Scientists are finding fungi in cancerous tumors(smithsonianmag.com)
smithsonianmag.com
Scientists are finding fungi in cancerous tumors
https://www.smithsonianmag.com/smart-news/scientists-are-finding-fungi-in-cancerous-tumors-180980881/
66 comments
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?
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?
> $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.
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.
Thanks for giving me my reading material this week, as someone with stage 4 colon cancer :) I also read about promising outcomes with fenbendazole (dog deworming medicine) and colon/lung cancer, hope these finally unlock the fix for metastasis.
Sorry to hear about the stage 4 prognosis. I know its insanely unlikely, but here's hoping for a quick game changing recovery that will flip the table on your cancer.
>Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination.
Can you provide a source for this? There are a lot of cranks right now claiming that there's no such thing as a virus because we've never been able to get a non-contaminated sequence (something I've assumed was due to culturing). If this is true of everything there's no limit to what can and cannot exist per their insane arguments.
Can you provide a source for this? There are a lot of cranks right now claiming that there's no such thing as a virus because we've never been able to get a non-contaminated sequence (something I've assumed was due to culturing). If this is true of everything there's no limit to what can and cannot exist per their insane arguments.
Did you even try to look before throwing FUD? Into is really sketchy to me when people call for citations without noting at least in passing that they either found the opposite or tried something reasonable and failed to find something.
In this case, I don't really know much about this either way, but 30 seconds of effort by just copy/pasting the exact sentence you quoted into Google found me something that seems to fit the bill, showing that contaminants in sequencing is "pervasive" and must be accounted for--such as by filtering things that look out of scope--to get reasonable results.
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-02...
> Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
> We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling.
In this case, I don't really know much about this either way, but 30 seconds of effort by just copy/pasting the exact sentence you quoted into Google found me something that seems to fit the bill, showing that contaminants in sequencing is "pervasive" and must be accounted for--such as by filtering things that look out of scope--to get reasonable results.
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-02...
> Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
> We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling.
The source is at least TFA published in Cell, axg11 discarded it without providing any. Thanks!
> 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 guide people through the process.
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 guide people through the process.
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)
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)
If anyone is thinking of doing this, it is both this easy and way harder.
Yes, this is an approximate workflow. It doesn’t take that much specialized knowledge to get it running.
However step 2/3 (find/download a dataset of interest) is harder. Finding whole genome sequencing data for a cancer that you can download without being part of a research institution is difficult. There are a lot of controls over who can access raw DNA sequences from patients. RNA data are much more readily available as they are less identifiable.
Specifically, here is the type of access you need:
https://gdc.cancer.gov/access-data/obtaining-access-controll...
The reasons for this are good and I’m not trying to say otherwise. Just that from a practical perspective, being able to technically perform the analysis is doable for many non-biomedical people here. However, accessing the raw data is much more difficult.
Yes, this is an approximate workflow. It doesn’t take that much specialized knowledge to get it running.
However step 2/3 (find/download a dataset of interest) is harder. Finding whole genome sequencing data for a cancer that you can download without being part of a research institution is difficult. There are a lot of controls over who can access raw DNA sequences from patients. RNA data are much more readily available as they are less identifiable.
Specifically, here is the type of access you need:
https://gdc.cancer.gov/access-data/obtaining-access-controll...
The reasons for this are good and I’m not trying to say otherwise. Just that from a practical perspective, being able to technically perform the analysis is doable for many non-biomedical people here. However, accessing the raw data is much more difficult.
I am reaching for something - that software is now enabling a minimal access level to amazing corners of science and technology - we can luck satellite photos from the ether, have whole dna sequences on our desktop.
I feel there is a "basic bootcamp for the 21C" that I missed
I feel there is a "basic bootcamp for the 21C" that I missed
If you just wanted to see if a particular sequence was fungi, you could just use BLAST.
If you had thousands of sequence reads from multiple unknown organisms, then you’d have to implement a meta genomics pipeline.
All the software for this is already made. You take your sequence reads, trim them a bit, assemble them into “contigs”, and then map those contigs to known genomes in the magical tree of life.
