When Processing, Not Presence, Determines Visibility

It is easy to assume that if a protein accumulates in a diseased cell, the immune system will eventually see it. In the case of p53, that assumption has always had an intuitive appeal. p53 is one of the central stress-response proteins in biology, frequently altered in cancer, often stabilized, and deeply woven into the molecular logic of cell fate. If any intracellular protein should become immunologically visible, it ought to be p53.

But the deeper one looks at antigen presentation, the less that simple view holds. What matters is not merely whether p53 is present. What matters is whether peptide fragments derived from p53 are generated in the right form, survive intracellular trimming, fit the preferences of a particular HLA groove, and remain stable enough on the cell surface to be interrogated by either a T cell receptor or an NK-cell receptor system. The 2022 Codondex article, Expanding Treatment Horizons, was already moving in that direction by highlighting an underappreciated observation from the HLA-C ligandome literature: a TP53-derived peptide, TAKSVTCTY, was identified as a naturally presented ligand of HLA-C*02:02. That observation comes from Moreno Di Marco and colleagues’ immuno-peptidomics study, which also listed MAGEA3-derived peptides among ligands presented by the same allotype.

That point remains important, but it also needs sharpening. The HLA-C paper tells us that a TP53-derived peptide can be naturally presented by HLA-C02:02. It does not tell us that HLA-C02:02 is already a dominant or clinically validated p53 presentation route in the way that HLA-A02:01 has become. For that, the literature is far stronger on the HLA-A side. A substantial body of work has shown that **wild-type p53 peptides presented by HLA-A02:01**, especially the well-known p53(264–272) epitope LLGRNSFEV, can stimulate cytotoxic T-cell responses and can be recognized on tumor cells. This was shown in studies such as Chikamatsu et al. Hoffmann et al. Gnjatic et al. and later vaccine-oriented work including Svane et al and the broader review literature on p53-targeting vaccines. In other words, for HLA-A*02:01, p53 is not just a theoretical ligand source; it is already part of a fairly mature immunotherapeutic story.

The most useful contribution of the recent Nature paper, The DNA virome varies with human genes and environments, is that it sharpens the mechanistic frame through which both HLA-C02:02 and HLA-A02:01 should now be viewed. The paper is not a p53 paper. It does not center tumor antigens, and it does not establish anything directly about TP53 peptide presentation. What it does show, at population scale, is that viral DNA load is shaped not only by HLA variation but also by the antigen-processing machinery, especially ERAP1 and ERAP2. That matters because it shifts the center of gravity away from a simplistic “does the peptide bind?” model and toward a more realistic “does the peptide survive the whole processing pipeline?” model.

That shift is especially important for p53. The HLA-A02:01 literature had already hinted that presentation of the classic p53(264–272) epitope depends on more than sequence alone. The work by Kuckelkorn et al showed that generation of this epitope is influenced by the interferon-γ-inducible processing machinery and that a hotspot mutation at residue 273 can prevent proper generation of the epitope. This is a reminder that even for the most familiar p53/HLA-A02:01 peptide, presentation is a processing problem before it becomes a recognition problem. The Nature virome study widens that principle: inherited variation in antigen processing can have measurable biological consequences at human scale. Read together, these papers suggest that p53 visibility is governed not simply by the existence of a fitting sequence, but by whether intracellular processing delivers that sequence intact to the appropriate HLA molecule.

This is where the contrast between HLA-A02:01 and HLA-C02:02 becomes genuinely interesting. HLA-A02:01 has a long experimental trail behind it: peptides were mapped, CTLs were induced, tumors were shown to present certain epitopes, and vaccine studies were built on top of that scaffold. HLA-C02:02, by contrast, remains more conditional. The ligandome study establishes that TAKSVTCTY from TP53 can indeed appear on HLA-C02:02, and it also gives a broader view of the peptide preferences of that allotype. In that same work, HLA-C02:02 is described as favoring small aliphatic or hydrophilic residues at position 2, with additional motif features helping define its ligand space. That does not diminish the importance of the TP53 observation; it means the TP53 peptide should be treated as a real but selective presentation event rather than assumed to be broadly immunodominant.

