Improving Public Trust in Biobanking: Roundtable Discussions from the 2021 ISBER Annual Meeting.

Biobanking is a relatively newly recognized and innovative branch of science, which includes the collection of samples and associated data from hospitals, diagnostic centers, and voluntary donations for biomedical and environmental research. It involves diverse stakeholders at the junction of society, science, ethics, law, and politics. A key element in the success of a biobank is the trust and support of public donors, clinicians, and scientists. To achieve trust, it is important to implement strategies that can increase biobank awareness in common people, and different types of communities. Biobank laws and regulations and transparent governance by the biobanks are also crucial to achieving public trust.

Decarbonization in Biobanking: A Potential New Scientific Area.

Calls to reduce or entirely remove the carbon footprint of ongoing activities, collectively termed as decarbonization, have become increasingly more vocal in health care with a number of recent, high profile consensus statements. These calls encourage the biobanking field, as one of the foundational health care research infrastructures, to consider decarbonization as a potential novel research area both in terms of the molecules and the equipment used in research. The current article provides a summary of the roundtable discussion during the 2022 ISBER Annual Meeting and Exhibits, highlighting the current knowledge gaps, challenges, and opportunities in this field. In particular, technological innovation, a greater awareness of the current situation, and behavioral change are important pieces of the puzzle to improving the future of decarbonization in biobanking, even if the eventually implemented routes between resource-abundant and resource-restricted settings might be distinctly different. This article sets the foundation for raising awareness of the subject and of subsequent steps that need to be undertaken.

Preparation of the "Lexique" for ISBER Best Practices 4th Edition for Biobankers in Indo-Pacific Rim Region.

Statement of the Problem: Several standards and guidelines for biobanks or biorepositories have been published by various parties (e.g., the International Society for Biological and Environmental Repositore [ISBER] and the International Organization for Standardization [ISO]). These documents are invaluable for improving the routine practices of the biobanks but the implementation has proven to be challenging for those biobanks from the non-English regions because these resources are mostly written in English. Proposed Solution: The World Health Organization (WHO) has recently published the International Classification of Diseases 11th Revision (ICD-11) along with a translation tool (lexique) for potential users. This has inspired us to make a similar contribution in the biobanking field. All the regional ambassadors (RAs) and director-at-large (DAL) in the Indo-Pacific Rim (IPR) region worked together to produce a similar lexique for potential users of ISBER's Best Practices (BPs) 4th edition. A lexique with languages of Hindi, Indonesian, Vietnamese, and Japanese has been prepared. Conclusions: This lexique is a comparison table between various languages and is expandable to other languages. In addition, this lexique will be a good tool for understanding the ISBER BPs 4th edition.

Quality Control of Breast Cancer Surgery Samples: Introducing Time Stamp Checking.

Background: Analytical information obtained from clinical tissue samples has recently become more important due to recent advancements in the clinical practice of medicine, for example, gene panel testing. However, acquiring and managing the sample quality, which greatly influences the analyses, are not sufficient and hence requires immediate attention. We introduced time stamp (TS) recording and documentation using the Standard PREanalytical Code (SPREC) for breast cancer surgery samples to monitor and control their quality. Materials and Methods: The TS recording used SPREC for quality control of each sample by recording seven factors: type of sample, type of collection, warm ischemia time (WIT), cold ischemia time (CIT), fixation type, fixation time (FT), and long-term storage. The responsibilities to record each factor were assigned among group members (breast surgeons, anesthesiologists, pathologists, operating room nurses, and medical technologists in pathology). Results: Records based on SPREC were recorded for 393 surgical cases of first-time breast cancer patients performed at the Kanagawa Cancer Center from May 2018 to April 2019. The vascular clamp time was defined as when skin flap formation was completed, regardless of the surgical procedure. An anesthesiologist recorded the vascular clamp time and sample collection time, and the pathologist recorded the fixation start time and fixation end time. WIT was 23 (3-116) minutes (breast-conserving surgery, 11 [3-38] minutes; mastectomy, 26 [5-116] minutes; and nipple-sparing mastectomy, 39 [31-43] minutes), CIT was 37 (3-1052) minutes, and FT was 43 (17-115) hours. The median CIT and FT were significantly shortened after introducing the TS system, and the variabilities were reduced. Conclusion: A TS system for quality control of breast cancer surgical sample functions well due to the establishment of highly versatile WIT and a working group consisting of multiple members of different occupations who shared roles.

Biobanking in the COVID-19 Era and Beyond: Part 2. A Set of Tool Implementation Case Studies.

