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Michael Fischbach Profile
Michael Fischbach

@mfgrp

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Liu (Liao) Family Professor of Bioengineering, ChEM-H @Stanford .

Stanford, CA
Joined February 2011
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@mfgrp
Michael Fischbach
4 years
Quick recap: We posted a public letter saying, basically: "Scott Atlas is giving the president bad advice. It will hurt people." Today, we got this love note from @SWAtlasHoover . I stand by everything we said. More facts, more science. Less Kasowitz.
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@mfgrp
Michael Fischbach
6 months
How to pick a problem. Today in @CellCellPress . 1/53
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@mfgrp
Michael Fischbach
2 years
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent immune response against a distant tumor. @yerinchen led the charge w/ help from @DjenetBousbaine , @VeinbachsA , @BelkaidLab . @ScienceMagazine 1/26
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Michael Fischbach
1 year
Today we report a detailed map of interactions between the immune system and the gut microbiome. @MicrobiomeTcell led the charge w/ help from Aishan Zhao and Kat Atabakhsh. @Nature 1/40
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Michael Fischbach
2 years
Today we report a new model system for the gut microbiome: hCom2, a defined community of 119 strains. @AliceCheng107 led the charge, with major contributions from Po-Yi Ho, @DrChilennial , and @SunitJain . Co-led by my longtime collaborator KC Huang. 1/22
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Michael Fischbach
1 year
Today we report that removing a strain from a complex microbiome can ripple through the community in an unpredictable (& useful) way. @MinWang_18 was the mastermind, with help from Mark Brown, Stan Hazen & crew. @CellCellPress 1/25
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Michael Fischbach
2 years
Christopher Walsh: 1944-2023 A giant indeed: the impact of his work is staggering. But Chris was even more impressive as a mentor. He was immeasurably devoted to, & loved by, his trainees. Nothing made him happier than doling out his wisdom. Superhuman & human at the same time.
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@mfgrp
Michael Fischbach
4 years
1/ We are 105 doctors, scientists, and public health experts and faculty members at Stanford University who expressed our serious concerns about statements made by Scott Atlas.
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@mfgrp
Michael Fischbach
4 years
The bile acid pool, which recirculates between the liver and gut 10x/day, is central to metabolic & immune function. Its composition is heavily influenced by gut bacteria. Excited to share Masa/Tyler's work on the core pathway, w/🙏 to Almo for the collab.
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Michael Fischbach
6 years
We spend days choosing a problem and years solving it. But our choice of problem has a huge influence on likelihood of success and impact of our work. @Stanford grad students: Chris Walsh and I unpack this in a new springQ seminar that treats problem choice as a game of strategy.
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Michael Fischbach
4 years
This one still blows my mind: Soil smells earthy only because bacteria are trying to hitch a ride on an arthropod.
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@mfgrp
Michael Fischbach
3 years
Celebrating 10 years together
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@mfgrp
Michael Fischbach
3 years
We spend days choosing a problem and years solving it. But our choice of problem has a huge influence on likelihood of success and impact of our work. @Stanford grad students: Chris Walsh and I unpack this in a spring qtr class that treats problem choice as a game of strategy.
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@mfgrp
Michael Fischbach
3 years
Big day — ⁦ @cobarnes27 ⁩ has arrived!!
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@mfgrp
Michael Fischbach
4 years
Extraordinary fact: The pool of ATP in a human (~75 grams) turns over 1000x/day. So a typical human uses 75 kilograms (165 pounds) of ATP per day. h/t Chris Walsh, from a new book on phosphorus (in press)
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Michael Fischbach
4 years
Every morning before class starts, Isabel builds one of these as her zoom background. Instant gravitas with the other 1st graders.
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@mfgrp
Michael Fischbach
6 months
Having observed that grad students are taught almost everything about science and engineering except how to pick a problem, me and Chris Walsh started a class at Stanford on the topic in 2019 (BIOE 395). What follows are eight lessons from the course. 3/53
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@mfgrp
Michael Fischbach
6 years
SCIENTISTS WANTED (please RT): Long hours, high expectations, uncertain path, constant failure. Honor and recognition in case of success.
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@mfgrp
Michael Fischbach
6 months
Your career = a finite number of weeks. Most would agree that time is precious & should be used for maximum impact, but acknowledging this and practicing it are two different things. Especially important when choosing a problem, which can impact time allocation for years. 2/53
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Michael Fischbach
4 years
No, we're not. Just a reminder that you threatened >100 of us with a lawsuit. We stand by everything we said. Your advice is hurting people.
