Since the tumor after surgery (removed 99%) increased again in the same size (3.5 x 5 x 5 cm) in 3 weeks and the tumor did not decrease after radiotherapy + TMZ, we probably have a very unusual cocktail for the first line:
- cycle 42 days: Avastin (3mg/kg/week) + CCNU (1 day 75mg/m2) + TMZ (5 days 90mg/m2),
- disulfiram 500mg (+Copper 5mg + DHA) and verapamil 200mg only on the days of TMZ + CCNU administration, and 2 days before and after. I'm not sure, maybe it's advisable to take Disulfiram every day? Otherwise, disulfiram may not start to influence so quickly?
- every day: cloroquine phosphate 250mg, telmisartan 80mg, alfacalcidol 2mcg, oxaloacetate 100mg, melatonin 20mg, curcumin longvida 2000mg, Berberine 1000mg, DHA/EPA 1000mg, PSK / PSP 1800mg, Methimazole + T3, R-lipoic acid + hydroxycitrate
My mother has been responding well to taking DCA + caffeine for a week in the form of black tea and coffee. However, my mom's pulse increased to 90-95 after sleep or rest. To reduce it, we now take 10 mg of propranolol per day. An increase in the pulse may also be caused by the intake of the hormone T3.
Also I consider the addition of a low dose of naltrexone before bed.
We also ordered perillyl alcohol at www.sigmaaldrich.com and expect it soon.
Today we received a report from OncoDNA. The last 3 months I read and search for any information about glioblastoma, but unfortunately I find it difficult to understand this report. Doctors in Russia do not order such reports at all! Our doctor in Germany said that unfortunately, such reports will not help us in any way.
Maybe you can tell me what to look for in this report? Any comments?
For example, I can not understand, is there overexpression (amplification) of EGFR?
"Damaging TP53" = mutation of TP53? Not understanding this, I can not draw conclusions from this review (http://astrocytomaoptions.com/exploring-strategies-for-tp53-mutated-gliomas/) and other studies.
"Damaging PTEN" = loss or mutation PTEN? An interesting article in this case: http://btcocktails.blogspot.ru/2018/01/parp-inhibitors-for-pten-mutant-cancer.html
Which of the drugs on the list of potential clinical benefits to pay attention to ?
Here is a link to the report itself and some pictures of him:"Damaging TP53" = mutation of TP53? Not understanding this, I can not draw conclusions from this review (http://astrocytomaoptions.com/exploring-strategies-for-tp53-mutated-gliomas/) and other studies.
"Damaging PTEN" = loss or mutation PTEN? An interesting article in this case: http://btcocktails.blogspot.ru/2018/01/parp-inhibitors-for-pten-mutant-cancer.html
Which of the drugs on the list of potential clinical benefits to pay attention to ?
https://drive.google.com/open?id=1A3dophOME6gY1GNdOHWE48wVYJUu_nHc
About the low level of FGFR3.
ReplyDeleteDoes this article relate to this case, because this report indicates that FGFR3 is not detected?
2017 https://link.springer.com/article/10.1007%2Fs10637-017-0503-7
"Patients whose tumors expressed low levels of FGFR3 and AKT2 responded poorly to TMZ. Combination treatment of vinblastine (VBL) plus mebendazole (MBZ) with TMZ was more effective in reducing cell number in most cultures when compared to TMZ alone, especially in cells with low expression levels of FGFR3 and AKT2."
The report says nothing about protein expression of FGFR3. It simply says there is no *mutation* in FGFR3, which is not surprising, as FGFR genes are rarely mutated in GBM.
Delete"Overexpression" of EGFR refers to protein overexpression, which wasn't tested. "Amplification" refers to having many copies of the EGFR gene per cell rather than the normal two copies.
ReplyDeleteIt's not clear to me whether the OncoDEEP test detects gene amplifications (such as EGFR amplification). It would be worth emailing them to ask. The OncoDEEP product sheet available as a download on the website doesn't go into detail about what is and isn't included.
