Phenotype Harmonization in the GLIDE2 Oral Health Genomics Consortium

Genetic risk factors play important roles in the etiology of oral, dental, and craniofacial diseases. Identifying the relevant risk loci and understanding their molecular biology could highlight new prevention and management avenues. Our current understanding of oral health genomics suggests that dental caries and periodontitis are polygenic diseases, and very large sample sizes and informative phenotypic measures are required to discover signals and adequately map associations across the human genome. In this article, we introduce the second wave of the Gene-Lifestyle Interactions and Dental Endpoints consortium (GLIDE2) and discuss relevant data analytics challenges, opportunities, and applications. In this phase, the consortium comprises a diverse, multiethnic sample of over 700,000 participants from 21 studies contributing clinical data on dental caries experience and periodontitis. We outline the methodological challenges of combining data from heterogeneous populations, as well as the data reduction problem in resolving detailed clinical examination records into tractable phenotypes, and describe a strategy that addresses this. Specifically, we propose a 3-tiered phenotyping approach aimed at leveraging both the large sample size in the consortium and the detailed clinical information available in some studies, wherein binary, severity-encompassing, and "precision," data-driven clinical traits are employed. As an illustration of the use of data-driven traits across multiple cohorts, we present an application of dental caries experience data harmonization in 8 participating studies (N = 55,143) using previously developed permanent dentition tooth surface-level dental caries pattern traits. We demonstrate that these clinical patterns are transferable across multiple cohorts, have similar relative contributions within each study, and thus are prime targets for genetic interrogation in the expanded and diverse multiethnic sample of GLIDE2. We anticipate that results from GLIDE2 will decisively advance the knowledge base of mechanisms at play in oral, dental, and craniofacial health and disease and further catalyze international collaboration and data and resource sharing in genomics research.

Abstract P4-06-06: Comparison of the immunological and clinical effect of personalized peptide vaccination for patients with breast cancer

Background: Selected therapeutic personalized peptide vaccines (PPV) were effective for boosting anticancer immune response that was associated with the clinical outcome as a prognostic factor for metastatic recurrent breast cancer (mrBC) 1-2. In this study, we investigated the immunological and clinical effect of PPV as the prophylactic cancer vaccine for non-recurrent but high-risk BC (nrhrBC) patients (pts), and we compared it's features to those of the mrBC pts who had active cancers or became resistant to the standard therapies(TR-mrBC). Methods: Material and Patient eligibility criteria: The peptides were selected from the 31 PPVs according to the results of HLA typing and peptide-specific IgG titers. Pts with a histological diagnosis of BC and their HLA-A molecules should be each of -A2, A3, A11, A24, A26, A31 or A33. The clinical protocols were approved by the institutional review board. (UMIN000003081and 00000184400000). Treatment schedule: A maximum of 4 peptides was administrated as weekly for initial four vaccinations and as biweekly for further inoculations. The concomitant standard endocrine therapy and the chemo-endocrine therapy were available for nrhrBC pts after finishing the standard adjuvant chemotherapy, and for mrBC pts concurrently. Immune and clinical response assessment: Specific T-cell responses, IgG titers and cytokines were evaluated using by interferon (IFN)-γ ELISPOT, Luminex assay and ELISA system in every 6-8 vaccinations. Toxicity, clinical response and correlation with the immune responses were investigated. Results: 16 pts with nrhrBC, 41 pts with mrBC and 79 pts with TR-mrBC received median 18, 16 and 14 vaccines, respectively. After PPV therapies, peptide-specific IgG and CTLs increased significantly in a total of 47 (77%) and 37(60%) in nrhrBC pts, 102 (63%) and 98 (61%) in mrBC pts, and 150(53%) and 100 (42%) in TR-mrBC pts. Pts experienced Grade 1-3 skin reaction at injection site, no other grade 3 or 4 SAEs were associated with PPV but with the disease progression or combination therapy. The median time to progression (TTP) and overall survival (OS) were not reached in nrhrBC pts, 7.8 and 29 months in mrBC pts, and were 7.5 and 15.9 months in TR-mrBC pts, respectively. The peptide specific CTL response was correlated significantly with OS in nrhrBC pts and the IgG levels were associated with the better OS in either non TR-mrBC pts or TR-mrBC pts. High levels of IL-6, GM-CSF, IFN-g, IL-2 receptor, BAFF were associated with worse prognosis for pts with TR-mrBC. And high levels of GM-CSF and BAFF were associated with worse prognosis for pts with nrhrBC and mrBC, respectively. In contrast, High levels of IL-2 were associated with the better prognosis for pts with mrBC. Conclusion: This study indicated that immunological features of these three groups were different from each other with most potent PPV-induced immune boosting for nrhrBC pts. Pts with mrBC who had lower immune-suppressive cytokine levels had the better prognosis. These results suggested the PPV therapy could be effective for postoperative prophylactic vaccination in patients with nrhrBC. References: 1. Takahashi R, Toh U, et al. Breast Cancer Res. 2014; 2. Toh U, Okabe M, et al. THE BREAST 2015.

