STABILITY 🔀⏩️LIFESPAN

 STABILITY 🔀⏩️LIFESPAN

 

The lifespan of objects in the universe is dependent on the stability of its unit ©2023 akshay Sanghavi 

 

All matter moves towards stability.

 

Atom is more stable when it is in a lower energy state and so it tries to move towards the lesser energy state.

 

 Unstable atom isotopes will spontaneously decay and change to another more stable element. The rate of radioactive decay is inversely proportional to the stability of the isotope. Radon-222 has a half life of just 4 days so every 4 days it will reduce to half. Which creates the spontaneous move towards a more stable form. Universal law of survival: a stable atom can exist for billions of years. Xenon-124’s half life is 18 billion trillion years. Despite its incredible lifespan and stability, it’s not immortal: it will also eventually die and turn to tellurium-124. 

 

Atom of Xenon-124 from Descopera.ro

 

I have been thinking about the different lifespans of biological species on our planet. My fascination and desperate curiosity to unravel the mystery of variable lifespans has obsessed me with constantly researching the potential causes. I have been sharing my findings in some of my previous posts like Mechanism of Aging, Headwaters, Autologous Regulation and Agents of Time. In the last few posts I have shared the realization that a cell’s destiny is strongly linked to regulatory changes enforced by regulators like non coding RNAs. Of course, there is incredible complexity to this process. Nothing else on this planet has brilliant, complex, autonomous engineering like our biology. But can there be one simple factor behind the variance that we see in the lifespans? It’s not size for example as the exceptions demonstrate. My mind is blown by the study by Professor Richard Dixon on Ginkgo Biloba tree. So much that it features in all my longevity related posts since it was published. If these hardcoded transcription plans are making deliberate changes starting after puberty setting off a cascade that ends in death, then how did Ginkgo Biloba make adaptive changes to bypass such a universal recycling mechanism of Nature? Professor Dixon called it almost immortal. The best part is that not only is it almost immortal but it’s almost immortal in a youthful state! Who wants to live a thousand years looking like shrunken bag of bones and crumpled skin? So, what is this one single cause of lifespan variance? We will arrive at that after some more deliberation. 

 

As we read in a paper by Morimoto and Labbadia called ‘Repression of the heat shock response is a programmed event at the onset of reproduction’ that just after puberty there is a change that reduces the ability of chaperones, that are key to the protein production process in our cells, by 60%-70%. This results in higher number of malformed proteins. This starts a cascade of many other drops in important functions in the cell and these drops snowball making us age. For example, as we read in Agents of Time, the debris of the 450 billion cells that die every single day in our body is cleared by phagocytes. But thanks to various regulatory changes and their ensuing cascades their mitochondrial batteries begin to fail them. This leads to accumulating number of sharp debris that enters cells and causes 1 quadrillion double strand DNA breaks everyday! In this chain of events germline cells triggered epigenetic changes that resulted in the fall of efficiency of protein production chaperones. What if these epigenetic changes were not allowed to be made or after they were made they were ‘repaired’ back to their original epigenetic configuration. In order to prioritize reproduction the germline stem cells trigger epigenetic repression of heat shock proteins which act as chaperones to support protein production and as stress response. When we get a hurt while playing sports the injury is repaired over a period of time. What if similarly the epigenetic mark that germline stem cells make after puberty is demethylated or removed to restore back the full strength of heat shock proteins? That would stop the chain of events that eventually cause so many double strand DNA breaks every day. Just to demonstrate how this cascade snowballs when those breaks keep happening in the DNA, even though almost all are repaired, they succeed in creating roadblocks in the hurtling train of transcription in our DNA. This than has serious repercussions as many transcription programs get blunted. In the Agents of Time blog another change causing aging is mentioned wherein our long, coding and noncoding, transcripts begin to fade. The authors of the cited paper also mentioned that these longest transcripts were activating prolongevity genes. Thereby repressing or silencing the genes associated with making us live longer. So when we prevent or significantly reduce the huge number of double strand DNA breaks we restore smooth transcription and thereby prevent the loss of longer transcripts and silencing of longevity genes. Do you see where this is leading us? 

1,400 year old Gingko Biloba Tree

 

The mechanism that Ginkgo Biloba tree has figured out is probably how to keep its epigenome stable! We are a collection of cells and all cells have the same DNA and yet they are transformed into 200 types to form eye and stomach and liver and skin etc. The DNA is the same but each type of cell has its own configuration of epigenetic marks on its DNA. These marks do not change the DNA physically but result in silencing majority of the genes and activating only the10%- 20% that transform it into its type of cell.  Around puberty we achieve our homeostatic peak where all our systems are working at their best. But due to the changes mentioned above we experience what is called as ‘epigenetic’ drift where the beautiful epigenetic configuration found around puberty is slowly changing leading to unwanted genes being activated and wanted genes becoming silent. This epigenetic drift manifests into what we know as aging. The Ginkgo Biloba tree does not seem to succumb to this epigenetic drift which can be seen in almost all multicellular life forms leading to cell nuclear instability that slowly grows into cellular, tissue and organ instability. In a fascinating paper titled ‘Multifeature analyses of vascular cambial cells reveal longevity mechanisms in old Ginkgo biloba trees’ by Professor Richard Dixon and Dr. Jinxing Lin et.al. the authors try to reveal the longevity mechanisms of Ginkgo Biloba trees. The table below shows the miraculous stability of really old Ginkgo Biloba trees:

The authors selected nine trees for further study and divided them into three groups: 20 y (15Y, 20Y, and 22Y, young trees; VC20), 200 y (193Y, 211Y, and 236Y, older trees; VC200), and 600 y (538Y, 553Y, and 667Y, oldest trees; VC600). Below we can see the comparison of the average leaf area, seed germination rates, efficiency of stress resistance, photosynthetic capacity and chlorophyll content of the 3 groups:

 Ginkgo Biloba Trees Comparison of 20 year olds, 200 olds and 600 year olds

 

Unlike almost all plants and trees that grow old and die Ginkgo Biloba’s environmental stress resistance, photosynthesis capacity, autophagy, sexual fertility and immune defense doesn’t drop with age! It’s cambial cells equivalent of our stem cells remain active even in oldest trees in the group but tempered with reduction in cell division, expansion and differentiation allows it to remain young without any uncontrolled growth or senescence. In human aging we begin to lose stability of the epigenome and our transcription track and its machinery leading to loss of beneficial genes and activation of unwanted genes. The exact opposite is happening with Ginkgo Biloba tree. In the same paper authors compared around 27,500 genes of the three groups: 20 year old, 200 year olds and 600 year olds there was only 4.4% difference in gene expression between the young trees and the older trees! How does Ginkgo Biloba tree maintain such stability of its epigenome, transcription, gene and protein expression???

This kind of beneficial stability is quite different then the longer lived species: the latter like Naked Mole Rats or Bowhead whales have some protective genes that are overexpressed even in old age. That does give longer than average life span associated with their species but they do grow old and die. Whereas Gingko Biloba trees seem to live forever in youthful prime. 

