Getting Respect

Lebanon created Sanjoub the Squirrel, a mascot who teaches children and villagers about preventing forest fires.

Thus states the Voice Of America. OK, it is the end of the year and the only other news is that stuff about some cliff, or as the French call it the mur or wall. But a squirrel being a national symbol, how great can it get!

Happy New Year to all you Cliff watchers.

What is Retail?

Retail is selling to people, you, me, other people. Starbucks is in retail, Dunkin Doughnuts is in retail, LL Bean is in retail, and yes Amazon is in retail. Retail means having the customer come back again and spend more money, and having the customer tell their friends how great the stuff was. Retail is a happy customer.

What else characterizes retail? First, if all else fails, listen to the customer. And who is the customer? The person buying your stuff, simple. Now take Amazon, if I buy something and I don't like it, for any reason, I get to send it back, free, no questions asked, almost. It works, it is simple, and I feel comfortable buying from Amazon. Bezos gets it, he knows retail. That is why Amazon gets so many customers. Now Apple is retail, they make a product, the design it well, they stand behind it, and they demonstrate their love of their customer. It is a religion, it works.

Now for Google. Google is NOT in retail. It seems to see its only customer those who pay them, namely advertisers. And for a long while that is exactly what they were. Then someone thought of selling the Nexus. Well, now the customer was you and me, dear readers, and Google was clueless. The Nexus has it appears a fantastic failure rate, by that I mean it appears to be quite high, and I can personally attest to it.

Now try and go back and remedy it with Google, I did, no luck. I even sent it with a nice note to Eric Schmidt, the Chairman, who I worked with on a Presidential Commission a decade ago, so I was not some schlub from the street, and any luck, no way. Had I written say Ivan Seidenberg at Verizon, in hours there would have been a response, and for years there was. Verizon is in retail, Google seems clueless.

So what is Retail, at its core it is keeping your customer happy, secure in knowing if its broke you will fix it, one way or the other. For Google in my opinion and in my experience, we the customer are a dumb annoyance. So what did I do at Christmas, got the team Kindles, yes, Kindles, not Nexus, would never go there. And oh by the way, I try and tell this tale to everyone. If I buy a Nexus from Google, I am terrified if it is defective, no warranty helps, the characters on their customer service just want to tell me they feel my pain, they really do. But fixing anything, are you nuts, they are Google.

Now one final note, I also have seen that somehow the Googleniks have in my opinion seemed to get to slam bad reviews on Amazon, perhaps Amazon would want to investigate, just a thought. Will Google ever understand Retail, after all Apple did, but then Jobs had his walk in the Desert, Google has not had that, yet.

USDA: An Example of Waste

Now the USDA is one of the largest branches of the Executive. It controls much of our life. For example, I have a small, 0.25 A, daylily hybridizing business, not really big, I generate and sell, a few, daylilies. Now I am not big Agribusiness. I have been doing this for 27 years and it is a nice small sum from time to time, not going to be Hedge Fund level stuff. It also has helped our work in genomics, as some of you may have seen on our other Blog entries.

So today I got my annual 50 page USDA National Agricultural Statistics Service Questionnaire. By Law I must fill it out and send it in. Yes, if I fail to do this I guess the USDA cops will be at my door. I have about 550 daylily hybrids, on small plots and some 4,000 seeds! But I had to tell them how many people are caring for my goats, how many peas I grew, my race, my income, my prperty value, how much water I used, how many immigrants I hired, and the list went on for hours!

This is an example of Government waste.The last question was what type of Internet connection I had. One would have thought that I could have answered the whole thing on line. But no, this is USDA, caught somewhere in 1921 to 1922!

The USDA building in DC is massive, halls upon halls of workers who in turn contract out to other workers, who in turn ... you get the point. Why in the good Lord's name do I have to tell them, under penalty of law, what I did with my 0.25 A of daylilies! I get inspected, I pay my fees, and then I have to, under penalty of law, make a report on nothing, really, it is almost nothing. But someone will read the data, enter it, put it in a data base and make monumental decisions.