Citation Format: Toh U, Okabe M, Takao Y, Tanaka Y, Shigaki T, Takenaka M, Iwakuma N, Sudo T, Yamada A, Shichijo S, Itoh K, Akagi Y. Comparison of the immunological and clinical effect of personalized peptide vaccination for patients with breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-06-06.

Association of NOD2 Mutations with Aggressive Periodontitis

Aggressive periodontitis (AgP) is characterized by rapid alveolar bone destruction and tooth loss early in life, and its etiology remains unclear. To explore the genetic risk factors of AgP, we performed genome-wide single-nucleotide polymorphism genotyping for identity-by-descent mapping and identified 32 distinct candidate loci, followed by whole exome sequencing with 2 pedigrees of AgP consisting of 3 cases and 1 control in 1 family and 2 sibling cases in the other. After variant filtering procedures and validation by targeted Sanger sequencing, we identified 2 missense mutations at 16q12 in NOD2 (p.Ala110Thr and p.Arg311Trp), which encodes nucleotide-binding oligomerization domain protein 2. We further examined 94 genetically unrelated AgP patients by targeted sequencing of NOD2 and found that 2 patients among them also carried the p.Arg311Trp variant. Furthermore, we found 3 additional missense mutations in this gene (p.His370Tyr, p.Arg459Cys, and p.Ala868Thr). These mutations either had not been previously observed or are extremely rare (frequency <0.001) in Asian populations. NOD2 plays a crucial role in innate immunity as an intracellular receptor initiating nuclear factor κB-dependent and mitogen-activated protein kinase-dependent gene transcription. These results demonstrated NOD2 as a novel gene involved in AgP.

Intestinal epithelial culture under an air-liquid interface: a tool for studying human and mouse esophagi

This study investigated whether an intestinal epithelial culture method can be applied to mouse and human esophageal cultures. The esophagi harvested from 1-day-old mice and adult humans were maintained in collagen gels. A commercially available culture medium for human embryonic stem cells was used for the human esophageal culture. We discovered that the intestinal epithelial culture method can be successfully applied to both mouse and human esophageal cultures. The long-term cultured esophageal organoids were rod-like luminal structures lined with myofibroblasts. We discovered that regeneration of the esophageal mucosal surface can be almost completely achieved in vitro, and the advantage of this method is that organoid cultures may be generated using host-derived fibroblasts as a niche. This method is a promising tool for mouse and human research in intestinal biology, carcinogenesis, and regenerative medicine.

Concurrent analysis of human equilibrative nucleoside transporter 1 and ribonucleotide reductase subunit 1 expression increases predictive value for prognosis in cholangiocarcinoma patients treated with adjuvant gemcitabine-based chemotherapy

BACKGROUND

The aim of this study was to investigate the predictive and prognostic values of intratumoural human equilibrative nucleoside transporter 1 (hENT1) and ribonucleotide reductase subunit 1 (RRM1) expression in advanced cholangiocarcinoma patients treated with adjuvant gemcitabine-based chemotherapy (AGC).

