GLP-1s vs. Autoimmune Disease

Happy Monday!

I got this message last week from a reader in my question box and thought it would be a great topic to address:

I love this question, because it speaks to where so many people are right now.

Tired.

Frustrated.

Ready for something that actually works, but skeptical because the latest “miracle” is almost always another dead end.

So let’s break it down—what’s really going on with autoimmune disease, how GLP-1 peptides like Retatrutide work on a cellular level, and how I’d use them if I were starting from scratch today.

How the Modern World Breeds Autoimmune Disease

Let me tell you a story you might recognize: You start out life eating whatever’s around—maybe it’s Pop-Tarts, pizza, and the occasional apple.

For most kids these days, school means stress, sports, fast food, and hours hunched over a phone or laptop.

You get a bit older.

College adds late nights, more stress, energy drinks, cheap beer.

Adult life comes with less movement, processed meals, work deadlines, and mounting anxiety.

What’s happening under the surface?

Your gut lining gets hammered by food dyes, gluten, seed oils, and sugar.

Chronic stress and poor sleep send cortisol and inflammation through the roof.

Over time, your gut barrier starts to leak.

Now, particles that should stay in your intestines (undigested food, bacterial byproducts, even environmental chemicals) slip through the cracks.

The immune system, seeing these new invaders, sounds the alarm.

What should be a “one-off” inflammatory response becomes chronic, and eventually, your immune system gets confused.

It starts attacking your own tissues—thyroid, joints, skin, even your brain.

Doctors call it Hashimoto’s, Crohn’s, lupus, rheumatoid arthritis—but it’s all rooted in the same process: a compromised immune system.

How GLP-1 Peptides Work Once They’re in the Body

Here’s where GLP-1 peptides—like Retatrutide—step in, and why they’re so much more than “diabetes” or “weight loss” drugs.

When you inject a GLP-1 agonist, you mimic your body’s own glucagon-like peptide-1 hormone, released naturally in the gut after eating.

But these peptides do so much more than help with blood sugar.

First, they’re potent anti-inflammatories. GLP-1 agonists decrease the production of “fire-alarm” cytokines—the molecules that fan the flames in autoimmune conditions—like TNF-alpha, IL-1β, and IL-6.

Second, they increase the body’s anti-inflammatory response by boosting IL-10 and similar molecules, essentially telling your immune system, “Chill out.”

Third, GLP-1 peptides remodel immune cell function. They lower the activity of Th1 and Th17 cells, which drive autoimmunity, and increase regulatory T cells (Tregs) that calm the whole system down.

Fourth—and crucially—they repair the gut barrier. By tightening up those “leaks,” they reduce the constant immune activation coming from the gut.

This is why many people first notice better digestion, less bloating, and improved food tolerance even before their “main” autoimmune symptoms improve.

Retatrutide Microdosing for Autoimmune Disease

Now, let’s talk protocol.

Most people using GLP-1s for diabetes or weight loss get put on big weekly doses.

But for autoimmunity, I recommend microdosing.

We’re trying to nudge the immune system back to sanity.

Here’s my base protocol:

• Retatrutide, 250mcg (0.25mg), three times per week (Monday, Wednesday, Friday)

• Inject subcutaneously, ideally in the morning while fasted.

• Stick to this for at least 4–6 weeks before you even think about increasing the dose.

Why microdose?

At this low level, you get all the immune-calming, gut-healing benefits with almost zero risk of nausea, dizziness, or blood sugar crashes.

If you’re wondering about “stacking,” many also benefit from adding gut-specific peptides like BPC-157 or thymosin alpha 1, but Retatrutide alone is a phenomenal reset switch.

What to Expect from Retatrutide

I want to set realistic expectations.

Here’s what I see most often in people microdosing GLP-1s for autoimmune disease:

Weeks 1–3:

• Subtle shifts—less joint pain, slightly better digestion, a general “easing off” of symptoms.

• Many report improved sleep and energy as inflammation drops.

Weeks 4–8:

• Gut issues (bloating, food intolerance, constipation/diarrhea) usually improve first.

• Joint pain, skin rashes, and brain fog begin to fade.

• Lab markers like CRP, ESR, or autoantibodies may improve—but be patient.

Weeks 8–16:

• Flare frequency drops. The immune system is less “hair-trigger.”

• Some people can reintroduce foods they thought were gone forever (start slow!).

Is it a miracle cure? No—nothing is.

But for many, it’s the missing piece that allows all their other healing strategies (diet, sleep, stress management) to finally work.

And because you’re working at the level of root cause (immune rebalancing and gut repair), results are more durable.

Further Reading & Real Studies

Here’s where you can dig in to see the actual science behind everything above:

• https://pmc.ncbi.nlm.nih.gov/articles/PMC10823863/

• https://pmc.ncbi.nlm.nih.gov/articles/PMC9772276/

• https://pmc.ncbi.nlm.nih.gov/articles/PMC10230051/

• https://pmc.ncbi.nlm.nih.gov/articles/PMC10496996/

If you’re reading this and wondering if it’s finally your time to try something different—maybe it is.

Microdosed Retatrutide is the closest thing I’ve found to a “reset” button for the immune system that actually heals the root cause of the symptoms.

Best,

Hunter Williams