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Sensory Guillain-Barré syndrome (GBS) is a rare heterogeneous subgroup of GBS characterized by the primary involvement of sensory neurons resulting in a distinctive clinical presentation. Sensory GBS usually occurs with acute and monophasic sensory symptoms, and no or minimal muscle weakness. Sensory GBS patient show hypo- or areflexia, distal paresthesia, and normal cerebrospinal fluid finding or albumino-cytologic dissociation which are suggesting that these conditions are a GBS variant. Autonomic dysfunctions have rarely been reported in sensory GBS patient presenting with postural hypotension, abnormal heart rate response to respiration. In this case, we demonstrate a patient with autonomic symptoms dominant sensory GBS in systemic lupus erythematosus.

Background/Aims: Histamine-2 receptor antagonists (H2RA) are used to treat acid-related disorders and functional dyspepsia. In contrast to other H2RAs, nizatidine promotes gastric emptying (GE). We investigated the effects of nizatidine and famotidine on intragastric pH and the GE rate in rats exposed to stress.Materials and Methods: We used 8-week-old male Wistar rats. Based on administration of water or drugs after an overnight fast, the animals were categorized into the nonstress-water, stress-water, stress-nizatidine, stress-famotidine, and stress-nizatidine with mosapride groups. The rats had access to pre-weighed food for 10 minutes, and those in the stress groups were exposed to 1 hour of restraint stress. Intragastric pH was measured under isoflurane anesthesia, and the GE rate was measured after the rats were sacrificed.Results: The GE rate was significantly lower in the stress-water and stress-famotidine groups than in the nonstress-water group. However, GE in the stress-nizatidine and stress-nizatidine with mosapride group did not significantly differ from that in the nonstress- water group. The GE rate was significantly higher in the stress-nizatidine with mosapride than in the stress-famotidine group. Intragastric pH was significantly higher in the stress-nizatidine and stress-famotidine groups than in the stress-water group. Nonetheless, there was no significant difference in pH between the stress-nizatidine and stress-famotidine groups. The intragastric pH was slightly but significantly higher in the stress-nizatidine with mosapride group than in the stress-nizatidine and stress-famotidine groups.Conclusions: In contrast to famotidine, nizatidine prevents stress-induced GE delay, which suggests that nizatidine is superior to other H2RAs for treatment of functional dyspepsia associated with delayed GE.

Smoking is a risk factor for gastric cancer (GC) and causes oxidative stress. Antioxidant vitamins may protect against oxidative stress. This study aimed to determine the association between dietary antioxidant vitamin intake and GC risk according to smoking status and the histological subtype. This case-control study included 286 pairs of patients with GC and controls aged 20-79 years enrolled at two hospitals from 2002 to 2006, matched by age (± 2 years), sex, hospital, and participation period (± 1 years). Dietary information was collected using a quantitative food frequency questionnaire (FFQ). When stratified by smoking status, increased intake of vitamin C (OR = 0.38; 95% CI = 0.17-0.84 for highest vs. lowest

Diet is a critical risk factor for gastric cancer, and Koreans consume significantly high amounts of carbohydrates. This study examined the association between carbohydrate intake, glycemic index, and glycemic load and the risk of gastric cancer and whether the association varied based on the general risk factors for gastric cancer. We hypothesized that carbohydrate intake, glycemic index, and glycemic load elevated gastric cancer risk and the relationship differed by the gastric cancer risk factors. This was a case-control study with a total of 307 matched pairs aged 20 to 79 years. Data collection was completed at two hospitals from December 2002 to September 2006. A food frequency questionnaire was applied for dietary assessment. Carbohydrate intake was not related to gastric cancer risk. However, a high glycemic index (odds ratio [OR], 1.88; 95% confidence interval (95% CI), 1.18-2.97) and glycemic load (OR, 2.51; 95% CI, 1.53-4.12) were significantly associated with the elevated risk of gastric cancer. When the relationship between glycemic load and gastric cancer risk was stratified by risk factors for gastric cancer, the gastric cancer risk especially increased among men, ≥65 years, smokers, drinkers, and people with Helicobacter pylori infection. Although there was no association between carbohydrate consumption and gastric cancer, high glycemic index and glycemic load were associated with the increased gastric cancer risk.

