1/21
@DeryaTR_
I asked o3, “What are the top 10 most important questions or challenges that need to be solved or answered in T cell immunobiology?” This is what I have been studying for the past 35 years.
o3 came up with not one, not two, not three, but 10/10 top-notch questions that I could not improve upon!
Not only that, it explained why each of these questions matters, outlined the roadblocks and leverage points, and offered insights that were simply amazing! At the end it even unified and linked all these

(shared in the thread).
This is a topic I understand extremely deeply, yet o3 effortlessly identified the best 10 questions in my field-better rate than I could have myself!
Here are the first 5 grand questions; the rest are in the thread. Each one them is so densely packed with knowledge that unpacking them would require PhD-level courses! This is why I called o3 genius-level, it’s just too damn smart!
Top 10 open problems that will decide the next decade of T‑cell immunobiology:
1.Crack the “TCR code” at scale
Grand question: Can we reliably predict which peptide‑MHC (or CD1/MR1) any given T‑cell receptor will recognise—and design new receptors on demand?
Why it matters: Unlocking this would transform cancer neoantigen targeting, infectious‑disease vaccines, autoimmunity screening and truly personalised immunology.
Roadblocks: Astronomical sequence space, cross‑reactivity, sparse ground‑truth data, and context‑dependent recognition rules.
Leverage points: Deep‑learning models trained on multi‑omic single‑cell datasets, high‑throughput yeast/RNA display pMHC libraries, and federated data‑sharing across clinics.
2.Rewire exhaustion and senescence instead of merely blocking checkpoints
Grand question: How do we durably restore proliferative capacity and killing potential in chronically stimulated or aged T cells without triggering cytokine storms?
Why it matters: Exhaustion limits CAR‑T efficacy, chronic infection control, and anti‑tumour immunity; senescence fuels “inflamm‑aging”.
Roadblocks: Layered transcriptional/epigenetic locks, mitochondrial dysfunction, and suppressive metabolites in the TME.
Leverage points: Metabolic rewiring (FAO ↔ glycolysis toggling), chromatin editing, combinatorial cytokine cocktails, and synthetic “reset” circuits.
3.Master tissue‑resident memory (T RM) formation and control
Grand question: What signals decide when effector T cells park long‑term in skin, gut, lung or brain, and how can we amplify or silence them at will?
Why it matters: T RM cells underpin frontline immunity against respiratory and mucosal pathogens, drive relapse in psoriasis/vitiligo, and protect—or aggravate—tumours.
Leverage points: Decoding local cytokine + metabolic niches, microbiome crosstalk, and TRM–stromal cell interactions; epigenetic “TRM locks” as drug targets.
4.Make engineered T cells work in solid tumours
Grand question: How do we ensure CAR/TCR‑T cells infiltrate, persist and kill in hypoxic, cytokine‑hostile, antigen‑heterogeneous solid tumours?
Roadblocks: Physical exclusion, suppressive myeloid nets, on‑target off‑tumour toxicity, and antigen escape.
Leverage points: Logic‑gated multi‑antigen CARs, chemokine‑armoured cells, regional (e.g., intratumoural) delivery, and on‑demand suicide switches.
http://5.Build truly universal, off‑the‑shelf T cells
Grand question: Can we generate banked iPSC‑derived or genome‑edited T cells that evade host rejection and GVHD yet retain vigorous function?
Why it matters: Autologous products are expensive, slow and inconsistent; scalable allogeneic cells would democratise cellular therapy and allow rapid pandemic response.
Roadblocks: HLA matching, alloreactivity, residual pluripotent cells, manufacturing QC, and regulatory hurdles.
Leverage points: MHC‑knockout plus HLA‑E/G over‑expression, multiplex base‑editing, orthogonal cytokine receptors, closed‑system robotic production.
2/21
@DeryaTR_
Here are the other 5 grand questions and how to attack / approach them, at the end:
6.Induce antigen‑specific tolerance on command
Grand question: How can we expand or engineer regulatory T cells (or CAR‑Tregs) to quench autoimmunity, tame transplant rejection, and resolve fibrotic inflammation without blanket immunosuppression?
Roadblocks: Treg instability in inflammatory milieus, specificity gaps, manufacturing yields, and safety monitoring.
