Cancer in 3D

Incorrect Cancer Knowledge?

Is what we think we know about cancer wrong? Or at least some major assumptions? Probably yes. Since the genome project allowed us to learn so much more about the human genome and perhaps as importantly or more so, bringing down the cost and increasing the speed of tests by many fold, advances are accelerating. They are now finding that all that “junk DNA” that supposedly had no purpose is very important and codes for non-coding RNA that doesn’t make proteins, but control the making of them and many other functions. However, other than the DNA studies, there have been many studies on a more macro level and primarily in petri dishes. This could be a big mistake.

Petri dishes basically create a two dimensional environment for the cancer cells to grow in. The Johns Hopkins Health Review describes research being done at Hopkins by Denis Wirtz on how cancer behaves when it is in a 3D format as it would be in the body.

Zig Zag Path

Cancer cells have been thought to take zigzag path when they move, almost a random pattern. (That isn’t because they used zig zags.) When Dr. Wirtz and his team put cancer cells in a 3D matrix that better replicates the environment in the body, the cancer cells behave very differently. They move in a straight line through the cells. In a petri dish they look flat and tend to adhere to the bottom and have problems moving. In the 3D environment, the cells were rounder and had long protrusions at each end. The proteins that predict is virulence were spread through the cell instead of mostly on the bottom of the cell. They didn’t stick to the bottom of the medium and move slowly. They moved rapidly through the medium and in straight lines.

Bad research and New Life for Drugs?

So a lot of what research has shown to be the behavior of cancers was just caused by the two dimensional environment of the petri dish. Dr. Wirtz thinks that a lot of the research has to be re-examined and possibly thrown out. Of course, other scientists aren’t too pleased with this. He also thinks that drug companies might want to reexamine some of the drugs that failed clinical trials. They might work very differently on cancer cells in a 3D environment.

Kenneth Yamada has also published some important papers on the need to investigate in a 3D environment. He is one of the most cited scientists and has published on a range of topics.

Problems to Solve

Using 3D matrices should help research, but there will be problems too. Scientists sometimes do things because they are easy even though they don’t replicate the in vivo environment. Petri dishes are easy. The problem is that electron microscopy works great in a dish, not so much in a 3D matrix.  Same goes for other important research tools. That problem needs to be resolved.


Most research has been on tumor shrinkage. Why? Once again because it is easy to study and measure. But a big problem with cancer is metastasis, when the cancer spreads to other parts of the body. This is still poorly understood but very little research dollars are going toward this. We really need for more money to be put into metastasis research using 3D matrices.

Preventing Nosocomial Infections

Nosocomial Infections – So what is that? Infections picked up in the hospital. Proper cleaning can reduce it, such as wound cleaning, hand cleaning, facilities cleaning such as carpet cleaning, floor cleaning, and any other surface you can think of. It is not a trivial matter. Five to ten percent of all patients get a hospital acquired infection and about 100,000 people die of the complications each year. Continue reading Preventing Nosocomial Infections

RNAs – Diagnostic & Therapeutic

There was a lot of DNA, 90% or so that used to be called junk DNA. Seems odd that no one would wonder what the purpose of that 90% was. Well, researchers have recently realized that like the other 10%, it creates RNA. But, whereas the 10% creates RNA that codes for proteins, the other 90% is called noncoding RNA. Some is called microRNA (miRNA) and others are called long noncoding RNAs (lncRNA), both names being descriptive.

Noncoding RNA Function

So what does this 90% do? It is involved in epigenetic mechanisms, gene expression and protein activity. It does this for both normal functioning and in disease states like cancer.

In other words, these RNAs regulate protein activity and gene function. So, the race is on to discover what all these RNAs do and see if they can be used as a diagnostic test for disease or infection or if they can be used as a treatment.


In one example involving patients with hepatitis C, an miRNA, miR-122 was targeted. A drug called miravirsen, which is an antisense oligonucleotide, was used to treat the patients. It binds with miR-122 and keeps it from working. But hepatitis C needs it to replicate and also for stability, which should cure or reduce the affect of the hepatitis C. It is still in trials, so the final results aren’t know yet.


Cancer is a major of study. Because noncoding RNAs are so ubiquitous, they are not only involved in just about every aspect of normal functioning, they are involved in almost every aspect of cancer as well: initiation, progression and proliferation and metastasis.

Dr. Calin at MD Anderson Cancer Center at the University of Texas is looking for miRNAs that are in the range of 21-22 nucleotides long. If these can be associated with certain cancers or stages of cancers, they will have great benefit as a diagnostic tool. They are of interest because they are not only found in the tumors but also circulating in the blood and other bodily fluids.

The technology has progressed enough that it isn’t holding back discovery as much designing and running studies that prove the predictive value of the biomarkers.

Therapeutic Use Issues

It is one thing to use a noncoding RNA as a diagnostic tool. You can look for variations from normal levels. But to use them for therapeutic tools is a lot trickier.  Usually, one of these RNAs has roles in many pathways. So if you disrupt it to fix something in one pathway, you may mess up something else in a number of other pathways. So you need to look for an RNA that very specific activity.

Cancer Transcriptome Diagnostics

Cancer is constantly changing and methods to detect those changes can be very important. By looking at the entire cancer transcriptome it can quickly tell what expression changes have happened in the cancer.

Kathy Liszewski wrote an interesting article on this in Genetic Engineering News which will be briefly summarized here.

RNA and Cancer

Also, by looking at how RNA expression is changing, it can give information on how the cancer will respond to different therapies in addition to giving information on their oncogenic properties.