The biology becomes even more layered because HLA-C is not simply a lower-profile version of HLA-A. HLA-C occupies a distinct place in immune regulation. Compared with HLA-A and HLA-B, HLA-C is generally expressed at lower surface levels and is more tightly integrated with KIR-mediated NK-cell regulation. That broader point is well summarized in the Nature Communications paper Structural and regulatory diversity shape HLA-C protein expression levels, which notes both the lower surface expression of HLA-C and its extensive functional relationship with KIRs. This makes HLA-C particularly interesting for p53 because a peptide displayed by HLA-C is not only a possible T-cell target; it is also part of a signaling surface read by NK cells.

That NK dimension turns out not to be merely background context. More recent work has shown that KIR recognition of HLA-C is often peptide-dependent. The point is made clearly in studies such as Sim et al. 2017 and Sim et al. 2023: the HLA-C molecule is not being read in a peptide-blind way. Inhibitory and activating KIRs can be strongly shaped by the identity of the peptide bound in the groove. That has profound implications for any discussion of TP53 peptides on HLA-C02:02. A TP53-derived peptide on HLA-C02:02 may not simply mark a cell for CD8 T-cell inspection; it may also alter the threshold for NK inhibition or activation. This is one of the most important places where the older Codondex article and the newer immunogenetic literature genuinely converge.

So the corrected reading is not that the 2026 Nature paper newly proves something specific about HLA-C*02:02 presenting p53. It does not. What it does is make the older HLA-C02:02 observation more meaningful by placing it inside a stronger mechanistic framework. The question is no longer only whether TAKSVTCTY can bind HLA-C02:02; the question is whether an individual’s processing machinery, inflammatory state, and HLA context allow that peptide to be generated, preserved, loaded, displayed, and then interpreted by either T cells or NK cells in a biologically consequential way. That is a more demanding question, but it is also a more interesting one.

This also helps explain why HLA-A*02:01 remains the more established p53 route. The A02:01 pathway has yielded peptides that are repeatedly recoverable in experimental systems, repeatedly recognized by CTLs, and repeatedly leveraged in translational work. The HLA-C02:02 pathway looks more contingent: real, but likely more dependent on peptide selection pressure, trimming, and the NK-facing consequences of peptide-loaded HLA-C. Seen this way, HLA-A02:01 is the clearer adaptive pathway, while HLA-C02:02 may be a narrower but potentially more intriguing bridge between tumor antigen presentation and innate immune tuning.

That may be the most useful lesson from putting these papers together. p53 is not simply “presented” or “not presented.” It passes through a filter. In HLA-A02:01, that filter has already produced a clinically legible signal. In HLA-C02:02, the signal is fainter, but perhaps more information-rich, because it may be read simultaneously by T cells and NK-cell receptor systems. If that is right, then the next real step is not more speculation about binding motifs alone. It is experimental work that directly compares TP53 peptide generation, ERAP dependence, surface abundance, and KIR/TCR consequences across HLA-A02:01 and HLA-C02:02 backgrounds. That is where the overlap becomes testable rather than merely suggestive.

Cancer and The PEPCK Clutch!

Key Points

• Research suggests mediated mechanical stretch can mimic localized increases in blood pressure and inflammation, based on studies showing stretch affects vascular cells and induces inflammatory responses.

• It seems likely that PEPCK, an enzyme involved in metabolism, can be induced to support a metabolic cell state that promotes outcomes like prolonged cell life and disease, especially in cancer, where it supports cell survival under stress.

• The evidence leans toward mechanical stretch influencing cancer cell metabolism, potentially involving PEPCK, though direct links need further study.

Background

Mediated mechanical stretch refers to controlled mechanical forces applied to cells or tissues, often used in lab settings to simulate physiological conditions like increased blood pressure. This can affect how cells behave, particularly in blood vessels and potentially in cancer. PEPCK, or Phosphoenolpyruvate Carboxykinase, is an enzyme key to gluconeogenesis, the process of making glucose from non-carbohydrate sources, and is notably active in cancer cells under nutrient stress.

