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Melanoma Checkpoint and Gut Microbiome Alteration With Microbiome Intervention

A Multicenter Phase 1b Randomized, Placebo-controlled, Blinded Study to Evaluate the Safety, Tolerability and Efficacy of Microbiome Study Intervention Administration in Combination With Anti-PD-1 Therapy in Adult Patients With Unresectable or Metastatic Melanoma

Status
Completed
Phases
Phase 1
Study type
Interventional
Source
ClinicalTrials.gov
Registry ID
NCT03817125
Acronym
MCGRAW
Enrollment
14
Registered
2019-01-25
Start date
2019-01-28
Completion date
2022-03-04
Last updated
2024-06-06

For informational purposes only — not medical advice. Sourced from public registries and may not reflect the latest updates. Terms

Conditions

Metastatic Melanoma

Keywords

Metastatic Melanoma, anti-PD1, Nivolumab, Microbiome, SER-401

Brief summary

This study is designed to evaluate the safety and tolerability of treatment with oral microbiome study intervention (SER-401) or matching placebo in combination with anti-programmed cell death 1 (anti-PD-1) therapy (nivolumab) in participants with unresectable or metastatic melanoma. The study also intends to assess clinical outcomes, the impact of microbiome study intervention administration on the microbiome profile, and its association with clinical and immunological outcomes.

Detailed description

This is a Phase 1b, multicenter, randomized, placebo-controlled, blinded study in adult participants with anti-PD-1 therapy naïve, unresectable or metastatic melanoma to evaluate the safety and tolerability of SER-401, or matching placebo in combination with anti-PD-1 therapy (nivolumab). Prior to initiating microbiome study intervention and nivolumab, participants will undergo an antibiotic or antibiotic placebo treatment lead-in to prime the gut microbiome for engraftment of the oral microbiome study intervention. Study intervention groups will be assessed for safety, changes in the microbiome, changes in the percentage of tumoral CD8 T cells, and antitumor activity. Participants must have measurable disease that can be biopsied and consent to baseline and on-treatment biopsies, as well as stool and blood biomarker collection throughout the study.

Interventions

Placebo for antibiotic will be administered orally four times a day for 4 days, followed by a 2-3 day washout.

DRUGVancomycin pretreatment

Vancomycin (125mg) will be administered orally four times a day, followed by a 2-3 day washout.

DRUGNivolumab

Nivolumab (480 mg) will be administered intravenously (IV) according to institutional guidelines every 4 weeks for up to 12 cycles. A cycle is defined as 4 calendar weeks.

DRUGMatching Placebo for SER-401

Administered once a day for 7 days during the lead-in phase, followed by once a day for 8 weeks during the microbiome/anti-PD-1 treatment phase.

DRUGSER-401

Administered once a day for 7 days during the lead-in phase, followed by once a day for 8 weeks during the microbiome/anti-PD-1 treatment phase.

Sponsors

Seres Therapeutics, Inc.
CollaboratorINDUSTRY
Parker Institute for Cancer Immunotherapy
Lead SponsorOTHER

Study design

Allocation
RANDOMIZED
Intervention model
PARALLEL
Primary purpose
TREATMENT
Masking
TRIPLE (Subject, Caregiver, Investigator)

Masking description

Participants will be randomly assigned in a 2:1 ratio to oral microbiome study intervention or matching placebo. Nivolumab will be administered open-label as standard of care to all groups. Investigators, site personnel, and participants will remain blinded to the assignment of microbiome study intervention throughout the course of the study. Select Sponsor personnel, including but not limited to the Medical Monitor, Clinical Scientists, Biostatistician, and Patient Safety, will be unblinded to treatment assignment for ongoing safety monitoring.

