Mastering Dynamic Cell Signaling

The following article was first published on Al Fin Longevity blog

Cells make decisions in fluctuating environments using inherently noisy biochemical mechanisms. Such effects create considerable, unpredictable variation – known as ‘stochasticity’– both over time and between genetically identical cells. To understand how cells exploit and control these biochemical fluctuations, scientists must identify the sources of stochasticity, quantify their effects, and distinguish variation that carries information about the biological environment from confounding noise.

In their PNAS paper, Dr Bowsher and Professor Swain show how to decompose the fluctuations of biochemical networks into multiple components and how to design experimental ‘reporters’ to measure these components in living cells.

The paper, which describes the application of this approach to yeast cells, shows that the majority of cellular variation may be informational in origin and due to fluctuations in the cellular environment. The results pave the way to a better understanding of the dynamics of signal processing and decision-making by cells. _SD

Cell Signaling Network, Preliminary Sketch
We begin to comprehend the potential power of cell signaling mastery, when we observe research breakthroughs such as the following:

In laboratory experiments with mouse cells, the researchers found that a specific protein that regulates cell aging also controls a process that causes blood-making stem cells to age. Using drugs to inhibit the action of this protein (called Cdc42) reversed aging of the hematopoietic stem cells and restored their function to a level similar to that of younger stem cells.

It had been [previously] believed that the aging of hematopoietic stem cells was locked in by nature and could not be reversed by using drugs, according to a hospital news release.

...The study by scientists at Cincinnati Children's Hospital Medical Center and Ulm University Medicine in Germany appeared online May 3 in the journal Cell Stem Cell. _USN

Turning old hematopoietic stem cells into young hematopoietic stem cells is nothing to sneeze at. And it is only a slight foretaste of what is becoming possible, as we better understand cell signaling networks and the signaling involved in gene expression.

One of the more exciting near-to-intermediate term possibility arising from the coming mastery of cell signaling, is the ability to reverse neurodegenerative diseases which involve abnormal protein folding. Diseases such as Alzheimer's, Huntington's, Parkinson's, and "mad cow disease," for example, involve abnormal proteins leading to cell destruction and loss of neural function.

Researchers at the University of Leicester uncovered how the build-up of proteins in mice with prion disease resulted in brain cells dying.

They showed that as misfolded protein levels rise in the brain, cells respond by trying to shut down the production of all new proteins.

...The team at the Medical Research Council laboratory in Leicester then tried to manipulate the switch which turned the protein factory off. When they prevented cells from shutting down, they prevented the brain dying. The mice then lived significantly longer.

Each neuro-degenerative disease results in a unique set of misfolded proteins being produced, which are then thought to lead to brain cells dying.

Prof Giovanna Mallucci told the BBC: "The novelty here is we're just targeting the protein shut-down, we're ignoring the prion protein and that's what makes it potentially relevant across the board."

The idea, which has not yet been tested, is that if preventing the shut down protects the brain in prion disease - it might work in all diseases that have misfolded proteins.

Prof Mallucci added: "What it gives you is an appealing concept that one pathway and therefore one treatment could have benefits across a range of disorders. _BBC

Nature article

Complex cell signaling is also involved in the control of gene expression, including critically important DNA repair, and control of telomere length in cells -- which controls the number of cell doublings allowed.

If you click on the image above, you can view an enlarged version of a portion of a cell signaling network. Such complexity explains the need for high powered computational backup in the attempt to decode these networks, as a prelude to their mastery.

Cellular processes take place very quickly, and in a closely controlled and balanced chemical milieu. If we are to learn to intervene on the level of the cell in a beneficial way, we must proceed with care. But we definitely aim to proceed.

Marvelous Video of Protein Messenger Traversing a Cell

The protein Paxillin is involved in the growth and movement of cells. UCSD researchers have produced an amazing video of paxillin molecules transiting a cell along with actin filaments. This research suggests a future where more and more of the complex cell signaling pathway of proteins will be captured on video for study and experiment.

