Human sample authentication in biomedical research: comparison of two platforms.

Samples used in biomedical research are often collected over years, in some cases from subjects that may have died and thus cannot be retrieved in any way. The value of these samples is priceless. Sample misidentification or mix-up are unfortunately common problems in biomedical research and can eventually result in the publication of incorrect data. Here we have compared the Fluidigm SNPtrace and the Agena iPLEX Sample ID panels for the authentication of human genomic DNA samples. We have tested 14 pure samples and simulated their cross-contamination at different percentages (2%, 5%, 10%, 25% and 50%). For both panels, we report call rate, allele intensity/probability score, performance in distinguishing pure samples and contaminated samples at different percentages, and sex typing. We show that both panels are reliable and efficient methods for sample authentication and we highlight their advantages and disadvantages. We believe that the data provided here is useful for sample authentication especially in biorepositories and core facility settings.

The Application of the Tissue Microarray (TMA) Technology to Analyze Cerebral Organoids.

"Multi-Omics" technologies have contributed greatly to the understanding of various diseases by enabling researchers to accurately and rapidly investigate the molecular circuitry that connects cellular systems. The tissue-engineered, three-dimensional (3D), in vitro disease model "organoid" integrates the "omics" results in a model system, elucidating the complex links between genotype and phenotype. These 3D structures have been used to model cancer, infectious disease, toxicity, and neurological disorders. Here, we describe the advantage of using the tissue microarray (TMA) technology to analyze human-induced pluripotent stem cell-derived cerebral organoids. Compared with the conventional processing of individual samples, sectioning and staining of TMA slides are faster and can be automated, decreasing labor and reagent costs. The TMA technology faithfully captures cell morphology variations and detects specific biomarkers. The use of this technology can scale up organoid research results in at least two ways: (1) in the number of specimens that can be analyzed simultaneously and (2) in the number of consecutive sections that can be produced for analysis with different probes and antibodies.

New Challenges for Biobanks: Accreditation to the New ISO 20387:2018 Standard Specific for Biobanks.

BACKGROUND: The emergence of "multi-omics" and "multi-parametric" types of analysis based on a high number of biospecimens enforces the use of a great number of high-quality "Biological Materials and Associated Data" (BMaD). To meet the demands of biomedical research, several Biological Resource Centers (BRCs) or Biobanks world-wide have implemented a specific Quality Management System (QMS) certified ISO 9001:2015 or accredited by CAP9 ISO 20387:2018. For the first time, ISO, with the support of several Biobanking experts, issued the ISO 20387:2018 which is the first ISO norm specific for Biobanks. The fundamental difference with present certification/accreditation standards is that the ISO 20387:2018 focuses not only on the operational aspects of the Biobank, but also on the "competence of the Biobank to carry our specific Biobanking tasks". METHODS: The accreditation process for ISO 20387:2018 required the definition of: (1) objectives, goals and organizational structure of the Biobank, including procedures for governance, confidentiality and impartiality policies; (2) standard operating procedures (SOPs) of all activities performed, including acquisition, analysis, collection, data management, distribution, preparation, preservation, testing facility and equipment maintenance, calibration, and monitoring; (3) procedures for control of documents and records, the identification of risks and opportunities, improvements, corrective actions, nonconforming records and evaluation of external providers (4) an internal audit and management reviews, verification of QMS performance, monitoring of quality objectives and personnel qualification and competency in carrying out specific Biobanking tasks. RESULTS: The accreditation process is performed by an independent authorized organization which certifies that all processes are performed according to the QMS, and that the infrastructure is engineered and managed according to the GDP and/or GMP guidelines. CONCLUSION: Accreditation is given by an accreditation body, which recognizes formally that the Biobank is "competent to carry out specific Biobanking tasks".

SEL1L plays a major role in human malignant gliomas.