 

As I had shared in my post Mechanism of Aging, Nature manages optimum levels of various activities and functions in our biology by the triage of activators and inhibitors and sensors. This works like a tap of hot water and cold water and a thermometer. Equilibrium is when taps are turned just the right amount to create ideal temperature of water. Any disturbance in this ratio can cause either too hot water or too cold water causing damage. In our prime, just after puberty, we enjoy optimum equilibrium or homeostasis between the activators, inhibitors and sensors. But soon after starts the slow offsets in this balance leading to all the accumulation of unrepaired damage and nuclear instability which manifests as age related changes. We can see and feel this happening especially after our 50s but since it’s not overnight and since we see others too showing similar negative changes we accept them. Ginkgo Biloba has been around longer than us: for more than 270 million years. Whereas we humans have been around only 200,000 to 300,000 years. Ginkgo Biloba has had 270 million more years to win the adaptation lottery. We humans too have won another genetic lottery: of higher intelligence that is compounding rapidly like an umbrella curve. We are developing great technologies and tools like CRISPR and AI and will soon figure out how to safely inculcate stability in our epigenome and nucleus. Then we too will have the option to live for thousands of years in the prime of our youth. Every known thing in observable universe seems to be recycled. The stars too die and leave behind a super dense spinning ball with no fusion or light just fading heat. These white dwarfs or neutron/pulsar remnants and planets and their debris all get recycled by black holes. All of the galaxies are probably held together by the gravitational pull of the super massive black hole at their core. This central black hole eventually will eat up the entire galaxy and break it down into fresh units of matter and radiation and spew them out as astrophysical jets long distances into space. So all the different bodies in a galaxy are broken down to sub atomic particles in the intense gravitational crush of the super massive black hole and slowly recycled into basic units of matter and radiation which then forms new stars and planets. So to outwit such a pervasive norm of recycling in the universe is a phenomenal achievement of Ginkgo Biloba. 

Super massive black hole spewing recycled matter and radiation deep into space. By Newsweek. 

 

Has Ginkgo Biloba developed some technology based in the futuristic world of science fiction? No. We see some mindblowing processes in biology all around us. During early embryogenesis there is global epigenetic reprogramming. For example in male embryos 96% of the methylation is wiped out to clear all accumulated errors from parents and later globally re-methylated as per template to create a brand new error free baby. This is the reason why Nature has created a program of aging so that continuous recycling will ensure cleaning out of errors every generation. So such an all encompassing and powerful epigenetic reprogramming technology is already being used in every embryo. Second technology is of self repair. Everyone of us would have got various degrees of hurt as a child while playing and see how over a few days or weeks it’s fully healed. Third technology is seen in some reptiles that regrow limbs even after they are fully severed. So biology already has some incredible engineering technologies to reset and restore any disturbance back to its optimum configuration. Can these technologies be harnessed to restore any erosion in our epigenome so that after every disturbance, whether it is stochastic or programmed, the epigenome is reset back to its optimum, youthful pattern? 

To understand the cause of nuclear and cellular instability further let us borrow from my last post Agents of Time: We read that Aging is associated with loss of longer transcripts including long non coding RNA: https://www.nature.com/articles/s43587-022-00317-6

Plus they found: ‘we find that in humans and mice the genes with the longest transcripts enrich for genes reported to extend lifespan, whereas those with the shortest transcripts enrich for genes reported to shorten lifespan’

This is one of main reasons why longer transcripts fade away with aging:

https://www.nature.com/articles/s41588-022-01279-6

‘The drops were not due to drop in promoter activity or drop in RNAP II activity. Even the launch of transcription was unaffected. The authors postulate that DNA breaks interrupted and stalled transcription – and as longer genes/transcripts have greater chances of being broken somewhere they can be the primary cause of their reduced transcription during aging.’

A recent paper gives us glimpse of one of the ways this loss of long non coding RNAs cause the damage to tissues and organs during aging:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10834948/

“LncREST localises to chromatin (the structure in which DNA is organised in the cell). Its main function is to facilitate the localisation of key proteins in the process of DNA replication and DNA damage repair where they are needed. In fact, the absence of lncREST has been shown to cause impaired stress signalling, leading to the accumulation of severe DNA defects and, ultimately, cell death“

A few deliberate changes like the sudden massive drop in heat shock chaperone efficiency just after puberty start this cascade of errors leading to the instability of epigenome, genome, nuclear architecture and the cell. If these errors can be stopped/repaired as soon as they occur we too can’ live forever’ in youth like the Ginkgo Biloba tree. E5 does this partially by feeding older cells and its nucleus suffering from epigenetic drift with regulatory workers like longer transcripts from a youthful system that fill in some of the gaps or missing pieces in the old cell/nucleus. This restores the broken epigenetic pattern partially back to its original template. The amazing part is that old, damaged cells bounce back to youthful healthy fitness once it’s epigenetic pattern is reversed closer to its optimum design. This is a safer engineering intervention than any that needs the cell to move towards pluripotent state. As it creates a fluid epigenetic state which can lead to tripping into loss of cell identity and loss of controls which can result in development of cancerous growth. The idea is to create stability in the epigenome not fluidity.

We already have the engineering peak around puberty where our biology works beautifully. But there are a thousand negative changes that occur as we age. We have to now learn how not to slip into the epigenetic drift and to keep our cell stable at its homeostatic peak as long as we want. Ultimately, we want to install a Ginkgo Biloba type of mechanism that restores the cell and its nuclear architecture after any disturbance. The secret to long youthful lifespan is achieving long lasting nuclear stability after reaching adult biology. We just have to observe the Universe to unmask this secret. Stability is the difference between a lifespan of 4 days and 18 billion trillion years. 

 

 

AGENTS OF TIME

 AGENTS OF TIME

 

Human biology is finite and yet so incredibly complex. We are constantly surprised by new components and systems being discovered. So far we relied on ‘Hallmarks of Aging’ as a reference for what all changes in us with aging but there have been a flood of papers recently that go much more deeper or upstream, closer to the source of these macro changes. They are giving us another perspective on the changes occurring in us with aging.

All of them not only sit very well with but also embellish what I shared in my two previous posts: Headwaters and Autologous Regulation. 

So let’s go over some of them here:

Cell-free chromatin particles from dead cells accumulate in our plasma and cut DNA in healthy cells making 1 Quadrillion double strand DNA breaks everyday in each of us as we grow older!

https://www.nature.com/articles/s41598-022-21388-w

A Shocking discovery of how shrapnel from exploding dead cells cause Double Strand DNA fractures in healthy cells and a simple oral supplement may protect against that. 

Dr. Indraneel Mittra is a brilliant scientist and a cancer surgeon with Tata Memorial Center for cancer research. He worked against all odds for 20 years to confirm, with evidence of 150,000 volunteers, the importance of regular low cost screening for breast and cervical cancers thereby saving lives of millions of women. Recently he was perplexed by the very high occurrence of double strand DNA breaks in our cells: 10 to 50 per cell per day! These DDBs are constantly repaired to maintain the viability of the cell but any error leads to cell death or worse cancer. So he and his team began to investigate the cause. They were surprised by what they found. Every day around 450 billion cells die in our body (our body is a collection of avg 33 trillion cells). This huge number of dead cells leave fragments or debris which circulates in our blood. Phagocytes work relentlessly to ‘eat’ this debris and digest it - clear it. But Dr. Mittra found that cell free chromatin particles released from the dead cell fragments enter healthy cells and cause double strand DNA breaks which basically snaps both the strands of the DNA. He found that the plasma consists of large quantities of these dangerous bullets circulating all across our bodies as we age they inflict dsDNA breaks, activate apoptotic pathways and induce inflammatory cytokines. This could be one of key causes of rising chronic inflammation during aging. Chronic inflammation is a precursor to most of our mortal diseases. Their group has successfully isolated and characterised cfChPs from human serum, which upon EM examination revealed extensive size heterogeneity ranging between ~ 10 and ~ 1000 nm13. They have also reported that blood levels of cfChPs increase with age. No surprise there. This is a BIG discovery! Dr. Mittra hypothesizes that the that lifelong assault on healthy cells by cell- free chromatin particles or cfChPs is the underlying cause of aging. Again a very major discovery if it turns out to be true. I personally do not fully attribute the circulation of these dangerous particles as the cause of aging because I am sure in the young, healthy body they can be more or less cleared by our amazing phagocytes. What happens with aging is that the efficiency of the phagocytic cells goes down which would leave accumulating amounts of this harmful circulating debris. An example of why phagocytes may lose their efficiency is the disruption of mitochondria seen in aging. Phagocytes especially require huge amount of energy provided by the mitochondria. Here is a paper on that: https://www.cuimc.columbia.edu/news/change-mitochondria-critical-clearing-dead-cells