Well I followed the law, filled out the form in complete, and then signed it and sent it back. I could have been making some money, but alas, with taxes going where they are why work. I will have too many forms to fill out under penalty of law. Kafka, where are you when we really need you?

Medicare Cuts

As of next Tuesday Medicare payments will be cut 28.5% from where they are now. What will that mean?

Medpage states:

It's looking less and less likely that Congress and the White House will strike a deal to keep the country from falling over the "fiscal cliff" next week, so physicians are preparing for a 28.5% cut in Medicare payments that will take effect on Jan. 1.

That figure includes a 26.5% cut under Medicare's sustainable growth rate (SGR) reimbursement formula and a 2% cut mandated by the Budget Control Act, the piece of legislation that outlined the tax increases and spending cuts that define the fiscal cliff.

"Given the current progress with the legislation, CMS [the Centers for Medicare and Medicaid Services] must take steps to implement the negative update," the agency said in a Dec. 19 notice on its website.

 CMS states:

The negative update of 27% under current law for the 2013 Medicare Physician Fee Schedule is scheduled to take effect on January 1, 2013. 

Medicare Physician Fee Schedule claims for services rendered on or before December 31, 2012, are unaffected by the 2013 payment cut and will be processed and paid under normal procedures and time frames.

The Administration is disappointed that Congress has failed to pass a solution to eliminate the sustainable growth rate (SGR) formula-driven cuts, and has put payments for health care for Medicare beneficiaries at risk.  We continue to urge Congress to take action to ensure these cuts do not take effect.  Given the current progress with the legislation, CMS must take steps to implement the negative update.

Under current law, clean electronic claims are not paid sooner than 14 calendar days (29 days for paper claims) after the date of receipt.  CMS will notify you on or before January 11, 2013, with more information about the status of Congressional action to avert the negative update and next steps.

 So what might that mean for those 55 million on Medicare:

1. Generally according to Medical Ethics if you have a physician they must see you if you are returning or being treated. Perhaps you may pushed to the end of the line but you will get an appointment, sometime.

2. If you are seeking a new physician, good luck, many will no longer take Medicare. You will be providing reimbursement lower than Medicaid. If for example you have a cancer and need special treatment and it is discovered January 1, 2013 or later, you may very well not find a physician available where the best ones are.

3. The level and quality of care may actually suffer, in small ways. You may find you are treated akin to food stamp holders at a candy store, with scorn.

So will the Fiscal Cliff cause harm? We don't really know, it does solve some problems but it creates many more. Add the ACA to the mix and one sees an explosive disruption in Health Care, a disaster which will soon expand on all fronts. Welcome to 2013.

Micro RNAs and Melanoma

We have previously examined the impact of miRNAs in the development of cancers from several perspectives. In this new White Paper we take a recent finding regarding melanoma and a specific miRNA and then use it as a baseline to examine miRNAs in a broader context, focusing specifically on melanoma. The interest here is twofold; first, as a potential therapeutic target and second as a potential prognostic marker.

miRNAs have been examined for the past twenty years but just the last decade have they been understood specifically as elements in cancer control. Even more so, only in the past five years has their full impact been understood and the ability to manipulate certain miRNA paths controlled.

This section details many of the elements of miRNA as regards to cancer and metastatic control as well as the therapeutic control via miRNAs. What is of most significant interest is that miRNAs have such a pervasive set of control paths via activating oncogenes and suppressing genes which control metastatic growth. The miRNAs are not just control elements in select paths but appear to be control elements in the day to day paths of cellular homeostasis. This makes modeling of pathways significantly more complex.

It is critical to understand that as we have seen genomic models built around proteins, genes and pathways, we have also not seen the clear presence of miRNAs as integral parts of this process. One need just look at the many papers on pathway dynamics and almost to each one there is a total absence of miRNAs. We had proposed about five years ago that we look at miRNAs as noise, as at best epigenetic accidents which result in loss of expression. Now however it may be argued that they play as significant a role as the well-known pathways, albeit not yet fully understood.