Scientists have captured on video the intracellular version of a postal delivery service. Reporting in the journal Biochemical and Biophysical Research Communications (BBRC), bioengineering researchers at UC San Diego published videos of a key message-carrying protein called paxillin moving abruptly from hubs of communication and transportation activity on the cell surface toward the nucleus. Paxillin was labeled with a red fluorescence marker to make it stand out in live cells.

“It’s amazing to us. We thought the cell was so simple,” said Shu Chien, the senior author of the BBRC paper and a professor of bioengineering at UCSD’s Jacobs School of Engineering. “But it’s really very complex and I’m not sure we’re covering much as yet. We certainly don’t know all the interactions among these molecules that bring the cell into action.”

Examining living cells through a microscope, Chien and the paper’s co-author, associate project scientist Ying-Li Hu, filmed red-fluorescence-tagged paxillin molecules traveling from cells’ outer membrane along green-fluorescence-labeled traces of cytoskeleton. Even without video evidence, scientists have confirmed over the past 10 years that higher organisms use paxillin as a transmitter of locomotion and gene-expression signals from several classes of growth-factor receptors to the nucleus.

Cancer researchers are eager to understand paxillin’s many interactions because their malfunctions have been linked to a variety of cancers, tumor metastasis, and other disease processes. Tumor-causing versions of signaling molecules may attach to paxillin and disturb the normal adhesion and growth factor signaling steps required for controlled proliferation and cell growth. For example, human papilloma virus, which can cause cervical cancer, makes a protein that binds to paxillin and that interaction may contribute to the carcinogenic potential of the sexually transmitted virus.

Source

Click here to view the video and accompanying report.

Forcing Cancer to Revert to Normal Cells

Cancer is one of the leading causes of death in the developed western world, and the leading cause of disability. What if physicians could simply "turn back the clock" on cancer, and make the cancer cells into normal cells?

Now, in the American Association of Anatomists’ plenary lecture and symposium, at Experimental Biology 2007 in Washington, DC, Dr. Hendrix describes new research that used an innovative experimental approach to provide unique insights into how scientists can change human metastatic melanoma cells back to normal-like skin cells - by exposing the tumor cells to the embryonic microenvironment of human embryonic stem cells, the zebra fish and the chick embryo.

Dr. Hendrix’s plenary lecture on April 29 is a highlight of the scientific program of the American Association of Anatomists. Her presentation is titled "the convergence of embryonic and cancer signaling pathways: role in tumor cell plasticity." Plasticity refers to the ability of the tumor cell, like the embryonic cell, to express or change into multiple, different types of cells.

....When aggressive melanoma and other tumor cells (recent findings also report Nodal expression in breast cancer and testicular cancer) regain the ability to express a potent embryonic morphogen like Nodal, the presence of the Nodal and the signals it sends and receives appear to play a key role in tumor cell plasticity and progression.

Most noteworthy, Dr. Hendrix’s team’s also has shown that inhibition of Nodal signaling leads to a reduction in melanoma cell invasiveness and ability to create new tumors. In fact, with inhibition of Nodal, the metastatic melanoma cells are reverted to a more benign skin cell without the ability to form tumors.

More details at source

After fertilisation of the egg, early cells are unspecialised. With development of the embryo, cells differentiate to form specialised tissues and organs. Recently it has been learned that cells can de-differentiate--or go back to simpler cell types. It is possible to create stem cells from differentiated cells, just as cancer cells can be regressed to normal cells.

There is a startling variety of cell types in the human body. But each cell type possesses essentially the same DNA as all other cell types. Differentiation of cells dictates which genes can be expressed. De-differentiation turns back the clock. From cancer to normal cells. From normal cells to stem cells.

Humans vs. Bacteria: An Unfair Advantage?

There is an arms race between humans and bacteria. My opinion for decades now, has been that the human brain gives humans the long term advantage in this race. Here is more detail on an approach to fight bacterial resistance that I alluded to in an earlier post:

In 2005, biochemist Floyd Romesberg of the Scripps Research Institute, near San Diego, announced that his lab had discovered a gene called LexA that switches on the error-prone DNA, enabling the microbe to mutate rapidly.

