The Availability of Human Biospecimens to Support Biomarker Research

Tarling, Tamsin; Byrne, Jennifer A.; Watson, Peter H.

doi:10.1177/11772719221091750

Cited by 5 publications

(4 citation statements)

References 59 publications

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“…The photonic chip is made of three layers (see Figure 1a), namely, a substrate of silicon (Si), an intermediate layer of silicon dioxide (SiO 2 ), and a top optical waveguide layer of silicon nitride (Si 3 N 4 ). The high refractive index contrast between the waveguide material (𝑛𝑛 ≈ 2.0) and the sample medium (n ≈ 1.4), allows a confined propagation of the Supplementary page I Supplementary Information Super-resolution histology of paraffin-embedded samples via photonic chip-based microscopy Luis E. Villegas-Hernández 1 , Vishesh K. Dubey 1 , Hong Mao 1 , Manohar Pradhan 2 , Jean-Claude Tinguely 1 , Daniel H. Hansen 1 , Sebastián Acuña 1 , Bartłomiej Zapotoczny 3 , Krishna Agarwal 1 , Mona Nystad 4,5,6 , Ganesh Acharya 4,10 , Kristin A. Fenton 7 , Håvard E. Danielsen 2,8,9 , Balpreet Singh Ahluwalia…”

Section: Author Contributionmentioning

confidence: 99%

“…Moreover, the FFPE processing method supports several labeling procedures, including light-absorbing dyes such as hematoxylin and eosin (H&E), immunohistochemical markers, and fluorophores. Nowadays, FFPE is estimated to be the most common histological preservation method, with hundreds of millions of samples stored in biobanks around the world 2,3 . All these features make FFPE a valuable source of biological material for a wide variety of studies ranging from genomics 4,5 and proteomics 6 to aid in diagnosis 1 and prognosis 7,8 of diseases.…”

Section: Introductionmentioning

confidence: 99%

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Super-resolution histology of paraffin-embedded samples via photonic chip-based microscopy

Villegas-Hernández

Dubey

Mao

et al. 2023

Preprint

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Fluorescence-based super-resolution optical microscopy (SRM) techniques allow the visualization of biological structures beyond the diffraction limit of conventional microscopes. Despite its successful adoption in cell biology, the integration of SRM into the field of histology has been deferred due to several obstacles. These include limited imaging throughput, high cost, and the need for complex sample preparation. Additionally, the refractive index heterogeneity and high labeling density of commonly available formalin-fixed paraffin-embedded (FFPE) tissue samples pose major challenges to applying existing super-resolution microscopy methods. Here, we demonstrate that photonic chip-based microscopy alleviates several of these challenges and opens avenues for super-resolution imaging of FFPE tissue sections. By illuminating samples through a high refractive-index waveguide material, the photonic chip-based platform enables ultra-thin optical sectioning via evanescent field excitation, which reduces signal scattering and enhances both the signal-to-noise ratio and the contrast. Furthermore, the photonic chip provides decoupled illumination and collection light paths, allowing for total internal reflection fluorescence (TIRF) imaging over large and scalable fields of view. By exploiting the spatiotemporal signal emission via MUSICAL, a fluorescence fluctuation-based super-resolution microscopy (FF-SRM) algorithm, we demonstrate the versatility of this novel microscopy method in achieving superior contrast super-resolution images of diverse FFPE tissue sections derived from human colon, prostate, and placenta. The photonic chip is compatible with routine histological workflows and allows multimodal analysis such as correlative light-electron microscopy (CLEM), offering a promising tool for the adoption of super-resolution imaging of FFPE sections in both research and clinical settings.

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Section: Author Contributionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Super-resolution histology of paraffin-embedded samples via photonic chip-based microscopy

Villegas-Hernández

Dubey

Mao

et al. 2023

Preprint

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“…The discovery of novel biomarkers depends on the availability of relevant types of biological specimens (blood, fluids, tissue samples, cells or nucleic acids, etc) and associated data from representative groups of patients assembled under specific clinical settings. 3 Thus, biobanking is essential to precision medicine progress.…”

Section: Introductionmentioning

confidence: 99%

Ethical navigation of biobanking establishment in Ukraine: learning from the experience of developing countries

Sulaieva,

Artamonova,

Dudin

et al. 2023

J Med Ethics

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Building a biobank network in developing countries is essential to foster genomic research and precision medicine for patients’ benefit. However, there are serious barriers to establishing biobanks in low-income and middle-income countries (LMICs), including Ukraine. Here, we outline key barriers and essential milestones for the successful expansion of biobanks, genomic research and personalised medicine in Ukraine, drawing from the experience of other LMICs. A lack of legal and ethical governance in conjunction with limited awareness about biobanking and community distrust are the principal threats to establishing biobanks. The experiences of LMICs suggest that Ukraine urgently needs national guidelines covering ethical and legal aspects of biospecimen-related research. National guidelines must be consistent with international ethical recommendations for safeguarding participants’ rights, welfare and privacy. Additionally, efforts to educate and engage physicians and patient communities are essential for achieving biobanking goals and benefits for precision medicine and future patients.

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“…2 Human biobanks, on the other hand, are composed of patient-specific clinical data as found in a registry and include stored specimens such as blood, stool, or tissue. 3 These specimens may be processed to provide isolated cell lines, microbes, organoids, DNA, RNA, and proteins attributed to the individual patient. 4 Biobanks range in size and can be university-based, national, international, or commercial repositories.…”

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confidence: 99%

Creating a Surgical Biobank: The Hershey Medical Center Experience

Mankarious

Connelly

Harris

et al. 2023

Diseases of the Colon &Amp; Rectum

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BACKGROUND: Tissue harvesting at the time of surgery offers surgeons and scientists a unique opportunity to discover and better understand disease pathophysiology. Tissue biobanking presents challenges in patient consents, specimen collection, preparation, and storage, but the potential for scientific discovery justifies the effort. Although the number of tissue biobanks is increasing worldwide, information regarding necessary infrastructure, process flow, and management of expected obstacles is lacking. OBJECTIVE: To provide a framework and motivation for clinician scientists intending to start an intestinal tissue biobank under their direction. DATA SOURCES: The Carlino Family Inflammatory Bowel and Colorectal Diseases Biobank is housed at the Milton S. Hershey Medical Center. STUDY SELECTION: Review. INTERVENTION: Implementation of a surgical tissue biobank at a large tertiary care institution. MAIN OUTCOME MEASURES: Assess critical challenges and obstacles over the years as well as keys to the success of the program. RESULTS: Over 2 decades, the institutional biobank grew from an IBD biobank to one which now incorporates thousands of surgical specimens representing numerous colorectal diseases. This was done through a process of refinement focusing on patient recruitment and an efficient consenting and specimen management process. The biobank’s success is further insured by institutional, external, and philanthropic support; scientific collaborations; and sharing of biological specimens with other groups of dedicated researchers. LIMITATIONS: This is a single-center experience in collecting surgically resected colorectal specimens. CONCLUSIONS: Surgical specimen biobanks are essential in studying disease cause using genomics, transcriptomics, and proteomic technologies. Therefore, surgeons, clinicians, and scientists should build biobanks at their institutions to promote further scientific discovery and improve specimen diversity.

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The Availability of Human Biospecimens to Support Biomarker Research

Cited by 5 publications

References 59 publications

Super-resolution histology of paraffin-embedded samples via photonic chip-based microscopy

Super-resolution histology of paraffin-embedded samples via photonic chip-based microscopy

Ethical navigation of biobanking establishment in Ukraine: learning from the experience of developing countries

Creating a Surgical Biobank: The Hershey Medical Center Experience

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