METHODS

Intratumoural hENT1 and RRM1 expression levels were investigated immunohistochemically in 127 patients with advanced cholangiocarcinoma who underwent surgical resection (68 with AGC and 59 without AGC). The impacts of hENT1 and RRM1 expression on survival were evaluated.

RESULTS

High intratumoural hENT1 and RRM1 expression levels were observed in 86 (68%) and 67 (53%) patients, respectively. In a multivariate analysis of 68 patients who received AGC, high hENT1 (P=0.044) and low RRM1 expression (P=0.009) were independently associated with prolonged disease-free survival (DFS), whereas low RRM1 expression (P=0.024) was independently associated with prolonged overall survival (OS). Moreover, concurrent high hENT1 and low RRM1 expression was a powerful independent predictor of prolonged DFS (P<0.001) and OS (P=0.001) when the combined classification of hENT1 and RRM1 was introduced.

CONCLUSIONS

Concurrent analysis of hENT1 and RRM1 expression may increase the predictive value of these biomarkers for survival of advanced cholangiocarcinoma patients treated with AGC.

Amplification of PVT-1 is involved in poor prognosis via apoptosis inhibition in colorectal cancers

Background:

We previously conducted gene expression microarray analyses to identify novel indicators for colorectal cancer (CRC) metastasis and prognosis from which we identified PVT-1 as a candidate gene. PVT-1, which encodes a long noncoding RNA, mapped to chromosome 8q24 whose copy-number amplification is one of the most frequent events in a wide variety of malignant diseases. However, PVT-1 molecular mechanism of action remains unclear.

Methods:

We conducted cell proliferation and invasion assays using colorectal cancer cell lines transfected with PVT-1siRNA or negative control siRNA. Gene expression microarray analyses on these cell lines were also carried out to investigate the molecular function of PVT-1. Further, we investigated the impact of PVT-1 expression on the prognosis of 164 colorectal cancer patients by qRT–PCR.

Results:

CRC cells transfected with PVT-1 siRNA exhibited significant loss of their proliferation and invasion capabilities. In these cells, the TGF-β signalling pathway and apoptotic signals were significantly activated. In addition, univariate and multivariate analysis revealed that PVT-1 expression level was an independent risk factor for overall survival of colorectal cancer patients.

Conclusion:

PVT-1, which maps to 8q24, generates antiapoptotic activity in CRC, and abnormal expression of PVT-1 was a prognostic indicator for CRC patients.

Temperature distributions of electron beam-irradiated samples by scanning electron microscopy

An electron beam (EB) generated by a scanning electron microscope (SEM) was used to irradiate two samples having different thermal conductivities, and the resulting temperatures of the EB-irradiated areas as well as the temperature distributions within the samples were then measured using a thermal camera. These measurements showed overall increases in sample temperatures, as well as revealed temperature rises at the EB-irradiated areas that had little difference with one of the theoretical predictions. Differences between the actual and the predicted temperature measurements were analysed in terms of the accuracy with which parameters could be estimated. The temperature distributions of the samples were measured and, On the basis of the results, it was hypothesized that the temperature differential over an irradiated sample will be inversely correlated with its thermal conductivity.

The indications for a diverting stoma in low anterior resection for rectal cancer: a prospective multicentre study of 222 patients from Japanese cancer centers

AIM

The aim of the study was to determine the present state of diverting stoma construction in Japanese cancer centres and to investigate the relationship between symptomatic leakage and diverting stoma after low anterior resection for rectal cancer.

METHOD

Two hundred and twenty-two consecutive patients undergoing low anterior resection for rectal cancer located within 10 cm from the anal verge were investigated in a prospective, multicenter study.