Regardless of whether cfChPs are the cause of aging or result of aging Dr. Mittra also found that just by taking a combination of resveratrol and copper in a particular ratio one can drastically reduce the cfChPs and in his experiment he saw reversal of many key pathologies of aging. Basically this combination which is absorbed from the stomach after an oral pill generated oxygen radicals that degraded cfChPs. I always like to share some way one could intervene against age related damage whenever something was available. Dr. Mittra’s lab found that oxygen radicals that are generated upon oral administration of R–Cu are apparently absorbed from the stomach to have systemic effects in the form of deactivation/eradication of extracellular cfChPs. In that  study they have taken advantage of cfChPs deactivating property of R–Cu to investigate whether prolonged administration of R–Cu to aging mice will retard the hallmarks of aging and neurodegeneration. The dose of Resveratrol used in our study was 1 mg/kg, and that of Copper was 0.1 μg/kg, given by oral gavage twice daily. This dose of Copper was 20,000 times less, and that of Resveratrol 5 times less, than those that have been used in pre-clinical studies to investigate their health promoting properties by other investigators.

Using confocal microscopy and antibodies against DNA and histone they detected copious presence of extra-cellular cfChPs in brain of aging mice, and observed that cfChPs were deactivated/eradicated following prolonged oral administration of R–Cu. Deactivation/eradication of cfChPs was associated with down-regulation of multiple biological hallmarks of aging in brain cells. At a systemic level, R–Cu treatment led to significant reduction in blood levels of glucose, cholesterol and C-reactive protein. Such a combination in the ratio discovered by Dr. Mittra can be an inexpensive, non-toxic solution which can be easily incorporated into our daily supplement regimen.

 

Global loss of Heterochromatin and disorganization of nuclear architecture in aging

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3414389/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253059/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8673774/

During youth DNA is tightly packed in heterochromatin but in aging we see rising disorganization in the heterochromatin leading to loosely packed DNA and aberrant transcription of silenced genes. We have 200 types of cells but to create a particular type of cell and maintain that identity nearly 80% of the DNA needs to be permanently silenced and made inaccessible in tightly packed heterochromatin. Aging causes global disorganization of chromatin architecture. Disruption of nuclear lamina/INM proteins and decondensation of associated heterochromatin are common features of normative aging. This initially leads to transcription of genes that should not have been transcribed and later leads to loss of cellular identity causing pro inflammatory secretions and loss of function. Nuclear envelope dysfunction leads to alterations in nuclear transport, chromatin organization, and telomere maintenance and  are correlated with nuclear protein alterations, namely nucleoporins, nuclear transport factors, lamins, INM proteins, chromatin‐associated factors, histones modifications, and sheltering complex proteins, revealing that NE proteins are essential determinants of aging. There are also morphological changes that are observed of the nucleus. For example in the young the nuclear periphery is smooth but over time, an increasing number of nuclei started to show a rather convoluted nuclear periphery, with multiple folds. As we grow older we see nuclei that showed increasingly abnormal shape and/or extensive stretching and fragmentation. 

 

 

Lipotoxic accumulation of lipid droplets in cellular nuclear compartments during aging

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10086520/

The authors say: Age‐dependent deterioration of lipid metabolism and nuclear morphology are common features in evolutionary divergent organisms. Nuclear lipid droplet (nLDs) deposition and LMN‐1/LMNA accumulation lead to cellular dysfunction and, subsequently, to tissue homeostasis collapse, with age. Nothing is kept by Nature and evolution without a purpose. Nuclear lipid droplets would have beneficial functions during embryogenesis, development and youthful homeostasis but during aging they begin to accumulate abnormally within the nucleus causing lipotoxic and mechanospatial damage to nuclear compartments and membrane. The authors found that longevity interventions like fasting and inhibition of IGF-1 reduced such lipotoxic burden. They also examined long lived nematodes and found some commonality with longevity mediation. HLH-30 is a crucial regulator of autophagy and it was found to reduce lipid accumulation in the nucleus in both cases. Specifically an enzyme ATLG-1 which is transcriptionally regulated by HLH-30 maintains lipid droplet homeostasis in nuclear compartments. ATLG-1 deficiency is seen in aging cells of normal worms but not in long lived works and is also upregulated during longevity interventions like fasting in normal worms. This interesting research paper shows how we could investigate further upregulation of ATLG-1 during aging by a natural extract called Oridonin: https://www.nature.com/articles/s41419-023-05613-6

Another deficiency they found in patients suffering from metabolic syndrome is deficiency in Phosphatidylethanolamine PE. Supplementation of PE or Oridonin led to restoration of lipid homeostasis by activating LXRa which in turn activated ATLG-1 and another enzyme EPT-1.

The loss of cellular bioelectricity and polarity in aging

https://www.sciencedirect.com/science/article/abs/pii/S1568163712000992

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896621/

A fundamental need of our cells is bioelectricity otherwise it would shut down just like any mobile phone when batteries run out. Similarly cells in our body progressively loose polarity as we age (or during cancer and disease). Polarity is important for the spatial organization of a cell. We read above what happened when a tight, stable configuration of heterochromatin and nucleus becomes loose and unstable in aging and the damage it can cause. So cell polarity plays an important role in maintaining that tight configuration. 

https://journals.biologists.com/jcs/article/121/8/1141/30524/Cell-polarity-and-cancer-cell-and-tissue-polarity As this paper adds to new evidence that restoration of cell polarity may differentiate the dedifferentiated cancer cells and normalize them. As we age we lose proteins that support bioelectrical

 generation and cell polarity. This leads to the fading of both and  further leading to eventual loss of the cell. 

Cell transcription speed increases with age and leads to more errors in transcription

https://www.nature.com/articles/s41586-023-05922-y

A very interesting paper by Andreas Beyer et. al. Shows us that Transcription of genes is fast but sloppy with age. Six research groups from the University of Cologne Cluster of Excellence on Cellular Stress Responses in Age-Associated Diseases (CECAD), the Max Planck Institute for Biology of Aging (MPI) in Cologne and the University of Göttingen discovered a new molecular mechanism that contributes to ageing by studying the transcription process in five different model organisms and in a wide variety of tissues. 26 scientists investigated genome-wide, age-related changes in transcription processes in nematodes, fruit flies, mice, rats and humans, including diverse tissues. And they discovered that the average speed at which the transcript grows through the attachment of RNA building blocks, the nucleotides, increased with age in all five species. With this increase in the speed of transcription they also saw increase in transcriptional and splicing errors. They observed that increase in transcription speed led to decrease in unspliced exons and intron retention. Basically increased splicing and splicing errors were seen with aging. In my previous blog post Headwaters I have written about how transcription is the beginning of the cascade of biological changes through out our life. So errors in transcription and splicing leads to multiple missexpression of genes which would further lead to cell, tissue and organs becoming impaired and diseased as we see with progressive aging. The authors also found that  calorie restriction and inhibition of IGF signaling led to slowing down of transcription speed and corresponding reduction in errors. This also extended their lifespan. Another finding shared by the authors was that overexpression of histones led to reduction transcription speed and increase in lifespan. Also the genes affected were not completely random, as they observed consistent changes across replicates for a subset of introns. As the speed increase in transcription and rise in errors in splicing are global and occur in all 

the 5 species including humans studied by the authors and they are not random one can conclude that these age related changes 
are encoded in our DNA deliberately causing the biological  deterioration we see during aging. 

