Interesting aspects of Herpetic Infections

No infection is as intriguing as the Herpetic infection.  Its interest lays in several facts
1. The mere fact that a Third of the US population may be involved makes this disease one of the most prevalent ones,  but it is also feared.  Whether the fear is justified or not remains a question.
2. Certainly it has something to do with horrific stories of potential recurrence of horrific burning neuropathic pains that we have heard about. Science does not know for sure whether only specific viral serotypes lead to this or whether certain hosts genes isoforms or inflammatory reactions  may be contributing to this presentation.
3. The outbreak is accompanied with guilt and sense of guiltiness that is mostly unjustified...many questions arise after the realization that those painful skin or otherwise lesions could be herpetic...that a partner you have gave this to you and that you may give this to a new partner?  Those questions are valid but with the prominence of the prevalence of this disease in the US, who and when one got exposed to Herpes is one of the great mysteries in herpetic disease.  Herpes 1 has been linked to Over crowding, and Herpes 2 is the one with a sexual connotation.  But one should remember that the Herpetic Virus will invade teguments (particularly abrasions) when contact happens, sexual or not!  And very often this happens in our tender ages of infancy.  Remember the infection can be symptomatic, but most of the time completely without any clinical manifestations. And enters quietly a dormancy.
4. The dormancy itself is quite a puzzling event!  All we know is that the capsule to this double stranded DNA viral particule is from the host!  This may help it to be "tolerated " by the host.  We can speculate that class I MHC will not be bothered. Only the class II may note the invader most likely and provide the Antibody that we can measure!
5. The exacerbation of the herpetic infection is also puzzling in many ways
-It happens when we are under stress (menstruation and exposure to UV light), pregnancy state and post chemotherapy, the so called state of "when the immune system" is down!
-To the writer this is a state of activity of the c-JUN and Fos, the NF-kB and full epigenetic phenomena as if cyclines and TNF, TGFs are in full swing!  Epigenetic events seem to free or unleash genes (regulators or not) that will reactivate the Virus.
-How and where these events occur (Golgi, Nucleus, or cytosolic) remains to be clarified.

 (Let raise the eyelid of this dormant disease and look at it through its eyes/pupils without awakening it!)

6. The bad exacerbation could be virally induced or it could be in fact a reaction of the Host  (Neutrophilic Grazymes) or Cyclin effects.  ie. In post Brain trauma injury (TBI) we know that post synaptic nerve death is due to  Cytokins that kill post synaptic nerve, is it the same in this herpetic disease?And if it is, what would be the therapeutic implications?!

Profiling through at the CRBCM!

At the CRBCM something is coming through:

1. Deterioration at membrane receptor by lack of stimulation or "false or abnormal stimulation" could not only alter the nature of the "glycan" covering the protein portion of the receptor, but also induce stress like molecules.(HSP)
2. As a result of receptor failure new cytokines and TGFs are secreted which unfortunately fail at the initial receptor, but induce other receptors, amplifying standard pathways like RAS or PIK
3. Certains TGFs have an intrinsic power to maintain life of cells no matter what and induce metastasis.
4. Certain genes have an auto-phosphorylation or self-limiting mechanism that can easily go wrong  (RAS, FAK) driving to neoplastic process
5. FAK plays a larger role in aggressive prostate cancer than it has been recognized!
6. FAK has a closer relation to Androgen than recognized
7. NOTCH has closer relation with MEK and "stem cell potential" than recognized.
8. FAK disturbance prominence in cancer explains its sensitivity to Taxanes!  That is on top of Microtubule disturbances induced by the drug!
9. Metalloproteases are the ultimate Biomarkers of membrane events !
10.  Epigenetic methylation and its patterns are one of the largest mystery still to be elucidated!

CRITICAL GENES IN (SECONDARY) LEUKEMIA

Aside from the the genes that can block Tumor Growth factors, our discussion on leukemia had shown that Leukemia is driven also by proteins located at CBF.  Indeed we now know that the proteins found in the CBF indeed determine the direction and intensity of the the neoplastic process.  Attacking growth factors effectiveness at stimulating its relevant receptor appears to be a decent strategy.   However there are other gene that should be in the focus of our attention.
AP-1
TFE-3
SMAD2-4
FOXG1
and at the border JARID1B
(we will add some gene regulators to this list)
==========================================================
'"The SMAD4 gene provides instructions for making a protein involved in transmitting chemical signals from the cell surface to the nucleus. This signaling pathway, called the transforming growth factor beta (TGF-β) pathway, allows the environment outside the cell to affect how the cell produces other proteins. The signaling process begins when a TGF-β protein attaches (binds) to a receptor on the cell surface, which activates a group of related SMAD proteins. The SMAD proteins bind to the SMAD4 protein and form a protein complex, which then moves to the cell nucleus. In the nucleus, the SMAD protein complex binds to specific areas of DNA where it controls the activity of particular genes and regulates cell growth and division (proliferation).

