Sunday, 28 February 2016


2nd of the two biggest debates of biomedical world: Are we programmed to die?

DEBATE II: Do we die because we succumb to wear and tear of our biology over the years or due to a DNA code programmed in us before we were born? Longevity has a good explanation for this theory: The wear and tear theory of aging believes that the effects of aging are caused by damage done to cells and body systems over time. Essentially, these systems "wear out" due to use. Once they wear out, they can no longer function correctly. It was first expressed in science by German biologist Dr. August Weismann in 1882. We simply expect that the body, as a mechanical system, is going to break down with use over the years. 
A range of things can damage body systems. Exposure to radiation, toxins, and ultraviolet light can damage our genes. The effects of our body's own functioning can also cause damage. When the body metabolizes oxygen, free radicals are produced that can cause damage to cells and tissues. There are some cellular systems that don't replace themselves throughout life, such as the nerve cells of the brain. As these cells are lost, function eventually will be lost. Within cells that continue to divide, the DNA can sustain damage errors can accumulate. Simply the act of dividing again and again shortens the telomeres of the chromosomes, eventually resulting in a senescent cell that can no longer divide. Oxidative damage in cells results in cross-linking of proteins, which prevents them from doing the jobs they are intended to do in the cells. Free radicals inside mitochondria, the powerhouses of our cells, injures their cell membranes so they can't function as well. 
Not all damage can be repaired fully, and mistakes in repairs may accumulate over time leading to our death.

Programmed aging and death theory is based on aging related slow decline of cellular functions being caused by a epigenetic clock programmed into our DNA. One major development in a Japanese lab of Jun-ichi Hayashi from Tsukuba University may tilt the scales towards this theory. The Tsukuba team has performed some compelling research that has led them to propose that age-associated mitochondrial defects are not controlled by the accumulation of mutations in the mitochondrial DNA but by another form of genetic regulation. The research, published this month in the prestigious journal Nature’s ‘Scientific Reports’, looked at the function of the mitochondria in human fibroblast cell lines derived from young people (ranging in age from a fetus to a 12 year old) and elderly people (ranging in age from 80-97 years old). The researchers compared the mitochondrial respiration and the amount of DNA damage in the mitochondria of the two groups, expecting respiration to be reduced and DNA damage to be increased in the cells from the elderly group. While the elderly group had reduced respiration, in accordance with the current theory, there was, however, no difference in the amount of DNA damage between the elderly and young groups of cells.

This led the researchers to propose that another form of genetic regulation, epigenetic regulation, may be responsible for the age-associated effects seen in the mitochondria. Epigenetic regulation refers to changes, such as the addition of chemical structures or proteins, which alter the physical structure of the DNA, resulting in genes turning on or off. Unlike mutations, these changes do not affect the DNA sequence itself. If this theory is correct, then genetically reprogramming the cells to an embryonic stem cell–like state would remove any epigenetic changes associated with the mitochondrial DNA. In order to test this theory, the researchers reprogrammed human fibroblast cell lines derived from young and elderly people to an embryonic stem cell-like state. These cells were then turned back into fibroblasts and their mitochondrial respiratory function examined. Incredibly, the age-associated defects had been reversed – all of the fibroblasts had respiration rates comparable to those of the fetal fibroblast cell line, irrespective of whether they were derived from young or elderly people. This indicates that the aging process in the mitochondrion is controlled by epigenetic regulation, not by mutations. The researchers then looked for genes that might be controlled epigenetically resulting in these age-associated mitochondrial defects. Two genes that regulate glycine production in mitochondria, CGAT and SHMT2, were found. The researchers showed that by changing the regulation of these genes, they could induce defects or restore mitochondrial function in the fibroblast cell lines. In a compelling finding, the addition of glycine for 10 days to the culture medium of the 97 year old fibroblast cell line restored its respiratory function. This suggests that glycine treatment can reverse the age-associated respiration defects in the elderly human fibroblasts. These findings reveal that, contrary to the mitochondrial theory of aging, epigenetic regulation controls age-associated respiration defects in human fibroblast cell lines. Can epigenetic regulation also control aging in humans? That theory remains to be tested, and if proven, could result in glycine supplements giving our older population a new lease of life.
Similarly David Sinclair's lab at Harvard showed that by upregulating NAD+ in the mitochondria the musculosketal infrastructure of the body rejuvennated to youthful peak levels.
Harvard's David Sinclair's Formula to Reverse Aging 
Parallely the Conboys and Wager demonstrated the rejuventation of muscles, brain, liver and other organs and systems by parabosis in two linked mice circulating young blood in old mice. Which proved that when signal proteins from young plasma circulated in an already age ravaged body were still able to reverse aging on the old mice.

