Research for the PKD Protocol

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In this post, I have collected all quotes that have led me to develop the PKD Protocol.
The links to sources and my personal comments are included.
If you read this in the provided order, you can draw some conclusions easily.
Most of these are animal models. But since I have had success with the Protocol already, it is reasonable to assume at least some of them work in humans as well.
This is not spell-checked.

http://tetralogicpharma.com/smac-mimetics-apoptosis/
Tumor Necrosis Factor, or TNF, is an extracellular signaling molecule that induces apoptosis. Cancer cells and certain virally infected cells can use IAPs to convert a TNF induced self destruction signal into a pro survival signal through a protein complex called NF κB. While a number of cancer therapies induce TNF, the TNF self destruction signal may be blocked by the IAPs.

http://www.sciencedirect.com/science/article/pii/S0167488913002243
Starvation and other environmental and hormonal cues such as nutrient deprivation, growth factor depletion and hypoxia are known to activate autophagy

http://www.news-medical.net/health/What-is-Autophagy.aspx
(Autophagy) maintains homeostasis or normal functioning by protein degradation and turnover of the destroyed cell organelles for new cell formation.
During cellular stress the process of Autophagy is upscaled and increased. Cellular stress is caused when there is deprivation of nutrients and/or growth factors.
(…)
Autophagy is termed a nonapoptotic programmed cell death with different pathways and mediators from apoptosis.
Autophagy mainly maintains a balance between manufacture of cellular components and break down of damaged or unnecessary organelles and other cellular constituents.

http://www.sciencedirect.com/science/article/pii/S0301008213001044
The decision for a cell to die is based on the balance between intracellular pro- and antiapoptotic factors, i.e., the caspases and intracellular inhibitors of apoptosis (IAPs), respectively.
(…)
IAPs are recognized by the presence of a ~ 70 amino acid BIR (baculovirus IAP repeat)
- Possible virus link??

http://www.ncbi.nlm.nih.gov/pubmed/23831571
Furthermore, we found that autophagy activation resulted in c-IAP1 and c-IAP2 degradation and formation of the Ripoptosome that contributes to necroptosis.

https://www.bulletproofexec.com/what-is-protein-fasting-bulletproof-diet/
By protein fasting once a week, you are essentially allowing your body a day to use its digestive machinery to perform self-maintenance. This is because dramatically lowering your protein intake once a week induces autophagy

http://www.ncbi.nlm.nih.gov/pubmed/16261996 (baby chicks)
(…) cathepsin B, and caspase-3 mRNA expression were likewise increased by fasting

http://www.ncbi.nlm.nih.gov/pubmed/16939413 (rats)
Activities of caspases 3, 6, 8 and 9 were increased significantly in lymphocytes from rats fasted for 24 h, whereas only an increase in caspase 3 and 9 activities were observed in rats fasted for 48 h.

http://www.sciencedirect.com/science/article/pii/S0925443911000196 (SBM mice)
Increased apoptosis and proliferation occur early in the course of the disease and precede cystogenesis in SBM mice
(…)
Apoptosis in PKD seems to act like a double-edged sword. The literature can be split into two groups: one accusing apoptosis of being the primary cause of the decline in renal function and the other, claiming that inducing apoptosis slows down disease progression
(…)
It seems that it is an imbalance between proapoptotic and pro-proliferative factors, rather than the absolute expression levels that play a critical role in the development of cystic kidney disease. This imbalance leads to aberrant cell cycle progression in a similar fashion to cancer, such that PKD has been labeled “neoplasia in disguise” [57]. Cancers are generally characterized by suppression of apoptosis and the goal of cancer therapy is to induce apoptosis in malignant cells
(…)
whether apoptosis is secondary to proliferation or vice versa, is still a subject of debate.
(…)
Particularly, apoptosis was detected in normal-appearing, noncystic tubules suggesting that it may be associated with the progressive loss of normal nephrons in PKD

Code:

- Remark: PKD Kidneys get apoptosis only where they are healthy. (maybe the body puts out an abundance of Knf-aplha to kill the cysts, but they fight it with IAPs while the healthy tissue cant fight) This would make the loss of kidney function an independent process of the cystogenesis itself (growing cysts). However, shrinking cysts are likely to reduce the total amount of KNF-alpha, slowing down apoptosis in healthy cells.

