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Supproting Materials for "Cross-Linked Selenoctanoic Acid Nanoplatform Enables Bidirectional Regulation of Intra- and Extracellular ROS: A New Avenue for Enhanced Cancer Immunotherapy" - section A
<p><strong>Table of Content</strong></p> <h1>1. Synthesis and characterization</h1> <h2> 1.1. SeLA</h2> <h3> 1.1.0. Lab book pages</h3> <h3> 1.1.1. NMR</h3> <h3> 1.1.2. HR-MS</h3> <h3> 1.1.3. UV</h3> <h3> 1.1.4. IR</h3> <h2> 1.2. cSeLAN</h2> <h3> 1.2.0. Lab book pages</h3> <h3> 1.2.1. NMR</h3> <h3> 1.2.2. UV</h3> <h3> 1.2.3. IR</h3> <h3> 1.2.4. GPC</h3> <h3> 1.2.5. MALDI-TOF-MS</h3> <h3> 1.2.6. DLS</h3> <h3> 1.2.7. Critical melle cncentration</h3> <h3> 1.2.8. ICP-MS</h3> <h3> 1.2.9. TEM</h3> <h2> 1.3. cLAN</h2> <h3> 1.3.0. Lab book pages</h3> <h3> 1.3.1. NMR</h3> <h3> 1.3.2. UV</h3> <h3> 1.3.3. DLS</h3> <h3> 1.3.4. GPC</h3> <h1>2. <em>In vitro</em> intra- and extracellular ROS regulation</h1> <h2> 2.0. Lab book pages</h2> <h2> 2.1. Raman scattering spectra</h2> <h2> 2.2. HPLC</h2> <h3> 2.2.1. Standard peaking</h3> <h3> 2.2.2. HPLC analysis</h3> <h2> 2.3. ICP-MS</h2> <h2> 2.4. MTT</h2> <h2> 2.5. Intracellular ROS generation</h2> <h3> 2.5.1. Fluorescence images</h3> <h3> 2.5.2. Flow fluorescence quantification</h3> <h2> 2.6. Intracellular pro-oxidation mechanism</h2> <h3> 2.6.1. Quantification of intracellular ATP</h3> <h3> 2.6.2. Quantification of intracellular NADH</h3> <h3> 2.6.3. Quantification of intracellular <strong>·</strong>OH</h3> <h3> 2.6.4. Quantification of intracellular ROS</h3> <h2> 2.7. Quantification of extracellular ROS</h2> <h1>3. <em>In vitro</em> ICD-inducing ability</h1> <h2> 3.0. Lab book pages</h2> <h2> 3.1. ATP release</h2> <h2> 3.2. HMGB1</h2> <h2> 3.3. CRT</h2> <h1>4. T cell proliferation and activation</h1> <h2> 4.0. Lab book pages</h2> <h2> 4.1. Flow cytometry analysis of the T cell proliferation</h2> <h2> 4.2. Quantification of IFN-γ secretions</h2> <h1>5. Biosafety evaluation of cSeLAN</h1> <h2> 5.0. Lab book pages</h2> <h2> 5.1. Hemolytic and hemagglutination assay</h2> <h3> 5.1.1. Hemolytic assay</h3> <h3> 5.1.2. Hemagglutination assay</h3> <h2> 5.2. Acute toxicity test</h2> <h3> 5.2.1. The amounts of dead mice</h3> <h3> 5.2.2. Body weight of mice</h3> <h3> 5.2.3. Hematological assay</h3> <h3> 5.2.4. Blood biochemistry</h3> <h3> 5.2.5. H&E staining of main organs</h3> <h1>6. Pharmacokinetic evaluation of cSeLAN</h1> <h2> 6.0. Lab book pages</h2> <h2> 6.1 Pharmacokinetic evaluation of cSeLAN</h2> <h1>7. <em>In vivo</em> anti-tumor immune response</h1> <h2> 7.0. Lab book pages</h2> <h2> 7.1. Chemiluminescence images</h2> <h3> 7.1.1. Chemiluminescence images of isoluminol</h3> <h3> 7.1.2. Chemiluminescence images of luminol</h3> <h3> 7.1.3. Related quantifications upon various treatments</h3> <h2> 7.2. Immunofluorescence images</h2> <h2> 7.3. T cell proliferation</h2> <h2> 7.4. DC proliferation</h2> <h1>8. <em>In vivo</em> anti-tumor efficacy</h1> <h2> 8.0. Lab book pages</h2> <h2> 8.1. Tumor growth</h2> <h3> 8.1.1. Tumor volume</h3> <h3> 8.1.2. Tumor weight</h3> <h3> 8.1.3. Tumor images</h3> <h2> 8.2. Body weight</h2> <h2> 8.3. Lung tissues with metastatic nodules</h2> <h3> 8.3.1. Lung tissues images</h3> <h3> 8.3.2. Number of pulmonary metastatic nodules</h3> <h3> 8.3.3. H&E</h3> <h2> 8.4. H&E of tumor and main organs</h2> <h2> 8.5. Cytokine secretions</h2> <h2> 8.6. Kaplan−Meier survival curves</h2> <h1>9. <em>In vitro</em> NK cytotoxicity and activity</h1> <h2> 9.0. Lab book pages</h2> <h2> 9.1. NK cytotoxicity</h2> <h2> 9.2. NK activity</h2>
Flow cytometry data and image data -A dendritic cell vaccine for both vaccination and neoantigen-reactive T cell preparation for cancer immunotherapy in mice
Open the record for dataset details and reuse information.