The above two have been covered in my earlier post called 'Can we cure aging?' in more detail.
All the three put together provides clear evidence that aging does not create permanent damage or is not caused by wear and tear.

My Conclusion: There is a code that has been planted in the DNA of ALL living things on this planet which is triggered by a epigenetic clock and leads to decline and death of the host. Steve Horvath of UCLA has not recieved the fame and appreciation he deserves for discovering the DNA methylation clock that accurately measures human age. Various strips of DNA has codes that make us grow to adulthood from babies and later, on reproductive maturity, trigger a slow decline leading to death. I don't expect these strips to be in one long chain but in different locations. What is remarkable is zero error rate - we do not see anyone due to DNA mutations cheating death. There are errors which cause various handicaps and deformities but never ever since record of humanity have we observed an error in code regulating aging and death. This shows that Nature gives a lot of importance to death and must have programmed multiple pathways to ensure decline and death in all living things. When we upregulate NAD+ or glycine or AMPK or whatever else has been shown to prolong life in lab animals we are only trying to cure the symptoms. Which can not lead to cure of aging and avoidance of death. There are only two ways it seems that one can aim to achieve this:

1. By disrupting the epigenetic clock by infusion of plasma of a young donor into the patient wanting to reverse aging. The noch protein signals of a donor whose epigenetic clock is signaling body to works at its peak is expected to do the same for the new recipients body as seen in parabiosis models in lab mice pairs. The question is will it do the same in human parabiosis or plasma exchange? Also if it does would the new signals flooding the body in sufficient numbers be able to reset the epigenetic clock of the old human to the age of its young donor or will the benefitial rejuvenation last only up to the life of the signal proteins? If it is the former the parabiosis or plasma exhange would be needed only once every 10 years to reset the epigenetic clock back to the age of 25 (from 35) and if it is the latter then the parabiosis or plasma exchange would need to be done every 4 months.

2. The other way would be identifying which section or sections of the human DNA has the triggers for decline messages to be relayed linked to the progress of the epigenetic clock. DNA does not need to have a message for effecting death. The total body decline ensures that it leads to death. This would be quite a challenge compared to the first option which can be implemented today by any qualified physician using the plasmapheresis machine. Identifying from the 20,000 to 25,000 protein coding genes - it may be a single one that triggers a cascade or it may be multiple ones that work independently or in synergy - too many permutations and combinations to evaluate. It may also be from the huge amount of non coding genes which now are no longer considered junk but also seem to be having some biological function. Needle in a haystack type of situation. But we have already mapped the entire human genome and have invented incredibly powerful gene editing tools like CRISPR - The importance of CRISPR - We are Nature's Robots with a software that dictates everything that happens to us - CRISPR is a tool that allows us to edit this software. We still don't know what to edit but when we do CRISPR will help us execute it.
Once the genes are identified we would need specific binding agents to block it from triggering the functional decline messages. Assuming that the identified genes also do not have other needed functions. Testing which genes play a role in triggering aging decline is very difficult to do as we can not try editing out genes on a living human. So is it impossible to eventually identify the genes triggering aging decline? Of course not. We will achieve this - it is only a matter of time.

Half a Million DVDs of Data Stored in Gram of DNAhuman longevity


One of two biggest debates of the biomedical world (second debate covered in separate blog post)

DEBATE I: Are all cancer cells mutagenic and proliferative or only the core mother stem cells? 
Dr John Dick sparked this debate in 1994 when he isolated the first cancer stem cell, and showed that these rare cells cause leukemia to grow in mice. Researchers at the University of Michigan made the case in 2003 that the same was true in breast cancer. In 2004  Dr Dirk a scientist and neurosurgeon at Toronto's Hospital for Sick Children discovered cancer-causing stem cells in the brain tumours of mice. The idea began gaining wider acceptance that a tiny number of cancer stem cells cause cancers to grow. As reported in Wkipedia under Cancer Stem Cells (CSCs): CSCs may generate tumors through the stem cell processes of self-renewal and differentiation into multiple cell types. Such cells are hypothesized to persist in tumors as a distinct population and cause relapse and metastasis by giving rise to new tumors. The theory suggests that conventional chemotherapies kill differentiated or differentiating cells, which form the bulk of the tumor but do not generate new cells. A population of CSCs, which gave rise to it, could remain untouched and cause relapse. The debate over the existence of a minority of CSCs at the root of all cancers or not has been continuing since the last 12 years. Both sides have been citing lab and murine studies to validate their argument. One example for each:

Evidence for Refuting the CSC theory: Sean Morrison director of the University of Michigan Center for Stem Cell Biology and his team of researchers  have determined in Nov 2010 that most types of melanoma cells can form malignant tumors, providing new evidence that the deadliest form of skin cancer does not conform to the increasingly popular cancer stem cell model. In addition, the researchers found that melanoma tumor cells can change their appearance by switching various genes on and off, making the malignant cells a stealthy, shape-shifting target for researchers seeking new treatments. As reported in Michigan News Both findings fly in the face of the cancer stem cell model, which states that a handful of rare stem cells drive the formation, growth and progression of malignant tumors in many cancers. Some supporters of the model have suggested that melanoma might be more effectively treated by taking aim specifically at these rare cancer stems cells, rather than attempting to eliminate all melanoma cells. But after conducting an exhaustive search for this elusive sub-population of tumor-forming melanoma cell, the U-M team concluded that it probably does not exist. The researchers analyzed 44 sub-populations of human melanoma cells, and all 44 had a similar ability to form tumors when transplanted into mice. "Some have suggested that melanoma follows a cancer stem cell model in which only rare cells are able to proliferate extensively and form new tumors. Our results suggest that most melanoma cells are capable of driving disease progression and that it won't be possible to cure patients by targeting rare sub-populations of cells," Morrison said. "We think you need to kill all the cells."
Are all Melanoma cells are cancer stem cells in disguise? Melanoma cells under an elctron microscope
The study found that tumor-forming melanoma cells have the ability to throw a genetic switch that changes the types of proteins expressed on the cells' surface. The study is the first to present evidence for this type of pervasive "phenotypic plasticity" among melanoma cells from patients. Patterns of surface proteins are used to identify different cell types and are commonly called cell surface markers. "The fact that these markers are turned on and off by melanoma cells raises the possibility that melanoma cells may also turn on and off genes that regulate clinically important characteristics like drug resistance and metastatic ability," Morrison said. "The ability to transition between various states may make melanoma more difficult to treat." The authors stress that while their results argue against a cancer stem cell model for melanoma, their findings do not invalidate the model. In fact, certain leukemias and other cancers appear to follow the model.
"It will be critical to determine which cancers follow a stem cell model and which do not, so therapies designed to target rare sub-populations of cells are not inappropriately tested in patients whose disease is driven by many diverse cancer cells," Quintana also from the UM Stem Cell Center said. "The cancer stem cell model says that tumor cells are organized hierarchically, and that only the cells at the top of the hierarchy form tumors. Cells at the bottom of the hierarchy can't," Morrison said. "In our model, all these cells can form tumors," he said. "And they're phenotypically different from each other not because they're hierarchically organized but because they're just turning these surface markers on and off." The U-M team found that all tumor-forming melanoma cells gave rise to progeny with a variety of marker patterns, and that all of those sub-populations retained the ability to form tumors. The marker changes appeared to be reversible, rather than being associated with a transition from tumor-forming to non-tumor-forming states, as the cancer stem cell model would predict.

Evidence for existence of CSCs and their role in cancer: In a study published in the journal Cancer Cell in 2014, researchers at Oxford University and Sweden’s Karolinska Institutet said they had tracked gene mutations responsible for a form of blood cancer back to a distinct set of cells which they say are at the root of the cancer’s spread. 'It's like having dandelions in your lawn. You can pull out as many as you want, but if you don't get the roots they’ll come back,' explains first author Dr Petter Woll of the MRC Weatherall Institute for Molecular Medicine at the University of Oxford. The 15 patients involved in the study had myelodysplastic syndrome (MDS), a blood disorder which causes a drop in the number of healthy blood cells, and develops into acute myeloid leukaemia in around half of all cases.
Cancer cell and lymphocytes
Genetic tracking identifies cancer stem cells in patients. Photo: University of Oxford