(…)
there is also evidence that increased apoptosis in tubular cells may be associated with decreased cyst formation. For example, Pax2 deficient mice that have increased apoptosis, were backcrossed into congenital polycystic kidney (cpk) mice have increased renal apoptosis yet less cystic disease
(…)

Apoptosis (in PKD) is localized primarily to the interstitium with little evidence of cell death in cyst epithelium or noncystic tubules.  

Code:

>HEISST: Apoptose findet bei PKD nur in der gesunden Region statt. (Hinweis- dort gibt es keine Zystenflüssigkeit mit IAPs?)

(…)
apoptosis in normal tubules further contributes to the progression of loss of renal function in ADPKD.
(…)
(c-FLIP) is structurally related to caspase-8, but its caspase domain is altered, rendering it inactive. It is therefore a natural inhibitor of activated caspase-8.
(…)
c-FLIP was detectable in large cysts from end-stage ADPKD kidneys^
(…)
Inhibition of the mTOR pathway reverses renal cystogenesis in PKD and has been associated with an increased rate in apoptosis in vitro

Code:

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- Remark: mTOR suppression is one of the effects of protein fasting. Bulletproof Coffee and other "Bulletproof" techniques aswell: „There are 3 known ways to compress mTOR. Intermittent fasting, exercise, and coffee (or more weakly, chocolate, green tea, turmeric, or resveratrol)”

(…)
In four patients who received rapamycin (mTOR inhibiter) as part of their post-transplant immunosuppression, the volume of the native cystic kidneys was reduced by 24% compared to 8.6% in three patients treated with other immunosuppressants.
(…)
The CDK inhibitors, both endogenous (p21) and synthetic (roscovitine) (…)
…resulted in arrest of cyst growth [10]. Intermittent administration of roscovitine has a long-lasting anti-cystic effect[113]. At high concentrations, roscovitine results in caspase-3 activity being significantly increased from control cells.
(…)
Intermittent administration of roscovitine has a long-lasting anti-cystic effect
(…)
the dedifferentiation occurring in cystic epithelial cells is not simply a “step backwards”, but likely a reaction to the environment encountered in PKD kidneys. Analysis of cyst fluid has revealed the presence of multiple cytokines, among them are TGF-β, TGF-α, and EGF[123] and [124]. These cytokines are closely involved in apoptosis, proliferation, and differentiation.
(…)
There are two lines of evidence for a common pathway of apoptosis and proliferation involving adhesion-dependent control of apoptosis and overexpression of the proto-oncogene c-myc.
(…)
apoptosis in PKD, beyond its role in cyst cavitation, contributes to the loss of renal tissue and may be responsible for the progressive deterioration of renal function that occurs in patients with ADPKD [8]. On the other hand, however, apoptosis can be viewed as the last line of defense against oxidative or other form of DNA damage, thus reducing the risk for neoplastic transformation and explaining the lack of a convincingly increased risk for renal cell carcinoma in this condition despite the high rate of epithelial cell proliferation. Therefore, elucidation of the mechanisms responsible for the coupled stimulation of cell proliferation and apoptosis in ADPKD may provide opportunities for interventions that avoid the potential risk of selectively inhibiting apoptosis alone. Exciting times are awaiting us in the near future.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459378/
…the mTOR pathway is inappropriately activated in cyst-lining epithelial cells in human ADPKD patients and mouse models. Rapamycin, an inhibitor of mTOR, is highly effective in reducing renal cystogenesis in two independent mouse models of PKD. Treatment of human ADPKD transplant-recipient patients with rapamycin results in a significant reduction in native polycystic kidney size.

