Failure to replicate the STAP cell phenomenon

Quantum contextuality and cognitive contextuality: The significance of violations of Bell-type inequalities

Quantum contextuality (or non-locality called "spooky action at a distance" by Einstein) is witnessed by violations of Bell-type inequalities, which are purely statistical inequalities and can in principle be applied to any statistical correlations observed in empirical experiments. It has been reported recently that Bell-type inequalities are violated in cognitive experiments, which formally shows that contextuality does exist in cognition as well as physical reality. It is unclear, however, whether quantum and cognitive contextualities are essentially the same kind of phenomena, and the nature of cognitive contextuality has been debated whereas the nature of quantum contextuality has been explicated by foundational physicists and philosophers of physics. In the present paper, thus, we aim at elucidating similarities and dissimilarities between quantum and cognitive contextualities. We argue, in particular, that cognitive contextuality as shown by the violation of Bell-type inequalities never entails that the brain is indeterministic; rather, cognitive contextuality is caused by the statistical nature of collective state dynamics and the special structure of experimental set-ups, whereas quantum contextuality is caused by the statistical nature of single state dynamics and the existence of special states or operations.

Expression of SSEA-4 and Oct-4 from somatic cells in primary mouse gastric cell culture induced by brief strong acid

Environmental changes can stress and alter biology at the molecular and cellular level. For example, metal-protein interaction is a classic physic and biological property of nature, which is fundamentally influenced by acidity. Here, we report a unique cellular reprogramming phenomenon in that a brief strong acid treatment induced the expression of pluripotent stem cell (PSC) markers. We used strong acid to briefly challenge mix-cultured gastric cells, and then subcultured survived cells in a normal cell culture medium. We found that survival acid-treated cells expressed PSC markers detected by commonly used pluripotent antibodies such as SSEA-4 and Oct4. In addition, we observed that the survived cells from the acid challenge grew faster during the second and third weeks of subculture and had a relative short doubling time (DT) than the controls. PSC marker-labeled 'older' cells also presented immature cell-like morphology with some having marker Oct4 in the nucleus. Finally, the expression of the markers appeared to be sensitive to metal ion chelation. Removal of the metals during a brief acid treatment reduced pluripotent marker-positive cells, suggesting the dissociation of metals from metal-binding proteins may be a factor involved in the induction of stem cell markers. Our findings reveal that somatic cells appear to possess a plasticity feature to express pluripotent marker proteins or to select cell subpopulations that express pluripotent marker proteins when cells are transiently exposed to strong acid. It opens new directions for understanding conserved regulatory mechanisms involved in cellular survival under stressful stimulation.

Postnatal Pluripotent Cells: Quarter of a Century of Research

Almost quarter of a century long studies aimed at identification, isolation, culturing, and use of postnatal pluripotent cells for the development of cell-based technologies have not met with success and failed to provide reliable and reproducible protocols of cell isolation, identification, and culturing. At the same time, experimental data in this field suggest that postnatal pluripotent cells are not the copies of embryonic cells and, therefore, the tests routinely used for identification of embryonic pluripotent cells are not fully adequate for characterization of their postnatal analogues. Therefore, cell lineage tracing methods showing the differentiation routes of the studied cells in human or animal body after birth should be developed and used.

Microvessel occlusions alter amyloid-beta plaque morphology in a mouse model of Alzheimer's disease

Vascular dysfunction is correlated to the incidence and severity of Alzheimer's disease. In a mouse model of Alzheimer's disease (APP/PS1) using in vivo, time-lapse, multiphoton microscopy, we found that occlusions of the microvasculature alter amyloid-beta (Aβ) plaques. We used several models of vascular injury that varied in severity. Femtosecond laser-induced occlusions in single capillaries generated a transient increase in small, cell-sized, Aβ deposits visualized with methoxy-X04, a label of fibrillar Aβ. After occlusions of penetrating arterioles, some plaques changed morphology, while others disappeared, and some new plaques appeared within a week after the lesion. Antibody labeling of Aβ revealed a transient increase in non-fibrillar Aβ one day after the occlusion that coincided with the disappearance of methoxy-X04-labeled plaques. Four days after the lesion, anti-Aβ labeling decreased and only remained in patches unlabeled by methoxy-X04 near microglia. Histology in two additional models, sparse embolic occlusions from intracarotid injections of beads and infarction from photothrombosis, demonstrated increased labeling intensity in plaques after injury. These results suggest that microvascular lesions can alter the deposition and clearance of Aβ and confirm that Aβ plaques are dynamic structures, complicating the interpretation of plaque burden as a marker of Alzheimer's disease progression.

