Immuno-genomic analysis reveals eosinophilic feature and favorable prognosis of female non-smoking esophageal squamous cell carcinomas.

Most of esophageal squamous cell carcinoma (ESCC) develop in smoking males in Japan, but the genomic etiology and immunological characteristics of rare non-smoking female ECSS remain unclear. To elucidate the genomic and immunological features of ESCC in non-smoking females, we analyzed whole-genome or transcriptome sequencing data from 94 ESCCs, including 20 rare non-smoking female cases. In addition, 31,611 immune cells were extracted from four ESCC tissues and subject to single-cell RNA-seq. We compared their immuno-genomic and microbiome profiles between non-smoking female and smoking ESCCs. Non-smoking females showed much better prognosis. Whole-genome sequencing analysis showed no significant differences in driver genes or copy number alterations depending on smoking status. The mutational signatures specifically observed in non-smoking females ESCC could be attributed to aging. Immune profiling from RNA-seq revealed that ESCC in non-smoking females had high tumor microenvironment signatures and a high abundance of eosinophils with a favorable prognosis. Single-cell RNA-sequencing of intratumor immune cells revealed gender differences of eosinophils and their activation in female cases. ESCCs in non-smoking females have age-related mutational signatures and gender-specific tumor immune environment with eosinophils, which is likely to contribute to their favorable prognosis.

Mitochondrial DNA Variants at Low-Level Heteroplasmy and Decreased Copy Numbers in Chronic Kidney Disease (CKD) Tissues with Kidney Cancer.

The human mitochondrial genome (mtDNA) is a circular DNA molecule with a length of 16.6 kb, which contains a total of 37 genes. Somatic mtDNA mutations accumulate with age and environmental exposure, and some types of mtDNA variants may play a role in carcinogenesis. Recent studies observed mtDNA variants not only in kidney tumors but also in adjacent kidney tissues, and mtDNA dysfunction results in kidney injury, including chronic kidney disease (CKD). To investigate whether a relationship exists between heteroplasmic mtDNA variants and kidney function, we performed ultra-deep sequencing (30,000×) based on long-range PCR of DNA from 77 non-tumor kidney tissues of kidney cancer patients with CKD (stages G1 to G5). In total, this analysis detected 697 single-nucleotide variants (SNVs) and 504 indels as heteroplasmic (0.5% ≤ variant allele frequency (VAF) < 95%), and the total number of detected SNVs/indels did not differ between CKD stages. However, the number of deleterious low-level heteroplasmic variants (pathogenic missense, nonsense, frameshift and tRNA) significantly increased with CKD progression (p < 0.01). In addition, mtDNA copy numbers (mtDNA-CNs) decreased with CKD progression (p < 0.001). This study demonstrates that mtDNA damage, which affects mitochondrial genes, may be involved in reductions in mitochondrial mass and associated with CKD progression and kidney dysfunction.

Mapping the delineation of practice to the AMIA foundational domains for applied health informatics.

OBJECTIVE: This article reports on the alignment between the foundational domains and the delineation of practice (DoP) for health informatics, both developed by the American Medical Informatics Association (AMIA). Whereas the foundational domains guide graduate-level curriculum development and accreditation assessment, providing an educational pathway to the minimum competencies needed as a health informatician, the DoP defines the domains, tasks, knowledge, and skills that a professional needs to competently perform in the discipline of health informatics. The purpose of this article is to determine whether the foundational domains need modification to better reflect applied practice. MATERIALS AND METHODS: Using an iterative process and through individual and collective approaches, the foundational domains and the DoP statements were analyzed for alignment and eventual harmonization. Tables and Sankey plot diagrams were used to detail and illustrate the resulting alignment. RESULTS: We were able to map all the individual DoP knowledge statements and tasks to the AMIA foundational domains, but the statements within a single DoP domain did not all map to the same foundational domain. Even though the AMIA foundational domains and DoP domains are not in perfect alignment, the DoP provides good examples of specific health informatics competencies for most of the foundational domains. There are, however, limited DoP knowledge statements and tasks mapping to foundational domain 6-Social and Behavioral Aspects of Health. DISCUSSION: Both the foundational domains and the DoP were developed independently, several years apart, and for different purposes. The mapping analyses reveal similarities and differences between the practice experience and the curricular needs of health informaticians. CONCLUSIONS: The overall alignment of both domains may be explained by the fact that both describe the current and/or future health informatics professional. One can think of the foundational domains as representing the broad foci for educational programs for health informaticians and, hence, they are appropriately the focus of organizations that accredit these programs.