Connection to Blood Pressure and Inflammation

Studies show mechanical stretch can mimic conditions of high blood pressure and inflammation. For instance, stretch on vascular cells increases reactive oxygen species and inflammation markers, similar to what happens with hypertension (Mechanical stretch: physiological and pathological implications for human vascular endothelial cells). This suggests stretch can create a microenvironment akin to diseased states.

Role of PEPCK in Disease

PEPCK is crucial in cancer, where it helps cells survive by altering metabolism under stress, such as low glucose. Research indicates PEPCK supports cancer cell growth by enhancing glucose and glutamine use, potentially prolonging cell life and promoting disease progression (PEPCK coordinates the regulation of central carbon metabolism to promote cancer cell growth).

Linking Mechanical Stretch and PEPCK

While direct studies linking mechanical stretch to PEPCK in cancer are limited, the connection seems plausible. Mechanical stretch can induce inflammation and metabolic changes, and in cancer, this could upregulate PEPCK, supporting a cell state that aligns with prolonged survival and disease promotion. This is an unexpected detail, as stretch is often seen as beneficial (e.g., exercise), but here it may exacerbate cancer conditions.

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Survey Note: Detailed Analysis of Mechanical Stretch, PEPCK, and Disease Promotion

This section provides a comprehensive exploration of the user's query, examining the potential for mediated mechanical stretch to mimic localized increases in blood pressure and inflammation, and whether PEPCK can be induced to support a metabolic cell state promoting outcomes that prolong cell life and promote disease. The analysis draws on various studies and blog posts referenced, ensuring a thorough understanding for readers with a scientific background.

Understanding Mediated Mechanical Stretch

Mediated mechanical stretch involves applying controlled mechanical forces to cells or tissues, often to simulate physiological or pathological conditions. Research indicates that such stretch can replicate the effects of increased blood pressure and inflammation at a localized level. For example, a study on vascular endothelial cells showed that mechanical stretch, especially under conditions mimicking hypertension, leads to the formation of reactive oxygen species and inflammation, aligning with pathological consequences (Mechanical stretch: physiological and pathological implications for human vascular endothelial cells). Another study, "The Effect of Pressure-Induced Mechanical Stretch on Vascular Wall Differential Gene Expression" (The Effect of Pressure-Induced Mechanical Stretch on Vascular Wall Differential Gene Expression), further supports that stretch can induce gene expression changes similar to those seen in high blood pressure, validating the user's premise.

Blood Pressure and Inflammation: Detailed Mechanisms

The connection between mechanical stretch and blood pressure is evident in studies showing stretch affects arterial stiffness and blood pressure regulation. For instance, regular stretching exercises have been shown to reduce blood pressure in hypertensive patients, suggesting a link between mechanical forces and vascular responses (Compliance of Static Stretching and the Effect on Blood Pressure and Arteriosclerosis Index in Hypertensive Patients). Inflammation is also induced by stretch, as seen in studies where cyclic mechanical stretch upregulates pro-inflammatory pathways, particularly in vascular smooth muscle cells, contributing to conditions like chronic venous insufficiency (The Effect of Pressure-Induced Mechanical Stretch on Vascular Wall Differential Gene Expression).

A detailed breakdown of relevant findings is presented in the following table, extracted from blog posts and studies:

Topic	Details	Exact Numbers	Relevant URLs
Mechanical Stretch	Causes sustained molecular signaling of pro-inflammatory and proliferative pathways, tied to p53, occurs in disturbed flow and undirected stretch at branch points and complex regions.	-	journals.physiology.org, blog.codondex.com
Blood Pressure	Meta-analysis of 7017 individuals identified 34 differentially expressed genes, 6 linked to BP and hypertension, MYADM (19q13) the only gene across diastolic, systolic BP, and hypertension.	7017, 34, 6	journals.plos.org, www.ncbi.nlm.nih.gov
Inflammation	Controlled by interaction between plasma membrane and submembrane at endothelial surface; MYADM knockdown induces inflammatory phenotype via ICAM-1 (19p13) increase, mediated by ERM actin cytoskeleton proteins; S1P2 (19p13) involved in immune, nervous, metabolic, cardiovascular, musculoskeletal, renal systems.	-	blog.codondex.com, www.ncbi.nlm.nih.gov, rupress.org, www.ncbi.nlm.nih.gov, www.jimmunol.org, www.ncbi.nlm.nih.gov, onlinelibrary.wiley.com, www.researchgate.net, www.ncbi.nlm.nih.gov, journals.asm.org, journals.plos.org, www.jbc.org, www.gastrojournal.org, www.spandidos-publications.com

This table highlights the molecular and physiological impacts, providing a foundation for understanding how stretch influences blood pressure and inflammation.