The Acidic Tumor Microenvironment as a Driver of Cancer

Acidic metabolic waste products accumulate in the tumor microenvironment because of high metabolic activity and insufficient perfusion. In tumors, the acidity of the interstitial space and the relatively well-maintained intracellular pH influence cancer and stromal cell function, their mutual interplay, and their interactions with the extracellular matrix. Tumor pH is spatially and temporally heterogeneous, and the fitness advantage of cancer cells adapted to extracellular acidity is likely particularly evident when they encounter less acidic tumor regions, for instance, during invasion. Through complex effects on genetic stability, epigenetics, cellular metabolism, proliferation, and survival, the compartmentalized pH microenvironment favors cancer development. Cellular selection exacerbates the malignant phenotype, which is further enhanced by acid-induced cell motility, extracellular matrix degradation, attenuated immune responses, and modified cellular and intercellular signaling. In this review, we discuss how the acidity of the tumor microenvironment influences each stage in cancer development, from dysplasia to full-blown metastatic disease.

Ethical development of stem-cell-based interventions

The process of developing new and complex stem-cell-based therapeutics is incremental and requires decades of sustained collaboration among different stakeholders. In this Perspective, we address key ethical and policy challenges confronting the clinical translation of stem-cell-based interventions (SCBIs), including premature diffusion of SCBIs to clinical practice, assessment of risk in trials, obtaining valid informed consent for research participants, balanced and complete scientific reporting and public communications, regulation, and equitable access to treatment. We propose a way forward for translating these therapies with the above challenges in mind.

Designing a rigorous microscopy experiment: Validating methods and avoiding bias

Images generated by a microscope are never a perfect representation of the biological specimen. Microscopes and specimen preparation methods are prone to error and can impart images with unintended attributes that might be misconstrued as belonging to the biological specimen. In addition, our brains are wired to quickly interpret what we see, and with an unconscious bias toward that which makes the most sense to us based on our current understanding. Unaddressed errors in microscopy images combined with the bias we bring to visual interpretation of images can lead to false conclusions and irreproducible imaging data. Here we review important aspects of designing a rigorous light microscopy experiment: validation of methods used to prepare samples and of imaging system performance, identification and correction of errors, and strategies for avoiding bias in the acquisition and analysis of images.

Therapeutic Targeting of Cancer Stem Cells: Integrating and Exploiting the Acidic Niche

Cancer stem cells (CSC) or tumor-initiating cells represent a small subpopulation of cells within the tumor bulk that share features with somatic stem cells, such as self-renewal and pluripotency. From a clinical point of view, CSC are thought to be the main drivers of tumor relapse in patients by supporting treatment resistance and dissemination to distant organs. Both genome instability and microenvironment-driven selection support tumor heterogeneity and enable the emergence of resistant cells with stem-like properties, when therapy is applied. Besides hypoxia and nutrient deprivation, acidosis is another selection barrier in the tumor microenvironment (TME) which provides a permissive niche to shape more aggressive and fitter cancer cell phenotypes. This review describes our current knowledge about the influence of the "acidic niche" on the stem-like phenotypic features of cancer cells. In addition, we briefly survey new therapeutic options that may help eradicate CSC by integrating and/or exploiting the acidic niche, and thereby contribute to prevent the occurrence of therapy resistance as well as metastatic dissemination.