Single-cell RNA-Seq and TCR-Seq analysis of PD-1+ CD8+ T-cells responding to anti-PD-1 and anti-PD-1/CTLA-4 immunotherapy in melanoma
<p><strong>This dataset details the scRNASeq and TCR-Seq analysis of sorted PD-1+ CD8+ T cells from patients with melanoma treated with checkpoint therapy (anti-PD-1 monotherapy and anti-PD-1 & anti-CTLA-4 combination therapy) at baseline and after the first cycle of therapy. A major publication using this dataset is accessible here: (reference) </strong></p> <p> </p> <p><strong>*experimental design</strong></p> <p> Single-cell RNA sequencing was performed using 10x Genomics with feature barcoding technology to multiplex cell samples from different patients undergoing mono or dual therapy so that they can be loaded on one well to reduce costs and minimize technical variability. Hashtag oligomers (oligos) were obtained as purified and already oligo-conjugated in TotalSeq-C format from BioLegend. Cells were thawed, counted and 20 million cells per patient and time point were used for staining. Cells were stained with barcoded antibodies together with a staining solution containing antibodies against CD3, CD4, CD8, PD-1/IgG4 and fixable viability dye (eBioscience) prior to FACS sorting. Barcoded antibody concentrations used were 0.5 µg per million cells, as recommended by the manufacturer (BioLegend) for flow cytometry applications. After staining, cells were washed twice in PBS containing 2% BSA and 0.01% Tween 20, followed by centrifugation (300 xg 5 min at 4 °C) and supernatant exchange. After the final wash, cells were resuspended in PBS and filtered through 40 µm cell strainers and proceeded for sorting. Sorted cells were counted and approximately 75,000 cells were processed through 10x Genomics single-cell V(D)J workflow according to the manufacturer’s instructions. Gene expression, hashing and TCR libraries were pooled to desired quantities to obtain the sequencing depths of 15,000 reads per cell for gene expression libraries and 5,000 reads per cell for hashing and TCR libraries. Libraries were sequenced on a NovaSeq 6000 flow cell in a 2X100 paired-end format.</p> <p> </p> <p><strong>*extract protocol</strong></p> <p> PBMCs were thawed, counted and 20 million cells per patient and time point were used for staining. Cells were stained with barcoded antibodies together with a staining solution containing antibodies against CD3, CD4, CD8, PD-1/IgG4 and fixable viability dye (eBioscience) prior to FACS sorting. Barcoded antibody concentrations used were 0.5 µg per million cells, as recommended by the manufacturer (BioLegend) for flow cytometry applications. After staining, cells were washed twice in PBS containing 2% BSA and 0.01% Tween 20, followed by centrifugation (300 xg 5 min at 4 °C) and supernatant exchange. After the final wash, cells were resuspended in PBS and filtered through 40 µm cell strainers and proceeded for sorting. Sorted cells were counted and approximately 75,000 cells were processed through 10x Genomics single-cell V(D)J workflow according to the manufacturer’s instructions.</p> <p> </p> <p><strong>*library construction protocol</strong></p> <p> Sorted cells were counted and approximately 75,000 cells were processed through 10x Genomics single-cell V(D)J workflow according to the manufacturer’s instructions. Gene expression, hashing and TCR libraries were pooled to desired quantities to obtain the sequencing depths of 15,000 reads per cell for gene expression libraries and 5,000 reads per cell for hashing and TCR libraries. Libraries were sequenced on a NovaSeq 6000 flow cell in a 2X100 paired-end format.</p> <p> </p> <p><strong>*library strategy</strong></p> <p> scRNA-seq and scTCR-seq</p> <p> </p> <p><strong>*data processing step</strong></p> <p> Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline.</p> <p> Further processing was done with Seurat (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis based on gene expression).