Almost all GBMs are missing one copy of PTEN due to loss of chromosome 10, and in your mom's case the second copy has been knocked out by mutation (premature stop codon leading to a truncated protein). This is confirmed by immunohistochemistry showing negative protein expression for PTEN.
PTEN is a suppressor of PI3K signaling. The report also shows high expression of phosphorylated 4EBP1 which suggest high mTOR activity. (mTOR can be activated through increased PI3K activity following loss of PTEN). There are a number of experimental PI3K or dual PI3K and mTOR inhibitors in clinical trials, but the only ones approved so far are rapalogs (rapamycin, everolimus, temsirolimus) which are specific to mTOR complex 1. PARP inhibitors may be useful on the basis of total loss of PTEN.
The "damaging" TP53 mutation had a variant allele frequency of 58%, which suggests only one copy is altered, and the other copy is normal. Many of the suggestions in the "Exploring Strategies for TP53 mutated gliomas" are specific to gain-of-function TP53 missense mutations, rather than frameshift mutation like the one in your mother's case (a frameshift mutation is a loss of function, rather than gain of function mutation).
The TP53 mutations allows us to infer that her tumor belongs to either the proneural or mesenchymal subgroups rather than the classical subgroup. The classical subgroup is most likely to have high level EGFR amplifiation, while the proneural and mesenchymal group are more likely to have either low level EGFR amplification or normal EGFR copy number.
Near the end of the report it states "To view the full report, go to our web platform OncoSHARE". Is there a more detailed report available?
The TOP2A inhibitors listed will be of limited use due to poor blood-brain barrier crossing - probably the reason they are not generally used for brain tumors.
More comments to follow...
Thanks Semyon, I copied (then deleted) the login info.
Deletehttp://astrocytomaoptions.com/exploring-strategies-for-tp53-mutated-gliomas/
Delete"The low-carb diet effectively inhibited tumours in all three groups, but most significantly in the p53-mutant and p53-null groups.
...This study is in agreement with a previous study by a different group which showed that colon cancer xenografts in which p53 was knocked out were inhibited by metformin treatment, while the same xenografts with normal p53 expression were completely resistant to metformin treatment [8]."
Stephen, forgive me, but I read your message and the OncoDeep report again and again. I can not understand which TP53 is in my mother's tumor. The report states: "We also identified a damaging TP53 variant (Q191Sfs * 18)."
Simply put, with this TP53, the effect of adding Metformin and (or) a low-carb diet is possible?
In recent months, I have been focusing on low-carbohydrate (ketogenic diet) and taking Metformin. And I'm afraid of not understanding something from your interesting article (http://astrocytomaoptions.com/exploring-strategies-for-tp53-mutated-gliomas/), your answers, the incomprehensible value of TP53 my mom's tumor and draw the wrong conclusions.
I apologize again, but the question of the theoretical benefits of Metformin and a low-carbohydrate diet is very important to me and I'm afraid of making a mistake ...
To understand your mom's TP53 is going to require some scientific background.
DeleteThe DNA code is made up of 4 bases ("letters"): A, G, C, and T. The DNA code letters are read in groups of 3, which are the equivalent of codons in mRNA. In RNA, each group of 3 letters is called a codon, and usually each codon provides the blueprint for making an amino acid, or alternatively a codon can signal that translation should stop (this is called a "termination" or "stop" codon.
http://www.brooklyn.cuny.edu/bc/ahp/BioInfo/GP/GeneticCode.html
https://www.mun.ca/biology/scarr/Exons_Introns_Codons.html
When there are small insertions or deletions of "letters" that are not equal to 3 or a multiple of 3, this cases a shift in the reading frame: this is called a frameshift mutation. What generally happens with a frameshift mutation is that you get a premature "stop" codon, resulting in a non-functional truncated protein. Also, any amino acids coded downstream of the frameshift mutation but before the stop codon, are not the correct ones, because of the alternation of the reading frame.