PEPCK and Its Role in Metabolic Cell States

PEPCK, or Phosphoenolpyruvate Carboxykinase, is a key enzyme in gluconeogenesis, converting oxaloacetate to phosphoenolpyruvate. Its role extends beyond normal physiology into cancer, where it supports metabolic flexibility under nutrient stress. Studies show PEPCK, particularly the mitochondrial isoform PCK2, is expressed in lung and other cancer tissues, aiding cell survival by enhancing glucose and glutamine utilization (PEPCK in cancer cell starvation). This metabolic adaptation can prolong cell life, especially in cancer, and promote disease progression by supporting tumor growth (PEPCK coordinates the regulation of central carbon metabolism to promote cancer cell growth).

Linking Mechanical Stretch, PEPCK, and Disease Promotion

The user's query posits whether PEPCK can be induced to support a single metabolic cell state that promotes outcomes similar to those from mechanical stretch, which mimics increased blood pressure and inflammation, and whether this prolongs cell life and promotes disease. While direct studies linking mechanical stretch to PEPCK induction are scarce, indirect evidence suggests a connection. Mechanical stretch induces inflammation and alters glucose metabolism, as seen in skeletal muscle studies where stretch increases glucose uptake via ROS and AMPK pathways (Stretch-stimulated glucose uptake in skeletal muscle is mediated by reactive oxygen species and p38 MAP-kinase). In cancer, where inflammation is a known promoter, mechanical stretch could create a microenvironment that upregulates PEPCK, supporting a metabolic state conducive to prolonged cell survival and disease, particularly in tumors under stress.

For instance, a study on lung cancer progression under mechanical stretch highlights its role in tumor microenvironment changes, potentially affecting metabolic pathways (An Overview of the Role of Mechanical Stretching in the Progression of Lung Cancer). Given PEPCK's role in cancer metabolism, it's plausible that such conditions could induce PEPCK, aligning with the user's hypothesis. This is an unexpected detail, as stretch is often viewed positively (e.g., exercise benefits), but here it may exacerbate cancer by supporting a disease-promoting metabolic state.

Conclusion and Implications

Based on the analysis, it seems likely that mediated mechanical stretch, by mimicking localized increases in blood pressure and inflammation, can create conditions where PEPCK is induced to support a metabolic cell state. This state, particularly in cancer, can promote outcomes like prolonged cell life and disease progression, fitting the user's query. Further research is needed to confirm direct links, but the evidence leans toward this possibility, offering insights into how mechanical forces influence cancer metabolism.

Key Citations

• Mechanical stretch: physiological and pathological implications for human vascular endothelial cells

• The Effect of Pressure-Induced Mechanical Stretch on Vascular Wall Differential Gene Expression

• Compliance of Static Stretching and the Effect on Blood Pressure and Arteriosclerosis Index in Hypertensive Patients

• PEPCK in cancer cell starvation

• PEPCK coordinates the regulation of central carbon metabolism to promote cancer cell growth

• Stretch-stimulated glucose uptake in skeletal muscle is mediated by reactive oxygen species and p38 MAP-kinase

• An Overview of the Role of Mechanical Stretching in the Progression of Lung Cancer

Can Ancient Pathways Defeat Cancer?

It has been widely acknowledged that non-coding RNAs are master-regulators of genomic function. The association between human introns and ncRNAs has a pronounced synergistic effect with important implications for fine-tuning gene expression patterns across the entire genome. There is also strong preference of ncRNA from intronic regions particularly associated with the transcribed strand. 

Accumulating evidence demonstrates that, analogous to other small ncRNAs (e.g. miRNAs, siRNA's etc.) piRNAs have both oncogenic and tumor suppressive roles in cancer development. Functionally, piRNAs maintain genomic integrity and cell age by silencing repetitive, transposable elements, and are capable of regulating the expression of specific downstream target genes in a post-transcriptional manner. 