Suppressor of Lin-12-like (C. elegans) (SEL1L) participates in the endoplasmic reticulum-associated protein degradation pathway, malignant transformation and stem cell biology. We explored the role of SEL1L in 110 adult gliomas, of different molecular subtype and grade, in relation to cell proliferation, stemness, glioma-associated microglia/macrophages (GAMs), prognostic markers and clinical outcome. SEL1L protein expression was assessed by immunohistochemistry and Western blotting. Genetic and epigenetic alterations were detected by molecular genetics techniques. SEL1L was overexpressed in anaplastic gliomas (World Health Organization [WHO] grade III) and in glioblastoma (GB, WHO grade IV) with the highest labelling index (LI) in the latter. Immunoreactivity was significantly associated with histological grade (p = 0.002) and cell proliferation index Ki-67/MIB-1 (p = 0.0001). In GB, SEL1L co-localised with stemness markers Nestin and Sox2. Endothelial cells and vascular pericytes of proliferative tumour blood vessels expressed SEL1L suggesting a role in tumour neo-vasculature. GAMs consistently expressed SEL1L. SEL1L overexpression was significantly associated with TERT promoter mutations (p = 0.0001), EGFR gene amplification (p = 0.0013), LOH on 10q (p = 0.0012) but was mutually exclusive with IDH1/2 mutations (p = 0.0001). SEL1L immunoreactivity correlated with tumour progression and cell proliferation, conditioning poor patient survival and response to therapy. This study emphasises SEL1L as a potential biomarker for the most common subgroup of TERT mutant/EGFR amplified/IDH-WT GBs.

Correction: SEL1L SNP rs12435998, a predictor of glioblastoma survival and response to radio-chemotherapy.

[This corrects the article DOI: 10.18632/oncotarget.3611.].

Trehalose to cryopreserve human pluripotent stem cells.

The successful exploitation of human pluripotent stem cells (hPSCs) for research, translational or commercial reasons requires the implementation of a simple and efficient cryopreservation method. Cryopreservation is usually performed with dimethylsulphoxide (DMSO), in addition to animal proteins. However, even at sub-toxic levels, DMSO diminishes the pluripotency capacity of hPSCs and affects their epigenetic system by acting on the three DNA methyltransferases (Dnmts) and histone modification enzymes. Our study aimed to test trehalose-based cryosolutions containing ethylene glycol (EG) or glycerol (GLY) on hESCs RC17, hiPSCs CTR2#6 and long-term neuroepithelial-like stem cells (lt-NES) AF22. Here, we demostrate the effectiveness of these cryosolutions in hPSCs by showing an acceptable rate of cell viability and high stability compared to standard 10% DMSO freezing medium (CS10). All cell lines retained their morphology, self renewal potential and pluripotency, and none of the cryosolutions affected their differentiation potential. Genotoxicity varied among different stem cells types, while trehalose-based cryopreservation did not sensibly alter the homeostasis of endoplasmic reticulum (ER). This study provides evidence that pluripotent and neural stem cells stored in trehalose alone or with other cryoprotectants (CPAs) maintain their functional properties, indicating their potential use in cell therapies if produced in good manufacturing practice (GMP) facility.

Generation of Human-Induced Pluripotent Stem Cells from Wolfram Syndrome Type 2 Patients Bearing the c.103 + 1G>A CISD2 Mutation for Disease Modeling.

Wolfram syndrome (WFS) is a rare autosomal premature aging syndrome that shows signs of diabetes mellitus, optic atrophy, and deafness in addition to central nervous system and endocrine complications. The frequent form of WFS type 1 (WFS1) harbors causative mutations in the WFS1 gene, whereas the rare form or WFS type 2 (WFS2) involves CISD2. Mutations in these two genes are recognized by a subset of variable clinical symptoms and a set of overlapping features. In this study, we report on the generation of stable human-induced pluripotent stem cells (hiPSCs) derived from primary fibroblasts of a previously reported Italian family with CISD2 mutation (c.103 + 1G>A), occurring in the consensus intron 1 splicing site in two sisters, deleting the first exon of the transcript. The generated hiPSCs provide a cell model system to study the mutation's role in the multisystemic clinical disorders previously described and test eventual drug effects on the specific and associated clinical phenotype.

Sel1l knockdown negatively influences zebrafish embryos endothelium.

