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March 13, 2024 | by Kara McGaughey, PennNeuroKnow and IAES Collaboration

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The staff at IAES is proud to present to all of you another wonderful article/blog from the amazing team at PennNeuroKnow. Since 2019 IAES has been extremely lucky to be in partnership with the PennNeuroKnow(PNK) team to help us all better understand complex medical issues related to AE and neurology in general. The talented PNK team continues to keep us up-to-date and help clarify the complexities we face each day along our AE journey, and we are eternally grateful! You can find out much more about this stellar group at:


Receiving a diagnosis of any kind can be overwhelming. In cases like autoimmune encephalitis (AE) where the diagnostic process is often long and complicated, finally getting an answer can bring a sense of relief. At the same time, coming to terms with new information about your body and your health might be unsettling and full of uncertainty. What happens next? What should you know? How can you best advocate for yourself?

In this post, we will explore 7 questions you can ask while beginning the process of navigating an AE diagnosis. While this list is certainly not exhaustive (and not medical advice), we hope it can be a resource as you and your loved ones begin to make sense of the barrage of new information that comes with an AE diagnosis. These questions can be helpful discussion points so you can head into your next appointment with an AE specialist feeling confident and empowered.

1. Can you explain why we have landed on a diagnosis of autoimmune encephalitis?

When settling on a diagnosis, clinicians often make use of a checklist of expected symptoms and test results called the diagnostic criteria. Having your doctor explain the diagnostic criteria for AE (Figure 1) can help you understand how your symptoms and recent test results relate to the bigger picture. It is one of the easiest and most helpful ways to make sense of a new AE diagnosis.

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Figure 1. The requirements for an AE diagnosis are seen in bold above. Notably, there are subtypes of AE that are “seronegative,” meaning that patients will not have AE-associated autoantibodies. The asterisk next to this diagnostic criteria indicates that, because of this seronegativity, not all patients with AE will satisfy the requirement. It’s important to recognize that while these diagnostic criteria represent the current consensus, they may change as researchers and clinicians continue to learn more about AE.1-3

It’s important to keep in mind that there are many subtypes of AE, each with their own assortment of symptoms and caveats for diagnosis. In other words, some of the symptoms and test results listed as part of the AE diagnostic criteria are more likely to occur in some subtypes of AE than others. For instance, patients with some subtypes of AE (like anti-NMDAR, anti-GABAB, or anti-LGI1) experience frequent, severe seizures, while patients with other AE subtypes will have no seizure activity.4 As another example, while most AE subtypes are defined by the antibodies causing inflammation in the brain, there are some subtypes of AE, called antibody-negative AE or “seronegative” AE, where patients have no detectable autoantibodies in their blood or cerebrospinal fluid (CSF) samples.5 All this to say, don’t be alarmed if there are symptoms present on the diagnostic criteria list that you’ve never experienced. Because of AE’s diverse presentation, understanding exactly which AE subtype you have is crucial for beginning to interpret the ins and outs of your particular diagnosis. It can also be tremendously helpful for filtering information if you’re wanting to read more about AE or AE research online as sometimes literature only applies to particular kinds of AE. You should also keep in mind that even people with the same AE diagnosis might present with drastically different symptoms, receive different treatments, and recover on totally different timelines.

2. Given my diagnosis, what is the best treatment available?

In some sense, the best treatment for AE is one you can start quickly and keep up with consistently. Research shows that, given the rapid onset of AE, early treatment is key for getting the body’s inflammation under control and achieving a good outcome.6-7 Specifically, early access to therapeutics plays an important role in both promoting complete recovery and decreasing long-term complications.7-8 With this in mind, in some cases, a doctor might advise that you begin treatment for AE before all the test results come in and you’re officially diagnosed.

There are a variety of different treatment options that aim to reduce inflammation and provide relief from the symptoms of AE. Oftentimes, treatment begins with first-line therapies, like steroids, plasma exchange (PLEX), or intravenous immune globulin (IVIG).2,6 If there is no meaningful response after 2-4 weeks of therapy, physicians often move to second-line therapeutics, like Rituximab or Cyclophosphamide.6 When meeting with an AE specialist, it’s important to understand which treatment you’ll be trying first as well as what the range of future treatment options might look like in your case. Like with most conditions, the treatment plan may vary depending on your AE diagnosis as well as any other health conditions you may have. Patients with paraneoplastic AE (AE triggered by a tumor present somewhere in the body), for example, generally require the tumor to be removed to achieve remission.7 Regardless of treatment specifics, it can be reassuring to know that there is a Plan B in place if Plan A isn’t going perfectly.

Importantly, new treatments for autoimmune conditions like AE are a hot area of research. Immunotherapy drugs, for example, are increasingly emerging as “third-line” therapy for AE patients whose symptoms are not resolved by traditional treatment options.9 So, while AE symptoms can be stubborn and unrelenting for some patients, there is hope to be found in the fact that new options continue to move through the drug-development pipeline.