Designing audit and feedback dashboards for dentists to monitor their opioid prescribing.

BACKGROUND AND OBJECTIVE: Prescription drug abuse is a major factor leading to drug overdose deaths in the US and dentists are one of the leading prescribers of opioid pain medication. Knowing that Audit & Feedback (A&F) dashboards are an effective tool and are used as quality improvement interventions, we aimed to develop such dashboards personalized for dental providers which could allow them to monitor their own opioid prescribing performance. METHODS: In this paper we report on the process for designing the A&F dashboards for dentists which were developed by using an iterative human-centered design process. The results obtained from each iteration were used to enrich the information needs analyses, provide function testing, and guide the design decisions of the next iteration. RESULTS: Engaging dentists in the development and refinement of the dashboards while using the think-aloud protocol for user-testing, provided rapid feedback and identified areas that were confusing and needed either a redesign or additional explanatory content. The final version of dashboards consisted of displaying necessary information through easy to interpret visualizations and interactive features. These included providing access to current national and organizational prescribing guidelines, displaying changes in individual prescribing behavior over time, comparing individual prescribing rate to peer group rate and target rate, displaying procedure specific prescribing, integrating patient reported post-operative dental pain experience and providing navigation and interpretation tips for users. The dashboards were easy to learn and understand for the dentists and were deemed as worth using often in dental practice. CONCLUSION: Our research was able to demonstrate the creation of useful and usable A&F dashboards using data from electronic dental records and patient surveys, for dentists to effectively monitor their opioid prescribing behavior. Efficacy of the dashboards will be tested in future work.

Comparative analyses define differences between BHD-associated renal tumour and sporadic chromophobe renal cell carcinoma.

BACKGROUND: Birt-Hogg-Dubé (BHD) syndrome, caused by germline alteration of folliculin (FLCN) gene, develops hybrid oncocytic/chromophobe tumour (HOCT) and chromophobe renal cell carcinoma (ChRCC), whereas sporadic ChRCC does not harbor FLCN alteration. To date, molecular characteristics of these similar histological types of tumours have been incompletely elucidated. METHODS: To elucidate renal tumourigenesis of BHD-associated renal tumours and sporadic renal tumours, we conducted whole genome sequencing (WGS) and RNA-sequencing (RNA-seq) of sixteen BHD-associated renal tumours from nine unrelated BHD patients, twenty-one sporadic ChRCCs and seven sporadic oncocytomas. We then compared somatic mutation profiles with FLCN variants and RNA expression profiles between BHD-associated renal tumours and sporadic renal tumours. FINDINGS: RNA-seq analysis revealed that BHD-associated renal tumours and sporadic renal tumours have totally different expression profiles. Sporadic ChRCCs were clustered into two distinct clusters characterized by L1CAM and FOXI1 expressions, molecular markers for renal tubule subclasses. Increased mitochondrial DNA (mtDNA) copy number with fewer variants was observed in BHD-associated renal tumours compared to sporadic ChRCCs. Cell-of-origin analysis using WGS data demonstrated that BHD-associated renal tumours and sporadic ChRCCs may arise from different cells of origin and second hit FLCN alterations may occur in early third decade of life in BHD patients. INTERPRETATION: These data further our understanding of renal tumourigenesis of these two different types of renal tumours with similar histology. FUNDING: This study was supported by JSPS KAKENHI Grants, RIKEN internal grant, and the Intramural Research Program of the National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research.

Why is biomedical informatics hard? A fundamental framework.

Building on previous work to define the scientific discipline of biomedical informatics, we present a framework that categorizes fundamental challenges into groups based on data, information, and knowledge, along with the transitions between these levels. We define each level and argue that the framework provides a basis for separating informatics problems from non-informatics problems, identifying fundamental challenges in biomedical informatics, and provides guidance regarding the search for general, reusable solutions to informatics problems. We distinguish between processing data (symbols) and processing meaning. Computational systems, that are the basis for modern information technology (IT), process data. In contrast, many important challenges in biomedicine, such as providing clinical decision support, require processing meaning, not data. Biomedical informatics is hard because of the fundamental mismatch between many biomedical problems and the capabilities of current technology.

Genotype-phenotype mapping of a patient-derived lung cancer organoid biobank identifies NKX2-1-defined Wnt dependency in lung adenocarcinoma.

