P53 - Stability and Life Or Disorder and Death!

Chromosomal stability is central to good health, but the push and shove war of genesis, division, transcription, replication and restraint can promote disorder. Disruption can also be retained resulting in ageing, reduced organ function or diseases that often follow. Recently a man escaped his genetic predisposition, to becoming a victim of Alzheimer's disease, illustrating how far we are from understanding even the most well studied conditions. 

Active or passive, mobile Transposable Elements (TE) represent around 40-50% of the human genome and around 30% are found in the non-coding introns of genes. The first intron is conserved as a site of downstream methylation with an inverse relationship to transcription and gene expression. Our understanding of non-coding RNA (ncRNA) suggests one of its primary functions is the restraint of mobile TE's. Several species of ncRNA are associated with this restraint and genomic stability, most contain p53 binding sites that are also known to be involved in tumor suppression. 

Of the short ncRNA species, LINE-1 (L1), siRNAs are typically 21-23 nucleotides long and play a role in silencing L1 transcripts, thus preventing retro-transposition. p53 binds the L1 promoter to restrict autonomous copies of these mobile elements in human cells. Alu elements are the most abundant transposable elements (capable of shifting their positions) containing over one million copies dispersed throughout the human genome. As little as 0.7% sequence divergence resulted in a significant reduction in recombination after double stranded breaks. piRNAs, usually 26-31 nucleotides, derived from Alu repeats restrain transposable elements. Endogenous Retroviruses (ERVs) can give rise to microRNAs (miRNAs) of 22 nucleotides, that can regulate the expression of ERV sequences and other cellular genes.  

TE's serve as templates for the generation of p53- binding-sites on a genome-wide scale . The formation of the p53 binding motifs was facilitated via methylation and deamination that distributes  p53-binding sites and recruits new target genes to its regulatory network in a species-specific manner. This p53 mechanism conducts genomic restraint, where instability and loss or mutation of p53 are commonly associated with hallmark's of cancer. 

Through a novel piRNA of the KIR3DL1 gene, antisense transcripts mediate Killer Ig-like receptor (KIR) transcriptional silencing in Natural Killer (NK) cell lineage that may be broadly used in orchestrating immune development. Silencing  individual KIR genes is strongly correlated with the presence of CpG dinucleotide methylation within the promoter. 

The emergence of recombination-activating genes (RAGs) in jawed vertebrates endowed adaptive immune cells with the ability to assemble a diverse set of antigen receptor genes. Innate NK cells are unable to express RAGs or RAG endonuclease activity during ontogeny. However, RAG expression in uncommitted hematopoietic progenitors and NK cell precursors mark functionally distinct subsets of NK cells in the periphery, a surprising and novel role for RAG in the functional specialization of the NK cell lineage. 

The p53 C-terminal including amino acids 360-393 of the full-length protein locate to the mitochondrial permeability transition pore and facilitate apoptosis. However fragments of p53 at amino acid 1-186 and 22-186 drive the most mitochondrial depolarization. Crystal structures demonstrate amino acid 239 binds 106 and 241 binds 105 for one p53 unit and 243 binds 103-264-265 for a second unit, which are both are required to bind BCL-xl for apoptosis.

p53 regulates the expression of major histocompatibility complex (MHC) class I on cell surfaces. p53 peptides presented on HLA/MHC-I could attract immune surveillance as in the target-specific antitumor effects of p53 amino acids at positions 264-272, epitope 264scTCR with IL-2 on p53+/HLA-A2.1+ tumors that are primarily mediated by NK cells.  

Initially, NK cells might be activated due to the combined effect of reduced inhibition (due to decreased KIR3DL1) and increased activation signals from p53 epitopes. This NK cell activation could lead to the release of cytokines that not only enhance further NK activity but also attract and activate T cells. 

To summarize, p53 can influence both the presentation of its antigens through MHC-I and the regulation of NK cell inhibitory receptors like KIR3DL1 via piRNA. This could lead to a more effective immune response against cells with compromised p53 function, although the exact dynamics would depend on the specific context of cancer development, immune cell status, and individual genetic variations.

Electrons Rule Your Biology!

The mitochondrial Electron Transport Chain (ETC) is responsible for almost all cellular energy - ATP. One protein, GPD2 was adopted into the inner mitochondrial membrane, perhaps because it enabled ETC production to move to its electron processing limit. To do this, lipids are metabolized when cytoplasmic GPD1-DHAP convert Glycerol Kinase to G3P, which passes two additional electrons from the cytoplasm, through GPD2, to the internalized ETC complexes. 

