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Total RNA-seq from Patient-Derived Xenograft models of Breast Cancer developed at Baylor College of Medicine

ABSTRACT: Total RNA-seq from Patient-Derived Xenograft models of Breast Cancer developed at Baylor College of Medicine

PROVIDER: PRJNA759581 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15687228_1.fastq.gz	Fastqsanger.gz
	SRR15687228_2.fastq.gz	Fastqsanger.gz
	SRR15687230_1.fastq.gz	Fastqsanger.gz
	SRR15687230_2.fastq.gz	Fastqsanger.gz
	SRR15687232_1.fastq.gz	Fastqsanger.gz

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Total RNA-seq from Patient-Derived Xenograft models of Breast Cancer developed at Baylor College of Medicine

Project description:This study is a repository for all RNAseq data obtained from High Throuput Seqeuncing of Patient Derived Xenograft models of Breast Cancer studied at the Baylor College of Medicine Breast Center.

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A Patient-Derived Xenograft Preclinical Model for Triple Negative Breast Cancer to Evaluate PDJ Amplicon Heterogeneity and Chemotherapeutic Induction

Project description:We applied DNA content flow cytometry to ten patient derived triple negative breast cancer (TNBC) xenografts (PDXs) from the Baylor College of Medicine (BCM). We interrogated purified sorted tumor fractions from each sample with whole genome copy number variant (CNV) analyses. These identified a variety of somatic genomic lesions that are common in TNBC including three cases with 9p24.1 amplification targeting PD-L1-PDL2 and JAK2 (PDJ amplicon) and recurring focal amplicons of oncogenic drivers found commonly in the TNBC PDXs including MYC and EGFR. In addition, homozygous deletions of known tumor suppressor genes including PTEN, CDKN2A, RB1, and BRCA2, and unique targets such as CUX1 and FYN were identified. Of the three PDJ-positive amplified PDXs, 2/3 two had focal MYC amplifications and 1/3 had a RB1 homozygous deletion.

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Project description:The purpose of this study was to search for microgravity-sensitive genes, specifically for apoptotic genes influenced by the microgravity environment and other genes related to immune response. Experiment Overall Design: Two-group design with paired samples, i.e., one 1G and one MMG culture came from the same donor. Therefore, 6 samples came from 3 different donors. Experiment Overall Design: Donor 1 :GSM96146,GSM96147 Experiment Overall Design: Donor 2: GSM96148, GSM96149 Experiment Overall Design: Donor 3: GSM96150,GSM96151 Experiment Overall Design: Total RNA was submitted to, and then labeled, hybridized and data generated by the Baylor College Medicine Microarray Core Facility (333E One Baylor Plaza, Houston, TX 77030).

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Project description:The survival rate of pediatric acute myeloid leukemia (pAML) is currently around 60%. While survival has slowly increased over the past few decades, the development of novel agents likely to further improve survival for this heterogeneous patient population has been limited by gaps in the pAML pre-clinical pipeline. One of the major hurdles in evaluating new agents for pAML is the lack of pAML patient-derived xenograft (PDX) models. Unlike solid tumors and other types of leukemias, AML is notoriously hard to establish in mouse models, likely due in part to the need for specific human microenvironment elements. Our laboratory at TCH/BCM addressed this gap by establishing a systematic PDX workflow, leveraging advanced immunodeficient hosts and capitalizing on our high volume of pAML patients and close coordination between labs and clinical sections. Patients treated at TCH are offered the chance to participate in specimen banking protocols that allow blood and bone marrow collection as well as the collection of relevant clinical data. All patients who consent and have samples available are trialed for PDX development. In addition, samples from the Children's Oncology Group (COG) are also trialed for PDX generation. Serially transplanting PDX models are validated using short tandem repeat (STR) and characterized using both targeted DNA/RNA next generation sequencing and RNAseq. As of March 2023, this systematic approach has resulted in 26 serially transplanting models. Models have been shared with requesting labs to facilitate external pAML pre-clinical studies. Available PDX models can be located through the BCM PDX Portal. We expect our growing PDX resource to make a significant contribution to expediting the testing of promising novel therapeutics for pAML.

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