Frontiers of Pluripotency

Humans develop from a unique group of pluripotent cells in early embryos that can produce all cells of the human body. While pluripotency is only transiently manifest in the embryo, scientists have identified conditions that sustain pluripotency indefinitely in the laboratory. Pluripotency is not a monolithic entity, however, but rather comprises a spectrum of different cellular states. Questions regarding the scientific value of examining the continuum of pluripotent stem (PS) cell states have gained increased significance in light of attempts to generate interspecies chimeras between humans and animals. In this chapter, I review our ever-evolving understanding of the continuum of pluripotency. Historically, the discovery of two different PS cell states in mice fostered a general conception of pluripotency comprised of two distinct attractor states: naïve and primed. Naïve pluripotency has been defined by competence to form germline chimeras and governance by unique KLF-based transcription factor (TF) circuitry, whereas primed state is distinguished by an inability to generate chimeras and alternative TF regulation. However, the discovery of many alternative PS cell states challenges the concept of pluripotency as a binary property. Moreover, it remains unclear whether the current molecular criteria used to classify human naïve-like pluripotency also identify human chimera-competent PS cells. Therefore, I examine the pluripotency continuum more closely in light of recent advances in PS cell research and human interspecies chimera research.

Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research

The use of phylogenetics in HIV molecular epidemiology has considerably increased our ability to understand the origin, spread, and characteristics of HIV epidemics. Despite its potential to advance knowledge on HIV transmission dynamics, the ethical issues associated with HIV molecular epidemiology have received minimal attention. In-depth interviews were conducted with scientists from diverse backgrounds to explore their perspectives on ethical issues associated with phylogenetic analysis of HIV genetic data as applied to HIV transmission dynamics studies. The Emanuel framework was used as the analytical framework. Favorable risk-benefit ratio and informed consent were the most invoked ethical principles and fair participant selection the least. Fear of loss of privacy and disclosure of HIV transmission were invariably cited as key ethical concerns. As HIV sequence data become increasingly available, comprehensive guidelines should be developed to guide its access, sharing and use, cognizant of the potential harms that may result.

When the research is not reproducible: the importance of author-initiated and institution-driven responses and investigations

Important and potentially useful findings in the sciences are under more intense public scrutiny now more than ever. Other researchers in the field dive into replicating and expanding the findings while the media swamps the community and the public with peripheral reporting and analyses. How should authors and the hosting/funding institutions respond when other workers in the field could not reproduce or replicate their published results? To illustrate the importance of author-initiated and institution-driven investigations in response to outcries of research irreproducibility, I draw on comparisons between three recent and well-publicized cases in the life sciences: betatrophin, Stimulus-Triggered Acquisition of Pluripotency (STAP) cells, and Natronobacterium gregoryi Argonaute (NgAgo). Swift, transparent responses and investigations facilitate activation of the self-correcting mechanism of science and are likely also critical in preserving the community's resources, public trust, and the reputation of the institutions and individuals concerned. Operational guidelines for "author and institutional responses" towards external reports of irreproducibility should therefore be in place for all research intensive institutions.

Enhancing reproducibility: Failures from Reproducibility Initiatives underline core challenges

Efforts to address reproducibility concerns in biomedical research include: initiatives to improve journal publication standards and peer review; increased attention to publishing methodological details that enable experiments to be reconstructed; guidelines on standards for study design, implementation, analysis and execution; meta-analyses of multiple studies within a field to synthesize a common conclusion and; the formation of consortia to adopt uniform protocols and internally reproduce data. Another approach to addressing reproducibility are Reproducibility Initiatives (RIs), well-intended, high-profile, systematically peer-vetted initiatives that are intended to replace the traditional process of scientific self-correction. Outcomes from the RIs reported to date have questioned the usefulness of this approach, particularly when the RI outcome differs from other independent self-correction studies that have reproduced the original finding. As a failed RI attempt is a single outcome distinct from the original study, it cannot provide any definitive conclusions necessitating additional studies that the RI approach has neither the ability nor intent of conducting making it a questionable replacement for self-correction. A failed RI attempt also has the potential to damage the reputation of the author of the original finding. Reproduction is frequently confused with replication, an issue that is more than semantic with the former denoting "similarity" and the latter an "exact copy" - an impossible outcome in research because of known and unknown technical, environmental and motivational differences between the original and reproduction studies. To date, the RI framework has negatively impacted efforts to improve reproducibility, confounding attempts to determine whether a research finding is real.