Eligibility

Sex/Gender
ALL
Age
18 Years to No maximum
Healthy volunteers
No

Inclusion criteria

1. Participant must be willing to provide a baseline stool sample. 2. Histologically-confirmed Stage IV cutaneous melanoma or Stage III cutaneous, acral or mucosal melanoma that is judged inoperable. Participants with a history of uveal melanoma are not eligible. 3. Measurable disease as defined by Response Evaluation Criteria in Solid Tumors version 1.1 (RECIST v1.1; ie, defined as at least 1 lesion that can be accurately measured in at least 1 dimension \[longest diameter to be recorded\] with a minimum size of ≥ 10 mm by computerized tomography \[CT\] scan or caliper measurement on clinical exam or ≥ 20 mm by chest X-ray). 1. Malignant lymph nodes must be ≥ 15 mm in short axis when assessed by CT scan to be considered pathologically enlarged and measurable. 2. Participants must have at least one measurable lesion by RECIST and a separate lesion amenable to biopsy that has not been previously irradiated. i. Participants must be willing to undergo a newly-obtained core needle or incisional biopsy at baseline (prior to antibiotic or antibiotic placebo administration). Fine needle aspiration is not acceptable. 4. Participants must be willing to undergo tumor biopsy on treatment. 5. Prior adjuvant or neoadjuvant melanoma therapy is permitted if completed at least 6 weeks prior to randomization and all related AEs have either returned to baseline or stabilized. 1. Prior anti-CTLA-4 therapy in the adjuvant setting is allowed if completed at least 12 weeks prior to the first dose of anti-PD-1.

Exclusion criteria

1. Participants who require hemodialysis. 2. Participants with a history of another cancer in the last 5 years, except for: a) curatively resected non-melanoma skin cancer; b) curatively treated cervical carcinoma in situ; c) localized prostate cancer not requiring systemic therapy; and c) other primary tumors with no known active disease present that, in the opinion of the Investigator and the Sponsor, will not affect participant outcome in the setting of the current diagnosis. 3. Any known, untreated brain metastases. Participants with brain metastases are eligible if these have been treated, and provided: 1. Brain metastases must be stable (image-documented) 4 weeks after completion of treatment for brain metastases and require treatment with less than 10 mg/day prednisone equivalent for at least 2 weeks prior to study intervention administration. 2. Neurological symptoms should be absent or returned to baseline. 4. Prior checkpoint inhibitor therapy with anti-PD-1 or anti-PD-L1 in the adjuvant setting. a. Exception: Participants with stage 3 or 4 cutaneous melanoma status post-resection who have received up to one year of adjuvant anti-PD-1 therapy who have recurred \> 6 months after their last dose of anti-PD-1 therapy are eligible. 5. Other prior systemic treatment (ie, anticancer chemotherapy, immunotherapy, or investigational agents) for unresectable or metastatic melanoma EXCEPT: 1. Prior BRAF-targeted therapy (ie, BRAF or BRAF-MEK) in the metastatic setting is allowed if completed at least 4 weeks prior to the first dose of anti-PD-1. 2. Prior anti-CTLA 4 therapy in the adjuvant setting are allowed if completed at least 12 weeks prior to the first dose of anti-PD-1. 6. History of active inflammatory bowel disease (eg, active Crohn's disease or ulcerative colitis) with diarrhea OR major gastrointestinal surgery (not including appendectomy or cholecystectomy) within 3 months of enrollment (ie, signed informed consent for the study), OR any history of total colectomy or bariatric surgery (bariatric surgery which does not disrupt the gastrointestinal lumen, ie, restrictive procedures such as banding, are permitted). 7. Any diagnosis of autoimmune disease. Participants with Type I diabetes mellitus, hypothyroidism only requiring hormone replacement, adrenal insufficiency on replacement dose steroids, skin disorders (such as vitiligo, psoriasis or alopecia) not requiring systemic treatment, or conditions not expected to recur in the absence of an external trigger are permitted to enroll. a. Participants with controlled Type 1 diabetes mellitus on a stable insulin regimen may be eligible. 8. Has a condition requiring systemic treatment with either corticosteroids (\> 10 mg daily prednisone equivalents) or other immunosuppressive medications within 14 days of study intervention administration or has a contrast allergy requiring premedication with corticosteroids. Inhaled or topical steroids, and adrenal replacement doses \> 10 mg daily prednisone equivalents are permitted in the absence of active autoimmune disease. 9. History of idiopathic pulmonary fibrosis, pneumonitis (including drug induced), organizing pneumonia (ie, bronchiolitis obliterans, cryptogenic organizing pneumonia, etc.), or evidence of active pneumonitis on screening chest CT scan. a. History of radiation pneumonitis in the radiation field (fibrosis) is permitted. 10. Has a transplanted organ or has undergone allogeneic bone marrow transplant. 11. Has received a live vaccine within 30 days prior to first dose. Participants must not receive live, attended influenza vaccine (eg, FluMist) within 30 days prior to Cycle 1, Day 1 or at any time during the study and 100 days after last dose of nivolumab. 12. Has used antibiotics within 30 days prior to randomization or has planned or required need for antibiotic prophylaxis for more than 24 consecutive hours during the course of the study.

