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jubei33
3rd March 11, 07:29 AM
Micro RNA Revolution: a Groundbreaking Discovery?

A molecular understanding of the human body and its processes has enabled us to produce relatively effective treatments for diseases that 100 years ago were death sentences for those who had the misfortune of getting them. One of the biggest discoveries to come out of this in depth study in the last 30 years was the knowledge of G-proteins and their regulation of receptor signaling. This led directly to new drug treatments that paved the way to making diseases like cancer survivable and manageable to a certain extent. A direct understanding of the processes led to treatments that were focused on blocking specific targets and for the most part had less severe side effects than their earlier chemotherapeutic counterparts. Recently, there has been a flurry of research on the new discovery of micro RNAs (http://en.wikipedia.org/wiki/Micro_Rna). As a direct importance to genetic therapy these hold great promise to produce further advances and more effective treatment of diseases like cancer and developmental disorders. Micro-RNAs are involved heavily in the regulation of messenger RNA transcripts and the repression and silencing of genes. They also may hold the key to specifically targeting cancer cells and thus may allow for more effective diagnosis and treatment.

Any discussion on this topic must begin with the process of gene transcription (http://en.wikipedia.org/wiki/Transcription_%28genetics%29). This is the process of converting the information in our DNA into the instructions RNA ribosomes can use to produce the proteins at the center of system control. Our genome is written in DNA with the familiar sequence of nucleotides thymine (T), guanine (G), cytosine (C) and adenine (A). However, before this can be turned into proteins, it must first be converted into RNA. The major physical difference between DNA and RNA is that the thymine (T) nucleotide is replaced with uracil (U). During the process the DNA strand is unzipped and an enzyme called RNA polymerase reads and converts it into an RNA copy of the information called mRNA, or messenger RNA. mRNA is used by ribosomes to manufacture proteins from the raw amino acids in a process called translation (http://en.wikipedia.org/wiki/Translation_%28biology%29). Here is where micro RNAs come in. MicroRNAs have small sequences that match portions of the mRNA products of certain genes. These bind to the mRNA and can either promote translation or stop it from happening and cause degradation of the mRNA. In this way, miRNAs have the ability to regulate gene expression and other important cell processes.

miRNAs were first discovered in a species of flatworm commonly used in genetic experiments called C. elegans(1). Scientists were looking to sequence their genome and found that these small pieces of RNA seemed to have regulatory functions in some of their gene expression. At the time it was thought to be an idiosyncrasy of the species, but the same finding began to pop up in other animals as well. Eventually, they were discovered in the human genome and it was shown that these are highly conserved in most animals. To date, we have discovered about 550 of these in humans and it is probably that there are many more. They are thought to correspond with approximately 60% of human genes and have been found to be involved with the regulation of developmental timing, cell differentiation, cell fate, aging, metabolism and the cell cycle just to name a few critically important processes. It is an understatement to note that when these systems receive aberrant signaling caused by a mutation of some kind the result is usually disease.

Recent studies have shown that all cancers have alterations in their micro RNA expression and in general miRNA genes map to known areas of cancer causing mutations, especially those of tumor suppressor (http://en.wikipedia.org/wiki/Tumor_suppressor) and oncogenes (http://en.wikipedia.org/wiki/Oncogene)(2). This finding is big news, because at the very least this could hold a path to more efficient diagnosis, quicker testing and more effective therapeutic intervention. One of the major problems with cancer therapy is diagnosis is often late stage, and at the time when our current collection of drugs is the least effective. The ability to selectively differentiate between cancer and normal cells has been long sought after for this reason and it’s possible that they may have found it with miRNAs. Numerous studies have shown connections between irregular miRNA expression and specific kinds of cancer. For example, Calin et'al published results in the NEJM showing mutations in miR15a and miR16-1 are associated with CCL and breast cancer(3). They later noted 13 different miRNAs were linked to specific kinds of cancers and individual expression patterns correlated with CLL prognosis. Furthermore, Yanaihara et al showed that lung cancer prognosis is identifiable by its miRNA signature(4). They found that mutations involving hsa-miR-15 had almost a 3.5 fold increase in pathology and mutations to hsa-let-7a-2 had greater than 2 fold increase compared to other mutations.