SEL1L (suppressor/enhancer of Lin-12-like) is a highly conserved gene associated with the endoplasmic reticulum-associated degradation (ERAD) pathway and involved in mediating the balance between stem cells self-renewal and differentiation of neural progenitors. It has been recently shown that SEL1L KO mice are embryonic lethal and display altered organogenesis. To better characterize the function of SEL1L in the early stages of embryonic development, we turned to the zebrafish model (Danio rerio). After exploring sel1l expression by RT-PCR and in situ hybridization, we employed a morpholino-mediated down-regulation approach. Results showed extensive impairments in the vasculature, which supports the mice knock-out findings.

mSEL-1L deficiency affects vasculogenesis and neural stem cell lineage commitment.

mSEL-1L is a highly conserved ER-resident type I protein, involved in the degradation of misfolded peptides through the ubiquitin-proteasome system (UPS), a pathway known to control the plasticity of the vascular smooth muscle cells (VSMC) phenotype and survival. In this article, we demonstrate that mSEL-1L deficiency interferes with the murine embryonic vascular network, showing particular irregularities in the intracranic and intersomitic neurovascular units and in the cerebral capillary microcirculation. During murine embryogenesis, mSEL-1L is expressed in cerebral areas known to harbor progenitor neural cells, while in the adult brain the protein is specifically restricted to the stem cell niches, co-localizing with Sox2 and Nestin. Null mice are characterized by important defects in the development of telenchephalic regions, revealing conspicuous aberration in neural stem cell lineage commitment. Moreover, mSEL-1L depletion in vitro and in vivo appears to affect the harmonic differentiation of the NSCs, by negatively influencing the corticogenesis processes. Overall, the data presented suggests that the drastic phenotypic characteristics exhibited in mSEL-1L null mice can, in part, be explained by the negative influence it plays on Notch1 signaling pathway.

Epigenetic and transcriptional modulation of WDR5, a chromatin remodeling protein, in Huntington's disease human induced pluripotent stem cell (hiPSC) model.

DNA methylation (DNAm) changes are of increasing relevance to neurodegenerative disorders, including Huntington's disease (HD). We performed genome-wide screening of possible DNAm changes occurring during striatal differentiation in human induced pluripotent stem cells derived from a HD patient (HD-hiPSCs) as cellular model. We identified 240 differentially methylated regions (DMRs) at promoters in fully differentiated HD-hiPSCs. Subsequently, we focused on the methylation differences in a subcluster of genes related to Jumonji Domain Containing 3 (JMJD3), a demethylase that epigenetically regulates neuronal differentiation and activates neuronal progenitor associated genes, which are indispensable for neuronal fate acquisition. Noticeably among these genes, WD repeat-containing protein 5 (WDR5) promoter was found hypermethylated in HD-hiPSCs, resulting in a significant down-modulation in its expression and of the encoded protein. A similar WDR5 expression decrease was seen in a small series of HD-hiPSC lines characterized by different CAG length. The decrease in WDR5 expression was particularly evident in HD-hiPSCs compared to hESCs and control-hiPSCs from healthy subjects. WDR5 is a core component of the MLL/SET1 chromatin remodeling complexes essential for H3K4me3, previously reported to play an important role in stem cells self-renewal and differentiation. These results suggest the existence of epigenetic mechanisms in HD and the identification of genes, which are able to modulate HD phenotype, is important both for biomarker discovery and therapeutic interventions.

A Review of Research-Grade Human Induced Pluripotent Stem Cells Qualification and Biobanking Processes.

Human induced pluripotent stem cell (hiPSC) biobanks are invaluable resources for basic and clinical research, since they provide a sustainable supply of accessible cell lines that meet high quality and safety standards. hiPSCs are particularly useful for understanding disease mechanisms, creating cell models for drug development, and generating novel clinical therapies. For clinical applications and drug discovery, it is fundamental that the acquired pluripotent cell lines never touch animal-derived products nor xenogeneic reagents (Good Manufacturing Practice-grade); whereas for research grade, it is sufficient to operate under Good Laboratory Practice conditions. However, regardless of the end use, it is important that every step in the whole process, starting from the original cells throughout expansion and manipulation, must be performed and recorded rigorously. Here, we describe our biobanking management system that is applied specifically to human pluripotent stem cells.

Investigating DNA methylation dynamics and safety of human embryonic stem cell differentiation toward striatal neurons.