Design outcomes

Primary

MeasureTime frameDescription
Percentage of Patients With Adverse Events (AEs)Up to 2 yearsInvestigators recorded AEs during each participant interaction. Symptoms were evaluated by the Investigator using the CTCAE version 5.0. This system grades AEs on a 1 to 5 scale: Grades 1 and 2 indicate mild to moderate events; Grade 3 denotes severe events; Grades 4 and 5 signify life-threatening or fatal outcomes. A treatment-emergent adverse event (TEAE) is defined as any event that either occurs after the initiation of study intervention, having been absent at baseline, or, if present at baseline, appears to have worsened in severity or frequency, regardless of its relation to the intervention. Adverse events deemed 'Possibly', 'Probably', or 'Definitely' related to the intervention were labeled as treatment-related adverse events (TRAE).

Secondary

MeasureTime frameDescription
Objective Response Rate (ORR)Up to week 52Objective Response Rate (ORR) is defined as the proportion of participants who attain a best overall response of complete response (CR; disappearance of all target lesions) or partial response (PR; \>=30% decrease in the sum of the longest diameter of target lesions), as determined by RECIST version 1.1. Confirmation of response by a repeat tumor assessment is not required.
Disease Control Rate (DCR)Up to week 52Defined as CR, PR, or stable disease (SD) for ≥ 24 weeks as best response by RECIST v1.1.
Progression-free Survival (PFS)Up to 2 yearsDefined as the time from randomization to date of first documented progression of disease, date of death due to any cause, or date of most recent participant contact that documented progression-free status
Mean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesUp to 2 yearsEngraftment was defined as the number of spore-forming species detected in SER-401 that were absent in participant baseline samples, and present post-microbiome-treatment, also referred to as newly appearing dose species.
Duration of ResponseUp to 2 yearsDefined as time from date of documented CR or PR to date of first documented progression of disease, date of death due to any cause, or date of most recent participant contact that documented response (ie, scan date).
Absolute Change in the Percentage of CD8 Cells in Tumor Tissue From Baseline at Cycle 2.At cycle 2 (each cycle is 28 days)Absolute change in the percentage of CD8 cells in tumor tissue from baseline at Cycle 2.
Overall Survival (OS)Up to 2 yearsDefined as the time from randomization until death or last contact if still alive at the time of final data collection (after completion of anti-PD-1 therapy).

Countries

United States

Participant flow

Participants by arm

ArmCount
SER-401 Matching Placebo/ Nivolumab
Participants will undergo a 4-day lead-in pretreatment with antibiotic placebo, then matching placebo for SER-401 and nivolumab (480 mg) treatment. Placebo for antibiotic: Placebo for antibiotic will be administered orally four times a day for 4 days, followed by a 2-3 day washout. Nivolumab: Nivolumab (480 mg) will be administered intravenously (IV) according to institutional guidelines every 4 weeks for up to 12 cycles. A cycle is defined as 4 calendar weeks. Matching Placebo for SER-401: Administered once a day for 7 days during the lead-in phase, followed by once a day for 8 weeks during the microbiome/anti-PD-1 treatment phase.
6
SER-401/ Nivolumab
Participants will undergo a 4-day lead-in pretreatment with antibiotic (vancomycin) to prime the gut microbiome for engraftment of the oral microbiome study intervention, then SER-401 and nivolumab treatment. Vancomycin pretreatment: Vancomycin (125mg) will be administered orally four times a day, followed by a 2-3 day washout. Nivolumab: Nivolumab (480 mg) will be administered intravenously (IV) according to institutional guidelines every 4 weeks for up to 12 cycles. A cycle is defined as 4 calendar weeks. SER-401: Administered once a day for 7 days during the lead-in phase, followed by once a day for 8 weeks during the microbiome/anti-PD-1 treatment phase.
8
Total14

