Clinicogenomic characteristics and synthetic lethal implications of germline homologous recombination-deficient hepatocellular carcinoma.

BACKGROUNDS AND AIMS: We performed an in-depth examination of pathogenic germline variants (PGVs) and somatic variants in DNA damage response (DDR) genes in hepatocellular carcinoma (HCC) to explore their clinical and genomic impacts. APPROACH AND RESULTS: We used a merged whole-exome or RNA sequencing data set derived from in-house ( n = 230) and The Cancer Genome Atlas ( n = 362) databases of multiethnic HCC samples. We also evaluated synthetic lethal approaches targeting mutations in homologous recombination (HR) genes using HCC cells selected from five genomic databases of cancer cell lines. A total of 110 PGVs in DDR pathways in 96 patients were selected. Of the PGV carriers, 44 were HR-altered and found to be independently associated with poorer disease-free survival after hepatectomy. The most frequently altered HR gene in both germline and somatic tissues was POLQ , and this variant was detected in 22.7% (10/44) and 23.8% (5/21) of all the corresponding carriers, respectively. PGVs in HR were significantly associated with upregulation of proliferation and replication-related genes and familial risk of HCC. Samples harboring PGVs in HR with loss of heterozygosity were most strongly correlated with the genomic footprints of deficient HR, such as mutation burden and denovoSig2 (analogous to Catalogue of Somatic Mutations in Cancer [COSMIC] 3), and poor outcome. Pharmacologic experiments with HCC cells defective in BRCA2 or POLQ suggested that tumors with this phenotype are synthetic lethal with poly(ADP-ribose) polymerase inhibitors. CONCLUSIONS: Our findings suggest that germline HR defects in HCC tend to confer a poor prognosis and result in distinctive genomic scarring. Tests of the clinical benefits of HR-directed treatments in the affected patients are needed.

Artificial Intelligence-based Radiomics in the Era of Immuno-oncology.

The recent, rapid advances in immuno-oncology have revolutionized cancer treatment and spurred further research into tumor biology. Yet, cancer patients respond variably to immunotherapy despite mounting evidence to support its efficacy. Current methods for predicting immunotherapy response are unreliable, as these tests cannot fully account for tumor heterogeneity and microenvironment. An improved method for predicting response to immunotherapy is needed. Recent studies have proposed radiomics-the process of converting medical images into quantitative data (features) that can be processed using machine learning algorithms to identify complex patterns and trends-for predicting response to immunotherapy. Because patients undergo numerous imaging procedures throughout the course of the disease, there exists a wealth of radiological imaging data available for training radiomics models. And because radiomic features reflect cancer biology, such as tumor heterogeneity and microenvironment, these models have enormous potential to predict immunotherapy response more accurately than current methods. Models trained on preexisting biomarkers and/or clinical outcomes have demonstrated potential to improve patient stratification and treatment outcomes. In this review, we discuss current applications of radiomics in oncology, followed by a discussion on recent studies that use radiomics to predict immunotherapy response and toxicity.

PET-Based Radiogenomics Supports mTOR Pathway Targeting for Hepatocellular Carcinoma.

PURPOSE: This work aimed to explore in depth the genomic and molecular underpinnings of hepatocellular carcinoma (HCC) with increased 2[18F]fluoro-2-deoxy-d-glucose (FDG) uptake in PET and to identify therapeutic targets based on this imaging-genomic surrogate. EXPERIMENTAL DESIGN: We used RNA sequencing and whole-exome sequencing data obtained from 117 patients with HCC who underwent hepatic resection with preoperative FDG-PET/CT imaging as a discovery cohort. The primary radiogenomic results were validated with transcriptomes from a second cohort of 81 patients with more advanced tumors. All patients were allocated to an FDG-avid or FDG-non-avid group according to the PET findings. We also screened potential drug candidates targeting FDG-avid HCCs in vitro and in vivo. RESULTS: High FDG avidity conferred worse recurrence-free survival after HCC resection. Whole transcriptome analysis revealed upregulation of mTOR pathway signals in the FDG-avid tumors, together with higher abundance of associated mutations. These clinical and genomic findings were replicated in the validation set. A molecular signature of FDG-avid HCCs identified in the discovery set consistently predicted poor prognoses in the public-access datasets of two cohorts. Treatment with an mTOR inhibitor resulted in decreased FDG uptake followed by effective tumor control in both the hyperglycolytic HCC cell lines and xenograft mouse models. CONCLUSIONS: Our PET-based radiogenomic analysis indicates that mTOR pathway genes are markedly activated and altered in HCCs with high FDG retention. This nuclear imaging biomarker may stimulate umbrella trials and tailored treatments in precision care of patients with HCC.

Comprehensive characterization of viral integrations and genomic aberrations in HBV-infected intrahepatic cholangiocarcinomas.