https://de.wikipedia.org/wiki/MTOR

Code:

An inhibition of mTOR is responsible for rapamycin's success.
so: temporary suppression of mTOR by Bulletproof fasting has rapamycin-like effects

http://www.scopus.com/record/display.uri?eid=2-s2.0-0031974527&origin=inward&txGid=0 (SBM mice)
We conclude that the pathogenesis of PKD hinges on a critical imbalance in c-myc regulation of the opposing processes of cell proliferation and apoptosis, recapitulating the cellular phenomena in developing fetal kidney.

http://www.ncbi.nlm.nih.gov/pubmed/15698430 (Han:SPRD rats)
There are two pathways of caspase-3 and caspase-7-mediated apoptosis: (1) the "extrinsic" pathway involving the death receptor Fas, Fas ligand (FasL), and caspase-8 and (2) the "mitochondrial" or "intrinsic" pathway involving Bcl-2 proteins, caspase-2, cytochrome c release, and caspase-9.
(…)
There was an increase in the proform of caspase-8 demonstrating involvement of the extrinsic pathway. No differences in FasL mRNA were seen suggesting that the extrinsic pathway is independent of the death receptor ligand, FasL.

http://www.pkdiet.com/pdf/VitB3.pdf
“Sirtuin 1 inhibition delays cyst formation in autosomal-dominant polycystic kidney disease”
SIRT1 was upregulated through c-MYC in embryonic and postnatal Pkd1-mutant mouse renal epithelial cells and tissues and could be induced by TNF-α, which is present in cyst fluid during cyst development.
(…)
treatment with a pan-sirtuin inhibitor (nicotinamide) (…) delayed cyst growth in Pkd1 knockout mouse embryonic kidneys
(…)
Increased SIRT1 expression in Pkd1 mutant renal epithelial cells regulated cystic epithelial cell proliferation through deacetylation and phosphorylation of Rb and regulated cystic epithelial cell death (APOPTOSIS?)
(…)
Our findings provide a molecular basis for the potential use of nicotinamide to delay cyst formation in ADPKD patients.
(…)
SIRT1 expression was also increased in kidneys from well-characterized hypomorphic homozygous Pkd1nl/nl mice (15) compared with that in age-matched WT kidneys
(…)
Cyst formation was significantly delayed in the absence of SIRT1
(…)
nicotinamide induced tubular epithelial cell apoptosis in kidneys from Pkd1–/– E15.5 embryos
(…)
Nicotinamide (0.25 mg/g)
(…)
Silence or inhibition of SIRT1 decreases renal epithelial cell growth, but increases apoptosis

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-Anmerkung: MORE APOPTOSIS, LESS PROLIFERATION leads to FEWER CYSTS. This proves, Apoptosis is what we want in PKD, and we should encourage, not limit it.

(…)
We further found that treatment with nicotinamide markedly increased the level of active caspase-3 (…) which suggests that caspase-3 is the downstream executioner of nicotinamide-induced apoptosis in Pkd1-mutant renal epithelial cells.
(…)
It has been reported that a 3-g/d dosage of nicotinamide is safe for adults (36)

Code:

- Remark: To match the rat model by dosage, we would need 250mg/kg body weight. Too high for humans.

(…)
We found that treatment with nicotinamide not only induced cystic epithelial cell apoptosis (Figure 7), but also increased p53 acetylation.


nicotinamide delayed cyst formation in MEKs when administered to pregnant females (Figure 4) suggest the possibility that at-risk fetuses, based on family history, may be treated in utero by administration of nicotinamide to the pregnant mother. In addition, since nicotinamide delayed cyst growth in postnatal Pkd1-knockout mouse kidneys (Figures 5 and 6), administration of nicotinamide to a neonate, toddler, or adolescent may delay cyst growth

https://www.clinicaltrials.gov/ct2/show/NCT02055079
Sirolimus (SIR) has lead to a reduction of overall kidney size (…) In this study we will investigate if pulsed administration of SIR in a fixed weekly oral dose of 3 mg over 24 months compared to placebo significantly reduces cyst growth
Sirolimus = mTOR inhibiter

Code:

- Remark: Once per week. This would match Protein Fasting Once a week probably. Study from Vienna. interesting.