The COVID-19 era has brought about a number of novel challenges for the global biobanking community. An array of diverse tools (e.g., standards, best practices, and plans) exists to support quality and fitness-for-purpose in biobank operations. The International Society for Biological and Environmental Repositories (ISBER) COVID-19 Response Task Force has set out to identify needs and gaps in these tools and make recommendations for the next generation of available tools, having closely examined the COVID-19-related challenges. While conducting this work to examine the relationships between tools and biobank adaptability, a subgroup of the task force conducted a parallel effort to develop and describe individual COVID-19 era case studies based on a number of operating biobanks. Each case study presents a different combination of implemented tools. Observations and lessons learned from these case studies are provided, and experiences with tool implementation are discussed. This information is supplemented by data relating to tool usefulness that was obtained through an ISBER survey discussed in a companion article. The knowledge gained from this study will be combined with other task force efforts to make recommendations to better position the biobanking community in their response to future emergencies.

Biobanking in the COVID-19 Era and Beyond: Part 1. How Early Experiences Can Translate into Actionable Wisdom.

The era of COVID-19 has brought about a number of novel challenges for the global biobanking community. To better position the biobanking community to cope with current and future challenges, the International Society for Biological and Environmental Repositories (ISBER) COVID-19 Response Task Force was convened to identify needs and gaps in biobanking tools (existing resources that support good practice), for example, standards, best practices, business, etc. and to make recommendations to benefit the community. Toward these goals, the Task Force assembled a set of questions to explore individual biobanks' experiences, with emphasis on identification of key challenges and approaches, including tools employed. A survey was designed with the use of these questions and administered by ISBER. This article presents a summary of the aggregated data obtained from the survey responses, illustrating some of the major issues encountered and identifying which tools the survey respondents found most useful. In particular, this article focuses on the challenges identified during the early months of the COVID-19 era. Recommendations are provided to support biobank emergency preparedness for the future, address lessons learned, and propose solutions to bridge identified gaps. The analysis and the complete survey dataset will also inform the larger Task Force goal to develop specific tool recommendations.

Diverse Responses of the Biobanks in Indo-Pacific Rim Region During the COVID-19 Pandemic: Case Scenarios from Two Low- and Middle-Income Countries and Two High-Income Countries in the Indo-Pacific Rim Region.

Background: Biobankers have been unexpectedly involved in the pandemic of COVID-19 since early 2020. Although specific guidance was not available, the International Society for Biological and Environmental Repositories (ISBER) Best Practices and the ISO 20387 document have been utilized to deal with the pandemic disaster. The ISO experts and best practice experts in ISBER teamed up to share the available information and learn the experiences of biobanks concerning COVID-19 through organizing webinars, surveys, and town hall meetings. Four ISBER regional ambassadors (RAs) from the Indo-Pacific Rim (IPR) region were also actively involved at one of the town hall meetings. These RAs, who are from Australia, India, Indonesia, and Japan, and the Director-at-Large of the region, have summarized their experiences in this article. Materials and Methods: The ISBER Standards Committee COVID-19 Task Force has kindly provided the survey results. The extracted glossary from the results was categorized into 10 factors: (1) crisis management; (2) sample-related issues; (3) logistics-related issues; (4) equipment-related issues; (5) ethical, legal, and social implication-related issues; (6) operation-related issues; (7) personnel-related issues; (8) management-related issues; (9) infection-related issues; and (10) research-related issues. Each IPR RA has provided a case considering these 10 factors. Results and Discussion: Two key points have emerged from the scenarios, which are as follows: (1) impacts of the biobanks in low- and middle-income countries (LMICs) are similar to those in high-income countries (HICs) and (2) tolerance of the biobanks in LMICs is not so robust as those in HICs. Furthermore, communication strategies with internal and external stakeholders are critical for a biobank to manage this crisis. This article summarizes the impacts, indicates the opportunities that COVID-19 has brought to the biobank community, and highlights the usefulness of the network beyond biobank services. Lastly, the biobanks need to turn the challenges into opportunities to overcome the crisis.

Monitoring of cancer patients via next-generation sequencing of patient-derived circulating tumor cells and tumor DNA.

