KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER | |
|---|---|---|---|
| Antibodies | |||
| MEL-A | Dako | M7196 | |
| PRAME | Abcam | Cat#Ab219650; RRID:AB_219650 | |
| CCR7 BV421 | BD Biosciences | Cat#150503 | |
| CD8 BV605 | BD Biosciences | Cat#564116; RRID:AB_2869551 | |
| CD25 BV786 | BD Biosciences | Cat#741035; RRID:AB_2740625 | |
| CD45RA PE | BD Biosciences | Cat#561883; RRID:AB_10895572 | |
| CD69 APC | BD Biosciences | Cat#555533; RRID: AB_398602 | |
| CD3 APCR700 | BD Biosciences | Cat#565119; RRID:AB_2744385 | |
| CXCR3 PerCP-Cy5.5 | BD Biosciences | Cat#560832; RRID:AB_2033945 | |
| IL17A FITC | Invitrogen | Cat#11-7179-42 | |
| IFNG PE-CF594 | BD Biosciences | Cat#562392; RRID:AB_11153859 | |
| TNFA APC-CY7 | BioLegend | Cat#502944; RRID:AB_2562870 | |
| HLADR BV605 | BD Biosciences | Cat#562845 | |
| TLR5 APCR700 | Bio-techne R&D Systems | Cat#FAB6704N; RRID:AB_3651878 | |
|
Biological Samples | |||
| Fecal and Blood Samples from Patients with Melanoma | Istituto Europeo di Oncologia; Istituto Nazionale Tumori IRCCS Fondazione G. Pascale | R845/18-IEO 889; 37/22 oss | |
|
Chemicals, Peptides, and Recombinant Proteins | |||
| Stool Sample Collection & Stabilization Kit | Canvax | Cat#SC0012 | |
| Bovine Serum Albumin | Seqens | Cas#1005-70 | |
| Goat Serum | Invitrogen | Cat#10000 C | |
| HRP-Secondary Antibody (Anti-Rabbit) | Agilent Dako | Cat#K4003; RRID:AB_2630375 | |
| Aminoethyl Carbazole (AEC) + High Sensitivity Substrate Chromogen | Agilent Dako | Cat#K3461 | |
| Hematoxylin | Sigma | Cat#MHS 16-500ML | |
| RPMI-1640 | Euroclone | Cat#ECM2001L | |
| DMEM | Euroclone | Cat#ECM0103L | |
| FBS | Euroclone | Cat#ECS0165L | |
| Hepes | Sigma | Cat#H0087 | |
| Sodium Pyruvate | Euroclone | Cat#ECM0742D | |
| Pen/Strep | Euroclone | Cat#ECB3001D | |
| Glutamine | Euroclone | Cat#LOBE17605E | |
| Normocin | InvivoGen | Cat#ant-nr | |
| Recombinant Human IL-2 | Novartis | Cat#CLB-P-476-800-13980 IT | |
| Anti-CD28/49d | BD Biosciences | Cat#347690; RRID:AB_647457 | |
| Golgi Plug | BD Biosciences | Cat#555029 | |
| Fixation/Permeabilization Solution Kit | BD Biosciences | Cat#554714 | |
| Cytofix/Cytoperm | BD Biosciences | Cat#554722 | |
| Fixable Viability Stain BV510 | BD Biosciences | Cat#564406 | |
| Purified Custom Peptides | GenScript (See Table S7) | NA | |
| UltraPure Flagellin from Salmonella typhimurium | InvivoGen | Cat#TLR-STFLA | |
|
Critical Commercial Assays | |||
| DNeasy PowerSoil Pro Kit | Qiagen | Cat#47016 | |
| MiSeq Reagent Kit V2 | Illumina | Cat#MS-102-2003 | |
| Nextera XT Index Kit V2 Set A | Illumina | Cat#FC-131-2001 | |
| Qubit dsDNA HS Assay Kit | Thermofisher | Cat#Q32851 | |
| Kapa HiFi HotStart ReadyMix | Fisher Scientific | Cat#50-196-5299 | |
| Human Magnetic Luminex Screening Assay | Bio-techne | Cat#LXSAHM-23 | |
|
Deposited Data | |||
| Raw 16S and/or Shotgun data | This paper; Baruch et al.9; Davar et al.10; Routy et al.5; Bjork et al.14 | PRJEB61942; PRJNA678737; PRJNA672867; PRJNA928744; PRJEB70966, PRJEB43119 | |
| Analyzed Shotgun data | Lee et al.8; Bjork et al.14 | https://bioconductor.org/packages/curatedMetagenomicData/ | |
| Source code/scripts to analyse the data | This paper; Biobakery63 |
https://github.com/ADGM/melanoma-longitudinal-paper
https://github.com/SegataLab/preprocessing |
|
| SILVA 128 database; SILVA 132 database | Quast et al.64 |