Leverage points: Antigen‑targeted CAR‑ /TCR‑Tregs, low‑dose IL‑2 variants, metabolic “Treg fitness” boosters, and non‑viral precision gene editing.
7.Rejuvenate the aging T‑cell compartment
Grand question: Can we restore thymic output, diversify the repertoire, and reverse inflamm‑aging so 70‑year‑olds respond to vaccines like 20‑year‑olds?
Roadblocks: Thymic epithelial atrophy, clonal expansions, chronic CMV load, metabolic drift.
Leverage points: RANKL/IL‑7 agonism, thymic organoid transplantation, senolytics targeting dysfunctional T cell clones, and epigenetic re‑programming.
8.Write and edit the metabolic & epigenetic “source code” of T‑cell fate
Grand question: What are the precise metabolic and chromatin states that lock a cell into effector, memory, stem‑like or regulatory lineages, and how can we flip them therapeutically?
Why it matters: Metabolism is a master switch—tweak it and you can dial efficacy, persistence, or quiescence at will.
Leverage points: Small‑molecule or CRISPR epigenome editors, nutrient‑sensor circuit rewiring, and programmable mitochondrial transfer.
9.Control stem‑like progenitor T cells and plasticity
Grand question: How do TCF1⁺ “stem‑like” T cells sustain chronic responses, and can we expand them ex vivo or in vivo without tipping into exhaustion or malignancy?
Roadblocks: Niche requirements in tumour‑draining lymph nodes, competition with terminally exhausted clones, and uncertain safety of massive in vivo expansion.
Leverage points: Wnt/β‑catenin and IL‑15 signalling tuning, lymph‑node‑targeted nanocarriers, and selective depletion of late dysfunctional clones.
10.Translate high‑dimensional immune maps into bedside decisions
Grand question: How do we turn single‑cell, spatial‑omics and longitudinal repertoire data into actionable predictions for each patient—dosing, targets, toxicity risks—in real time?
Roadblocks: Data sparsity by tissue, batch effects, lack of integrated clinical‑omic repositories, and “black‑box” regulatory skepticism.
Leverage points: Federated learning across centres, causal inference models that incorporate mechanistic constraints, and AI copilots embedded into electronic health records for adaptive trial design.
⸻
How to attack them strategically
•Pick leverage over novelty – many labs chase incremental checkpoint combos; instead, own the data layer (challenge 10) and feed it back into rational engineering (challenges 1, 4, 5).
•Exploit convergences – exhaustion, aging and Treg instability share common metabolic choke‑points (AMPK, SIRT1, NAD⁺). One well‑designed modulator could move three needles at once.
•Design for manufacturability on day 1 – every elegant genetic tweak adds QA/QC cost; ruthless minimalism will decide which platforms leave the pilot plant.
•Keep safety optics front‑and‑centre – secondary T‑cell malignancies flagged by regulators (EMA/FDA) have already reshaped CAR‑T labels; build kill‑switches and longitudinal monitoring into every protocol.
•Push uncomfortable collaborations – immunologists, systems biologists, and AI engineers still talk past each other; joint sandboxes and shared incentive structures are essential if we’re serious about cracking the biggest questions.
3/21
@DannysWeb3
It’s scary how intelligent it is :
ChatGPT - Emergent Consciousness and Life
4/21
@DeryaTR_
Wow!
5/21
@iamai_eth
I have been suffering from atopic dermatitis many years and I asked o3: “What are the 5 most important issues or challenges to curing atopic dermatitis?”
This was its answer:
1. Disease heterogeneity and tangled endotypes
AD is not a single disorder but a family of sub‑diseases driven by different genetic backgrounds, barrier defects, and immune pathways (Th2, Th17, Th22, IL‑31, IL‑33, etc.). Because there is still no practical, widely accepted way to classify these endotypes, it is difficult to match each patient with precisely targeted therapy. Large multi‑omics projects and machine‑learning–based clustering are beginning to map these molecular subtypes, but they have not yet reached daily clinical use.
2. Durable and comprehensive skin‑barrier reconstruction
Loss‑of‑function mutations in filaggrin and other barrier genes leave the stratum corneum inherently fragile; altered lipids and dysbiosis make things worse. To “cure” AD we would need to restore corneocyte architecture, lipid profiles, surface pH and the microbial film—far beyond what current emollients and barrier creams can do. Experimental approaches include physiological 3:1:1 lipid formulations, micro‑bubble lipid vesicles, local gene delivery and tactics for suppressing Staphylococcus aureus (e.g., bacteriophages or probiotic sprays).