If you had thousands of sequence reads from multiple unknown organisms, then you’d have to implement a meta genomics pipeline.
All the software for this is already made. You take your sequence reads, trim them a bit, assemble them into “contigs”, and then map those contigs to known genomes in the magical tree of life.
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.
Yet.
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!
[deleted]
> Bhatt tells Nature News that the researchers took most of their samples from databases that didn’t aim to minimize fungal contamination during collection. So, she’d like to see if other studies can get the same results with samples taken in a sterile environment.
For me, this is the real question. I expect for a certain level of bacterial and fungal contamination in sequencing experiments. Hell, I've even seen sequencing reads contaminated by the sequencing facility and not from tissue collection lab.
For me, this is the real question. I expect for a certain level of bacterial and fungal contamination in sequencing experiments. Hell, I've even seen sequencing reads contaminated by the sequencing facility and not from tissue collection lab.
Something similar to this was recently found in the mouth
"Across-kingdom partnership between bacteria and fungi can result in the two joining to form a “superorganism”
...
They were stickier, more resistant to antimicrobials, and more difficult to remove from teeth than either the bacteria or the fungi alone
...
What’s more, the assemblages unexpectedly sprout “limbs” that propel them to “walk” and “leap” to quickly spread on the tooth surface, despite each microbe on its own being non-motile"
https://penntoday.upenn.edu/news/microbes-cause-cavities-can...
"Across-kingdom partnership between bacteria and fungi can result in the two joining to form a “superorganism”
...
They were stickier, more resistant to antimicrobials, and more difficult to remove from teeth than either the bacteria or the fungi alone
...
What’s more, the assemblages unexpectedly sprout “limbs” that propel them to “walk” and “leap” to quickly spread on the tooth surface, despite each microbe on its own being non-motile"
https://penntoday.upenn.edu/news/microbes-cause-cavities-can...
They also sometimes test delicious: https://asm.org/Articles/2020/June/The-Sourdough-Microbiome
That is really cool. Reminds of this paper:
Swimming bacteria promote dispersal of non-motile staphylococcal species https://pubmed.ncbi.nlm.nih.gov/28398350/
Swimming bacteria promote dispersal of non-motile staphylococcal species https://pubmed.ncbi.nlm.nih.gov/28398350/
Lycan is also an assemblage of fungi and cyanobacteria or algae if I'm not mistaken..
Lichen are. (Lycan are werewolves I think.)
Huh, whoops. Is your username a reference to the cossotat river?
They’re also stunningly beautiful. They’re one of my favourite things to find and observe in the woods.
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".
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".
Interesting. I would have called bs too it it weren't for your comment, but there is actually peer reviewed research around this [1].
[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7249593/
[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7249593/
Perspiration?
Some Spanish "magufo" (think of Alex Jones but without the far right ideology and being a fake practicioner) are like that, search for Pamies in Google/DDG.
I'm worried about the reaction from these snake-oil scammers, too.
EDIT: I found an article in English:
https://english.elpais.com/elpais/2018/10/18/inenglish/15398...
EDIT: I found an article in English:
https://english.elpais.com/elpais/2018/10/18/inenglish/15398...
[deleted]
Are there not also sometimes fungi in non-cancerous human tissues?
There are around 50 fungi in our guts alone[1].
>Mahmoud Ghannoum, Ph.D., an NIH-funded researcher since 1993, who’s spent his career studying fungi in the body (there are about 50 different species living in our gut specifically). Dr. Ghannoum is credited with uncovering the significant interplay between bacteria and fungi, which affects the critical balance of the body’s microbiome. (Much of this interaction occurs at a digestive plaque wall that Ghannoum discovered with his research team at Case Western Reserve University in 2016.)
[1] https://goop.com/wellness/health/new-in-gut-health-fungis-im...
>Mahmoud Ghannoum, Ph.D., an NIH-funded researcher since 1993, who’s spent his career studying fungi in the body (there are about 50 different species living in our gut specifically). Dr. Ghannoum is credited with uncovering the significant interplay between bacteria and fungi, which affects the critical balance of the body’s microbiome. (Much of this interaction occurs at a digestive plaque wall that Ghannoum discovered with his research team at Case Western Reserve University in 2016.)