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Michael Fischbach
6 years
Multiple postdoc positions open. All are welcome, especially those with an interest in highly complex synthetic communities (& synthetic ecology), new genetic tools for difficult organisms in the microbiome, and molecular mechanisms of microbiome-host interactions.
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Michael Fischbach
6 months
2) Exercise intuition pumps and avoid common traps. There is no single way to generate new ideas, but certain prompts can help jumpstart the ideation process… 9/53
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@mfgrp
Michael Fischbach
4 years
There once was a Miller named Stephen, Who wanted brown people a-leavin’. They voted en masse, Kicked him out on his ass, And deported his boss—now we’re even.
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@mfgrp
Michael Fischbach
4 years
@stevenstrogatz You can be recombobulated, at least at the Milwaukee airport.
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@mfgrp
Michael Fischbach
4 years
Plants seem so peaceful, but they love to harpoon each other when nobody is watching. Rice is especially vicious: it secretes a chemical from its roots that prevents other plants from germinating. Its pathway (see 👇) could replace the need for herbicides.
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@mfgrp
Michael Fischbach
6 months
1) Spend more time on problem choice. In science and (non-software) engineering, a typical project for a grad student might involve 1-2 weeks of planning and 2-5 years of execution. That is way out of balance, especially considering that… 4/53
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@mfgrp
Michael Fischbach
2 years
RIP my little guy. You brought us so much love.
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@mfgrp
Michael Fischbach
6 months
Instead, think of new ideas as leeches trying to make a meal of your time. Treat them with skepticism and evaluate several of them in parallel—comparison shopping leads to better decision making. 8/53
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Michael Fischbach
4 years
Before it becomes a red blood cell, the erythroblast *ejects its own nucleus*, turning itself into a zombie. This happens 200 billion times/day in a human. Macrophages eat the leftover brains (i.e., nuclei). Strange job even for the butler, @RMedzhitov .
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@mfgrp
Michael Fischbach
4 years
4/ We stand together and we reiterate clearly and with great affirmation that public health policy must be guided by established scientific principles and not opinions, especially ones that could harm individuals and the health of our nation.
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@mfgrp
Michael Fischbach
4 years
We're looking for a scientific director for a new DARPA program in the area of microbiome therapeutics. Our lab + @Geneticdesigner and @Omar_Akbari_ . Job ad will be up soon; if interested, send me a note.
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@mfgrp
Michael Fischbach
4 years
3/ Today, we stand by our 9/9 letter & reaffirm our concerns. In addition, we are deeply troubled by the legal threats that Dr. Atlas has made against us in an attempt to intimidate & silence us in the midst of a pandemic, as we speak out on important public health issues.
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@mfgrp
Michael Fischbach
4 years
Good point! If you compress the y-axis a little more, you could just make those deaths ... go away.
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@mfgrp
Michael Fischbach
4 years
This paper remains extraordinary, five years later. A magnificent observation, with no understanding of mechanism, can be publication worthy.
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@mfgrp
Michael Fischbach
4 years
Let’s take this energy to Georgia and win the Senate!
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@mfgrp
Michael Fischbach
4 years
This is 11/10 stupid.
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@mfgrp
Michael Fischbach
6 months
…once you choose a project, you are confined to a relatively narrow ‘impact band��. It is hard to make the solution to a mediocre problem impactful. So the problem you choose will influence the impact of your work just as much as your execution. 5/53
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@mfgrp
Michael Fischbach
4 years
Getting ready to be Hamilton for Halloween. Eat your heart out @Lin_Manuel !
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Michael Fischbach
3 years
If you want to climb the unclimbable, be inspired here: @AlexHonnold If you want to dream the undreamable, donate here: @UNITEDWEDREAM And if you want to manage the unmanageable, well do I have an opportunity for you: 👇
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@mfgrp
Michael Fischbach
2 years
In a very real sense, S. epi-OVA is a cancer vaccine in which *the adjuvant is a commensal*. S. epi is exciting as an adjuvant because it colonizes persistently (and safely) & the T cells it elicits are capable of acting against solid tumors. 20/26
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@mfgrp
Michael Fischbach
6 months
…and there are common traps to avoid (below). In addition, focus on areas where you will have a competitive advantage from your expertise, access to data, or love of a problem and exuberance for solving it (this will help you dig deeper than others). 10/53
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@mfgrp
Michael Fischbach
2 years
Erin realized that we could address this by engineering S. epi to express a tumor antigen. By colonizing mice with this bacterium, we would trick the host into developing CD8+ T cells that *it thinks* are against the bug, but *we know* are also specific for a tumor. 5/26
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@mfgrp
Michael Fischbach
4 years
We knew a pandemic was coming. If we had prepared in advance we could have saved millions of lives & trillions of $. The ROI would have been stunning. Now that logic is back in the building, 4 other problems we should invest in before they become crises:
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@mfgrp
Michael Fischbach
2 years
In prior work, Littman, @BelkaidLab & others showed that certain colonists induce a potent T cell response w/ 3 attributes: T cell "flavor" is determined by the microbe, T cells are antigen-specific, and this happens preemptively: w/o infection, across an intact barrier. 2/26
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@mfgrp
Michael Fischbach
4 years
. @SWAtlasHoover : I'll support your herd immunity plan if you agree to be treated at a community hospital when you get infected. No special care, no compassionate use antibody therapy. Same risk you're asking most Americans to take. Deal?