https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_128_release.tgz; https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_132_release.zip |
|
| CHOCOPhlAnSGB v202103 database | Blanco-Míguez et al.65 | =https://github.com/biobakery/humann?tab=readme-ov-file#download-the-chocophlan-database | |
| UniRef90 database | Suzek et al.66 | https://www.uniprot.org/ | |
| Pathway–KO mapping file | PICRUSt2 | https://github.com/picrust/picrust2/blob/master/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv | |
| KO–pathway mapping file | Beghini et al.63 | https://github.com/biobakery/humann/blob/master/humann/data/misc/map_kegg-pwy_name.txt.gz | |
|
Experimental models: Cell lines | |||
| HEK-Blue hTLR5 | Invivogen | Cat#hkb-htlr5; RRID:CVCL_IM83 | |
|
Oligonucleotides | |||
| 16S Amplicon PCR Forward Primer TCGTCGGCAGCGTCAGATGTGTATA AGAGACAGCCTACGGGNGGCWGCAG |
Illumina | NA | |
| 16S Amplicon PCR Reverse Primer GTCTCGTGGGCTCGGAGATGTGTA TAAGAGACAGGACTACHVGGGTATCTAATCC |
Illumina | NA | |
|
Software and algorithms | |||
| R version v4.1.1 (2021-08-10) | R Core Team67 | https://www.r-project.org | |
| RStudio v2022.07.2+576 | RStudio | https://posit.co | |
| Inkscape v1.2.2 | Inkscape Developers | https://inkscape.org/ | |
| BioRender | BioRender | https://www.biorender.com/ | |
| qiime2-2018.11; qiime2-2019.7 | Bolyen et al.68 | https://qiime2.org/ | |
| qiime2-2018.11 DADA2 plug-in | Callahan et al.69 | https://docs.qiime2.org/2018.11/plugins/available/dada2/index.html | |
| qiime2-2019.7 SEPP fragment insertion plug-in; qiime2-2019.7 naive Bayes feature classifier plug-in |
Janssen et al.70; Bokulich et al.71 | https://docs.qiime2.org/2019.7/plugins/available/fragment-insertion/sepp/; https://docs.qiime2.org/2019.7/plugins/available/feature-classifier/fit-classifier-naive-bayes/ | |
| Bowtie 2 | Langmead and Salzberg72 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml | |
| MetaPhlAn v4.0.3 | Blanco-Míguez et al.65 | https://github.com/biobakery/MetaPhlAn | |
| HUMAnN v3.6 | Beghini et al.63 | https://github.com/biobakery/humann | |
| NetMHCstabpan v4.1 | Rasmussen et al.73 | https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ | |
| Molsoft Mol Browser v3.8-7d | Molsoft | https://www.molsoft.com/icm_browser.html | |
| phyloseq v1.36.0 | McMurdie et al.74 | https://joey711.github.io/phyloseq/ | |
| vegan v2.6-8 | Oksanen et al.75 | https://github.com/vegandevs/vegan | |
| picante v1.8.2 | Kembel76 | https://github.com/skembel/picante | |
| rstatix v0.7.2 | Kassambara77 | https://github.com/kassambara/rstatix | |
| sva v3.40.0 | Johnson et al.78 | https://bioconductor.org/packages/release/bioc/html/sva.html | |
| usedist v0.4.0 | Bittinger79 | https://github.com/kylebittinger/usedist | |
| gtools v3.9.5 | Warnes et al.80 | https://cran.r-project.org/web/packages/gtools/index.html | |
| dplyr v1.1.4 | Wickham et al.81 | https://dplyr.tidyverse.org/ | |
| Maaslin2 v1.7.3 | Mallick et al.82 | https://github.com/biobakery/Maaslin2 | |
| clusterProfiler v4.0.5 | Wu et al.83 | https://guangchuangyu.github.io/software/clusterProfiler/ | |
| ggplot2 v3.5.1 | Wickham et al. 81 | https://ggplot2.tidyverse.org/ | |
| ComplexHeatmap v2.8.0 | Gu84 | https://github.com/jokergoo/ComplexHeatmap | |
| ggridges v0.5.6 | Aldahmani and Zoubeidi85 | https://wilkelab.org/ggridges/ | |
| ggpubr v0.6.0 | Kassambara86 | https://github.com/kassambara/ggpubr/releases | |
| gridExtra v2.3 | Auguie87 | https://CRAN.R-project.org/package=gridExtra | |