By controlling gene activity and regulating cell proliferation, the SMAD4 protein serves both as a transcription factor and as a tumor suppressor. Transcription factors help control the activity of particular genes, and tumor suppressors keep cells from growing and dividing too fast or in an uncontrolled way.

Does the SMAD4 gene share characteristics with other genes?

"The SMAD4 gene belongs to a family of genes called SMAD (SMAD, mothers against DPP homologs).
A gene family is a group of genes that share important characteristics. Classifying individual genes into families helps researchers describe how genes are related to each other. For more information, see What are gene families? in the Handbook."  

 "Common SMAD (co-SMAD) is the coactivator and mediator of signal transduction by TGF-beta (transforming growth factor). Component of the heterotrimeric SMAD2/SMAD3-SMAD4 complex that forms in the nucleus and is required for the TGF-mediated signaling. Promotes binding of the SMAD2/SMAD4/FAST-1 complex to DNA and provides an activation function required for SMAD1 or SMAD2 to stimulate transcription. Component of the multimeric SMAD3/SMAD4/JUN/FOS complex which forms at the AP1 promoter site; required for syngernistic transcriptional activity in response to TGF-beta. May act as a tumor suppressor. Positively regulates PDPK1 kinase activity by stimulating its dissociation from the 14-3-3 protein YWHAQ which acts as a negative regulator."
(NIH)

Ovarian Cancer

*Researchers who conducted the study who conducted the use of Selumetinib in low grade serous Ovarian cancer were still puzzled because its activity did not follow presence of KRAS or BRAF. They have been wondering if it used another pathway.  But remember MEK is the revolving door to de-differentiation and to the reversal of mesengialization and as such increase tor susceptibility not only to chemotherapy drugs, but also to the secondary angiogenic potentiation of MEK.  That is, with anti-MEK, there is a down regulation of MAPK (as suggested) and therefore  the C-JUN and TGF and cyclins, but also down regulation of the VEGF!

They say " Our results suggest that selumetinib is an active agent, but not necessarily because of BRAF or KRAS mutational activation per se,” the authors concluded.

In an interview, Gershenson said that one reason for the lack of correlation could be biomarker instability. Among the 52 patients, specimens were available for only 40, mutational analysis was done in 34, and in 28 of those the tissue was from the primary therapy and not from the recurrent tumor. “The question arises, are these biomarkers stable over time or do they change, so that what you find in the primary tumor may not be what you find in the recurrent tumor,” he said."   They suggesting here that the lack of correlation could be due to a changing nature of Biomarker.  But the existence of other factors and pathways could not be be excluded!

Gene-Expression Profiling May Help Select Best Drugs for Pancreatic Cancer

Caroline Helwick 

---------------------------------------------------------------------------------------------------

In this study patient with pancreatic cancer had reportedly circulating cell and their genes could predict response to therapy but unfortunately they did not spell out which genes were reviewed.  We will investigate further this article...

The AML discussion continues!

AML-1 mostly corresponds to the alpha subunit of the CBF and contains the RUNX-1 which specializes in hematologic differentiation of the cell, the other portion already contains among other things regulatory or catalytic molecules facilitating many processes of the cell combination with EVI-1 will control signal pathways and growth factors.
This type of AML, or AML in general, appears to be a disease mostly driven by dysregulation of promoters and regulator genes with global suppression of the NK-kB a nd the cyclins/TGF. 
?role of ANDROGEN, interferon and growth factor in EVI-1 positive AML can be raised as a question.  On top of standard induction chemotherapy of course!  This is where Cyclosporine and Antithymocyte Globulin could still have a role (in EVI-1 AML)

One may wonder why TGF is suppressed?  Maybe to stop the cancerous process to form a mass and stay "fluid"?   That is, in granulocytic sarcoma, TGF would be less suppressed?