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@mfgrp
Michael Fischbach
3 years
It’s 2007, I’m in grad school. I need a tie but I’m short on money. So I go to Filene’s Basement looking for the cheapest one I can find. To my delight, it was so cheap I could afford two.
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@mfgrp
Michael Fischbach
4 years
2/ We believe that his statements and the advice he has been giving fosters misunderstandings of established science and risks undermining critical public health efforts.
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@mfgrp
Michael Fischbach
2 years
What did we learn? First, the T cells induced by S. epi are fully capable of traveling systemically and killing tumor cells. Second, the host appears to be "vaccinating" itself against this commensal by developing immunity in the absence of infection. 18/26
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@mfgrp
Michael Fischbach
6 months
A few notes of gratitude: First, I developed and taught this course with Chris Walsh, who passed away as we began writing this piece. All of these ideas were developed together. I consider him a co-author & owe him an immeasurable debt of gratitude. 47/53
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@mfgrp
Michael Fischbach
2 years
She saw the effect in the very first experiment: mice that were uncolonized, or colonized with a control strain of S. epi, had very large tumors. But if they were colonized with S. epi-OVA, the tumors were much smaller. 9/26
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@mfgrp
Michael Fischbach
6 months
The key to navigating the decision tree is to move back and forth frequently between two types of work: getting stuff done (Level 1) and evaluating it critically (Level 2). These cannot be done at the same time. 27/53
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@mfgrp
Michael Fischbach
2 years
We decided to focus on the skin colonist Staphylococcus epidermidis; in prior work, @BelkaidLab showed that it induces CD8+ T cells in mice & non-human primates. Erin devised a genetic system for S. epi, which was previously difficult to manipulate. 3/26
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@mfgrp
Michael Fischbach
6 months
If you’re writing software, cycle time is short. Just try it & see if it works; if not, you only lose a couple weeks. Doesn’t work in science & non-software engineering, where go/no-go = months and whole project = years. Inertia takes over; sunk cost fallacy hard to avoid. 6/53
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Michael Fischbach
2 years
...if you're still here, I encourage you to read this amazing paper from Jeff Dangl's group (of which I just became aware). Amazing work assembling and deconstructing a complex defined community to identify strains responsible for a phenotype.
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@mfgrp
Michael Fischbach
2 years
We learned three important things about how this works. First, heat-killed S. epi is inactive, even when Erin applied it repeatedly to the mouse. --> So S. epi-OVA is not simply acting as an adjuvant + antigen - it has to be alive for this to work. 10/26
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@mfgrp
Michael Fischbach
4 years
I’m a staunch believer in free speech, but this is way over the line. @CondoleezzaRice and @HooverInst should disavow this unambiguously.
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@mfgrp
Michael Fischbach
2 years
The combination was powerful; most mice rejected the tumor outright, leading to a large survival advantage. When re-challenged, tumors failed to grow, indicating that the colonized mice had immune memory against the tumor. 15/26
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@mfgrp
Michael Fischbach
2 years
Second, S. epi-OVA is effective not only when the tumor cells are injected subcutaneously (forming a primary mass in the flank) but also intravenously (forming metastases in the lungs). This suggests the bacterium can act at a distance. 11/26
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@mfgrp
Michael Fischbach
6 months
To score a project’s likelihood of success, we suggest an ‘assumption analysis’. List every assumption you are making from the project’s inception through its conclusion. Assign two scores to each one: likelihood of success and duration of effort. 12/53
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@mfgrp
Michael Fischbach
2 years
Initially we wanted to know *how* S. epi induces CD8+ T cells (i.e., molecular mechanism). But as we went deeper, we became more puzzled by *why* this happens: what is the host's goal in responding to a commensal? 4/26
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@mfgrp
Michael Fischbach
1 year
From all of this work, it's clear that the microbiome is a strong immune stimulus. But we don't know how this works at the community level - what each strain contributes to the composite phenotype of immune modulation. 4/40
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@mfgrp
Michael Fischbach
2 years
If this is true, then by engineering S. epi to express a tumor antigen, we have tricked the immune system into thinking the tumor is bacterially infected. It responds aggressively and specifically. 19/26
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@mfgrp
Michael Fischbach
4 years
This is so fucking cool
@SpaceX
SpaceX
4 years
Liftoff!