Acquired resistance to inhibitors of anaplastic lymphoma kinase (ALK) is a major clinical challenge for ALK fusion-positive non-small-cell lung cancer (NSCLC). In the absence of secondary ALK mutations, epigenetic reprogramming is one of the main mechanisms of drug resistance, as it leads to phenotype switching that occurs during the epithelial-to-mesenchymal transition (EMT). Although drug-induced epigenetic reprogramming is believed to alter the sensitivity of cancer cells to anticancer treatments, there is still much to learn about overcoming drug resistance. In this study, we used an in vitro model of ceritinib-resistant NSCLC and employed genome-wide DNA methylation analysis in combination with single-cell (sc) RNA-seq to identify cytidine deaminase (CDA), a pyrimidine salvage pathway enzyme, as a candidate drug target. CDA was hypomethylated and upregulated in ceritinib-resistant cells. CDA-overexpressing cells were rarely but definitively detected in the naïve cell population by scRNA-seq, and their abundance was increased in the acquired-resistance population. Knockdown of CDA had antiproliferative effects on resistant cells and reversed the EMT phenotype. Treatment with epigenome-related nucleosides such as 5-formyl-2′-deoxycytidine selectively ablated CDA-overexpressing resistant cells via accumulation of DNA damage. Collectively, our data suggest that targeting CDA metabolism using epigenome-related nucleosides represents a potential new therapeutic strategy for overcoming ALK inhibitor resistance in NSCLC.

Background Colorectal cancer (CRC) is the third most common type of diagnosed cancer in the world and has the second-highest mortality rate. Meanwhile, South Korea has the second-highest incidence rate for CRC in the world. Objective To assess the possible influence of ethnicity on the molecular profile of colorectal cancer, we compared genomic and transcriptomic features of South Korean CRCs with European CRCs. Methods We assembled a genomic and transcriptomic dataset of South Korean CRC patients (KOCRC; n = 126) from previous studies and European cases (EUCRC; n = 245) selected from The Cancer Genome Atlas (TCGA). Then, we compared the two datasets in terms of clinical data, driver genes, mutational signature, gene sets, consensus molecular subtype, and fusion genes. Results These two cohorts showed similar profiles in driver mutations but differences in the mutation frequencies of some driver genes (including APC, TP53, PABPC1, FAT4, MUC7, HSPG2, GNAS, DENND5B, and BRAF). Analysis of hallmark pathways using genomic data sets revealed further differences between these populations in the WNT, TP53, and NOTCH signaling pathways. In consensus molecular subtype (CMS) analyses of the study cases, no BRAF mutations were found in the CMS1 subtype of KOCRC, which contrasts with previous findings. Fusion gene analysis identified oncogenic fusion of PTPRK-RSPO3 in a subset of KOCRC patients without APC mutations. Conclusions This study presents insights into the genomic landscape of KOCRCs and reveals some similarities and differences with EUCRCs at the molecular level.

Gastrointestinal (GI) prokinetic agents are drugs that increase GI motility and promote the movement of contents in the GI tract by amplifying and controlling the contraction of GI smooth muscle. Currently used prokinetics increase GI motility by acting as a dopamine D2 receptor antagonist (e.g., metoclopramide, domperidone, levosulpiride) and 5-HT4 receptor agonist (e.g., mosapride, prucalopride). Some prokinetics also have a cholinesterase inhibitory property (e.g., itopride), and herb-derived prokinetics (e.g., motilitone) affect multiple receptors. Depending on the type and distribution of receptors on which the prokinetics bind, the effect(s) may be regional or throughout the GI tract. Most prokinetics have been used for functional dyspepsia and gastroparesis because they mainly affect upper GI motility. However, prucalopride, a highly selective 5-HT4 receptor agonist, is used primarily to treat chronic constipation and pseudo-obstruction. Dopamine D2 receptor antagonists also inhibit the D2 receptor in the medulla oblongata chemoreceptor trigger zone; therefore, they can treat nausea and vomiting. However, short term use of dopamine D2 antagonists at an appropriate dose is recommended because of their potential for central nervous system side effects by penetrating the blood-brain barrier. It is necessary to know the mechanism of action, each clinical trial’s characteristics, and the side effects of prokinetics to obtain the best clinical outcomes. This article aims to summarize the results of clinical studies related to the impact of currently available prokinetic agents in Korea on GI motility.