Human lung cancer is a constellation of tumors with various histological and molecular properties. To build a preclinical platform that covers this broad disease spectrum, we obtained lung cancer specimens from multiple sources, including sputum and circulating tumor cells, and generated a living biobank consisting of 43 lines of patient-derived lung cancer organoids. The organoids recapitulated the histological and molecular hallmarks of the original tumors. Phenotypic screening of niche factor dependency revealed that EGFR mutations in lung adenocarcinoma are associated with the independence from Wnt ligands. Gene engineering of alveolar organoids reveals that constitutive activation of EGFR-RAS signaling provides Wnt independence. Loss of the alveolar identity gene NKX2-1 confers Wnt dependency, regardless of EGFR signal mutation. Sensitivity to Wnt-targeting therapy can be stratified by the expression status of NKX2-1. Our results highlight the potential of phenotype-driven organoid screening and engineering for the fabrication of therapeutic strategies to combat cancer.

Variant spectrum of von Hippel-Lindau disease and its genomic heterogeneity in Japan.

Von Hippel-Lindau (VHL) disease is an autosomal dominant, inherited syndrome with variants in the VHL gene, causing predisposition to multi-organ neoplasms with vessel abnormality. Germline variants in VHL can be detected in 80-90% of patients clinically diagnosed with VHL disease. Here, we summarize the results of genetic tests for 206 Japanese VHL families, and elucidate the molecular mechanisms of VHL disease, especially in variant-negative unsolved cases. Of the 206 families, genetic diagnosis was positive in 175 families (85%), including 134 families (65%) diagnosed by exon sequencing (15 novel variants) and 41 (20%) diagnosed by multiplex ligation-dependent probe amplification (MLPA) (one novel variant). The deleterious variants were significantly enriched in VHL disease Type 1. Interestingly, five synonymous or non-synonymous variants within exon 2 caused exon 2 skipping, which is the first report of exon 2 skipping caused by several missense variants. Whole genome and target deep sequencing analysis were performed for 22 unsolved cases with no variant identified and found three cases with VHL mosaicism (variant allele frequency: 2.5-22%), one with mobile element insertion in the VHL promoter region, and two with a pathogenic variant of BAP1 or SDHB. The variants associated with VHL disease are heterogeneous, and for more accuracy of the genetic diagnosis of VHL disease, comprehensive genome and DNA/RNA analyses are required to detect VHL mosaicism, complicated structure variants and other related gene variants.

Alphaviruses Detected in Mosquitoes in the North-Eastern Regions of South Africa, 2014 to 2018.

The prevalence and distribution of African alphaviruses such as chikungunya have increased in recent years. Therefore, a better understanding of the local distribution of alphaviruses in vectors across the African continent is important. Here, entomological surveillance was performed from 2014 to 2018 at selected sites in north-eastern parts of South Africa where alphaviruses have been identified during outbreaks in humans and animals in the past. Mosquitoes were collected using a net, CDC-light, and BG-traps. An alphavirus genus-specific nested RT-PCR was used for screening, and positive pools were confirmed by sequencing and phylogenetic analysis. We collected 64,603 mosquitoes from 11 genera, of which 39,035 females were tested. Overall, 1462 mosquito pools were tested, of which 21 were positive for alphaviruses. Sindbis (61.9%, N = 13) and Middelburg (28.6%, N = 6) viruses were the most prevalent. Ndumu virus was detected in two pools (9.5%, N = 2). No chikungunya positive pools were identified. Arboviral activity was concentrated in peri-urban, rural, and conservation areas. A range of Culicidae species, including Culex univittatus, Cx. pipiens s.l., Aedes durbanensis, and the Ae. dentatus group, were identified as potential vectors. These findings confirm the active circulation and distribution of alphaviruses in regions where human or animal infections were identified in South Africa.

Survey of West Nile and Banzi Viruses in Mosquitoes, South Africa, 2011-2018.

We collected >40,000 mosquitoes from 5 provinces in South Africa during 2011-2018 and screened for zoonotic flaviviruses. We detected West Nile virus in mosquitoes from conservation and periurban sites and potential new mosquito vectors; Banzi virus was rare. Our results suggest flavivirus transmission risks are increasing in South Africa.

Hereditary cancer variants and homologous recombination deficiency in biliary tract cancer.