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Michael Fischbach
6 months
It can help to reverse the polarity of our relationship with new ideas. Don’t treat them with reverence; confirmation bias will set in. Definitely don’t jump on the first idea and get started—that is the worst thing you can do. 7/53
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@mfgrp
Michael Fischbach
2 years
Third, if we engineer S. epi to express tumor-derived neoantigens instead of ovalbumin, the effect is comparably potent. So this isn't simply a consequence of having used an efficient model antigen; it works with a real-world antigen. 13/26
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@mfgrp
Michael Fischbach
2 years
We tested these strains in B16 melanoma, a syngeneic tumor model (WT mouse, normal immune system). This is a feisty, immunologically 'cold' tumor. We didn't prep the mice in any way; Erin dipped a q-tip in the culture and gently swabbed the head of the mouse. 8/26
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@mfgrp
Michael Fischbach
6 months
Finally, an important rule of thumb is to perform the go/no-go experiment at the earliest feasible moment. This is true even if it requires some compromise; build a clunky prototype and see if it works, even a little. 15/53
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@mfgrp
Michael Fischbach
4 years
Interesting prequel: David Hopwood, who pioneered Streptomyces research, made it a policy at JIC that people couldn't keep potted plants in the lab. Why? Because something was crawling out of the soil and into the plates, tracking Streptomyces spores around. (h/t Mark Buttner)
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@mfgrp
Michael Fischbach
3 years
If you haven’t read QED (Feynman), I highly recommend it. Mind blowing content and a master class in explaining tough concepts in a simple way.
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@mfgrp
Michael Fischbach
2 years
She reasoned that this would enable us to differentiate between two possibilities: 1) S. epi-induced CD8+ T cells remain near the site of colonization & keep the peace, vs. 2) they migrate to the tumor and kill tumor cells. 6/26
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@mfgrp
Michael Fischbach
1 year
Heartfelt congratulations to @MEBirnbaum , one of my favorite collaborators and an all-around delightful human.
@MITdeptofBE
MIT Dept of BE
1 year
Prof Michael Birnbaum among this year’s newly tenured engineering faculty. @MITEngineering
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Michael Fischbach
2 years
Finally, we are deeply grateful to @Benioff , @mleslie45 , and Solina Chau for supporting this work via the Microbiome Therapies Initiative. 26/26
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Michael Fischbach
4 years
This is an amazing story... ...and the science behind it is extraordinary (). Showcases the mind-blowing power of cell therapy.
@Rainmaker1973
Massimo
4 years
The story of Hassan, the boy whose whole body looked like an open wound because of a genetic condition which led his skin to be paperthin. He had his DNA repaired and the modified skin cells grew to make skin totalling 0.85 sq m. He now leads a normal life
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Michael Fischbach
2 years
We are interested in seeing whether the persistent supply of antigen-specific T cells it elicits might perform comparably to, or in some ways better than, cells generated by ex vivo engineering (CAR-T or TCR-T). 21/26
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@mfgrp
Michael Fischbach
6 months
Some people gather tons data or write reams of code, but rarely stop to consider its implications. Others are brilliant strategists but have trouble reducing plans to practice. The most successful folks move back and forth frequently between planning and doing. 32/53
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Michael Fischbach
6 months
3) Don’t avoid risk; befriend it. A useful starting point for evaluating a new idea is to place it on the graph below. We will consider the axes one at a time. 11/53
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@mfgrp
Michael Fischbach
2 years
More broadly, can other commensals be engineered to generate different kinds of antigen-specific T cells? And can other components of the adaptive immune system be brought into play? 22/26
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@mfgrp
Michael Fischbach
4 years
Meanwhile on Fox News, top story is @SWAtlasHoover telling everyone not to worry. Says Covid "is very difficult to avoid." Total BS. Masks and distancing are highly effective. Could have used this opportunity to stick with science and help keep folks safe.
