Search

Supplementary Figure Legends

Supplementary Materials and Figure Legends

Purpose: Current immunomagnetic enrichment method can only detect general epithelial antigens of circulating tumor cells (CTC). Further characterization of the CTCs to provide specific information on the tumor type is not possible. We attempted to overcome this drawback by developing the methodology for using a gastrointestinal-specific anti-cytokeratin (CK) 20 antibody to detect CTCs in colorectal cancer patients' blood.Experimental Design: The protocol was validated using a colorectal cancer SW480 cell line. The clinical significance of findings in colorectal cancer was investigated by detecting CK20-positive CTCs (pCTC) in patients with colorectal cancer, other common cancers, colorectal adenoma, benign colorectal diseases, and normal subjects. Moreover, the malignant nature of CK20 pCTCs was examined by comparing chromosome 17 aberration patterns with those from the corresponding primary tumors.Results: The assay successfully showed CK20-positive SW480 cells. When applied in patient samples, the detection rates were 62% (132 colorectal cancer patients; median number = 11 CTCs), 0% (120 patients with other common cancers), 6% (50 colorectal adenoma patients), 0% (120 patients with benign colorectal diseases), and 0% (40 normal subjects). Furthermore, statistical analysis showed that CK20 pCTC numbers were associated with tumor-node-metastasis stage and lymph node status. Using the median CK20 pCTC numbers as the cutoff points, stratified groups of colorectal cancer patients had significant differences in their recurrence, metastasis, and survival. Finally, chromosome 17 aneusomy in 90% of colorectal cancer patients with CK20 pCTCs matched with those from the primary tumors.Conclusions: Detection of CK20 pCTCs using the new protocol could generate clinically important information for colorectal cancer patients.

Supplementary Figure 1. Validation of the lncRNA microarray data using qRT-PCR. Supplementary Figure 2. Expression levels of DZnep-induced lncRNAs in a panel of HCC cell lines and non-tumor cell lines. Supplementary Figure 3. Expression levels of DZnep-induced lncRNAs in paired human HCC tissues and adjacent non-tumor tissues. Supplementary Figure 4. High specificity of ChIP assay in measuring true interaction between EZH2 and the promoters of EZH2 targeted genes. Supplementary Figure 5. Inhibition of TCAM1P-004 and RP11-598D14.1 with siRNAs promoted cell proliferation. Supplementary Figure 6. Knockdown of TCAM1P-004 and RP11-598D14.1 with shRNAs inhibited cell apoptosis, promoted colony formation ability and transformation ability, and stimulated tumor growth in xenograft mice model. Supplementary Figure 7. Overexpression of TCAM1P-004 and RP11-598D14.1 repressed cell colony formation and transformation abilities, and tumor growth in xenograft mice model. Supplementary Figure 8. Overexpression of TCAM1P-004 or RP11-598D14.1 promoted apoptosis in subcutaneous tumors derived from Hep3B cells. Supplementary Figure 9. Inhibition of TCAM1P-004 or RP11-598D14.1 could induce tumorigenesis of non-tumor MIHA cells. Supplementary Figure 10. KEGG pathway enrichment analysis of TCAM1P-004 and RP11-598D14.1 regulated genes. Supplementary Figure 11. qRT-PCR validated signaling pathways related to TCAM1P-004 and RP11-598D14.1. Supplementary Figure 12. Expression of DDIT and PFKFB4 in HCC cell lines and HCC tumor samples. Supplementary Figure 13. Expression of PFKFB4 in HCC tumor samples. Supplementary Figure 14. Alignment analysis between lncRNA TCAM1P-004 and RP11-598D14.1. Supplementary Figure 15. EZH1 showed no significant role in HCC.