Smooth Muscle Myosin & Leukemia

1.SMMHC, a Smooth Muscle Myosin related marker of differentiation, but also implying the use of multiple regulatory genes that ultimately depress P53 as a way to decrease repair of DNA and allow leukemia to proceed with proliferation. this marker is  seen in Inv-16 Leukemia.  Through interaction with SMAD3, it affects TGF driven migration of leukemic cells.  It also interfere with ACTA 2, TGFBR-2 AND FBN-1,
THIS SUGGEST THAT BLOCKING MIGRATION AND IMMUNE BETA-2 RECEPTOR OF TGF COULD ADD TO ACUTE EOSINOPHILIC LEUKEMIA.  BLOCKING NUCLEAR INTERNALIZATION OF THE BETA SUBUNIT OF THE CBF WOULD HELP IN THE CBF DRIVEN LEUKEMIA IN GENERAL.


2.HOXD3
" Mutations in this particular gene cause synpolydactyly and Brachydactyly. The product of the mouse Hoxd13 gene plays a role in axial skeleton development ...
remember the role of Anti-VEGF /MEK in people with gene that impairs morphogenesis.  leukemia with this mutation could a get a trial!

3 MEIS, a cofactor to the "soul of AML" E3
remember we discussed the AML is characterized by suppression of NF-kB
that suppression is achieved by this MEIS over-expression.  it is the over expression to 
HOS protein which is
 'The homologue of Slimb (HOS) F-box protein is a receptor of the Skp1-Cullin1-F-box protein (SCF(HOS)) E3 ubiquitin ligase, which mediates ubiquitination and degradation of beta-catenin and the inhibitor of NFkappaB, IkappaB.''

Stability of homologue of Slimb F-box protein is regulated by availability of its substrate.

Li Y, Gazdoiu S, Pan ZQ, Fuchs SY.

 You block this stuff, you release NF-kB, you slow down leukemia or at least decrease co-existing infection rates (role in transplant patients).

HYPOTHESIS : WHERE DO CYCLINS COME FROM?

There is increasing evidence that Cyclins are integrins and so are Tumor growth factors, Tumor Necrosis factors, interleukins and interferons.
All these are membrane proteins with a particularity to be released from Metalloprotease and related adhesion molecules depending on the nature of stimuli.  The discovery and description of ADAMs as type I membrane protein containing Metalloproteinase and an integrin domain locate the growth factors and Cyclins squarely at the membrane  (surface and reticulum membrane).  These proteins, once released, go straight to the Nucleus to unveil their might by activating transcription factor.  In their track to the nucleus they can amplify and activate signal transduction pathways as well as either molecules. The cyclins find cytoplasmic and protein substrates (mostly enzymes)  which have their specific domains and link to the site to activate them most of the time, changing their shapes so as to expose hidden electrons or atomic groups (such SH) to cause downstream chain activation.

Now as the pathway unfolds at light speed (or electronic speed) it may overwhelm the cell, protection has to be assured to hide death domains (which also are integrins and therefore at the membrane) and pathways to Apoptosis.  Protection at the membrane seems to be offered by the INK while the CIP/Kip.  But deep in the cell are the Bcl-like proteins. The CIP/Kip seems to work like Decoy specific proteins since the have Cyclin domain to stop them from stimulating their respective CDKs (Cyclin dependent Kinases).  Some CDKs need 2 or more different stimulations to accomplish their deed. And with the number of stimulations comes the consequent activation of various substrates.  The Retinoblastoma substrate governs the G1 progression phase in the cell cycle, but it needs at least 2 activations, first by Cyclin D followed by activation by Cyclin E in order for it to free E2F that light up tarnscrptions genes which control the path to S-phase.  This Cyclin E also activates processes leading to Histone Biosynthesis, Centrosome activity and DNA replication.  And in fact, Cyclin E is the one that leads to gene instability that characterize many triple negative breast cancers

(E2F AND CYCLIN E, ARE POWERFUL TARGETS FOR CANCER CURE)

One of the CIP/Kip(s) is the P21 which plays a role in the cell cycle arrest due to P53 activation.
I should note that the Kinase itself may be mutated.  CDK4 is mutated in Melanoma, it renders the INK4 protein unable to occupy its domain and therefore is free to affect the nuclear transcription factor.  Therefore the solution is to increase the ligand to INK4 so as to increase its ubiquitination and and degradation through the proteasome (Ipilimumab/CTLA 4 in T cell/ does not do this unfortunately, so there is more room for you to research).  YES, LIKE FOR MERCEDES, WE NEED THE E CLASS OF PROTEINS TO FURTHER UBIQUITINATION.  A MUTATION IN E CLASS (WHICH INCLUDES MDM2) WILL BE BAD IN MELANOMA!

Suffice is to show that what starts at the membrane moves quickly to the nucleus in a milli-milli second in a flash and turn the life of the host around!

