Data S1. Immunohistochemistry protocol

Automated IHC was performed using the Ventana Benchmark ULTRA (Ventana Medical Systems Inc.). Sequential sections of 4 µm thickness were prepared from the formalin fixed paraffin embedded tissues and stained for p16, p53, NFIB, and STAT1 using Optiview universal DAB detection Kit (#760‑700, Ventana). In brief, following de‑paraffinization and heat‑induced antigen retrieval with CC1 (#950‑500, Ventana) for 64 min, the tissue samples were incubated with the antibody of interest for 32 min at 37˚C. Incubation was followed by hematoxylin II counter stain for 8 min and then a blue coloring reagent for 8 min according to the manufactures instructions (Ventana). Positive controls were used on every slide; tonsil tissue was used for p16 and p53, normal cervical tissue was used for STAT1 and breast tissue was used for NFIB. Additional relevant information on the antibodies are presented in Table S1. Figure S1. Box‑plots depicting the distribution of STAT1 and NFIB expression for each tissue type. Horizontal lines in the boxes represent the medians and the whiskers represent the 5 and 95th percentiles. STAT1, signal transducer and activator of transcrip‑ tion 1; NFIB, nuclear factor IB; HPV, papilloma virus; VSCC, vulvar squamous cell carcinoma; dVIN, differentiated vulvar intraepithelial neoplasias; HSIL, high grade squamous intraepithelial lesions. Figure S2. Bar‑charts depicting the genomic alterations of nuclear factor IB detected in various cancers (derived from cBioPortal). Figure S3. Bar‑charts depicting the genomic alterations of signal transducer and activator of transcription 1 detected in various cancers (derived from cBioPortal). Table SI. Antibodies used for immunohistochemistry.

Antibody Type Dilution Company Clone p16 Anti-mouse 1.0 µg/ml Ventana Medical Systems, Inc. CintecR© p53 Anti-mouse 2.5 µg/ml Ventana Medical Systems, Inc. Bp53 -11 STAT1 Anti-Rabbit 1/750 Novus Biologcials, LLC SD20-75 NFIB Anti-Rabbit 1/800 Novus Biologicals, LLC Polyclonal

STAT1, signal transducer and activator of transcription 1; NFIB, nuclear factor IB. Table SII. Differentially expressed in human papilloma virus-related vulvar squamous cell carcinoma that were similarly regulated in both datasets.

No. Symbol Name Location Type(s) Canonical Pathways

1 MMP3 Matrix metallopeptidase 3 Extracellular Space Peptidase Agranulocyte Adhesion and Diapedesis; Bladder Cancer Signaling; Colorectal Cancer Metastasis Signaling 2 MMP12 Matrix metallopeptidase 12 Extracellular Space Peptidase Agranulocyte Adhesion and Diapedesis; Bladder Cancer Signaling; Colorectal Cancer Metastasis Signaling 3 CDKN2A Cyclin dependent kinase inhibitor 2A Nucleus Transcription regulator Aryl Hydrocarbon Receptor Signaling; Cell Cycle: G1/S Checkpoint Regulation; Wnt/β-catenin Signaling 4 IFI44L induced 44 like Nucleus Other NA 5 RBP1 Retinol binding protein 1 Extracellular Space Transporter Acute Phase Response Signaling 6 STAT1 Signal transducer and activator of Nucleus Translation regulator Activation of IRF by Cytosolic Pattern Recognition Receptors; transcription 1 CNTF Signaling; Dendritic Cell Maturation; EGF Signaling; ERK/MAPK Signaling; IL-12 Signaling and Production in Macrophages; IL-15 Production; IL-22 Signaling 7 MT2A Metallothionein 2A Cytoplasm Other Oncostatin M Signaling; SPINK1 General Cancer Pathway 8 EPSTI1 Epithelial stromal interaction 1 Other Other NA 9 IFIT3 Interferon induced protein with Cytoplasm Other Interferon Signaling tetratricopeptide repeats 3 10 CCL20 C-C motif chemokine ligand 20 Extracellular Space Cytokine Agranulocyte Adhesion and Diapedesis; Granulocyte Adhesion and Diapedesis; IL-17A Signaling in Airway Cells; IL-17A Signaling in Gastric Cells; Role of IL-17A in Arthritis; Role of IL-17A in Psoriasis; Th17 Activation Pathway 11 LAMP3 Lysosomal associated membrane Plasma Membrane Other NA protein 3 12 OAS2 2'-5'-oligoadenylate synthetase 2 Cytoplasm Enzyme Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses 13 XPR1 Xenotropic and polytropic retrovirus Plasma Membrane G-protein coupled NA receptor 1 receptor 14 PLOD2 Procollagen-lysine,2-oxoglutarate Cytoplasm Enzyme NA 5-dioxygenase 2 15 CKS1B CDC28 protein kinase regulatory Other Kinase Cell Cycle: G2/M DNA Damage Checkpoint Regulation subunit 1B 16 IGF2BP3 Insulin like growth factor 2 mRNA Cytoplasm Translation regulator NA binding protein 3 17 RPL39L Ribosomal protein L39 like Other Other EIF2 Signaling 18 IFI44 Interferon induced protein 44 Cytoplasm Other NA 19 SOD2 Superoxide dismutase 2 Cytoplasm Enzyme Acute Phase Response Signaling 20 XAF1 XIAP associated factor 1 Nucleus Other NA 21 HCP5 HLA complex P5 Other Other NA 22 IGF2BP2 Insulin like growth factor 2 mRNA Cytoplasm Translation regulator NA binding protein 2 Table SII. Continued.