Long noncoding RNAs (lncRNA) play critical roles in the development of cancer, including hepatocellular carcinoma (HCC). However, the mechanisms underlying their deregulation remain largely unexplored. In this study, we report that two lncRNAs frequently downregulated in HCC function as tumor suppressors and are epigenetically silenced by histone methyltransferase EZH2. lncRNAs TCAM1P-004 and RP11-598D14.1 were inhibited by EZH-mediated trimethylation of H3K27me3 at their promoters. Downregulation of TCAM1P-004 and RP11-598D14.1 was frequently observed in HCC tumors compared with adjacent normal tissues. Both lncRNAs inhibited cell growth, cell survival, and transformation in HCC cells in vitro as well as tumor formation in vivo. Using RNA pull-down and mass spectrometry, we demonstrated that TCAM1P-004 bound IGF2BP1 and HIST1H1C, whereas RP11-598D14.1 bound IGF2BP1 and STAU1. These lncRNA–protein interactions were critical in regulating p53, MAPK, and HIF1α pathways that promoted cell proliferation in HCC. Overexpression of EZH2 was critical in repressing TCAM1P-004 and RP11-598D14.1, and EZH2-TCAM1P-004/RP11-598D14.1–regulated pathways were prevalent in human HCC. Aberrant suppression of TCAM1P-004 and RP11-598D14.1 led to loss of their tumor-suppressive effects by disrupting the interaction with IGF2BP1, HIST1H1C, and STAU1, which in turn promoted HCC development and progression. Collectively, these findings demonstrate the role of TCAMP1P-004 and RP11-598D14.1 in suppressing tumor growth and suggest that EZH2 may serve as a therapeutic target in HCC.Significance:EZH2-mediated loss of lncRNAs TCAM1P-004 and RP11-598D14.1 hinders the formation of tumor suppressor lncRNA–protein complexes and subsequently promotes HCC growth.

Supplementary Tables S1-S3 from Clinical Significance of Cytokeratin 20-Positive Circulating Tumor Cells Detected by a Refined Immunomagnetic Enrichment Assay in Colorectal Cancer Patients

Background & Aims\ud Metabolic syndrome can lead to the clinical manifestation of non-alcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC) as part of the natural history of NAFLD. Despite a strong causative link, NAFLD-HCC is often underrepresented in systematic genome explorations.\ud Methods\ud Here, tumor-normal pairs from 100 subjects diagnosed with NAFLD-HCC were subject to next generation sequencings. Bioinformatic analyses were performed to identify key genomic, epigenomic and transcriptomic events associated with the pathogenesis of NAFLD to NAFLD-HCC. Establishment of primary patient-derived NAFLD-HCC culture was used as a representative human model for downstream in vitro investigations of underlying CTNNB1 S45P driver mutation. Syngeneic immunocompetent mouse model was used to further test the involvement of CTNNB1mut and TNFRSF19 in reshaping the tumor microenvironment.\ud Results\ud Mutational process operative in NAFLD-liver inferred susceptibility to tumor formation through defective DNA repair pathways. Dense promoter mutations and dysregulated transcription factors accentuated activated transcriptional regulation in NAFLD-HCC, in particular the enrichment of MAZ-MYC activities. Somatic events common in HCCs arising from NAFLD and viral hepatitis B infection underscore similar driver pathways, although an incidence shift highlights CTNNB1mut dominance in NAFLD-HCC (33%). Immune exclusion correlated evidently with CTNNB1mut. ChIP-seq integrated with transcriptome and immune profiling showed for the first time a transcriptional axis of CTNNB1mut/TNFRSF19/repressed senescence-associated secretory phenotype-like (SASP-like) cytokines (including IL6 and CXCL8). This phenomenon could be reverted by Wnt-modulator ICG001.\ud Conclusions\ud The unique mutational processes in NAFLD-liver and NAFLD-HCC alludes to a “field effect”. Whereby, distinct aberrations and shift in driver events reveal a gain-of-function role of CTNNB1 mutations in immune exclusion via TNFRSF19 inhibition of SASP-like features.\ud LAY SUMMARY\ud The increasing prevalence of metabolic syndrome in adult populations poised NAFLD-induced HCC to be the major type of liver cancer of the 21st century. We showed a strong “field effect” in NAFLD-liver from mutational signatures detected and a mechanistic path of activated β-catenin in reshaping the tumor-immune microenvironment.