BACKGROUND AND AIMS: Despite the epidemiological association between intrahepatic cholangiocarcinoma (iCCA) and HBV infection, little is known about the relevant oncogenic effects. We sought to identify the landscape and mechanism of HBV integration, along with the genomic architecture of HBV-infected iCCA (HBV-iCCA) tumors. APPROACH AND RESULTS: We profiled a cohort of 108 HBV-iCCAs using whole-genome sequencing, deep sequencing, and RNA sequencing, together with preconstructed data sets of HBV-infected HCC (HBV-HCC; n = 167) and combined hepatocellular cholangiocarcinoma (HBV-cHCC/CCA; n = 59), and conventional (n = 154) and fluke-related iCCAs (n = 16). Platforms based on primary iCCA cell lines to evaluate the functional effects of chimeric transcripts were also used. We found that HBV had inserted at multiple sites in the iCCA genomes in 45 (41.7%) of the tumors. Recurrent viral integration breakpoints were found at nine different sites. The most common insertional hotspot (7 tumors) was in the TERT (telomerase reverse transcriptase) promoter, where insertions and mutations (11 tumors) were mutually exclusive, and were accompanied by promoter hyperactivity. Recurrent HBV integration events (5 tumors) were also detected in FAT2 (FAT atypical cadherin 2), and were associated with enrichment of epithelial-mesenchymal transition-related genes. A distinctive intergenic insertion (chr9p21.3), between DMRTA1 (DMRT like family A1) and LINC01239 (long intergenic non-protein coding RNA 1239), had oncogenic effects through activation of the mammalian target of rapamycin (mTOR)/4EBP/S6K pathway. Regarding the mutational profiles of primary liver cancers, the overall landscape of HBV-iCCA was closer to that of nonviral conventional iCCA, than to HBV-HCC and HBV-cHCC/CCA. CONCLUSIONS: Our findings provide insight into the behavior of iCCAs driven by various pathogenic mechanisms involving HBV integration events and associated genomic aberrations. This knowledge should be of use in managing HBV carriers.

Inspiring hope through sources of strength among predominantly Pacific Islander communities.

Suicide death rates for Indigenous Hawaiians and other Pacific Islanders are amongst the highest in the world for youth, taking a tremendous toll on local communities (Else et al., 2007; Goebert, 2014). Comprehension of community perspectives of suicide and well-being can enhance suicide prevention interventions. This community-initiated project aimed to culturally adapt the components of an evidence-based youth suicide prevention intervention and refine the intervention methodology to align with these adaptations. Formative qualitative work was conducted with community members to obtain information on community strengths and program fit. Narrative analyses were emergent and emphasized components for suicide prevention, incorporating cultural auditing to ensure information reflected group views. Participants highlighted cultural aspects pertaining to the program philosophy, the importance of cultural protocol, local innovation in suicide prevention, and culturally grounded advancements that give back to their community. This insight was applied to two adjacent but distinct communities to integrate suicide prevention in a sustainable way by culturally adapting the program. Effective suicide prevention for rural and Indigenous youth requires a broad-based community commitment, connection, and network.

Endoscopic navigation system with extended field of view using augmented reality technology.

BACKGROUND: While endoscopic skull base surgery (ESBS) has emerged as an alternative surgical option, the limited field of view of the endoscope may lead to the surgeon's fatigue and discomfort. METHODS: The developed navigation system includes extended augmented reality (AR), which can provide an extended viewport to a conventional endoscopic view by overlaying 3D anatomical models generated from preoperative medical images onto endoscope images. To enhance the accuracy of the developed system, we adopted state-of-the-art endoscopic calibration and tracking techniques based on an optical tracking system. RESULTS: The mean spatial errors of AR was ~1 mm, which falls in the acceptable range of accuracy for ESBS. For the simulated surgical tasks with the developed system, the number and duration of error events were decreased. CONCLUSIONS: The results show that the human subject can perform the task more precisely and safely with the developed AR-based navigation system than with the conventional endoscopic system.

Aquimarina seongsanensis sp. nov., isolated from sea water.

An orange, rod-shaped, gliding bacterium, designated strain CBA3208T, was isolated from sea water of Jeju Island, Republic of Korea. Cells were observed to be Gram-stain negative, strictly aerobic, catalase positive and oxidase negative and to hydrolyse starch, gelatin, and Tweens 40 and 80. The major fatty acids were identified as iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. The only isoprenoid quinone was found to be menaquinone-6 (MK-6) and the major polar lipids were identified as phosphatidylethanolamine, two aminolipids and four unidentified polar lipids. The DNA G+C content of strain CBA3208T was determined to be 34.9 mol%. Strain CBA3208T is considered to represent a novel species of the genus Aquimarina, for which the name Aquimarina seongsanensis sp. nov. is proposed based on this polyphasic taxonomic analysis. The type strain is CBA3208T (=KACC 17667T =JCM 19529T).