In your mom's TP53 gene, there was an insertion of 4 "letters": CTCC, which shifted the reading frame. This resulted in the protein alteration:
Q191Sfs*18
This means that at codon 191, because of the small insertion of "CTCC", a glutamine (Q) was replaced by a serine (S) amino acid. That was the first codon to be affected by the frameshift. The * symbolizes the termination or stop codon, which in this case is predicted to be at codon 18 downstream from the first affected codon (which was codon 191).
So to summarize, one of the copies of TP53 in your mom's tumor would be cut-off (shortened, truncated) shortly after codon 191. "The p53 protein is a phosphoprotein made of 393 amino acids". But in this case only the first 191 codons (about the first half) would have been translated into the proper amino acids. This half-length p53 protein is most likely non-functional.
However, this TP53 mutation was only found in 58% of sequencing reads, implying that a "wild-type" or non-mutated copy of TP53 also exists in the tumor.
In my TP53 article on Astrocytoma Options where I'm summarizing the study on glucose restriction, the mutations described there are missense mutations resulting in a full-length, functional protein, with a single amino acid alteration. This is unlike the frameshift mutation in your mother's tumor. We also can't describe your mom's tumor as "p53 null", because there is evidently a wild-type TP53 still remaining, and the frameshift mutation only took out one copy.
Regardless, the function of the remaining p53 can be reduced in other ways, for example by increased expression of metallothioneins. So even a non-mutant p53 is not necessarily functional. http://astrocytomaoptions.com/exploring-strategies-for-tp53-mutated-gliomas/
In short, I don't see any reason to stop with the carb restriction and metformin as they could be giving some benefit.
Thank you for such a detailed analysis. I'm very uncomfortable that you have given me so much time!
DeletePlease don't feel uncomfortable. This is why the blog exists, to educate and share information!
DeleteThere is a high expression of phosphorylated ERK1/2. ERK1 and 2 is phosphorylated by MEK1/2. Therefore a MEK1/2 inhibitor like trametinib could be useful. However, brain penetration of trametinib is likely sub-optimal.
ReplyDeletehttps://www.ncbi.nlm.nih.gov/pubmed/24875464
Combining with a P-glycoprotein inhibitor such as verapamil, or fluoxetine (Prozac) might aid its passage into the tumor. Trametinib isn't approved for brain tumors though, and it might be challenging to get it prescribed and/or expenses covered.
Negative expression of CD8 and PD-L1 suggests checkpoint inhibitors (nivolumab, pembrolizumab, durvalumab) on their own would be of no benefit. Your mom's tumor would most likely be classed as a "non T-cell inflamed".
https://www.ncbi.nlm.nih.gov/pubmed/29275462
I'm currently researching ways of increasing T-cell infiltration into tumors and hope to write a summary of my research soon. Much of the evidence is mouse rather than human unfortunately.
Thank you very much, Stephen, I will now very carefully study your answers.
DeleteAs I see, I also should carefully study your article and the link in it:
http://btcocktails.blogspot.ru/2018/01/parp-inhibitors-for-pten-mutant-cancer.html
Preliminary, probably I should consider PARP + mTOR inhibitors and study the information on Trametinib?
You probably did not find in the full report the study of the amplification of EGFR? It's strange. When they sold me this test, they assured me that this research will be done.
_____________________
You may not believe it, but unfortunately in Russia even the most expensive oncologists do not analyze such reports. I do not think that this report, like anything else, will help us much, I have no illusions, but at the moment I want to do for my mom maximum. And thank you very much for spending time with people like me from all over the world.
I'm sure that your blog has prolonged the life of many patients (as you yourself say cocktail approach is unpredictable), or brought them a bit of peace and hope.
Thanks for your kind words Semyon. If I've prolonged somebody's life or even brought them some peace and light in a dark time, it makes my work worthwhile.
DeleteIt's possible that no gene amplifications were detected, and therefore nothing about that made it onto the report. I would email OncoDNA to clarify whether EGFR amplification would have been detected if it was present.
1. Stephen, forgive my obsessive questions, I do not quite understand.
DeleteYou write that "PARP inhibitors may be useful on the basis of the total loss of PTEN." Does this apply to my mom's case?
