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ClaverolMass SpectrometryBottom-up proteomicsCsccDhodhCutaneous squamous cell carcinomaCancer therapyDifferentiationPyrimidine biosynthesishttps://www.ebi.ac.uk/pride/archive/projects/PXD070860Vehicle- and leflunomide-treated A431 xenografts, as well as xenografts derived from shCtrl- and shDHODH-transduced A431 cells (hr240913), were subjected to proteomic analysis. Similarly, xenografts from vehicle-, leflunomide-, and PTC299-treated mice, along with xenografts derived from shPLKO- and shDHODH-transduced SCC13 cells (hr250519_A1), were analyzed. A total of six xenografts per condition were sent for analysis. Protein samples were solubilized in Laemmli buffer and separated by SDS–PAGE. After colloidal blue staining, each lane was excised and further cut into approximately 1 × 1 mm gel pieces. The gel pieces were destained in 25 mM ammonium bicarbonate containing 50% acetonitrile (ACN), rinsed twice with ultrapure water, and dehydrated in ACN for 10 min. After removal of ACN, the gel pieces were air-dried at room temperature, covered with sequencing-grade trypsin solution (10 ng/µL in 50 mM ammonium bicarbonate), rehydrated at 4 °C for 10 min, and incubated overnight at 37 °C. Peptides were first extracted by incubating the gel pieces for 15 min in 50 mM ammonium bicarbonate with gentle shaking. The supernatant was collected, and extraction was repeated twice with a H₂O/ACN/formic acid (47.5:47.5:5, v/v/v) solution for 15 min each. The combined extracts were pooled and dried in a vacuum centrifuge. The resulting peptide digests were resuspended in 0.1% formic acid prior to LC–MS/MS analysis. Peptide mixtures were analyzed using an Ultimate 3000 nanoLC system (Dionex, Amsterdam, The Netherlands) coupled to an Orbitrap Fusion™ Lumos™ Tribrid™ Mass Spectrometer (Thermo Fisher Scientific, San Jose, CA). Ten microliters of each peptide digest were loaded onto a C18 PepMap™ trap column (300 µm × 5 mm, LC Packings) at a flow rate of 10 µL/min. Peptides were separated on a C18 PepMap™ analytical column (75 µm × 50 cm, LC Packings) using a linear gradient of 4–25% solvent B over 87 min, followed by an increase from 25% to 40% solvent B in 30 min (solvent A: 0.1% formic acid in water; solvent B: 0.1% formic acid in 80% ACN). The flow rate was set to 200 nL/min. The mass spectrometer was operated in positive ion mode with a spray voltage of 2 kV. Data were acquired in data-independent acquisition (DIA) mode using Xcalibur 4.4 software. Each cycle consisted of a full MS scan (resolution 60,000; AGC target 4 × 10^5; maximum injection time 50 ms; scan range 350–1400 m/z) followed by 34 DIA MS/MS scans (resolution 30,000; AGC target 5 × 10^5; maximum injection time 54 ms) with variable-width isolation windows covering 380–980 m/z. Higher-energy collisional dissociation (HCD) was performed with a collision energy of 25%.prideDIA data were analyzed with Chimerys in Proteome Discoverer 3.1 (Thermo Fisher Scientific) against the Homo sapiens protein database (2021-03 release, 20,324 entries). Spectra corresponding to peptides <350 Da or >5000 Da were excluded. The maximum precursor mass tolerance was set at 10 ppm. Up to two missed cleavages were allowed. Carbamidomethylation of cysteines (+57 Da) was set as a fixed modification, while oxidation of methionine (+16 Da) was considered as a variable modification. Only peptides with high confidence (corresponding to a 1% false discovery rate at the peptide level) were retained. Quantification was performed using the Fragment Ion Quantifier node, and normalization was based on the total human peptide abundance. Protein ratios were calculated as the median of all pairwise peptide ratios. Statistical analysis was performed using a t-test with Benjamini–Hochberg correction. Only proteins quantified with at least two peptides and with an adjusted p-value < 0.05 were considered significant.ProteomicsStephane ClaverolPARTIALUniv. Bordeaux, Bordeaux Proteome, Bordeaux, FranceHomo Sapiens (human)42049699 Khalife F, Muzotte E, Naji F, Mahfouf W, Izotte J, Pinson B, Claverol S, Amoedo N, Fayyad-Kazan H, Dousset L, Rossignol R, Rezvani HR. DHODH inhibition suppresses cutaneous squamous cell carcinoma growth by the induction of differentiation through perturbation of the cellular redox balance. Cell Death Dis. 2026 17(1):566 10.1038/s41419-026-08815-wstephane.claverol@u-bordeaux.frBordeaux ProteomeFranceDihydroorotate dehydrogenase (DHODH), a key enzyme in de novo pyrimidine biosynthesis, has recently emerged as a therapeutic target in various cancers. We have previously identified a pivotal role of DHODH in the initiation of cutaneous squamous cell carcinoma (cSCC), the second most common type of non-melanoma skin cancer. We also showed that pharmacological inhibition of this enzyme suppresses ultraviolet (UV)-induced tumor formation. However, the key mechanisms driving the anticancer activity of DHODH inhibition remain unexplored in cSCC. We investigated the biological consequences of pharmacological and genetic DHODH inhibition in cSCC using xenograft models derived from two human cell lines, A431 and SCC13, implanted in immunodeficient NSG mice. DHODH activity was suppressed pharmacologically with leflunomide (LFN) and the potent DHODH inhibitor PTC299, or genetically via lentiviral shRNA-mediated