Disruption of RNA at different points in its life or in different ways can lead to or make a difference in cancers.

Radiation exposure can lead to  fusion oncogenes, some affecting the MAPK pathways and others caused overexpression of a nuclear receptor that is connected with malignancy.

RNA Variety

One new area of research is looking at the many modifications of RNA of which 110 are known so far. Something as simple as a change in methylation can change everything. It can affect where it goes, its interpretation, and affect stability. All can help lead to cancer.

This has allowed new diagnostic indicators to be found that can give an indication of time until relapse.

RNA Editing

The amount of RNA editing that goes on in the body is just beginning to be appreciated. It allows changes in proteins  that will change the function. Interestingly, different tissues in the body can have different RNA editing profiles. Dr. Li of Stanford thinks that there may be more editing enzymes in cancer tissue.

He found an example of this in human heptocellular carcinoma increased the tumor initiating potential of a protein.

The Cancer Genome Atlas should help researchers. It does large scale sequencing of cancers and then distributes the data to researchers.


There is a family of 9 DNA editing enzymes (APOBEC) that aid in viral immunity. Some of the 9 also help diversify antibody gene DNA and also edit mRNA. Although 4 of the family can target retroviruses like HIV-1, one of them, APOBEC3B can interfere. Dr. Reuben Harris of the Masonic Cancer Center hypothesized that APOBEC3B would be an important cause or factor in a wide range of cancers.

His research showed its involvement in mutagenesis in many cancers and was corroborated by separate research done by Drs. Gordenin and Stratton. So this may lead to useful diagnostic tests and identify cancers that are more difficult to treat and help suggest targeted treatments.


MicroRNAs are critical for normal tissue functioning. Many of them though are found in regions of the genome that are fragile. As cancer progresses the functioning of the microRNAs is changed.

Two microRNAs, miR-143 and miR-145 have been found to be  greatly reduced in colon cancer and both are in the 5q32 chromosome.

SKIP and Apoptosis

The enzyme complex, RNA polymerase II catalyzes DNA transcription. It sometimes stops and needs SKIP to get restarted. SKIP is Ski-interacting protein.  That part is good, but SKIP can also help cancer cells survive. Dr. Katherine Jones found that by reducing SKIP, it increased the likelihood of p53-mediated apoptosis. So if small molecule SKIP inhibitors can be found, chemotherapy agents can become more effective.



Liquid Biopsies Up & Coming

New diagnostic blood tests are rapidly changing cancer treatment. They are called liquid biopsies. They are eliminating needle or surgical biopsies for some patients.

Rather than capturing cells from the tumor itself, the process is to take a blood sample and capture cancer cells or the DNA from cancer cells in the sample. It is not clear how these tests will be used and how much of a change they will make in medicine, but a number of doctors see it as leading to a major change that will allow for an increase in personalized medicine.

More frequent timely testing

It makes it possibly to repeatedly sample what a cancer is doing in a noninvasive manner. This has several important implications. It hasn’t been easy to sample cancer on a repeated basis in the past and never non-invasively. This allows not only profiling the cancer’s genes, but it also makes it possible to track mutations and to target drugs to them. Plus, you can get faster feedback and therefore tell whether a protocol is working and how it might need to be changed over time.

The technology is improving rapidly, as is its use. It was only used in research two years ago. There are now several available on the market and  more than ten in development. Some doctors are starting to use them on a regular basis, and more are beginning to try them.

Examples of usefulness

One example of their benefit is in breast cancer recurrences where the recurrence can be found far sooner than it normally would be, which can give an edge in treatment.

University of Texas MD Anderson Cancer Center now uses liquid biopsies on about 10 percent of its metastatic colon cancer patients. It is also useful in place of, or to support lung biopsies, which can be difficult to do.

Treatment effectiveness

Some doctors are quite excited because most cancer drugs are quite toxic and many times are not effective. This will allow doctors to determine the effectiveness more quickly and save the cost of the drugs and the damage and suffering that the patient goes through.

Currently, doctors are using them when they don’t know where the cancer is, or when it is difficult to get to it for a regular biopsy. It is also useful when the patient’s current drug no longer works and it is necessary to figure out what direction to take treatment going forward.

The problem at present though is that studies of the process haven’t caught up to the liquid biopsy process. It is clear that there is great potential, but there are no studies proving that they are beneficial or if they are accurate and what their specificity is.

Dr. M. Cristofanilli of Thomas Jefferson University in Philadelphia points out several features of liquid biopsies and cancer that make them useful. When you do a tissue biopsy, in most cases a sample is taken from only one spot in the tumor. But, different regions of the tumor can vary dramatically, having different genes and/or hormones active.

Two other items make liquid biopsies useful. When tumors metastasize, just as with different regions within the tumor, they can vary quite a bit in the different locations that they spread to. On top of that, they change again due to the treatment drugs and radiation.

For most tissue biopsies,  you don’t or can’t do them on a regular basis. That means you are frequently working with outdated information. Considering the speed with which cancer can change, this is a problem.

The first liquid biopsy tests looked for entire cancer cells in the blood stream that had been shed by the tumor. Now they are targeting DNA from the tumor that is circulating in the blood stream.

Cost effective?

One more question about them is cost. At present, they aren’t cheap, so they are not something you are going to do on a daily basis. The price may come down, but you also need to look at how much they cost versus the entire cost of treating a patient for cancer. If liquid biopsies can dramatically decrease the overall cost of treatment and improve outcome, they will be widely used in short order. But the data isn’t yet in.

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