Shortly before this announcement, Romesberg presented some startling findings during a meeting at the institute I cofounded, the BioAgenda Institute. Romesberg, a short, intense man with a graying beard and an ability to explain complex ideas to nonscientists, told us that his lab had learned how to turn off LexA. Several major biotechnology figures at the meeting said to me, "This is huge." At the time, several top-tier venture-capital firms were vying for Romesberg's attention in hopes of starting a company. Ned David was one of the lucky cofounders who later named the company Achaogen--"achao" means "against chaos" in Latin.

Now Romesberg has announced the discovery of a molecule that inhibits LexA'sability to cause mutations; it was found after the lab screened more than 100,000 possible compounds. The molecule also slips easily into a bacterial cell, which is critical to creating an effective tool to zap the bugs.

This new mutation killer does not prevent bacterial infections. Taken in combination with antibiotics, it would prevent the bugs from mutating in response to the antibiotics, thereby preventing resistant strains from developing. The drug could also be used to restore the effectiveness of older antibiotics that have been rendered almost useless by bacterial resistance.

Source

I particularly like the idea of restoring efficacy to older antibiotics--since those tried and true drugs are much less expensive than the newer "uber-antibiotics."

Using bacterial cell signaling proteins as drug targets is logical, and much easier with modern lab techniques. It is the current explosion of discovery in the biological sciences--combined with bioinformatics software AND proper economic incentives--that will change the face of medical treatment. This revolution will happen in the developed world and in the third world, thanks to the generosity of the people of western nations.


Perhaps the idea of western aid to impoverished and underdeveloped nations originated in the protestand missionaries of the 18th, 19th, and 20th centuries. But now the concept is thoroughly secularized and mainstreamed in the west.

Contrast the many billions of dollars of private aid from western organisations with muslim "aid" from wealthy oil states that is oriented toward spreading violent islamism around the world. Russian and Chinese "aid" is oriented toward strategic alliances and natural resources of the third world. In contrast, the many private, non-state organisation of the western world generally try to address the most serious humanitarian problems. Often this effort is opposed by the dictatorships and other political entities that cause most of the hardship in the first place.

DNA Repair: BRIT1 in Cancer--Built-In Telomerase Inhibitor Blocks Cell Immortalisation

BRIT1 is a gene that functions as a transcriptional inhibitor of hTERT (human telomerase reverse transcriptase), the catalytic subunit of human telomerase. hTERT is the rate limiting determinant of telomerase and cell immortalisation.

This Newswise newsrelease discusses recent developments in uncovering the relationship between BRIT1, hTERT, DNA repair, and cancer onset.

A single gene plays a pivotal role launching two DNA damage detection and repair pathways in the human genome, suggesting that it functions as a previously unidentified tumor suppressor gene, researchers at The University of Texas M. D. Anderson Cancer Center report in Cancer Cell.

The advance online publication also reports that the gene - called BRIT1 - is under-expressed in human ovarian, breast and prostate cancer cell lines.

Defects in BRIT1 seem to be a key pathological alteration in cancer initiation and progression, the authors note, and further understanding of its function may contribute to novel, therapeutic approaches to cancer.

"Disruption of BRIT1 function abolishes DNA damage responses and leads to genomic instability," said senior author Shiaw-Yih Lin, Ph.D., assistant professor in the Department of Molecular Therapeutics at M. D. Anderson. Genomic instability fuels the initiation, growth and spread of cancer.

A signaling network of molecular checkpoint pathways protects the human genome by detecting DNA damage, initiating repair and halting division of the damaged cell so that it does not replicate.

In a series of laboratory experiments, Lin and colleagues show that BRIT1 activates two of these checkpoint pathways. The ATM pathway springs into action in response to damage caused by ionizing radiation. The ATR pathway responds to DNA damage caused by ultraviolet radiation.

By using small interfering RNA (siRNA) to silence the BRIT1 gene, the scientists shut down both checkpoint pathways in cells exposed to either type of radiation.