Let us recall that the miRNA functions in a manner shown below:

We shall detail this process later in the document. However it is good to understand the nature of the miRNA. One key factor is that reproducing and introducing miRNAs appears to be rather straightforward. This perhaps they represent a powerful tool in the therapeutic arsenal.

The specific focus here is on miRNA-26a[1]. There are many databases now with a great deal of information regarding the miRNAs and we refer to them as in course.

Recent Observations

We begin by examining a recent paper regarding miR-26a. As we shall discuss later this miRNA is found to be aberrant in multiple cancers and in the case of melanoma the disruption associated with several pathways is somewhat clearly understood. In a recent paper by Reuland et al the authors make the following observations[2]: 

Melanoma is an aggressive cancer that metastasizes rapidly and is refractory to conventional chemotherapies. Identifying microRNAs (miRNAs) that are responsible for this pathogenesis is therefore a promising means of developing new therapies. We identified miR-26a through microarray and quantitative reverse-transcription–PCR (qRT-PCR) experiments as a miRNA that is strongly downregulated in melanoma cell lines as compared with primary melanocytes. Treatment of cell lines with miR-26a mimic caused significant and rapid cell death compared with a negative control in most melanoma cell lines tested. 

In surveying targets of miR-26a, we found that protein levels of SMAD1 (mothers against decapentaplegic homolog 1) and BAG-4/SODD were strongly decreased in sensitive cells treated with miR-26a mimic as compared with the control. 

The luciferase reporter assays further demonstrated that miR-26a can repress gene expression through the binding site in the 3′ untranslated region (3′UTR) of SODD (silencer of death domains). Knockdown of these proteins with small interfering RNA (siRNA) showed that SODD has an important role in protecting melanoma cells from apoptosis in most cell lines sensitive to miR-26a, whereas SMAD1 may have a minor role. Furthermore, transfecting cells with a miR-26a inhibitor increased SODD expression. Our findings indicate that miR-26a replacement is a potential therapeutic strategy for metastatic melanoma, and that SODD, in particular, is a potentially useful therapeutic target.

The observations focus on several key areas:

1. The impact of miRNAs on melanoma metastasis. As we will discuss there have been many previous studies implicating many miRNAs in this area. Thus seems to expand the results.

2. There appears to be a therapeutic approach to the issue by increasing the miRNA26a to further reduce by binding to the SODD facilitator product. There again have been several studies along this line recently. SODD is an interesting controlling gene/protein complex and the control via miR-26a is of significance.

3. There may be a prognostic indicator here as well. Again there has been a great deal of work in this field.

First we examine both the miRNA26a and SODD respectively and then we examine the issues discussed above in some detail. This represents just another of many studies regarding the use of miRNAs for the potential control of melanoma.

Before continuing it is useful to examine some of the additional comments the authors of the referred to article have made to the trade press relating to the release of the paper. Now one trade press article states[3]: 

A University of Colorado Cancer Center study in this month's edition of the Journal of Investigative Dermatology describes a new target and potential treatment for melanoma, the most dangerous form of skin cancer. MicroRNA can decide which genes in a cell's DNA are expressed and which stay silent. Melanoma tends to lack microRNA-26a, which makes the gene SODD go silent.

"It's a double negative," says Yiqun Shellman, PhD, investigator at the CU Cancer Center, associate professor at the CU School of Medicine, and the study's co-senior author. "miR-26a works to stop the growth of cancer. You turn off this thing that should stop growth, and you have growth." When Shellman, David Norris and colleagues reintroduced microRNA-26a to melanoma cell lines that lacked it, they saw a marked decrease in cancer cell survival. MicroRNA-26a killed melanoma cells while leaving healthy cells unharmed. In fact, the discovery started back a couple steps. First the group compared microRNA expression in healthy cells to that of microRNA expression in melanoma cells. "We hoped the difference between microRNA expression in healthy and melanoma cells would show which ones were contributing to tumorgenesis," Shellman says. The microRNA most consistently different between healthy and cancerous cells was 26a. The discovery of how it works and what exactly it does was serendipitous. "We started by testing the effect of microRNA-26a on known gene targets to see if it was effecting the expression of logical, cancer-causing pathways, but none of them seemed affected in melanoma," Shellman says.  "We were working with the SODD gene in an unrelated project, and SODD has a putative but not high-scored binding site for miR-26a, and thought, why not test it? Sure enough, it turned out to be the target – microRNA-26a downregulates this gene." Shellman hopes this robust finding in cell cultures will help pave the way for future work with microRNA-26a as a therapeutic target in animal models and eventually a human trial.  "The first step is to further pinpoint the genetic signatures of the patients likely to benefit from microRNA-26a replacement therapy," Shellman says, noting that only some and not all melanoma cells were killed by miRNA replacement. "Maybe it's simply the downregulation of microRNA-26a itself, or maybe we can use SODD expression as the biomarker," Shellman says. Once Shellman and colleagues discover the characteristics of a melanoma susceptible to microRNA-26a treatment, they hope funding will allow the lab to follow the promising therapy up the evolution from cells to humans.