It’s good to be able to identify who has cancer, but the whole point is to help those stricken by it. Aside from better diagnostics, this knowledge of miRNAs could also lead to better therapeutic drugs. In cancer cells miRNAs follow two patterns of expression: overexpression and down regulation. Overexpression patterns usually function to promote a stem cell-like state where uncontrolled proliferation is established outside of the normal structured growth. Y. Hayashita in 2005, showed that overexpression of miR-17-92 enhanced lung cancer cell proliferation (5). By using drugs that inhibit this activity, it may be possible to pull a cancerous cell back in line with normal function. The hopeful result in this case is apoptosis of the rouge cells and reduction of the tumor. Drugs that bind to and block the function of overexpressed miRNAs can be specifically designed to match the miRNA sequence, leading to therapies that favor the cancer cells over normal cells. H. Matsubara in 2007 published a study using antisense oligonucleotides to attack overexpressed miR-17-5p and miR-20a in human lung cancer cell lines (6). Antisense means that a complimentary copy of the mRNA had been made that matches the opposite ‘sense’ coding piece of the miR-17-5p. When a ‘sense’ copy interacts with an ‘antisense’ copy it blocks translation of the mRNA script stopping it from being copied at the ribosome. Without the extra miRNAs suppressing the cell’s normal function, the chemical induced apoptosis in the cells, destroying the tumor.

The opposite route with miRNA down regulation also has a variety of possible therapies. Because of the small size of miRNAs (only ~ 22 nucleotides long) it may be possible to use viral vectors to reintroduce the missing or blocked components into cancer cells (7). This tactic has recently been shown successful in proof of concept studies for the treatment of Duchenne muscular dystrophy (http://en.wikipedia.org/wiki/Duchenne_muscular_dystrophy). In the study, using knowledge gleaned from mutations of the dystrophin (http://en.wikipedia.org/wiki/Dystrophin) gene (the gene producing the critical disfunctional protein in the disease), they trimmed down and produced a smaller version of the gene just able to fit inside an adenovirus capsid. The gene had enough functionality to replace the activity of the broken protein in affected muscle cells. In mouse studies it had enough effect to reduce symptoms to a less serious variant of the disease: Becker muscular dystrophy (http://en.wikipedia.org/wiki/Becker%27s_muscular_dystrophy). In this way, miRNAs could be used as the payload in a viral capsid or other similar vector and reintroduced into rouge cells. Reintroduction may replace the regulatory function and protective action of the miRNAs in question and hopefully cause target specific apoptosis of damaged cells.

The ability to discern the fundamental difference between cancer cells and normal cells has long been seen as the holy grail of cancer research. It was thought that this could lead to quicker diagnosis and targeted, more effective therapies. It is very possible that the patterns of miRNA expression found in cancer cells could hold the key to these kinds of therapies, but in any case more research needs to be done before this yields benefits in clinical medicine. Time will tell if miRNAs will live up to their promise, but at the very least a small piece of the puzzle has been discovered.




1. Lee RC, Feinbaum RL, Ambros V (December 1993). "The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14". Cell 75 (5): 843–54. doi:10.1016/0092-8674(93)90529-Y. PMID 8252621.
2. A large list of papers: Calin et al, PNAS 2002; Lu et al, Nature, 2005; Volinia & Calin et al, PNAS 2006; Landgraf et al, Cell 2007, MicroRNA genes map to cancer loci. Calin, G.A., et al.,2004. PNAS101:2999-3004 (specifically)
3. Calin et al, N Engl J Med, 2005; Raveche et al, Blood 2007 Germline abnormalities in miR15a/miR16-1 transcripts are associated with CLL and breast cancer aggregation.
4. Yanaihara et al, Cancer Cell, 2006 A unique miRNA signature is associated with lung cancer prognosis
5. Hayashita Y, et al. A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res. 2005 65(21):9628-32.
6. Matsubara H, et al. Apoptosis induction by antisense oligonucleotides against miR-17-5p and miR-20a in lung cancers overexpressing miR-17-92. Oncogene. 2007 Mar 26;
7. Wang CL, et al. Activation of an oncogenic microRNA cistron by provirus integration. Proc Natl Acad Sci U S A. 2006 103(49):18680-4.