Unlike miRNAs and siRNAs, the precursors of piRNAs are single stranded transcripts without any prominent secondary hairpin structures. These precursors are usually generated from specific genomic locations containing repetitive elements, a process that is typically orchestrated via a Dicer-independent pathway. 

Without restraint, the ancient, L1 class of transposable elements can interrupt the genome through insertions, deletions, rearrangements, and copy number variations. L1 activity has contributed to instability and evolution of genomes, and is tightly regulated by DNA methylation, histone modifications, and piRNA. They can impact genome variation by mispairing and unequal crossing-over during meiosis due to repetitive DNA sequences. Indeed meiotic double-strand breaks are the proximal trigger for retrotransposon eruptions as highlighted in animals lacking p53.

Through a novel 28-base small piRNA of the KIR3DL1 gene, antisense transcripts mediate Killer Ig-like receptor (KIR) transcriptional silencing in immune somatic, Natural Killer (NK) cell lineage, a mechanism that may be broadly used in orchestrating immune development. Expressed on NK cells, KIR's are important determinants of NK cell function. Silencing  individual KIR genes is strongly correlated with the presence of CpG dinucleotide methylation within the promoter. 

Structural research exposed the enormous binding complexity behind KIR haplotypes and HLA allotypes. Not only via protein structures, but also plasticity and selective binding behavior's as influenced by extrinsic factors. One study links a specific recognition of HLA-C*05:01 by KIR2DS4 receptor through a peptide highly conserved among bacteria pathogenic in humans. Another demonstrated a hierarchy of functional peptide selectivity by KIR–HLA-C interactions, including cross-reactive binding, with relevance to NK cell biology and human disease associations. Additionally a p53 peptide most overlapped other high performance peptides for a HLA-C allotype C*02:02 that shares identical contact residues with C*05:01.

Ancient pathways linking p53 to attenuation of aberrant stem cell proliferation may predate the divergence between vertebrates and invertebrates. Human stem cell proliferation, as determined by p53 transposable element silencing, may also serve a NK progenitor to promote the repertoire of more than 30,000 NK cell subsets. 

A recent study showed that wild type p53 can restrain transposon mobility through interaction with PIWI-piRNA complex. Also, cellular metabolism regulates sensitivity to NK cells depending on P53 status and P53 pathway is coupled to NK cell maturation leaving open the possibility that a direct relationship exists. Further, functional interactions between KIR and HLA modify risks of basal cell carcinoma (BCC) and squamous cell carcinomas (SCC) and KIR B haplotypes provide selective pressure for altered P53 in BCC tumors. 

Anticipating p53's broader influences or responses, cells, extracted from 48 different sections of 7 tumor biopsies were sequenced and TP53 DNA computed using Codondex algorithm. Each section produced a TP53 Consensus Variant (CV), represented by its intron1, ncDNA Key Sequence's (KS). Bioinformatic correlations between each KS and cytotoxicity resulting from NK coculture with the section may predict KIR-HLA and extrinsic factor plasticity to reliably determine from KS's, optimal cell/tissue selections for NK cell education and licensing. 

First Intron DNA - Site for a Genetic Brain?

DNA Methylation

The first intron of a gene, regardless of tissue or species is conserved as a site of downstream methylation with an inverse relationship to transcription and gene expression. Therefore, it is an informative gene feature regarding the relationship between DNA methylation and gene expression. But, expression in induced pluripotent stem cells (iPSC's) has been a major challenge to the stem cell industry, because by comparison these cells have not yet reached the state of natural pluripotent or embryonic stem cells (ESC's).

In mice two X chromosomes (XC) are active in the epiblasts of blastocysts as well as in pluripotent stem cells. One XC is inactivated triggered by Xist (non coding) RNA transcripts coating it to become silent. Designer transcription factor (dTF) repressors, binding the Xist intron 1 enhancer region caused higher H3K9me3 methylation and led to XC's opening and X-linked gene repression in MEFs. This substantially improved iPSC production and somatic cell nuclear transfer (SCNT) preimplantation embryonic development. This also correlated with much fewer abnormally expressed genes frequently associated with SCNT, even though it did not affect Xist expression. In stark contrast, the dTF activator targeting the same enhancer region drastically decreased both iPSC generation and SCNT efficiencies and induced ESC differentiation. 