3. Safe, long‑lasting immune recalibration
Systemic immunosuppressants such as cyclosporine and oral JAK inhibitors work quickly but cannot be used indefinitely; biologics (dupilumab, tralokinumab, etc.) are more specific, yet flares frequently return after discontinuation. The central question is how to achieve immunological tolerance rather than mere suppression without compromising host defence. A crowded pipeline of anti‑IL‑4Rα, IL‑13, TSLP and IL‑31RA agents is under way, and tolerance‑induction ideas—micro‑dose antigen delivery via skin and mucosa, Treg enhancers—are being explored.
4. Lack of predictive biomarkers and an early‑intervention window
Many children show first manifestations before the age of two. If the disease could be reversed before it becomes “programmed,” lifelong chronicity might be avoided. Unfortunately, we still lack blood or skin biomarkers that reliably predict who will outgrow AD and who will not, as well as clarity on the best time to intervene. Serum TARC and IL‑13 correlate with severity but are not specific enough, while wearable sensors that track sweat or stratum‑corneum cytokines are only now entering feasibility studies.
5. Patient adherence and environment / lifestyle co‑management
Heat, sweat, fabrics, stress, insomnia and infections all trigger AD, but each patient’s triggers differ. Long‑term treatment relies on daily moisturising (often twice a day), significant out‑of‑pocket costs, and rigorous allergen or irritant avoidance—tasks that hinge on patient and family discipline. No single drug can replace this “engineering of everyday life.” Smartphone apps that remind patients to apply medication and log triggers have improved adherence, and school‑ or kindergarten‑based education programs have lowered relapse rates in pilot trials.
6/21
@DeryaTR_
Amazing response! Every one of them are just outstanding!
7/21
@itechnologynet
how would you score o3 vs o1 pro currently ?
(o3 pro is coming in a few weeks)
8/21
@DeryaTR_
o3 is way better than o1-pro! It’s not even close!
9/21
@alpex704
Just incredible
10/21
@DoctorYev
A general AI can read an article from you or another expert in the field in some website and likely come up with a similar list or consensus, no?
I think context is important to ask it modifiers to rank the list or come up with newer ideas.
The roadblocks part is interesting if you think it added unique insights. In this case, especially if points towards unique solutions, then in that case exciting stuff!
11/21
@DCbuild3r
This is exactly what I love to see! The years upon us will be wonderful
12/21
@acidbrn
This well above and beyond my understanding, but how many of the suggestions are actionable today, or are most of the ideas still years or decades off from being viably carried out?
13/21
@DeryaTR_
Every one of them are actionable, but major projects that require several years of research.
14/21
@TheValueist
Please share the exact prompt you gave it for this task. I would like to know exactly how you produced this output. Thanks!
15/21
@IamEmily2050
I really hope the virtual cell is less than five years away



16/21
@RobertHaisfield
Whatever its response is to this question, respond:
“I think you can do so much better with these questions. Try again.”
Be amazed
[Quoted tweet]
Basically, Prompt Reasoning Models to Overthink. If you criticize them, that gives them an outcome to evaluate against. If you set a really high bar for your expectations and communicate them clearly, the model will figure out how to reach that bar.
17/21
@glio_dao
o3 didn’t just understand, it elevated the conversation. This is insane
18/21
@lukestanley
This is very useful though I do wonder how much is based upon the direct message prompt and how much is based on your existing conversation? Recently the magic synthesis of retrieval augmented generation ChatGPT is using was improved.
19/21
@RichAboutRE
This is profound. I learned about cutaneous T-cell lymphoma, Sézary syndrome, from doctors over 13 years while my dad battled this aggressive cancer. It's remarkable he survived 13 years. Progress on this rare cancer was incredible to witness.
I believe AI will soon analyze genomics and proteomics to predict personalized treatments. This was the biggest challenge towards the end, but the team of doctors was incredible.
20/21
@RaconteurR2D2
Wow
21/21
@NeuralCatAccel
Memory is on, sir