No. Symbol Entrez Gene Name Location Type(s) Canonical Pathways

23 PARP9 Poly(ADP-ribose) polymerase family Nucleus Enzyme Death Receptor Signaling member 9 24 RSAD2 Radical S-adenosyl methionine domain Cytoplasm Enzyme Role of Lipids/Lipid Rafts in the Pathogenesis of Influenza containing 2 25 DCBLD2 Discoidin, CUB and LCCL domain Plasma Membrane Other NA containing 2 26 GBP1 Guanylate binding protein 1 Cytoplasm Enzyme NA 27 FNDC3B Fibronectin type III domain Cytoplasm Other NA containing 3B 28 DSE Dermatan sulfate epimerase Cytoplasm Enzyme Dermatan Sulfate Biosynthesis 29 PARP14 Poly(ADP-ribose) polymerase family Cytoplasm Enzyme Death Receptor Signaling; Retinoic acid Mediated Apoptosis member 14 Signaling; UVA-Induced MAPK Signaling 30 RUVBL1 RuvB like AAA ATPase 1 Nucleus Translation regulator NA 31 CCDC50 Coiled-coil domain containing 50 Cytoplasm Other NA 32 KLHL5 Kelch like family member 5 Extracellular Space Other NA 33 HSPE1 Heat shock protein family E (Hsp10) Cytoplasm Enzyme Aldosterone Signaling in Epithelial Cells member 1 34 TMEM44 Transmembrane protein 44 Other Other NA 35 FOXM1 Forkhead box M1 Nucleus Translation regulator NA 36 EIF2AK2 Eukaryotic translation initiation factor Cytoplasm Kinase EIF2 Signaling; NF-κB Activation by Viruses 2 alpha kinase 2 37 PTK2 Protein tyrosine kinase 2 Cytoplasm Kinase Actin Cytoskeleton Signaling; IL-15 Signaling; VEGF Signaling 38 ASAP1 ArfGAP with SH3 domain, Plasma Membrane Other FAK Signaling; Integrin Signaling ankyrin repeat and PH domain 1 39 H2AFZ H2A family member Z Nucleus Other NA 40 PSMB7 Proteasome subunit beta 7 Cytoplasm Peptidase Protein Ubiquitination Pathway 41 COMMD2 COMM domain containing 2 Other Other NA 42 MARCKS Myristoylated alanine rich protein Plasma Membrane Other Phagosome Formation kinase C substrate 43 PABPC1L Poly(A) binding protein cytoplasmic Cytoplasm Other NA 1 like 44 RAB32 RAB32, member RAS oncogene Cytoplasm Enzyme NA family 45 SHISA2 Shisa family member 2 Cytoplasm Other NA 46 PDCD10 Programmed cell death 10 Cytoplasm Other NA 47 PSMA4 Proteasome subunit alpha 4 Cytoplasm Peptidase Protein Ubiquitination Pathway 48 SNRPA1 Small nuclear ribonucleoprotein Nucleus Other Systemic Lupus Erythematosus Signaling polypeptide A' Table SII. Continued.