BACKGROUND & AIMS: The heritability and actionability of variants in homologous recombination-related genes in biliary tract cancers (BTCs) are uncertain. Although associations between BTC and BRCA germline variants have been reported, homologous recombination deficiency has not been investigated in BTCs. METHODS: We sequenced germline variants in 27 cancer-predisposing genes in 1,292 BTC cases and 37,583 controls without a personal nor family history of cancer. We compared pathogenic germline variant frequencies between cases and controls and documented the demographic and clinical characteristics of carriers. In addition, whole-genome sequencing of 45 BTC tissues was performed to evaluate homologous recombination deficiency status. RESULTS: Targeted sequencing identified 5,018 germline variants, which were classified into 317 pathogenic, 3,611 variants of uncertain significance, and 1,090 benign variants. Seventy-one BTC cases (5.5%) had at least one pathogenic variant among 27 cancer-predisposing genes. Pathogenic germline variants enriched in BTCs were present in BRCA1, BRCA2, APC, and MSH6 (p <0.00185). PALB2 variants were marginally associated with BTC (p = 0.01). APC variants were predominantly found in ampulla of Vater carcinomas. Whole-genome sequencing demonstrated that three BTCs with pathogenic germline variants in BRCA2 and PALB2, accompanied by loss of heterozygosity, displayed homologous recombination deficiency. Conversely, pathogenic germline variants without a second hit or variants of other homologous recombination-related genes such as ATM and BRIP1 showed homologous recombination-proficient phenotypes. CONCLUSIONS: In this study, we describe the heritability and actionability of variants in homologous recombination-related genes, which could be used to guide screening and therapeutic strategies for BTCs. IMPACT AND IMPLICATIONS: We found that 5.5% of biliary tract cancers (BTCs) in a Japanese population possessed hereditary cancer-predisposing gene alterations, including in BRCA and genes associated with colorectal cancer. Two hits in homologous recombination-related genes were required to confer a homologous recombination-deficient phenotype. PARP inhibitors and DNA-damaging regimens may be effective strategies against BTCs exhibiting homologous recombination deficiency. Hence, in this study, genome-wide sequencing has revealed a potential new therapeutic strategy that could be applied to a subset of BTCs.

Genomic features of renal cell carcinoma developed during end-stage renal disease and dialysis.

Patients with end-stage renal disease (ESRD) or receiving dialysis have a much higher risk for renal cell carcinoma (RCC), but carcinogenic mechanisms and genomic features remain little explored and undefined. This study's goal was to identify the genomic features of ESRD RCC and characterize them for associations with tumor histology and dialysis exposure. In this study, we obtained 33 RCCs, with various histological subtypes, that developed in ESRD patients receiving dialysis and performed whole-genome sequencing and transcriptome analyses. Driver events, copy-number alteration (CNA) analysis and mutational signature profiling were performed using an analysis pipeline that integrated data from germline and somatic SNVs, Indels and structural variants as well as CNAs, while transcriptome data were analyzed for differentially expressed genes and through gene set enrichment analysis. ESRD related clear cell RCCs' driver genes and mutations mirrored those in sporadic ccRCCs. Longer dialysis periods significantly correlated with a rare mutational signature SBS23, whose etiology is unknown, and increased mitochondrial copy number. All acquired cystic disease (ACD)-RCCs, which developed specifically in ESRD patients, showed chromosome 16q amplification. Gene expression analysis suggests similarity between certain ACD-RCCs and papillary RCCs and in TCGA papillary RCCs with chromosome 16 gain identified enrichment for genes related to DNA repair, as well as pathways related to reactive oxygen species, oxidative phosphorylation and targets of Myc. This analysis suggests that ESRD or dialysis could induce types of cellular stress that impact some specific types of genomic damage leading to oncogenesis.

Immuno-genomic profiling of biopsy specimens predicts neoadjuvant chemotherapy response in esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive cancers and is primarily treated with platinum-based neoadjuvant chemotherapy (NAC). Some ESCCs respond well to NAC. However, biomarkers to predict NAC sensitivity and their response mechanism in ESCC remain unclear. We perform whole-genome sequencing and RNA sequencing analysis of 141 ESCC biopsy specimens before NAC treatment to generate a machine-learning-based diagnostic model to predict NAC reactivity in ESCC and analyzed the association between immunogenomic features and NAC response. Neutrophil infiltration may play an important role in ESCC response to NAC. We also demonstrate that specific copy-number alterations and copy-number signatures in the ESCC genome are significantly associated with NAC response. The interactions between the tumor genome and immune features of ESCC are likely to be a good indicator of therapeutic capability and a therapeutic target for ESCC, and machine learning prediction for NAC response is useful.

