Monday, January 13, 2020

Impotent Natural Killers by Cancer Stem Cells and Ageing

Cancer stem cells have been found, through various mechanisms to alter the sentinel function and innate, immune surveillance of Natural Killer cells (NK). In senescent cells that have stopped cell division, including in cancer stem cell niches and NK induced vascular remodeling (as found in the developing placenta) NK's sentinel vigilance is also reduced.

Senescence-associated mitochondrial dysfunction, a significant trigger of multiple dimensions of the senescent phenotype is caused by disruption of normal mitochondrial autophagy (mitophagy). Mitophagy increases with aging and this age-dependent rise is abrogated by PINK1 or parkin deficiency. Deletion of a p53 response element on PINK1 promoter impacts p53-mediated PINK1 transcriptional repression. This p53-mediated negative regulation of autophagy has been found to be PINK1-dependent and constitutes a p53-PINK1 loop in nucleus and cytoplasm.

Further, mitophagy controls the activities of tumor suppressor p53 to regulate, at least hepatic cancer stem cells via Nanog. Prostate cancer cells escape NK attack by Nanog down-regulating ICAM1 (LFA1), to which NK would normally bind its target. In lung cancer NK have been found to limit the efficient clearance of senescent tumor cells from the mouse lung after p53 restoration. This indicated p53 may promote conditions for cellular survival and NK induced vascular remodeling or angiogenesis, necessary for the growth of tumors.

When under stress and inner mitochondrial membrane pressure gradient moves toward depolarization, Pink1 slots into the membrane, binds and phosphorylates p53 at Serine 392 (p53s392) and aids phagophore formation to enhance mitophagy. Mitophagy traps cytoplasmic p53s392, which reduces its transport to the nucleus where it would otherwise disrupt transcription of Nanog. (As illustrated below). 
Activated p53s392 nucleoside concentrations are effected by mitophagy
On the other hand, the sentinel function of NK may be subject to this PINK1 mediated mitochondrial switch. In prostate cancer cells Nanog promoted ICAM1 transcription required for NK binding target and cell killing. In prostate cancer cells Nanog over-expression restricts ICAM1, which would promotes tumor formation. (As illustrated below). Investigating further, the direct functional link between p53 and ICAM-1 in senescence and age-related disorders appears to be deeply integrated in mitophagy, senescence and immunity.

Nanog over-expression appears to be deterministic 
In stem cells where normal expression of Nanog transcribes ICAM1 and cancer stem cells where over-expression of Nanog restricts ICAM1, the variable PINK1-p53 switch may represent a "canary" that signals the state of  mitochondrial health to sentinel NK. However in some cancer cells where normal mitophagy is impaired and Nanog expression is restricted by p53s392, other p53 isoforms may directly promote the transcription of ICAM1.

In  two manipulation experiments using five different fibroblast cell lines that accelerated development of senescent associated secretory phenotypes a striking result was observed: oncogenic RAS expression, which causes genotoxic stress and senescence in normal cells, and functional loss of the p53 tumor suppressor protein. Both loss of p53 and gain of oncogenic RAS also exacerbated pro-malignant paracrine signaling activities. Experiments show that PINK1 and Parkin, which are regulated by p53 specifically regulate mitochondrial antigen presentation of both MHC classes.

So, the question is whether the p53-PINK1 mitochndrial switch acts as cell-health "canary" for sentinel NK, where its inherent variables and regulatory loop may be fertile ground for the challenges of developing cancers? 

Thursday, December 19, 2019

Therapeutic Coding and non-Coding DNA Relationships

Relationships of coding and non-coding intra-gene DNA are good cause for intense research and scientific debate. Many cellular functions of non coding DNA have been discovered in the past 30 years, but prior to that these genomic regions were mostly considered 'junk'.

Probing relationships between a genes' protein coding, cDNA and at least one non-coding DNA section of the transcript, which in our work is intron1 can yield important data about genomic features in the combination. Over the past 7 years we focused on interrogating combination relationships, across multiple transcripts to construct intra-gene DNA signatures from apparently disparate DNA elements that are known to perform vastly different biological functions, yet are proximal and often adjacent.

