Fecal Microbiota Transplantation (FMT) of FMP30 in Relapsing-Remitting Multiple Sclerosis

In this Phase 1b open-label prospective clinical trial, patients with relapsing- remitting MS
will undergo FMT of FMP30 (donor stool) via colonoscopy and immunological efficacy endpoints
will be assessed at various time points. The active phase of the study will continue for 12
weeks post-FMT with safety and biomarker (engraftment) follow-up for 48 weeks. A parallel
observational control arm of MS patients who otherwise satisfy study inclusion criteria based
on their MS phenotype, demographics, disease duration and prior use of allowable MS
therapies, will be recruited as a comparison observational group to measure stability of
stool and serum immunological measures.

The primary hypotheses are that:

1. FMT will be safe and tolerable in patients with MS.

2. FMT preceded by antibiotic preconditioning will lead to a change in fecal microbiota
community structure

Secondary hypotheses are that:

1. FMT preceded by antibiotic preconditioning will induce a favorable shift from
pro-inflammatory to immunomodulatory T cell profiles in patients with
relapsing-remitting MS

2. That engraftment will not appreciably decay over time

3. That FMT will favorably change humoral function

4. That FMT will favorably influence short-term clinical and radiological endpoints.

FMP30 donor stool will be obtained from OpenBiome (Somerville, MA; OpenBiome.org), an
established nonprofit stool bank with stringent safety protocols and quality control. Donor
stool will be obtained from donors without MS and without other known autoimmune diseases and
will be screened for transmissible pathogens. In collaboration with OpenBiome, UCSF will
additionally screen donor stool on in vitro assays for immunological properties thought to be
favorable in MS, including decreasing TH17 and increasing T regulatory cells, in order to
select the final donor stool for to be used in this study for FMT. UCSF will obtain an IND
from the FDA for FMT of FMP30 donor stool in MS.

After providing written informed consent and reviewing inclusion and exclusion criteria,
subjects will participate in either the FMT Treatment Arm or the Observational Control Arm.

Subjects in the FMT Treatment Arm will first undergo screening assessments according to the
study schedule of activities and provide blood samples for eligibility and research, and
stool samples for research. Subjects who pass screening will have their pre-treatment
baseline visit with 21 days of their screening visit where they will have an MRI, safety and
biomarker research blood sample collection, stool sample collection for research, complete
study activities according to the study visit schedule, be given antibiotics, bowel
preparation, a medication compliance diary and directions on when and how to start the
antibiotics and bowel preparation before their scheduled FMT colonoscopy procedure.

The week before their Baseline FMT visit, subjects will be contacted by study staff to
initiate an oral antibiotic regimen for 5 days to precondition the gut for FMT and optimize
engraftment of the donor microbiome. Study staff will ensure that the subjects understand how
to complete their oral antibiotic regimen, compliance diary, and bowel preparation correctly.

At the study Baseline Visit, following standard bowel preparation for colonoscopy, subjects
will then undergo colonoscopy with FMT of FMP30 by an experienced gastroenterologist.
Subjects will return for scheduled assessments of stool and blood sampling, questionnaires,
physical examination and MS rating scales, and follow-up MRI for 12 weeks, with additional
safety and biomarker blood sample collection, and followed at weeks 24, 36 and 48. The active
study time of 12 weeks was designed to be short to minimize time off MS disease modifying
therapies (should the subject wish to go on a MS disease modifying therapy).

Subjects participating in the Observational Control Arm will not undergo the interventional
FMT treatment. Participants in this arm will have a total of 5 visits over the course of 12
weeks. At the Screening/Baseline visit, subjects will provide blood and stool samples for
research along with other study activities according to the study visit schedule. Subjects
will mail in a stool sample at week 2 and come in for follow-up visits at weeks 4, 8 and 12.

Inclusion Criteria:

1. Age 18-60 inclusive (at time of screening).

2. Diagnosis of relapsing-remitting multiple sclerosis (MS) by International Panel
McDonald Criteria (2010)(1) incorporating 2017 revisions which reclassify select
high-risk Clinically Isolated Syndromes under 2010 criteria as RRMS under 2017
criteria, and Lublin criteria (2014)(2).

