Scholars@Duke
Nicholas Fredric Parrish

Nicholas Fredric Parrish

Medical Instructor in the Department of Surgery
Surgery, Abdominal Transplant Surgery

Selected Publications

An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases.

Journal Article Science · July 5, 2024 Transcribed enhancer maps can reveal nuclear interactions underpinning each cell type and connect specific cell types to diseases. Using a 5' single-cell RNA sequencing approach, we defined transcription start sites of enhancer RNAs and other classes of co ... Full text Link to item Cite

Fetal cord plasma herpesviruses and preeclampsia: an observational cohort study.

Journal Article Sci Rep · June 25, 2024 A previous study suggested that fetal inheritance of chromosomally integrated human herpesvirus 6 (ici-HHV6) is associated with the hypertensive pregnancy disorder preeclampsia (PE). We aimed to study this question utilizing cord plasma samples (n = 1276) ... Full text Link to item Cite

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

Journal Article Hum Mol Genet · June 5, 2023 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 d ... Full text Link to item Cite

Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk.

Journal Article Nat Genet · June 2023 Mobile genetic elements (MEs) are heritable mutagens that recursively generate structural variants (SVs). ME variants (MEVs) are difficult to genotype and integrate in statistical genetics, obscuring their impact on genome diversification and traits. We de ... Full text Link to item Cite

Bridging multiple dimensions: roles of transposable elements in higher-order genome regulation.

Journal Article Curr Opin Genet Dev · June 2023 Transposable elements (TEs) such as endogenous retroviruses (ERVs), long interspersed nuclear elements (LINEs), and short interspersed nuclear elements (SINEs) occupy nearly half of typical mammalian genomes. Previous studies show that these parasitic elem ... Full text Link to item Cite

Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning.

Journal Article Nat Biomed Eng · June 2023 Gene transcription is regulated through complex mechanisms involving non-coding RNAs (ncRNAs). As the transcription of ncRNAs, especially of enhancer RNAs, is often low and cell type specific, how the levels of RNA transcription depend on genotype remains ... Full text Link to item Cite

The regulation of persistent Borna disease virus infection by RNA silencing factors in human cells.

Journal Article Biochem Biophys Res Commun · May 28, 2023 Viral infection induces diverse cellular immune responses. Some viruses induce the production of antiviral cytokines, alterations of endogenous gene expression, and apoptosis; however, other viruses replicate without inducing such responses, enabling them ... Full text Link to item Cite

A hominoid-specific endogenous retrovirus may have rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells.

Journal Article PLoS Genet · May 2022 Mammalian germ cells stem from primordial germ cells (PGCs). Although the gene regulatory network controlling the development of germ cells such as PGCs is critical for ensuring gamete integrity, substantial differences exist in this network among mammalia ... Full text Link to item Cite

Preface

Journal Article Methods in Molecular Biology · January 1, 2022 Cite

Mammalian antiviral systems directed by small RNA.

Journal Article PLoS Pathog · December 2021 There are strong incentives for human populations to develop antiviral systems. Similarly, genomes that encode antiviral systems have had strong selective advantages. Protein-guided immune systems, which have been well studied in mammals, are necessary for ... Full text Link to item Cite

Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more.

Journal Article PLoS Comput Biol · October 2021 Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequen ... Full text Link to item Cite

Virus-derived variation in diverse human genomes.

Journal Article PLoS Genet · April 2021 Acquisition of genetic material from viruses by their hosts can generate inter-host structural genome variation. We developed computational tools enabling us to study virus-derived structural variants (SVs) in population-scale whole genome sequencing (WGS) ... Full text Link to item Cite

Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome.

Journal Article Proc Natl Acad Sci U S A · February 2, 2021 Understanding the genetics and taxonomy of ancient viruses will give us great insights into not only the origin and evolution of viruses but also how viral infections played roles in our evolution. Endogenous viruses are remnants of ancient viral infection ... Full text Link to item Cite

Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa.

Journal Article Mol Biol Evol · January 4, 2021 Human herpesvirus 6A and 6B (HHV-6) can integrate into the germline, and as a result, ∼70 million people harbor the genome of one of these viruses in every cell of their body. Until now, it has been largely unknown if 1) these integrations are ancient, 2) ... Full text Link to item Cite

Prevalence and Spectrum of Pathogenic Germline Variants in Japanese Patients With Early-Onset Colorectal, Breast, and Prostate Cancer.

Journal Article JCO Precis Oncol · November 2020 PUPOSE: We investigated the prevalence and spectrum of pathogenic germline variants in patients with early-onset colorectal cancer (CRC), breast cancer (BC), and prostate cancer (PCA) in the Japanese population. We also identified pathogenic variants in ot ... Full text Link to item Cite

Endogenous retroviruses drive species-specific germline transcriptomes in mammals.

