Genomic Characterization of Familial Pancreatic Cancer Leads to Discovery of a Novel Structural Variant in Cancer

Despite dramatic increases in the survival of cancer in general over the last 5 decades, the 5-year survival of pancreatic ductal adenocarcinoma (PDAC) remains relatively unchanged at 6%. Approximately 10% of PDAC cases are familial pancreatic cancer (FPC), involving two or more affected first-degree relatives. Despite large sequencing efforts over the past decade, less than 20% of FPC cases have an identified causal germline mutation, despite recent large-scale sequencing efforts by our group and others. Unlike the majority of familial cancer syndromes, our analysis shows that FPC is not associated with an earlier age of onset compared to its sporadic counterpart. We theorized that the similar age of onset may be the result of shared between sporadic and familial PDAC driver genes, KRAS, TP53, CDKN2A/p16, and DPC4/SMAD4. Our analysis of PDAC driver genes in our cohort of FPC cancer cell lines, using high density SNP microarray, whole exome sequencing (WES), whole genome sequencing (WGS), and RNA-Seq, confirmed that FPC has alterations in the PDAC driver genes and at the same prevalence as sporadic. Given that the genes p16 and SMAD4 are commonly inactivated by deletions, we hypothesized that the underlying structural rearrangements could provide insight into the mechanism of driver gene deletions in cancer. Our breakpoint analysis of the p16 and SMAD4 deletions using WGS data revealed a novel structural variant that we have termed “TransFlip mutations.” A TransFlip mutation is an inter-chromosomal translocation on one side and an inversion on the other side, flanking a deletion. My thesis work highlights the similarity of FPC with sporadic PDAC, both in the driver genes and in the age of onset. Here I report the discovery of TransFlip mutations, a new structural variant in cancer, highlighting the complexity of cancer genomes and the challenges of reliably calling structural variants. Advisor: Dr. James R. Eshleman (Reader) Thesis Committee: Dr. Sarah J. Wheelan (Reader) Dr. Kenneth Kinzler (Chair) Dr. Ralph H. Hruban Dr. Alison P. Klei

Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19

Neutralizing autoantibodies against type I interferons (IFNs) have been found in some patients with critical coronavirus disease 2019 (COVID-19), the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the prevalence of these antibodies, their longitudinal dynamics across the disease severity scale, and their functional effects on circulating leukocytes remain unknown. Here, in 284 patients with COVID-19, we found type I IFN–specific autoantibodies in peripheral blood samples from 19% of patients with critical disease and 6% of patients with severe disease. We found no type I IFN autoantibodies in individuals with moderate disease. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 patients with COVID-19 and 26 non–COVID-19 controls revealed a lack of type I IFN–stimulated gene (ISG-I) responses in myeloid cells from patients with critical disease. This was especially evident in dendritic cell populations isolated from patients with critical disease producing type I IFN–specific autoantibodies. Moreover, we found elevated expression of the inhibitory receptor leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) on the surface of monocytes isolated from patients with critical disease early in the disease course. LAIR1 expression is inversely correlated with ISG-I expression response in patients with COVID-19 but is not expressed in healthy controls. The deficient ISG-I response observed in patients with critical COVID-19 with and without type I IFN–specific autoantibodies supports a unifying model for disease pathogenesis involving ISG-I suppression through convergent mechanisms

Increased Protein Insolubility in Brains From a Subset of Patients With Schizophrenia.

OBJECTIVE: The mechanisms leading to schizophrenia are likely to be diverse. However, there may be common pathophysiological pathways for subtypes of the disease. The authors tested the hypothesis that increased protein insolubility and ubiquitination underlie the pathophysiology for a subtype of schizophrenia. METHODS: Prefrontal cortex and superior temporal gyrus from postmortem brains of individuals with and without schizophrenia were subjected to cold sarkosyl fractionation, separating proteins into soluble and insoluble fractions. Protein insolubility and ubiquitin levels were quantified for each insoluble fraction, with normalization to total homogenate protein. Mass spectrometry analysis was then performed to identify the protein contents of the insoluble fractions. The potential biological relevance of the detected proteins was assessed using Gene Ontology enrichment analysis and Ingenuity Pathway Analysis. RESULTS: A subset of the schizophrenia brains showed an increase in protein insolubility and ubiquitination in the insoluble fraction. Mass spectrometry of the insoluble fraction revealed that brains with increased insolubility and ubiquitination exhibited a similar peptide expression by principal component analysis. The proteins that were significantly altered in the insoluble fraction were enriched for pathways relating to axon target recognition as well as nervous system development and function. CONCLUSIONS: This study suggests a pathological process related to protein insolubility for a subset of patients with schizophrenia. Determining the molecular mechanism of this subtype of schizophrenia could lead to a better understanding of the pathways underlying the clinical phenotype in some patients with major mental illness as well as to improved nosology and identification of novel therapeutic targets

RoB-SPEO: A tool for assessing risk of bias in studies estimating the prevalence of exposure to occupational risk factors from the WHO/ILO Joint Estimates of the Work-related Burden of Disease and Injury

BACKGROUND: The World Health Organization (WHO) and the International Labour Organization (ILO) are developing joint estimates of the work-related burden of disease and injury (WHO/ILO Joint Estimates). For this, systematic reviews of studies estimating the prevalence of exposure to selected occupational risk factors will be conducted to provide input data for estimations of the number of exposed workers. A critical part of systematic review methods is to assess risk of bias (RoB) of individual studies. In this article, we present and describe the development of such a tool, called the Risk of Bias in Studies estimating Prevalence of Exposure to Occupational risk factors (RoB-SPEO) tool; report results from RoB-SPEO's pilot testing; note RoB-SPEO's limitations; and suggest how the tool might be tested and developed further. METHODS: Selected existing RoB tools used in environmental and occupational health systematic reviews were reviewed and analysed. From existing tools, we identified domains for the new tool and, if necessary, added new domains. For each domain, we then identified and integrated components from the existing tools (i.e. instructions, domains, guiding questions, considerations, ratings and rating criteria), and, if necessary, we developed new components. Finally, we elicited feedback from other systematic review methodologists and exposure scientists and agreed upon RoB-SPEO. Nine experts pilot tested RoB-SPEO, and we calculated a raw measure of inter-rater agreement (Pi) for each of its domain, rating Pi  0.80 as almost perfect agreement. RESULTS: Our review found no standard tool for assessing RoB in prevalence studies of exposure to occupational risk factors. We identified six existing tools for environmental and occupational health systematic reviews and found that their components for assessing RoB differ considerably. With the new RoB-SPEO tool, assessors judge RoB for each of eight domains: (1) bias in selection of participants into the study; (2) bias due to a lack of blinding of study personnel; (3) bias due to exposure misclassification; (4) bias due to incomplete exposure data; (5) bias due to conflict of interest; (6) bias due to selective reporting of exposures; (7) bias due to difference in numerator and denominator; and (8) other bias. The RoB-SPEO's ratings are low, probably low, probably high, high or no information. Pilot testing of the RoB-SPEO tool found substantial inter-rater agreement for six domains (range of Pi for these domains: 0.51-0.80), but poor agreement for two domains (i.e. Pi of 0.31 and 0.33 for biases due to incomplete exposure data and in selection of participants into the study, respectively). Limitations of RoB-SPEO include that it has not yet been fully performance-tested. CONCLUSIONS: We developed the RoB-SPEO tool for assessing RoB in prevalence studies of exposure to occupational risk factors. The tool will be applied and its performance tested in the ongoing systematic reviews for the WHO/ILO Joint Estimates.status: publishe