3. Recent documented MS disease activity, defined as at least 1 clinical relapse within
the past 1 year prior to baseline OR 2 clinical relapses in the past 2 years prior to
baseline OR at least 1 new T2/FLAIR lesion on brain or spine MRI OR at least 1
gadolinium enhancing lesion on brain or spine MRI in the past 1 year prior to
baseline.

4. Expanded Disability Status Scale (EDSS) less than or equal to 6.0; EDSS 5.5 or less if
MS disease duration is greater than 15 years (no other disease duration restriction).

5. Must have positive serology for Epstein-Barr Virus (EBV) (IgG anti-EBNA positive) at
screening, indicating prior exposure.

6. No prior MS disease modifying therapy or a 12 week washout period for subjects on
glatiramer acetate or interferon-beta therapy.

7. At least 4 weeks from baseline since last use of IV or oral glucocorticoids Protocol:
MS-BIOME Study.

8. Agree to maintain a stable diet during the course of the study (over the counter
probiotics are allowable).

9. Premenopausal women and women <12 months after the onset of menopause must have a
negative serum pregnancy test unless they have undergone surgical sterilization.

10. Female subjects of childbearing potential who are sexually active with a
non-sterilized male partner must agree to use a highly effective method of
contraception; non-sterilized male subjects who are sexually active with a female
partner of childbearing potential must agree to use a highly effective method of
contraception.

11. Not actively participating in another interventional MS clinical trial (participation
in other observational research studies is allowable).

Exclusion Criteria:

1. Prior use of fingolimod, dimethyl fumarate, teriflunomide, natalizumab, alemtuzumab,
mitoxantrone, cyclophosphamide, rituximab, ocrelizumab, daclizumab, methotrexate,
azathioprine, mycophenolate mofetil, cyclosporine, leflunomide or induction
chemotherapy.

2. No use of diuretics like furosemide (Lasix) 1 week before the first dose oral
antibiotics. The use of hydrochlorothiazide (HCTZ) for hypertension at a dose < 50
mg/day is allowable.

3. Progressive MS by Lublin criteria (2014).

4. No oral or IV antibiotics within 8 weeks of screening and 12 weeks of scheduled of the
planned FMT procedure if in the FMT arm or first stool collection if in control arm
(note that topical, otic, ocular antibiotics are specifically allowable which is
consistent with the IMSMS.org protocol for collaborative gut microbiome research in
MS).

5. Hypersensitivity or allergy to study antibiotics, conscious sedation medications or
bowel preparation.

6. Contraindication to study procedures including MRI, anesthesia (ASA criteria IV and
V), colonoscopy, phlebotomy.

7. History of inflammatory bowel disease (Crohn's Disease, Ulcerative Colitis) Protocol:
MS-BIOME Study.

8. Active symptomatic C. Difficile infection (colonization is not an exclusion).

9. Active gastrointestinal condition being investigated (i.e. GI bleeding, colon cancer,
active GI workup); history of known or suspected toxic megacolon and/or known small
bowel ileus, major gastrointestinal surgery (e.g. significant bowel resection) within
3 months before enrollment (note that this does not include appendectomy or
cholecystectomy); or history of total colectomy or bariatric surgery.

10. History of malignancy (except excised cutaneous basal cell carcinoma or squamous cell
carcinoma which are allowable) including no concurrent induction chemotherapy,
radiation therapy or biological treatment for active malignancy.

11. Pregnant or lactating women or intention of getting pregnant during the trial period.

12. Active infection including untreated latent or active tuberculosis, HIV, hepatitis,
syphilis or other major active infection.

13. Known immunodeficiency including CVID.

14. INR>1.5, Platelets<100, Hemoglobin <8.5, WBC<2.0, Absolute lymphocyte count <0.8,
Absolute Neutrophil Count <0.5, CD4<200, eGFR<45.

15. Any condition that in the opinion of the study PI could jeopardize the safety of the
subject, would make it unlikely for the subject to complete the study or could
confound the results of the study.

16. Unable or unwilling to comply with study protocol requirements.