John Hemming's Web Log

Prompt: ""of the diseases of aging which are assocated with changes to RNA splicing" Diseases of Aging Associated with Changes to RNA Splicing Many major age-related diseases have documented links to altered RNA splicing—both via age-related drift in the spliceosome and via disease-specific mutations in splicing factors or cis-elements. Below are key examples by system (not exhaustive, but covering major, well-supported cases). 1. Neurodegenerative Diseases Alzheimer’s disease (AD) What’s altered? Alternative splicing of tau (MAPT) , shifting 3R/4R isoform balance. Splicing of APP , PSEN2 , and various synaptic genes. Mechanism: Mis-spliced tau isoforms are more aggregation-prone and disturb microtubules; age-related decline in spliceosome components (e.g. SRSF and hnRNP proteins) pushes splicing patterns in a pro-pathology direction. Frontotemporal dementia (FTD) and other tauopathies What’s altered? ...

I put a couple of prompts into Gemini and the following came out as answers: Impact of RNA Splicing on Endothelial Function in CVD User Query To what extent are protein changes as a result of RNA splicing changes that cause endothelial problems part of cardiovascular disease? AI Analysis Protein changes resulting from aberrant RNA splicing in endothelial cells are not merely bystanders but are increasingly recognized as active drivers of cardiovascular disease (CVD). To answer your question directly: these changes contribute to CVD to a significant extent by creating "molecular switches" that can flip a healthy endothelial cell into a diseased state without necessarily changing the total amount of the gene being expressed. This process often explains why a patient might have "normal" levels of a protein but impaired function. The following s...

The principal mitochondrial K+ uniport is associated with respiratory complex I is an interesting preprint that has been withdrawn "due to disagreement with UCSF over data rights. This withdrawal decision is not related to the validity of the data presented in this study, and these authors understand that this work cannot be cited as reference for the project until the disagreement is resolved." It remains, however, interesting. The reason I find it interesting is that there is clear evidence that there is a link between the delta pH between the mitochondrial matrix and Intermembrane Space and the mitochondrial membrane potential. This was evidenced in experiments which varied one and saw the proton motive force (which is the total of the two adjusted for the same units) remain essentially constant. Furthermore it seems that where Potassium Ion transport changes with age we can also see a reduction in the membrane potential, but an increase in delta pH. This is signif...

These are two lists of reviews looking at mainly acetyl-CoA, but also other acyl-CoAs. They were selected by a search using chatGPT for the first one and Claude for the second one. Some are behind a paywall. My plan is to read through these and draw out conclusions I will separate out the ones which are behind a paywall. Acetyl-CoA: a central metabolite and second messenger (Cell Metab, 2015) Acetyl-CoA and the regulation of metabolism (Trends Biochem Sci, 2015) Spatiotemporal control of acetyl-CoA metabolism in chromatin regulation (Trends Biochem Sci, 2018) Compartmentalised acyl-CoA metabolism and roles in chromatin regulation (Molecular Metabolism, 2020) Should we consider subcellular compartmentalization of metabolism? (Trends Cell Biol, 2019) The multiple facets of acetyl-CoA metabolism: Energetics, biosynthesis, regulation, acylation and inborn errors (Mol Genet Metab, 2023) Molecular targets and small molecules modulating acetyl-CoA metabolism (ACS Pharmacol Transl...

I recently read a paper Ribonucleotide incorporation into mitochondrial DNA drives inflammation which I found very interesting. The reason I found it interesting is perhaps summarised in the first paragraph of the discussion section which I will quote: We demonstrate that increased incorporation of rNTPs into mtDNA during replication leads to the release of mtDNA fragments from mitochondria and proinflammatory signalling. Our results therefore highlight the challenge that the high molar excess of rNTPs relative to dNTPs poses to cells. Although RNase H2 removes incorporated rNMPs from nuclear DNA as part of the ribonucleotide excision repair pathway, this repair mechanism is not present in mitochondria, which are therefore prone to accumulating rNMPs in their genome. Similar to the effect of rNMPs on nuclear DNA replication27,40, due to the inherent reactivity of the 2′-OH group of the ribose ring or collisions with the replication fork, misincorporated rNMPs may cause DNA strand br...

People who study NCD (Non Communicable Diseases) and particularly those that focus on the diseases of aging (which I think include many of the NCDs, but not all of them) have a concept of someone having a biological age as well as a chronological age. This guides things like how frail someone is, how well their cognition works, whether they are at the risk of cancer or diabetes or indeed how they look. Human beings are quite good at judging each other's general health by appearance. That is because the various NCDs tend to correlate with how well the body maintains the skin and when someone is frail it is quite easy to see this by how they move around. Regular readers of my blog will know that I think this is because the genome stops functioning properly as people get older. In essence cells stop producing the right proteins. I provide full details of this hypothesis on this web page https://citrate.science/2025poster/poster2025.html . Various approaches have been used to cal...

I tend to ask chatGPT for a summary of the transcript of videos so that I don't have to spend the time watching them. I have done this for the ALS Scientific Advisory Council from about a month ago which follows (the critique is of chatGPT - my critique is that they don't talk about mitochondria, the closest they come to epigenetics is DNA methylation): International Alliance of ALS/MND Associations Scientific Advisory Council Webinar – Transcript Summary Opening & Housekeeping Jessica Mabe (Programs Coordinator, International Alliance) welcomed attendees and introduced the webinar, noting caption availability (via Zoom chat or QR code) and thanking sponsor Mitsubishi Tanabe Pharma . The Scientific Advisory Council Chair & Moderator: Dr Nicholas Cole (Head of Research, MND Association, UK) Panelists: Dr Kuldip Dave – Vice President of Research, ALS Association (USA) Dr Nadia Sethi – Co‑chair, NE...