Objectives Gastric cancer (GC) is the fourth most common cancer worldwide, with the highest incidence and mortality regardless of sex. Despite technological advances in diagnosing and treating gastric cancer, GC still has high incidence and mortality rates. Therefore, continuous research is needed to overcome GC. In various studies, cell lines are used to find and verify the cause of specific diseases. Large-scale genomic studies such as ENCODE and Roadmap epigenomic projects provide multiomics data from various organisms and samples. However, few multi-omics data for gastric tissues and cell lines have been generated. Therefore, we performed RNA-seq, Exome-seq, and ChIP-seq with several gastric cell lines to generate a multi-omics data set in gastric cancer. Data description Multiomic data, such as RNA-seq, Exome-seq, and ChIP-seq, were produced in gastric cancer and normal cell lines. RNA-seq data were generated from nine GC and one normal gastric cell line, mapped to a human reference genome (hg38) using the STAR alignment tool, and quantified with HTseq. Exome sequence data were produced in nine GC and two normal gastric lines. Sequenced reads were mapped and processed using BWA-MEM and GATK, variants were called by stralka2, and annotation was performed using ANNOVAR. Finally, for the ChIP-seq, nine GC cell lines and four GC cell lines were used in two experimental sets; chip-seq was performed to confirm changes in H3K4me3 and H3K27me3. Data was mapped to human reference hg38 with BWA-MEM, and peak calling and annotation were performed using the Homer tool. Since these data provide multi-omics data for GC cell lines, it will be useful for researchers who use the GC cell lines to study.

Regulatory T cells (Treg) are targeted for cancer immunotherapy because they suppress antitumor immunity. Although the importance of neuropilin-1 (NRP1) in the stability and function of intratumoral Tregs is well-documented, targeting of NRP1+ Tregs for anticancer immunotherapy has not been well explored. Here, we found that an NRP1 antagonist [Fc(AAG)-TPP11], generated by fusion of the NRP1-specific binding peptide TPP11 with the C-terminus of an effector function–deficient immunoglobulin Fc(AAG) variant, inhibits intratumoral NRP1+ Treg function and stability. Fc(AAG)-TPP11 triggered the internalization of NRP1, reducing its surface expression on Tregs and thereby inhibiting the suppressive function of Tregs. In two murine syngeneic tumor models, Fc(AAG)-TPP11 retarded tumor growth, comparable with a Treg-depleting anti–CTLA-4 antibody, without noticeable toxicity. Fc(AAG)-TPP11 inhibited NRP1-dependent Treg function, inducing unstable intratumoral Tregs, with reduced expression of Foxp3 and enhanced production of IFNγ, which subsequently increased the functionality and frequency of intratumoral CD8+ T cells. We also observed selective expression of NRP1 on Tregs isolated from human tumors, but not from the blood of healthy donors and patients with cancer, as well as ex vivo inhibition of intratumoral NRP1+ Treg function by Fc(AAG)-TPP11. Our results suggest that the NRP1 antagonist Fc(AAG)-TPP11 has therapeutic potential for the inhibition of intratumoral NRP1+ Tregs with limited unfavorable effects on peripheral Tregs.