 

Changes in plasma extracellular vesicles, volume and content, with aging

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430958/

Cells release lipid-bound extracellular vesicles (EVs; exosomes, microvesicles and apoptotic bodies) containing proteins, lipids and RNAs into the circulation. Vesicles mediate intercellular communication between both neighboring and distant cells. Here the authors analyzed circulating plasma EVs in a cross-sectional and longitudinal study in order to address age-related changes in circulating EVs. They found that EV concentration decreases with advancing age. They also observed increased internalization of EVs by B cells which are immune cells. They found more tumorigenous surface proteins and cargo with age and also more misfolded proteins as cargo. Loss of proteostasis is also cited as a reason by the authors for the reduction of circulating secretome in aging. There are some papers that mention the opposite by showing how EVs increase with age. They cite increase in senescent cells and their EVs increasing the overall volume. But these are harmful EVs and carry cargo that leads to turning an healthy cell into a senescent cell a little like Zombies. That may not change the fact that secretome from healthy cells may decrease with age. 

Another paper: 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7811845/

Sort of corroborates this. The same authors of the paper cited above Eitan et. al. state in this paper that

 They examined whether mtDNA (mitochondrial DNA) can be detected in human plasma EVs and whether mtDNA levels are altered with human age. They found that Plasma EV mtDNA was significantly and negatively associated with age in their cross‐sectional analyses. Basically mtDNA in EVs reduced with age. Did this have any consequences? To determine whether age‐related changes in plasma EV mtDNA affect mitochondrial function, they pooled EV populations of young and old EVs and measured the cell’s respiration rate. They found that cells treated with young EVs had significantly higher levels of both basal and maximal respiration compared to those cells treated with old EVs. So the reduction of mtDNA in EVs in aging did hamper mitochondrial functions. 

 

Longer transcripts decrease with age and shorter transcripts increase with age

https://www.nature.com/articles/s43587-022-00317-6

This has been one of the most interesting papers recently in the aging research field. Not only did they find that longer transcripts seem to fade away as we age and shorter transcripts seem to be of higher abundance but they also found the correlation of longest transcripts with pro-longevity genes and shortest transcripts with genes reported to shorten life. 

https://www.nature.com/articles/s41588-022-01279-6

This paper by Joris Pothof et.al. also finds in old mice (2year old) liver cells that there is 40% drop in transcription. This change was pronounced especially in longer transcripts. They did not find any changes or drops due to drop in promoter activity or drop in RNAP II activity. Even the launch of transcription was unaffected. They postulate that DNA breaks interrupted and stalled transcription – and as longer genes/transcripts have greater chances of being broken somewhere they can be the primary cause of their reduced transcription during aging. If we see the first listed change in aging in this post it is talking about rising Double Strand DNA breaks due to cell-free chromatin shards from dead cells which explains why the authors found a 40% drop in transcription. This may also explain what we read above where transcription errors increase with age. Breaks in DNA could stall transcription or create an error in transcription. 

 

 

The role of retrotransposable elements in aging

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8600649/

There is an on going war from 100s of thousands of years within us. It’s not just against outside pathogens and parasites but also against parasites that have virus like capabilities that have inserted in our genome – not just our genome but it seems in all living life forms-in a big way. These foreign invaders that have made our genome their permanent home since the dawn of life are called Transposons. Scarily they also have the ability to fly from one genomic location to another and insert themselves there. Transposons belong to two main groups: those that move using a DNA intermediate (‘DNA transposons’) in a ‘cut and paste’ mechanism, and retrotransposable elements (retrotransposons) that move using a ‘copy and paste’ mechanism that involves an RNA intermediate. Thirty five percent of the human genome is comprised of retrotransposon DNA sequence! Retrotransposons are further divided into Long Terminal Repeat (LTR) elements, derived from exogenous retrovirus infections, and more primitive and ancient non-LTR elements with an obligate intra-cellular life cycle. Non-LTR retrotransposons consist of two main groups: the Long INnterspersed Elements (LINEs), which encode their own proteins necessary for retrotransposition, and the Short INnterspersed Elements (SINEs), which are short, non-coding RNAs that hijack the LINE protein machinery. Our original genome continues to build tools and mechanisms to silence these elements and the transposons keep trying to outrun them. Both try to outsmart each other but also coexist and adapt from each other. A retrotransposon onslaught can be profoundly deleterious and hence the germline is guarded with multiple defenses. Host defenses are highly effective, and hence the majority of retrotransposons in our genome are passive passengers, slowly accumulating mutations, deletions or other rearrangements. While some older elements can still affect host function through cis-acting gene regulatory or recombinational mechanisms,  the deleterious effects of retrotransposons increasingly being linked with aging appear to be largely dependent on the activities of their encoded proteins, and fall into three general mechanisms: genetic and epigenetic effects associated with retrotransposition, DNA damage associated with active or abortive retrotransposition, and activation of immune pathways associated with detection of retrotransposon nucleic acids. One of the key defense mechanisms is heterochromatization which represses these elements. The other retrotransposon silencing mechanism is through methylation. Our genome has proteins that activate these repressive mechanisms on transposons. One example is KRAB domain containing Zinc Finger proteins or KZFPs. KZFPs, of which there are over 400 in the human genome, co-evolve with retrotransposons as part of an ongoing ‘arms race’. Many of these KZFPs bind to retrotransposon elements in the genome and promote their heterochromatinization via the recruitment of KAP1.  Retrotransposons mutate to avoid this surveillance, and the host organisms evolve variant KZFPs that can again repress the new generation of retrotransposons. Other such transposon surveillance and repression elements are siRNAs and piRNAs, we have CRISPR like RNA editing enzymes like APOBEC and ADAR, MOV10, BRCA1, SAMHD1 and TREX1. 

Some of these factors are defenses against exogenous viruses and act by diverse mechanisms such as editing of viral/retrotransposon genomes to mis-code the protein sequences (APOBEC), decreasing nucleotide triphosphate pools to limit viral/retrotransposon cDNA synthesis (SAMHD1) or degrading viral/retrotransposon nucleic acids (TREX1). These are our intelligent weapons to watch over and overpower transposons. As we read above aging is associated with loss of heterochromatin in various locations in the genome. Decreases of heterochromatin or heterochromatin-establishing factors contribute to elevated retrotransposon activity with age. Genetic interventions that promote heterochromatin formation and/or retrotransposon silencing, remarkably, can increase life span. Aging also sees loss of methylation which also derepresses transposons. Mobilisation of transposons can lead to genomic instability: if a transposon jumps into a functional (coding or regulatory) region of the genome, the insertion often results in loss of function, thereby, facilitating the death of the affected cell. The mass occurrence of transposition events can lead to various degenerative processes. Unwanted  activation of transposons in aging can lead to diseases even cancer. Their activation also led to immune response which is part of rise of chronic inflammation seen in aging. Studies suggest that retrotransposons causally contribute to the aging process, and that interventions that oppose retrotransposon activity might improve healthy longevity and lifespan. To quote the authors further: The most proximal approach to inhibiting retrotransposons would be to strengthen the epigenetic mechanisms responsible for their silencing, especially those that become compromised with age. One such epigenetic regulator is SIRT6. Male mice overexpressing SIRT6 show increased life span, which may be due in part to more efficient silencing of L1 elements and reduced inflammation. SIRT6 is involved in multiple processes which include DNA repair, telomere maintenance and metabolism. Small molecule activators of SIRT6 are being developed and may provide an array of health benefits, including improved retrotransposon silencing. Several experiments also show that that a key intervention already known to increase lifespan, a low-calorie diet, dramatically delays the onset of increased transposon activity.