The report also says about PARP inhibitors: "preclinical studies have shown that PTEN deficient tumors may be sensitive to PARP inhibitors; PARP inhibitors, such as olaparib, are being studied in clinical trials".
Probably the best PARP inhibitor for glioblastoma is while Olaparib?
In December, I specially flew to Delhi (India) when I wanted to buy Plerixafor and now I'll probably go there for a copy of Olaparib. It's much cheaper there. I think that the quality of the drug should be acceptable.
I also need to think about when to add Olaparib. I think this will depend on the results of MRI.
2. The report also says that "Altogether, those results suggest that mTOR inhibitors would be associated with a clinical benefit for this patient whereas PIK3 inhibitors would be associated with a clinical benefit for this patient."
Thus, I will draw attention to rapamycin, everolimus, temsirolimus. I'll probably add Rapamycin (2mg / day) to Chloroquine and I'll think later about replacating rapamycin for everolimus or temsirolimus, their dose and schedule.
3. I also study information about Trametinib
4. Specialists from OncoDNA told me that "According to the results of the analysis, the amplification of EGFR was not found, since according to information on EGFR - there are no variants of damage."
Also in the letter they ask especially to pay attention to mTOR inhibitors (PTEN and p4EBP1 IHCs and PIK3CA wild type and PTEN variant NGS)
Yes, I did mean that a PARP inhibitor could be useful in your mom's case. Here is another study showing increased sensitivity to PARP inhibitors in PTEN-deficient endometrial cancer cells
Deletehttp://stm.sciencemag.org/content/2/53/53ra75
PTEN Deficiency in Endometrioid Endometrial Adenocarcinomas Predicts Sensitivity to PARP Inhibitors
https://www.nature.com/articles/onc2017326
PTEN deficiency sensitizes endometrioid endometrial cancer to compound PARP-PI3K inhibition but not PARP inhibition as monotherapy
http://stm.sciencemag.org/content/2/53/53ra75
Olaparib is a reasonable choice, but like trametinib it is a P-glycoprotein substrate and might get into the brain better with a P-glycoprotein inhibitor (eg. verapamil).
A more brain penetrant PARP inhibitor called BGB-290 might turn out to be the best choice for brain tumors, but is currently only available in clinical trials in Australia and the USA.
Everolimus is a modification of sirolimus (rapamycin) and temsirolimus can be converted to sirolimus inside the body. A big difference is that rapamycin is off-patent and has generic versions available, while everolimus and temsirolimus are still protected by patents and so are much more expensive.
The lack of EGFR amplification confirms her tumor is not in the "classical" subgroup, and EGFR inhibitors (eg. lapatinib, afatinib) would be less useful.
Thank you very much for your detailed answers! It's very important to me...
DeleteStephen, in the comments to my mom's report you wrote: "There is a high expression of phosphorylated ERK1/2. ERK1 and 2 is phosphorylated by MEK1/2."
DeleteAlso, in your library in the file "Matching drugs to targets", the medicine Minocycline is indicated for the target "Mek1 / 2, Erk1 / 2".
I correctly think that Minocycline is theoretically suitable for the case of my mother?
Stephen, once again I want to thank you for your incredible work. Your "Brain Tumor Library" is very useful!
Theoretically it could be useful. I would add that I would not use minocycyline or other antibiotics if pursuing vaccine or checkpoint inhibitor immunotherapy, in light of the importance of gut bacteria in immune-based therapies.
DeleteIt is also one of the drugs that often brings adverse side effects at the higher doses. CUSP9v3 escalates to 100 mg twice daily for minocycline, but you might find 50 mg twice daily to be more tolerable.
I found this record about the loss of PTEN and Trametinib:
Deletehttp://www.pdr.net/drug-summary/Mekinist-trametinib-3157.4424
"Potential mechanisms of resistance to trametinib include upregulation of MAPK signaling, phosphatase tensin homologue (PTEN) loss, hepatocyte growth factor (HGF)/MET signaling, amplified cyclin D1 (CCND1), and amplified receptor tyrosine kinase (RTK) signaling through PI3K and mTOR."