[1] https://goop.com/wellness/health/new-in-gut-health-fungis-im...
Ok, but how many in your blood?
definitely are
(athlete's foot, ringworm, candida, ...)
Do fungi lurking inside cancers speed their growth? (nature.com) - 82 comments
https://news.ycombinator.com/item?id=33133477
https://news.ycombinator.com/item?id=33133477
As far as I can gather from reading this - contamination cannot be ruled out.
> Although the researchers developed methods to filter any potential contaminants out of the sequencing data, she would like to see the results replicated using samples taken in a sterile environment.
This isn't terribly surprising since one of the first things a cancerous tumor does (often) is create an "cold" immune environment to evade detection by the hosts immune system. This is why certain infections can actually kill a tumor: no immune system to kill the new pathogen and it ends up destroying the cancerous cells.
Do doctors ever purposely infect someone to fight cancer?
Single, methodologically flawed, unreplicated studies have no business being publicised as scientific results in the popular media.
I thought to myself...is there anything else out there that may show a similar clue. So I searched for a common known lung cancer cause...asbestos. By searching (using wrong search terms) for "fungus growing on asbestos" I scrolled down and found this. https://pubmed.ncbi.nlm.nih.gov/6754414/
Aspergillus is also mentioned in the linked paper. I do not have the background to evaluate....but interesting. Maybe another link.
I really hope these sorts of things make their way to trials soon. recently found out that I have a recurrance of colon cancer...
Here is a physician ( Tullio Simoncini ) that thinks that cancer is almost entirely cause by fungus: https://simoncinicancertherapy.com/en/index.html
He is considered a quack by most people though I would give him the benefit of doubt.
He is considered a quack by most people though I would give him the benefit of doubt.
I'm going to assume they are fighting the tumors and take it as a sign to increase my dosages of reishi and chaga powders.
Feed the chaganaut!
The same scientists were amazed to find that the loaf of bread they left next to the PCR machine became moldy even though their lab was spotless!
Their next paper will demonstrate that contrary to popular belief, wheat is not a plant but a composite organism!
Their next paper will demonstrate that contrary to popular belief, wheat is not a plant but a composite organism!
There is a theory that sometimes stuff gets through the gut wall into the blood stream. This can cause for some allergies.
I wouldn't be very surprised to learn that fungae somehow survive the immune system and their ongoing battle creates cancer.
For my own experiences... my depression is linked to sugar somehow, and green veggies seem to cause some mental bouts where I don't want to exist. There's almost always 4 days in between ingestion and symptom. (I found notes from 2016 but only made the connection around 2018 and have been testing around with different foods after that)
I wouldn't be very surprised to learn that fungae somehow survive the immune system and their ongoing battle creates cancer.
For my own experiences... my depression is linked to sugar somehow, and green veggies seem to cause some mental bouts where I don't want to exist. There's almost always 4 days in between ingestion and symptom. (I found notes from 2016 but only made the connection around 2018 and have been testing around with different foods after that)
I told you people not to turn your back on fungi and you didn't listen. now look what they're doing
https://news.ycombinator.com/item?id=31197031
https://news.ycombinator.com/item?id=31197031
My personal non scientific thought on tumours (non cancerous fatty tumours)
Is that they are your bodies away of wrapping up something bad that it can't otherwise deal with. In a protective layer to contain. Similar to how a clams makes a pearl layer by layer around a foreign particle.
Is that they are your bodies away of wrapping up something bad that it can't otherwise deal with. In a protective layer to contain. Similar to how a clams makes a pearl layer by layer around a foreign particle.
So we're just making things up now, yeah? In that case I think that tumours are parts of your body from other universes popping into our universe
Can your mind only resolve the likely? Thinking outside the box is the first step in the scientific pursuit.
Its called thinking it doesn't always have to be logical.
Its called thinking it doesn't always have to be logical.
Sounds legit
This study hasn’t ruled out contamination as the cause for the results. Given that, it’s very likely to be BS.