BUTYRATE

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413450/
Pharmacological inhibition of HDAC activity has been found to reduce the progression of cyst formation and slow the decline of kidney function
(…)
the expression of HDAC6 is upregulated in cystic epithelial cells
(…)
inhibition of HDAC5 with HDAC inhibitor may prevent cyst formation.
(…)
In all Pkd2−/− embryos (n=7) from TSA-injected mothers, kidney cyst formation was drastically reduced compared to those from control DMSO-injected mothers. This finding suggests that HDACs are the potential therapeutic targets for the treatment of ADPKD

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- Remark: TSA seems to only inhibit HDAC 1,3,4,6,10. Conclusion for HDAC5 not possible. Butyrate does NOT inhibit HDAC6 & 10, but all others.

(…)
We and others have reported that class I HDAC inhibitor, VPA, and class II HDAC inhibitor, TSA, reduce the progression of cyst formation and slow the decline of kidney function.
(…)
VPA belongs to the short-chain fatty acids derived HDAC inhibitors, which also includes sodium phenylbuty-rate and sodium butyrate.
(……)
These data and studies in cancer biology suggest that a combination of HDAC inhibitors along with the inhibitors of growth factor signaling may provide an effective therapy for prevention of cyst formation.

http://jn.nutrition.org/content/133/7/2485S.long
Sodium butyrate has multiple effects on cultured mammalian cells that include inhibition of proliferation, induction of differentiation and induction or repression of gene expression.
(…)
Butyrate inhibits most HDAC except class III (SIRT1) and class IIb (HDAC6 and HDAC10)

http://www.jbc.org/content/275/27/20436.full
p53, the most commonly mutated gene in cancer cells
(…)
histone deacetylase (HDAC)-1, -2, and -3 are all capable of down-regulating p53 function. Down-regulation of p53 activity by HDACs is HDAC dosage-dependent

Code:

- Remark: p53 is necessary for apoptosis.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799791/
we demonstrated that inhibiting class I HDACs, either by valproic acid (VPA), a class I specific HDAC inhibitor structurally unrelated to TSA, or by knocking down hdac1, suppressed kidney cyst formation and body curvature caused by pkd2 deficiency. Finally, we show that VPA was able to reduce the progression of cyst formation and slow the decline of kidney function in a mouse ADPKD model.
(…)
our results also reveal a critical role for HDACs in PKD pathogenesis and point to HDAC inhibitors as drug candidates for PKD treatment.

http://www.ncbi.nlm.nih.gov/pubmed/16126250
Alternate fasting, that was initiated in middle age mice through a 4 month period, reduced significantly the incidence of lymphoma (0% versus 33% for controls)

Comparability of Butyrate and VPA in effectiveness for HDAC inhibition

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165640/

Code:

- upper left corner. the thinner the line, the better the HDAC2 inhibition. Butyrate is a little less strong, but still comparable to VPA.

http://link.springer.com/article/10.1007%2Fs001250051536
High-dose nicotinamide should still, however, be considered as a drug with toxic potential at adult doses in excess of 3 gm/day and unsupervised use should be discouraged

http://www.doctoryourself.com/JOM1.html
Severely crippled arthritic patients needed up to a total of 4,000 mg/day (of niacinamide).  Divided into 10 doses per day.

http://etd.library.pitt.edu/ETD/available/etd-03252008-114622/
The mammalian sirtuin SIRT1 activates the same pathway that conveys longevity via calorie restriction
(…)
Furthermore, SIRT1 activator reduces, whereas SIRT1 inhibitor nicotinamide activates the mTOR pathway.  

Code:

- Remark: Niacinamide shouldnt be taken when inhibiting mTOR, because it activates it. Best to take it with protein containing meals.