Supplementary Figures 1-7

The limited localization and penetration of monoclonal antibodies (mAb) into solid tumors restricts their antitumor efficacy. Here, we describe a solid tumor–targeting antibody with enhanced tumor penetration activity. We designed a 22-residue peptide (A22p), which was extracted from the C-terminal basic region of semaphorin 3A (Sema3A) but modified to have higher affinity with neuropilin receptors (NRP), and genetically fused it to the C-terminus of Fc of human immunoglobulin G1 via a 15-residue (G4S)3 linker, generating Fc-A22p, for the bivalent binding to NRPs. In contrast to Fc or the monovalent A22p peptide alone, Fc-A22p homed to tumor vessels and induced vascular permeability through VE-cadherin downregulation and penetrated tumor tissues by interacting with NRPs in mice bearing human tumor xenografts. We extended the Fc-A22p platform by generating mAb-A22p antibodies of two clinically approved solid tumor–targeting mAbs, the anti-EGF receptor mAb cetuximab (erbitux), and the anti-Her2 mAb trastuzumab (herceptin). The mAb-A22p antibodies retained the intrinsic antigen binding, natural Fc-like biophysical properties, and productivity in mammalian cell cultures, comparable with those of the parent mAbs. In mouse xenograft tumor models, the mAb-A22p antibodies more efficiently homed to tumor vessels and spread into the extravascular tumor parenchyma, which significantly enhanced antitumor efficacy compared with the parent mAbs. Our results suggest that mAb-A22p is a superior format for solid tumor–targeting antibodies due to its enhanced tumor tissue penetration and greater antitumor efficacy compared with conventional mAbs. Mol Cancer Ther; 13(3); 651–61. ©2014 AACR.

PDF - 2613K, Figure S1: Structural analysis of NRP1, NRP2, and Sema3A, and their interactions to facilitate the understanding of the interactions between Sema3A and NRP1/2. Figure S2: SDS-PAGE analyses of the purified proteins showing that NRP1/2-b1b2 domains, Fc-A22, and Fc-A22p are well prepared. Figure S3: FACS and confocal fluorescence data showing that Fc-A22p, but not Fc, specifically interacts with cell-surface expressed NRP1/2 undergoing cellular internalization. Figure S4: Cell viability data showing that Fc-A22p does not cause significant cytotoxicity on HUVECs and tumor cells. Figure S5: Tumor tissue analyzing data showing that Fc-A22p homes to tumor, induces vascular permeability, and downregulates VE-cadherin in endothelial cells and E-cadherin in tumor cells. Figure S6: Confocal fluorescence data showing that Fc-A22p causes downregulation of VE-/E-cadherin and their dissociation from F-actin cytoskeleton resulting in disruption of cell-cell contacts. Figure S7: Data showing the expression and biochemical characterization of mAb-A22p antibodies, cetuximab-A22p and trastuzumab-A22p, compared with the parent mAbs. Figure S8: Cell proliferation and Western blotting data showing that cetuximab-A22p exerts in vitro biological activities comparable to those of cetuximab in A431 and FaDu tumor cells. Figure S9: Human tumor xenografted mouse data showing that mAb-A22p antibodies show increased tumor homing and penetration and thus superior in vivo anti-tumor efficacy, compared with the parent mAbs. Table S1: SPR data showing the kinetic binding parameters for the interactions of Fc-A22, Fc-A22p, VEGF165, and Sema3A with soluble NRP1-b1b2 and NRP2-b1b2 fragments. Table S2: Purification yields of Fc proteins and antibodies obtained from transient expression in HEK293F cells. Table S3: SPR data showing the kinetic binding parameters for the interactions of mAbs and mAb-A22p antibodies with the indicated proteins. Supplementary Materials and Methods: Detailed description of Reagents; Recombinant protein expression and purification; Construction, expression, and purification of antibodies; Binding analysis by ELISA; Surface plasmon resonance (SPR); Flow cytometric analysis; Cell proliferation assay; Western blotting and immunoprecipitation; Co-localization studies by confocal immunofluorescence microscopy; RNA Interference; Ex vivo tumor penetration assays.

