Genes Are Not The Only Drivers Of Colon Cancer

gdpawel said:

Metabolism Is The Principal Driver Of Human Cancer
Sometimes the genetic signal may not be the driver mutation. Other signaling pathways, like passenger mutations, could be operative.

Driver mutations are the ones that cause cancer cells to grow, whereas passengers are co-travellers that make no contribution to cancer development. It turns out that most mutations in cancers are passengers.

However, buried among them are much larger numbers of driver mutations than was previously anticipated. This suggests that many more genes contribute to cancer development than was thought.

Cells speak to each other and the messaages they send are interpreted via these intracellular pathways. You wouldn't know this using analyte-based genomic and proteomic methodologies. However, functional phenotype analysis provides the window. It can test various cell-death signaling pathways downstream.

While most scientists use genomic or proteomic platforms to detect mutations in these pathways that might result in response to chemicals, functional cytometric platforms have taken a different tack. By applying functional analysis, to measure the end result of pathway activation or deactivation, they can predict whether patients will actually respond.

The functional cytometric profiling platform has the capacity to measure genetic and epigenetic events as a functional, real-time adjunct to static genomic and proteomic platforms.

As virtually every presentation at the 2012 American Association for Cancer Research (AACR) meeting made obligatory reference to genomic analysis, almost every one of them then doubled back to metabolism as the principal driver of human cancer.

It may be very important to zero in on different genes and proteins. However, when actually taking the "targeted" drugs, do the drugs even enter the cancer cell? Once entered, does it immediately get metabolized or pumped out, or does it accumulate? In other words, will it work for every patient?

All the validations of this gene or that protein provides us with a variety of sophisticated techniques to provide new insights into the tumorigenic process, but if the "targeted" drug either won't "get in" in the first place or if it gets pumped out/extruded or if it gets immediately metabolized inside the cell, it just isn't going to work.

To overcome the problems of heterogeneity in cancer and prevent rapid cellular adaptation, oncologists are able to tailor chemotherapy in individual patients. This can be done by testing "live" tumor cells to see if they are susceptible to particular drugs, before giving them to the patient. DNA microarray work will prove to be highly complementary to the parellel breakthrough efforts in targeted therapy through cell function analysis.

Gene Mutation vs Chromosomal Theory of Cancer

http://cancerfocus.org/forum/showthread.php?t=3666

Driver Mutations and Passenger Mutations on the road to cancer

http://cancerfocus.org/forum/showthread.php?t=3808

gdpawel said:

Cancer cells hide by going dormant

In a major breakthrough that will change the way cancer is studied and treated in the future, Toronto scientists have discovered a key reason why many tumours may return after chemotherapy.

In a new study, researchers at the Princess Margaret Cancer Centre have shown that some of the cells that drive tumour growth hide from common chemotherapy drugs by going “dormant” — reigniting the disease when they awaken after treatments end.

“That’s where this paper lies is to begin to add more depth (and) complexity to why cancers come back, why they recur,” says renowned stem cell scientist John ****, whose paper was released Thursday by the journal Science.

“This will stimulate a lot of activity,” says ****, the study’s senior author.

Luba Slatkovska, head of research with Canadian Cancer Society’s Ontario division agrees, saying the discovery represents a paradigm shift for research into the disease.

“John **** is one of those researchers who is really changing the way we think about cancer, and this is another example,” Slatkovska says.

“We think that it’s going to become one of the new hot topics in cancer research,” she says.

****, also a molecular geneticist at the University of Toronto, says the newly-discovered dormant cells have precisely the same genetic mutations as those active ones that drove the original tumour to begin with.

Cancers occur when genetic mutations to a cell’s DNA cause them to replicate in an out-of-control fashion.

And it was assumed, **** says, that cancers returned after chemotherapy because of subsequent genetic mutations that made them resistant to the drugs being used against the original tumours.

“And that is certainly true in many cases,” he says.

But the discovery of the genetically-identical dormant cells shows that other forces are at play in cancer recurrence and that these nongenetic forces must now command the attention of the oncology community.

“We thought that there would have been a different set of (genetic) mutations, a different spectrum of mutations that would have explained why (the recurring) cells were resistant to chemotherapy,” **** says.

“And in a sense that’s not what we saw. We saw that they seemed to be quite similar or essentially identical (genetically) and so something else was driving their resistance to therapy.”

****, who last made headlines in 2011 when he led the team that first isolated blood stem cells, says that “something else” could include the micro-environments in which the dormant cells are located within the tumour.