Researchers investigated malignant cells in the bone marrow of the patients and tracked them over time. Using genetic analysis, they were able to isolate a small and distinct group of MDS cells which were the origin of the cancer-driving DNA changes which were causing the disease to progress. 'This is conclusive evidence for the existence of cancer stem cells in myelodysplastic syndromes,' says Dr Woll. 'We have identified a subset of cancer cells, shown that these rare cells are invariably the cells in which the cancer originates, and also are the only cancer-propagating cells in the patients. It is a vitally important step because it suggests that if you want to cure patients, you would need to target and remove these cells at the root of the cancer – but that would be sufficient, that would do it.'Dr Peter Woll, first author, said that it did give future researchers “a target” for development of more efficient “cancer stem cell-specific” therapies. However, even if cancer stem cells were eliminated, Dr Woll added, there would still be a chance that genetic mutations could lead to other stem cells later becoming cancer stem cells. Professor Kamil Kranc, a Cancer Research UK stem cell expert based at the University of Edinburgh, said that the findings were a “a huge leap towards understanding the roots of blood cancers”. Dr Neil Rodrigues, of the European Cancer Stem Cell Research Institute at Cardiff University, said that the new study was “very important”, as it “precisely defines the provenance and biological composition of the cancer stem cell in MDS.”

Leader of the Pack: There are more than a dozen companies that have reached clinical trials in patients specifically targetting cancer stem cells including Boston BIomedical which was acquired by Dainippon Sumitomo Pharma Co. for US$ 2.63 billion and Oncomed at US$ 300 million valuation on NASDAQ.
The leader of he pack of cancer stem cell tergetting biotech companies is Stemcentrix. It has achieved an astounding valuation of US$ 5 billion without any sales and has raised half a billion dollars. This Californian start up is backed by heave weight investors Fidelity Investments, Artis Ventures, Silicon Valley Bank, Sequoia Capital, Elon Musk,  and a US$ 200 million investment from one of the most successful investors in the world Peter Thiel and his Founders Fund (earlier co-founder of Paypal, dscovered Facebook and invested in AirBnB and Palantir).
Scott J. Dylla
Scott Dylla co-founder Stemcentrix
Image result for brian slingerland stemcentrx
Brian Slingerland co-founder Stemcentrix
Image result for peter thiel
Peter Thiel The backer with the midas touch
Stemcentrx, formed in 2008, is developing a small-cell lung cancer therapy that homes in on a target, DLL3. The product, which uses an antibody to guide a cell-killing drug to its target, appears to be effective in some small-cell lung cancer patients. In a recent trial of 80 small-cell lung cancer patients, which was testing safe dosage, tumors shrank more often than they did in response to the only approved drug to treat the cancer, topotecan. For patients whose cancer exhibits the stem-cell marker the drug aims at, benefits were larger. It’s one of three drugs the company is already testing in human trials. Why do top investors put in so much money at such crazy valuations in such early stage highly risky venture? Probably based on the success of Pharmacyclics Inc., a cancer drug developer that was acquired by AbbVie Inc., for $21 billion in May 2015. Scott Dylla an ex Stanford stem cell targetting researcher and ex tech banker Brian Slingerland co-founded Stemcentrix. All this smart money is betting that CSCs are present in cancer biology and play the role of the mother bee in a beehive.

My conclusion: Both sides are showing evidence in this debate. It is finally irrefutable results in human clinicals of stem cell targetting drugs that will put in the last word. It may be that both are right. Different cancers may have different biologies some with CSCs and some without. Or cancer may be the most scary shape shifter of them all constantly changing its avatar. But if the CSCs are the cause of all recurrences of resistant cancers and we can kill the CSCs with allopathic and natural drugs then we may be able to save millions of lives.

I leave you with some useful information from European Cancer Stem Cell Research Institute at Cardiff University:

Diagram showing how cancer stem cells could arise
This shows how a normal stem cell creates a new stem cell and a progenitor cell. The normal progenitor cell then matures into differentiated (specialised) cell required by the body. An event such as a direct genetic mutation or effect from external factors could make these cells mutate or de-differentiate i.e. lose their specialisation at any stage. These affected cells could then produce a cancer stem cell. (With inspiration from Therese Winslow’s artwork)

Cancer stem cell theory
his shows the initial theory of how cancer stem cells can maintain a tumour. Even with conventional cancer therapy the cancer stem cells survive and the cancer can relapse but if we can identify cancer stem cells and develop specific treatment the patient outcome could be improved as the tumour would regress or enter remission.

Cancer stem cell theory 2
This shows another theory of how cancer stem cells can conserve a tumour. There may in fact be more than one type of cancer stem cell so with conventional cancer therapy the tumour mass is maintained. But again if we can identify cancer stem cells treatment could be improved.

Tumour regression
Pictures from Dr Richard Clarkson (Cardiff University) showing how Cancer Stem Cells grown in the laboratory can be killed over time – a model of tumour regression.