It is worth noting that not only Cyclins can be blocked from entering the Nucleus where they trigger transcription factor formation, but sometimes the Decoy (Cip/Kip) is stopped from entering the nucleus and cannot stop Cyclins which have entered the nucleus: this happens in breast cancer (p27 mislocation)
-----------------------------------------------------------------------------------------
THE INTEGRINS, PRESUMED SOURCE OF CYCLINS!

STRATEGIES FOR THE CURE

Since the work of Weinberg and Hanahan, we know that despite the varieties of cancer, 6 driving forces lead to cancer cell survival.  The "Hallmarks of cancer" result from:

1.Self sufficiency in growth signals: Cancer cells escape Anoikis,  They secrete their own growth factors to achieve an autocrine stimulation.

2.Insensitivity to anti-growth signals. This is achieved by changing membranes' receptors composition and number, boosting its own global growth, and secreting Tumor Necrosis factors to tamper with surrounding cell machinery.

3.Sustained Angiogenesis, to maintain "feeding" of the new tumor mass.  This is mostly critical for solid tumors.  It is critical in tumors that bleed easily such as renal cell cancers.

4.Limitless replicative potential.  By removing stops to mass formation, natural boundary sensors which contribute to shaping organs, Telomerase activation again.

5. Suppressing or escaping Apoptosis: By using cyclins and Bcl-2 and related molecules. Shielding Mitochondria and avoiding FAS/BAX, activating loopholes routes and impairing ubiquitination of growth molecules!

6.Tissue invasion and metastasis. Here the tumor cells alter composition, nature and amount of the cell receptors and adhsions molecules, cluster of differentiation (CD), and produce Tumor growth factors (TGF) which give it growth advantage vis-a-vis the surrounding tissue.

This list is by no mean exhaustive given the variety of possible oncogene mutations.  However, when one gene is causing one of the 6 pathways, it is dubbed a DRIVER mutation for that cancer, and may have significant therapeutic importance.

This 6 venues are made of important molecular structures that can be a Target for therapy. Researcher are combing them one by one and targeting them.  The successful experience with Multikinase therapy suggest that interrupting several points of the cascade appears beneficial.  Computer models are being developed to see if sequential attacks or coordinated combinations would be better models for future therapies.  The CRBCM is working to develop such a model. Our model will be complete after we enumerate all laws of nature (see our related series).

Model of cures should embrace these 6 venues in a mathematical equation...the challenge is launched!
 

Understanding the Laws of Biology

IMPORTANCE OF UNDERSTANDING BIOLOGIC LAWS

With every research performed around the world, scientists learn a little more.  It is important that research focuses on a particular molecule and its interactions, specificity and efficacy. Point location research should be understood within a general plan of advances in biomolecular research.  To find that, TGF Beta, when produced, will make a cancer grow and therefore make the cancer more resistant to treatment, is nice. It adds to the detailed knowledge.  TGF(s) act on membrane receptors, therefore it will harvest the signal pathways to display its might.  We know that it will reach or may emanate from some transcription genes.  The tract its actions have to follow to affect the cell is full of loopholes and pitfalls.  Going after TGF(s) should be part of a planned combination approach.  It cannot work in over 30% of the people because of genetic heterogeneity which in itself is nature's protection for host survival.

Here at CRBCM, we understand that to cross the 50% effectiveness, our current treatment strategies must include the activity of the 2nd law well described here.  And better yet the first 2 laws.  Disruption of gene, and that of Microtubule that will lead to caspase release (Cytochrome c disruption implied).  Membrane based effects are only as good as they are able to involve an increased activity of fas and Bax.  Short of that, they are 70% ineffective.  (You can't discount 30% though)

TGF could present an opportunity for treatment.  We made an early allusion to the JUDO.  Use the power of the attacker to send him to the floor "in the general direction of his attack".  TGF wants to achieve acceleration of growth and cellular multiplication.  Disruption of gene and microtubule may in fact be more effective when faster multiplication is achieved? This is risky, but not a crazy a approach.  That is also why chemotherapy works only on dividing cells!

Globally, however, TGF and Bcl-2 tend to protect cancer cell. TGF seems to give a growth advantage to cancer cells vis-a-vis surrounding cells.  Bcl-2 seems rather to be a protection mechanism from reaching the mitochondrial Caspase,  protecting therefore cancer cell from Apoptosis, the cure to cancer. 
With this background info, we can now judge any research coming along as to its importance, and see how it fits in the general strategy to achieve the cure we all want.