No. Symbol Entrez Gene Name Location Type(s) Canonical Pathways

49 C1orf112 1 open reading Other Other NA frame 112 50 RAB7A RAB7A, member RAS oncogene Cytoplasm Enzyme AMPK Signaling; IL-12 Signaling and Production in family Macrophages 51 SSB Sjogren syndrome antigen B Nucleus Enzyme NA 52 B2M Beta-2-microglobulin Plasma Membrane Translation regulator Antigen Presentation Pathway; Communication between Innate and Adaptive Immune Cells; Virus Entry via Endocytic Pathways 53 MED30 Mediator complex subunit 30 Nucleus Transcription regulator Estrogen Receptor Signaling 54 PARP1 Poly(ADP-ribose) polymerase 1 Nucleus Enzyme Sirtuin Signaling Pathway; Apoptosis Signaling; Death Receptor Signaling 55 PSMD11 Proteasome 26S subunit, non-ATPase Cytoplasm Other Protein Ubiquitination Pathway 11 56 HIST1H1D Histone cluster 1 H1 family member d Nucleus Other Granzyme A Signaling; Protein Kinase A Signaling; Sirtuin Signaling Pathway 57 ATP6V1C1 ATPase H+ transporting V1 subunit C1 Cytoplasm Transporter Iron homeostasis signaling pathway; Phagosome Maturation 58 RPA3 Replication protein A3 Nucleus Other Cell Cycle Control of Chromosomal Replication 59 PSMB4 Proteasome subunit beta 4 Cytoplasm Peptidase Protein Ubiquitination Pathway 60 LSM5 LSM5 homolog, U6 small nuclear Cytoplasm Other Systemic Lupus Erythematosus Signaling RNA and mRNA degradation associated 61 VAV2 Vav guanine nucleotide exchange Cytoplasm Transcription regulator Actin Cytoskeleton Signaling factor 2 62 NUP37 Nucleoporin 37 Nucleus transporter NA 63 SETMAR SET domain and mariner transposase Nucleus Enzyme NA fusion gene 64 RPL3 Ribosomal protein L3 Nucleus Other EIF2 Signaling 65 RETSAT Retinol saturase Cytoplasm Enzyme NA 66 RPL13A Ribosomal protein L13a Cytoplasm Other EIF2 Signaling 67 PURA Purine rich element binding protein A Nucleus Transcription regulator NA 68 DUOX1 Dual oxidase 1 Plasma Membrane Enzyme NA 69 BNIPL BCL2 interacting protein like Cytoplasm Other NA 70 EIF4B Eukaryotic translation initiation Cytoplasm Translation regulator mTOR Signaling factor 4B 71 CYB561D1 Cytochrome b561 family member D1 Other Other NA 72 LRP10 LDL receptor related protein 10 Plasma Membrane Transmembrane receptor NA 73 ACAD8 Acyl-CoA dehydrogenase family Cytoplasm Enzyme Isoleucine Degradation I; Valine Degradation I member 8 74 ZNF493 Zinc finger protein 493 Nucleus Transcription regulator NA Table SII. Continued.

No. Symbol Entrez Gene Name Location Type(s) Canonical Pathways

75 TSPO Translocator protein Cytoplasm Transmembrane receptor Sirtuin signaling pathway 76 SLC35C1 Solute carrier family 35 member C1 Cytoplasm Transporter NA 77 ACOX2 Acyl-CoA oxidase 2 Cytoplasm Enzyme LPS/IL-1 Mediated Inhibition of RXR Function 78 ARSF Arylsulfatase F Extracellular Space Enzyme NA 79 SUSD4 Sushi domain containing 4 Other Other NA 80 SNHG8 Small nucleolar RNA host gene 8 Other Other NA 81 CMSS1 Cms1 ribosomal small subunit Other Other NA homolog 82 HIPK2 Homeodomain interacting protein Nucleus Kinase Cell Cycle: G2/M DNA Damage Checkpoint Regulation; kinase 2 Molecular Mechanisms of Cancer; p53 Signaling 83 HMCES 5-hydroxymethylcytosine binding, ES Other Other NA cell specific 84 HSPB11 Heat shock protein family B (small) Extracellular Space Other Aldosterone Signaling in Epithelial Cells member 11 85 ISY1 ISY1 splicing factor homolog Nucleus Other NA 86 NDUFAF6 NADH:ubiquinone oxidoreductase Cytoplasm Other NA complex assembly factor 6 87 SKA3 Spindle and kinetochore associated Nucleus Other NA complex subunit 3 88 U2SURP U2 snRNP associated SURP domain Nucleus Other NA containing

No. 1-69 were upregulated in both datasets. No. 70-88 were downregulated in both datasets. NA, not applicable. Table SIII. Differentially expressed genes in human papilloma virus-independent vulvar squamous cell carcinoma that were similarly regulated in both datasets.