 

 

 

The decline of the extracellular matrix begins just after puberty

https://karger.com/ger/article/66/3/266/148307/The-Matrisome-during-Aging-and-Longevity-A-Systems

 

We assume that ECM begins to deteriorate due to accumulation of AGE’s and cross linking of collagen over decades but actually ECM is deliberately hurtled towards destruction much earlier: During development and growth, cells constantly remodel the ECM by degrading parts of their ECM and through de novo synthesis of matrisome components in order to maintain homeostasis. This dynamic and energy-intensive process declines  after reproduction. Either because natural selection, as defined as reproductive fitness, is ineffective after reproduction, or because of a shift in resource allocation from somatic to germline tissue during the onset of reproduction. Irrespective of the etiology, this predicts that after reproduction the homeostasis of matrisome components, that is, de novo synthesis and ECM remodeling, would decline and should be reflected in the temporal change of matreotypes during aging. Thus, the matreotype of a young ECM is different compared to an old ECM. In this paper the authors also give  an explanation of the kind vicious cycle such early decline would lead to: During aging, either through collagen fragmentation or loss of adherence proteins,  cells detach from the ECM potentially leading to cell dysfunction and loss of ECM synthesis and turnover. In fact, the loss of ECM-to-cell connection might start a vicious downward spiral. For instance, during aging, there is an increase in activity of ECM-degrading enzymes, such as matrix metalloproteases (MMP). Increased MMP activity leads to collagen fragmentation, causing cell detachment, which leads to altered -integrin signaling and an increase in mitochondrial -reactive oxygen species, which in turn promotes the -expression of more MMPs, leading to further ECM fragmentation. 

So the aging program seems to select our most important components and systems for early start in deterioration -another example is 60% loss of heat shock protein chaperone support to protein product also happening just after puberty. ECM is as important as protein production because it makes up a staggering 50–70% of the human body mass and any change in that would be felt systemically. Another way to estimate importance of decline of ECM in aging is from this paper: 

https://www.aginganddisease.org/EN/10.14336/AD.2022.1116

The authors found that 12 most established longevity-promoting transcription factors (i.e., CREB1, FOXO1,3, GATA1,2,3,4, HIF1A, JUN, KLF4, MYC, NFE2L2/Nrf2, RELA/NF-κB, REST, STAT3,5A, and TP53/p53), directly and indirectly transcriptionally regulate ECM genes. 

Healthy cell-ECM crosstalk is vital for cellular homeostasis

Cells synthesize their own surrounding ECM. Each type of cell has its own unique type of EVM. Throughout the life of a cell there is constant cross talk with its ECM-in fact during aging when the damage to ECM is so great that a cell detached from it, which is called anoikis leading to the cell either dying or turning cancerous. A fascinating finding is that placing senescent cells or aged stem cells in a “younger ECM” has been shown to rejuvenate these old cells. The ECM provides instructive signals that change cellular function and identity. For instance, placing tumor cells into an embryonic ECM reprograms them to lose their tumorigenicity and become normal cells. Furthermore, the lost regenerative potential of old muscles is rejuvenated by grafting them into young, but not old hosts. And so a young and healthy ECM is vital for the survival of the cell it surrounds. During aging, components of the ECM become damaged through fragmentation, glycation, crosslinking, and accumulation of protein aggregation, all of which contribute to age-related pathologies. Since ECM is pervasive throughout our body it’s decline is linked to catastrophic tissue failure and multiple organ failure. ECM is a dynamic structure that is continuously built and remodeled but in aging Advanced Glycation End products that build up on the ECM blocking remodeling enzymes making it stiff. This leads to diseases like fibrosis seen in various organs like heart, lungs, kidneys, etc. So far it was believed that once formed AGEs can not be destroyed. But in 2020 Nam Y Kim et.al. published this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768434/

In which they shared about an altered enzyme and it’s variant were able to reverse AGEs. This is a great breakthrough and hopefully all types of AGEs can soon be eliminated. 

 

  

These are just a few of the thousands of changes occurring during aging. From this we can see why addressing one or a few of these changes will not be able to reverse aging. Only those interventions that work to reverse all these changes back to normal or youthful configuration can actually reverse aging. The entire universe is made up of only one building material: atoms. Atoms are incredibly mysterious full of magical forces but atomic, nuclear and quantum physics deserve a separate blog post. What is fascinating is what happened on Earth: these mystical atoms in different configurations formed molecules. From these molecules came living forms and their unit is cells. Cells are intricately beautiful with their components and engineering. Along with other tiny life forms like microbes and and another mysterious object: virus-it’s like a non-living zombie code that can jump from living cells to living cells housed in various bodies. Various collections have developed of these three to form a variety of life forms including us humans. Another principle of the universe seen in everything, living or inanimate, is recycling. May fly lives just 24 hours and our Sun 4.5 billion years but despite that difference both have one thing in common: both will perish and be recycled into something else. And there is black holes from which nothing seems to escape: the ultimate recycler of the known universe. On Earth cells have DNA and RNA which is DNA’s master and servant. But emerging evidence over the last few decades points to a recycling code embedded in the DNA which is altered due to various paths of adaptationary changes adopted by each life form or each unique collection of cells, microbes and viruses. No matter what alterations almost all seem to participate in the universal principle of recycling. In some life forms reproduction is asexual and automatic as part of their life journey. In other forms with higher intelligence where a factor of choice comes in reproduction is incentivized with pleasurable sensations. So the birth and death cycle continues millions of times. In life forms with even more complex engineering, like humans, we can witness an army of agents of time which chip away at a thousand different locations till one day the life form succumbs and dies. Our awareness of our biology is growing rapidly and every now and then we keep discovering another agent of time. Our gift from adaptions to survive is highest intelligence amongst all life forms on Earth due to which we have come to totally dominate Earth just like our predecessors the dinosaurs. This intelligence will also allow us at some point to synthesize our own adaptation to overpower these agents of time. We have the potential to become one of the first forms in the universe to bypass the principle of recycling at least from our own short recycling cycles. Although eventually one of the powerful forces of the universe would end our run. If we reach the point of immortality who knows we may get enough time to avoid or prevent total oblivion through interstellar travel and building our own defenses manipulating matter. Becoming biologically immortal is not such a big jump as we think now because as I have said in my previous posts there are complex life forms on Earth not gifted with our intelligence that have already achieved this by way of adaptation lottery win. So our intelligence will surely allow us to create indefinite lifespan in perpetual youthful homeostasis. We are going to build technologies which we can’t even imagine today. Tempted to throw in just one example of possibility: The virus that recently created a global epidemic is considered an enemy but we have the capability to turn an enemy into our greatest weapon. One song that all agents of time sing is dialing down of our amazing repair systems so imagine tiny nano robotized virus like codes that continuously repair damage as it occurs in our 30 trillion cells and their microenvironment. We can literally blow this virus from various points in a city to ensure everyone remains infected. The virus can be engineered to sit in a cell and get activated at any sign of damage and repair it. Similar virus can also be created to prevent or treat cancer our other great enemy. May be we can learn from cancer cell and reengineer it to make us young – after all a cancer cell makes itself immortal. It would be technologies we can’t even begin to comprehend now. 