I think it is useful to try to identify: a) The most heavily energy using neurons b) The balance in those cells between OxPhos (which produces Reactive Oxygen Species - ROS) and Glycolysis I will be using various LLMs to search for information relating to this and will be spending time checking the responses for hallucinations, but I may not at the time of you reading this page finished validating everything. I will also be concentrating on validating the analysis for dopaminergic and motor neurons because those are the neurons which cause PD and ALS/MND. In principle the rank is not really valid. Although this table is produced using a ranking that is not going to be reliable, it is still useful. What I am trying to get from this is to identify the cells which would be vulnerable to rapid deterioration through ROS. The first step is those with a high energy usage. This, however, I would expect to vary from time to time and any actual accurate calculation for one human being ...

Regular readers of my blog will have seen that I think there is solid evidence that some neurodegenerative diseases such as ALS (MND) and Parkinsons are caused by a deterioration of mitochondrial DNA primarily because of damage by free radicals (Reactive Oxygen Species - ROS) in the cells. This gradually causes the cells to fail to produce the right proteins and the cells stop working. I think the reason this happens in ALS (MND) and Parkinson's disease is that the cells that suffer are ones which both have a high energy demand, but also make high use of Oxidative Phosphorylation (OxPhos). Hence the mitochondria generate damaging molecules at higher rate which damages the mitochondria at a higher rate than normal. Cells have systems to deal with this, but once it gets to a certain point the deterioration becomes more rapid. Cells in the Central Nervous System have a supply of melatonin via the CerebroSpinal Fluid (CSF) that helps to resist this, but if there is a shortage for...

Given the links between mtDNA damage, splicing, ALS (MND) and PD, an obvious thing to look at is Multiple Sclerosis. MS is a failure of the myelin sheaf. It has been thought to be as a result of an auto-immnue response, but an alternative perspective would be a failure of homeostasis. I thought I would ask chatGPT to look at both sides of the argument about splicing and this is the response: chatGPT O3 response to question: " what are the arguments for and against multiple sclerosis resulting from aberrant splicing in the production of myelin " The summary result from chatGPT is: Bottom line The case for aberrant splicing in myelin production as a contributor to MS is biologically plausible and experimentally supported, but the case against it being the primary cause remains strong. At present, the weight of population genetics and virology favours a model in which immune dysregulation (often EBV-driven) comes first, with myelin-splice errors acti...

Obviously when mtDNA is damaged in neurons that can have various effects depending on the damage. A key point, however, is that if there is a process which is damaging mtDNA then if that continues then the mtDNA will get further damaged. As some relatively minor damage appears to be caused by the replication of mtDNA itself then it is like there is a very slow moving footpath moving towards cell failure. Hence when looking at how to rectify this then certain points need to be made. When mtDNA is damaged this will not immediately affect the structure of the cell. What it does is to change how the cell produces or fails to produce proteins in the future. Hence if the process of mtDNA damage stops, the cell is unlikely to be in its stable state and can be expected to deteriorate in function to a point at which homeostasis is achieved. It is hard, but possible, to improve mtDNA. However, that will not immediately improve the function of the cell and it may need a stimulus to rege...

I aim to write this blog so that people don't need a detailed understanding of genetics to read it. I assume people know that genetics involves DNA being used to produce proteins. DNA is comprised of four nucleotides. Two of these are purines Adenine (A) and Guanine (G). The other two are pyrimidines Thymine (T) and Cytosine (C). They pair in two pairs A to T and G to C. Each pair is called a base pair. To produce a protein they are copied to mRNA (messenger RNA) which is then used by the ribosome to create proteins. There is DNA in the nucleus of the cell and there is also DNA in the mitochondria (the little chemical factories that generate ATP and other molecules used by the cell). There is a three base pair code (identifying which amino acid to use) used to convert DNA into protein (via mRNA). Interestingly the code is slightly different in the nucleus/ribosome to the mitochondria. So far so good. DNA can be mutated where one nucleotide for some reason or other is ch...

I wrote previously about how babies are born young. The essence is that for youth you need efficient mitochondria with a high membrane potential (when running in a steady state generating ATP). When an egg is created it is created with a mitochondrial bottleneck. This reduces the variation in mitochondrial DNA (mtDNA) to about 3 copies (according to recent research). However, this does not as far as research indicates select for better mtDNA (and hence more efficient mitochondria). Relatively few babies are born with mitochondrial disease because the eggs don't get fertilised, don't start replicating, don't implant into the uterine wall or miscarry. This is not the only reason for non-viability, but it is a reason. This is seen in how older eggs tend to be less viable. However, there is another selection process for eggs which is called "Follicular Atresia". Follicular Atresia is a really interesting process and the Wikipedia article that I link to does ...

In Parkinson’s disease, dopaminergic neurons (primarily those in the substantia nigra pars compacta) undergo progressive dysfunction and death. In amyotrophic lateral sclerosis (ALS aka MND in the UK), both upper and lower motor neurons progressively degenerate. The cells deteriorate in different ways. However, the nub of both of theses diseases is the deterioration of a particular type of neuron. An interesting question is what it is about these neurons that makes them vulnerable to rapid deterioration. Neurons are high energy cells. Dopaminergic neurons have to maintain a massive network of axons linking them to other cells. Similarly motor neurons need to maintain long axons of possibly 1 metre in length. All of this takes energy. However, what distinguishes these two types of cells is that they rely to a greater extent on Oxidative Phosphorylation (that is using the Krebs cycle to produce energy) than other neurons. OxPhos, has the effect of generating more free radical...