EvilSteve
3rd March 11, 04:19 PM
Very interesting. A novel approach to cancer treatment I was unaware of. To date I'd only known about standard chemo / radiation therapy (which ranks up there with such enlightened medical techniques such as bleeding and trepanning), and anti-angiogenesis therapies which were a long ways off.

This strikes me as related to something I heard recently- I heard it second hand from Joe Rogan, but I believe it's legit- that cancer can be more accurately modeled as cells that have gone into "default" mode. That is, rather than something abnormal, they're unsure of what to do, so they act like a single-celled organism would and just try to eat and reproduce as much as possible. Anyway, this sounds like a promising avenue of research.

By the way, weren't you considering moving back to the US to study pharmacy? You seem to know quite a bit about molecular biology. Why not stick with that?

jubei33
3rd March 11, 04:52 PM
who's Joe Rogan? --Anyway, there's a bunch of theories out there: mitochondrial disease,cancer stem cells, etc. The miRNA version is that mutations cause the cell to act like a pluripotent stem cell in that they can travel and infect other places in the body, which is the basis of metastasis.

older chemo and radiation are similar to carpet bombing, in a way, but they have gotten more and more selective over the years. There are a lot of cancers now that are curable if caught in time. The drugs they use now are generally selective to rapidly dividing cells, as with the CCS and NCCS drugs (cell cycle specific). Others, called alkylating agents, are used to alkylate DNA to effect apoptosis in cancer cells. Still others, like the infamous methotrexate, block DNA synthesis. Most of these are semi-selective towards cancer cells, as they are dividing more often.

Antiangiogenesis therapies are in use now, actually, and depending on case can be standard therapy. Monoclonal antibodies are used as well to treat breast cancer etc.

trust me, with miRNAs, you will see more of these guys in the future.

------------
Yeah I want to very much. My main "20 year" goal is to work as a drug designer. Pharmacy will give me a back bone in the fundamental skills necessary for it, plus give a job with skills that are useful outside of academia, plus give me a job I want to do. The school(s) that I'm looking at also have additional specializations, like manufacture and design that I want to invest in. They also have a bunch of people that I want to learn from, especially in miRNA and cancer therapies. I already got a decent score on the entrance exam for it, but its competitive to get in and I might have to choose somewhere or something else..

I'm working towards it and I'm looking at 2012 next year, but we'll see how it goes. Right now I'm looking at funding for the rest of the year and finding a good location to live for my family. MY plan B would be to go to grad school for something, probably medicinal chemistry/organic chem.

resolve
3rd March 11, 05:52 PM
I, for one, really hope you get into a school that will help you along this path.

I really see alot of promise in you to do really good things for human health.

jubei33
4th March 11, 03:27 AM
Thanks, I appreciate that vote of confidence.

SFGOON
5th March 11, 10:42 AM
Probably not going to work. Too hard to get the RNAi into the cytoplasm selectively. Best to look into M. El Sayed's work first - has better ideas.

jubei33
5th March 11, 04:49 PM
Probably not going to work. Too hard to get the RNAi into the cytoplasm selectively. Best to look into M. El Sayed's work first - has better ideas.

Which part do you disagree with? By what tactic?

El Sayed's work, it relies on getting monoclonal antibodies for patient specific cancer cells. This tactic is an idea and seen all over the place, but its also going to be expensive to produce on a per patient basis, which is fine for Ricky Rich I suppose. Its a good idea, though, but in a way, it also reminds me of royal rife's machine too.

As for getting it into the cytoplasm, I don't think the technical difficulties are terribly insurmountable, at least unheard of in recent contexts:

Local Dystrophin Restoration with Antisense Oligonucleotide PRO051
Judith C. van Deutekom, Ph.D., Anneke A. Janson, B.S., Ieke B. Ginjaar, Ph.D.,Wendy S. Frankhuizen, B.S., Annemieke Aartsma-Rus, Ph.D.,Mattie Bremmer-Bout, B.S., Johan T. den Dunnen, Ph.D., Klaas Koop, M.D.,Anneke J. van der Kooi, M.D., Ph.D., Nathalie M. Goemans, M.D., Ph.D.,Sjef J. de Kimpe, Ph.D., Peter F. Ekhart, M.Sc., Edna H. Venneker, M.D.,Gerard J. Platenburg, M.Sc., Jan J. Verschuuren, M.D., Ph.D.,and Gert-Jan B. van Ommen, Ph.D.