“Is it that cells are sitting in the tumour in a location that makes them dormant?” he asks.

**** says that along with cancer cells, tumours contain a number of normal tissues, including blood vessels and immune system agents.

“And it appears that tumour cells can lie in proximity to these non-tumour cells and that can influence their behaviour,” **** says.

“So that is one of the properties we should be looking for, we should be looking for where tumour cells are sitting, who they’re close to and what kind of signals they are receiving.”

****, whose team grew human colorectal cancers in mice for the research, says only one in every several thousand cells in a tumour can actually drive its growth.

And many of these tumour drivers are susceptible to chemotherapies because most of the drugs now used in cancer treatment target cells that multiply at abnormal speeds — a signature of the disease in all its forms.

But if some of these stem-cell-like cancer drivers are dormant — in effect hiding their ability to rapidly replicate — the drugs will pass them over.

“Some of (the cancer driver cells) are actually quite sensitive (to chemotherapy) and other ones, particularly those ones that come from these so-called dormant cells are much more resistant,” **** says.

“And that can be responsible for relapse.”

**** says scientists now need to look for ways to kill these skulking cells or to control the factors that can awaken them.

“We need to understand the biological properties — not necessarily the genetic properties — that are driving dormancy,” he says.

An understanding of these nongenetic properties could lead to an entirely new generation of cancer medications, **** says.

Slatkovska, whose society has funded **** in the past but was not involved in the current study, says she can imagine the creation of drugs that could wake up the sleeping cells and expose them to killer chemo.

Drugs that could interfere with the external signals that call the dormant cells out of sleep could also become a weapon in the oncology arsenal, **** says.

“What our paper is saying is that on top of (targeting) the genetic properties of these cells you have to target the biological properties to be more effective,” **** says. “Everything doesn’t just rest on genetics.”

This is the second significant cancer advance out of Toronto hospitals just this month, and the second to home in on the healthy tissues that lie in proximity to tumours.

In a major breakthrough, Toronto scientists have discovered a new approach to cancer treatment that would target the “normal” cells embedded around tumours.

In a study just released, researchers at Mount Sinai Hospital show that it’s the non-cancerous cells that grow in and around a tumour that actually coax it to spread to other parts of the body.

“Basically the normal cells and the cancer cells are engaged in a dialogue which is controlling (spread),” says Dr. Jeff Wrana, the study’s senior author.

“The tumour cells are tweaking the normal cells, causing them to misbehave a little bit and causing those normal cells to produce signals, words if you will, that flow back to the tumour cells and promote the tumour cell’s growth.”

Wrana’s study, which appears in the journal Cell, revealed that the words delivered by the normal cells, in a tiny protein vocabulary, were actually telling their cancerous counterparts to spread or metastasize.

In particular, his team identified a protein signal labelled Cd81 — a so-called exosome — as the key instructional culprit in kicking off tumour spread.

Classical oncology research has almost always searched for ways to kill or halt the mutant cancer cells themselves.

But Wrana’s team, at the hospital’s Samuel Lunenfeld Research Institute, suggested that stopping the successful transmission of Cd81 from normal to cancer cells could arrest metastasis, the tumour spread that causes most deaths from the disease.

“It (Cd81) is a mass of information, not just a word or two, but a whole collection of information,” Wrana says.

“And these signals weren’t just telling cancer cells to metastasize, what they were doing is sort of teaching the cancer cells how to use their own machinery to spread,” he says.

Wrana says scientists can now search for drugs that would stop normal cells from sending out their signals or that would block those Cd81 instructions from attaching to tumour cells.

Researchers at the Princess Margaret Cancer Centre speculated that some cancer cells evaded chemotherapy treatment by going dormant.

This dormancy, which would essentially hide them from cancer drugs, could well have been caused by instructions from the healthy tissues nearby, the Princess Margaret study said.

Wrana says the common understanding of cancer sees tumours as separate entities from normal tissues, an alien lump of horror growing inside one or other of our organs.

But cancer is in fact hooked into our normal tissues, dependent on them for food and — as it turns out — directions on how to spread.

“People think of cancer as a kind of independent tissue growing inside them, the same way they might think of a bacterial infection,” Wrana says.

“But in reality cancer grows within the context of the normal tissue that surrounds it. So cancer really is a part of us that’s transformed and changed.”

