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CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10 [R08_MgliaDep]

ABSTRACT: We performed CITE-seq (10x Genomics-based) to profile and compare the transcriptomes and cell surface expression of immune epitopes in the brains and blood of different transgenic mice (Cx3cr1CreERT; Cx3cr1CreERT-ROSA-iDTR) during homeostasis or brain metastasis with or without DT-based microglia depletion. We sequenced a total of eight different samples. We created an antibody pool consisting of 35 different antibodies and stained each sample individually with this antibody pool. Then, we stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all sight samples and finally separate each sample in silico by it's unique hashing antibody. The samples are as follows: (1) HTO1: brain of naïve Cx3cr1CreERT mouse (non-microglia depleted); (2) HTO2: brain of metastasis-burdened Cx3cr1CreERT mouse (non-microglia depleted); (3) HTO3: brain of metastasis-burdened Cx3cr1CreERT mouse (non-microglia depleted); (4) HTO4: brain of naïve Cx3cr1CreERT-ROSA-iDTR mouse (microglia depleted); (5) HTO5: brain of metastasis-burdened Cx3cr1CreERT-ROSA-iDTR mouse (microglia depleted); (6) HTO6: brain of metastasis-burdened Cx3cr1CreERT-ROSA-iDTR mouse (microglia depleted); (7) HTO7: blood of metastasis-burdened Cx3cr1CreERT mouse (non-microglia depleted); (8) HTO8: blood of metastasis-burdened Cx3cr1CreERT-ROSA-iDTR mouse (microglia depleted). The following sample comparisons were made: HTO1 versus HTO4; HTO2 and HTO3 versus HTO5 and HTO6; HTO7 versus HTO8.

ORGANISM(S): Mus musculus

PROVIDER: GSE139971 | GEO | 2020/10/29

REPOSITORIES: GEO

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CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10 [R07_Cx3cr1]

Project description:We performed CITE-seq (10x Genomics-based) to profile and compare the transcriptomes and cell surface expression of immune epitopes in the brains of Cx3cr1+/- and Cx3cr1-/- mice during homeostasis or brain metastasis. We sequenced a total of eight different samples. We created an antibody pool consisting of 35 different antibodies and stained each sample individually with this antibody pool. Then, we stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all sight samples and finally separate each sample in silico by it's unique hashing antibody. The samples are as follows: (1) HTO1: brain of naïve Cx3cr1+/- mouse; (2) HTO2: brain of naïve Cx3cr1+/- mouse; (3) HTO3: brain of metastasis-burdened Cx3cr1+/- mouse; (4) HTO4: brain of metastasis-burdened Cx3cr1+/- mouse; (5) HTO5: brain of naïve Cx3cr1-/- mouse; (6) HTO6: brain of naïve Cx3cr1-/- mouse; (7) HTO7: brain of metastasis-burdened Cx3cr1-/- mouse; (8) HTO8: brain of metastasis-burdened Cx3cr1-/- mouse. The following sample comparisons were made: HTO1 and HTO2 versus HTO5 and HTO6; HTO3 and HTO4 versus HTO7 and HTO8.

2020-10-29 | GSE139970 | GEO

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Project description:We performed CITE-seq (10x Genomics-based) to profile and compare the transcriptomes and cell surface expression of immune epitopes in the brains and blood of different transgenic mice (Cx3cr1+/-; Cx3cr1-/-; CCR2+/-; CCR2-/-) during homeostasis or brain metastasis. We sequenced a total of eight different samples. We created an antibody pool consisting of 35 different antibodies and stained each sample individually with this antibody pool. Then, we stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all sight samples and finally separate each sample in silico by it's unique hashing antibody. The samples are as follows: (1) HTO1: brain of naïve CCR2+/- mouse; (2) HTO2: brain of naïve CCR2+/- mouse; (3) HTO3: brain of naïve CCR2-/- mouse; (4) HTO4: brain of naive CCR2-/-; (5) HTO5: blood of naïve Cx3cr1+/- mouse; (6) HTO6: blood of metastasis-burdened Cx3cr1+/- mouse; (7) HTO7: blood of naïve Cx3cr1-/- mouse; (8) HTO8: blood of metastasis-burdened Cx3cr1-/- mouse.The following sample comparisons were made: HTO1 and HTO2 versus HTO3 and HTO4; HTO5 versus HTO7; HTO6 versus HTO8.

2020-10-29 | GSE139969 | GEO

Chemotherapy-mediated changes in the immune cell landscape of murine triple negative breast cancer.

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Project description:Metastasis is a multistage process that requires cancer cells to escape from the primary tumor, survive in the circulation, seed at distant sites and colonize these foreign tissue environments. Each of these processes involves rate-limiting steps that are influenced by stromal cells of the tumor microenvironment. While the tumor microenvironment has emerged as a major regulator of cancer progression in other organ sites, our knowledge of the brain metastatic microenvironment is currently very limited. Thus, we aim to dissect signatures of tumor-stroma interactions in brain metastasis in order to identify factors that regulate the homing, seeding and outgrowth of cancer cells in this highly specialized microenvironment. We took advantage of an experimental metastasis model in which variants of the human breast cancer line MDA-MB-231 home to the brain in xenografted animals. To simultaneously capture gene expression changes in the tumor and stromal compartment, we used a dual species-specific microarray platform, the HuMuProtIn array, to discriminate between differentially expressed protease or protease inhibitor genes of human (tumor) or murine (stromal) origin. RNA was isolated from early and late brain, bone and lung metastases from xenograft models of breast metastasis. RNA was also isolated from non-tumor-burdened mouse brain, bone and lung as normal tissue controls. RNA from tissue homing cell lines was isolated in vitro to serve as a control for the human-derived RNA. Samples were collected from 24 total tumor-burdened mice, with 3 replicates for each condition and control. A total of 36 samples are included here.

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Mus musculus strain:C57BL6J

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| PRJDB17062 | ENA

CSF-1R inhibition alters macrophage polarization and blocks gliomagenesis

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2013-09-20 | E-GEOD-37475 | biostudies-arrayexpress

CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10

Project description:We used CITE-seq (10x Gemoics-based) to profile and compare the transcriptomes and cell surface expression of a set of immune markers of naïve brain myeloid cells from wild type C57Bl/6 mice to brain metastasis-associated myeloid cells (Br.MAM) from C57Bl/6 mice bearing E0771 brain metastases. In each sequencing round, we sequenced a total of four different mouse brains (2 naive and 2 metastasis-burdened). We created an antibody pool consisting of 6 different antibodies (CD45, CD25, CD3, CD4, CD11b, and CD86) and stained each brain individually with this antibody pool. Then, we stained each brain with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all six samples and finally separate each sample in silico by it's unique hashing antibody.

2020-10-29 | GSE134284 | GEO

CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10

Project description:We used CITE-seq (10x Genomics-based) to profile and compare the transcriptomes and cell surface expression of a set of immune markers of naïve brain myeloid cells from wild type C57BL/6 mice to brain metastasis-associated myeloid cells (Br.MAM) from C57BL/6 mice bearing E0771 brain metastases. In each sequencing round, we sequenced a total of four different mouse brains (2 naive and 2 metastasis-burdened). We created an antibody pool consisting of 6 different antibodies (CD45, CD25, CD3, CD4, CD11b, and CD86) and stained each brain individually with this antibody pool. Then, we stained each brain with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all six samples and finally separate each sample in silico by it's unique hashing antibody.

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2021-06-15 | E-MTAB-10021 | biostudies-arrayexpress

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