Is this a good reason not to consider taking Trametinib (+ P-glycoprotein inhibitors) in our case?
This would be a good reason to address both the PTEN/PI3K/mTOR pathway as well as the MEK/ERK pathway.
DeleteThe study below shows that combined targeting of MEK (with trametinib), and mTOR complex 1 (with everolimus, sirolimus/rapamycin etc.) can be useful in NF1 mutant cancers.
https://www.ncbi.nlm.nih.gov/pubmed/24913553
NF1 is a negative regulator of RAS. If NF1 is deactivated, it allows increased RAS activity and then downstream RAF, MEK and ERK activity.
While your mom's tumor may or may not have NF1 mutation (this gene wasn't included in the OncoDEEP panel), the report did show high expression of phosphorylated (activated) ERK1/2 (NF1/RAS/RAF/MEK/ERK pathway).
So theoretically a combination of MEK and mTOR inhibitors could be useful (trametinib + rapamycin for example). My questions would be about tolerability of the combination (especially in addition to all the other cocktail drugs), as well as availability and access. Trametinib is an expensive patented cancer drug with the earliest patent expiries in the USA not before the year 2025.
I just saw in your April 22 post you were able to purchase trametinib in India.
DeleteStephen, thank you again for your detailed answers!
DeleteMom takes such a cocktail of many medicines with great risk (((
Sometimes there are side effects and I try to change the schedule of medications or take breaks. In general, my mother tolerates all well.
We do detailed blood tests every week. We also regularly do ultrasound of the organs.
Especially I'm afraid for Trametinib. It has the greatest number of side effects.
Official price in Russia: 30х2mg - $4500. In India, I bought it for $2000.
Thanks for the link to perillyl alcohol - I've been looking to add that to my daughter's cocktail for a while! However, do you know which of the products there I should order (https://www.sigmaaldrich.com/catalog/search?term=perillyl+alcohol&interface=All&N=0&mode=match%20partialmax&lang=en®ion=GB&focus=product)? And how should it be administered?
ReplyDeleteBest of luck to your mum, Semyon - much love x
We ordered 100 grams of this:
Deletehttps://www.sigmaaldrich.com/catalog/product/aldrich/w266418?lang=en®ion=US
Probably, we were mistaken, I will also re-order this:
https://www.sigmaaldrich.com/catalog/product/aldrich/218391?lang=en®ion=US
About how to use perillyl alcohol there is a lot of information in this wonderful blog:
Deletehttps://btcocktails.blogspot.ru/search/label/perillyl_alcohol
We did not use it ourselves, so I can not advise anything yet. But as soon as we start, I will definitely post in this blog all the photos and the report.
Also on this site there are solutions of EGCg, resveratrol, withaferin A and others. It would be very, very interesting to know how it can be used!
DeleteI see promising and more studied intravenous injections of Curcumin and Resveratrol.
Steven,
Deletehere on this link, kindly indicated by Stephen in one of the message, is very well written about the reception of perillyl alcohol:
https://www.cancertreatmentsresearch.com/perillyl-alcohol-poh/
This recently published study concluded that ketogenic diet + perillyl alcohol is effective against the usual diet and perillyl alcohol.
Deletehttps://www.ncbi.nlm.nih.gov/pubmed/29391903
"These results are encouraging and suggest that KD associated with intranasal POH may represent a viable option as an adjunct therapy for recurrent GBM."
Semyon, does your mom use the perillyl alcohol at present? Could you please share, at spare time, your experience (side effects, the actual solution you prepared - I mean which of the two products from Sigma Aldrich did you decided to use). Many thanks.
DeleteHello! Here all the information:
Deletehttp://btcocktails.blogspot.ru/2018/02/perillyl-alcohol-full-information-about.html
First I bought a ready-made solution in Italy, now I ordered 96% perillic alcohol in Sigma Aldrich.
If there are other questions, I am always happy to answer!
This comment has been removed by the author.
ReplyDelete