As can be seen from the conversation above, there still may exist some questions of the details of the process. What is critical, however, is the fact that the miRNA plays such a prominent role, that one may target the miRNA, and that a pathway is a fundamental part of the development of a putative therapeutic. But fundamentally the last sentence above does diminish the ultimate enthusiasm.

The critical observations made here is the relationship between the controlling proteins, their related mRNA and the interference coming from miRNA. This has not been explored in significant detail until of late.

Another trade press review states as follows[4]: 

Researchers from the University of Colorado Cancer Center say that they have discovered a new, more targeted way of treating melanoma, the most deadly form of skin cancer

The findings, described in a recent edition of the Journal of Investigative Dermatology, describe how small pieces of genetic material known as MicroRNA can choose the genes in a DNA cell that are either expressed or kept silent. With melanoma in particular, the researchers discovered a deficiency of microRNA-26a that usually silences the gene SODD. “It’s a double negative,” explained the study’s co-senior author Yiqun Shellman, an investigator at the University of Colorado Cancer Center and associate professor at the University of Colorado School of Medicine, in a prepared statement. “MiR-26a works to stop the growth of cancer. You turn off this thing that should stop growth, and you have growth.” 

In the study, melanoma cell lines that lacked microRNA-26a were reintroduced to the cell in a lab. As a result, there was a reduction in cancer cell survival and the microRNA-26a eliminated melanoma cells while leaving healthy cells alive. The team of investigators was able to compare the expression of microRNA in healthy cells to the expression of microRNA in melanoma cells. “We hoped the difference between microRNA expression in healthy and melanoma cells would show which ones were contributing to tumorgenesis,” continued Shellman in the statement. The researchers saw that the expression of micro-RNA-26 was consistently different between healthy and cancerous cells. Some, but not all, of the melanoma cells were eliminated by the replacement introduction of mRNA. “The first step is to further pinpoint the genetic signatures of the patients likely to benefit from microRNA-26a replacement therapy,” noted Shellman in the statement. “Maybe it’s simply the downregulation of microRNA-26a itself, or maybe we can use SODD expression as the biomarker.” Moving forward, Shellman believes that her team’s discovery of the role of MicroRNA in the development of carcinoma in cell cultures may eventually help develop new therapeutic techniques that could be used in real cancer patients.

This above statement is a simple reiteration of some of the prior work. Again it is clear that although experimentally observed, one is still quite a way from clinical reality.

Other researchers have examined miRNAs and melanoma as well. For example the work of Segura et al (2012) state:

Melanoma incidence and associated mortality continue to increase worldwide. The lack of treatments with durable responses for stage IV melanoma may be due, at least in part, to an incomplete understanding of the molecular mechanisms that regulate tumor initiation and/or progression to metastasis. Recent evidence supports miRNA dysregulation in melanoma impacting several well-known pathways such as the PI3K/AKT or RAS/MAPK pathways, but also underexplored cellular processes like protein glycosylation and immune modulation. There is also increasing evidence that miRNA can improve patient prognostic classification over the classical staging system and provide new therapeutic opportunities. The integration of this recently acquired knowledge with known molecular alterations in protein coding genes characteristic of these tumors (i.e., BRAF and NRAS mutations, CDKN2A inactivation) is critical for a complete understanding of melanoma pathogenesis. Here, we compile the evidence of the functional roles of miRNAs in melanomagenesis and progression, and of their clinical utility as biomarkers, prognostic tools and potential therapeutic targets. Characterization of miRNA alterations in melanoma may provide new angles for therapeutic intervention, help to decipher mechanisms of drug resistance, and improve patient classification for disease surveillance and clinical benefit.