Withdrawals & dropouts

PeriodReasonFG000FG001
Overall StudyAdverse Event10
Overall StudyLack of Efficacy15
Overall StudyPhysician Decision01

Baseline characteristics

CharacteristicSER-401/ NivolumabSER-401 Matching Placebo/ NivolumabTotal
Age, Categorical
<=18 years
0 Participants0 Participants0 Participants
Age, Categorical
>=65 years
3 Participants3 Participants6 Participants
Age, Categorical
Between 18 and 65 years
5 Participants3 Participants8 Participants
Age, Continuous66.3 years
STANDARD_DEVIATION 11.73
55.5 years
STANDARD_DEVIATION 22.31
61.6 years
STANDARD_DEVIATION 17.21
Age, Customized64 years60.5 years64 years
Cancer Stage at Enrollment
IIIA
0 Participants1 Participants1 Participants
Cancer Stage at Enrollment
IIIB
0 Participants1 Participants1 Participants
Cancer Stage at Enrollment
IIIC
2 Participants1 Participants3 Participants
Cancer Stage at Enrollment
IV
6 Participants3 Participants9 Participants
Cancer Stage at Initial Diagnosis
IIA
2 Participants0 Participants2 Participants
Cancer Stage at Initial Diagnosis
IIC
2 Participants2 Participants4 Participants
Cancer Stage at Initial Diagnosis
IIIA
0 Participants1 Participants1 Participants
Cancer Stage at Initial Diagnosis
IIIB
1 Participants1 Participants2 Participants
Cancer Stage at Initial Diagnosis
IIIC
2 Participants0 Participants2 Participants
Cancer Stage at Initial Diagnosis
IV
1 Participants1 Participants2 Participants
Cancer Stage at Initial Diagnosis
Unknown
0 Participants1 Participants1 Participants
ECOG Performance Score at Screening
0
7 Participants6 Participants13 Participants
ECOG Performance Score at Screening
1
1 Participants0 Participants1 Participants
Ethnicity (NIH/OMB)
Hispanic or Latino
1 Participants0 Participants1 Participants
Ethnicity (NIH/OMB)
Not Hispanic or Latino
7 Participants6 Participants13 Participants
Ethnicity (NIH/OMB)
Unknown or Not Reported
0 Participants0 Participants0 Participants
Melanoma Subtype
Acral
0 Participants1 Participants1 Participants
Melanoma Subtype
Cutaneous
7 Participants3 Participants10 Participants
Melanoma Subtype
Mucosal
0 Participants1 Participants1 Participants
Melanoma Subtype
Unknown
1 Participants1 Participants2 Participants
Race (NIH/OMB)
American Indian or Alaska Native
0 Participants0 Participants0 Participants
Race (NIH/OMB)
Asian
0 Participants0 Participants0 Participants
Race (NIH/OMB)
Black or African American
0 Participants0 Participants0 Participants
Race (NIH/OMB)
More than one race
0 Participants0 Participants0 Participants
Race (NIH/OMB)
Native Hawaiian or Other Pacific Islander
0 Participants0 Participants0 Participants
Race (NIH/OMB)
Unknown or Not Reported
1 Participants1 Participants2 Participants
Race (NIH/OMB)
White
7 Participants5 Participants12 Participants
Ruminococcaceae abundance-based metric at Screening
High
3 Participants2 Participants5 Participants
Ruminococcaceae abundance-based metric at Screening
Low
5 Participants4 Participants9 Participants
Sex: Female, Male
Female
1 Participants3 Participants4 Participants
Sex: Female, Male
Male
7 Participants3 Participants10 Participants