A genome-wide, tissue-independent quasi-linear, inverse relationship exists between DNA methylation of the first intron and gene expression. More tissue-specific, differentially methylated regions exist in the first intron than in any other gene feature. These have positive or negative correlation with gene expression, indicative of distinct mechanisms of tissue-specific regulation. CpGs in transcription factor binding motifs are enriched in the first intron and methylation tends to increase with distance from the first exon–first intron boundary, with a concomitant decrease in gene expression.

Since the relationship between sequence, methylation, repression and transcription is determinative in ESC differentiation it may also suggest a broader link to differential translation. Translation is required for miRNA-dependent transcript destabilization that alters levels of coding and noncoding transcripts. But, steady-state abundance and decay rates of cytosolic long non-coding RNA's (lncRNAs) are insensitive to miRNA loss. Instead lncRNAs fused to protein-coding reporter sequences become susceptible to miRNA-mediated decay. 

In this model, first intron DNA sequences that are differentially methylated, bind transcription factors that effect transcription, impact splicing, expressions of coding or non-coding transcripts and transcript destabilizations resulting in differential rates and possible variations in translation. This bottom-up, dynamic view of the classical process may elevate the first intron from 'junk' to a DNA 'brain' because it plays a more extensive role, heading the process toward translation of any gene or switching it off entirely.  

For this reason, among others Codondex uses first intron k-mers relative to the transcripts mRNA as the basis for comparing same gene transcripts in diseased cells or tissue samples. Further, p53 and BRCA1 miRNA key sequences, discovered using Codondex iScore algorithm, when transfected into HeLa cells resulted in significantly reduced proliferation that may result from this accelerated, transfected miRNA dependent decay.

 

Short Sequences of Proximally Disordered DNA

Oxford Nanopore Device Reducing Sequencing Cost

Relationships exist between short sequences of proximal DNA (SSPD) of a gene that when transcribed into RNA present stronger or weaker binding attractions to RNA binding proteins (RBP'S) that settle, edit, splice and resolve messenger RNA (mRNA). Responsive to epigenetic stimuli on Histones and DNA, mRNA are constantly transcribed in different quantity, at different times such that different mRNA strands are transported from the nucleus to cytoplasm where they are translated into and produce any of more than 30,000 different proteins.

Single nucleotide polymorphisms and DNA mutations can alter SSPD combinations in different diseased cells thus altering sequence proximity, ordering that affects transcribed RNA's attraction and optimal binding of RBP's. This may result in modified splicing of RNA, assembly of mRNA and slight or major variations in some or all translated protein derived from that gene. 

The specific effects of these DNA variations, on the multitude of proteins produced are generally unknown. However, it remains important to understand their effects in disease, diagnosis and therapy. Typically these have historically been researched by large scale analysis of RBP on RNA as opposed to the more fundamental, yet underrepresented massive array of diseased variant DNA to mRNA transitions.

Most pharmaceutical research is directed to a molecular interference targeting an aberrant protein to cure widely represented or highly impactful disease conditions of society. Economic assessments generally influence government decisions to support research based on loss of GDP contribution by a specific disease in a  patient cohort. However, in the modern multi-omics era top down research into protein-RNA activity is descending deeper into the cell to include RNA-mRNA and mRNA-DNA customizable therapies that will eventually resolve individually assessed diseases at a price that addresses much larger array of patient needs.  

SNP's and other mutations can vary considerably in cells. These variations can cause instability during division and lead to translated differences that can ultimately drive cancerous cell growth to escape patient immunity. Like a 'whack-a-mole' game, pattern variation and mechanistic persistence eventually beat the player. Without effective immune clearance these cells can replicate into tumors and contribute to microenvironments that support their existence.

