Fig 2: Expression levels of miR-200c-3p, ERCC3 and ERCC4 in gastric cancer cell lines following lentiviral transduction. (A) Relative miR-200c-3p expression levels in SGC7901 cells and SGC7901/DDP cells, as measured by reverse transcription-quantitative polymerase chain reaction. The fold-change between SGC7901 cells and SGC7901/DDP cells was 1.788. (B) Western blot analysis detected higher ERCC3 and ERCC4 expression in SGC7901/DDP cells than in SGC7901 cells. (C and D) Semi-quantification of western blotting results shown in (B) via densitometry. *P<0.05. ERCC3, ERCC excision repair 3, TFIIH core complex helicase subunit; ERCC4, ERCC excision repair 4, endonuclease catalytic subunit; miR-200c-3p, microRNA-200c-3p.

Fig 3: TRABI-seq detects divergent transcription and provides evidence for XPF sequence preference.Strand-specific profile of the mean DNA break count and its 95% c.i. (shade) throughout the gene body and adjacent regions in U2OS WT (a), CSB-KO (b), XPC-KO (c) and XPA-KO (d) after 2h exposure to trabectedin and subsequent 2h recovery. n = 4425 protein-coding genes (top 30% expressed in unexposed U2OS WT) are considered to compute the means and c.i. Solid, dashed, and dotted curves: means of different biological replicates. Strand- and gene-length-specific profile of the mean DNA break count and its 95% c.i. (shade) in the ±5 kilobase (Kb) proximity of TSS in TC-NER proficient cell lines U2OS WT (e) and XPC-KO (f), zooming out (left panel) and in (right). The same gene set as in a–d. Methods provide gene numbers per gene-length group. DNA break count in two branches of divergent transcription in U2OS WT (g) and XPC-KO (h) versus gene expression. +5 Kb: within 5 Kb downstream of; −5 Kb: within 5 Kb upstream of. The plots are built analogously to Fig. 4a–d (lower panels). Supplementary Fig. 6g–h presents respective correlation analysis for all replicates. Gray band: endogenous DNA breaks not caused by trabectedin treatment (upper quartile of DNA break count in unexpressed genes); this threshold shows that around 25% (lower boundary of boxes) of highly expressed genes may not have trabectedin-induced breaks upstream of the TSS. Sequence logos around DNA breaks in U2OS WT (i) and XPC-KO (j). We considered DNA breaks located in the indicated regions of the gene set used in a–f. The percentage of G at position 1 (+2 relative to the break) is shown. Data: all biological replicates united per cell line. Supplementary Fig. 6i–j: analogous analysis for TC-NER-deficient cell lines. a–f: bin sizes are absolute (a base number) or relative (a percentage of gene length; the corresponding average base number indicated in parentheses). a–h: arb. unit: Methods describe DNA break count normalization. a–j TSS and TES: transcription start and end sites; Kb: kilobase; b: base. Source data are provided as a Source Data file.

Fig 4: Schematic illustration of the structure of the GOx/TPZ@Lipo-Pt HYDRI NMs and hypoxia-induced reversal of cisplatin resistance.Hypoxia-cascade DNA repair–inhibiting (HYDRI) NMs (also denoted as GOx/TPZ@Lipo-Pt NMs) were formulated from platinum(IV) prodrug as a building block with payloads of GOx and hypoxia-activatable chemodrug TPZ. The oxygen consumption upon the GOx-catalyzed oxidation of glucose was able to greatly amplify the intracellular hypoxia of drug-resistant cancer cells, which could boost the cytotoxicity and bioactivity of TPZ. The activated TPZ results in reinforced antitumor activity and spontaneously down-regulating the expression of XPF protein known for DNA repair, which thus realizes synergistic effects with platinum(IV) complex against the cisplatin-resistant tumors.

Fig 5: Portraits of FA-Q patient 3104 at different age, and characterization of her genetic and cellular defects. a: Typical FA puppet-like face, small head, light brown hair, absence of the right and severe hypoplasia of the left thumb (arrows) at about 15 months. b: High slanting eye lids and beginning freckling of the face at age 12 years. c: Low-set auricles, early hair graying and actinic keratosis-like skin changes with erythema, atrophy and patchy pigmentation in her fifth decade. d: A heterozygous substitution of adenine with guanine (asterisk) 2 bp upstream of exon 5 in the XPF/ ERCC4/FANCQ gene was maternally inherited. e: The mutation shown in (d) leads to aberrant splicing (upper panel). Gel extraction and sequence analysis of a major splice product reveals skipping of exon 5 (lower panel). f: The second heterozygous FANCQ mutation c.1765C > T (asterisk) is located in exon 8 and was paternally inherited. g: 3104 fibroblasts transduced with mock vector (green line) or with vector containing XPF/ ERCC4/FANCQ with the missense mutation c.1765C > T (red line) are MMC-sensitive, though not quite to the degree of fibroblasts from an FA-B patient serving as a control (black line). Complementation of 3104 fibroblasts with wildtype FANCQ (FANCQWT, blue line) restores MMC resistance. Error bars designate SDs of three experiments. LC50 levels are indicated by dotted lines of corresponding colors; they equal 42.6 ± 5.7 nM for 3104 + mock, 52.8 ± 2.7 nM for 3104 + FANCQMUT and 20.7 ± 2.4 nM for FA-B fibroblasts. The survival rates of 3104 + FANCQMUT and 3104 + mock are not significantly different, however the proportions for all concentrations (except 0) of these curves and 3104 + FANCQWT are different with p < 0.001. h: Immunoblot using fibroblast extracts from the FA-Q cell line 3104 and of the previously reported FA-Q cell line 1333 [9] with different FANCQ missense mutations showing immunoreactive residual FANCQ protein of normal size but reduced abundance in comparison to a normal (CON) and a FANCD2-deficient (FA-D2) control. One thousand three hundred thirty-three reveals an additional FANCQ band resulting from a truncating mutation on the second allele. Loading control: tubulin. i: Cell fractionation demonstrates residual mutant FANCQ protein in 3104 cells detectable in the chromatin fraction. j and k: Normal ERCC1-XPF interactions in 3104 transformed fibroblasts. ERCC1 (j) or XPF (k) were immunoprecipitated with antibodies against ERCC1 or XPF, respectively. Unspecific bands are marked by asterisks while the visible antibody heavy chain is indicated by an arrow