The above work readily complements the work upon which we have focused this analysis. Additional melanoma analyses has been done by Zehavi et al. Zehavi et al state[5]:

We show that the expression of miRNAs from a large cluster on human chromosome 14q32 is significantly down-regulated in melanoma cell lines, benign nevi and melanoma samples relative to normal melanocytes. This miRNA cluster resides within a parentally imprinted chromosomal region known to be important in development and differentiation. In some melanoma cell lines, a chromosomal deletion or loss-of-heterozygosity was observed in the cis-acting regulatory region of this cluster. In several cell lines we were able to re-express two maternally induced genes and several miRNAs from the cluster with a combination of de-methylating agents and histone deacetylase inhibitors, suggesting that epigenetic modifications take part in their silencing. Stable over-expression of mir-376a and mir-376c, two miRNAs from this cluster that could be re-expressed following epigenetic manipulation, led to modest growth retardation and to a significant decrease in migration in-vitro. Bioinformatic analysis predicted that both miRNAs could potentially target the 3'UTR of IGF1R. Indeed, stable expression of mir-376a and mir-376c in melanoma cells led to a decrease in IGF1R mRNA and protein, and a luciferase reporter assay indicated that the 3'UTR of IGF1R is a target of both mir-376a and mir-376c. Our work is the first to show that the large miRNA cluster

Note in the above the selection and determination of other miRNAs as well. It is not expected that any single miRNA will be considered the sole controlling element. In fact one may anticipate a progression as the tumor develops. The setting off of miRNAs as the tumor stage changes would be an interesting by-product of this analysis.

Another quite useful analysis of miRNAs and melanoma has been done by Taveira da Cruz and Jasiulionis. In their work the two authors state:

miRNAs are non-coding RNAs that bind to mRNA targets and disturb their stability and/or translation, thus acting in gene posttranscriptional regulation. It is predicted that over 30% of mRNAs are regulated by miRNAs. Therefore these molecules are considered essential in the processing of many biological responses, such as cell proliferation, apoptosis, and stress responsiveness. As miRNAs participate of virtually all cellular pathways, their deregulation is critical to cancer development. Consequently, loss or gain of miRNAs function may contribute to tumor progression. Little is known about the regulation of miRNAs and understanding the events that lead to changes in their expression may provide new perspectives for cancer treatment. Among distinct types of cancer, melanoma has special implications. It is characterized as a complex disease, originated from a malignant transformation of melanocytes. 

Despite being rare, its metastatic form is usually incurable, which makes melanoma the major death cause of all skin cancers. Some molecular pathways are frequently disrupted in melanoma, and miRNAs probably have a decisive role on these alterations. Therefore, this review aims to discuss new findings about miRNAs in melanoma fields, underlying epigenetic processes, and also to argue possibilities of using miRNAs in melanoma diagnosis and therapy.

The conclusions drawn from the above paper are considerable. After just a few years there is now a well-accepted understanding of how miRNAs function and that they play critical roles in pathways. However, and this is a very significant however, we do not understand what precipitates them nor do we fully understand their relationship in pathway analysis. What is clear is that they are found in a multiple set of cancers, that that are pathway control elements, but the complex interactions we would anticipate are still unknown.

Micro RNAs

miRNAs are small (19-25 nucleotide single strand RNA) which have been created off intron sections of the DNA of a cell through pol II or pol III. They then operate on mRNA from exons which have escaped from the nucleus and are putatively maturing to proteins in the cytoplasm. Some of the proteins may be beneficial and some may not. The miRNAs seem to be secondary, and in some cases primary, pathway control elements. miRNAs contain RNA nucleotides, U, A, C, G. Thus simply stated if any possible combination is available there could be 4²² such miRNAs or about one trillion, equal to the national debt each year! This is a simplistic statement but it does provide a metric. We have discovered just more than a 1,000 miRNAs to data, with variants on some. Therefore a great deal more can be determined.