First we considered codon to amino acid coding may operate a little different to the classical view if reading a first and second nucleotide made the third deterministic. This method would not alter the outcome of known protein coding, but it may alter the way we consider combination relationships between nucleotide's. For a transcript, any given length of cDNA and its respective intron1 sequence could possess undiscovered intrinsic order. In a model where order was tightly honored, transcript relativity may identify cDNA sequences that caused significant change in the order at each next nucleotide step.

To investigate transcripts, from the first nucleotide we computed every length cDNA k-mer. We associated k-mer's, of every possible length with the cDNA transcripts intron1 signature. Then, for a set of multiple same gene transcripts, in nucleotide order our algorithm ordered the transcripts into a vector based on their respective cDNA-kmer:intron1-signatures. Stepping through from one k-mer to the next we observed whether next k-mer significantly changed the order of transcripts in the vector. After filtering domino effects we ranked k-mers with the most significantly changed transcript order from the previous k-mer.  

Size of  circle 'K' in the example indicates k-mer length, but we only compare same length K

In the above example, it is evident that k-mer2 vs k-mer3 was the most changed because all three transcript positions moved without a domino effect. From the vector we identify intra:inter transcript conditions in next nucleotide relationships as represented in the k-mers. 

As an example, in our work with 15 viable consensus transcripts for p53 occasionally all 15 transcripts in the vector changed positions at the next k-mer. These intra transcript k-mer relationships govern the transcripts order in the vector, but when, at the next k-mer transcript order is relaxed and positions move, particularly where the significant majority of positions move it is indicative that the intra transcript k-mer condition is relative to other transcript k-mers in the vector. The more and the further transcripts move positions in the vector the more relevant their intra transcript k-mer relationships are likely to be to gene.

This transcript comparative presents a new method for diagnosis and therapy because each new transcript, when compared to the consensus set has the capacity to disrupt order in the vector and yield k-mers that are specifically relevant to the gene. In our assay testing we were able to predict and synthesize ncRNA sequences that significantly reduced proliferation of HeLa cells. In our pre-clinical work, based on comparisons to transcripts of the TP53 consensus we will be predicting the efficacy of cell and tissue selections that educate and activate Natural Killer cells.

Pre-clinical flow chart to educate NK cells with tumor tissue/cell co-cultures and prove prediction


Monday, November 25, 2019

Synapses By p53 And CD40L in Reproduction and Immunity

Cell membranes constitute a diverse range of lipid molecules each attached to a varying, odd or even length hydrocarbon chain (a tail) that, collectively pack together to form a membrane. Packing is a dynamic that generally occurs according to surrounding pressure, concentration, hydrophobic conditions and motion. The mix of molecules and their hydrocarbon chains in each membrane play a crucial role in determining functions of complex organisms in cells.

Two complex membrane bound organisms of eukaryotic cells are mitochondria - primary provider of ATP energy powering reactions of the cell and endoplasmic reticulum (ER) - protein folding organelle surrounding the nucleus. The mitochondria comprise a double membrane containing electron transport chains - sets of four membrane bound proteins which pump protons between inner and outer membranes to maintain optimal inner mitochondrial membrane pressure through which oxygen is metabolized into water by phosphorylation of ADP to ATP molecules, which are the basic energy unit of the cell.

ER is a convoluted extension of the nucleus membrane into which translated amino acids are transported and where they fold before being released and packaged in the golgi apparatus and cytoplasm. The process of translation, folding and transport requires significant energy as such mitochondria and ER are closely associated. Recently and for the first time C18 ceramide transportation between ER and outer mitochondrial membrane was described as a cellular stress response mechanism.