 

AUTOLOGUS REGULATION

AUTOLOGOUS REGULATION

 Our biological destiny is inherited by us in every cell. Our DNA is the repository of this information in every cell. DNA is another incredible wonder of Nature. Todd Smith gives a great description (1): Six billion base pairs of DNA are packaged into 22 pairs of chromosomes, plus two sex chromosomes. Each base pair is 34 angstroms in length (.34 nanometers, or ~0.3 billionths of a meter), so six billion base pairs (all chromosomes laid out head to toe) form a chain that's two meters long. If we could hang this DNA chain from a hook, it would be slightly taller than an average human. But that's just the DNA from one cell. Each of us have around 50 trillion cells (50,000 billion). If we took the DNA from all of those cells and laid it out in a linear fashion, it could wrap around the earth 2.5 million times, or reach to the sun and back 300 times! Yet cells manage to pack all that DNA into a structure so small we can't even see it without a microscope. 

This long hard disk is twisted and braided and compressed so amazingly in the tiny nucleus of our tiny cell. Each tiny cell contains all the information to build a complete living organism or human being. Basically it carries two types information: one for autologous regulation- continuously managing itself as per inherited temporal program. This silences most of the genes and activates only those that give it its identity and characteristics. It uses multiple layers of tools and collaborations between those tools to accomplish this as per instructions embedded in it. Second type of information is its mesh like behaviour. Cell functions on its own as per the type of cell it becomes but it also functions collectively with other cells to build as per the design of the organism. On top of this mesh there are non cellular players like bioelectrical networks that influence each cell and also collectively as another language of communication amongst them. 

Cells are very crowded places: there are some 42 million protein molecules in a simple cell, revealed a team of researchers led by Grant Brown, a biochemistry professor in the University of Toronto's Donnelly Centre for Cellular and Biomolecular Research. The majority of proteins exist within a narrow range -- between 1000 and 10,000 molecules. Some are outstandingly plentiful at more than half a million copies, while others exist in fewer than 10 molecules in a cell. These molecules move very very fast inside the cell. In a blog by Ken Shiriff where he quotes from the book Molecular Biology of the Cell: You may wonder how things get around inside cells if they are so crowded. It turns out that molecules move unimaginably quickly due to thermal motion. A small molecule such as glucose is cruising around a cell at about 250 miles per hour, while a large protein molecule is moving at 20 miles per hour. Note that these are actual speeds inside the cell, not scaled-up speeds. I'm not talking about driving through a crowded Times Square at 20 miles per hour; to scale this would be more like driving through Times Square at 20 million miles per hour!

Because cells are so crowded, molecules can't get very far without colliding with something. In fact, a molecule will collide with something billions of times a second and bounce off in a different direction. Because of this, molecules are doing a random walk through the cell and diffusing all around. A small molecule can get from one side of a cell to the other in 1/5 of a second.

 As a result of all this random motion, a typical enzyme can collide with something to react with 500,000 times every second. Watching the video, you might wonder how the different pieces just happen to move to the right place. In reality, they are covering so much ground in the cell so fast that they will be in the "right place" very frequently just by chance.

 A rendition of a cross section of a cell and how crowded it is.

 In addition, a typical protein is tumbling around, a million times per second. Imagine proteins crammed together, each rotating at 60 million RPM, with molecules slamming into them billions of times a second. This is what's going on inside a cell.

In super tiny tightly packed strands of DNA heritable intelligence decides which gene (a segment of the DNA) will be read and which part of the strands will be tightly sealed to avoid being read. The ‘reading’ of the strands is by a process using enzymes and many floppy phase changing proteins as described in previous post. So many things have to come together at the right place for the gene to be read – all inside a tiny tightly packed part of a tiny cell. 

From what is not read and what is read in our DNA a cell gets it’s identity and function. Only 10%to 20%  of the coding genes are active at any given time in a cell. There is intelligence even in the spatial arrangement of each of the 200 types of cells. It’s like each type of cell is of a particular color and shape in a puzzle and Nature arranges them to form 80 different 3-D organs with incredible functions like our eyes which allow us to see and liver that does complex processing. Cells also form bones and cartilage and tendons and muscles. All of this different things made from the same basic cell. And each cell can be made to turn into any other type of cell. Unbelievably each cell has information on its ‘hard disk’ to build each and every of the organs, bones, muscles and skin. We literally start from a single cell! 

As we read in my earlier post Headwaters, this ‘reading’ or  transcription of our DNA is quite pervasive and is observed in 85% of our genome. Out of this only 2% is involved in protein coding. Rest is involved in regulating this 2% and it’s translation. The more the complex organism the bigger the ratio between coding and non coding but this tells only one part of the story. 

Even in such a crowded cell with such a huge genome Nature maximizes this space by alternatively splicing 95% of the genome. So instead 50,000 genes (coding and non coding) generating 50,000 transcripts not only 85% of the genome transcribes but 98% of this transcriptome undergoes alternative splicing! Creating uncountable isoforms. By alternative splicing we mean that same region of our genome can be ‘read’ in multiple versions. Supposing we mark a region from 1 to 10 and  neighbouring region is marked from 11 to 20 as two genes but those genes due to alternative splicing can be transcribed as 5 to 9 or 3 to 6 or 2 to 9 making 3 transcripts from the same gene. This splicing can also include neighbours so it can go 7 to 15 or 3 to 12, etc. to explain it simply. So in the preceding Headwaters post we learnt about how most of the transcription from non coding regions and some proteins create layer upon layer of regulation of the protein coding genes driving the changes that make us from an egg to an adult and after puberty it launches the process of aging. Now in this post we find that that is not all that happens in the genome and it’s housing structures like histones and  chromosomes. On top of this there is spliceosome that cuts up the genome into not just linear transcripts across its length but unending variety of isoforms due to rampant alternative splicing. Look at the packaging brilliance of Nature: a 2 meter long DNA 85% of which transcribes into transcripts in a nucleus that is 10 microns (one micron is one millionth of a meter) would be miraculous enough but Nature maximizes this by adding pervasive alternative splicing that creates multiple transcripts from same gene! Thereby multiplying the number of transcripts by multifold that are produced from the 2 meters. 

 

 

From Universal Alternative Splicing of Non Coding Exons by Tim Mercer et. al

 Only a limited number of transcripts whether of a full gene or alternatively spliced gene translates into protein. In my previous post Headwaters we read about how these shapeless, floppy proteins gather near a gene activation site and magically phase change into a condensate that hovers over the site. Similarly a different condensate activates splicingAn article published in Genome Biology Journal on 28^th November 2018 by Dr. Steven Salzburg et. Al. states the following: “We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. The new database contains 42,611 genes, of which 20,352 are potentially protein-coding and 22,259 are noncoding, and a total of 323,258 transcripts. These include 224 novel protein-coding genes and 116,156 novel transcripts. We detected over 30 million additional transcripts at more than 650,000 genomic loci, nearly all of which are likely nonfunctional, revealing a heretofore unappreciated amount of transcriptional noise in human cells.”

