Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA202379

Local Sample ID:	BW45-21
Subject ID:	SU002194
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

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Subject:

Subject ID:	SU002194
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
BW45-21	SA202379	FL024607	Responder	Phenotype
BW45-21	SA202379	FL024607	Post	Treatment

Collection:

Collection ID:	CO002187
Collection Summary:	This was a multi-center, prospective, single-arm phase I/Ib safety trial. Patients eligible for treatment had to be diagnosed with non-metastatic, biopsy-proven p16-negative histology squamous cell carcinoma of the oral cavity, oropharynx, larynx, or hypopharynx, and had to be eligible and amenable to surgical resection. This study enrolled using a 3+3 model. Patients received one dose of neoadjuvant Durvalumab 1500 mg approximately 3-6 weeks before standard-of-care surgery given concurrently with the first dose of radiation (RT). The starting RT dose level was 6 Gy for 2 fractions (12 Gy total) every other day over approximately one week to sites of gross disease (Table 1) to minimize exposure to normal tissue. If toxicity developed and surgery was delayed by more than 6 weeks due to treatment toxicity (qualifying as a DLT), the radiation dose was set to be dropped per protocol for the next set of patients. If this dose was tolerated, the dose was increased to 6 Gy for 3 fractions (18 Gy total) for the next 3 patients. Patients proceeded to surgical resection approximately 3-6 weeks after radiation as recommended by the ENT surgeon. Post-operatively, pathology was reviewed at the multi-disciplinary head and neck conference, and the need for adjuvant therapy was discussed. For the first 8 patients, all patients were given adjuvant therapy based on presenting features. However, after patient 8, adjuvant therapy was dictated based on high-risk pathologic features as per the NCCN guidelines and treating physician recommendations. Adjuvant radiation included intensity-modulated radiation therapy of 60 Gy in 2 Gy once-daily fraction size once-daily fraction size (total of 30 fractions). If indicated, adjuvant systemic therapy included cisplatin or other cytotoxic chemotherapy or targeted biologics (Cetuximab) per physician discretion. All patients received adjuvant durvalumab to be initiated approximately 6-12 weeks post-surgery. It was given as 1500 mg intravenously once every 4 weeks for a maximum of 6 doses, or until progression, toxicity, or withdrawal from study. This was delivered either as monotherapy or concurrently with adjuvant radiation +/- systemic therapy for high-risk patients. Safety and toxicity evaluations were done throughout the study process. DLTs and adjustment of radiation doses were done during the neoadjuvant period.
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR002206
Treatment Summary:	This was a multi-center, prospective, single-arm phase I/Ib safety trial. Patients eligible for treatment had to be diagnosed with non-metastatic, biopsy-proven p16-negative histology squamous cell carcinoma of the oral cavity, oropharynx, larynx, or hypopharynx, and had to be eligible and amenable to surgical resection. This study enrolled using a 3+3 model. Patients received one dose of neoadjuvant Durvalumab 1500 mg approximately 3-6 weeks before standard-of-care surgery given concurrently with the first dose of radiation (RT). The starting RT dose level was 6 Gy for 2 fractions (12 Gy total) every other day over approximately one week to sites of gross disease (Table 1) to minimize exposure to normal tissue. If toxicity developed and surgery was delayed by more than 6 weeks due to treatment toxicity (qualifying as a DLT), the radiation dose was set to be dropped per protocol for the next set of patients. If this dose was tolerated, the dose was increased to 6 Gy for 3 fractions (18 Gy total) for the next 3 patients. Patients proceeded to surgical resection approximately 3-6 weeks after radiation as recommended by the ENT surgeon. Post-operatively, pathology was reviewed at the multi-disciplinary head and neck conference, and the need for adjuvant therapy was discussed. For the first 8 patients, all patients were given adjuvant therapy based on presenting features. However, after patient 8, adjuvant therapy was dictated based on high-risk pathologic features as per the NCCN guidelines and treating physician recommendations. Adjuvant radiation included intensity-modulated radiation therapy of 60 Gy in 2 Gy once-daily fraction size once-daily fraction size (total of 30 fractions). If indicated, adjuvant systemic therapy included cisplatin or other cytotoxic chemotherapy or targeted biologics (Cetuximab) per physician discretion. All patients received adjuvant durvalumab to be initiated approximately 6-12 weeks post-surgery. It was given as 1500 mg intravenously once every 4 weeks for a maximum of 6 doses, or until progression, toxicity, or withdrawal from study. This was delivered either as monotherapy or concurrently with adjuvant radiation +/- systemic therapy for high-risk patients. Safety and toxicity evaluations were done throughout the study process. DLTs and adjustment of radiation doses were done during the neoadjuvant period.

