, antigen processing and presentation, natural killer cell-mediated cytotoxicity and T cell receptor signal transduction. In conclusion, we found that DSF could up-regulate PD-L1 in TNBC cells and elucidated its mechanism. Our findings revealed that the combination of DSF and anti-PD-1 Ab could activate the tumor immune microenvironment (TIME) to show much better antitumor efficacy than monotherapy.
2021-11-05 | GSE186885 | GEO
Project description:Cancer treatment has been transformed by checkpoint blockade therapies, with the highest anti-tumor activities of anti-programmed death 1 (PD-1) antibody (Ab) therapy seen in Hodgkin lymphoma. Disappointingly, response rates have been low in the non-Hodgkin lymphomas, with no activity seen in relapsed chronic lymphocytic leukemia (CLL) with anti-PD-1 Ab. Thus, identifying more powerful combination therapy is required for these patients. Here, we pre-clinically demonstrate enhanced T cell mediated anti-CLL activity following combinational therapy with anti-PD-1 or anti-PD-1 ligand (PD-L1) Ab and avadomide, a cereblon-modulating agent. Next-generation RNA sequencing was performed on highly purified T cells from treatment naïve CLL patients treated for 18 hours with avadomide or anti-PD-1 (nivolumab) or PD-L1 (durvalumab) alone or in combinations. Patient samples were selected to represent extremes of prognosis (n=6 good and n=6 poor prognostic groups). Total RNA was extracted using the RNeasy isolation kit (Qiagen) while the library preparation of extracted mRNA was performed by utilizing the TruSeq stranded mRNA kit (Illumina) and the resulting library sequencing was performed on an Illumina HiSeq 2500 system. In all analyses the primary assembly of hg38 was used (ENCODE version) and the annotation from Gencode v24. Alignment was performed using a two-pass mode with STAR (v2.5.2b) on the full genome and counts were obtained using the quantmode GeneCounts option. Salmon (v 0.7) was used to obtain pseudoalignments on transcripts and genes on the trimmed fastq files. Differentially expressed genes were identified by application of the voom R package. Each treatment group was compared to vehicle to estimate the effect size and statistical significance of gene expression changes between treatment and control. Differential expression pathway analysis revealed that the top functional gene categories common for all the avadomide and combination treated patient samples were related to the response to both type I and II interferon (IFN) signalling, as well as inflammatory, TNF-α signalling, IL-6/JAK/STAT3 and IL-2/STAT5 signalling responses. Pathway analysis revealed a strong enrichment of genes involved in T cell proliferation, cytokine and chemokine signalling, F-actin polymerization, T cell differentiation and co-stimulation. Notably, avadomide induced the expression of IFN type I inducible chemokines Cxcl9, Cxcl10 and Cxcl11 that have been associated with activation of Th1 immunity and favourable response to immunotherapy in solid cancer. In addition, genes associated with IFN-induced counter-regulatory pathways including Cd274 (PD-L1), Lag3 (lymphocyte-activation gene 3) and Ido1 (indoleamine 2,3 deoxygenase) were also upregulated by avadomide. Our analysis revealed that avadomide and the combination treatments induced IFN signaling in both good and poor prognostic disease subtypes, suggesting that therapies targeting patient T cells could be effective for all CLL patients. Thus, these results demonstrate the ability of avadomide to normalize dysfunctional IFN and chemokine responses in patient T cells that are linked to anti-tumor immunity.
2020-04-11 | GSE148476 | GEO
Project description:We sought to more precisely characterize the different alpha-synuclein (aSyn) 3M-bM-^@M-^YUTR mRNA species in normal and PD human brain. High-throughput, whole-transcriptome sequencing of the 3M-bM-^@M-^YUTR ends of polyadenylated mRNA transcripts (termed pA-RNAseq; see Methods) was performed on a cohort of 17 unaffected and 17 PD cerebral cortical tissue samples. This revealed 5 aSyn 3M-bM-^@M-^YUTR isoforms, with lengths of 290, 480, 560, 1070 and 2520 nt. Of these, the 560 nt and 2520 nt forms were predominant. The existence and relative preponderance of these species was further confirmed by Northern Blot. We next hypothesized, that aSyn 3M-bM-^@M-^YUTR selection might be altered in PD. Comparison of pA-RNAseq profiles from PD and unaffected cerebral cortex samples revealed an increase in the preponderance of the long 3M-bM-^@M-^YUTR species (>560 nt) relative to shorter species (<560 nt). Such a relative increase in aSynL was confirmed by Quantitative real-time RT-PCR (rt-qPCR) and appeared specific for PD, as the increase was also observed by comparison to RNA from amyotrophic lateral sclerosis patient samples. We note that the modified aSyn 3M-bM-^@M-^YUTR selection associated with PD patient tissue was detected in cerebral cortex tissue, which typically harbors pathological evidence of the disease process without frank cell loss; thus, this phenotype is unlikely to be a secondary consequence of neurodegeneration. Comparison of 3'UTR ends of alpha-synuclein in PD and unaffected brain cortex
2012-10-04 | E-GEOD-40710 | biostudies-arrayexpress