The interesting thing to note is the huge number of transcripts they found: 30 million! They claim that most of them are non functional but Nature rarely spends resources to construct huge volumes of non-function things. The non protein coding transcripts too have very important roles. In a paper titled ‘Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs’ by Matthew J. Hangaue et. Al. the authors say “It is now becoming more and more clear instead that, far from being genetic “deadwood” these repetitive expanses are actively and deliberately transcribed into non-coding RNAs which play a major role in regulating gene expression and silencing, organizing nuclear architecture, compartmentalizing the nucleus, and modulating protein function.” My previous post explains in detail the various types of non coding transcripts and the regulatory roles they play but here we additionally examined the alternative splicing that generates not only variety of coding transcripts but also as we read above huge number of non coding transcripts. 

 What is fascinating is how these transcripts govern their own births: if you recall we covered Long non coding RNAs in the previous post-in a paper titled ‘Epigenetic regulation of alternative splicing: How LncRNAs tailor the message’ by authors Pisignano and Lafomery they write about some of the ways in which LncRNAs regulate alternative splicing which in turn leads to various transcripts including LncRNAs. An excerpt from their paper “Both short (<200 nt) and long (>200 nt) non-coding RNAs can contribute to the regulation of alternative splicing in many different ways; either indirectly by regulating the activity of splice factors; or directly, by interacting with pre-mRNAs. Long non-coding RNAs (lncRNAs) are particularly well suited to these roles due to their demonstrated capacity to act as regulatory molecules that modulate gene expression at every level. Either alone, or in association with partner proteins, these long RNA polymerase II transcripts have been shown to take part in a wide range of developmental processes and disease in complex organisms.” So which are the ways they mentioned in which LncRNAs regulate alternative splicing:

1.     LncRNAs regulate alternative splicing through chromatin modification: An intimate relationship exists between lncRNAs and chromatin conformation.  LncRNAs regulate chromatin modifications by recruiting or directly interacting with histone-modifying complexes or enzymes at specific chromosomal loci. A possible lncRNA-mediated crosstalk between histone modifications and the pre-mRNA splicing machinery has also been proposed. Several lncRNAs appear to control important aspects of chromatin organization including chromatin looping, either remaining tethered to the site of transcription or moving over distant loci. 

2.     LncRNAs regulate pre-mRNA splicing through RNA-DNA interactions: LncRNAs can tether DNA forming an RNA-dsDNA triplex by targeting specific DNA sequences and inserting themselves as a third strand into the major groove of the DNA duplex. These are known as R-loops; three-stranded nucleic acid structures, composed of RNA–DNA hybrids, frequently formed during transcription. Aberrant R-loops are generally associated with DNA damage, transcription elongation defects, hyper-recombination and genome instability. Recent lines of evidence indicate a potential role for R-loops in alternative pre-mRNA splicing. A class of lncRNAs, the so-called circular RNAs (circRNAs) are abundant, conserved transcripts originate from a non-canonical AS process (back-splicing) leading to the formation of head-to-tail splice junctions, joined together to form circular transcripts. 

3.     LncRNAs regulate pre-mRNA splicing through RNA-RNA interactions: Identified in multiple eukaryotes, Natural Antisense Transcripts (NATs) are a class of long non-coding RNA molecules, transcribed from both coding and non-coding genes on the opposite strand of protein-coding ones. Regardless of their genomic origin, NATs can hybridize with pre-mRNAs and form RNA-RNA duplexes. In some cases, a double function is also possible, and NATs can encode for proteins on one hand, while at the same time working as non-coding molecules modulating the splicing of a neighbouring gene’s transcript. 

4.     LncRNAs regulate pre-mRNA splicing by modulating the activity of Splicing Factors: lncRNAs interact in a dynamic network with many SFs and their pre-mRNA target sequences to modulate transcriptome reprogramming in eukaryotes. LncRNAs regulate the localization and phosphorylation status of Splicing Factors. 

 The authors conclude by stating that “With the increasing prevalence of splicing events and the discovery of over a hundred thousand lncRNAs, it is likely that the involvement of lncRNAs in regulating AS is far greater than the currently known.”

 

  

Regulation of pre-mRNA splicing by lncRNAs. LncRNAs (red) are able to control pre-mRNA splicing by (a) modifying chromatin accessibility through recruiting or impeding access to chromatin modifying complexes at the transcribed genomic locus. In some cases, this might result in more drastic long-range structural changes; (b) interacting with the transcribed genomic locus through an RNA-DNA hybrid; (c) hybridizing with the pre-mRNA molecule (light blue); (d) promoting SF recruitment or by sequestering SFs into specific subnuclear compartments, thereby interfering with SF activities. Credit: Epigenetic Regulation of Alternative Splicing: How LncRNAs Tailor the Message. Authors: Giuseppina Pisignano and Michael Ladomery. 

In my preceding post Headwaters we see various ways in which many types of non coding RNAs regulate gene expression not only inside the cell but also through the circulating secretome. Here we saw how alternative splicing leads to protein diversity and non coding transcription by creating alternative transcripts from the same gene. But what is amazing is that non coding RNAs influence the alternative spliceasome. A very interesting paper titled Aging is associated with a systemic length-associated transcriptome imbalance by Dr. Luis Amaral et. Al. in which they find out that as we age longer transcripts reduce and many of them are associated with longevity genes. They cite various possible causes as the source of the origin of these change like heat shock protein leaving translation with truncated protein lengths and spliceosome and splice factors deliberately transcribing shorter transcripts. But the best clue is that they also found in some subset of tissues and cell types exact opposite is seen happening! In these short transcripts are seen reducing and long transcripts are seen increasing. So what is this a dead giveaway of? Temporal program of autologous regulation. The age related changes are not random but are orchestrated by transcription and splicing machinery and their coplayers. In a paper titled Aging associated changes in the expression of LncRNAs in human tissues reflect a transcriptional modulation of ageing pathways by Dr. Joao Pedro de Megalhaes et. Al they observed that LncRNAs are very tissue and lineage specific and typically highly specific spatio-temporal expression patterns. This again shows evidence of an intricately designed regulatory plan that unfolds with timeline of the living organisms. All this intricately complex regulation in such tiny environment is for spatial and temporal organization of a life form:

Spatial organization: Imagine a tiny cell 1/10^th the diameter of a human hair has information that it reads which tells it where it should locate itself with respect to other cells in our body. So a cell that is designated to be an eye cell, as it emerges from the multiplication of cells from one single fertilized egg, knows it has to move precisely towards the sockets being formed in the head and then through epigenetic changes it becomes an eye cell! It will not float and land up on the hand or turn into a skin cell in the eye. The precision is mind boggling. Where is that information, that instruction that it must move there to become an eye cell? It’s already labeled in its DNA. Imagine tens of trillions of cells each knowing exactly where it needs to locate itself in a 3 dimensional space of the life form and then what it needs to become to form various organs and tissues and muscles and bones! It must need to coordinate and jostle with its neighbours to land at its physical destination. Dr. Michael Levin says there is Bioelectrical memory which connects all cells in a mesh and guides each cell to where it needs to be. This process is called spatial organization. 