Treatment ID:

TR002206

Treatment Summary:

This was a multi-center, prospective, single-arm phase I/Ib safety trial. Patients eligible for treatment had to be diagnosed with non-metastatic, biopsy-proven p16-negative histology squamous cell carcinoma of the oral cavity, oropharynx, larynx, or hypopharynx, and had to be eligible and amenable to surgical resection. This study enrolled using a 3+3 model. Patients received one dose of neoadjuvant Durvalumab 1500 mg approximately 3-6 weeks before standard-of-care surgery given concurrently with the first dose of radiation (RT). The starting RT dose level was 6 Gy for 2 fractions (12 Gy total) every other day over approximately one week to sites of gross disease (Table 1) to minimize exposure to normal tissue. If toxicity developed and surgery was delayed by more than 6 weeks due to treatment toxicity (qualifying as a DLT), the radiation dose was set to be dropped per protocol for the next set of patients. If this dose was tolerated, the dose was increased to 6 Gy for 3 fractions (18 Gy total) for the next 3 patients. Patients proceeded to surgical resection approximately 3-6 weeks after radiation as recommended by the ENT surgeon. Post-operatively, pathology was reviewed at the multi-disciplinary head and neck conference, and the need for adjuvant therapy was discussed. For the first 8 patients, all patients were given adjuvant therapy based on presenting features. However, after patient 8, adjuvant therapy was dictated based on high-risk pathologic features as per the NCCN guidelines and treating physician recommendations. Adjuvant radiation included intensity-modulated radiation therapy of 60 Gy in 2 Gy once-daily fraction size once-daily fraction size (total of 30 fractions). If indicated, adjuvant systemic therapy included cisplatin or other cytotoxic chemotherapy or targeted biologics (Cetuximab) per physician discretion. All patients received adjuvant durvalumab to be initiated approximately 6-12 weeks post-surgery. It was given as 1500 mg intravenously once every 4 weeks for a maximum of 6 doses, or until progression, toxicity, or withdrawal from study. This was delivered either as monotherapy or concurrently with adjuvant radiation +/- systemic therapy for high-risk patients. Safety and toxicity evaluations were done throughout the study process. DLTs and adjustment of radiation doses were done during the neoadjuvant period.

Sample Preparation:

Sampleprep ID:	SP002200
Sampleprep Summary:	Metabolomics analyses were performed as extensively described in previous studies (Issaian et al., Hematologica 2021). A volume of 20μl of frozen plasma was extracted in either 480μl of methanol:acetonitrile:water (5:3:2, v/v/v) (D'Alessandro et al. JCI Insight 2021). After vortexing at 4°C for 30 min, extracts were separated from the protein pellet by centrifugation for 10 min at 10,000g at 4°C and stored at −80°C until analysis. Ultra-High-Pressure Liquid Chromatography-Mass Spectrometry analyses were performed using a Vanquish UHPLC coupled online to a Q Exactive mass spectrometer (Thermo Fisher, Bremen, Germany) (Nemkov et al. Methods Mol Bio 2019). Samples were analyzed using a 5-minute gradient as described ( Nemkov et al. Methods Mol Bio 2019, Nemkov et al. JCI Insight 2020). Solvents were supplemented with 0.1% formic acid for positive mode runs and 1 mM ammonium acetate for negative mode runs. MS acquisition, data analysis and elaboration were performed as described.

Sampleprep ID:

SP002200

Sampleprep Summary:

Metabolomics analyses were performed as extensively described in previous studies (Issaian et al., Hematologica 2021). A volume of 20μl of frozen plasma was extracted in either 480μl of methanol:acetonitrile:water (5:3:2, v/v/v) (D'Alessandro et al. JCI Insight 2021). After vortexing at 4°C for 30 min, extracts were separated from the protein pellet by centrifugation for 10 min at 10,000g at 4°C and stored at −80°C until analysis. Ultra-High-Pressure Liquid Chromatography-Mass Spectrometry analyses were performed using a Vanquish UHPLC coupled online to a Q Exactive mass spectrometer (Thermo Fisher, Bremen, Germany) (Nemkov et al. Methods Mol Bio 2019). Samples were analyzed using a 5-minute gradient as described ( Nemkov et al. Methods Mol Bio 2019, Nemkov et al. JCI Insight 2020). Solvents were supplemented with 0.1% formic acid for positive mode runs and 1 mM ammonium acetate for negative mode runs. MS acquisition, data analysis and elaboration were performed as described.

Combined analysis:

Analysis ID	AN003450	AN003451
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	NEGATIVE	POSITIVE
Units	Relative Abundance	Relative Abundance

Chromatography:

Chromatography ID:	CH002548
Chromatography Summary:	Negative Mode: Samples were analyzed using a 5-minute gradient as described (Nemkov et al. Methods Mol Bio 2019, Nemkov et al. JCI Insight 2020). Solvents were supplemented with 1 mM ammonium acetate for negative mode runs.
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
Chromatography Type:	Reversed phase

Chromatography ID:	CH002549
Chromatography Summary:	Positive Mode: Samples were analyzed using a 5-minute gradient as described (Nemkov et al. Methods Mol Bio 2019, Nemkov et al. JCI Insight 2020). Solvents were supplemented with 0.1% formic acid for positive mode runs.
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003213
Analysis ID:	AN003450
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS acquisition, data analysis and elaboration were performed as described. (Nemkov et al. Methods Mol Bio 2019).
Ion Mode:	NEGATIVE

MS ID:	MS003214
Analysis ID:	AN003451
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS acquisition, data analysis and elaboration were performed as described. (Nemkov et al. Methods Mol Bio 2019).
Ion Mode:	POSITIVE