Diagnosing cancer by profiling the immune system

[marymkearney]

This is really cool. Thanks for sharing. It validates the perspective of the late great Pieter Hintjens on this topic. https://github.com/hintjens/confessions/blob/master/ch08.txt

"In my body right now there is a holy war going on, and has been raging for years. My immune system has been doing its damned best to kill these rogue cells. And the rogue cells, unaware that they're destroying their own host, have been fighting back.

"The odds are on the cancer, of course, which is why this family of diseases is a major killer. Our bodies have to keep winning, year after year. Any given cancer has to win only once, and it's Game Over. The only way to beat cancer, really, is to die from something else first.

"Everyone fights cancer, all our lives long. From birth, our immune systems are hunting down and killing rogue cells.... We are all cancer survivors, until we're not. "

[Rodeoclash]

“I’m pretty sure, I’m not a doctor, but I’m pretty sure if you die, the cancer dies at the same time. That’s not a loss. That’s a draw."

- Norm Macdonald

[jvanderbot]

I discovered ZMQ after his death. Reading his last posts were perspective-shifting. I genuinely felt sad, both for him as an individual, and because many of his best works are not going to survive much longer than he did. Life is short and our impacts are transient.

[tuxguy]

Thanks for this reminder about Pieter Hintjens. I have been greatly influenced by his writing, including his use of Alice & Bob, in "a protocol for dying" ! So witty, so clever - such a tragic loss.

[whistle650]

Wow, thank you for sharing that link. It was rational and humane and I found it very moving. I didn't know who he was, but I'm glad to know of him and his work now.

[ajb]

Getting a readout of the immune system sounds like a huge advance. I'm a little surprised to first hear about it as a cancer diagnosis tool rather than as an autoimmune disease diagnosis tool

[nextos]

I've been working on this area for quite long, and I think it's just a matter of time it becomes huge. Right now, a major roadblock is that single-cell RNA-seq, which may also give paired TCR alpha and beta chain data, is too expensive compared to bulk TCR-seq. The latter has limited resolution and more technical variability.

However, Microsoft Research has a preprint that employs bulk TCR-seq where they are able to detect Lyme, which is particularly difficult to do using antibody assays and often mistaken for multiple sclerosis: https://www.medrxiv.org/content/10.1101/2021.07.30.21261353v...

AFAIK, there are a few startups in stealth mode and non-stealth mode collecting big repertoire datasets. In those datasets, one can even measure the effects of vaccinations that occurred decades ago.

[jostmey]

Trying to raise money for something like that! We have exciting preliminary results

[genomer]

I'm surprised as well. I thought the problem with cancer is that the immune system doesn't react/detect it and therefore might not provide a discernible signal.

[jostmey]

Author here. We’re bringing this technology to market. We’ve identified specific use cases where these methods can impact clinical decision making. Here’s our LinkedIn page: https://www.linkedin.com/company/immunoscope . We’re looking to do our first raise

[ugh123]

What studies, experiments, and/or trials has this gone through? Also, I see a list of "Publications" linked, but unsure how they relate to the work done here.

"Diagnosing cancer by profiling the immune system" is a bold statement to make while merely linking to a github repo. The readme still leaves A LOT of questions

[adamredwoods]

I don't understand what Atchley factors are, here's the paper: https://www.pnas.org/doi/full/10.1073/pnas.0408677102

[jjtheblunt]

This was a plot twist in an episode of CSI:Miami several years ago.

Identical twins were implicated in a crime for which DNA was left behind, and they thought they were safe by being twins. But they also had distinct T cell (etc) signatures and that solved the case.

[robocat]

Human Chimeras[1] are even more weirder: one person with cells from two fraternal twins. Causes real problems with maternal[2] and paternal[3] DNA testing. Even more problems[4] if the twins are male and female.

[1] https://duckduckgo.com/?q=human+chimera

[2] https://wikipedia.org/wiki/Lydia_Fairchild — Fairchild stood accused of fraud by either claiming benefits for other people's children, or taking part in a surrogacy scam, and records of her prior births were put similarly in doubt . . .

[3] https://time.com/4091210/chimera-twins/ — the father had absorbed some of his twin's cells when he was a fetus, effectively becoming a chimera of himself and his brother. The man's previous child's DNA matched his . . .

[4] https://wikipedia.org/wiki/46,XX/46,XY Sex-chromosome discordant chimerism (XX/XY chimerism)

[thfuran]

Due to mutations, identical twins probably don't even have identical DNA by the time they're born, let alone in their adult life. I don't think forensic DNA testing is a full sequencing though.

[Aardwolf]

How do you get your data into this software though? What devices do you need for that?

[moneywoes]

As someone with a lot of auto immune diseases how do I get tested

[penny11k]

Regarding cancer treatment, wonder how much more advancement did they get on that polio treatment. Where lot of test subjects with a brain tumor was treated by injecting polio virus into them.

https://www.uhhospitals.org/blog/articles/2020/01/clinical-t...

[rosywoozlechan]

All the really interesting stuff is always written in python, (AI, science research stuff like this). Here I am and I haven't written any python in over 10 years now, ever since go overtook python after it's v3 debacle.

[jkingsman]

> go overtook python > All the really interesting stuff is always written in python

Those might not be super compatible statements ¯\_(ツ)_/¯