3. What treatment side effects should I be aware of?

When agreeing to a particular treatment plan, it’s important to not just ask about treatment options, but also their potential side effects. Exactly which side effects to look out for depends entirely on which treatment you’re taking. But, whatever they are, you’ll probably feel most confident starting a particular medication or therapy if you know both the beneficial changes to anticipate and the symptoms or signs that might tag along for the ride. Some side effects are little, short-term nuisances you can push through in order to recover long-term. Others might be much harder to tolerate or signs that you might need to return to the doctor’s office. Explicitly asking your physician which side effects fall into which of these categories can help put your mind at ease.

4. Are there AE signs or symptoms I should look out for that would warrant a call to my doctor?

In addition to keeping track of treatment side effects, it’s important to have a clear sense of AE symptoms to look out for that might indicate treatment isn’t working and the condition is progressing. Asking your doctor to list reasons for concern can help you be proactive in monitoring your AE symptoms as they ebb and flow over the course of the treatment process. Knowing what to look out for can also help you distinguish any treatment side effects from AE symptoms. It might also be worth asking your doctor to clarify when AE symptoms warrant a call to your doctor’s office or a visit to the emergency room. Having a sense of what merits a mental note vs. immediate action will not only make a tremendous difference in your care, but also help you feel more confident and secure in your AE management skills.

5. Are there any clinical trials I should consider participating in?

All drugs that are available, either at the hospital or from your local pharmacy, have been carefully tested through the clinical trial process. However, you might have the opportunity to try new medications by participating in a clinical trial yourself. People choose to participate in clinical trials for a number of reasons. For one, these trials are a way to access the newest treatments coupled with additional care from physicians on the clinical trial team. Participating in a clinical trial is also an opportunity to help accelerate scientific research and the development of safer, more effective treatment options for your condition. For rarer conditions, like AE, participating in clinical trials can have an even larger impact since it can be much more difficult to recruit enough participants to fill and complete a successful clinical trial.10

While it is understandably a big decision to participate in the testing process for a new drug, it’s important to remember that clinical trials are closely supervised and heavily regulated.11-12 Before deciding to participate, you’re provided an “informed consent document” describing the study’s purpose, duration, required procedures, risks, and potential benefits. The potential risks and benefits depend largely on the specifics of the clinical trial (i.e., the drug involved and what phase of the clinical trial process you’d be participating in). However, in most cases and phases, clinical trials are organized such that participants receive at least the same care they otherwise would at their doctor’s office.11,13 Importantly, consenting to participate in the trial is not a contract. You are free to change your mind and withdraw at any time or refuse particular treatments and tests.

If you’re interested in considering a clinical trial, it’s a good idea to discuss the details with your AE specialist. They should be able to explain the nuances, know whether or not you qualify for a particular trial, and offer their opinion on whether participating is in your best interest. Often, AE clinical trials will focus on a new drug for a particular AE subtype, meaning you’d need a specific AE diagnosis to participate. It is also worth knowing that not all clinical trials involve testing new drugs (so-called “interventional trials”). Many, especially in the world of AE, are observational trials that track patients and their responses to existing treatments over time. You can learn more about the clinical trial process using these detailed guidelines from The National Institutes of Health, and explore a list of AE clinical trials here.

6. How will my condition be monitored moving forward?

Whether or not you choose to participate in a clinical trial, your AE journey will likely still involve a lot of visits to the clinic. One of the trickiest parts about AE is the long-term outpatient management required due to residual symptoms that some patients experience following their initial episode.6,14  While there is variation depending on the subtype of AE, it has been estimated that 10-20% of patients experience an AE relapse.7 In order to help AE patients achieve the highest possible level of functionality and reach complete remission, “maintenance therapy” is usually considered.7

Because of the diversity of AE subtypes and symptoms, identifying a single clinician with appropriate expertise can be a major obstacle. As such, AE patients often accumulate a team of clinicians, each tasked with managing a part of their long-term care. You might, for example, have follow-up appointments with a psychiatrist for psychiatric symptoms; a neurologist for seizures, movement disorders, or dysautonomia; a speech therapist; an occupational therapist; and so on. The specialists you see might also change over time. This is because, while in some cases the AE symptoms a patient experiences with relapses are the same ones they experienced with the condition’s onset, in others, relapses can present differently than the initial wave.14-15

All these clinicians should have access to your medical records and charts so they can read each other’s notes, thoughts, and observations. However, it can’t hurt to relay the big picture at each appointment to make sure both you and the doctor are up to date. You can find helpful tips for how to compile and maintain a record of your personal health information here on the IAES website.

7. What resources exist for both patient and caregiver support?

While your clinicians can help manage your physical and mental symptoms, an AE diagnosis can also have tremendous emotional and social impacts. In addition to managing new medications and other therapies, many patients with AE must learn to manage their expectations of what day-to-day life will look like for a while. While it can be difficult, it’s important to remember that you do not need to navigate your AE diagnosis alone.