Another important membrane lipid C16-ceramide was found to tightly bind within the p53 DNA-binding domain. This interaction was highly selective toward the C16 ceramide acyl chain length with its C10 atom being proximal to Ser240 and Ser241. This binding stabilized p53 and disrupted its complex with E3 ligase MDM2 leading to the p53 accumulation, nuclear translocation and activation of downstream targets. The p53-MDM2 axis has been extensively covered in previous articles describing allorecognition, reproduction, immunity and auto-regulation. Ser241 was the only residue that interacted with all three p53 DNA sequences (p21, puma and a non-specific DNA system) persistently, indicating that Ser241 is a [response element] sequence-independent H-bond donor/acceptor for DNA.

It was also determined that Folate stress induces apoptosis via p53-dependent de novo Ceramide synthesis and up-regulation of Ceramide synthase 6 [C16], which is a transcriptional target of p53. In particular, Folate metabolism affects ovarian function, implantation, embryogenesis and the entire process of pregnancy. We observed that folate withdrawal leads to CerS6 up-regulation and C16-ceramide accumulation in a p53-dependent manner as a pro-apoptotic cue.

It has been demonstrated that clustering of the CD40 receptor depends on reciprocal clustering of the CD40 ligand, which is mediated by an association with p53, a translocation of acid sphingomyelinase (ASM) to the cell membrane, activation of the ASM (enzyme for ceramide), and a formation of ceramide. Ceramide appears to modify preexisting sphingolipid-rich membrane microdomains to fuse and form ceramide-enriched signaling platforms that serve to cluster CD40 ligand. Genetic deficiency of p53 or ASM or disruption of [C16] ceramide-enriched membrane domains prevents clustering of CD40 ligand. If the ligand is membrane-bound, the contact site between clustered ligands and receptors forms an immune synapse.

Finally, immune activation during the implantation phase causes preeclampsia-like symptoms via the CD40–CD40 ligand pathway in pregnant mice. The CD40 ligand (CD40L) is expressed by T cells and has a critical role in immune system regulation. Interventions targeting CD40L interactions following embryo implantation represent an approach to preventing preeclampsia (PE).

Here we have demonstrated a relationship between p53, C16 ceramide in reproduction and immunity via CD40 receptor-ligand in membrane bound concentrations of cells, particularly in respect of immunological synapse formation and blastocyst implantation. This further supports the notion that immunity and reproduction share common innate origins linked by p53.

Saturday, September 28, 2019

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.

Wednesday, September 4, 2019

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 has enabled them, at the front line of reproduction to interact with incoming trophoblasts that invade the uterine wall where NK cells perform functions that 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 mechanisms 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 which 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.

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.

Tuesday, July 16, 2019

Natural Killer Shaping A Life

As explained in previous posts, reproduction and innate immunity conspire when maternal Natural Killer (NK) cells of the decidua, lining the uterine wall are coerced to attack maternal epithelial cells, lining spiral arteries that penetrate the decidua to supply nutrients into the rapidly forming placenta. The culprit, extravillous cytotrophoblasts that originate from the external wall of the blastocyst, penetrate the decidua and replace disrupted maternal epithelial cells of advancing spiral arteries. This rejection paradox by the maternal innate immune system, of the foreign male contribution to the blastocyst is mitigated by its trohphoblasts that enable maternal-fetal interface and blastocyst implantation. By day 7 life begins, at least through the handshake of maternal epithelial cells and fetal trophoblasts thus transforming rejection to inception.

Maternal NK enable extravillous cytotrophoblasts to converge with epithelial cells of spiral arteries
Decidual NK constitute 70% of lymphocytes up to the first 20 weeks of pregnancy. They are characterized by their low cytotolytic capacities, but adequately secrete cytokines, chemokines and angiogenic factors. As of 2018 it was unknown as to the effect of these decidual NK cells on earliest stages of pregnancy or how they may transform in context of the developing placenta. As previously discussed allorecognition by decidual NK cells is emerging as the key maternal-fetal immune mechanism that ultimately regulates placentation and that immuno-metabolism played a more significant role in NK activation and cellular transformation.

