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

> **NIH NIH R42** · MATCHSTICK TECHNOLOGIES, INC. · 2022 · $155,792

## 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 a 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,
inefficient, 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, RNA, DNA and proteins for the
discovery of biomarkers for personal medicine.
We have previously developed and marketed a high-throughput PIXUL sonicator which generates high-intensity
focused ultrasound (HIFU) in wells of 96-well microplate to advance chromatin, RNA, DNA and protein
preparation from cultured cells and tissues.
As proposed in our current Fast Track STTR application (now in year 2 of Phase 2), we have established
protocols for extraction of chromatin, DNA, and RNA from FFPEs using PIXUL. We have benchmarked these
FFPE retrieval protocols against matched mouse frozen tissues (brain, heart, kidney and liver) using microplate
Matrix-ChIP-qPCR/seq, Matrix-MeDIP-qPCR/seq, Matrix-RT-qPCR/seq platforms. Still, test-tubes and heat
block are necessary for heat retrieval of analytes. The process can be simplified if all the sample preparation
steps, including sonication and heating, are done in one instrument using the same 96-well microplate. Thus, an
important goal of the current STTR grant was to engineer a more versatile PIXUL instrument for processing
FFPEs. Accordingly, we designed a 96-well microplate dual functionality laboratory PIXUL iteration instrument
that allows to program ultrasound and heating/cooling parameters, PIXUL H&C. The library preparation,
sequencing kits and PIXUL engineering costs are still limiting our ability to optimize and commercialize PIXUL
H&C for high throughput analysis of tissues including FFPEs. The administrative supplement is requested to
expedite PIXUL-FFPE R&D by increasing the number of tissues for NGS testing and allowing more
engineering resources to develop PIXUL H&C commercial prototype and custom microplates.
 Genome-wide tissue multiomic studies have provided valuable resources for discoveries. Thus, the high-
throughput, fast and efficient user-friendly dual-function PIXUL H&C device that we propose to optimize for NGS
applications and to commercialize will demonstrate its utility to researchers as an important means to interrogate
the vast repositories of FFPEs to discover disease pathways, candidate biomarkers and drug targets. Given that
FFPE are most often used in clinical laboratories for testing molecular biomarkers we expect that PIXUL H&C,
alike PCR machines, will also hav...

## Key facts

- **NIH application ID:** 10650670
- **Project number:** 3R42HG010855-03S1
- **Recipient organization:** MATCHSTICK TECHNOLOGIES, INC.
- **Principal Investigator:** Karol Bomsztyk
- **Activity code:** R42 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $155,792
- **Award type:** 3
- **Project period:** 2022-06-21 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10650670

## Citation

> US National Institutes of Health, RePORTER application 10650670, PIXUL-FFPE:  High throughput platform for chromatin and DNA sample preparation from formalin fixed paraffin embedded (FFPE) tissue samples- supplement application. (3R42HG010855-03S1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10650670. Licensed CC0.

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