The potential use of human embryonic stem cells (hESCs) in cell-based therapies points out the critical importance of epigenomic evaluation for cell-based therapies. Specifically, DNA methylation appears to be a crucial player in establishing cell fate commitment and lineage choices. In this study, we report the global changes observed on the CpG islands distributed in promoters, gene bodies, and intergenic regions and the major biochemical pathways and genes involved in methylation changes as H9-hESCs turn into a neuronal culture containing medium-sized spiny striatal neurons (MSNs). Using an ontogeny-recapitulating protocol of striatal neuron differentiation, we analyzed DNA methylation profiles during the conversion from pluripotency to neuropotency up to the acquisition of a mature neuronal phenotype. H9-hESCs changed the methylation pattern both through de novo methylation and hypomethylation of specific gene promoters. Bioinformatic analysis allowed us to identify a panel of striatal-associated genes, which were regulated by DNA methylation and differentially expressed during striatal commitment. Importantly, DNA methylation analysis revealed that H9-hESCs did not acquire methylation-based oncogenic properties after differentiation. Indeed, hypermethylation of cancer-associated genes that characterize transformed cells, such as Polycomb repressive complex-associated genes, was not detected in the neuronal cultures. However, the oncosuppressor gene, BCL2L11, became hypermethylated in H9-hESC-derived mature neurons. Whole-genome DNA methylation profiling could become a technological platform to predict the differentiative potential of hESC-derived cultures and establish further biosafety assessment quality control tools of the cell-based products.

SEL1L SNP rs12435998, a predictor of glioblastoma survival and response to radio-chemotherapy.

The suppressor of Lin-12-like (C. elegans) (SEL1L) is involved in the endoplasmic reticulum (ER)-associated degradation pathway, malignant transformation and stem cells. In 412 formalin-fixed and paraffin-embedded brain tumors and 39 Glioblastoma multiforme (GBM) cell lines, we determined the frequency of five SEL1L single nucleotide genetic variants with regulatory and coding functions by a SNaPShot™ assay. We tested their possible association with brain tumor risk, prognosis and therapy. We studied the in vitro cytotoxicity of valproic acid (VPA), temozolomide (TMZ), doxorubicin (DOX) and paclitaxel (PTX), alone or in combination, on 11 GBM cell lines, with respect to the SNP rs12435998 genotype. The SNP rs12435998 was prevalent in anaplastic and malignant gliomas, and in meningiomas of all histologic grades, but unrelated to brain tumor risks. In GBM patients, the SNP rs12435998 was associated with prolonged overall survival (OS) and better response to TMZ-based radio-chemotherapy. GBM stem cells with this SNP showed lower levels of SEL1L expression and enhanced sensitivity to VPA.

BRCA1 point mutations in premenopausal breast cancer patients from Central Sudan.

Premenopausal breast cancer (BC) is one of the most common cancers of women in rural Africa and part of the disease load may be related to hereditary predisposition, including mutations in the BRCA1 gene. However, the BRCA1 mutations associated with BC in Africa are scarcely characterized. We report here 33 BRCA1 point mutations, among which 2 novel missense variants, found in 59 Central Sudanese premenopausal BC patients. The high fractions of mutations with intercontinental and uniquely African distribution (17/33, 51.5 % and 14/33, 42.4 %, respectively) are in agreement with the high genetic diversity expected in an African population. Overall 24/33 variants (72.7 %) resulted neutral; 8/33 of unknown significance (24.3 %, including the 2 novel missense mutations); 1 (3.0 %) overtly deleterious. Notably, in silico studies predict that the novel C-terminal missense variant c.5090G>A (p.Cys1697Tyr) affects phosphopeptide recognition by the BRCA1 BRCT1 domain and may have a pathogenic impact. Genetic variation and frequency of unique or rare mutations of uncertain clinical relevance pose significant challenges to BRCA1 testing in Sudan, as it might happen in other low-resource rural African contexts.

Tissue microarray design and construction for scientific, industrial and diagnostic use.

CONTEXT: In 2013 the high throughput technology known as Tissue Micro Array (TMA) will be fifteen years old. Its elements (design, construction and analysis) are intuitive and the core histopathology technique is unsophisticated, which may be a reason why has eluded a rigorous scientific scrutiny. The source of errors, particularly in specimen identification and how to control for it is unreported. Formal validation of the accuracy of segmenting (also known as de-arraying) hundreds of samples, pairing with the sample data is lacking. AIMS: We wanted to address these issues in order to bring the technique to recognized standards of quality in TMA use for research, diagnostics and industrial purposes. RESULTS: We systematically addressed the sources of error and used barcode-driven data input throughout the whole process including matching the design with a TMA virtual image and segmenting that image back to individual cases, together with the associated data. In addition we demonstrate on mathematical grounds that a TMA design, when superimposed onto the corresponding whole slide image, validates on each and every sample the correspondence between the image and patient's data. CONCLUSIONS: High throughput use of the TMA technology is a safe and efficient method for research, diagnosis and industrial use if all sources of errors are identified and addressed.