To demonstrate the recent occurrence of miRNA, it was not until the 6^th edition of Watson’s Biology of the Gene in 2008 that we see a Chapter on controlling RNAs with miRNA (See Chapter 18). In addition even some of the recent literature lends miRNAs a place as a curiosity. In fact the more they are understood the more powerful they become.

In the classic review paper by Esquela-Kerscher, A. and F, Slack, they present an excellent discussion on miRNAs. First we present the overall construct. miRNAs are produced like all RNA and then pass through the Drosha/Pasha complex and emerge from the nucleus as a double RNA with a loop. Dicer cuts the loop creating single strand short RNAs which are the miRNA.

 Now from the paper we have the more detailed description where we show how miRNA can interfere with RNA translation by either inhibiting it or by slicing the RNA and in turn also inhibiting it. We depict that below 

 We rely upon that here, They state:

The biogenesis of microRNAs. MicroRNA (miRNA) genes are generally transcribed by RNA Polymerase II (Pol II) in the nucleus to form large pri-miRNA transcripts, which are capped (7MGpppG) and polyadenylated (AAAAA). These pri-miRNA transcripts are processed by the RNase III enzyme Drosha and its co-factor, Pasha, to release the ~70-nucleotide pre-miRNA precursor product. (Note that the human let-7a-1 miRNA is shown here as an example of a pre-miRNA hairpin sequence. The mature miRNA sequence is shown in red.) RAN–GTP and exportin 5 transport the pre-miRNA into the cytoplasm. Subsequently, another RNase III enzyme, Dicer, processes the pre-miRNA to generate a transient ~22- nucleotide miRNA:miRNA* duplex. This duplex is then loaded into the miRNA-associated multiprotein RNA-induced silencing complex (miRISC) (light blue), which includes the Argonaute proteins, and the mature single-stranded miRNA (red) is preferentially retained in this complex. The mature miRNA then binds to complementary sites in the mRNA target to negatively regulate gene expression in one of two ways that depend on the degree of complementarity between the miRNA and its target. miRNAs that bind to mRNA targets with imperfect complementarity block target gene expression at the level of protein translation owever, recent evidence indicates that miRNAs might also affect mRNA stability (not shown). Complementary sites for miRNAs using this mechanism are generally found in the 3′ untranslated regions (3’ UTRs) of the target mRNA genes. miRNAs that bind to their mRNA targets with perfect (or nearly perfect) complementarity induce target-mRNA cleavage (lower right). miRNAs using this mechanism bind to miRNA complementary sites that are generally found in the coding sequence or open reading frame (ORF) of the mRNA target.

They further detail it as follows:

MicroRNAs can function as tumour suppressors and oncogenes. a. In normal tissues, proper microRNA (miRNA) transcription, processing and binding to complementary sequences on the target mRNA results in the repression of target-gene expression through a block in protein translation or altered mRNA stability. The overall result is normal rates of cellular growth, proliferation, differentiation and cell death. b. The reduction or deletion of a miRNA that functions as a tumour suppressor leads to tumour formation. c. A reduction in or elimination of mature miRNA levels can occur because of defects at any stage of miRNA biogenesis (indicated by question marks) and ultimately leads to the inappropriate expression of the miRNA-target oncoprotein (purple squares). The overall outcome might involve increased proliferation, invasiveness or angiogenesis, decreased levels of apoptosis, or undifferentiated or de-differentiated tissue, ultimately leading to tumour formation. The amplification or overexpression of a miRNA that has an oncogenic role would also result in tumour formation. In this situation, increased amounts of a miRNA, which might be produced at inappropriate times or in the wrong tissues, would eliminate the expression of a miRNA-target tumour-suppressor gene (pink) and lead to cancer progression. Increased levels of mature miRNA might occur because of amplification of the miRNA gene, a constitutively active promoter, increased efficiency in miRNA processing or increased stability of the miRNA (indicated by question marks). ORF, open reading frame.