Liquid biopsy of circulating tumor cells (CTC) and circulating tumor DNA (ctDNA) is gaining attention as a method for real-time monitoring in cancer patients. Conventional methods based upon epithelial cell adhesion molecule (EpCAM) expression have a risk of missing the most aggressive CTC subpopulations due to epithelial-mesenchymal transition and may, thus, underestimate the total number of actual CTC present in the bloodstream. Techniques utilizing a label-free inertial microfluidics approach (LFIMA) enable efficient capture of CTC without the need for EpCAM expression. In this study, we optimized a method for analyzing genetic alterations using next-generation sequencing (NGS) of extracted ctDNA and CTC enriched using an LFIMA as a first-phase examination of 30 patients with head and neck cancer, esophageal cancer, gastric cancer and colorectal cancer (CRC). Seven patients with advanced CRC were enrolled in the second-phase examination to monitor the emergence of alterations occurring during treatment with epidermal growth factor receptor (EGFR)-specific antibodies. Using LFIMA, we effectively captured CTC (median number of CTC, 14.5 cells/mL) from several types of cancer and detected missense mutations via NGS of CTC and ctDNA. We also detected time-dependent genetic alterations that appeared during anti-EGFR therapy in CTC and ctDNA from CRC patients. The results of NGS analyses indicated that alterations in the genomic profile revealed by the liquid biopsy could be expanded by using a combination of assays with CTC and ctDNA. The study was registered with the University Hospital Medical Information Network Clinical Trials Registry (ID: UMIN000014095).

Standardization and Innovation in Paving a Path to a Better Future: An Update of Activities in ISO/TC276/WG2 Biobanks and Bioresources.

Recent advances in biotechnology are making it possible to advance science and improve healthcare with increasing speed and precision. Biobanking, as a foundation of the biotechnology infrastructure, is critical to the assurance of quality for many of the key components for these advancing technologies in both the human and nonhuman domains. Biobanking must advance to support the increased complexity and required precision needs of biological resources. Standards development can provide an important link for the research and development community by providing tools to ensure quality, fitness-for-purpose, and reproducibility in biobanking. ISBER has been developing the ISBER Best Practices revision. At the same time, ISO/TC276/ WG2 has been developing an International Standard (IS) ISO/DIS 20387 General requirements for biobanking standard. It is important that ISBER and ISO/TC276/WG2 harmonize and/or align their products to enable members of the diverse biobanking community to tailor their own suite of tools to support their specific needs. The availability of both standards and best practices that are complementary will maximize available support for all biobanks. The increased availability of complementary standards, tools, and best practices will facilitate the path to new biotechnology advances and a better future.

Clinicopathological, Immunohistochemical, and Genetic Features of Primary Lung Adenocarcinoma Occurring in the Setting of Usual Interstitial Pneumonia Pattern.

INTRODUCTION: An association between usual interstitial pneumonia (UIP) and carcinogenesis has been well established. However, few detailed analyses have investigated the clinicopathological, immunohistochemical, and genetic features of patients with primary lung adenocarcinoma (ADC) with UIP (UIP-ADC). METHODS: We identified 44 patients with ADC in the setting of UIP (the UIP-ADC group) (1.9%) from 2309 patients with primary ADC and compared clinicopathological, immunohistochemical, and genetic features between the UIP-ADC group and patients with ADC without UIP (the non-UIP-ADC group). RESULTS: Clinicopathological features of UIP-ADC included an older age at occurrence; male predominance; smoking history; predilection for the lower lobe; large tumor size; high incidence of lymph vessel invasion, pleural invasion, and lymph node metastasis; and poor survival rate. However, the cause of death of patients with UIP-ADC was largely influenced by respiratory complications. Histologically, patients in the UIP-ADC group could be stratified according to invasive mucinous-predominant subtype. Genetically, patients in the UIP-ADC group had lower EGFR and higher KRAS mutation rates compared with patients in the non-UIP-ADC group. CONCLUSIONS: UIP-ADC was associated with a poor prognosis owing to the high frequency of perioperative complications rather than the malignancy of the tumor itself. There was a high prevalence of the invasive mucinous-predominant subtype in cases of UIP-ADC. UIP-ADC also had a low prevalence of EGFR mutations and a high prevalence of KRAS mutations. These findings suggest that UIP-ADC should be distinct from non-UIP-ADC.

Association of variations in HLA class II and other loci with susceptibility to EGFR-mutated lung adenocarcinoma.