PDF file - 596K, Figure S1: Sequence alignment of CH3 domain of human IgG isotypes to compare the mutation sites introduced for heterodimeric Fc variants between our study and other approaches. Figure S2 : The vector maps of the scFv-Fc/Fc expression system and western blotting analysis of the purified scFv-Fc/Fc proteins carrying the indicated CH3 variant pair. Figure S3 : SPR data showing the kinetic interactions of msMet, tanibirumab, and bsVeMet antibodies with the antigens, Met and VEGFR-2. Figure S4: FACS data showing binding profiles of the msMet, tanibirumab and bsVeMet antibodies to HUVECs and MKN45 cells and effects of the antibodies on the cellular proliferation and signaling of the endothelial HUVECs stimulated by single ligand HGF or VEGF alone. Figure S5: Effects of the msMet, tanibirumab and bsVeMet antibodies on the tube formation of HUVECs stimulated by treatments of HGF and/or VEGF. Table S1: The list of CH3 variant pairs constructed in this study. Table S2: Purification yields of Fc-WT, Fc-EW-RVT, and Fc-KiH proteins obtained from transient expression in HEK293F cells. Table S3: The binding parameters of Fc-WT, Fc-EW-RVT, and Fc-KiH proteins with FcRn and FcγR proteins, determined by SPR analyses. Table S4: The binding parameters of the msMet, tanibirumab and bsVeMet antibodies with the antigens, Met or VEGFR-2, determined by SPR analyses. Supplementary Materials and Methods : Detailed description of Reagents; design and evaluation of heterodimeric Fc; construction, expression, and purification of antibodies; SEC analysis; far-UV CD spectroscopy; DSC experiments; SPR analysis; sandwich ELISA; flow cytometry; cell proliferation assay; western blotting; animal experiments; immunofluorescence of tumor tissues.

Heterodimeric Fc designed by engineering the CH3 homodimeric interface of immunoglobulin G1 serves as an attractive scaffold for the generation of bispecific antibodies (bsAb) due to the favorable properties of the Fc region. In this study, we describe a heterodimeric Fc generated by substituting the conserved electrostatic interactions at the CH3 core interface with asymmetric hydrophobic interactions and introducing asymmetric, long-range electrostatic interactions at the rim of the CH3 interface. Coexpression of Fc proteins carrying the combined CH3 variant pairs in HEK293F cells produced the heterodimer, which was purified with more than 90% yield, and retained wild-type Fc biophysical properties. The heterodimeric Fc was exploited to generate a bsAb simultaneously targeting both the Met receptor tyrosine kinase and the VEGF receptor 2 (VEGFR-2), with two respective antigen-specific, single-chain variable fragments (scFv) into the N-terminus. The Met × VEGFR-2 bsAb bound concurrently to the two target antigens, efficiently inhibited the downstream signaling and tube formation stimulated by the two receptors in human endothelial cells, and exhibited more potent antitumor efficacy in MKN45 human gastric cancer xenograft models than both the parent monospecific antibody alone. Collectively, based on the newly designed heterodimeric Fc-based bsAb, our results provide the therapeutic potential of bsAb targeting both Met and VEGFR-2 simultaneously for the treatment of human cancers. Mol Cancer Ther; 12(12); 2748–59. ©2013 AACR.

Gene expression levels in H3122, LR, and panobinostat treated LR cells and the promoter or enhancer H3K27 ac gain or loss

Supplementary Data from A novel agonistic antibody to human death receptor 4 induces apoptotic cell death in various tumor cells without cytotoxicity in hepatocytes

Supplementary Figure S1 shows the distribution of chromatin features around mutations across multiple cancer types. Sup S2 and S3 shows the average signal distributions of nucleosome occupancy across several cancer types. Sup S4 shows correlation between histone modifications and mutation rates of indels and SNVs. Sup S5 shows mutation rates in intragenic enhancer relative to non-enhancer Sup S6 shows the relative cumulative frequencies of missense and silent SNVs. Sup S7, S8, S9, S10 shows counts of each of the four indel types across multiple cancer types. Sup S11 shows the average signal distributions of DNA methylation around mutation positions. Sup S12, S13, S14, S15 shows the average signal distribution of a few histone marks and nucleosomes around SNV and indel positions in several tumor types. Sup S16 shows the binding pattern of NER machineries around mutation positions. Sup S17 shows the average distribution of H3K3me3, XPB, and XPD around indel positions from STAD. Sup S18 shows the average distributions of CSB and Pol II around a few TFBS. Sup S19 shows NER activity around mutations. Sup S20 shows relationship between mutation acquisition and chromatin features in MMR- and POLE-deficient tumors. Sup S21 summarizes epigenomic features that distinguish SNVs, indels, and non-mutated positions. Sup S22 shows the signal intensity of TC-NER on 12 types of missense SNVs