We depict these three cases shown as follows. First, miRNA acting in a normal manner. This is below:

 Notice above the miRNA is assumed to be a normal part of the control mechanism of the control of the conversion of the mRNA into a protein. It block the conversion.

Second, we now consider the second case. Here we have an oncogene which is not blocked by the miRNA and it results in many oncoproteins as shown below.

 Third and finally in case 2 we have a massive explosion of miRNAs acting as onco activators as shown below.

 These methods demonstrate in a somewhat simple manner how the miRNA functions in the case of certain cancers. It also demonstrates how the miRNA can become a target for therapeutics.

 

Observations

Much of what we know about miRNAs and their functions has evolved in the past five years to a decade at most. In fact in the past decade one has seen a great opening to RNAs in general. Before that it could be said that RNAs were the poor cousin in the process, the glory given the DNA and then the pathway dynamics dominated by proteins. We now appear to have opened a door on control mechanisms at the RNA level, dominated by miRNA and their control of mRNA before it becomes a protein. Thus RNA is somewhat exciting, and the miRNA have presented an added level of complexity to our modeling of complex cellular dynamics.

Based upon the analysis herein:

miRNA present new Paradigms for Cell Signalling

The most significant result from the explosion of miRNA effects is that what we have seen as now classic pathways may have significant undercurrent resulting from the miRNAs. Are miRNAs dominant control elements, is so where do they impact the most. We have seen many of the miRNA discoveries as just incidental to studying pathways. In our prior analysis we assumed them to be just noise. Now we can no longer accept such a proposition. In fact they seem to play significant if not dominant roles.

miRNA provide opportunistic targets for Therapeutics

The use of miRNAs as therapeutic targets is of significant interest. We have discussed some of the results and we have tried to place miRNAs in context of a broad therapeutic approach. The true reason is the simplicity of the miRNA structure. It is not a complex protein of hundreds of nucleic acids folded in a complex manner. The miRNA is just some 22 nucleotides on a sugar backbone.

miRNA expand the Interest in Introns as Control Elements

We have been trained to ignore the introns. It was the trash heap of evolution, perhaps of some use in the past. However since miRNAs are intro sourced, we now have a new window on the importance of introns.

miRNA may have Broader Roles in Metastatic Growth

We have looked at such proteins as PTEN, p53, and others as the control element. We looked at kinases and receptors and instigating ligands as part of that process. When we examine miRNA we see control coming from within. What instigates the processing and release of miRNAs. What are the feedback loops, if any, between the surface changes on receptors and the activation of miRNAs.

miRNA can be a Significant Target for Diagnostic and Prognostic Analysis

One of the problems we have in many cancers is both diagnosis and prognosis. In melanoma unfortunately prognosis may often be dire, but not always. In addition diagnosis of pigmented lesions is often problematic. Take a simple melanoma in situ, where it is diagnosed based on upward movement of the melanocyte. Are there differences in the MIS? Namely is each MIS identical, just losing its stability, say through loss of E-cadherin, and if not are there simple miRNAs which can be targeted and profiled.

There are many more observations which will evolve as we better understand miRNAs. Since we are at the beginning of understanding them we must keep in mind the ever changing field of play, and thus any analysis must include miRNAs as significant participants.

References

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23.            Watson, J., et al, Molecular Biology of the Gene, 6^th Edition, Pearson (New York) 2008.

24.            Zehavi, et al, Silencing of a large microRNA cluster on human chromosome 14q32 in melanoma: biological effects of mir-376a and mir-376c on insulin growth factor 1 receptor, Molecular Cancer 2012, 11:44 Page 8 of 15, http://www.molecular-cancer.com/content/11/1/44.

25.            Zhu, Y., MicroRNA-26a/b and their host genes cooperate to inhibit the G1/S transition by activating the pRb protein, Nucleic Acids Research, 2011, 1–11.