Lung adenocarcinoma driven by somatic EGFR mutations is more prevalent in East Asians (30-50%) than in European/Americans (10-20%). Here we investigate genetic factors underlying the risk of this disease by conducting a genome-wide association study, followed by two validation studies, in 3,173 Japanese patients with EGFR mutation-positive lung adenocarcinoma and 15,158 controls. Four loci, 5p15.33 (TERT), 6p21.3 (BTNL2), 3q28 (TP63) and 17q24.2 (BPTF), previously shown to be strongly associated with overall lung adenocarcinoma risk in East Asians, were re-discovered as loci associated with a higher susceptibility to EGFR mutation-positive lung adenocarcinoma. In addition, two additional loci, HLA class II at 6p21.32 (rs2179920; P =5.1 × 10(-17), per-allele OR=1.36) and 6p21.1 (FOXP4) (rs2495239; P=3.9 × 10(-9), per-allele OR=1.19) were newly identified as loci associated with EGFR mutation-positive lung adenocarcinoma. This study indicates that multiple genetic factors underlie the risk of lung adenocarcinomas with EGFR mutations.

Multiplex Diagnosis of Oncogenic Fusion and MET Exon Skipping by Molecular Counting Using Formalin-Fixed Paraffin Embedded Lung Adenocarcinoma Tissues.

INTRODUCTION: Fusions of the anaplastic lymphoma receptor tyrosine kinase gene (ALK), ret proto-oncogene (RET), ROS proto-oncogene 1, receptor tyrosine kinase gene (ROS1), B-Raf proto-oncogene, serine/threonine kinase gene (BRAF), and neuregulin 1 gene (NRG1) and intronic MMNG HOS Transforming gene (MET) mutations are druggable oncogene alterations in lung adenocarcinoma that cause expression of aberrant transcripts. Because these aberrant transcripts are both infrequent (incidence <5%) and mutually exclusive, multiplex assays are required to detect them in tumor samples. METHODS: Aberrant transcripts of the six aforementioned oncogenes (36 transcripts in total) were examined in a molecular counting (MC) assay, which counts RNA molecules by simultaneous hybridization of several probes. Forty-one samples of surgically resected lung adenocarcinoma tissue found to express one of these aberrant oncogenic transcripts upon whole transcriptome sequencing (test cohort: n = 22) or reverse transcription polymerase chain reaction (validation cohort: n = 19) analyses were subjected to MC, after which biopsies were performed on tumor tissue samples. RESULTS: Threshold values for the diagnosis of each of the 36 transcripts were determined in frozen and formalin-fixed paraffin-embedded samples from the test cohort. On the basis of these threshold values, the MC assay diagnosed expression of oncogenic transcripts in the validation cohort samples with 100% accuracy. The assay also accurately detected oncogenic fusions in bronchial lavage fluid and transbronchial biopsy samples. CONCLUSIONS: The MC assay allows multiplex detection of oncogenic fusion and exon-skipped transcripts in tumor samples, including in formalin-fixed paraffin-embedded samples obtained in the clinic.

Frequent BRAF or EGFR Mutations in Ciliated Muconodular Papillary Tumors of the Lung.

INTRODUCTION: Ciliated muconodular papillary tumors (CMPTs) are recently characterized, rare peripheral nodules of the lung. These small tumors are histologically comprised of a vaguely organized mixture of nonatypical ciliated columnar cells, mucous cells, and basal cells, and consistently follow a benign clinical course. However, the histogenesis of CMPTs remains uncertain. METHODS: We performed detailed genomic analyses of 10 archived CMPT cases, using next-generation sequencing and high-resolution melting analysis. RESULTS: Mutations were identified in eight of the 10 cases (80%); four cases harbored the BRAF-V600E mutation, one case harbored the BRAF-G606R mutation, and three cases harbored deletions in exon 19 of EGFR. All of the deletions in EGFR were of the E746-T751/S752V subtype. CONCLUSIONS: The high prevalence of driver gene mutations in CMPTs supports the notion that these lesions are neoplastic rather than reactive or metaplastic.

Serum level of hepatocyte growth factor is a novel marker of predicting the outcome and resistance to the treatment with trastuzumab in HER2-positive patients with metastatic gastric cancer.