Injectable ECM Scaffolds for Cardiac Repair.

Injectable biomaterials have been developed as potential minimally invasive therapies for treating myocardial infarction (MI) and heart failure. Christman et al. first showed that the injection of a biomaterial alone into rat myocardium can improve cardiac function after MI. More recently, hydrogel forms of decellularized extracellular matrix (ECM) materials have shown substantial promise. Here, we present the methods for fabricating an injectable cardiac-specific ECM biomaterial with demonstrated positive outcomes in small and large animal models for cardiac repair as well as initial safety in a Phase I clinical trial. This chapter also covers the methods for the injection of a biomaterial into rat myocardium using a surgical approach through the diaphragm. Although the methods shown here are for injection of an acellular biomaterial, cells or other therapeutics could also be added to the injection for testing other regenerative medicine strategies.

Myositis ossificans of the breast - A rare case report with radiologic-pathologic correlation.

Myositis ossificans is a pathologic process of ossification in soft tissues. The breast is an exceptionally rare location for myositis ossificans with less than 5 cases documented in the English literature. We present a case of a 66-year-old woman with myositis ossificans of the left breast and no known initiating trauma. The significance of the progression of clinical and radiological findings are discussed in detail. This case shows the importance of radiology for identifying unique pathology as well as close radiological follow up.

Caries Risk Documentation And Prevention: eMeasures For Dental Electronic Health Records.

BACKGROUND: Longitudinal patient level data available in the electronic health record (EHR) allows for the development, implementation, and validations of dental quality measures (eMeasures). OBJECTIVE: We report the feasibility and validity of implementing two eMeasures. The eMeasures determined the proportion of patients receiving a caries risk assessment (eCRA) and corresponding appropriate risk-based preventative treatments for patients at elevated risk of caries (appropriateness of care [eAoC]) in two academic institutions and one accountable care organization, in the 2019 reporting year. METHODS: Both eMeasures define the numerator and denominator beginning at the patient level, populations' specifications, and validated the automated queries. For eCRA, patients who completed a comprehensive or periodic oral evaluation formed the denominator, and patients of any age who received a CRA formed the numerator. The eAoC evaluated the proportion of patients at elevated caries risk who received the corresponding appropriate risk-based preventative treatments. RESULTS: EHR automated queries identified in three sites 269,536 patients who met the inclusion criteria for receiving a CRA. The overall proportion of patients who received a CRA was 94.4% (eCRA). In eAoC, patients at elevated caries risk levels (moderate, high, or extreme) received fluoride preventive treatment ranging from 56 to 93.8%. For patients at high and extreme risk, antimicrobials were prescribed more frequently site 3 (80.6%) than sites 2 (16.7%) and 1 (2.9%). CONCLUSION: Patient-level data available in the EHRs can be used to implement process-of-care dental eCRA and AoC, eAoC measures identify gaps in clinical practice. EHR-based measures can be useful in improving delivery of evidence-based preventative treatments to reduce risk, prevent tooth decay, and improve oral health.

An Adaptive, Affordable, Open-Source Robotic Hand for Deaf and Deaf-Blind Communication Using Tactile American Sign Language.

Currently, ~ 1.5 million American deaf-blind individuals depend on the availability of interpreting services to communicate in their primary conversational language, tactile American Sign Language (ASL). In an effort to give the deaf-blind community access to a device that facilitates independent communication using tactile ASL, we developed TATUM (Tactile ASL Translational User Mechanism). TATUM employs 15 degrees of actuation in a hand-wrist system that is capable of signing the 26-letter ASL alphabet. Leveraging Interpres, an independent cloud-based service, all servo sequences that render desired fingerspelled letters and ASL words are stored in a web application programming interface (API). A validation study including both deaf and deaf-blind participants confirmed that the TATUM hand mimics a human hand both in size and feel. The current design of TATUM attained an average recognition rate of 94.7% in visual validation, indicative of the potential to support deaf and deaf-blind individuals in communicating via visual and tactile ASL.

Potential Mosquito Vectors for Shuni Virus, South Africa, 2014-2018.

Shuni virus is associated with neurologic and febrile illness in animals and humans. To determine potential vectors, we collected mosquitoes in South Africa and detected the virus in species of the genera Mansonia, Culex, Aedes, and Anopheles. These mosquitoes may be associated with Shuni virus outbreaks in Africa and emergence in other regions.