Normal cells sending out the spread signals could include the organ tissues in which a tumour is growing or the blood vessel and immune system cells that are actually embedded within.

gdpawel said:

Gene Mutations Alone Cannot Explain Drug-Resistant Cancer

(ChemotherapyAdvisor) - The appearance of new genetic mutations during cancer therapy has long been correlated with drug resistance, treatment failure, and ultimately, relapse. But using single-cell genome sequencing, researchers at the Ontario Cancer Institute and Princess Margaret Cancer Center in Toronto, Canada have shown that gene mutations alone cannot explain drug-resistant cancer.

Tracking individual human colorectal tumor subclone cells that had been xenografted into mice, and sequencing their exomes (the gene-encoding regions of subclone genomes), the team discovered dramatic functional heterogeneity even among genetically identical clones; these included different tumor propagation patterns and different susceptibilities to oxaliplatin, which was reported by the the researchers in Science.

The findings represent “a major conceptual advance in understanding tumor growth and treatment response,” said senior author John ****, PhD, a pioneer in cancer stem cell research. “The data show that gene sequencing of tumors to find the spectrum of their mutations is definitely not the whole story when it comes to determining which therapies will be most effective.”

While some cells of a subclone contributed to tumor growth, others quickly became dormant, even though they harbored the same mutations as the more active cells, Dr. ****'s team found—and these dormant cells survived oxaliplatin therapy.

“This is a paradigm shift that shows research also needs to focus on the biological properties of cells,” Dr. **** said. Treatments that force dormant cells back into growth cycles could make them more sensitive to chemotherapies, he theorizes.

“Targeting the biology and growth properties of cancer cells could expand the repertoire of usable therapeutic agents and provide better outcomes for patients,” he added.

The study is “avante garde in its documentation that types of subcloning can happen against a stability of genetic changes—a clone within a given set of genetic changes can evolve into subpopulations within that clone without changing their genetic background, their mutations,” said Stephen Baylin, MD, Professor of Oncology and Deputy Director of the Cancer Center at the Johns Hopkins University School of Medicine.

Epigenetic factors, such as different DNA-methylation patterns that can silence gene expression, might help explain behavioral heterogeneity among genetically identical subclones, Dr. Baylin postulates.

“If you have got such genetic stability, then it's likely that the other facets of the subclones that emerged could have an epigenetic basis—long-term changes in gene expression,” he told ChemotherapyAdvisor. “Things like epigenetic abnormalities could be contributing to the emergence of new subclones with distinct properties.”

The new study “emphasizes those possibilities,” he said. When dormant tumor cells “come out and replenish the tumor,” other studies have shown that they do so with a “different epigenetic state” that appears to contribute to their drug resistance, he noted.

The traditional paradigm, with new mutations causing some tumor cells' drug resistance, is not completely wrong, Dr. Baylin is quick to point out. “That can happen,” he said of mutation-driven resistance. However, Baylin believes,the new findings reported by Dr. **** and his colleagues strongly suggest epigenetics is another “big player” in drug resistance.

Epigenetics-targeting drugs already exist, he notes. For example, azacitidine (5-azacytidine) and decitabine (5-aza-2′deoxycytidine) inhibit DNA methylation and are approved by the FDA for myelodysplastic syndrome. Histone deacetylase inhibitors might also target epigenetic pathways in tumors.

At low doses, ongoing studies in Dr. Baylin's lab suggest that azacitadine “sensitizes patients to subsequent chemotherapies or a new form of immunotherapy,” he said.

The findings reported by Dr. ****'s team indeed suggest that nongenetic targets for personalized anticancer agents are waiting to be identified, agrees Charis Eng, MD, PhD, FACP. Candidate targets include both epigenetic alterations and tumor microenvironments (healthy cells adjacent to tumors), she said.

Dr. Eng is the Hardis and American Cancer Society Professor and founding Chair of the Genomic Medicine Institute and directs the Institute's clinical component, the Center for Personalized Genetic Healthcare at the Cleveland Clinic. She believes that even though tumors' subclone gene mutations were identical from cell to cell, their functional genomics—“the ways they interact with each other, the ways they signal and make transcripts”—might still be quite variable.

Gene mutations, in other words, are just one part of a larger puzzle. Epigenetics, proteomics, even microbiomes, or the genomes of bacteria living on epithelial tissues in which tumors emerge, may all help explain why some subclone cells go dormant and evade chemotherapeutic attacks, while others succumb to treatment, she believes.