Researchers then used siRNA to silence the gene in normal human mammary epithelial cells (HMEC). The result: Inactivation of the gene caused chromosomal aberrations in 21.2 to 25.6 percent of cells. Control group HMEC had no cells with chromosomal aberrations. In cells with the gene silenced that were then exposed to ionizing radiation, 80 percent of cells had chromosomal aberrations.

"We also found that BRIT1 expression is aberrant in several forms of human cancer," Lin said. The team found reduced expression of the gene in 35 of 87 cases of advanced epithelial ovarian cancer. They also found reduced expression in breast and prostate cancer tissue compared with non-cancerous cells.

Genetic analysis of breast cancer specimens revealed a truncated, dysfunctional version of the BRIT1 protein in one sample.

Loss of the DNA damage checkpoint function and the ability to proliferate indefinitely are two cellular changes required for the development of cancer. Lin and colleagues have now tied the gene to both factors. They previously identified BRIT1 as a repressor of hTERT, a protein that when reactivated immortalizes cells, allowing them to multiply indefinitely.

Source.

The cell signaling pathways that regulate detection of DNA damage and the subsequent halting of the cell cycle, DNA repair, and possibly trigger apoptosis, is very complex. By using tools such as siRNA to selectively block individual components of this complex network, researchers can get closer to understanding how this intricate cell machinery functions.

The relationship between BRIT1, hTERT, cancer and cell immortalisation, suggests tantalising clues to possible cancer treatments as well as anti-aging therapies. But it is still too early to be certain of the best avenue of approach. This is an intriguing line of research, nevertheless.

Decoding Cell Signaling: Struggle and Serendipity

In 1965, soil samples being screened for useful antibiotic candidates serendipitously yielded a microorganism that produced rapamycin. Although rapamycin was not a particularly good antibiotic, it did display interesting effects on yeast, insect larvae, and mammalian cells. Through careful research, the target of rapamycin inside the mammalian cell was located, and labeled mTOR (mammalian Target of Rapamycin). Due to its effect on mTOR, rapamycin is being investigated for a broad range of therapies.

Recent research is zeroing in on mTOR as a useful target for therapies for Glioma and other cancers.

Other recent research points to mTOR as a key to treating obesity.

mTor is key to the initiation of protein synthesis, and the initiation of cell cycling and division. The process of muscular hypertrophy utilises mTOR, both in skeletal muscle and smooth muscle. This places mTOR at the center of possible treatments for vascular stenosis due to smooth muscle hypertrophy.

It is the sheer complexity of the cell signaling pathways that causes potentially revolutionary research to proceed at a snail's pace. It is important that the therapeutic agent target only those molecules that achieve a useful result. Achieving the proper level of specificity involves both struggle and serendipity.

Stem Cells and Cancer: The Exquisite Dance

As many as 20% of cancers or more originate in stem cells. Our bodies are homes to hordes of stem cells, sometimes quiescent, sometimes regenerative, and sometimes proliferating out of control. The female breast is one organ that is amply supplied with stem cells.

"People have long suspected there should be a stem cell population in the human breast gland," said Sigurdsson who is part of the ESF-funded team led by Thorarinn Gudjonsson. A 'virgin' breast, before pregnancy, is very different to a fully functioning, milk-producing breast. With lactation, the breast becomes fully differentiated, and once this stage is over, it involutes. This cycle of proliferation, differentiation and apoptosis also happens in every menstrual cycle and in a more dramatic form during pregnancy. "This caught our attention, and has driven our research," Sigurdsson pointed out.

Breast cancer almost always occurs in the luminal epithelial compartment, which is also where milk is produced. Perhaps it is not surprising then, that stem cells reside in this compartment. In 2002, Thorarinn Gudjonsson, successfully isolated cells from the human breast with stem cell properties.

Gudjonsson immortalised these cells and grew them in three dimensional matrix that mimics the real, living tissue. Biologists have long relied on 2-dimensional cell cultures as the basic tool of their trade. But there is a big difference between a flat layer of cells and culturing cells in three-dimensions. The Icelandic researchers, realizing just how much a cells context matters, used the 3-D cell culture pioneered by Mina Bissell, at the Lawrence Berkeley National Laboratory in California. "We can build up a 3-D breast structure similar to what you have in vivo," says Gudjonsson.

