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Scientists are finding fungi in cancerous tumors

smithsonianmag.com

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Re: Scientists are finding fungi in cancerous tumors

#31

Post by bitL »

hondo77 wrote: post #9

Great./s Now the people who told me that drinking baking soda in water would cure my cancer "because cancer is a fungus" are going to go wild over this.

You might be laughing, but baking soda used to be injected to tumors to reduce lactic acidosis (cancer cells can't proliferate without being immersed in lactic acid). So the people you mentioned might have been running on older research and scientific beliefs. The new version is to use medication that actually decreases lactic acid to slow down/stop growth of tumors (DCA, mega-dose thiamine etc.)

Another funny fact - most cancer cells get energy the same way as fungus/yeast - by fermentation, and not like most human cells by perspiration. That might be why those people said "cancer is just fungus".

Re: Scientists are finding fungi in cancerous tumors

#33

Post by penumbragement »

yellsatclouds wrote: post #28
greggsy wrote: post #24

Earlier quoted context omitted.

> You can even check this yourself today. As much as I would love to be able to do this, I’m unsure where to start, and while I’m certain there would be a stackoverflow community for it, I wouldn’t even know what to ask. I know this sounds like a joke comment, but I feel like we live in a time where someone could post some Jupyter notebooks on the matter, and for someone to create a step by step video on YouTube to g…

we cerntainly have the technology... just not the social-political will to do it.

Not to be pedantic, but we do have the social-political will, just not enough of it.

Yet.

Re: Scientists are finding fungi in cancerous tumors

#34

Post by vavooom »

axg11 wrote: post #23

Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Every time. You can even check this yourself today. Analyse any publicly available (unprocessed) whole genome sequencing data. Usually the contamination is This study hasn’t ruled out contamination as the cause for the results. Given that, it’s very likely to be BS.

Assuming this was true and well documented, this sounds like an interesting classification problem to identify and quickly flag such instances in genome sequencing. As always - this requires good clean data!

Re: Scientists are finding fungi in cancerous tumors

#35

Post by jcampbell1 »

axg11 wrote: post #23

Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Every time. You can even check this yourself today. Analyse any publicly available (unprocessed) whole genome sequencing data. Usually the contamination is This study hasn’t ruled out contamination as the cause for the results. Given that, it’s very likely to be BS.

This is newsworthy because the Swedish healthcare system recently discovered that prostate cancer patients who took oral Terbinafine to treat toenail fungus had much better cancer outcomes. The same holds for Terbinafine and colon cancer.

We are currently in the WTF is going on here phase. $5 of anti-fungal medication cuts some cancer death rates in half? Is a tiny amount of fungus in cancer tissue driving growth and metastasis? Does Terbinafine have some other anti-cancer mechanism?

Re: Scientists are finding fungi in cancerous tumors

#36

Post by thimkerbell »

bitL wrote: post #31
hondo77 wrote: post #9

Great./s Now the people who told me that drinking baking soda in water would cure my cancer "because cancer is a fungus" are going to go wild over this.

You might be laughing, but baking soda used to be injected to tumors to reduce lactic acidosis (cancer cells can't proliferate without being immersed in lactic acid). So the people you mentioned might have been running on older research and scientific beliefs. The new version is to use medication that actually decreases lactic acid to slow down/stop growth of tumors (DCA, mega-dose thiamine etc.) Another funny fact -…

Perspiration?

Re: Scientists are finding fungi in cancerous tumors

#37

Post by flqn »

thimkerbell wrote: post #36
bitL wrote: post #31

Earlier quoted context omitted.

You might be laughing, but baking soda used to be injected to tumors to reduce lactic acidosis (cancer cells can't proliferate without being immersed in lactic acid). So the people you mentioned might have been running on older research and scientific beliefs. The new version is to use medication that actually decreases lactic acid to slow down/stop growth of tumors (DCA, mega-dose thiamine etc.) Another funny fact -…

Perspiration?

Respiration

Re: Scientists are finding fungi in cancerous tumors

#39

Post by smt88 »

jcampbell1 wrote: post #35
axg11 wrote: post #23

Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Every time. You can even check this yourself today. Analyse any publicly available (unprocessed) whole genome sequencing data. Usually the contamination is This study hasn’t ruled out contamination as the cause for the results. Given that, it’s very likely to be BS.

This is newsworthy because the Swedish healthcare system recently discovered that prostate cancer patients who took oral Terbinafine to treat toenail fungus had much better cancer outcomes. The same holds for Terbinafine and colon cancer. We are currently in the WTF is going on here phase. $5 of anti-fungal medication cuts some cancer death rates in half? Is a tiny amount of fungus in cancer tissue driving growth and…

> $5 of anti-fungal medication cuts some cancer death rates in half?

I read an interesting hypothesis that many cancers can be treated by changing (perhaps unpredictable) variables in the patient's body.

We already know cancers thrive in nutrient-rich environments and that many tumors have a narrower set of survival conditions than the normal tissue around them. That's why chemo works: you start to kill the whole person and the tumor (hopefully) dies first.

So what if you just randomly messed around with the conditions of the body? Give someone a diabetes drug, change their diet, add an antifungal... we've seen random successes like this, and the unifying theory might be that the cancer was thriving because it had exactly the right conditions, and now we can change them to cause the cancer to stop thriving.

Re: Scientists are finding fungi in cancerous tumors

#40

Post by aaauaucuggaa »

greggsy wrote: post #24
axg11 wrote: post #23

Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Every time. You can even check this yourself today. Analyse any publicly available (unprocessed) whole genome sequencing data. Usually the contamination is This study hasn’t ruled out contamination as the cause for the results. Given that, it’s very likely to be BS.

> You can even check this yourself today. As much as I would love to be able to do this, I’m unsure where to start, and while I’m certain there would be a stackoverflow community for it, I wouldn’t even know what to ask. I know this sounds like a joke comment, but I feel like we live in a time where someone could post some Jupyter notebooks on the matter, and for someone to create a step by step video on YouTube to g…

Start with downloading SRA toolkit: https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-To...

Find some data of interest: https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[... (This searches SRA for human genome sequences on illumina with fastq files available)

Run fasterq-dump on the SRR (listed as "Runs" in the SRA page of your choice): fasterq-dump SRR21812682

Download a microbial genome of interest, here is the link for common yeast: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF...

Install an alignment tool like bwa: https://github.com/lh3/bwa

Unzip the the genome file and create a bwa index: gunzip GCF_000146045.2_R64_genomic.fna.gz && bwa index GCF_000146045.2_R64_genomic.fna

Align: bwa GCF_000146045.2_R64_genomic.fna SRR21812682.fastq (or whatever the fastq files are named)

If you get any alignment results, you've "found" fungal DNA in a human sample. This is a highly simplified workflow, but covers the basic ideas. One of the papers is free and the method sections covers their workflow (it is much more complicated):

https://www.cell.com/cell/fulltext/S0092-8674(22)01127-8

Useful resources: https://www.biostars.org/ https://rosalind.info/problems/list-view/?location=bioinform... https://www.cancer.gov/about-nci/organization/ccg/research/s... (source data for this paper, cancer specific sequencing data)

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