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Supplementary Data from Hepatocellular Carcinoma in Mongolia Delineates Unique Molecular Traits and a Mutational Signature Associated with Environmental Agents

Purpose:Mongolia has the world's highest incidence of hepatocellular carcinoma (HCC), with ∼100 cases/100,000 inhabitants, although the reasons for this have not been thoroughly delineated.Experimental Design:We performed a molecular characterization of Mongolian (n = 192) compared with Western (n = 187) HCCs by RNA sequencing and whole-exome sequencing to unveil distinct genomic and transcriptomic features associated with environmental factors in this population.Results:Mongolian patients were younger, with higher female prevalence, and with predominantly HBV–HDV coinfection etiology. Mongolian HCCs presented significantly higher rates of protein-coding mutations (121 vs. 70 mutations per tumor in Western), and in specific driver HCC genes (i.e., APOB and TSC2). Four mutational signatures characterized Mongolian samples, one of which was novel (SBS Mongolia) and present in 25% of Mongolian HCC cases. This signature showed a distinct substitution profile with a high proportion of T>G substitutions and was significantly associated with a signature of exposure to the environmental agent dimethyl sulfate (71%), a 2A carcinogenic associated with coal combustion. Transcriptomic-based analysis delineated three molecular clusters, two not present in Western HCC; one with a highly inflamed profile and the other significantly associated with younger female patients.Conclusions:Mongolian HCC has unique molecular traits with a high mutational burden and a novel mutational signature associated with genotoxic environmental factors present in this country.

Supplementary Figure from Hepatocellular Carcinoma in Mongolia Delineates Unique Molecular Traits and a Mutational Signature Associated with Environmental Agents

Supplementary Material and Method

Supplementary Figure 1. Overview of XPO1's role in nuclear:cytoplasmic transport. Supplementary Figure 2. KPT-185 is much less toxic to patient-derived benign cells than patient-derived serous high grade OvCa cells. Supplementary Figure 3. FACS cell cycle analysis of indicated cell lines treated with KPT-185 at respective IC50 doses or control DMSO for 36 hours. Data shown as mean percentage in G1 phase. Supplementary Figure 4. Combinatorial effects of KPT-185 and cisplatin in OvCa cells. Supplementary Figure 5. Knockdown of p53 by p53 siRNA blocked the KPT-mediated apoptosis in CP70 cells. Supplementary Figure 6. P53 network following KPT-185 treatment in CP70 cells. Supplementary Figure7. Representative images and mutation status of original human tumor pathology specimens and paired PDX tumor sections.

Purpose: The high fatality-to-case ratio of ovarian cancer is directly related to platinum resistance. Exportin-1 (XPO1) is a nuclear exporter that mediates nuclear export of multiple tumor suppressors. We investigated possible clinicopathologic correlations of XPO1 expression levels and evaluated the efficacy of XPO1 inhibition as a therapeutic strategy in platinum-sensitive and -resistant ovarian cancer.Experimental Design: XPO1 expression levels were analyzed to define clinicopathologic correlates using both TCGA/GEO datasets and tissue microarrays (TMA). The effect of XPO1 inhibition, using the small-molecule inhibitors KPT-185 and KPT-330 (selinexor) alone or in combination with a platinum agent on cell viability, apoptosis, and the transcriptome was tested in immortalized and patient-derived ovarian cancer cell lines (PDCL) and platinum-resistant mice (PDX). Seven patients with late-stage, recurrent, and heavily pretreated ovarian cancer were treated with an oral XPO1 inhibitor.Results: XPO1 RNA overexpression and protein nuclear localization were correlated with decreased survival and platinum resistance in ovarian cancer. Targeted XPO1 inhibition decreased cell viability and synergistically restored platinum sensitivity in both immortalized ovarian cancer cells and PDCL. The XPO1 inhibitor–mediated apoptosis occurred through both p53-dependent and p53-independent signaling pathways. Selinexor treatment, alone and in combination with platinum, markedly decreased tumor growth and prolonged survival in platinum-resistant PDX and mice. In selinexor-treated patients, tumor growth was halted in 3 of 5 patients, including one with a partial response, and was safely tolerated by all.Conclusions: Taken together, these results provide evidence that XPO1 inhibition represents a new therapeutic strategy for overcoming platinum resistance in women with ovarian cancer. Clin Cancer Res; 23(6); 1552–63. ©2016 AACR.

Supplementary Figure Legend

Supplementary Table 1. cBIO data for XPO1 overexpression and association with survival. Supplementary Table 2. Clinical features of patient samples in TMA. Supplementary Table 3. Clinicopathologic features for patient-derived tumor cell lines.

