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Profiling protease and protease inhibitor gene expression in tumors and their microenvironment

ABSTRACT: To assist in the identification of proteases, their endogenous inhibitors, and proteins that interact with proteases or proteolytic pathways in biological tissues, a dual species oligonucleotide microarray has been developed in conjunction with Affymetrix, Inc. To investigate the performance of the array, gene expression profiles were analyzed in pure mouse and human samples and orthotopically implanted xenografts of human A549 lung and MDA-MB-231 breast carcinomas. The Hu/Mu ProtIn array is a valuable discovery tool for the identification of components of human and murine proteolytic pathways in health and disease, and has particular utility in the determination of cellular origins of proteases and protease inhibitors in xenograft models of human cancer. Keywords: gene expression profiles were analyzed in pure mouse and human samples and orthotopically implanted xenografts of human A549 lung and MDA-MB-231 breast carcinomas

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE6413 | GEO | 2008/07/21

SECONDARY ACCESSION(S): PRJNA99655

REPOSITORIES: GEO

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Profiling protease and protease inhibitor gene expression in tumors and their microenvironment

Project description:To assist in the identification of proteases, their endogenous inhibitors, and proteins that interact with proteases or proteolytic pathways in biological tissues, a dual species oligonucleotide microarray has been developed in conjunction with Affymetrix, Inc. To investigate the performance of the array, gene expression profiles were analyzed in pure mouse and human samples and orthotopically implanted xenografts of human A549 lung and MDA-MB-231 breast carcinomas. The Hu/Mu ProtIn array is a valuable discovery tool for the identification of components of human and murine proteolytic pathways in health and disease, and has particular utility in the determination of cellular origins of proteases and protease inhibitors in xenograft models of human cancer. Keywords: gene expression profiles were analyzed in pure mouse and human samples and orthotopically implanted xenografts of human A549 lung and MDA-MB-231 breast carcinomas Commercial pan human and mouse total RNA replicate samples (n=3) were profiled. In addition, human ductal stage II or III breast carcinoma biopsies (n=18) were compared to normal human breast biopsies (n=13). Spontaneous spontaneous murine mammary carcinomas from MMTV-PyMT+(FVB/n) (n=8) and MMTV-PyMT+/uPARAP-/-(FVB/n) (n=2) transgenic mice were compared to normal mouse mammary fat pads (n=4; female Rag-1 tm1Mom retired breeders at >6 weeks post lactation). In vitro cultures of MDA-MB-231 human breast carcinoma cells (n=3) and MDA-MB-231 orthotopic xenografts (n=3) were profiled. The xenografts were compared to normal mammary fat pads. A549 human lung adenocarcinoma cells (n=2), A549 orthotopic xenografts (n=3) and normal mouse lung tissue (n = 3) were profiled.

2008-07-20 | E-GEOD-6413 | biostudies-arrayexpress

Role of Ubc13 in Breast Cancer Metastasis

2014-08-18 | GSE55649 | GEO

Role of Ubc13 in Breast Cancer Metastasis

Project description:We recently found that Ubc13 controls breast cancer metastasis. However, the underlying molecular mechanisms remain elusive. In order to gain a better understanding of the signaling pathways controlled by Ubc13 in metastasis, we performed a gene array analysis on xenografts derived from orthotopically implanted MDA-MB-231 LM2 cells, which preferentially metastazize to lung in NOD/SCID mice. MDA-MB-231 LM2 cells were infected with lentivial shRNA constructs targeting either GFP (Control) or Ubc13 (ubc13). The resulting Control or Ubc13-silenced cells were implanted into fat pads of six weeks old female virgin NOD/SCID mice. After eight weeks, tumors were excised, followed by collagenase/hyaluronidase digestion to establish single cell suspension, from which epithelial cells were enriched by depleting mouse cells of hematopoietic, endothelial, and fibroblast origin (CD45, TER119, CD31 and BP-1). The enrihced epithelial cells (three Control and three Ubc13-KD cells) were lysed in TRIZOL to extract RNA, which were then used to run microarray.

2014-08-18 | E-GEOD-55649 | biostudies-arrayexpress

Differential gene expression analysis of RNAseq data comparing control and srGAP1 knockdown MDA-MB-231 primary tumors.

Project description:To investigate the differential expression of genes in human tumor xenografts of control MDA-MB-231 primary tumors (Ctrl) and srGAP1 knockdown MDA-MB-231 primary tumors.