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@mfgrp
Michael Fischbach
1 year
Two lines of prior work were essential here. First, Dan Littman, @BelkaidLab , Fiona Powrie, Greg Barton & others showed that certain colonists induce a potent T cell response. 2/40
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@mfgrp
Michael Fischbach
1 year
Kazuki does not mind putting in a little elbow grease (!!). 17/40
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@mfgrp
Michael Fischbach
2 years
3) Prior expts had been in 'prophylaxis mode': colonization first, then tumor cell injection. When we inject tumor cells first and wait 14d for tumors to establish ('treatment mode'), S. epi-OVA + checkpoint is still very potent, which is encouraging. 17/26
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@mfgrp
Michael Fischbach
2 years
A few notes of gratitude. First, many thanks to @carlzimmer for explaining this far better than I can. 19/22
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@mfgrp
Michael Fischbach
6 months
Importantly, the idea here is not to *eliminate* risk—risk-free projects tend to be incremental. Instead: name, quantify, and work steadily to chip away at risk. And when presenting a new idea, be candid about risk—it makes your case more convincing. 14/53
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@mfgrp
Michael Fischbach
2 years
We chose ovalbumin as a model antigen. Erin constructed variants of S. epi in which the full-length protein or smaller epitopes were expressed in the cytoplasm, anchored to the cell surface, or as secreted proteins. 7/26
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Michael Fischbach
4 years
Fox News joins the fun!
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@mfgrp
Michael Fischbach
6 months
Most of all, we’re hoping to convince people to spend more time thinking about problem choice. Perhaps we might even inspire some of you to teach a similar course in your shop. We will happily offer course materials to anyone who is interested. 46/53
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Michael Fischbach
2 years
Many thanks to @ElaineFuchsLab , @SairajSajjath , and @anita__gola for their perspective piece, which is clear and incisive.
@ElaineFuchsLab
The Fuchs lab
2 years
Fascinating paper out in @ScienceMagazine on T cells engineering skin microbiota. Read our perspective by @SairajSajjath & @anita__gola :
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Michael Fischbach
3 years
Lentivirus displaying pMHC in its envelope; virus enters T cells only if they express a TCR that binds the pMHC. Wild new technology from @MEBirnbaum and @ItsVirusTime .
@biorxivpreprint
bioRxiv
3 years
Antigen identification and high-throughput interaction mapping by reprogramming viral entry #bioRxiv
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Michael Fischbach
6 months
Getting stuff done requires full immersion in the details of experimentation or coding. Critical evaluation demands that you clear your head, step away from the work, and evaluate it as though it were performed by someone else. 28/53
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Michael Fischbach
1 year
@CarolynBertozzi @Stanford_ChEMH BIOE 395! As Carolyn mentioned, Chris and I taught an informal session of the same course to new PIs last fall; I'm planning to do this again. See also:
@JuliaBauman2
Julia Bauman
1 year
Can scientists be taught how to choose good projects? I took a fantastic class taught by @mfgrp last quarter where the foundational hypothesis is: Yes, they can! And I continually come back to these core insights as I think about project choice and direction in my 2nd year of
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Michael Fischbach
2 years
2) When we colonize 25 days ahead of tumor cell injection, the bacterium is gone by the time the tumor cells arrive (S. epi is an inefficient colonist of mice). Tumors are still small, showing that transient exposure is sufficient for prophylaxis. 16/26
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Michael Fischbach
1 year
Second, we found (by accident) that some of the expanded Treg clonotypes respond *not* to bacteria but to mouse chow. Kazuki, @JamieBlum7 & @Sattely_lab are taking advantage of this to clone food-derived epitopes that govern oral tolerance. More on this soon. 35/40
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@mfgrp
Michael Fischbach
1 year
OK, so what did we learn? Three main lessons. First, T cell induction by the microbiome is indeed a composite phenotype: many strains contribute. The data in Fig 2 are a good starting point for choosing species to study. 31/40
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@mfgrp
Michael Fischbach
2 years
Additional data suggest this works in the following way: antigen-specific CD8+ & CD4+ T cells are primed in the lymph node, then travel through circulation to the tumor, where we detect them as TILs if we dissect the tumor before it recedes. 12/26
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Michael Fischbach
1 year
Kazuki proposed that we could address this question by colonizing germ-free mice with a complex defined community. Since the community would be composed of known strains, we could then profile the T cell response to each strain, one at a time. 5/40
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Michael Fischbach
2 years
We couldn't have done this without generous financial support from @open_phil , @HelmsleyTrust , @SU2C , @czbiohub , and @NIH , and incredible institutional support from @Stanford_ChEMH , IMA, and @StanfordBioE . 25/26
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Michael Fischbach
1 year
Second, many groups have shown by transplantation that the gut microbiome (as a whole) influences immune function. One of the best known & most exciting examples is the impact on response to checkpoint inhibitors (Wargo, Zitvogel, Gajewski). 3/40
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