ObjectiveWe previously reported a characterisation of the hepatocellular carcinoma (HCC) immune contexture and described an immune-specific class. We now aim to further delineate the immunogenomic classification of HCC to incorporate features that explain responses/resistance to immunotherapy.DesignWe performed RNA and whole-exome sequencing, T-cell receptor (TCR)-sequencing, multiplex immunofluorescence and immunohistochemistry in a novel cohort of 240 HCC patients and validated our results in other cohorts comprising 660 patients.ResultsOur integrative analysis led to define: (1) the inflamed class of HCC (37%), which includes the previously reported immune subclass (22%) and a new immune-like subclass (15%) with high interferon signalling, cytolytic activity, expression of immune-effector cytokines and a more diverse T-cell repertoire. A 20-gene signature was able to capture ~90% of these tumours and is associated with response to immunotherapy. Proteins identified in liquid biopsies recapitulated the inflamed class with an area under the ROC curve (AUC) of 0.91; (2) The intermediate class, enriched inTP53mutations (49% vs 29%, p=0.035), and chromosomal losses involving immune-related genes and; (3) the excluded class, enriched inCTNNB1mutations (93% vs 27%, pPTK2overexpression due to gene amplification and promoter hypomethylation.CTNNB1mutations outside the excluded class led to weak activation of the Wnt-βcatenin pathway or occurred in HCCs dominated by high interferon signalling and type I antigen presenting genes.ConclusionWe have characterised the immunogenomic contexture of HCC and defined inflamed and non-inflamed tumours. Two distinctCTNNB1patterns associated with a differential role in immune evasion are described. These features may help predict immune response in HCC.

PurposeClinical analysis and reporting of somatically acquired copy number abnormalities (CNAs) detected through next-generation sequencing (NGS) is time consuming and requires significant expertise. Interpretation is complicated by other classes of variants such as coding mutations and gene fusions. Recent guidelines for the clinical assessment of tumor CNAs harmonize and simplify the reporting criteria but did not directly address NGS-specific concerns or the need for a standardized and scalable protocol for CNA analysis.MethodsWe developed a scalable NGS-derived CNA analysis protocol paired with a novel interactive web application, CNA Explorer and anaLyzer (CNAEL), to facilitate the rapid, scalable, and reproducible analysis and reporting of complex tumor-derived CNA profileshttps://CNAEL.sema4.com.ResultsNovel features of CNAEL include on-the-fly data rescaling to account for tumor ploidy, purity, and modal chromosomal copy number; integration of gene expression, coding, and fusion variants into review and automated genome-wide summarization to enable rapid reporting. We found that case curation times were significantly reduced when using CNAEL [median:7 mins, IQR = 4, 10.25] compared with our previous laboratory standard operating procedure [median: 61 mins, IQR = 23.75, 176,25] with p=4.631e-05.ConclusionCNAEL enables efficient and accurate clinical review and reporting of complex NGS-derived tumor copy number profiles.

The work is devoted to the creation and research of a model of a laser pulse location (LPL) system without the use of an electron-optical converter (EOC) as an external shutter. The system is designed to detect light reflecting objects (LROs), including optical and optoelectronic surveillance devices. The description of the hardware and capabilities of the created special software is presented. The results of measuring the dependence of the signal on the LRO rotation angle relative to the direction of the optical axis of the LPL system, on the distance to the object, and on the aperture of its lens are presented. The light reflecting characteristics (LRCs) of typical video recording devices in real conditions were experimentally determined. A method for calculating the maximum detection range of LROs in the presence of information about their LRCs by measuring an informative signal at obviously shorter ranges with an increased degree of aperture is proposed and demonstrated.

The method of pulse laser location is studied in relation to the problem of detecting retroreflective objects, including optical and optoelectronic surveillance devices. Using the created mobile specialized hardware and software stand, the retroreflection indicators of typical video recording devices in real conditions were experimentally determined. The effectiveness of periodic illumination, frame accumulation, and the formation of difference images for the detection of objects in conditions of intense sunlight is demonstrated.

