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Hope for Others: Research Results from the University of Pittsburgh Rapid Autopsy Program for Breast Cancer

ABSTRACT: Hope for Others: Research Results from the University of Pittsburgh Rapid Autopsy Program for Breast Cancer

PROVIDER: PRJNA1235297 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR32670550.fastq.gz	Fastqsanger.gz
	SRR32670551.fastq.gz	Fastqsanger.gz
	SRR32670553.fastq.gz	Fastqsanger.gz
	SRR32670554.fastq.gz	Fastqsanger.gz

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Hope for Others: Research Results from the University of Pittsburgh Rapid Autopsy Program for Breast Cancer

Project description:Breast cancer affects 1/8 of women throughout their lifetimes, with over 90% of cancer deaths being caused by metastasis. However, metastasis poses unique challenges to research, as complex changes in the microenvironment in different metastatic sites and difficulty obtaining tissue for study hinder the ability to examine in depth the changes that occur during metastasis. Rapid autopsy programs thus fill a unique need in advancing metastasis research. Here, we describe our protocol and processes for establishing and improving the US-based Hope for OTHERS (Our Tissue Helping Enhance Research and Science) program for organ donation in metastatic breast cancer. As of August 2024, we consented 114 patients and performed 37 autopsies, from which we collected 551 unique metastatic frozen tumor samples, 1244 FFPE blocks, 90 longitudinal liquid biopsy samples and developed 14 patient-derived organoid and 8 patient-derived xenograft models. We report in-depth clinical and histopathological information and discuss extensive new research and novel findings in patient outcomes, metastatic phylogeny, and factors in successful living model development. Our results reveal key logistical and protocol improvements that are uniquely beneficial to certain programs based on identifiable features, such as working closely with patient advocates, methods to rescue RNA quality in cases where tissue quality may degrade due to time delays, as well as guidelines and future expansions of our program.

2025-06-25 | GSE291822 | GEO

Hope for Others: Research Results from the University of Pittsburgh Rapid Autopsy Program for Breast Cancer.

Project description:Breast cancer affects 1/8 of women throughout their lifetimes, with 90% of cancer deaths being caused by metastasis. However, metastasis poses unique challenges to research, as complex changes in the microenvironment in different metastatic sites and difficulty obtaining tissue for study hinder the ability to examine in depth the changes that occur during metastasis. Rapid autopsy programs thus fill a unique need in advancing metastasis research. Here, we describe our protocol and processes for establishing and improving the US-based Hope for OTHERS (Our Tissue Helping Enhance Research and Science) program for organ donation in metastatic breast cancer. Our results reveal key logistical and protocol improvements that are uniquely beneficial to certain programs based on identifiable features, such as working closely with patient advocates, methods to rescue RNA quality in cases where tissue quality may degrade due to time delays, as well as guidelines and future expansions of our program with new research and novel research findings in patient outcomes, metastatic phylogeny, living model development and more.

| S-EPMC11580927 | biostudies-literature

Refractory Cancers (RC) HOPE-CARE

Project description:Refractory Cancers (RC) HOPE-CARE

| PRJNA671240 | ENA

COVID_19 lung autopsy samples

Project description:COVID_19 lung autopsy samples

| PRJNA839754 | ENA

Transcription profiling of human hippocampi from epilepsy patients with and without hippocampal sclerosis and autopsy controls

Project description:Genome wide gene expression was compared between nonHS, HS temporal lobe epilepsy patients (TLE) and autopsy control hippocampi in a 3-way analysis. In many TLE patients the hippocampus is subject to massive neuronal damage, gliosis and hippocampal sclerosis (HS), while in others there is no apparent hippocampal damage (nonHS). This three way analysis enabled us to differentiate between pathology and epilepsy related processes.

2008-01-01 | E-MEXP-744 | biostudies-arrayexpress

HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies

Project description:Hepes-glutamic acid buffer mediated Organic solvent Protection Effect (HOPE)-fixation has been introduced as an alternative to formalin fixation of clinical samples. Beyond preservation of morphological structures for histology, HOPE-fixation was demonstrated to be compatible with recent methods for RNA and DNA sequencing. However, suitability of HOPE-fixed materials for the inspection of proteomes by mass spectrometry so far remained undefined. This is of particular interest, since proteins constitute a prime resource for drug research and can give valuable insights into the activity status of signaling pathways. In this study, we extracted proteins from human lung tissue and tested HOPE-treated and snap frozen tissues comparatively by proteome and phosphoproteome analyses. High confident data from accurate mass spectrometry allowed the identification of 2603 proteins and 3036 phosphorylation sites. HOPE-fixation did not hinder the representative extraction of proteins and investigating their biochemical properties, covered subcellular localizations and cellular processes revealed no bias caused by the type of fixation. In conclusion, proteome as well as phosphoproteome data of HOPE lung samples were qualitatively equivalent to results obtained from snap frozen tissues. Thus, HOPE-treated tissues match clinical demands both in histology and retrospective proteome analyses of patient samples by proteomics.

2014-05-22 | PXD000836 | Pride

Gene Expression Profile of Synchronized Cells Identifies Alzheimer's Disease in Autopsy Validated Skin and Blood Samples

Project description:A gene expression profile has not been identified for late-onset Alzheimer's Disease (LOAD) in more than 95% of cases. However, autosomal dominant genes are known for their early-onset (EOAD) characteristics. Moreover, the genetic convergences between familial EOAD and sporadic LOAD have not previously been identified despite the common neuropathology. Here, synchronized skin fibroblast samples from individuals with LOAD, confirmed by autopsy, revealed 36 statistically significant (P<0.05) LOAD-dysregulated genes, with 26 showing an essential gap with non-Alzheimer's disease (non-ADD) dementia patients. Notably, five LOAD-dysregulated genes in the skin—FAM149B, NHLH1, SHISA5, URB2, and WASF2—were also dysregulated in blood B-lymphocytes. Importantly, an additional 18 LOAD-dysregulated gene families in the skin were validated in the blood. In total, 23 LOAD-dysregulated gene families in the skin were confirmed in the blood. An intriguing and novel aspect is the genetic convergence between late-onset and early-onset Alzheimer's disease, as demonstrated by dysregulated gene families, including ADAM, IL, and RAB. The gene expression profile aligns remarkably well with prior autopsy-validated biomarkers: Morphometric Imaging, PKC epsilon, Cell Size, Growth Rate, and Protein Amount. Our findings suggest a promising potential for personalized genomic profiling in the diagnosis and treatment of LOAD, offering hope for more effective and targeted approaches.

2025-07-30 | GSE303404 | GEO

Ovis aries breed:Barbarine and others

Project description:Ovis aries breed:Barbarine and others Raw sequence reads

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Transcriptional response to SARS-CoV-2 infection in human autopsy lung samples

Project description:RNA-sequencing of human lung samples derived from COVID-19 patient autopsy.

2023-03-03 | GSE200074 | GEO

COHCAP: City of Hope CpG Island Analysis Pipeline

Project description:COHCAP: City of Hope CpG Island Analysis Pipeline

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