Optimization of Breast Biopsy and Mastectomy Sample Collection Procedures for Biobanking, Personalized Medicine, and Research Applications

Summary

This article presents a detailed protocol for collecting breast cancer samples, designed to optimize their utility for biobanking, personalized medicine, and other research applications. The workflow for sample collection, including breast biopsy and mastectomy procedures, is described in detail, focusing on minimizing tissue damage and maximizing sample quality.

Abstract

Breast cancer is the most prevalent cancer affecting women, particularly in Asia, with the highest incidence in the Philippines. Despite ongoing efforts, the understanding of breast cancer biology remains inadequate, compounded by the lack of effective screening programs and timely treatments. Addressing these issues, biobanks and other repositories for biological specimens have gained global momentum. The University of the Philippines- Philippine General Hospital (UP-PGH) has established a cancer biobank, demonstrating the viability of a government-supported initiative for cancer research in the Philippines. The study involves a prospective observation of 100 Filipino breast cancer patients at various disease stages, leveraging the expertise of UP-PGH, Philippine Genome Center (PGC), and University of the Philippines Diliman - Institute of Biology (UPD-IB). It integrates the collection, processing, and storage of biospecimens alongside comprehensive patient data. Procedures include RNA extraction, library preparation, and sequencing. Additionally, a subset of patients participates in an in vitro three-dimensional (3D) cell culture experiment for chemotherapy pre-screening. The aggregated data aims to uncover therapeutic strategies that can lead to personalized treatments where standard clinical approaches are inadequate. Key techniques include ultrasound-guided core needle biopsy, meticulous normal breast tissue collection, and precise tumor percentage determination to ensure high-quality RNA extraction, sequencing, and 3D cell culture. The study also addresses challenges encountered in prior biobanking endeavors. Ultimately, this research aims to contribute significantly to breast cancer research, positioning itself as a model for collaborative research, biobank establishment, and the advancement of precision medicine in developing countries, such as the Philippines.

Introduction

Breast cancer stands as the most prevalent form of cancer among Filipino women. In Asia, the Philippines exhibits one of the highest breast cancer mortality rates and lowest mortality-to-incidence ratio¹. The rates may have been greatly affected by the absence of screening programs and timely and effective treatment for breast cancer. In the country, breast cancer is typically diagnosed in later stages since most cancer patients only seek consultation at advanced cancer stages. In the Philippines, where a high incidence rate of breast cancer is observed, 53% of breast cancer cases were diagnosed in Stages III and IV, and only 2-3% were diagnose....

Protocol

This is a prospective, observational study with a collection of de-identified biospecimens (tumor and normal breast tissue) and clinicopathologic, treatment, and outcome data from 100 Filipino breast cancer patients of various stages. This is a collaborative work between the Philippine General Hospital (PGH), the Philippine Genome Center (PGC), and the Institute of Biology (IB) of the University of the Philippines Diliman, each with designated tasks. The protocol was registered in the Research Grants Administration Office (RGAO-2020-0933), and reviewed and approved by the University of the Philippines Manila Research Ethics Board (UPMREB) for implementation under....

Results

For the collection of samples during core needle biopsy, doing the procedure under ultrasound guidance had a huge impact on patient convenience and efficiency of workflow, as well as on the RNA integrity of the samples. If this is not done, the expected results might not be obtained, and patients must go back to the clinics to repeat the procedure, therefore prolonging sample collection and processing.

In addition to that, identification of tumor percentages per sample, which was done by the p.......

Discussion

The successful implementation of this protocol relies not only on technical precision but also on the coordination of clinical and research teams to ensure consistent sample quality and data integrity. This protocol incorporates several key procedures designed to maximize diagnostic accuracy and generate high-quality biospecimens suitable for downstream molecular analyses. Key steps include ultrasound-guided core needle biopsy for obtaining both normal and tumor breast tissue, data collection on treatment response, .......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
37% Formalin solution	PHILUSA Corporation	N/A	Used as a preservative of tissues for histopathological analysis
70% Isopropyl alcohol	Green Cross Inc.	N/A	Used as a disinfectant
Barcode printer	Zebra	GC420t	For printing of barcode labels to be used in labelling tubes containing the samples
Bleach	Green Cross Inc.	N/A	Used as a disinfectant; for decontamination of surgical tools
Blue ice packs	Rubbermaid	1002	For keeping samples at low temperatures during transport
Core needle biopsy 14-G needle	Bard	MN1410	An invasive tubular surgical instrument designed to be connected to a biopsy gun handpiece for the automatic extraction of a small tissue sample from an anatomical structure (a biopsy), while causing minimal surrounding tissue damage, for tissue pathological examination/testing.
Core needle breast biopsy gun	Bard	MG1522	Reusable core biopsy instrument used in collecting tissue samples during core needle biopsy
Disposable Petri Dish 90 mm x 15 mm	Phoenix Biomedical Products	LOT: 20220206	Used in core needle biopsy specimen collection when submerging tissues in PBS
Dulbecco's phosphate-buffered saline (PBS)	Thermo Fisher Scientific	21600010	A balanced salt solution used for a variety of cell culture applications, such as washing cells before dissociation, transporting cells or tissue, diluting cells for counting, and preparing reagents.
Forceps	Local Supplier	N/A
Kimtech Science KimWipes Delicate Task Wipers	Kimberly Clark Professional	KC34120	4.3 x 8.4 in. (11.0 cm x 21.3 cm); 1-ply 280 Count; for cleaning surfaces, parts, instruments, and medical offices, these wipes easily clean liquids, dust and small particles.
MACS Tissue storage solution	Miltenyi Biotec	130-100-008	Storage solution used to allow an optimized storage of fresh organ and tissue samples
Micropipette	Shanghai Lichen Instrument Technology Co., Ltd.	STEM-GC-3197-Y	for pipetting/transferring liquids in small volumes
Micropipette tips	Tarsons	521100	for pipetting/transferring liquids in small volumes
Parafilm	Parafilm M	5259-04LC PM996	For airtight and moisture-proof sealing of tubes to prevent leaks
Primocin 250 mg (5 x 1 mL)	InvivoGen	ant-pm-05	Used to protect tissues from microbial contamination
Refrigerator (4 °C)	LG	Model: GR-Y331SLZB	For storage of tissue samples and reagents
RNAlater solution	Thermo Fisher Scientific	AM7021	RNA stabilization solution used in the storage and biobanking of tissues
Sterile 15 mL conical tube	Thermo Scientific	339650	Used to make aliquots of reagents/media used in tissue storage
Sterile 5 mL Cryovials	Thermo Scientific	5000-1020	Used to make aliquots of reagents/media used in tissue storage
Sterile scalpel blade (#11)	Surgitech	N/A	For cutting tumor and normal breast tissues
Surgical scissors (18.5 cm 7 ¼" str)	Olten Instruments	BO-0125	For cutting tumor and normal breast tissues
Temperature logger	Extech Instruments	42280	For recording temperature and humidity during transport of samples
Tissue ink	Epredia	3120123	For staining the margins of excised surgical specimens for histopathological analysis
Ultra-low freezer	Haier Biomedical	DW-86L579	For indefinite storage of tumor and normal breast tissues
Urine specimen container 60mL	Sure Guard	0016UCS06PC	For storage of tissues for histopathological analysis
Ziplock Bags	Reynolds Consumer Products LLC		Used in packing the samples for transport