The proapoptotic tumor necrosis factor–related apoptosis inducing ligand (TRAIL) receptors death receptor (DR) 4 and DR5 are attractive targets to develop the receptor-specific agonistic monoclonal antibodies (mAb) as anticancer agents because of their tumor-selective cell death–inducing activity. Here, we report a novel agonistic mAb, AY4, raised against human DR4 in mice. ELISA analysis revealed that AY4 specifically bound to DR4 without competition with TRAIL for the binding. Despite distinct binding regions of AY4 on DR4 from those of TRAIL, AY4 as a single agent induced caspase-dependent apoptotic cell death of several tumor types through the extrinsic and/or intrinsic pathways without substantial cytotoxicity to normal human hepatocytes. Further, the AY4-sensitive cells followed the same cell death characteristics classified as type I and type II cells by the response to TRAIL, suggesting that the cell death profiles in responses to DR4 and/or DR5 stimulation are determined by the downstream signaling of the receptor rather than the kind of receptor. Noticeably, AY4 efficiently induced cell death of Jurkat cells, which have been reported to be resistant to other anti-DR4 agonistic mAbs, most likely due to the unique epitope property of AY4. In vivo administration of AY4 significantly inhibited tumor growth of human non–small cell lung carcinoma preestablished in athymic nude mice. Conclusively, our results provide further insight into the DR4-mediated cell death signaling and potential use of AY4 mAb as an anticancer therapeutic agent, particularly for DR4-responsive tumor types. [Mol Cancer Ther 2009;8(8):2276–85]

Supplementary Figure S1. Viability of H3122-LR and H2228-LR cells Supplementary Figure S2. Gene set enrichment analysis and western blot Supplementary Figure S3. Effects of AXL inhibition on EMT gene expression in LR cells, related to Fig. 1E. Supplementary Figure S4. Mice with established H3122-derived tumors were treated with four doses (50, 75, 87.5, or 100 mg/kg) of ceritinib to derive ceritinib-resistant tumors Supplementary Figure S5. Enhancer remodeling during ceritinib resistance, related to Fig. 2. Supplementary Figure S6. Genes with H3K27ac loss or gain in their promoters during ceritinib resistance, related to Fig.2.

Supplementary Materials and Methods that contain detailed experimental procedures

Anaplastic lymphoma kinase (ALK) inhibitors are highly effective in patients with ALK fusion–positive lung cancer, but acquired resistance invariably emerges. Identification of secondary mutations has received considerable attention, but most cases cannot be explained by genetic causes alone, raising the possibility of epigenetic mechanisms in acquired drug resistance. Here, we investigated the dynamic changes in the transcriptome and enhancer landscape during development of acquired resistance to ALK inhibitors. Histone H3 lysine 27 acetylation (H3K27ac) was profoundly altered during acquisition of resistance, and enhancer remodeling induced expression changes in both miRNAs and mRNAs. Decreased H3K27ac levels and reduced miR-34a expression associated with the activation of target genes such as AXL. Panobinostat, a pan-histone deacetylase inhibitor, altered the H3K27ac profile and activated tumor-suppressor miRNAs such as miR-449, another member of the miR-34 family, and synergistically induced antiproliferative effects with ALK inhibitors on resistant cells, xenografts, and EML4-ALK transgenic mice. Paired analysis of patient samples before and after treatment with ALK inhibitors revealed that repression of miR-34a or miR-449a and activation of AXL were mutually exclusive of secondary mutations in ALK. Our findings indicate that enhancer remodeling and altered expression of miRNAs play key roles in cancer drug resistance and suggest that strategies targeting epigenetic pathways represent a potentially effective method for overcoming acquired resistance to cancer therapy.Significance: Epigenetic deregulation drives acquired resistance to ALK inhibitors in ALK-positive lung cancer. Cancer Res; 78(12); 3350–62. ©2018 AACR.

