Profiling the inflammatory signatures of bulk MC38, Pan02 and KPC tumors from wild-type mice and Sirpα-KO mice before and after radiation therapy
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PROVIDER: PRJNA630429 | ENA |
REPOSITORIES: ENA
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Project description:The inflammatory gene expression profile in MC38, Pan02 and KPC tumors from wild-type mice and Sirpα-KO mice before and after radiation was analyzed by nCounter Analysis System using nCounter Mouse Immunology kit including 561 immunology-related mouse genes .
2021-04-19 | GSE149882 | GEO
Project description:To compare the inflammatory responses of WT and SIRPα KO macrophage, we performed a complete transcript profiling of WT and SIRPα-KO M1 macrophage using transcriptome sequencing as a discovery platform. SIRPα-KO mice and WT mice were kept under the same condition. BMDMs were produced from WT and SIRPα-KO mice followed by M1 polarization. RNA was then isolated from the same number of BMDMs.
2021-03-19 | GSE169177 | GEO
Project description:Recently, Bailey et al (2016, Nature) defined four subtypes of pancreatic cancer that are associated with distinct histopathological characteristics and differential survival, namely, Squamous, Pancreatic Progenitor, Immunogenic, and ADEX (Aberrantly Differentiated Endocrine eXocrine). We set out to assess by RNASeq whether loss of CXCR2 was significantly associated with a specific PDAC subtype. Pancreatic tumors were harvested from KPC or KPC Cxcr2-/- mice at endpoint (n=5 v 5), RNA prepared, and RNASeq analysis carried out. Reads were analysed using the bcbio-nextgen framework (https://bcbio-nextgen.readthedocs.org/en/latest/). After quality control and adaptor trimming, reads were aligned to the mouse genome build (UCSC mouse mm10) using STAR. Counts for known genes were generated using the function featureCounts in the R/Bioconductor package \Rsubread\. The R/Bioconductor package edgeR was used to identify differentially expressed genes.
2018-03-31 | E-MTAB-4659 | biostudies-arrayexpress
Project description:Type-2 innate lymphoid cells (ILC2) are part of a growing family of innate lymphocytes known for their crucial role in both the development and exacerbation of allergic asthma. In this study, we aim to elucidate the critical role of the suppressor molecule signal regulatory protein alpha (SIRPα), which interacts with CD47, in controlling ILC2-mediated airway hyperreactivity (AHR). Our data indicate that activated ILC2s upregulate the expression of SIRPα, and the interaction between SIRPα and CD47 effectively suppresses both ILC2 proliferation and effector function. To evaluate the efficacy of SIRPα in regulating ILC2-mediated AHR, we utilized SIRPα and CD47 deficient mice in a murine model of allergen-induced AHR. Our findings suggest that the absence of SIRPα leads to the overactivation of ILC2s. Conversely, engagement with SIRPα reduces ILC2 cytokine production and effectively regulates ILC2-dependent AHR. Furthermore, the SIRPα-CD47 axis modulates mitochondrial metabolism through the JAK/STAT and ERK/MAPK signaling pathways, thereby regulating NF-κB activity and the production of type two cytokines. Additionally, our studies on human cells have revealed that SIRPα is inducible and expressed on human ILC2s, and administration of a SIRPα agonist effectively suppresses the effector function and cytokine production of ILC2s. Moreover, administering human CD47-Fc to humanized ILC2 mice effectively alleviated AHR and lung inflammation. These findings highlight the promising therapeutic potential of targeting the SIRPα-CD47 axis in the treatment of ILC2-dependent allergic asthma.
2024-08-10 | GSE264061 | GEO
Project description:mPDAC tumors of KPC mice
2019-02-12 | GSE126388 | GEO
Project description:We report the application of bulk RNAseq of live cells from pancreas of KPC or KPC-OG genetic mice at 6 weeks of age. These sponteneous tumors were unperturbed otherwise until timepoint.
2020-01-01 | GSE131602 | GEO
Project description:Pancreatic ductal adenocarcinoma (PDAC) continues to be a major health problem. A ketogenic diet (KD), characterized by a very low carbohydrate and high fat composition, has gained attention for its anti-tumor potential. We evaluated the effect and mechanisms of feeding a strict KD alone or in combination with gemcitabine in the autochthonous LSL-KrasG12D/+; LSL- Trp53 R172H/+; Pdx1-Cre (KPC) mouse model. For this purpose, both male and female pancreatic tumor-bearing KPC mice were allocated to a control diet (CD; %kcal: 70% carb, 14% protein, 16% fat), a KD (%kcal: 14% protein, 1% carb, 85% fat), a CD + gemcitabine (CG), or a KD + gemcitabine (KG) group. Mice fed a KD alone or in combination with gemcitabine showed significantly increased blood β-hydroxybutyrate levels compared to mice fed a CD or CG. KPC mice fed a KG had a significant increase in overall median survival compared to KPC mice fed a CD (increased overall median survival by 42%). Interestingly, when the data was disaggregated by sex, the effect of a KG was significant in female KPC mice (60% increase in median overall survival), but not in male KPC mice (28% increase in median overall survival). Mechanistically, the enhanced survival response to a KD combined with gemcitabine was multifactorial, including inhibition of ERK and AKT pathways, regulation of fatty acid metabolism and the modulation of the gut microbiota. In summary, a KD in combination with gemcitabine appears beneficial as a treatment strategy in PDAC in KPC mice, deserving further clinical evaluation.
2022-07-21 | GSE208398 | GEO
Project description:Background: Treatment with single-agent decitabine (5aza-dC; DAC), a well-tolerated DNA hypomethylating drug, in a mouse model of pancreatic ductal adenocarcinoma (PDAC), KPC-Brca1, extended the survival of the animals and upregulated immune-related pathways. Here we extend these findings to combination therapy, using DAC followed by the immune checkpoint inhibitor anti-PD-1H in the original more widely utilized KPC (Pdx-Cre Kras/p53) model. Methods: We treated tumor-bearing KPC mice with DAC, and with anti-PD-1H, separately and in combination, and assessed tumor growth, mouse survival, immune cell infiltration of the tumors, and gene expression, compared to historical and mock-treated control mice. Results: Treatment with single-agent DAC led to increased Cd8+ tumor-infiltrating T cells (TILs), increased tumor necrosis, and slower tumor growth. RNA-seq analysis revealed increased expression of a group of myeloid-lineage markers, including Chi3l3 (Ym1), which proved to reflect recruitment or expansion of a unique population of Chi3l3/Arginase-1 double-positive “M2-polarized” tumor-infiltrating myeloid cells. Anti-PD-1H alone had only modest effects on tumor growth and number of Cd8+ TILs. However, PD-1H-expressing TILs were significantly increased by single agent DAC, and DAC treatment followed by anti-PD-1H produced the strongest increase in Cd8+ TILS, inhibition of tumor growth, and prolongation of survival. Conclusions: Treatment with DAC alone, and DAC plus anti-PD-1H, inhibits PDAC tumor growth in the KPC model and produces changes in tumor-infiltrating lymphoid and myeloid cell populations, with an additive therapeutic benefit from combining the two agents. Since the influx of M2-polarized macrophages induced by DAC is predicted to antagonize the anti-tumor effects, future work should investigate eliminating or reprogramming these cells.
2018-07-01 | GSE101336 | GEO
Project description:MC38 tumors were photoconverted in Kade mice to assess the effect of photo conversion on the transcriptome
2022-04-08 | GSE193654 | GEO
Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling and TCR sequencing.
2022-08-16 | E-MTAB-9734 | biostudies-arrayexpress