Celiac misdiagnosis, ultra-sensitive NCGS, or something else? 


My celiac journey has been quite strange.

I was diagnosed with Celiac Disease about 8-9 years ago after a positive EMA (17) and a Marsh 3b biopsy. My initial symptoms which were mostly fatigue, diarrhea, and nausea, resolved majorly on a gf diet but then relapsed due to cross-contamination from uncertified GF foods (or so I thought). I was given a 10 days course of budesonide which helped, but once it was over my symptoms returned again.
I eventually started reacting to most processed GF foods and switched to an ultra-strict gluten contamination elimination diet. This resolved my symptoms, but I couldn't transition back to a standard GFD without symptoms relapsing. During this time, all my follow-up celiac panels, biopsies, colonoscopy, and tests for other autoimmune diseases were completely normal. (antiparasitic medication and rifaximin for any possible sibo/infection, tests for ibd etc). Also any IBS symptoms were well managed by a low fodmap diet that my dietitian prescribed. I rarely have any bloating now.

Years later, I still had the symptoms, then while seeing a different & reputable GI dr for another issue , I mentioned my celiac history, and he said that he doubted my initial diagnosis. He didn't think the EMA was reliable enough, saying that he trusted only TTG and that villous atrophy didn't always mean celiac . He suggested a two-month gluten challenge. Right before starting the challenge, my bloodwork (full celiac panel) was normal except for a positive EMA IgG. During the two months of eating gluten, I had severe fatigue, drowsiness, and nausea (manageable with otc anti-emetics), though surprisingly, these symptoms were less severe than before my original diagnosis (9 years ago). To my shock, at the end of the challenge, my entire celiac panel and biopsy came back completely negative. The GI concluded I likely had non celiac gluten sensitivity rather than CeD.

For over a year now, I've been eating gluten on and off. Sometimes I tolerate it fine and sometimes not, but my nausea has become so unbearable that normal antiemetics dont work, and I still have frequent fatigue & lethargy. I was prescribed Amitriptyline 50-100mg for IBS, which has helped immensely with the nausea, but I'm now almost dependent on 85-100mg. If I forget my daily dose, or take a lesser one, I get dizzy spells, hot flushes, and feel like I'll pass out from the severe nausea. My recent tTG tests (taken 1-2 times after the challenge) remain negative. An internist recently suggested that CeD might take longer than two months to relapse. She noted that negative serology doesn't rule out patchy villous atrophy and recommended another endoscopy. But my GI insists two months of gluten is definitive. I also have had osteopenia since my early twenties, which hasn't resolved over the years.

I’m perplexed as to what the issue could be. Is it actually possible for an original positive EMA and a "gold-standard" Marsh 3b biopsy to just be wrong? (diagnosed by someone known to be an expert pathologist, and a followup biopsy a year later on the gfd showed marsh 1)
I feel confused, not knowing whether or not I have celiac..

Could the disease have somehow become "dormant" , and would a full-blown, prolonged very high gluten challenge trigger a relapse (I wouldn't want to go back to being celiac now, honestly..) ?
But does avoiding a longer challenge put me at risk of missing unnoticed villous atrophy? And I wonder how long am I going to live on amitriptyline for this nausea?

I know I can't get official medical advice here, but I'd really appreciate hearing if anyone has navigated a similar experience with such conflicting results.