Adverse events

Event typeEG000
affected / at risk
EG001
affected / at risk
deaths
Total, all-cause mortality
1 / 64 / 8
other
Total, other adverse events
6 / 68 / 8
serious
Total, serious adverse events
1 / 61 / 8

Outcome results

Primary

Percentage of Patients With Adverse Events (AEs)

Investigators recorded AEs during each participant interaction. Symptoms were evaluated by the Investigator using the CTCAE version 5.0. This system grades AEs on a 1 to 5 scale: Grades 1 and 2 indicate mild to moderate events; Grade 3 denotes severe events; Grades 4 and 5 signify life-threatening or fatal outcomes. A treatment-emergent adverse event (TEAE) is defined as any event that either occurs after the initiation of study intervention, having been absent at baseline, or, if present at baseline, appears to have worsened in severity or frequency, regardless of its relation to the intervention. Adverse events deemed 'Possibly', 'Probably', or 'Definitely' related to the intervention were labeled as treatment-related adverse events (TRAE).

Time frame: Up to 2 years

Population: Safety Population is defined as all participants who received at least 1 dose of any study intervention

ArmMeasureGroupValue (COUNT_OF_PARTICIPANTS)
SER-401 Matching Placebo/ NivolumabPercentage of Patients With Adverse Events (AEs)Grade 3 or Grade 4 TRAE1 Participants
SER-401 Matching Placebo/ NivolumabPercentage of Patients With Adverse Events (AEs)Serious TRAE1 Participants
SER-401 Matching Placebo/ NivolumabPercentage of Patients With Adverse Events (AEs)Grade 5 TRAE0 Participants
SER-401 Matching Placebo/ NivolumabPercentage of Patients With Adverse Events (AEs)TRAE leading to treatment discontinuation1 Participants
SER-401 Matching Placebo/ NivolumabPercentage of Patients With Adverse Events (AEs)Treatment-related adverse event (TRAE)5 Participants
SER-401/ NivolumabPercentage of Patients With Adverse Events (AEs)TRAE leading to treatment discontinuation0 Participants
SER-401/ NivolumabPercentage of Patients With Adverse Events (AEs)Treatment-related adverse event (TRAE)4 Participants
SER-401/ NivolumabPercentage of Patients With Adverse Events (AEs)Grade 3 or Grade 4 TRAE0 Participants
SER-401/ NivolumabPercentage of Patients With Adverse Events (AEs)Grade 5 TRAE0 Participants
SER-401/ NivolumabPercentage of Patients With Adverse Events (AEs)Serious TRAE0 Participants
Secondary

Absolute Change in the Percentage of CD8 Cells in Tumor Tissue From Baseline at Cycle 2.

Absolute change in the percentage of CD8 cells in tumor tissue from baseline at Cycle 2.

Time frame: At cycle 2 (each cycle is 28 days)

Population: Only participants with available CD8 values at both baseline at Cycle 2 are included in the analysis.

ArmMeasureValue (MEDIAN)
SER-401 Matching Placebo/ NivolumabAbsolute Change in the Percentage of CD8 Cells in Tumor Tissue From Baseline at Cycle 2.62.7 percentage of CD8 cells
SER-401/ NivolumabAbsolute Change in the Percentage of CD8 Cells in Tumor Tissue From Baseline at Cycle 2.27.1 percentage of CD8 cells
Secondary

Disease Control Rate (DCR)

Defined as CR, PR, or stable disease (SD) for ≥ 24 weeks as best response by RECIST v1.1.

Time frame: Up to week 52

ArmMeasureValue (COUNT_OF_PARTICIPANTS)
SER-401 Matching Placebo/ NivolumabDisease Control Rate (DCR)5 Participants
SER-401/ NivolumabDisease Control Rate (DCR)3 Participants
Secondary

Duration of Response

Defined as time from date of documented CR or PR to date of first documented progression of disease, date of death due to any cause, or date of most recent participant contact that documented response (ie, scan date).