Single cell analysis at the Fetal - Maternal interface 
Studies of maternal microchimerism suggest that cell's and DNA transferred from mother to embryo can be traced and are prevalent in chord blood. These include NK cells that have been demonstrated to persist following re-transplantation of chord blood. Inferred in these findings, maternal microchimerism's, specifically NK cells transferred at a very early, even in single cell quantities may influence the earliest development of fetal immunity. Indeed at 6 weeks the earliest fetal NK cells are detected in the liver and tend to possess lower lytic potential a characteristic similar to decidual NK.

Maternal decidual NK cells that transfer into the developing placenta probably remain less cytolyic. Given the active environment they may even be metabolically exhausted, but are still capable of lytic activity and could play a critical role eliminating aberrant cells of the rapidly developing embryo. Further this activity could also educate fetal NK cells that start to develop from 6 weeks. Because this exposure occurs during early development of the fetal immune system, the primary response is to develop allospecific tolerance to maternal antigens.

A new concept is emerging in that the uterine immune system uses NK cell allorecognition to regulate placentation and to control the maternofetal interface. The jury is still out on microchimeric influences including exosomes, DNA and whole cells that transfer between mother and fetus. However, it seems entirely plausible that maternal immune cells may do much more than we presently know to shape conditions and determine cells of the fetus.

Our research interest relates to p53 peptides presented by MHC class receptors on targets of NK cells. We maintain the well conserved phospho-acceptor sites of p53 protein in axis with MDM2 is central to immunity and allorecognition. It is known that p53 plays an important role in blastocyst implantation and maternal reproduction through regulation of leukemia inhibitory factor (LIF) in mice. We expect p53 peptides, influenced by transcription regulatory factors determine outcomes of immune-target reactions including blastocyst implantation. Further that TP53 transcription can be triggered in a target by NK allorecognition nano-probe at a distance resulting in target p53 peptide presentation by MHC as NK's go-no-go cytolytic tipping point for immunity.

Sunday, May 26, 2019

The Deep Data of Cell Selection.

We identified 16 DNA sequences, each comprising 28 nucleotide's from 15 TP53 transcripts, each comprising ~10,000 intron1 nucleotide's and an mRNA isoform. To make the identification we computed and analyzed relationships between more than 225,000 derived sequences for each transcripts ~10,000 intron1 nucleotide's and mRNA with the same for each of the 15 transcripts.

During analysis we first discovered shorter (than 28 nucleotide) sequences, iterated from the same sequence start position in each transcript and compared them by using a highly ordered vector. The order of the sequences, for each of the 15 transcripts in each vector was compared with the vector computed for the sequences at the next start position. The final selection of shorter length sequences were made from sequences at the most disordered vectors. From these sequences we identified any consecutive 28 nucleotide's, from intron1 of all 15 TP53 transcripts that fully incorporated more than one of these shorter length sequences, no less than 8 nucleotide's.

In each of the 16 DNA sequences, 4 or 5 (complex) shorter length sequences were discovered in their  identical nucleotide combinations suggesting a broad sequence affinity with these shorter length intron1 sequences.

We ran a series of 8 sequence alignment tests to determine whether there was anything special about the 16 DNA sequences of length 28 and the shorter sequences used to identify them. Each test used an algorithm to optimize the ordering of the sequences according to a sort score. This score assigned points to each A|T|C or G character that was aligned with the next of the 16 length 28 sequences or the next sequence of any length in the ordering. Each of the 8 tests varied the points weighting assigned to the length 28 alignment, while points assigned to the next alignment were kept constant. This was expressed as a ratio but left un-normalized. As a control we scrambled the ordering of the letters in each sequence and applied the same algorithm to optimize for a sort score, obtaining the following results.

Scoring Ratio (L28:Next)
Sequence Score
Randomized Score

8 organizations of 16 x 28 oligonucleotide sequences and shorter lengths
The order bias toward Sequence Score (resulting from our selection process) is evident in the chart and numbers above. It indicates that the 16 identified DNA sequences and those used to select them have better alignments than the random alternatives. In previous randomization studies we determined the vector performs similarly against two methods of randomization's which are described in detail at the link.

These methods form part of our neural network initiative and will be used during the process of cell selections for autologus immune therapy using patient derived Natural Killer cells.