Link to video on tumor microenvironment https://youtu.be/Z9H2utcnBic

We thought to analyze DNA and mRNA transcripts from cells in tumors and their microenvironments to see if we could expose the SSPD disordered combinations that may have promoted sub-optimal RBP attractions and led to sustained immune escape. Given the complexity of DNA to mRNA transcription, for any given gene many distortions in gene data sets have to be filtered. To do that we focused on p53, the most mutated gene in cancer. We designed a method to compare sequences arrays of DNA and mRNA Ensembl transcripts, from the consensus of healthy patients to multiple cell samples extracted from different sections of a patients tumor and tumor microenvironment.     

We previously identified and measured different levels of Natural Killer (NK) cell cytotoxicity, produced from cocultures with the extracted samples of each of the multiple sites of a biopsy. We will measure the different p53 transcript SSPD combinations associated with each sample and determine whether disordered SSPD's corelate with NK cytotoxicity from each coculture. We expect to identify whether biopsied tumor cells, ranked by SSPD's predict the cytotoxicity resulting from NK cell cocultures. We will narrow our research to identify the varied expressions of receptor combinations associated with degrees of cytotoxicity. We will test immune efficacy to lyse and destroy tumor cells. Finally we will test for adaptive immune response. 

Our vision is for per-patient, predictable cell co-culture pairings, for innate immune cell education based on ranking DNA-mRNA combinations to lead to multiple effective therapies. The falling cost of sequencing and sophistication of GMP laboratories presently servicing oncologists may support a successful use of this analytical approach to laboratory assisted disease management.

   

 

A p53 Checkpoint For Cancer Therapy

Enormously complex signaling exists in the communication of antigens, receptors and ligands in DNA pathways between Natural Killer cells (NK) and target cells with which they interact. Based on observations, following NK formation of an immune synapse with its target cell two outcomes occur most often, termination or differentiation. The innate immune system comprises multiple cell types that are present and differentiated in tissues, but the predatory-like activity of NK has led to the general perception of its role in the immune system's front line.

As we have articulated many times on this blog, immunity and reproduction are tied, originally through allorecognition to the conserved p53-mdm2 axis. Further, it has become abundantly clear that auto-regulation of p53 occurs in multiple gene positive and negative feedback loops including mdm2. NK performance in young versus older patients showed a reduced capacity for, synaptic polarization and perforin release into the immune synapse before killing target cell. Further that the reduced release of perforin also reduced the capacity for NK to clear senescent cells associated with aging.

The activation of mitogen‐activated protein kinases (MAPK) is critical for lytic granule (perforin-granzyme) polarization, granule exocytosis and NK Cytotoxicity. It is possible that these proximal signalling events are compromised by aging. In addition, the studied p53 mutants regulated MAP2K3 gene whereas ectopic expression rescued the proliferative defect induced by mutant p53 knockdown.

In one series of experiments it was shown that the mutational status of p53 can facilitate cytotoxicity and different T cell recognition patterns. The p53 protein is presented by MHC molecules and the differential T cell recognition patterns seem confined to p53 as an antigen. The paper suggests p53 may behave differently to other classical tumor antigens, therefore a biomarker for immunotherapy targeting p53 should be the type of mutation expressed rather than protein levels only.

As previously reported, cytoskeleton superfamily member Talin1 has been uniquely tied to two essential NK functions;  activation of LFA1, required for binding ICAM on NK target cell and NK polarization that results. We know overexpression of talin head activates LFA1 and talin1 promotes cell proliferation by affecting the expression of BCL2 family and p53 network. But, mdm2 the conserved nemesis of p53 is neutralized by Merlin, another cytoskeleton superfamily protein also required for polarization. p53 also regulates the highly conserved Cdc42 which effects adhesion, actin cytoskeletal dynamics and cell movement including for angiogenesis in developing tumor microenvironments.

We found that activation of p53 augmented NK cell-mediated cytolysis of tumor cells via induction of ULBP2 expression on tumor cell surface. Further, we identified p53 as a direct transcriptional regulator of ULBP2 via an intron1 binding site, thus revealing previously unknown molecular mechanism controlling NKG2D ligand transcription. In mouse NK cells, talin is required for outside signaling by LFA1, which together with signaling by NKG2D induces granule polarization.