In addition to support from friends and family, it can be especially helpful to find and connect with other AE patients and caregivers. Organizations such as the International Autoimmune Encephalitis Society (IAES) have compiled a list of resources (including apps). Asking your doctor if they have additional recommendations — either online or in your area — can increase the chances that you’re able to find the support that’s right for you. It’s important to have lots of options as the type and level of support you need can change over the course of your AE journey.


  1. Graus, F., Titulaer, M. J., Balu, R., Benseler, S., Bien, C. G., Cellucci, T., Cortese, I., Dale, R. C., Gelfand, J. M., Geschwind, M., Glaser, C. A., Honnorat, J., Höftberger, R., Iizuka, T., Irani, S. R., Lancaster, E., Leypoldt, F., Prüss, H., Rae-Grant, A., … Dalmau, J. (2016). A clinical approach to diagnosis of autoimmune encephalitis. The Lancet Neurology, 15(4), 391–404.
  2. Lancaster, E. (2016). The Diagnosis and Treatment of Autoimmune Encephalitis. Journal of Clinical Neurology (Seoul, Korea), 12(1), 1–13.
  3. Cellucci, T., Van Mater, H., Graus, F., Muscal, E., Gallentine, W., Klein-Gitelman, M. S., Benseler, S. M., Frankovich, J., Gorman, M. P., Van Haren, K., Dalmau, J., & Dale, R. C. (2020). Clinical approach to the diagnosis of autoimmune encephalitis in the pediatric patient. Neurology Neuroimmunology & Neuroinflammation, 7(2), e663.
  4. Davis, R. & Dalmau, J. (2013). Autoimmunity, Seizures, and Status Epilepticus. Epilepsia 54, 46–49.
  5. Lee, W.-J., Lee, H.-S., Kim, D.-Y., Lee, H.-S., Moon, J., Park, K.-I., Lee, S. K., Chu, K., & Lee, S.-T. (2022). Seronegative autoimmune encephalitis: Clinical characteristics and factors associated with outcomes. Brain, 145(10), 3509–3521.
  6. Abboud, H., Probasco, J. C., Irani, S., Ances, B., Benavides, D. R., Bradshaw, M., Christo, P. P., Dale, R. C., Fernandez-Fournier, M., Flanagan, E. P., Gadoth, A., George, P., Grebenciucova, E., Jammoul, A., Lee, S.-T., Li, Y., Matiello, M., Morse, A. M., Rae-Grant, A., … Titulaer, M. J. (2021). Autoimmune encephalitis: Proposed best practice recommendations for diagnosis and acute management. Journal of Neurology, Neurosurgery & Psychiatry, 92(7), 757–768.
  7. Shin, Y.-W., Lee, S.-T., Park, K.-I., Jung, K.-H., Jung, K.-Y., Lee, S. K., & Chu, K. (2017). Treatment strategies for autoimmune encephalitis. Therapeutic Advances in Neurological Disorders, 11, 1756285617722347.
  8. Titulaer, M. J., McCracken, L., Gabilondo, I., Armangué, T., Glaser, C., Iizuka, T., Honig, L. S., Benseler, S. M., Kawachi, I., Martinez-Hernandez, E., Aguilar, E., Gresa-Arribas, N., Ryan-Florance, N., Torrents, A., Saiz, A., Rosenfeld, M. R., Balice-Gordon, R., Graus, F., & Dalmau, J. (2013). Treatment and prognostic factors for long-term outcome in patients with anti-NMDA receptor encephalitis: An observational cohort study. The Lancet Neurology, 12(2), 157–165.
  9. Yang, J., & Liu, X. (2021). Immunotherapy for Refractory Autoimmune Encephalitis. Frontiers in Immunology, 12.
  10. Blackburn, K. M., Denney, D. A., Hopkins, S. C., & Vernino, S. A. (2022). Low Recruitment in a Double-Blind, Placebo-Controlled Trial of Ocrelizumab for Autoimmune Encephalitis: A Case Series and Review of Lessons Learned. Neurology and Therapy, 11(2), 893–903.
  11. U.S. Department of Health and Human Services. (2022). NIH Clinical Research Trials and You: The Basics. National Institutes of Health.
  12. Van Norman, G. A. (2016). Drugs, Devices, and the FDA: Part 1: An Overview of Approval Processes for Drugs. JACC. Basic to Translational Science, 1(3), 170–179.
  13. American Cancer Society. (2020). Making Decisions and Managing Your Treatment: Types and Phases of Clinical Trials.
  14. Abboud, H., Briggs, F., Buerki, R., Elkasaby, M., BacaVaca, G. F., Fotedar, N., Geiger, C., Griggins, C., Lee, C., Lewis, A., Serra, A., Shrestha, R., Winegardner, J., & Shaikh, A. (2022). Residual symptoms and long-term outcomes after all-cause autoimmune encephalitis in adults. Journal of the Neurological Sciences, 434, 120124.
  15. Zeng, W., Cao, L., Zheng, J., & Yu, L. (2021). Clinical characteristics and long-term prognosis of relapsing anti-N-methyl-d-aspartate receptor encephalitis: A retrospective, multicenter, self-controlled study. Neurological Sciences, 42(1), 199–207.

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