Time frame: Up to 2 years

Population: The overall number of participants evaluated for duration of response includes only those who achieved a complete (CR) or partial response (PR) as per RECIST v1.1.

ArmMeasureValue (MEDIAN)
SER-401 Matching Placebo/ NivolumabDuration of ResponseNA month
SER-401/ NivolumabDuration of ResponseNA month
Secondary

Mean Change From Baseline in the Number of Newly Appearing Spore-forming Species

Engraftment was defined as the number of spore-forming species detected in SER-401 that were absent in participant baseline samples, and present post-microbiome-treatment, also referred to as newly appearing dose species.

Time frame: Up to 2 years

Population: Participants were excluded from analysis at a specific time point if a stool sample was not collected or there was insufficient material available to run the assay.

ArmMeasureGroupValue (MEAN)Dispersion
SER-401 Matching Placebo/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 1 Day 16.83 spore-forming speciesStandard Deviation 8.424
SER-401 Matching Placebo/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 3 Day 18.50 spore-forming speciesStandard Deviation 12.629
SER-401 Matching Placebo/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 2 Day 17.67 spore-forming speciesStandard Deviation 10.539
SER-401 Matching Placebo/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 4 Day 14.80 spore-forming speciesStandard Deviation 1.483
SER-401 Matching Placebo/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 1 Day 87.60 spore-forming speciesStandard Deviation 9.209
SER-401 Matching Placebo/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 7 Day 111.20 spore-forming speciesStandard Deviation 18.349
SER-401 Matching Placebo/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesDay -75.33 spore-forming speciesStandard Deviation 7.202
SER-401/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 7 Day 125.33 spore-forming speciesStandard Deviation 8.963
SER-401/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 2 Day 128.38 spore-forming speciesStandard Deviation 16.767
SER-401/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesDay -71.67 spore-forming speciesStandard Deviation 1.862
SER-401/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 1 Day 125.71 spore-forming speciesStandard Deviation 17.661
SER-401/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 1 Day 823.29 spore-forming speciesStandard Deviation 5.187
SER-401/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 3 Day 129.00 spore-forming speciesStandard Deviation 12.853
SER-401/ NivolumabMean Change From Baseline in the Number of Newly Appearing Spore-forming SpeciesCycle 4 Day 121.25 spore-forming speciesStandard Deviation 6.551
Secondary

Objective Response Rate (ORR)

Objective Response Rate (ORR) is defined as the proportion of participants who attain a best overall response of complete response (CR; disappearance of all target lesions) or partial response (PR; \>=30% decrease in the sum of the longest diameter of target lesions), as determined by RECIST version 1.1. Confirmation of response by a repeat tumor assessment is not required.

Time frame: Up to week 52

ArmMeasureValue (COUNT_OF_PARTICIPANTS)
SER-401 Matching Placebo/ NivolumabObjective Response Rate (ORR)4 Participants
SER-401/ NivolumabObjective Response Rate (ORR)2 Participants
Secondary

Overall Survival (OS)

Defined as the time from randomization until death or last contact if still alive at the time of final data collection (after completion of anti-PD-1 therapy).

Time frame: Up to 2 years

ArmMeasureValue (MEDIAN)
SER-401 Matching Placebo/ NivolumabOverall Survival (OS)NA month
SER-401/ NivolumabOverall Survival (OS)21.1 month
Secondary

Progression-free Survival (PFS)

Defined as the time from randomization to date of first documented progression of disease, date of death due to any cause, or date of most recent participant contact that documented progression-free status

Time frame: Up to 2 years

ArmMeasureValue (MEDIAN)
SER-401 Matching Placebo/ NivolumabProgression-free Survival (PFS)15 month
SER-401/ NivolumabProgression-free Survival (PFS)5.2 month

Source: ClinicalTrials.gov · Data processed: Feb 11, 2026