Targeting pH regulating proteins for cancer therapy-Progress and limitations

Tumour acidity induced by metabolic alterations and incomplete vascularisation sets cancer cells apart from normal cellular physiology. This distinguishing tumour characteristic has been an area of intense study, as cellular pH (pH_i) disturbances disrupt protein function and therefore multiple cellular processes. Tumour cells effectively utilise pH_i regulating machinery present in normal cells with enhancements provided by additional oncogenic or hypoxia induced protein modifications. This overall improvement of pH regulation enables maintenance of an alkaline pH_i in the continued presence of external acidification (pH_e). Considerable experimentation has revealed targets that successfully disrupt tumour pH_i regulation in efforts to develop novel means to weaken or kill tumour cells. However, redundancy in these pH-regulating proteins, which include Na⁺/H⁺ exchangers (NHEs), carbonic anhydrases (CAs), Na⁺/HCO₃^- co-transporters (NBCs) and monocarboxylate transporters (MCTs) has prevented effective disruption of tumour pH_i when individual protein targeting is performed. Here we synthesise recent advances in understanding both normoxic and hypoxic pH regulating mechanisms in tumour cells with an ultimate focus on the disruption of tumour growth, survival and metastasis. Interactions between tumour acidity and other cell types are also proving to be important in understanding therapeutic applications such as immune therapy. Promising therapeutic developments regarding pH manipulation along with current limitations are highlighted to provide a framework for future research directives.

Reproducibility Issues: Avoiding Pitfalls in Animal Inflammation Models

In light of an enhanced awareness of ethical questions and ever increasing costs when working with animals in biomedical research, there is a dedicated and sometimes fierce debate concerning the (lack of) reproducibility of animal models and their relevance for human inflammatory diseases. Despite evident advancements in searching for alternatives, that is, replacing, reducing, and refining animal experiments-the three R's of Russel and Burch (1959)-understanding the complex interactions of the cells of the immune system, the nervous system and the affected tissue/organ during inflammation critically relies on in vivo models. Consequently, scientific advancement and ultimately novel therapeutic interventions depend on improving the reproducibility of animal inflammation models. As a prelude to the remaining hands-on protocols described in this volume, here, we summarize potential pitfalls of preclinical animal research and provide resources and background reading on how to avoid them.

Acidic pH Is a Metabolic Switch for 2-Hydroxyglutarate Generation and Signaling

2-Hydroxyglutarate (2-HG) is an important epigenetic regulator, with potential roles in cancer and stem cell biology. The d-(R)-enantiomer (d-2-HG) is an oncometabolite generated from α-ketoglutarate (α-KG) by mutant isocitrate dehydrogenase, whereas l-(S)-2-HG is generated by lactate dehydrogenase and malate dehydrogenase in response to hypoxia. Because acidic pH is a common feature of hypoxia, as well as tumor and stem cell microenvironments, we hypothesized that pH may regulate cellular 2-HG levels. Herein we report that cytosolic acidification under normoxia moderately elevated 2-HG in cells, and boosting endogenous substrate α-KG levels further stimulated this elevation. Studies with isolated lactate dehydrogenase-1 and malate dehydrogenase-2 revealed that generation of 2-HG by both enzymes was stimulated severalfold at acidic pH, relative to normal physiologic pH. In addition, acidic pH was found to inhibit the activity of the mitochondrial l-2-HG removal enzyme l-2-HG dehydrogenase and to stimulate the reverse reaction of isocitrate dehydrogenase (carboxylation of α-KG to isocitrate). Furthermore, because acidic pH is known to stabilize hypoxia-inducible factor (HIF) and 2-HG is a known inhibitor of HIF prolyl hydroxylases, we hypothesized that 2-HG may be required for acid-induced HIF stabilization. Accordingly, cells stably overexpressing l-2-HG dehydrogenase exhibited a blunted HIF response to acid. Together, these results suggest that acidosis is an important and previously overlooked regulator of 2-HG accumulation and other oncometabolic events, with implications for HIF signaling.

Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq

Genomic instability has profound effects on cellular phenotypes. Studies have shown that pluripotent cells with abnormal karyotypes may grow faster, differentiate less and become more resistance to apoptosis. Previously, we showed that microarray gene expression profiles can be utilized for the analysis of chromosomal aberrations by comparing gene expression levels between normal and aneuploid samples. Here we adopted this method for RNA-Seq data and present eSNP-Karyotyping for the detection of chromosomal aberrations, based on measuring the ratio of expression between the two alleles. We demonstrate its ability to detect chromosomal gains and losses in pluripotent cells and their derivatives, as well as meiotic recombination patterns. This method is advantageous since it does not require matched diploid samples for comparison, is less sensitive to global expression changes caused by the aberration and utilizes already available gene expression profiles to determine chromosomal aberrations.