Antisense Oligonucleotides: Basic Concepts and Mechanisms
Nathalie Dias,C. A. Stein. Columbia University, New York, New York 10032

Gene-Specific Ebola Therapies Protect Nonhuman Primates from Lethal Disease
U.S. Army Medical Research Institute of Infectious diseases
Fort Detrick, Maryland
http://www.usamriid.army.mil/press%20releases/warfield_press_release.pdf

Weiss, B. (ed.): Antisense Oligodeoxynucleotides and Antisense RNA : Novel Pharmacological and Therapeutic Agents, CRC Press, Boca Raton, FL, 1997

Hell, even corporate gene engineering has been using mRNAs to ripen tomatoes since the 80's.

resolve
5th March 11, 05:04 PM
I hated living next to Fort Detrick... you always knew when the "burning days" were... :/.

Japuma
5th March 11, 05:16 PM
I hated living next to Fort Detrick... you always knew when the "burning days" were... :/.

lol, have you heard about the "cancer cluster" around Fort Detrick yet? There was agent orange sprayed on the the base back in the 60's and people are blaming it for an outbreak of cancer. I grew up 2 blocks from Detrick on Rosemont Ave.

http://www.tbd.com/articles/2011/02/new-evidence-for-possible-fort-detrick-cancer-cluster-54759.html

jubei33
5th March 11, 05:17 PM
Do you still get those itchy maculopapular rashes?

Japuma
5th March 11, 05:21 PM
Only when it's "burning day" :/

jubei33
5th March 11, 05:25 PM
haha! smear some aloe vera on that, you'll be fine.

I love it when the government uses us for test subjects and leaves us no recourse for recrimination. It's like those atomic veterans, big bro's just like: "can't hear you over my su-te-REE-OOOO!"

Blue Negation
12th March 11, 02:13 AM
These are absolutely a major incoming field of study for cancer research. Heck, I was working on RNAi+microRNA expression arrays (cell lines vs embryo vs primary culture) to isolate oncogenic vs tumor suppressor vs plastic shock noise a couple of weeks ago, and that's all the head honchos were chatting about. If they think there's something to it, I'm inclined to agree.

Together with the next-gen sequencers that will soon be replacing ChIPs, rapid RNAi/microRNA diagnoses and antisense prescriptions aren't that many years away, IMO.

jubei33
12th March 11, 06:37 AM
^yeah, what's that noise!? Let me turn that sound UP!

yeah, I'd have to say its a huge discovery and they've already had successes in limited test trials for antisense therapies in duchenne muscular dystrophy. These are not without their snags and extra passages, but every step closer...

Do you mind if I ask who you work for? What was the focus of the research you were working on?

Blue Negation
12th March 11, 05:51 PM
I only recently heard about the duchenne success. Pretty encouraging.

PM'd as for the other stuff.

SFGOON
31st March 11, 02:50 AM
STUPIDITY!! Look, analyzing the transcriptomes of tumors vs. the DNA of the patient is just a fast way to figure out what changed to cause the fucking oncocells and subsequent tumors. You highfalutin' science types like to hide behind your highfalutin' words for dumb simple shit. I'm fucking sick of it. For real. Just call it something everyone can understand. Make it analogous to something common, something the consensus understands. You can't fault the bridge and tunnel crowd for not giving a flying shit about science when you deliberately try to obfuscate (LOOK IT UP!) your discipline by using a shitty lexicon that basically amounts to ivory tower slang.

I could teach biochem to TLH, ICY, and Riddeck if they'd fucking sit still for it. It's not hard, and it's not complicated.

Cullion
31st March 11, 06:00 AM
ICY is one of the most intelligent people who's ever posted on sociocide.

SFGOON
31st March 11, 07:28 AM
It's the sitting still bit that's hard for him.