# PIXUL-FFPE:  High throughput platform for chromatin and DNA sample preparation from formalin fixed paraffin embedded (FFPE) tissue samples.

> **NIH NIH R42** · MATCHSTICK TECHNOLOGIES, INC. · 2020 · $995,238

## Abstract

Formalin fixed paraffin-embedded (FFPE) tissue archives represent the largest clinically annotated human
specimen repository. The estimated millions of available FFPE tissue samples provide vast resource for the
discovery of disease epigenetic pathways, biomarkers and drug targets, And yet, these samples are highly
underutilized because current methods for extracting molecular information from FFPE samples are slow, labor
intensive, insufficiently sensitive to detect gene-bound enzymes (drug targets) and have low throughput to fully
exploit their enormous research and clinical potential. There is an unmet need for better tools to take advantage
of these archived clinical samples to retrieve chromatin and DNA for the discovery of epigenetic biomarkers for
personal medicine.
 The chromatin immunoprecipitation (ChIP) assay, a widely used approach for identifying genome-
associated proteins or DNA modifications, is one of the most powerful tools used in epigenetic studies. To
facilitate chromatin analysis, we have developed a high-throughput microplate-based Matrix ChIP-qPCR
platform and engineered a device for fast chromatin shearing which uses an array of 96 miniature ultrasound
transducers PIXUL (PIXelated ULtrasound). Extraction of chromatin from FFPE samples is a multistep process
which includes chromatin shearing. Ultrasound facilitates chromatin extraction from FFPE samples. The goal of
this Matchstick Fast Track STTR project (working with UW partner laboratories) is to develop and
validate a user-friendly and efficient high throughout PIXUL-based technology, PIXUL-FFPE, to extract
and shear chromatin and DNA from small FFPE samples for epigenetic analysis for use in the research
market paving the way for use in clinical settings. The following aims are proposed. In Aim#1(Phase 1) We
will design and validate custom PIXUL 96-well microplate for more efficient extraction of chromatin and DNA
from FFPE tissue samples. In Aim#2 (Phase 2) we will optimize PIXUL-FFPE protocol for fast and high
throughput chromatin extraction from small FFPE samples while maximizing sample integrity. In Aim#3 (Phase
2) we will demonstrate the translational utility of PIXUL-FFPE by comparative ChIP analysis of matched pairs of
fresh-frozen and FFPE glioblastoma (GBM) tumor sections. In Aim#4 (Phase 2) we will modify PIXUL instrument
for extraction of chromatin from FFPE samples.
 Search for epigenetic therapies has slowed down by paucity of available data. Thus, integrating the custom
96-well plates and improved protocol with the modified PIXUL instrument will greatly increase utilization of FFPE
specimens in the research market place attracting greater numbers of investigators to explore the vast
repositories of archived human tissues and as such advancing precision medicine.

## Key facts

- **NIH application ID:** 10021842
- **Project number:** 4R42HG010855-02
- **Recipient organization:** MATCHSTICK TECHNOLOGIES, INC.
- **Principal Investigator:** Karol Bomsztyk
- **Activity code:** R42 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $995,238
- **Award type:** 4N
- **Project period:** 2019-09-18 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10021842

## Citation

> US National Institutes of Health, RePORTER application 10021842, PIXUL-FFPE:  High throughput platform for chromatin and DNA sample preparation from formalin fixed paraffin embedded (FFPE) tissue samples. (4R42HG010855-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10021842. Licensed CC0.

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