Supplementary Tables S1 and S2 describes the datasets used in this study. Supplementary Table 3 is a table of correlation between histone marks and NER activities

Purpose: This study aims to determine the relationship between CpG island DNA hypermethylation and global genomic DNA hypomethylation and their prognostic implications in hepatocellular carcinoma. The association of DNA methylation changes with clinicopathologic factors and the chronological ordering of DNA methylation changes along multistep hepatocarcinogenesis were also assessed.Experimental Design: Hepatocellular carcinoma (n = 20) and nonneoplastic liver samples (n = 72) were analyzed for their methylation status at 41 CpG island loci and 3 repetitive DNA elements (LINE-1, ALU, and SAT2) using MethyLight or combined bisulfite restriction analysis. After selection of 19 CpG island loci showing cancer-specific DNA methylation, another set of 99 hepatocellular carcinoma samples was analyzed for these loci.Results: The number of methylated genes in hepatocellular carcinoma was significantly higher in hepatocellular carcinoma patients with a cirrhotic liver than in hepatocellular carcinoma patients with a noncirrhotic liver (9.9 versus 7.0, P = 0.001). Hepatocellular carcinoma from female patients showed a higher number of methylated genes than hepatocellular carcinoma from male patients (11.2 versus 8.4, P = 0.006). The genes CRABP1 and SYK showed significant association between CpG island hypermethylation and patients' poor survival. SAT2 hypomethylation occurred earlier than LINE-1 or ALU hypomethylation along the multistep hepatocarcinogenesis. Depending on the type of CpG island locus, a direct, inverse, or no relationship between CpG island hypermethylation and repetitive DNA hypomethylation was observed in hepatocellular carcinomas.Conclusion: The varying relationships between the hypermethylation of individual CpG island loci and the hypomethylation of repetitive elements suggests that they are not mechanically linked. SYK and CRABP1 hypermethylation may serve as useful tumor markers for prognostication of hepatocellular carcinoma patients.

Supplementary figure legends S1 to S12

Dynamic chromatin structures result in differential chemical reactivity to mutational processes throughout the genome. To identify chromatin features responsible for mutagenesis, we compared chromatin architecture around single-nucleotide variants (SNV), insertion/deletions (indels), and their context-matched, nonmutated positions. We found epigenetic differences between genomic regions containing missense SNVs and those containing frameshift indels across multiple cancer types. Levels of active histone marks were higher around frameshift indels than around missense SNV, whereas repressive histone marks exhibited the reverse trend. Accumulation of repressive histone marks and nucleosomes distinguished mutated positions (both SNV and indels) from the context-matched, nonmutated positions, whereas active marks were associated with substitution- and cancer type–specific mutagenesis. We also explained mutagenesis based on genome maintenance mechanisms, including nucleotide excision repair (NER), mismatch repair (MMR), and DNA polymerase epsilon (POLE). Regional NER variation correlated strongly with chromatin features; NER machineries exhibited shifted or depleted binding around SNV, resulting in decreased NER at mutation positions, especially at sites of recurrent mutations. MMR-deficient tumors selectively acquired SNV in regions with high active histone marks, especially H3K36me3, whereas POLE-deficient tumors selectively acquired indels and SNV in regions with low active histone marks. These findings demonstrate the importance of fine-scaled chromatin structures and associated DNA repair mechanisms in mutagenesis. Cancer Res; 77(11); 2822–33. ©2017 AACR.

Supplementary Data from Prognostic Implications of and Relationship Between CpG Island Hypermethylation and Repetitive DNA Hypomethylation in Hepatocellular Carcinoma

Supplementary Table 2 from LRRC3B, Encoding a Leucine-Rich Repeat-Containing Protein, Is a Putative Tumor Suppressor Gene in Gastric Cancer

Supplementary Figure 1 from LRRC3B, Encoding a Leucine-Rich Repeat-Containing Protein, Is a Putative Tumor Suppressor Gene in Gastric Cancer