Temporal organization: Once a cell takes its place and it’s epigenetic buttons are clicked to transform it into a type of cell a whole different process of organization begins. In this process the 10% or 20% of the coding  genes which typically are active begin to print proteins that fulfill their various tasks in line with their cell’s type. So a pancreatic cell with code for insulin for example. These are functional tasks of the cell but parallely as we have read above there is also highly complex regulation that is happening of those protein coding genes and their transcripts. This continuous background regulation creates constant changes in the cell from birth till death. Initially these macro changes are related to development: to make us grow from an egg to an adult and after puberty the main theme of these changes is to dial down important repair and recycling systems so that within a given range the life form dies. These latter changes manifest as aging. These regulatory changes of the spliceosome, alternative splicing, non coding and coding gene transcription all together leading to a particular proteomic configuration which in turn influences the efficiency of all the tasks that are done by those proteins. The changes stop some proteins, change some proteins, reduce some proteins and increase some proteins. This is ongoing all our lives. Ironically these transcriptional and proteomic changes also affect the cells DNA itself as progressively double strand breaks increase as we age and their repair efficiency reduces when it’s needed even more. This brings us to the main observation driving this post: 

Autologus Regulation: Nature has created this unit of mind boggling complexity and intricate design: the cell. All life forms on our planet are built from this unit. Incredibly this unit produces regulators that governs itself! It produces transcripts and proteins that regulate the regulators! So basically it writes its own biological destiny. Inherited genetic factors and lifestyle factors do also influence our biological destiny but only in a narrow range. The main driver continues to remain the inherited repository of information in the cell itself. The information it carries enacts it’s spatial organization and the same source of information also enacts it’s temporal organization. It transcribes transcripts that influence the transcriptional machinery and splicing machinery to decide whether to transcribe the entire gene or whether to transcribe an alternate version or whether to silence it. Some of those transcripts along with some of the translated proteins will make further alterations to the transcriptional decisions and splicing decisions in a continuing loop of self regulation driving the two major themes: development before adulthood and aging after adulthood. Besides these two main themes there are also changes that occur due to environmental stimuli. But overall unless they are extreme or fatal these are dominated by the two main themes. Some of these instructions are exchanged between cells through direct connections with neighboring cells or through the secretions of one cell entering another. 

This self regulation is a very interesting process created by Nature which we rarely get to witness anywhere else. It’s easy to miss how incredibly remarkable is this technology developed by Nature and evolution. DNA carries information that when read sequentially builds us into an adult starting from a single cell and DNA also carries information that when read sequentially after puberty leads to gradual aging and death. We inherit both, our youth code and our death code,  from the moment we are a fertilized  egg. Let me try to explain it with an example. Let’s say a branch office is opened (cell) in which there is no manager but only an SOP manual – a standard operating procedure master handbook for the entire year that all the staff has to follow. It gives instructions to the HR dept on what kind of staff to hire. It has various printers that print out instructions daily giving tasks to all the staff. But imagine that only 30% of the employees actually do the tasks that produce the parts that the branch manufactures. 70% of the employees are getting instructions daily from the SOP to manage those 30% employees and what they produce by making changes in the master SOP that is daily giving instructions to those 30%. So the SOP itself has instructions to daily make changes in the SOP and thereby resulting in changes in the production. But those changes and their edits are so complex that it requires 70% of the employees just taking new instructions daily from the SOP and coming over and editing the future chapters of the SOP manual. These self edit instructions flow out sequentially as each new page of the SOP is read each new day of the year. Other branches also exchange data (secretome) and send their employees to also make edits in each other’s SOPs’.  In the beginning there is tremendous excitement and new teams are hired and production is going full swing making wonderful products that sell very well (puberty). At its peak the training reaches a point where a team of employees can go and open another branch (reproduction). But once that is done the SOP begins to give out instructions to edit itself (autologous regulation) so that in forthcoming pages the production quality, hiring quality, raw material quality all of it is purposely, gradually brought down (aging). In the beginning it’s hard to notice but after some months of such gradual changes the consequences begin to show and unsold products start piling up. Cash flow is affected, salaries are affected. And what at its peak was a dynamic factory full of enthusiastic, productive workers becomes demoralized and stressed out leading to even further degradation at the branch creating a snowballing stranglehold from which the branch can’t escape and at some point it shuts down which is death. This is done so that there is no over crowding of the branches creating over supply which would destroy the company itself and also to ensure fresh young staff is recruited with every new branch which is enthusiastic and hard working. 

 Coming back to our biology there are two basic goals of autologous regulation: One is to build an adult from a fertilized egg. Second is to gradually make the adult age that would culminate with sufficient degradation to cause death anywhere between average lifespan to maximum lifespan of that species. One of the key reasons for this regular recycling every generation is because thanks to a paper last year by Dr. Vadim Gladyshev we learnt of this marvelous event occurring during early embryogenesis: all the inherited errors and insults of germline cells is wiped clean to make a brand new error free baby. Have humans outgrown this need to regular recycling? Can our intelligence help us to resolve the challenge of accumulation of biological errors and insults? As mentioned in my previous post I continue to take inspiration from certain life forms which seem to be immortal in permanent youth. I cite the Ginkgo Biloba tree because a researcher Dr. Richard Dixon has studied it. Even after a thousand years the tree that he studied still had photosynthesis efficiency and immune resilience of a 20 year old tree. Question arises as to how it’s able to do this. In almost all other life forms the DNA harbors temporal instructions that, as we read above,  make changes to the spliceosome and the splicing factors and the transcription factors and the epigenetic marks which result in gradual collapse of our repair and recycling systems and ultimately death. How is Ginkgo Biloba allowing all the changes related to development to reach adulthood but freezing or blocking or erasing further regulatory changes thereby permanently remaining in youth? Many scientists wonder if we can prolong our youth would we still die when we reach 122 or 125? Ginkgo Biloba tree says no. 

Two technologies are moving towards reversing human biological age. One of them is partial reprogramming of the cell using some of the yamanaka factors. This will in effect reverse the epigenetic signature, the gene expression and the proteome back to an earlier point closer to our youth. Question is does it also change the transcriptome? If not,  aging related changes would again bring the cell back to an impaired state. If it does also turn back the temporal needle of the transcription program to where it was in our twenties then it would again take decades for the cell to get impaired again. The only catch is that this is the same path that cell would take if it were reverting back to embryogenic cell state and that state can lead to cancer. So does partial reprogramming fully protect against cancer? One can never know till many years later. Second technology is an arbitrage. Signaling and regulatory molecules circulating in the plasma of the young are injected into the circulatory system of the old. As those molecules enter the impaired cells they reset the proteome of that cell back to how it was in youth. Thereby rejuvenating those cells. This does not stop the legacy transcription in the cell which after a point would begin the degradation all over again. The question here is if the pro youth molecules are injected repeatedly would that at some point ‘flip’ the transcriptome to how it was during youth? If yes then it would take decades before the cell would get impaired again. 

Human biology is incredibly complex. But does it have to be this complex? The complexity arises to maintain autologous management of the entire body. But can it be improved? Why do we need to generate voltage only from the food we eat? Why can’t we re-engineer so that we need only sunlight for energy like trees and plants do so beautifully? So much of our body’s parts are devoted to eating, digestion and excretion. If we did not need to eat to generate electrical energy we could reduce 50% of of our organs. Also why can’t we store electrical  energy in our body/cell? We humans have created batteries to store electrical power so are we now ahead of evolution? Can we create alternate source of electrical energy in our cells? We have the intelligence to do it. Can we obviate the need for oxygen? We will also be able to edit the embryogenic process safely to alter our human organs and systems and form.  I guess all of this is possible in the distant future. It will all start with our control over biological age.