RESULTS

The overall leakage rate was 9.0% (20/222). Of 31 cases with an anastomosis within 2.0 cm from the anal verge, 22 (71%) had a diverting stoma. Of cases anastomosed within 5.0 cm, the absence of a diverting stoma and tumour size were significantly related to an increased rate of leakage [leakage in 13 (12.7%) of 102 cases without a diverting stoma; in three (3.8%) of 80 cases with a diverting stoma]. Among anastomoses within 2.0 cm from the anal verge, leakage occurred in four (44.4%) of nine cases without and in none (0%) of 22 cases with a diverting stoma.

CONCLUSION

We recommend a diverting stoma for an anastomosis within 5.0 cm of the anal verge and strongly recommend it for a very low anastomosis within 2.0 cm.

Phase II trial of cetuximab plus irinotecan for FOLFOX and FOLFIRI-refractory patients with EGFR-positive advanced and/or metastatic colorectal cancer: Evaluation of the efficacy and safety based on KRAS mutation status (T- CORE0801)

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Background: Activating mutation of the KRAS gene is a predictive biomarker for loss of efficacy to anti-EGFR antibody therapy. However, this was mainly established by the evidences of Caucasian studies. Then, this prospective study investigated the role of KRAS mutations on efficacy and safety to cetuximab plus irinotecan in Japanese patients with metastatic colorectal cancer (mCRC).

Methods: We conducted a prospective study to analyze objective response to cetuximab plus irinotecan in molecularly defined KRAS wild-type (WT) or mutant subgroups of chemotherapy-refractory mCRC. KRAS mutations were detected by direct sequence on DNA from formalin-fixed, paraffin-embedded tissue of patients treated in 11 centers in Japan. Additional EGFR related genes such as BRAF, PIK3CA etc. and antibody-dependent cellular cytotoxicity related polymorphism in FCγRIIa and RIIIa genes were also examined.

Results: Forty-three patients were enrolled. KRAS mutations were found in 31.7% of 41 eligible patients. Response rate (RR) to cetuximab plus irinotecan, the primary endpoint of the study, was 17.9% and 0% for the patients with tumor harboring WT and mutant KRAS, respectively. No significant differences in toxicity were observed between the KRAS WT and mutant groups. Detail statistical analyses are ongoing.

Conclusions: We confirmed that KRAS status is a useful predictive maker for the efficacy to cetuximab plus irinotecan therapy in Japanese mCRC patients, even though the response rate in the KRAS WT group was lower than expected.

[Table: see text]

The direct PAK1 inhibitor, TAT-PAK18, blocks preferentially the growth of human ovarian cancer cell lines in which PAK1 is abnormally activated by autophosphorylation at Thr 423

So far no effective therapeutic has been developed for the FDA-approved treatment of ovarian cancer patients. Recently we provided the first evidence indicating that an old antibiotic (antiparasitic drug) called Ivermectin suppresses the growth of a variety of human ovarian cancer cell lines in vitro by inactivating the oncogenic kinase PAK1 somehow (Hashimoto H, et al. Drug Discov Ther. 2009;3:243-246). This kinase is now known to be essential for the growth of more than 70% of all human cancers including breast, prostate, pancreatic, colon, gastric, lung, cervical, thyroid cancers as well as hepatoma, glioma, melanoma, MM (multiple myeloma) and NF (neurofibromatosis) tumors. In this study, using the cell-permeable PAK1-inactivating peptide TAT-PAK18 which blocks the essential PAK1-PIX interaction, we examined the relationship between the sensitivity of ovarian cancer cell lines to this anti-PAK1 peptide and the protein expression/autophosphorylation levels of PAK1 in these cell lines, and found that the more PAK1 is abnormally activated (autophosporylated at Thr 423), the more their growth is sensitive to this peptide, regardless of their PAK1 expression levels. This observation provides the first direct evidence that ovarian cancers also belong to the PAK1-dependent cancers which represent more than 70% of all human cancers, suggesting that anti-PAK1 drugs would be effective therapeutics for ovarian cancers.