536 Background: Cisplatin-based chemotherapy has been associated with functional cures (i.e., DDFTFS) in a small subset of patients with mUC. However, the mechanistic basis for this phenomenon has remained elusive. Immune checkpoint blockade may enhance the ability of cisplatin-based chemotherapy to cure mUC, particularly if the latter is achieved by promoting antitumor immunity. From a phase II trial evaluating a phased schedule of gemcitabine and cisplatin (GC) followed by GC plus Ipilimumab (Ipi) for mUC, 4/36 patients were treatment-free disease-free >7 years after initiation of treatment. We sought to identify the immunological mechanisms associated with functional cure of such patients. Methods: Whole exome sequencing was performed on pre-treatment archival tumor tissue. Neoantigen binding affinity was predicted using NetMHCcons. Neoantigen-specific T cell response was assessed via IFNγ ELISpot assays after co-culture of patient-derived peripheral blood CD4+ and CD8+ T cells with autologous neoantigen-pulsed antigen presenting B cells. Serum protein soluble analytes were measured using the Olink Target 96 Immuno-Oncology Panel at the pre-treatment, post-GC, and post-GC+Ipi timepoints. Results: CD4+ and CD8+ neoantigen-specific T cell reactivity was measured at serial timepoints in 2 patients achieving DDFTFS and 5 patients not achieving DDFTFS. Strikingly, peripheral blood CD4+ and CD8+ T cell reactivity to a predicted neoantigen emerged on cycle 6 day 1 (after 2 cycles of GC followed by 4 cycles of GC + Ipi) in 2/2 patients achieving DDFTFS (variant in TP53 or DHX9) but in 0/5 patients not achieving DDFTFS. Peripheral serum proteomic analysis at serial timepoints (n = 35 patients) revealed that pre-treatment, patients achieving DDFTFS demonstrated an immune activated phenotype with elevations in cytotoxic adaptive immunity markers and immune checkpoints (Table). After the addition of Ipi, patients achieving DDFTFS demonstrated decreased markers of tumor-promoting inflammation but increased markers of adaptive immunity, co-stimulation, and cytotoxicity. Conclusions: Anti-tumor immunity may underlie functional cures achieved in patients with mUC treated with cisplatin-based chemotherapy +/- immune checkpoint blockade. Probing the mechanistic basis for DDFTFS may facilitate the identification of pre- and on-treatment features, and therapeutic components and sequences, necessary to extend this ultimate therapeutic goal to a larger subset of patients. [Table: see text]

BACKGROUND AND AIMS Non-alcoholic steatohepatitis (NASH)-related hepatocellular carcinoma (HCC) is increasing globally, but its molecular features are not well defined. We aimed to identify unique molecular traits characterising NASH-HCC compared to other HCC aetiologies. METHODS We collected 80 NASH-HCC and 125 NASH samples from 5 institutions. Expression array (n = 53 NASH-HCC; n = 74 NASH) and whole exome sequencing (n = 52 NASH-HCC) data were compared to HCCs of other aetiologies (n = 184). Three NASH-HCC mouse models were analysed by RNA-seq/expression-array (n = 20). Activin A receptor type 2A (ACVR2A) was silenced in HCC cells and proliferation assessed by colorimetric and colony formation assays. RESULTS Mutational profiling of NASH-HCC tumours revealed TERT promoter (56%), CTNNB1 (28%), TP53 (18%) and ACVR2A (10%) as the most frequently mutated genes. ACVR2A mutation rates were higher in NASH-HCC than in other HCC aetiologies (10% vs. 3%, p

Ossifying fibromas are very rare tumors that are sometimes seen as part of the hyperparathyroidism-jaw tumor syndrome (HPT-JT), which is caused by inactivating mutations of the HRPT2/CDC73 tumor suppressor gene. CDC73 mutations have been identified in a subset of sporadic cases but aberrant expression of the encoded protein, parafibromin, has not been demonstrated in ossifying fibroma. We sought to determine if loss of parafibromin regularly contributes to the development of sporadic, nonsyndromic ossifying fibroma. We examined a series of 9 ossifying fibromas, including ossifying, cemento-ossifying, and juvenile active variants, for parafibromin protein expression by immunohistochemistry and for CDC73 sequence abnormalities by Sanger sequencing and/or targeted AmpliSeq panel sequencing. Four ossifying fibromas showed a complete absence of nuclear parafibromin expression; loss of parafibromin expression was coupled with aberrant cytoplasmic parafibromin expression in 1 case. CDC73 mutations were detected in 2 cases with aberrant parafibromin expression. These results provide novel evidence, at the level of protein expression, that loss of the parathyroid CDC73/parafibromin tumor suppressor may play a role in the pathogenesis of a subset of ossifying fibromas.