Journal Article Nat Struct Mol Biol · October 2020 Gene regulation in the germline ensures the production of high-quality gametes, long-term maintenance of the species and speciation. Male germline transcriptomes undergo dynamic changes after the mitosis-to-meiosis transition and have been subject to evolu ... Full text Link to item Cite

Endogenization and excision of human herpesvirus 6 in human genomes.

Journal Article PLoS Genet · August 2020 Sequences homologous to human herpesvirus 6 (HHV-6) are integrated within the nuclear genome of about 1% of humans, but it is not clear how this came about. It is also uncertain whether integrated HHV-6 can reactivate into an infectious virus. HHV-6 integr ... Full text Link to item Cite

piRNA-Guided CRISPR-like Immunity in Eukaryotes.

Journal Article Trends Immunol · November 2019 Eukaryotic genomes contain virus-derived sequences called endogenous virus elements (EVEs). The majority of EVEs are related to retroviruses, which integrate into the host genome in order to replicate. Some retroviral EVEs encode a function; for example, s ... Full text Link to item Cite

The Changing Face of Liver Transplantation in the United States: The Effect of HCV Antiviral Eras on Transplantation Trends and Outcomes.

Journal Article Transplant Direct · March 2019 BACKGROUND: Hepatitis C virus (HCV) cirrhosis is the leading indication for liver transplantation in the United States, although nonalcoholic steatohepatitis (NASH) is on the rise. Increasingly effective HCV antivirals are available, but their association ... Full text Link to item Cite

Species-specific host factors rather than virus-intrinsic virulence determine primate lentiviral pathogenicity.

Journal Article Nat Commun · April 10, 2018 HIV-1 causes chronic inflammation and AIDS in humans, whereas related simian immunodeficiency viruses (SIVs) replicate efficiently in their natural hosts without causing disease. It is currently unknown to what extent virus-specific properties are responsi ... Full text Open Access Link to item Cite

A Viral (Arc)hive for Metazoan Memory.

Journal Article Cell · January 11, 2018 Arc, a master regulator of synaptic plasticity, contains sequence elements that are evolutionarily related to retrotransposon Gag genes. Two related papers in this issue of Cell show that Arc retains retroviral-like capsid-forming ability and can transmit ... Full text Link to item Cite

Endogenized viral sequences in mammals.

Journal Article Curr Opin Microbiol · June 2016 Reverse-transcribed RNA molecules compose a significant portion of the human genome. Many of these RNA molecules were retrovirus genomes either infecting germline cells or having done so in a previous generation but retaining transcriptional activity. This ... Full text Link to item Cite

A global reference for human genetic variation.

Journal Article Nature · October 1, 2015 The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having recons ... Full text Link to item Cite

An integrated map of structural variation in 2,504 human genomes.

Journal Article Nature · October 1, 2015 Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we c ... Full text Link to item Cite

piRNAs derived from ancient viral processed pseudogenes as transgenerational sequence-specific immune memory in mammals.

Journal Article RNA · October 2015 Endogenous bornavirus-like nucleoprotein elements (EBLNs) are sequences within vertebrate genomes derived from reverse transcription and integration of ancient bornaviral nucleoprotein mRNA via the host retrotransposon machinery. While species with EBLNs a ... Full text Link to item Cite

Transcription Profiling Demonstrates Epigenetic Control of Non-retroviral RNA Virus-Derived Elements in the Human Genome.

Journal Article Cell Rep · September 8, 2015 Endogenous bornavirus-like nucleoprotein elements (EBLNs) are DNA sequences in vertebrate genomes formed by the retrotransposon-mediated integration of ancient bornavirus sequence. Thus, EBLNs evidence a mechanism of retrotransposon-mediated RNA-to-DNA inf ... Full text Link to item Cite

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Journal Article Nat Commun · June 1, 2015 Investigating genomic structural variants at basepair resolution is crucial for understanding their formation mechanisms. We identify and analyse 8,943 deletion breakpoints in 1,092 samples from the 1000 Genomes Project. We find breakpoints have more nearb ... Full text Link to item Cite

Neutralization properties of simian immunodeficiency viruses infecting chimpanzees and gorillas.

Journal Article mBio · April 21, 2015 UNLABELLED: Broadly cross-reactive neutralizing antibodies (bNabs) represent powerful tools to combat human immunodeficiency virus type 1 (HIV-1) infection. Here, we examined whether HIV-1-specific bNabs are capable of cross-neutralizing distantly related ... Full text Open Access Link to item Cite

Borna disease virus possesses an NF-ĸB inhibitory sequence in the nucleoprotein gene.

Journal Article Sci Rep · March 3, 2015 Borna disease virus (BDV) has a non-segmented, negative-stranded RNA genome and causes persistent infection in many animal species. Previous study has shown that the activation of the IκB kinase (IKK)/NF-κB pathway is reduced by BDV infection even in cells ... Full text Link to item Cite

Quantitative phosphoproteomics reveals extensive cellular reprogramming during HIV-1 entry.