2022-08-10 | GSE210488 | GEO

Modulation of protease expression by PITX transcription factors regulates protein quality control during aging

Project description:Protein quality control is important for healthy aging and is dysregulated in several age-related diseases. The autophagy-lysosome and ubiquitin-proteasome systems are key for proteostasis but it remains largely unknown whether other proteolytic systems maintain protein quality control during aging. Here, we find that the expression of proteolytic enzymes (proteases/peptidases) distinct from the autophagy-lysosome and ubiquitin-proteasome systems declines during skeletal muscle aging in Drosophila. Age-dependent downregulation of proteases undermines proteostasis, as demonstrated by the increase in detergent-insoluble poly-ubiquitinated proteins and pathogenic huntingtin-polyQ in response to protease RNAi. Transcriptomic analysis identifies Ptx1, homologous to human PITX1/2/3, as a transcriptional regulator of proteases. Specifically, RNAi for Ptx1 increases the expression of age-downregulated proteases and improves protein quality. Moreover, muscle-specific expression of Ptx1 RNAi extends lifespan. These findings indicate that protein quality control is ensured during aging by autophagy/proteasome-independent proteases that degrade misfolded and aggregation-prone proteins and by their transcriptional modulator Ptx1.

2022-08-15 | GSE156346 | GEO

Pubching spatial transcriptomics of MDA-MB-231 xenografts

Project description:Pubching spatial transcriptomics of MDA-MB-231 xenografts

| PRJNA765938 | ENA

The effect of MFNG knockdown on gene expression profile of xenograft tumor derived from MDA-MB231 cells

Project description:Mfng, a modulator of Notch signaling, is highly expressed in human claudin-low breast cancer (CLBC). To determine Mfng’s roles in CLBC pathogenesis,we knocked down Mfng in a CLBC cell line MDA-MB231, and found that Mfng knockdown altered Notch activation, decreased tumor sphere formation in vitro, and reduced tumor growth in xenograft model. To identify the potential downstream targets of Mfng during CLBC tumorigenesis, we compared the gene expression profiles between xenografts tumor derived from of MDA-MB231 cells carrying Mfng shRNA and the control vector. Mfng, a modulator of Notch signaling, is highly expressed in human claudin-low breast cancer (CLBC). To determine Mfng’s roles in CLBC pathogenesis,we knocked down Mfng in a CLBC cell line MDA-MB231, and found that Mfng knockdown caused alteration in Notch activation, associated with decreased tumor sphere formation in vitro, as well as reduced tumor growth in xenograft model. We intend to compare gene expression profiles between xenografts of MDA-MB231 cells carrying Mfng shRNA and the control vector. This project seeks to identify potential downstream targets of Mfng in CLBC. MDA-MB231 cells were transfected with shRNA against MFNG. Stable cell clones with knockdown of MFNG or corresponding control were selected and injected orthotopically into SCID mice. Total RNA was then extracted from the xenograph tumors for microarray analysis.

2015-05-01 | E-GEOD-62481 | biostudies-arrayexpress

Renal Cell Carcinoma (RCC) tumorgrafts exhibit similar gene expression profiling to corresponding primary tumors

Project description:Primary tumors of Renal Cell Carcinoma (RCC) were implanted orthotopically into mice and their gene expression profiling was compared to their corresponding tumors using Affymetrix Human Genome U133 Plus 2.0 arrays.

2012-06-05 | E-MTAB-1050 | biostudies-arrayexpress

Liver Transplantation for Non-Resectable Colorectal Liver Metastasis

Project description:The study aims to evaluate the efficacy of liver transplantation in the context of non-resectable colorectal liver metastasis. The primary endpoint is the overall survival in this group of patients while the secondary endpoint is the disease-free survival. Patients included in this protocol will be evaluated either for whole or partial liver transplantation from deceased or living donors. Type of different transplantations proposed are as follows: 1. Whole liver graft or partial liver (split) from a deceased donor 2. Partial liver graft retrieved from a deceased donor and orthotopically implanted after having performed a left hepatectomy in the recipient. 3. Partial liver graft retrieved from a deceased donor and heterotopically implanted if total hepatectomy can not be performed. 4. Partial liver graft retrieved from a living donor and orthotopically implanted after having performed total hepatectomy. 5. Partial liver graft retrieved from a living donor and orthotopically implanted after having after having performed a left hepatectomy in the recipient. 6. Partial liver graft retrieved from a living donor and heterotopically implanted if total hepatectomy can not be performed. In cases 2-3-5-6 total hepatectomy of native liver can be secondarily performed after having achieved a proper graft hypertrophy in order to avoid a small for size syndrome

| 2400483 | ecrin-mdr-crc

Tang2019 - Pharmacology modelling of AURKB and ZAK interaction in TNBC

Project description:Aurora Kinase B and ZAK interaction model Equivalent of the stochastic model used in "Network pharmacology model predicts combined Aurora B and ZAK inhibition in MDA-MB-231 breast cancer cells" by Tang et. al. 2018. The only difference is cell division and partitioning of the components, which are available in the original model for SGNS2.

2020-04-28 | BIOMD0000000940 | BioModels

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