Mesenchymal stromal cell cryopreservation.

The advent of stem cells and stem cell-based therapies for specific diseases requires particular knowledge of laboratory procedures, which not only guarantee the continuous production of cells, but also provide them an identity and integrity as close as possible to their origin. Their cryopreservation at temperatures below -80°C and typically below -140°C is of paramount importance. This target can be achieved by incorporating high molar concentrations of cryoprotectant mixtures that preserve cells from deleterious ice crystal formation. Usually, dimethyl sulfoxide (DMSO) and animal proteins are used as protectant reagents, but unexpected changes in stem cell fate and downstream toxicity effects have been reported, limiting their wide use in clinical settings. In scientific reviews, there are not much data regarding viability of mesenchymal stromal cells (MSCs) after the freezing/thawing process. During our routine analysis, a poor resistance to cryopreservation of these cells was observed, as well as their weak ability to replicate. This is an important point in the study of MSCs; moreover, it represents a limit for preservation and long-term storage. For this reason, MSCs isolated from equine, ovine, and rodent bone marrow and equine adipose tissue were compared using different cryopreservation solutions for this study of vitality. Our findings showed the best results regarding cell viability using a solution of fetal bovine serum with addition of 10% DMSO. In particular, we noted an increase in survival of equine bone marrow MSCs. This parameter has been evaluated by Trypan blue staining at fixed times (0, 24, and 48 hours post-thaw). This result highlights the fact that equine bone marrow MSCs are the frailest we analyzed. Therefore, it could be useful to delve further into this topic in order to improve the storage possibility for these cells and their potential use in cell-based therapies.

Basal-like phenotype in a breast carcinoma case series from Sudan: prevalence and clinical/pathological correlations.

Basal-like breast cancer, an aggressive subtype associated with high grade, poor prognosis, and younger age, is reported frequently in Africa. We analyzed the expression of the basal cytokeratins (CKs) 5/6 and 17 in a case series from Central Sudan and investigated correlations among basal CK status, ER, PgR, and Her-2/neu, and individual/clinicopathological data. Of 113 primary breast cancers 26 (23%), 38 (34%), and 46 (41%) were, respectively, positive for CK5/6, CK17, and combined basal CKs (CK5/6 and/or CK17). Combined basal CK+ status was associated with higher grade (P < .03) and inversely correlated with ER (P < .002), PgR (P = .004) and combined ER and/or PgR (P < .0002). Two clusters based on all tested markers were generated by hierarchical cluster analysis and k-mean clustering: I: designated "hormone receptors positive/luminal-like" and II: designated "hormone receptors negative", including both basal-like and Her-2/neu+ tumors. The most important factors for dataset variance were ER status, followed by PgR, CK17, and CK5/6 statuses. Overall basal CKs were expressed in a fraction of cases comparable to that reported for East and West African case series. Lack of associations with age and tumor size may represent a special feature of basal-like breast cancer in Sudan.

Comprehensive cancer control-research & development: knowing what we do and doing what we know.

Comprehensive cancer control is defined as an integrated and coordinated approach to reducing cancer incidence, morbidity, and mortality across the cancer control continuum from primary prevention to end-of-life care. This approach assumes that when the public sector, non-governmental organizations, academia, and the private sector share with each other their skills, knowledge, and resources, a country can take advantage of all its talents and resources to more quickly reduce the burden of cancer for all its population. One critical issue for comprehensive cancer control is the extent to which the private sector can contribute to cancer prevention and control programs and policies that have historically been lead by the public health sector, and similarly how can the public sector increase its investment and involvement in clinical research and practice issues that are largely driven by the private sector worldwide? In addition, building capacity to integrate research that is appropriate to the culture and context of the population will be important in different settings, in particular research related to cancer control interventions that have the capacity to influence outcomes. To whatever extent cancer control research is ultimately funded through the private and public sectors, if investments in research discoveries are ultimately to benefit the populations that bear the greatest burden of disease, then new approaches to integrating the lessons learned from science with the lessons learned from service (public health, clinical, and public policy) must be found to close the gap between what we know and what we do. Communities of practice for international cancer control, like the ones fostered by the first three International Cancer Control Congresses, represent an important forum for knowledge exchange opportunities to accelerate the translation of new knowledge into action to reduce the burden of cancer worldwide.