The functions of p53 are inextricably linked to multiple mechanisms in NK and target cells including recognition, antigen-receptor-ligand binding, cytoskeletal rearrangement, immune synapse, granzyme and perforin release. p53's mutation frequency and variances bearing p53 destabilizing mutations are recognized more effectively by p53-specific T cells than stabilized p53 mutants. Therefore, NK could operate its probe as a binding cipher that determines whether its target can be killed. Variable binding, and ectopic expression, resulting from a p53 feedback loop could be dependent on a p53 variable-kill-checkpoint that triggers the cascade of coordinated activities between NK and its target, generally referenced in the preceding paragraphs.

NK's p53 status, a targets MHC molecules presenting p53 antigens, ULBP2-NKG2D binding and relevant pathways confer with observations that the period of NK engagement is sufficient to allow downstream DNA transcription and translation to confirm and enable the kill event. Co-culture methods that could educate NK to better synchronize with targets, based on p53 status may usher in new regimes for organic immunotherapy. The Codondex research teams at Precision Autology are progressing through pre-clinical research using their computed cell selections.

Hope for a p53 Autologous Natural Killer Cell Therapy

Natural Killer Cells (NK) are much more than cell killers! They possess mechanisms and sensitivities that, among many functions, enables them at the front line of reproduction to interact with incoming trophoblasts that invade the uterine wall where NK cells are critical for blastocyst implantation and pregnancy. NK are members of the innate immune system, but they can be licensed to kill and re-purpose cells whereas most innate immune cells directly target invading pathogens.

Maternal decicdual NK may be redirected by PreImplantation Factor (PIF) expressing, anti-apoptopic, extra-villous trophoblasts that invade the endometrium (epithelioid) of the decidua of the uterine wall. This may result from epithelial LIF expression, and LIFR(eceptors) critical for blastocyst implantation. LIF allele's may act as a NK switch, the direct result of a p53 promoter allele that targets specific LIF transcription, that alters NK interactions with trophoblasts, the host endometria and vascular epithelia. If so, redirection of NK is an essential mechanism of conception that underwrites the development of the placenta.

Studies have revealed p53 targets LIF and demonstrated that, as a secreted protein LIF can function through the Stat3/ID1/MDM2 pathway to negatively regulate p53. Selected alleles in SNPs in LIF, Mdm2, Mdm4, and Hausp genes, each of which regulates p53 levels in cells, are also enriched in IVF patients. This association of SNPs in the p53 pathway with human fertility strongly suggests that p53 regulates human reproduction. It is distinctly possible enriched SNP's invoke regulation that negatively affects p53 and may also be the mechanism by which NK switches between modes that kill or transform its cell targets. In implantation, levels of p53  may lead to pre-eclampsia a condition that is the direct result of increased, p53 dependent apoptosis in extra-villous trophoblasts.

Pathogen-associated molecular pattern–mediated metabolic reprogramming can be considered as a manifestation of innate immune signaling, reprogramming a conserved phenomenon, that changes how we think about the biology and function of the innate immune network.

The mode of NK, in response to cancers may determine the fate of its target either by the binding of innate receptor combinations that initiate an immune synapse and perforin-mediated cytolysis or the release cytokines and chemokines that alters the inflammatory response. It was recently demonstrated these combinations are varied by different tissue and disease depending on p53 for example, in lung adenocarcinoma NK limited target killing and reduced inflammatory response allowing the cancer to spread. Further, peptides derived from p53 are presented by class I MHC molecules and may act as tumor-associated epitopes which could also be targeted by p53-specific T cells.  Results show that selected p53 mutations altering protein stability can modulate p53 presentation to T cells, leading to a differential immune reactivity inversely correlated with measured p53 protein levels.

These complex tissue dependent modes, through p53 pathways that contribute negative or positive feedback loop's, have prevented the most mutated gene in cancer from itself becoming a target of drug or immune therapy. Using a novel approach Precision Autology's Codondex algorithm computed the variable state of p53 isoforms, using a relative vector distance, from the consensus, to select patient cells for co-culture with, at least autologous NK for use in customized therapy. The approach will enable approved labs to identify highly specific cell targets, in part by their p53 state and to educate autologous NK cells based on a single p53 measure so that NK precision can be calibrated via the mismatch of target receptor combinations and p53.