James Chodosh

Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren’s syndrome

Sjögrens syndrome is a common autoimmune disease (affecting ∼0.7% of European Americans) that typically presents as keratoconjunctivitis sicca and xerostomia. Here we report results of a large-scale association study of Sjögrens syndrome. In addition to strong association within the human leukocyte antigen (HLA) region at 6p21 (Pmeta = 7.65 × 10−114), we establish associations with IRF5-TNPO3 (Pmeta = 2.73 × 10−19), STAT4 (Pmeta = 6.80 × 10−15), IL12A (Pmeta = 1.17 × 10−10), FAM167A-BLK (Pmeta = 4.97 × 10−10), DDX6-CXCR5 (Pmeta = 1.10 × 10−8) and TNIP1 (Pmeta = 3.30 × 10−8). We also observed suggestive associations (Pmeta < 5 × 10−5) with variants in 29 other regions, including TNFAIP3, PTTG1, PRDM1, DGKQ, FCGR2A, IRAK1BP1, ITSN2 and PHIP, among others. These results highlight the importance of genes that are involved in both innate and adaptive immunity in Sjögrens syndrome.

Evidence of Molecular Evolution Driven by Recombination Events Influencing Tropism in a Novel Human Adenovirus that Causes Epidemic Keratoconjunctivitis

In 2005, a human adenovirus strain (formerly known as HAdV-D22/H8 but renamed here HAdV-D53) was isolated from an outbreak of epidemic keratoconjunctititis (EKC), a disease that is usually caused by HAdV-D8, -D19, or -D37, not HAdV-D22. To date, a complete change of tropism compared to the prototype has never been observed, although apparent recombinant strains of other viruses from species Human adenovirus D (HAdV-D) have been described. The complete genome of HAdV-D53 was sequenced to elucidate recombination events that lead to the emergence of a viable and highly virulent virus with a modified tropism. Bioinformatic and phylogenetic analyses of this genome demonstrate that this adenovirus is a recombinant of HAdV-D8 (including the fiber gene encoding the primary cellular receptor binding site), HAdV-D22, (the ε determinant of the hexon gene), HAdV-D37 (including the penton base gene encoding the secondary cellular receptor binding site), and at least one unknown or unsequenced HAdV-D strain. Bootscanning analysis of the complete genomic sequence of this novel adenovirus, which we have re-named HAdV-D53, indicated at least five recombination events between the aforementioned adenoviruses. Intrahexon recombination sites perfectly framed the ε neutralization determinant that was almost identical to the HAdV-D22 prototype. Additional bootscan analysis of all HAdV-D hexon genes revealed recombinations in identical locations in several other adenoviruses. In addition, HAdV-D53 but not HAdV-D22 induced corneal inflammation in a mouse model. Serological analysis confirmed previous results and demonstrated that HAdV-D53 has a neutralization profile representative of the ε determinant of its hexon (HAdV-D22) and the fiber (HAdV-D8) proteins. Our recombinant hexon sequence is almost identical to the hexon sequences of the HAdV-D strain causing EKC outbreaks in Japan, suggesting that HAdV-D53 is pandemic as an emerging EKC agent. This documents the first genomic, bioinformatic, and biological descriptions of the molecular evolution events engendering an emerging pathogenic adenovirus.

Computational Analysis Identifies Human Adenovirus Type 55 as a Re-Emergent Acute Respiratory Disease Pathogen

ABSTRACT Novel human adenoviruses (HAdVs) arise from genome recombination. Analysis of HAdV type 55 from an outbreak in China shows a hexon recombination between HAdV-B11 and HAdV-B14, resulting in a genome that is 97.4% HAdV-B14. Sporadic appearances as a re-emergent pathogen and misidentification as “HAdV-B11a” are due to this partial hexon.

Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality.

Adenoviral infections are typically acute, self-limiting, and not associated with death. However, we present the genomic and bioinformatics analysis of a novel recombinant human adenovirus (HAdV-D56) isolated in France that caused a rare neonatal fatality, and keratoconjunctivitis in three health care workers who cared for the neonate. Whole genome alignments revealed the expected diversity in the penton base, hexon, E3, and fiber coding regions, and provided evidence for extensive recombination. Bootscan analysis confirmed recombination between HAdV-D9, HAdV-D26, HAdV-D15, and HAdV-D29 in the penton base and hexon proteins, centered around hypervariable loops within the putative proteins. Protein structure analysis of the fiber coding region revealed similarity with HAdV-D8, HAdV-D9, and HAdV-D53, possibly accounting for the ocular tropism of the virus. Based on these data, this virus appears to be a new HAdV-D type (HAdV-D56), underscoring the importance of recombination events in human adenovirus evolution and the emergence of new adenovirus pathogens.