Chromosomal aberrations can be detected by global gene expression analysis. Here, the authors report eSNP-Karyotyping, a new method that can detect chromosomal aberrations by measuring the ratio of expression between the two alleles without comparison to a matched diploid sample.

Investigation of the cellular reprogramming phenomenon referred to as stimulus-triggered acquisition of pluripotency (STAP)

In January 2014, it was reported that strong external stimuli, such as a transient low-pH stressor, was capable of inducing the reprogramming of mammalian somatic cells, resulting in the generation of pluripotent cells. This cellular reprograming event was designated 'stimulus-triggered acquisition of pluripotency' (STAP) by the authors of these reports. However, after multiple instances of scientific misconduct in the handling and presentation of the data were brought to light, both reports were retracted. To investigate the actual scientific significance of the purported STAP phenomenon, we sought to repeat the original experiments based on the methods presented in the retracted manuscripts and other relevant information. As a result, we have concluded that the STAP phenomenon as described in the original studies is not reproducible.

Results of an attempt to reproduce the STAP phenomenon

In 2014, Obokata and colleagues reported their observation of a novel cell reprogramming phenomenon they named ‘stimulus-triggered acquisition of pluripotency’ (STAP). The most conclusive evidence for the pluripotency of so-called STAP cells was the purported ability of such cells to contribute to chimera formation. Here, I report the results of an attempt by Haruko Obokata to replicate the phenomenon under the supervision of the Scientific Validity Examination Team of RIKEN. In this follow-up study, putative STAP cells prepared by Haruko Obokata were injected into 1051 embryos, of which 591 were recovered. However, the injected cells made no significant contribution in any of the embryos that developed.

Modified STAP conditions facilitate bivalent fate decision between pluripotency and apoptosis in Jurkat T-lymphocytes

Low extracellular pH (pHe) is not only the result of cancer metabolism, but a factor of anti-cancer drug efficacy and cancer immunity. In this study, the consequences of acidic stress were evaluated by applying STAP protocol on Jurkat T-lymphocytes (2.0 × 10(6) cells/ml, 25 min in 37 °C). We detected apoptotic process exclusively in pH 3.3 treated cells within 8 h with western blotting (WB). This programmed cell death led to significant drop of cell viability in 72 h measured by MTT assay resulting PI positive population on flow cytometry (FCM) at day 7. Quantified RT-PCR (qRT-PCR) data indicated that all of above mentioned responses are irrelevant to expression of OCT4 gene variants. Interestingly enough, pluripotent cells represented by positive alkaline phosphatase (AP) staining survived acidic stress and consequently proportion of AP positive cells was significantly increased after pH 3.3 treatment (day 7). In general, acidic treatment led to an apoptotic condition for Jurkat T-lymphocytes, which occurred independent of OCT4 induction.

Standard Operating Procedures (SOPs) for Evaluating the Heart in Preclinical Studies of Duchenne Muscular Dystrophy

A recent working group meeting focused on contemporary cardiac issues in Duchenne muscular dystrophy (DMD) was hosted by the National Heart, Lung, and Blood Institute in collaboration with the Parent Project Muscular Dystrophy. An outcome of this meeting was to provide freely available detailed protocols for preclinical animal studies. The goal of these protocols is to improve the quality and reproducibility of cardiac preclinical studies aimed at developing new therapeutics for the prevention and treatment of DMD cardiomyopathy.

Hallmarks of pluripotency

Stem cells self-renew and generate specialized progeny through differentiation, but vary in the range of cells and tissues they generate, a property called developmental potency. Pluripotent stem cells produce all cells of an organism, while multipotent or unipotent stem cells regenerate only specific lineages or tissues. Defining stem-cell potency relies upon functional assays and diagnostic transcriptional, epigenetic and metabolic states. Here we describe functional and molecular hallmarks of pluripotent stem cells, propose a checklist for their evaluation, and illustrate how forensic genomics can validate their provenance.