HER2-overexpression in tumor tissue is observed in 6 to 23% of advanced gastric cancer (GC) cases, and trastuzumab is an active molecular drug for these patients. There are no data available on whether serum levels of ligands are associated with the response and resistance to trastuzumab in HER2-positive patients with metastatic GC. HER2 screening of 502 patients with advanced gastric cancer was performed in our institution. Among these patients, 84 patients (16.8%) were diagnosed as HER2-positive, and those who were treated with trastuzumab and met the inclusion criteria were enrolled in the present study. Serum levels of ligands that affect the HER2 signal pathway were measured by an enzyme-linked immunosorbent assay. Forty-six HER2-positive patients were enrolled in this study, and 26 patients (56.5%) achieved a partial response to treatment with trastuzumab. Among several ligands, the serum level of hepatocyte growth factor (HGF) was significantly lower in responders compared with that in non-responders (p = 0.014). Multivariate analyses showed that a high level of serum HGF was a poor prognostic factor for overall survival (OS) compared with low levels of HGF (adjusted HR: 3.857, 95% CI: 1.309-11.361, p = 0.014). Among 25 patients without initial disease progression on the treatment with trastuzumab, the mean value of serum HGF at disease progression was significantly higher than that at pre-treatment (p = 0.041). As novel findings, our study indicated that serum level of HGF was associated with tumor shrinkage and time to progression of trastuzumab in HER2-positive patients with metastatic GC.

Mucinous micropapillary pattern in lung adenocarcinomas: a unique histology with genetic correlates.

AIMS: In lung adenocarcinoma (ADC), micropapillary carcinomas (MPCs) are associated with poor prognosis because these tumours exhibit higher metastatic potential. Despite this, there are no studies investigating the differences between mucinous and non-mucinous MPC. METHODS AND RESULTS: We evaluated the proportion of micropapillary components in lung ADCs, and compared the differences with respect to the presence or absence of associated mucin. Tumour specimens from 694 patients with consecutively resected primary lung ADC were reviewed, and 37 cases of invasive mucinous ADCs were excluded. A significant (≥5%) micropapillary component was noted in 320 (48.7%) of 657 evaluable cases. When the cases with micropapillary component were divided into 67 (20.9%) mucinous and 253 (79.1%) non-mucinous subtypes, tumours with mucinous micropapillary component exhibited significantly more aggressive pathological features, a higher proportion of HER2 mutations (P = 0.002) and ALK rearrangements (P < 0.001), and a lower proportion of EGFR mutations (P = 0.038) compared to those with a non-mucinous micropapillary component. In survival analyses, mucinous MPC tended to be more aggressive compared with non-mucinous MPC, but its prognostic value was not statistically significant (P = 0.076). CONCLUSIONS: Mucinous micropapillary pattern is an under-recognized unique growth associated significantly with HER2 mutation and ALK rearrangement.

[Harmonization of TSH Measurements.]

The measured concentration of thyroid stimulating hormone (TSH) differs depending on the reagents used. Harmonization of TSH is crucial because the decision limits are described in current clinical practice guide- lines as absolute values, e.g. 2.5 mIU/L in early pregnancy. In this study, we tried to harmonize the report- ed concentrations of TSH using the all-procedure trimmed mean. TSH was measured in 146 serum samples, with values ranging from 0.01 to 18.8 mIU/L, using 4 immunoassays. The concentration of TSH was highest with E test TOSOH and lowest with LUMIPULSE. The concentrations with each reagent were recalculated with the following formulas: E test TOSOH 0.855x-0.014; ECLusys 0.993x+0.079; ARCHITECT 1.041x- 0.010; and LUMIPULSE 1.096x-0.015. Recalculation eliminated the between-assay discrepancy. These formulas may be used until harmonization of TSH is achieved by the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC).

[Liquid Biopsy: Challenges and Possibilities Regarding Its Clinical Application.]

Cell-free DNA is "Fragmented DNA found in circulation in the Cell-free component of whole blood". Cell-free DNA derived from tumors is expressed as circulating tumor DNA. Examination of circulating tu- mor DNA for genetic alterations present in the tumor tissue is defined as liquid biopsy. Currently in the cancer field, Cell-free DNA or CTC (Circulating tumor cells) is the main target of "Liquid Biopsy". Acquir- ing Cell-free DNA or CTC presents little challenge because of the recent technological developments. However, we need to improve the efficiency of CTC retrieval, and we also need to establish how to culture the retrieved CTCs. For clinical applications, PGx (Pharmacogenomics) and PGt (Pharmacogenetics) fol- lowing NGS (Next Generation Sequencing) are attractive areas for new and future applications. The intro- duction of "Liquid Biopsy" to the area of clinical trials is already in progress. As an expert group, members of the JSLM (Japanese Society of Laboratory Medicine) need to indicate the presence of quality control or quality management in the area of "Liquid Biopsy". Besides these quality issues, we, as clinical pathologists, need to think about harmonizing our expertise with surgical pathologists, who have historically handled clas- sical biopsies of solid samples. The field of "Liquid Biopsy" has marked potential; however, we need to overcome various obstacles to realize this.