Ivermectin inactivates the kinase PAK1 and blocks the PAK1-dependent growth of human ovarian cancer and NF2 tumor cell lines

Ivermectin is an old anti-parasitic antibiotic which selectively kills nematodes at a very low dose (0.2 mg/kg) by inhibiting their GABA (gamma-aminobutyric acid) receptor, but not mammalian counterpart. Interestingly, several years ago it was reported by a Russian group that Ivermectin can suppress almost completely the growth of human melanoma and a few other cancer xenografts in mice at the much higher doses (3-5 mg/kg) without any adverse effect on mice. However, its anti-cancer mechanism still remained to be clarified at the molecular levels, that would determine the specific type of cancers susceptible to this drug. The first hint towards its anti-PAK1 potential was a recent finding that Ivermectin at its sublethal doses dramatically reduces the litter size (number of eggs laid) of the tiny nematode C. elegans. Interestingly, either a PAK1-deficiency (gene knock-out) or treatment with natural anti-PAK1 products such as CAPE (caffeic acid phenethyl ester) and ARC (artepillin C), the major anti-cancer ingredients in propolis, also causes the exactly same effect on this nematode, suggesting the possibility that the kinase PAK1 might be a new target of Ivermectin. This kinase is required for the growth of more than 70% of human cancers such as pancreatic, colon, breast and prostate cancers and NF (neurofibromatosis) tumors. Here we demonstrate for the first time that Ivermectin blocks the oncogenic kinase PAK1 in human ovarian cancer and NF2-deficient Schwannoma cell lines to suppress their PAK1-dependent growth in cell culture, with the IC50 between 5-20 μM depending on cell lines.

Hypoxia-inducible protein 2 (HIG2) as a new biomarker of ovarian clear cell adenocarcinoma

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Background: Epithelial ovarian cancer (EOC) can be subclassified into five major histologic types (Serous(SC), Mucinous(MC), Endometrioid(EC), Clear cell(CC), Undifferentiated (UC)). Among them, CC generally has a poor response to combination chemotherapy and its overall prognosis is poorer, as compared with other histologic types. In previous reports, we compared gene expression profiles in CC and SC using cDNA microarrays and suggested that HIG2 gene might be a new biomarker for CC (Clin Cancer Res, 2005). In this study, we generated a polyclonal antibody for HIG2 and further validated the expression of HIG2 in EOC. In addition, HIG2 expression was evaluated in CC derived from endometrium(EMCC) and kidney(KDCC). Methods: Formalin-fixed surgical samples from 254 EOC, 17 EMCC and 29 KDCC patients were included in this study. HIG2 expression was investigated by immunohistochemistry. HIG2 cytoplasmic staining were divided into positive or negative. Results: Histologic types and stages of EOC were as followed: (SC: 51; MC: 25; EC: 31; CC: 130; UC: 17) and (I: 96; II: 37; III: 100; IV: 21). In EOC, 175 of 254(69%) cases had HIG2 expression. The relationship between HIG2 expression and histologic types was shown in table . The positive rate of HIG2 in CC was significantly higher than other histologic types in EOC. However, there is no significant correlation between HIG2 expression and stages or grades. In addition, both CC of the ovary and endometrium showed significantly higher levels of HIG2 expression compared to those of CC of the kidney. Conclusions: HIG2 expression is a new biomarker for CC.

[Table: see text]

No significant financial relationships to disclose.

Radiotherapy negates the effect of retroperitoneal nonclosure for prevention of lymphedema of the legs following pelvic lymphadenectomy for gynecological malignancies: an analysis from a questionnaire survey