DHODH silencing (shDHODH). Proteomic and metabolomic analyses were integrated with histopathological, immunohistochemical, and immunoblotting evaluations to delineate the downstream effects of DHODH blockade. Comprehensive proteomic and metabolomic profiling revealed that DHODH inhibition induces a coordinated adaptive program involving keratinization, differentiation, redox homeostasis, and metabolic stress responses. Histological and immunostaining analyses demonstrated marked reductions in Ki67-positive proliferating cells and a corresponding increase in pan-cytokeratin (PanCK) and keratin 10 (Krt10) expression, indicative of enhanced epithelial differentiation. These changes were most pronounced in PTC299-treated and shDHODH xenografts, whereas LFN displayed minimal or no efficacy in SCC13 tumors. DHODH inhibition drives tumor differentiation and suppresses proliferation in cSCC, highlighting metabolic dependency as a potential therapeutic vulnerability. PTC299 exhibited superior antitumor activity and differentiation-inducing capacity compared with LFN. These findings position DHODH as a promising target for bioenergetic vulnerability-based cancer therapy in advanced or treatment-resistant cSCC.DHODH inhibition suppresses cutaneous squamous cell carcinoma growth by the induction of differentiation through perturbation of the cellular redox balance.Khalife Ferial F, Muzotte Elodie E, Naji Fatima F, Mahfouf Walid W, Izotte Julien J, Pinson Benoît B, Claverol Stéphane S, Amoedo Nivea N, Fayyad-Kazan Hussein H, Dousset Lea L, Rossignol Rodrigue R, Rezvani Hamid-Reza HRfalseDHODH inhibition suppresses cutaneous squamous cell carcinoma growth by the induction of differentiation through perturbation of the cellular redox balanceDihydroorotate dehydrogenase (DHODH), a key enzyme in de novo pyrimidine biosynthesis, has recently emerged as a therapeutic target in various cancers. We have previously identified a pivotal role of DHODH in initiation of cutaneous squamous cell carcinoma (cSCC), the second most common type of non-melanoma skin cancer. However, the key mechanisms driving the anticancer activity of DHODH inhibition remain unexplored in cSCC. To evaluate the impact of DHODH inhibition on cSCC growth, we employed three complementary approaches: (1) pharmacological inhibition of DHODH in mice bearing xenografts of A431 and SCC13 cells through oral administration of leflunomid (LFN) or PTC299 (PTC), and (2) genetic silencing of DHODH via transduction of cells with a lentiviral vector expressing shRNA targeting DHODH (shDHODH) prior to transplantation into NSG mice. After transplantation of A431 or SCC13 cells and once tumors reached an average volume of 150 to 200 mm3, mice were divided into two groups that receiving either vehicle alone or LFN administrated orally on a daily basis. The same procedure was applied for treatment with PTC299. To further investigate, DHODH expression was downregulated in A431 and SCC13 cells using shDHODH. Cells transduced with shCtrol used as control. Six days after transduction, the cells were subcutaneously engrafted into NSG mice. To investigate the molecular consequences of DHODH inhibition across distinct cSCC models, label-free quantitative proteomic analyses were performed on A431 and SCC13 xenografts treated with LFN or PTC299, as well as on tumors transduced with shDHODH (6 xenografts per group).2026-06-152025-11-18PXD070860NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:475174NEWT:111205NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:641809NEWT:38815NEWT:317447NEWT:4688NEWT:111225NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:270643NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:1185650NEWT:216778NEWT:294607NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:317047NEWT:460523NEWT:235443NEWT:1757312NEWT:85694NEWT:108458NEWT:5936NEWT:320637NEWT:1078283NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:470NEWT:5911NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:166313NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:906914NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:8655NEWT:5147NEWT:28108NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:298176NEWT:40674NEWT:1194669NEWT:51329NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:99488NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:29829NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:300273NEWT:4232NEWT:416348NEWT:11298NEWT:4236NEWT:7742NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:563041NEWT:72664NEWT:36599NEWT:41949NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:29835NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:35231NEWT:8644NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:192222NEWT:9963NEWT:1617910NEWT:637379NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:186801NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NEWT:194439NCBITaxon:12637NEWT:38727NEWT:218496NEWT:8618NEWT:70448NEWT:300251NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:2627626NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:54195NEWT:10136NEWT:38942NEWT:4762NEWT:6941NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:869728NEWT:6938NCBITaxon:39054NEWT:1736309NEWT:4751NEWT:194963NEWT:15819NEWT:109461NEWT:1085956NEWT:692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