</p> <p> </p> <p> <strong>*genome build/assembly</strong></p> <p> Alignment was performed using prebuilt Cell Ranger human reference GRCh38.</p> <p> </p> <p><strong>*processed data files format and content</strong></p> <p> RNA counts and HTO counts are in sparse matrix format and TCR clonotypes are in csv format.</p> <p>Datasets were merged and analyzed by Seurat and the analyzed objects are in rds format.</p> <p> </p> <table> <tbody> <tr> <td> <p><strong>file name</strong></p> </td> <td> <p><strong>file checksum</strong></p> </td> </tr> <tr> <td> <p>PD1CD8_160421_filtered_feature_bc_matrix.zip</p> </td> <td> <p>da2e006d2b39485fd8cf8701742c6d77</p> </td> </tr> <tr> <td> <p>PD1CD8_190421_filtered_feature_bc_matrix.zip</p> </td> <td> <p>e125fc5031899bba71e1171888d78205</p> </td> </tr> <tr> <td> <p>PD1CD8_160421_filtered_contig_annotations.csv</p> </td> <td> <p>927241805d507204fbe9ef7045d0ccf4</p> </td> </tr> <tr> <td> <p>PD1CD8_190421_filtered_contig_annotations.csv</p> </td> <td> <p>8ca544d27f06e66592b567d3ab86551e</p> </td> </tr> </tbody> </table> <p> </p> <table> <tbody> <tr> <td> <p><strong>*processed data file </strong></p> </td> <td> <p><strong>antibodies/tags</strong></p> </td> </tr> <tr> <td> <p>PD1CD8_160421_filtered_feature_bc_matrix.zip</p> </td> <td> <p>none</p> </td> </tr> <tr> <td> <p>PD1CD8_160421_filtered_feature_bc_matrix.zip</p> </td> <td> <p>TotalSeq™-C0251 anti-human Hashtag 1 Antibody - (HASH_1) - M1_base_monotherapy<br>TotalSeq™-C0252 anti-human Hashtag 2 Antibody - (HASH_2) - M1_post_monotherapy<br>TotalSeq™-C0253 anti-human Hashtag 3 Antibody - (HASH_3) - C1_base_combined_therapy<br>TotalSeq™-C0254 anti-human Hashtag 4 Antibody - (HASH_4) - C1_post_combined_therapy<br>TotalSeq™-C0255 anti-human Hashtag 5 Antibody - (HASH_5) - C2_base_combined_therapy<br>TotalSeq™-C0256 anti-human Hashtag 6 Antibody - (HASH_6) - C2_post_combined_therapy</p> </td> </tr> <tr> <td> <p>PD1CD8_160421_filtered_contig_annotations.csv</p> </td> <td> <p>none</p> </td> </tr> <tr> <td> <p>PD1CD8_190421_filtered_feature_bc_matrix.zip</p> </td> <td> <p>none</p> </td> </tr> <tr> <td> <p>PD1CD8_190421_filtered_feature_bc_matrix.zip</p> </td> <td> <p>TotalSeq™-C0251 anti-human Hashtag 1 Antibody - (HASH_1) - M2_base_monotherapy<br>TotalSeq™-C0252 anti-human Hashtag 2 Antibody - (HASH_2) - M2_post_monotherapy<br>TotalSeq™-C0253 anti-human Hashtag 3 Antibody - (HASH_3) - M3_base_monotherapy<br>TotalSeq™-C0254 anti-human Hashtag 4 Antibody - (HASH_4) - M3_post_monotherapy<br>TotalSeq™-C0255 anti-human Hashtag 5 Antibody - (HASH_5) - C3_base_combined_therapy<br>TotalSeq™-C0256 anti-human Hashtag 6 Antibody - (HASH_6) - C3_post_combined_therapy</p> </td> </tr> <tr> <td> <p>PD1CD8_190421_filtered_contig_annotations.csv</p> </td> <td> <p>none</p> </td> </tr> </tbody> </table> <p> </p>
Tackling hepatocellular carcinoma with individual or combinatorial immunotherapy approaches
<p>Hepatocellular carcinoma (HCC) is the third leading cause of death from cancer globally. Indeed, there is a single drug approved as first-line systemic therapy in advanced unresectable HCC, providing a very limited survival benefit. In earlier stages, 5-year survival rates after surgical and loco-regional therapies are extremely variable depending on the stage of disease.</p> <p>Nevertheless, HCC is considered an immunogenic tumor arising in chronically inflamed livers. </p> <p>In such a scenario, immunotherapy strategies for HCC, in particular combinations including cancer vaccines, may represent a key therapeutic tool to improve clinical outcome in HCC patients. However, a lot of improvement is needed given the disappointing results obtained so far.</p>
1454GCC: Anti-PD-1 (MK-3475) and IMiD (Pomalidomide) Combination Immunotherapy in Relapsed/Refractory Multiple Myeloma
ClinicalTrials.gov study NCT02289222. IPD Sharing: Not stated. Countries: 1. Publications: 1.