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[1] http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000083

 

[2] http://www.nature.com/jid/journal/vaop/ncurrent/full/jid2012400a.html

[3] http://medicalxpress.com/news/2012-12-serendipity-potential-therapy-melanoma.html also http://medicalxpress.com/news/2012-12-serendipity-potential-therapy-melanoma.html#jCp

[4] http://www.redorbit.com/news/health/1112752907/genetic-culprit-for-melanoma-found-122112/

 [5] http://www.molecular-cancer.com/content/11/1/44

Socrates and the Press

Over the Holidays I reread Gorgias, the debate Socrates had with the Sophists, today we would most likely call them politicians. Anything to get elected. It evoked the logic of the Greeks some two and a half millennia ago.

Then I read the piece in the NY Times about the Gannett paper in Westchester which printed an interactive map of every person with a gun license in Westchester and the surrounding counties. Now I do not know NY Law on the matter but in New Jersey one must have a gun license to have a Daisy BB gun. Not an AK47 or M16, but yes a BB gun. Thus the nexus between abiding by the law and having a firearm does not exist. The nexus between a gun license and the right to then buy a gun may exist but the possession of such gun is not in evidence. Socrates would have a field day with the morons who put this together.

I suspect that most individuals who have a gun license may have a gun but not all. Again in New Jersey they may like me have a single dated Daisy BB rifle in New Hampshire, but no heavy armament of any kind in New Jersey. (Just to let the folks know, the Daisy is to keep the deer from my daylilies, but it seems the newly imported wolves have done a great job). Yet I suspect that in Newark the murders for the most part were committed by unlicensed individuals. One does not go out and get a license for such a purpose, one gets a license to not break the law, or to obey the law, I suspect it is the same thing. I am not a gun fan, never used one other than having been trained, never liked the things, but that is my opinion. Upcountry they actually hunt and eat the result. I will stay with store bought stuff.

I read the comments and surprisingly they were overly negative. What purpose does this serve. Perhaps reckless endangerment by targeting homes a potential sources of weapons. Or homes weaponless. In either case there is no purpose, only the self aggrandizement one finds all too often in the Press. Perhaps it makes someone feel good, why not publish the names of all physicians dispensing oxycodone. None f this makes any logical sense.The consequences may be deadly, the positive effect is zero, and the problem is not avoided. Well it is our  Press after all.

Merry Christmas

1 And it came to pass in those days that a decree went out from Caesar Augustus that all the world should be registered.

2 This census first took place while Quirinius was governing Syria.

3 So all went to be registered, everyone to his own city.

4 Joseph also went up from Galilee, out of the city of Nazareth, into Judea, to the city of David, which is called Bethlehem, because he was of the house and lineage of David,

5 to be registered with Mary, his betrothed wife, who was with child.

6 So it was, that while they were there, the days were completed for her to be delivered.

7 And she brought forth her firstborn Son, and wrapped Him in swaddling cloths, and laid Him in a manger, because there was no room for them in the inn.

8 Now there were in the same country shepherds living out in the fields, keeping watch over their flock by night.

9 And behold, an angel of the Lord stood before them, and the glory of the Lord shone around them, and they were greatly afraid.

10 Then the angel said to them, “Do not be afraid, for behold, I bring you good tidings of great joy which will be to all people.

11 For there is born to you this day in the city of David a Savior, who is Christ the Lord.

12 And this will be the sign to you: You will find a Babe wrapped in swaddling cloths, lying in a manger.”

13 And suddenly there was with the angel a multitude of the heavenly host praising God and saying:

14 “ Glory to God in the highest, And on earth peace, goodwill toward men!

15 So it was, when the angels had gone away from them into heaven, that the shepherds said to one another, “Let us now go to Bethlehem and see this thing that has come to pass, which the Lord has made known to us.”

16 And they came with haste and found Mary and Joseph, and the Babe lying in a manger.

17 Now when they had seen Him, they made widely^[d] known the saying which was told them concerning this Child.

18 And all those who heard it marveled at those things which were told them by the shepherds.

19 But Mary kept all these things and pondered them in her heart.

20 Then the shepherds returned, glorifying and praising God for all the things that they had heard and seen, as it was told them.