"You can analyse cell-cell interactions and signaling pathways in these cells during morphogenesis and in cancer progression." The Icelandic researchers are now focusing their efforts on how endothelial cells convey signals to stem cells in normal breast formation and in cancer. In collaboration with another Icelandic research team, the Gudjonsson lab is now unraveling the role of tyrosine kinase receptors and their downstream signaling events. Source.

And so we see that stem cells are a two-edged sword in the breast. The same is true in other tissues. Stem cells are vital for regenerative functions, but must be held in check by tumour suppressor genes.

[A tumour suppressor gene,]PTEN functions to decide whether to progress further though the cell cycle or return to a quiescent (G0) state. Disrupting PTEN in stem cells results in more active cycling and a loss of the quiescent pool of stems cells that is necessary for long-term stem cell maintenance.

PTEN can be phosphorylated in response to other signals that modulate its function. The Li Lab's work demonstrated distinct populations of hematopoetic stem cells (HSCs) with phosphorylated and unphosphorylated forms of PTEN, suggesting that PTEN phosphorylation may be a 'sensor' that could help integrate external cues with the HSC quiescence/activation switch.

"Although the primary mutation occurs in stem cells, leading to short-term expansion of normal stem cells, this mutation alone is not enough to support unlimited expansion of either normal or cancer stem cells," said Dr. Li. "A secondary mutation is therefore required to empower the leukemia cells resulting from this mutation to undergo unlimited expansion. Exploring the nature of the secondary mutation, together with the primary mutation in PTEN, can help to understand the self-renewal ability of stem cells and perhaps will identify new molecules that can be targeted to provide effective leukemia treatment without adversely affecting normal stem cells." Source.

Sometimes the tumour suppressor genes are silenced, and if the tumour cells can maintain the silencing of the suppressor genes, the tumours are free to grow. Methylation is one means of gene silencing that tumours take advantage of.

Our cells become cancerous when the normal controls over cell growth and death go awry. This deregulation has traditionally been linked to DNA mutations of single genes or deletion of large sections of the chromosome. However more recently it has become clear that gene silencing in cancer can also occur, in the absence of changes to the DNA sequence: a phenomenon known as 'epigenetics'. DNA methylation is one of the main epigenetic processes.

In cancer, the DNA methylation pattern of many genes changes. However, until now, it was believed that only individual single genes were silenced by methylation. But this is not necessarily the case. "What we've found is that non-methylated genes that reside in a particular suburb near methylated genes are also silenced. Their physical proximity to the methylated genes affects their ability to function. It's a case of being in the wrong neighbourhood at the wrong time", says Assoc. Professor Clark.

The Garvan team developed a new method to scan the entire complement of the 30 000 plus genes - the entire genome - in the cancer tissue samples, which allowed widespread changes to be identified in specific parts of the genome.

They were amazed to find the extent of gene silencing. Assoc. Professor Clark adds: "What we want to do now is determine if these same regions are switched off in other types of cancers". Source.

Given that adult male testicles carry a sizable contingent of stem cells, it is perhaps surprising that testicular cancer is no more common than it is. There is considerable interest in testicular stem cells, and their possible potential in regenerative medicine. Projects are currently underway to learn how to extract and culture testicular stem cells in vitro. The following describes a project to culture specifically the spermatogonial stem cells, although more pluripotent cells are present.

"Our plan is to develop a culture system for spermatogonial stem cells" de Rooij told conference attendees. Although admitting the leap to humans is considerable, the colonised mouse testes are already providing useful insights.

"We'd like to know how to culture human spermatogenic stem cells to restore male fertility after cancer therapy," says Hannu Sariola, from the University of Helsinki in Finland who is also working towards a similar goal.