Summary Adenoid cystic carcinoma (ACC) is a rare cancer type that originates in the salivary glands. Tumors commonly invade along nerve tracks in the head and neck, making surgery challenging. Follow-up treatments for recurrence or metastasis including chemotherapy and targeted therapies have shown limited efficacy, emphasizing the need for new therapies. Here, we report a Drosophila-based therapeutic approach for a patient with advanced ACC disease. A patient-specific Drosophila transgenic line was developed to model the five major variants associated with the patient's disease. Robotics-based screening identified a three-drug cocktail—vorinostat, pindolol, tofacitinib—that rescued transgene-mediated lethality in the Drosophila patient-specific line. Patient treatment led to a sustained stabilization and a partial metabolic response of 12 months. Subsequent resistance was associated with new genomic amplifications and deletions. Given the lack of options for patients with ACC, our data suggest that this approach may prove useful for identifying novel therapeutic candidates., Graphical abstract, Highlights • Personalized therapy was developed for patient with Adenoid Cystic Carcinoma • Genomics analysis was leveraged to establish a Drosophila ‘personalized patient avatar’ • A robotics-based screen identified a novel three drug therapeutic cocktail • 12 months response was followed by relapse and significant tumor genomic re-wiring, Molecular physiology; genetics; biotechnology; cancer systems biology

Background Treatment options have been historically limited for cisplatin-ineligible patients with advanced urothelial carcinoma (UC). Given the need for alternatives to platinum-based chemotherapy, including non-chemotherapy regimens for patients with both impaired renal function and borderline functional status, in 2010 (prior to the immune checkpoint blockade era in metastatic UC), we initiated a phase II trial to test the activity of everolimus or everolimus plus paclitaxel in the cisplatin-ineligible setting. Methods This was an open-label phase II trial conducted within the US-based Hoosier Cancer Research Network (ClinicalTrials.gov number: NCT01215136). Patients who were cisplatin-ineligible with previously untreated advanced UC were enrolled. Patients with both impaired renal function and poor performance status were enrolled into cohort 1; patients with either were enrolled into cohort 2. Patients received everolimus 10 mg daily alone (cohort 1) or with paclitaxel 80 mg/m2 on days 1, 8, and 15 of each 28-day cycle (cohort 2). The primary outcome was clinical benefit at 4 months. Secondary outcomes were adverse events, progression-free survival (PFS), and 1-year overall survival (OS). Exploratory endpoints included genomic correlates of outcomes. The trial was not designed for comparison between cohorts. Results A total of 36 patients were enrolled from 2010 to 2018 (cohort 1, N = 7; cohort 2, N = 29); the trial was terminated due to slow accrual. Clinical benefit at 4 months was attained by 0 (0%, 95% confidence interval [CI] 0-41.0%) patients in cohort 1 and 11 patients (37.9%, 95% CI 20.7-57.7%) in cohort 2. Median PFS was 2.33 (95% CI 1.81-Inf) months in cohort 1 and 5.85 (95% CI 2.99-8.61) months in cohort 2. Treatment was discontinued due to adverse events for 2 patients (29%) in cohort 1 and 11 patients (38%) in cohort 2. Molecular alterations in microtubule associated genes may be associated with treatment benefit but this requires further testing. Conclusion Everolimus plus paclitaxel demonstrates clinical activity in cisplatin-ineligible patients with metastatic UC, although the specific contribution of everolimus cannot be delineated. Patients with both impaired renal function and borderline functional status may be difficult to enroll to prospective trials. (ClinicalTrials.gov Identifier NCT01215136).

Human insulinomas are rare, benign, slowly proliferating, insulin-producing beta cell tumors that provide a molecular “recipe” or “roadmap” for pathways that control human beta cell regeneration. An earlier study revealed abnormal methylation in the imprinted p15.5-p15.4 region of chromosome 11, known to be abnormally methylated in another disorder of expanded beta cell mass and function: the focal variant of congenital hyperinsulinism. Here, we compare deep DNA methylome sequencing on 19 human insulinomas, and five sets of normal beta cells. We find a remarkably consistent, abnormal methylation pattern in insulinomas. The findings suggest that abnormal insulin (INS) promoter methylation and altered transcription factor expression create alternative drivers of INS expression, replacing canonical PDX1-driven beta cell specification with a pathological, looping, distal enhancer-based form of transcriptional regulation. Finally, NFaT transcription factors, rather than the canonical PDX1 enhancer complex, are predicted to drive INS transactivation., Insulinomas are rare, benign beta cell tumours which overproduce insulin and have been associated to epigenetic alterations. Here the authors characterise insulinoma methylomes, finding changes in promoter methylation and chromatin structure proposed to drive the pathological expression of insulin.