Serologic and molecular surveillance of serum collected from 152 suspected scrub typhus patients in Myanmar revealed Orientia tsutsugamushi of genotypic heterogeneity. In addition, potential co-infection with severe fever with thrombocytopenia syndrome virus was observed in 5 (3.3%) patients. Both scrub typhus and severe fever with thrombocytopenia syndrome are endemic in Myanmar.

Background/Aims: ATP-binding cassette (ABC) transporters have been shown to regulate tumor initiating cells in various cancer types and specific genotype associated with cancer risk. ABCF1 was on priority among the ABC transporters because the gene located at 6p21, the chromosome region associated with a number of HCC risk genetic loci including the HLA genes. Its family member ABCF2 was also examined as their expression levels were highly correlated and associated with HCC recurrence. Subjects and Methods: A total of 300 HCC and 300 healthy blood samples (99.3% and 94.7% Chinese respectively) were prospectively collected with informed consent. All patients had been diagnosed with primary HCC and underwent partial hepatectomy. Clinical information including sex, age, tumor stage and survival outcomes were collected prospectively. Genomic DNA were extracted from blood samples and SNPs were examined by TaqMan genotyping assay, Sequenom MassARRAY platform and direct sequencing. Results: Sixteen SNPs and three INDELs were examined in ABCF1 and ABCF2 in the germline DNA of 300 HCCs and 300 healthy individuals. Among the 19 loci investigated, ABCF1 rs1264440 (916-99A>G) and rs4148252 (*1delA), ABCF2 rs3823589 (-43+219C>A) and rs75100208 (368-94C>A) were significantly associated with HCC risk (OR: 1.424, 95%CI: 1.03-1.97, P=0.032; OR: 1.446, 95%CI: 1.04-2.00, P=0.026; OR: 1.635, 95%CI: 1.09-2.46, P=0.018; OR: 1.479, 95%CI: 1.09-2.18, P=0.049, respectively). Patients with any two of the four variant genotype, compared with those with all wild type, revealed elevated HCC risks (OR: 1.657, 95%CI: 1.16-2.37, P=0.006). Importantly, patients with all four variant genotypes demonstrated augmented HCC risk (OR: 2.295, 95%CI: 1.27-4.15, P=0.006). Conclusions: ABCF1 genetic variants rs1264440, rs4148252 and ABCF2 genetic variants rs3823589, rs75100208 were associated with significantly increased HCC risk. Augmented cancer risk was observed among patients possessed all four variant genotypes in ABCF1 and ABCF2. Further mechanistic studies are warranted to comprehend the underlying mechanisms. Citation Format: Philip Chun Yeung, Kelvin Kwok Chai Ng, Tan To Cheung, Charing Ching-Ning Chong, Paul Bo San Lai, Siu Tim Cheung. ABCF1 and ABCF2 genetic variants in association with hepatocellular carcinoma (HCC) risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1436.

Postoperative pancreatic fistula (POPF) after pancreaticoduodenectomy (PD) remains a dreadful complication. Duct-to-mucosa pancreaticojejunostomy (DTMPJ) is a commonly performed anastomosis after PD. This study aims to evaluate whether there is a size limit of pancreatic duct below which POPF rate increases significantly after DTMPJ.A retrospective study was performed from a database with prospectively collected data on consecutive patients undergoing DTMPJ.Between the years 2003 and 2019, a total of 288 patients with DTMPJ were recruited. POPF occurred in 56.3% of the patients, of which 43.8% were biochemical leak, 8.7% were grade B, and 1.4% were grade C. Overall operative morbidity was 51.4%, of which 19.1% were major complications. Five patients (1.7%) died within 90 days of operation. Patients with grade B/C POPF had significantly soft pancreas (DTMPJ can be safely performed for pancreatic duct1 mm without significantly increased POPF risk.