Bizarrely, a brain cell growth factor also has a powerful influence on spermatogonial stem cells. Glial cell derived neurotrophic factor (GDNF) is also involved in spermatogenesis: levels are high during the neonatal period and drop in adulthood. Indeed, mice that have been genetically manipulated to express high levels of GDNF in the testes produce huge clusters of spermatogonial stem cells. But the risk of cancer is boosted too, so it is not just about turning on the GDNF tap indiscriminately. It must be tightly regulated, Sariola pointed out.

The Dutch researchers are also hunting for the ideal conditions and nutrients that will coax spermatogonial stem cells into becoming sperm. So far, they have found that growth factors GDNF and fibroblast growth factor (FGF) seem to be necessary to enhance cell growth. The team's next move is to transplant monkey and human cells into the mouse testes system. Source.

Such are a few of the many molecular moves of the exquisite dance of the cell. It is not surprising that so many things sometimes go wrong. Rather, it is amazing that so many things go right for so long. But then, that is evolution's doing--we cannot take credit. The things that are coming, well, that is another matter.

Dancing Molecules of Life Extension

It has been known for over a decade that the Insulin Growth Factor 1(IGF-1) signaling was involved in longevity. Reducing IGF-1 signaling in knockout mice led to longer lived mice, but the mice developed as dwarves. Now scientists are learning how to influence the IGF-1 signaling system to prolong lifespan, without interfering with normal growth and development, and other vital systems.

This newsrelease discusses the discoveries of Salk Institute researchers, into the IGF signaling system and its relationship to ageing.

Within a hormone-triggered cascade of molecular signals that plays a crucial for a wide range of physiological functions, researchers for the very first time have identified a protein that functions specifically to extend lifespan and youthfulness -- without disrupting fertility, immunity or the organism's response to stress.

"In past experiments, meddling with this versatile pathway to exploit its beneficial effects on aging and life span inevitably invited a host of problems," says Andrew Dillin, Ph.D., an assistant professor in the Molecular and Cell Biology Laboratory at the Salk Institute for Biological Studies and leader of the study, reported in the March 9 issue of the journal Cell.

The Salk scientists discovered the protein in studies with worms, a commonly used lab model in genetics; since this signaling cascade including the newly identified protein is conserved across many species, including humans, these findings raise the prospect that one day it might be possible to medically tweak this pathway to slow aging and improve the quality of life without harmful consequences to the body.

Read the entire report here. Here is a related SENS abstract.

The intricate dance of interacting molecules described in the report is fascinating, but it is typical of the complexity of biological systems. It is only now, when the tools of science and bioinformatics are growing so sophisticated, that scientists could hope to dig so deeply into the workings of cellular and organismic systems.

Growth Factor Blocker to Treat Advanced Cancers

Snowcrash provides another excellent posting at Biosingularity. Snowcrash describes research from the Max Planck Institute leading to a new drug for treating advanced renal cell carcinoma and gastro-intestinal stromal tumours. This research involves important aspects of proteomics, and an earlier posting by Snowcrash illuminates the important topic of cell signaling networks in proteomics.

Here is an excerpt from the article:
When particular growth factors are bound to specific receptors on the surface of a cell, this can cause the cell to propagate itself and build certain tissue similar to blood vessels. Worldwide, research into receptors has focused on a special class of proteins, called tyrosine kinases. They are responsible for causing the received signal to be transduced through a long signalling cascade into the nucleus, triggering cell division and multiplication. Signalling cascades are absolutely necessary, if various tissues - like blood vessels, nerve tissue, and connective tissue - are to be built up during the development of an organism and in the process of tissue regeneration.

Research has focussed on these tumour cell signalling cascades, because in cancers they are often disturbed. If there were a way to block growth factors, or the receptors on the cellular surface from tumour cells, that could lead to targeted therapies against cancers. Already in the 1980s, cancer researcher Axel Ullrich, then a scientist at Genentech (USA), working with colleagues in the UK and Israel, succeeded in describing the structure and function of a receptor for epidermal growth factor (EGF). Since then, tyrosine kinases and various growth factors have been at the focus of research and development of therapies against tumours.

If this incredibly important topic interests you, visitBiosingularity and read the whole thing.

Here is an abstract describing similar basic research.