3F8/GM-CSF Immunotherapy Plus 13-Cis-Retinoic Acid for Primary Refractory Neuroblastoma in Bone Marrow
ClinicalTrials.gov study NCT01183897. IPD Sharing: Not stated. Countries: 1. Publications: 1.
T Cell Receptor Immunotherapy Targeting MAGE-A3 for Patients With Metastatic Cancer Who Are HLA-DP0401 Positive
ClinicalTrials.gov study NCT02111850. IPD Sharing: NO. Countries: 1. Publications: 3.
Vaccine Immunotherapy for Recurrent Medulloblastoma and Primitive Neuroectodermal Tumor
ClinicalTrials.gov study NCT01326104. IPD Sharing: NO. Countries: 1. Publications: 0.
T Cell Receptor Immunotherapy Targeting NY-ESO-1 for Patients With NY-ESO-1 Expressing Cancer
ClinicalTrials.gov study NCT01967823. IPD Sharing: NO. Countries: 1. Publications: 3.
CAR-pNK Cell Immunotherapy for Relapsed/Refractory CD33+ AML
ClinicalTrials.gov study NCT02944162. IPD Sharing: YES. Countries: 1. Publications: 1.
An Investigational Immunotherapy Study of Nivolumab With Standard of Care Therapy vs Standard of Care Therapy for First-Line Treatment of Colorectal Cancer That Has Spread
ClinicalTrials.gov study NCT03414983. IPD Sharing: Not stated. Countries: 5. Publications: 1.
The Peanut Oral Immunotherapy Study: Safety, Efficacy and Discovery
ClinicalTrials.gov study NCT02103270. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Retreatment Protocol for BL22 Immunotherapy in Relapsed or Refractory Hairy Cell Leukemia
ClinicalTrials.gov study NCT00924040. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Immunotherapy Administered Under the Tongue to Treat Dust Mite Allergy
ClinicalTrials.gov study NCT00200850. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Testing the Use of the Immunotherapy Drugs Ipilimumab and Nivolumab Plus Radiation Therapy Compared to the Usual Treatment (Temozolomide and Radiation Therapy) for Newly Diagnosed MGMT Unmethylated Gl
ClinicalTrials.gov study NCT04396860. IPD Sharing: YES. Countries: 1. Publications: 2.
QUILT-3.038: Active Immunotherapy CEA Vaccine in Patients With Malignancies Expressing CEA
ClinicalTrials.gov study NCT01147965. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
INCB106385 Alone or in Combination With Immunotherapy in Advanced Solid Tumors
ClinicalTrials.gov study NCT04580485. IPD Sharing: YES. Countries: 6. Publications: 0.
Milk Oral Immunotherapy in Children to Treat Food Allergy
ClinicalTrials.gov study NCT01162473. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Tolerance Following Peanut Oral Immunotherapy
ClinicalTrials.gov study NCT01750879. IPD Sharing: YES. Countries: 1. Publications: 1.
CAR T Cell Receptor Immunotherapy Targeting VEGFR2 for Patients With Metastatic Cancer
ClinicalTrials.gov study NCT01218867. IPD Sharing: NO. Countries: 1. Publications: 3.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.