No. Symbol Entrez Gene Name Location Type(s) Canonical pathways

1 POSTN Periostin Extracellular Space Other NA 2 CELSR3 Cadherin EGF LAG seven-pass G-type receptor 3 Plasma Membrane G-protein coupled NA receptor 3 PRMT3 Protein arginine methyltransferase 3 Nucleus Enzyme Cysteine Biosynthesis III (mammalia); Methionine Degradation I (to Homocysteine); Superpathway of Methionine Degradation 4 CSTF3 Cleavage stimulation factor subunit 3 Nucleus Other Cleavage and Polyadenylation of Pre-mRNA; Tight Junction Signaling 5 SLC38A1 Solute carrier family 38 member 1 Plasma Membrane Transporter Glutamate Receptor Signaling 6 N4BP2L2 NEDD4 binding protein 2 like 2 Nucleus Transcription regulator NA 7 PGK1 1 Cytoplasm Kinase Gluconeogenesis I; Glycolysis I; Sirtuin Signaling Pathway 8 NCBP2 Nuclear cap binding protein subunit 2 Nucleus Other NA 9 KPNA2 Karyopherin subunit alpha 2 Nucleus Transporter RAN Signaling 10 BTBD3 BTB domain containing 3 Other Other NA 11 SLC25A15 Solute carrier family 25 member 15 Cytoplasm Transporter NA 12 MRPL19 Mitochondrial ribosomal protein L19 Cytoplasm Other NA 13 CAPRIN1 Cell cycle associated protein 1 Plasma Membrane Other NA 14 PAICS Phosphoribosylaminoimidazole carboxylase and Cytoplasm Enzyme Inosine-5'-phosphate Biosynthesis II; phosphoribosylaminoimidazolesuccinocarboxamide Purine Nucleotides De Novo Biosynthesis II synthase 15 KLHDC3 Kelch domain containing 3 Cytoplasm Other NA 16 USP4 Ubiquitin specific peptidase 4 Nucleus Peptidase Protein Ubiquitination Pathway 17 VAMP2 Vesicle associated membrane protein 2 Plasma Membrane Other Huntington's Disease Signaling; Insulin Receptor Signaling; Phagosome Maturation; Tight Junction Signaling 18 TFPI Tissue factor pathway inhibitor Extracellular Space Other Coagulation System; Extrinsic Prothrombin Activation Pathway 19 STX5 Syntaxin 5 Cytoplasm Transporter NA 20 SCARA3 Scavenger receptor class A member 3 Plasma Membrane Transmembrane Phagosome Formation receptor 21 JAZF1 JAZF zinc finger 1 Nucleus Transcription regulator NA 22 TACSTD2 Tumor associated calcium signal transducer 2 Plasma Membrane Other NA 23 PHYHD1 Phytanoyl-CoA dioxygenase domain containing 1 Other Other NA 24 FNDC1 Fibronectin type III domain containing 1 Plasma Membrane Other NA 25 ZNF423 Zinc finger protein 423 Nucleus Transcription regulator Adipogenesis pathway; BMP signaling pathway; TGF-β Signaling 26 COX7A1 subunit 7A1 Cytoplasm Enzyme Mitochondrial Dysfunction; Oxidative Phosphorylation Table SIII. Continued.

No. Symbol Entrez Gene Name Location Type(s) Canonical pathways

27 CPZ Carboxypeptidase Z Extracellular Space Peptidase SPINK1 Pancreatic Cancer Pathway 28 MASP1 Mannan binding lectin serine peptidase 1 Extracellular Space Peptidase Complement System; Neuroprotective Role of THOP1 in Alzheimer's Disease 29 IL11RA Interleukin 11 receptor subunit alpha Plasma Membrane Transmembrane Cardiac Hypertrophy Signaling (Enhanced); STAT3 receptor Pathway 30 ECM2 Extracellular matrix protein 2 Extracellular Space Other NA 31 ZBTB20 Zinc finger and BTB domain containing 20 Nucleus Transcription regulator NA 32 NFIB Nuclear factor I B Nucleus Transcription regulator Aryl Hydrocarbon Receptor Signaling 33 ATP8B2 ATPase phospholipid transporting 8B2 Plasma Membrane Transporter NA 34 DDAH2 Dimethylarginine dimethylaminohydrolase 2 Cytoplasm Enzyme NA 35 DLL1 Delta like canonical Notch ligand 1 Plasma Membrane Enzyme Epithelial Adherens Junction Signaling; Notch Signaling; Th1 and Th2 Activation Pathway 36 ADRB2 Adrenoceptor beta 2 Plasma Membrane G-protein coupled Glucocorticoid Receptor Signaling receptor 37 HEG1 Heart development protein with Plasma Membrane Other NA EGF like domains 1 38 TM4SF1 Transmembrane 4 L six family member 1 Plasma Membrane Other NA 39 DCN Decorin Extracellular Space Other Neuregulin Signaling; Osteoarthritis Pathway 40 CPQ Carboxypeptidase Q Extracellular Space Peptidase SPINK1 Pancreatic Cancer Pathway 41 EPHX3 Epoxide hydrolase 3 Other Enzyme NA 42 INTS13 Integrator complex subunit 13 Cytoplasm Other NA 43 MGP Matrix Gla protein Extracellular Space Other NA 44 PLPP1 Phospholipid phosphatase 1 Plasma Membrane Phosphatase Triacylglycerol Biosynthesis 45 SHTN1 Shootin 1 Plasma Membrane Other NA 46 SUN2 Sad1 and UNC84 domain containing 2 Nucleus Other NA

No. 1-16 were upregulated in both datasets. No. 17-46 were downregulated in both datasets. NA, not applicable.