Using patient questionnaires, we studied the long-term effect of leaving the peritoneum open on the incidence of lymphedema of the legs in patients following pelvic lymphadenectomy for gynecological malignancies. The patients were retrospectively assigned to one of two groups, depending on whether the retroperitoneum was closed or left open at surgery. Three years after surgery, we obtained valid questionnaire responses from 101 patients (43 cervical, 46 endometrial, and 12 ovarian cancers) in the closure group and 83 patients (34 cervical, 40 endometrial, and 9 ovarian cancers) in the nonclosure group. In patients' self-analysis, the overall incidence of lymphedema of the legs was significantly lower in the nonclosure group than in the closure group (25.3% and 50.5%, respectively; P < 0.01). The incidence of lymphedema of the legs was significantly increased by postoperative radiotherapy. Especially in the nonclosure group, the incidence of lymphedema was only 15.8% in patients who did not have radiotherapy, but it increased significantly (44.4%) (P < 0.05) when patients underwent radiotherapy. In conclusion, this questionnaire survey suggested that leaving the retroperitoneum open after lymphadenectomy is significantly effective in reducing the incidence of leg lymphedema, which impairs patients' quality of life more than expected by physicians.

Identification of EGFR mutations in esophageal cancer

BACKGROUND

It is well known that the prognosis for esophageal cancer is worse than for other digestive cancers in spite of multimodality treatment, and there is an urgent need to improve this situation. The epidermal growth factor receptor (EGFR) inhibitor, gefitinib, was approved in Japan to treat advanced non-small cell lung cancer patients and several papers have since reported that the successfully treated patients had genetic mutations in EGFR.

PURPOSE

The aim of this study was to investigate the existence of EGFR mutations in esophageal cancer cell lines and primary lesions, and also to explore the possibility of treating esophageal cancer using gefitinib.

MATERIALS AND METHODS

Nineteen esophageal cancer cell lines were cultured and DNA was extracted using an ultracentrifugation method. Fifty cases of primary cancer and corresponding normal tissue samples were obtained and DNA was extracted using the same protocol. Nested PCR and DNA sequencing targeting exons 18, 19, 20 and 21 of EGFR were performed to investigate the presence of mutations in esophageal cancer cell lines and primary tumors.

RESULTS

Three of the 19 cell lines had the same silent mutation at nucleotide 2607, a G-to-A substitution in exon 20. One of the 50 patients had an EGFR mutation in codon 719, resulting in an amino acid substitution from glycine to aspartic acid.

CONCLUSION

EGFR mutations in esophageal carcinoma are rare but do exist, and thus gefitinib could be included in esophageal cancer treatment regimens by selecting those patients who possess such mutations.

Reduction of radiation-induced apoptosis by specific expression of Bcl-2 in normal cells

Radiation-induced apoptosis is thought to underlie the toxicity of radiation to normal tissues as well as to cancer cells. We hypothesized that specific ectopic overexpression of the antiapoptotic molecule Bcl-2 in normal cells would inhibit radiation-induced apoptosis and thereby reduce radiation-induced toxicity in normal cells. To express Bcl-2 specifically in normal cells (which have wild-type (wt) p53) but not in cancer cells (which often have mutated p53), we constructed a Bcl-2 expression plasmid (PG13-Bcl-2) with a minimal promoter regulated by multiple wt p53 DNA-binding sites and found that the presence of wt p53 protein strongly upregulated Bcl-2 expression through this plasmid. Transfection of NIH 3T3 fibroblasts, which express wt p53, with PG13-Bcl-2 increased cell survival and reduced apoptosis; however, transfection of MDA-MB-231 breast cancer cells, which have mutated p53, did not affect survival and apoptosis of those cells. These results indicate that irradiation of normal cells rapidly upregulates the expression of wt p53, which binds to the p53 binding sequence of the PG13-Bcl-2 plasmid and increases the transcriptional activity of Bcl-2. Ectopic expression of Bcl-2 reduced radiation-induced apoptosis only in normal cells (not in cancer cells). Bcl-2 expression was detected in the lung from mice injected via a tail vein with LPD-PG13-Bcl-2 or LPD-CMV-Bcl-2, but did not in the lung from mice treated with DOTAP or LPD-PG13-mock. This novel approach to inhibiting radiation-induced apoptosis in normal cells may allow such cells to be protected from radiation-induced toxicity. Further preclinical in vivo studies are needed.