When Mitochondrial Membrane Potential "Δψm" is within normal range, the GPD2 electrons enhance ATP energy production. When damage to lipids, fatty chains, cholesterols or other elements, constituting the inner mitochondrial membrane, disrupt Δψm the anchored ETC proteins can move fractionally apart causing electrons passing along the chain of ETC complexes to leak.

During disrupted Δψm the additional flow of GPD2 electrons can burden the ETC complexes, resulting in unstable molecules that contain oxygen and are highly reactive known as reactive oxygen species (ROS). Prolific ROS can increase CA+ levels, damage lipids in mitochondrial membranes, which can cause dysfunction and disease. In  a normal cellular environment this process can lead to ferroptosis, an iron-dependent form of cell death, induced by lipid peroxidation. 

A key bidirectional regulator of ferroptosis, p53 can adjust metabolism of iron, lipids, glutathione peroxidase 4, reactive oxygen species, and amino acids via a canonical pathway. GPD2 is transcribed by multiple factors that interact with p53 including Nrf2 and others during stress, but findings with E2F suggest a critical function controls a p53-dependent axis that indirectly regulates E2F-mediated transcriptional repression and cellular proliferation. 

P53 can also induce apoptosis through the mitochondrial pathway, contribute to necrosis by accumulating in the mitochondrial matrix and regulating autophagy. Mitochondrial p53 accumulation is an early event  not merely a consequence of apoptosis or a consequence of binding to damaged organelles in dying cells. Now, emerging evidence shows that ferroptosis plays a crucial role in tumor suppression via p53. 

Immune cells require massive energy boosts during synapse formation and lysis of a target cell when mitochondrial fitness is essential. However, tumor micro environments (TME's) alter lipid metabolism disrupting Δψm causing immune cells to function sub-optimally. Stimulation of T cells triggers a spike in cellular ATP production that doubles intracellular levels in <30 s and causes prolonged ATP release into the extracellular space. ATP release and autocrine feedback, via purinergic receptors collectively contribute to the influx of extracellular Ca2+ that is required for IL-2 production. The process has also been described for Natural Killer (NK) cells.

In the TME innate NK cells are dysfunctional due to lipid peroxidation inhibiting glucose metabolism. If innate immune cells are initially successful, adaptive immune responses may still fail because mitochondria reposition to the immune synapse where they transfer, including to immune cells, which can assist the target to evade immune response. Rapidly proliferating cancer cells may overwhelm initial immune responses and modify immune signaling promoting cancer and vascular remodeling.

ΔΨm as a measure of functional integrity maybe the flawed alert, a blind spot for of a cells' ADP-ATP pipeline. Likewise the status of TP53, from transcription through p53 isoform, may signal wide ranging affects of ΔΨm changes that incorporate fragmentation, accumulating damaged mitochondria, mitophagy, apoptosis or normal immune signaling and response through mitochondrial biogenesis, differentiation and angiogenesis. This modal duality aligns known functions of NK cells that under physiological conditions promote angiogenesis growth (as in Blastocyst implantation and placental vascularization) or NK's classic, cytolytic role in the innate immune response. 

Mitochondrial Phospholipid (MitoPLD), is anchored to the mitochondrial surface. It regulates mitochondrial shape, facilitating fusion and in the electron-dense nuage, of adjacent mitochondria, performs a critical piRNA generating function that is known to generate a spermatocyte-specific piRNA required for meiosis. piRNA are known to be aberrantly expressed in cancer cells.

Changes in mitochondrial membrane potential and ETC complexes can also influence piRNA-mediated control of transposable elements (TE's) through energy availability, ROS generation, and direct or indirect effects on piRNA biogenesis and function. piRNA restrain TE's that disrupt genes, chromosomal stability, damage DNA, cause inflammation, disease and/or cell death. For example, increased levels of endogenous retroviruses (ERV's), a TE subclass, trigger fibro inflammation and play a role in kidney disease development.

In mammals, the transcription of TEs is important for maintaining early embryonic development and related vital aspects of NK cell immune development. Intriguingly, regardless of the cell type, p53 sites are highly enriched in the endogenous retroviral elements of the ERV1 family. This highlights the importance of this repeat family in shaping the transcriptional network of p53 and its transcriptional role in interferon-mediated antiviral immunity.