Journal Article Cell Host Microbe · May 15, 2013 Receptor engagement by HIV-1 during host cell entry activates signaling pathways that can reprogram the cell for optimal viral replication. To obtain a global view of the signaling events induced during HIV-1 entry, we conducted a quantitative phosphoprote ... Full text Link to item Cite

Phenotypic properties of transmitted founder HIV-1.

Journal Article Proc Natl Acad Sci U S A · April 23, 2013 Defining the virus-host interactions responsible for HIV-1 transmission, including the phenotypic requirements of viruses capable of establishing de novo infections, could be important for AIDS vaccine development. Previous analyses have failed to identify ... Full text Open Access Link to item Cite

Transmitted/founder and chronic HIV-1 envelope proteins are distinguished by differential utilization of CCR5.

Journal Article J Virol · March 2013 Infection by HIV-1 most often results from the successful transmission and propagation of a single virus variant, termed the transmitted/founder (T/F) virus. Here, we compared the attachment and entry properties of envelope (Env) glycoproteins from T/F and ... Full text Link to item Cite

Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones.

Journal Article Virology · February 5, 2013 We report the molecular identification, cloning and initial biological characterization of 12 full-length HIV-1 subtype A, D and A/D recombinant transmitted/founder (T/F) genomes. T/F genomes contained intact canonical open reading frames and all T/F virus ... Full text Link to item Cite

Mucosal simian immunodeficiency virus transmission in African green monkeys: susceptibility to infection is proportional to target cell availability at mucosal sites.

Journal Article J Virol · April 2012 African green monkeys (AGMs) are naturally infected with a simian immunodeficiency virus (SIVagm) that is nonpathogenic in its host. Although SIVagm is common and widespread, little is known about the mechanisms that govern its transmission. Since the earl ... Full text Link to item Cite

Transmitted/founder and chronic subtype C HIV-1 use CD4 and CCR5 receptors with equal efficiency and are not inhibited by blocking the integrin α4β7.

Journal Article PLoS Pathog · 2012 Sexual transmission of human immunodeficiency virus type 1 (HIV-1) most often results from productive infection by a single transmitted/founder (T/F) virus, indicating a stringent mucosal bottleneck. Understanding the viral traits that overcome this bottle ... Full text Link to item Cite

Primary infection by a human immunodeficiency virus with atypical coreceptor tropism.

Journal Article J Virol · October 2011 The great majority of human immunodeficiency virus type 1 (HIV-1) strains enter CD4+ target cells by interacting with one of two coreceptors, CCR5 or CXCR4. Here we describe a transmitted/founder (T/F) virus (ZP6248) that was profoundly impaired in its abi ... Full text Link to item Cite

Phenotypic and immunologic comparison of clade B transmitted/founder and chronic HIV-1 envelope glycoproteins.

Journal Article J Virol · September 2011 Sexual transmission of human immunodeficiency virus type 1 (HIV-1) across mucosal barriers is responsible for the vast majority of new infections. This relatively inefficient process results in the transmission of a single transmitted/founder (T/F) virus, ... Full text Link to item Cite

Genetic identity and biological phenotype of a transmitted/founder virus representative of nonpathogenic simian immunodeficiency virus infection in African green monkeys.

Journal Article J Virol · December 2010 Understanding the lack of disease progression in nonpathogenic simian immunodeficiency virus (SIV) infections is essential for deciphering the immunopathogenesis of human AIDS. Yet, in vivo studies have been hampered by a paucity of infectious molecular cl ... Full text Link to item Cite

A rev1-vpu polymorphism unique to HIV-1 subtype A and C strains impairs envelope glycoprotein expression from rev-vpu-env cassettes and reduces virion infectivity in pseudotyping assays.

Journal Article Virology · February 20, 2010 Functional studies of HIV-1 envelope glycoproteins (Envs) commonly include the generation of pseudoviruses, which are produced by co-transfection of rev-vpu-env cassettes with an env-deficient provirus. Here, we describe six Env constructs from transmitted ... Full text Link to item Cite

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection.

Journal Article J Exp Med · June 8, 2009 Identification of full-length transmitted HIV-1 genomes could be instrumental in HIV-1 pathogenesis, microbicide, and vaccine research by enabling the direct analysis of those viruses actually responsible for productive clinical infection. We show in 12 ac ... Full text Link to item Cite

Functional relationship between bacterial cell density and the efficacy of antibiotics.

Journal Article J Antimicrob Chemother · April 2009 OBJECTIVES: To determine the functional relationship between the density of bacteria and the pharmacodynamics of antibiotics, and the potential consequences of this inoculum effect on the microbiological course of antibiotic treatment of Staphylococcus aur ... Full text Link to item Cite