A novel imprinted transgene located near a repetitive element that exhibits allelic imbalance in DNA methylation during early development

Suitable Promoter for DNA Vaccination Using a pDNA Ternary Complex

In this study, we evaluated the effect of several promoters on the transfection activity and immune-induction efficiency of a plasmid DNA (pDNA)/polyethylenimine/γ-polyglutamic acid complex (pDNA ternary complex). Model pDNAs encoding firefly luciferase (Luc) were constructed with several promoters, such as simian virus 40 (SV40), eukaryotic elongation factor 1 alpha (EF1), cytomegalovirus (CMV), and chicken beta actin hybrid (CBh) (pSV40-Luc, pEF1-Luc, pCMV-Luc, and pCBh-Luc, respectively). Four types of pDNA ternary complexes, each with approximately 145-nm particle size and -30-mV ζ-potential, were stably constructed. The pDNA ternary complex containing pSV40-Luc showed low gene expression, but the other complexes containing pEF1-Luc, pCMV-Luc, and pCBh-Luc showed high gene expression in DC2.4 cells and spleen after intravenous administration. After immunization using various pDNA encoding ovalbumin (OVA) such as pEF1-OVA, pCMV-OVA, and pCBh-OVA, only the pDNA ternary complex containing pCBh-OVA showed significant anti-OVA immunoglobulin G (IgG) induction. In conclusion, our results showed that the CBh promoter is potentially suitable for use in pDNA ternary complex-based DNA vaccination.

The human EF1a promoter does not provide expression of the transgene in mice

In this work, we set out to create mice susceptible to the SARS-CoV-2 coronavirus. To ensure the ubiquitous expression of the human ACE2 gene we used the human EF1a promoter. Using pronuclear microinjection of the transgene construct, we obtained six founders with the insertion of the EF1a-hACE2 transgene, from which four independent mouse lines were established. Unfortunately, only one line had low levels of hACE2 expression in some organs. In addition, we did not detect the hACE2 protein in primary lung fibroblasts from any of the transgenic lines. Bisulfite sequencing analysis revealed that the EF1a promoter was hypermethylated in the genomes of transgenic animals. Extensive analysis of published works about transgenic animals indicated that EF1a transgenic constructs are frequently inactive. Thus, our case cautions against using the EF1a promoter to generate transgenic animals, as it is prone to epigenetic silencing.

Physiological tissue-specific and age-related reduction of mouse TDP-43 levels is regulated by epigenetic modifications

The cellular level of TDP-43 (also known as TARDBP) is tightly regulated; increases or decreases in TDP-43 have deleterious effects in cells. The predominant mechanism responsible for the regulation of the level of TDP-43 is an autoregulatory negative feedback loop. In this study, we identified an in vivo cause-effect relationship between Tardbp gene promoter methylation and specific histone modification and the TDP-43 level in tissues of mice at two different ages. Furthermore, epigenetic control was observed in mouse and human cultured cell lines. In amyotrophic lateral sclerosis, the formation of TDP-43-containing brain inclusions removes functional protein from the system. This phenomenon is continuous but compensated by newly synthesized protein. The balance between sequestration and new synthesis might become critical with ageing, if accompanied by an epigenetic modification-regulated decrease in newly synthesized TDP-43. Sequestration by aggregates would then decrease the amount of functional TDP-43 to a level lower than those needed by the cell and thereby trigger the onset of symptoms.

Summary: Identification of a cause-effect relationship between epigenetic modifications that occur on the promoter and histones of mouse TARDBP and the level of TDP-43 both in tissues and in cell culture.

Spontaneous Cancers, But Not Many Induced Ones in Animals, Resemble Semi-New Organisms that Possess a Unique Programmed Cell Death Mode Different from Apoptosis, Senescent Death, Necrosis and Stress-Induced Cell Death

There are four basic cell death modes in animals, i.e. physiological senescent death (SD) and apoptosis as well as pathological necrosis and stress-induced cell death (SICD). There have been numerous publications describing “apoptosis” in cancer, mostly focused on killing cancer cells using radio- or chemo-therapy, with few on exploring how cancer cells die naturally without such treatments. Spontaneous benign or malignant neoplasms are immortal and autonomous, but they still retain some allegiance to their parental tissue or organ and thus are still somewhat controlled by the patient's body. Because of these properties of immortality, semi-autonomy, and semi-allegiance to the patient's body, spontaneous tumors have no redundant cells and resemble “semi-new organisms” parasitizing the patients, becoming a unique tissue type possessing a hitherto unannotated cell death mode besides SD, apoptosis, necrosis and SICD. Particularly, apoptosis aims to expunge redundant cells, whereas this new mode does not. In contrast to spontaneous tumors, many histologically malignant tumors induced in experimental animals, before they reach an advanced stage, regress after withdrawal of the inducer. This mortal and non-autonomous nature disqualifies these animal lesions as authentic neoplasms and as semi-new organisms but makes them a good tissue type for apoptosis studies. Ruminating over cell death in spontaneous cancers and many inauthentic tumors induced in animals from these new slants makes us realize that “whether cancer cells undergo apoptosis” is not an easy question with a simple answer. Our answer is that cancer cells have an uncharacterized programmed cell death mode, which is not apoptosis.

While it is not deliberate, much of today's biomedical research contains logical and technical flaws, showing a need for corrective action

Biomedical research has advanced swiftly in recent decades, largely due to progress in biotechnology. However, this rapid spread of new, and not always-fully understood, technology has also created a lot of false or irreproducible data and artifacts, which sometimes have led to erroneous conclusions. When describing various scientific issues, scientists have developed a habit of saying "on one hand… but on the other hand…", because discrepant data and conclusions have become omnipresent. One reason for this problematic situation is that we are not always thoughtful enough in study design, and sometimes lack enough philosophical contemplation. Another major reason is that we are too rushed in introducing new technology into our research without assimilating technical details. In this essay, we provide examples in different research realms to justify our points. To help readers test their own weaknesses, we raise questions on technical details of RNA reverse transcription, polymerase chain reactions, western blotting and immunohistochemical staining, as these methods are basic and are the base for other modern biotechnologies. Hopefully, after contemplation and reflection on these questions, readers will agree that we indeed know too little about these basic techniques, especially about the artifacts they may create, and thus many conclusions drawn from the studies using those ever-more-sophisticated techniques may be even more problematic.