Iodine

http://www.jbc.org/content/281/28/19762.abstract
Western blot results showed a decrease in Bcl-2
results demonstrate that [molecular] iodine treatment activates a caspase-independent and mitochondria-mediated apoptotic pathway.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2199149/

We also investigated another well characterized function of c-myc, the regulation of apoptosis through pathways involving p53 and members of the bcl-2 family, which induce and inhibit apoptosis, respectively.

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- Remark: BCL-2 inhibits apoptosis. Iodine promotes apoptosis.

Mechanism

http://jasn.asnjournals.org/content/13/9/2384.full
cysts arise from the tubular portion of the nephron as well as the renal collecting system. However, although all cells of the nephron carry the same germline mutation, only a few cysts arise per nephron.
[…]
In this model, a mutated PKD1 (or PKD2) gene is inherited from one parent and a wild-type gene is inherited from the unaffected parent. During the lifetime of the individual, the wild-type gene undergoes a somatic mutation and becomes inactivated. Complete loss of PKD1 (or PKD2) in cells in which second mutations have occurred initiates cyst formation.
[…]
If each renal cyst arises from a discrete second hit, then a relatively high rate of somatic mutagenesis would be required to explain the large number of cysts that are found in polycystic kidneys. Recent studies indicate that the rate of somatic mutations in kidney epithelial cells is approximately 2 × 10^-4, which is more than tenfold higher than in other cells (37). The reason for the high rate of somatic mutagenesis in the kidney is not known.

https://web.archive.org/web/20150918231600/http://www.britannica.com/science/somatic-mutation
Somatic mutations are frequently caused by environmental factors, such as exposure to ultraviolet radiation or to certain chemicals.

Code:

- Annotation: More somatic mutations could be caused by heigthened sensitivity to mTOR. (Rapamycin study) Even if we could not influence this, we could still limit our exposure to known mutation inducers such as chemicals and radiation. Possible ways to do this are removal of chemicals from food and care products (substitute for better ones like real soap, baking soda, apple cider vinegar). eating organic and getting radiation protected phone pouches, as well as shutting off WiFi (get a landline and ethernet.) are bound to help.

Coffee/Caffeine

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2698317/
Theophylline and caffeine are naturally occurring methylxanthines[…]
Caffeine is the world’s most widely consumed stimulant and reaches plasma concentrations of ~50 μM in moderate coffee drinkers.[…]
Theophylline causes bronchodilator and antiinflammatory responses and has long been used clinically for the treatment of asthma and other respiratory diseases. The therapeutic serum levels range from 55–111 μM
[…]
Theophylline (5 mM) strongly inhibits mTOR kinase activity in vitro and blocked insulin activation of Akt in 3T3-L1 adipocytes [73]. However, since theophylline and caffeine also target class I PI3Ks with IC50 values ranging from 75 μM to 1 mM [74], effects on Akt cannot be attributed solely to mTOR inhibition.
[…]
Many biochemical actions of methylxanthines have been identified, including antagonism of adenosine receptors, inhibition of cyclic nucleotide phosphodiesterases, and increased Ca2+ release from the sarcoplasmic reticulum. These compounds also inhibit mTOR and related kinases, most likely by acting as low affinity ATP analogs. Theophylline (5 mM) strongly inhibits mTOR kinase activity in vitro

Code:


-   Remark: Triptolide (drug), as well as Caffeine trigger Ca2+ release.
-   Theophylline and Caffeine are part of coffee.
-   Coffee inhibits mTOR, inhibits Akt independently

https://www.researchgate.net/profile/Alexandre_Arcaro/publication/6202222_Mitotic_activation_of_Akt_signalling_pathway_in_Han__SPRD_rats_with_polycystic_kidney_disease/links/0912f50ab913e1ba26000000.pdf
Because Akt is a proximal target of mTOR, its inhibition with specific antagonists could be useful to prevent or halt cystogenesis in ADPKD.