“Genomic changes are like the skeleton. The genome is the skeleton and everything else—the methylation, microenvironment, the microbiome—will be the flesh, the meat, the muscle and the skin,” Dr. Eng explained to ChemotherapyAdvisor. “So a look at everything, a snapshot profile of all the –omes, or what I call ‘integrated –omics,' which is the strength of my lab, integrates all the –omic platforms to see whether we can come up with an integrated view of what a cancer looks like.”

Even the Cancer Genome Atlas Project has added RNA and epigenetic assays to its profiling of tumor genomes, she notes.

The “sum total of the integration of all the ‘-omes' from all the cancer cells,” rather than any one component, may dictate chemotherapy responses in many cancers, she suspects. If that's the case, gene mutation-targeting drugs could one day represent just one part of clinical oncology's personalized-therapy arsenal.

“I have a funny feeling that even the three-dimensional positioning of the cells (within tumors) and how they talk to each other—whether by message or protein or exchanging genes—also matters,” Dr. Eng said. 

But she is quick to point out that the Science study involved xenografting human tumors into mice. Even though that model worked elegantly to show that subclone heterogeneity is not attributable to genetic mutations alone, it may not be the best way to find out exactly what else is responsible, she cautioned—especially if tumor microenvironments are involved.

“When the microenvironment is not represented well, alterations in the microenvironment might be missed,” she explained. “We have to ask: what is the interaction of each of these subclones with the mouse environment?”

Taking human tumors out of their human microenvironmental context might itself “have effects on different expressions of genes in the cancer,” Dr. Eng noted.

“We'd been assuming the enemy was simple-minded,” she said. “The enemy is complex. We need a multidisciplinary approach to look at the DNA and to understand the microenvironment, how it turns genes off and on in different contexts and even in different (cell) positions within tumors.”

Dr. Baylin agrees that the new findings will open doors to new avenues of research.

“We need to work on extending these observations to other tumors and to really keep studying the mechanisms that account for how these subclones emerge,” he said. “And then we need to correlate those changes really carefully with drug resistance so we can understand the molecular underpinnings in resistance patterns, and learn how to tailor therapeutic approaches to those molecular mechanisms.”

Reference: Kreso A, O'Brien CA, van Galen P, et al. Variable clonal repopulation dynamics influence chemotherapy responses in colorectal cancer. Science. 

http://www.sciencemag.org/content/early/2012/12/12/science.1227670.abstract?sid=63872db4-97e2-4580-a9eb-46531083d53e

 

Robert A. Nagourney, M.D.

It was during the last weeks of December that a particularly interesting article crossed my desk. The study done by a group from Toronto, Canada, is entitled Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer. The study examined the proliferative capacity and drug sensitivity in colorectal cancer cells that were tracked using a process known as lentiviral lineage tracking. The investigators showed that despite serial passages, the cell populations remained stable from a genomic standpoint.

What was most interesting was the finding that these genomically related subpopulations became progressively more resistant to oxaliplatin after drug exposure, suggesting what they described as “inherent functional variability.”

As one of several investigators engaged in the field of functional profiling, I found the article both interesting and extremely consistent with our laboratory observations. First, cancer cells display biological differences that may reflect environmental (microenvironmental) influences, epigenetics and other drivers not readily identified at the DNA level.

Second, these investigators, using extremely sophisticated molecular techniques, found, as the lead investigator said, “We should not be putting our eggs exclusively in the genetics basket.” This quote from the lead investigator, John ****, was particularly resonant.

As many of you who read my blogs know, a recurring theme in these pages is the need to broaden our scope and examine the protein, metabolic and functional characteristics of the cancer cells in their native state. Once again we find that as our most accomplished molecular brethren drill down to the bedrock of cancer biology, they are confronted by complexities and crosstalk that can only be effectively studied at the level of cell biology.

http://www.the-scientist.com/?articles.view/articleNo/33640/title/Cancer-More-Diverse-than-Its-Genetics/

manwithnoname said:

Ketogenic

I still have concerns about this diet, ketones and lactate can stimulate CSCs, there is a paper about it somewhere; 

also strange to me that they xenograft human tumours in mice with no immune system, then test drug reactions...like the immune system plays no part!  we need a better system.

You have that right! The problem this kind of experiment (tumor grafting analysis) is that they are usually done on SCID (severe combined immunodeficiency) mice - aka, mice with zero immune system. They also use nude mice, which don't have a thymus (and therefore no T cells). T cells (T lymphocytes) play a central role in cell-mediated immunity.