Comparison of the American-European Consensus Group Sjögren's syndrome classification criteria to newly proposed American College of Rheumatology criteria in a large, carefully characterised sicca cohort

Abstract Objective To compare the performance of the American–European Consensus Group (AECG) and the newly proposed American College of Rheumatology (ACR) classification criteria for Sjögrens Syndrome (SS) in a well-characterised sicca cohort, given ongoing efforts to resolve discrepancies and weaknesses in the systems. Methods In a multidisciplinary clinic for the evaluation of sicca, we assessed features of salivary and lacrimal gland dysfunction and autoimmunity as defined by tests of both AECG and ACR criteria in 646 participants. Global gene expression profiles were compared in a subset of 180 participants. Results Application of the AECG and ACR criteria resulted in classification of 279 and 268 participants with SS, respectively. Both criteria were met by 244 participants (81%). In 26 of the 35 AECG+/ACR participants, the minor salivary gland biopsy focal score was ≥1 (74%), while nine had positive anti-Ro/La (26%). There were 24 AECG−/ACR+ who met ACR criteria mainly due to differences in the scoring of corneal staining. All patients with SS, regardless of classification, had similar gene expression profiles, which were distinct from the healthy controls. Conclusions The two sets of classification criteria yield concordant results in the majority of cases and gene expression profiling suggests that patients meeting either set of criteria are more similar to other SS participants than to healthy controls. Thus, there is no clear evidence for increased value of the new ACR criteria over the old AECG criteria from the clinical or biological perspective. It is our contention, supported by this report, that improvements in diagnostic acumen will require a more fundamental understanding of the pathogenic mechanisms than is at present available.

Molecular evolution of human adenoviruses

The recent emergence of highly virulent human adenoviruses (HAdVs) with new tissue tropisms underscores the need to determine their ontogeny. Here we report complete high quality genome sequences and analyses for all the previously unsequenced HAdV serotypes (n = 20) within HAdV species D. Analysis of nucleotide sequence variability for these in conjunction with another 40 HAdV prototypes, comprising all seven HAdV species, confirmed the uniquely hypervariable regions within species. The mutation rate among HAdV-Ds was low when compared to other HAdV species. Homologous recombination was identified in at least two of five examined hypervariable regions for every virus, suggesting the evolution of HAdV-Ds has been highly dependent on homologous recombination. Patterns of alternating GC and AT rich motifs correlated well with hypervariable region recombination sites across the HAdV-D genomes, suggesting foci of DNA instability lead to formulaic patterns of homologous recombination and confer agility to adenovirus evolution.

Effect of Anti-CXCL10 Monoclonal Antibody on Herpes Simplex Virus Type 1 Keratitis and Retinal Infection

ABSTRACT The inflammatory response to acute ocular herpes simplex virus type 1 (HSV-1) infection in mice involves the innate and adaptive immune response, with an associated increase in the secretion of chemokines, including CXCL10 (interferon-inducible protein 10 kDa [IP-10]). Neutralizing antibodies to mouse CXCL10 were used to determine the role of CXCL10 during the acute phase of HSV-1 ocular infection. Treatment of HSV-1-infected mice with antibody to CXCL10 significantly reduced CXCL10 levels in the eye and trigeminal ganglion and reduced mononuclear cell infiltration into the corneal stroma. These results coincided with reduced ICAM-1 and CXCR3 transcript expression, macrophage inflammatory protein-1α and CXCL10 levels, and corneal pathology but increased viral titers in the stroma and trigeminal ganglion. Progression of the virus from the corneal stroma to the retina during acute infection was significantly hindered in anti-CXCL10-treated mice. In addition, colocalization of viral antigen with infiltrating leukocytes in the iris and retina during acute infection suggests that one means by which HSV-1 traffics to the retina involves inflammatory cells (primarily CD11b+ cells). Collectively, the results suggest that CXCL10 expression in the eye initially orchestrates the inflammatory response to acute HSV-1 infection, which facilitates the spread of the virus to other restricted sites within the eye.

Using the whole genome sequence to characterize and name human adenoviruses.

We propose that human adenoviruses (HAdVs) be identified, characterized, and typed on the basis of complete genome sequence analyses rather than serological approaches. This idea has recently percolated through the community of adenovirologists. As a result, an open-floor discussion took place at the Ninth International Adenovirus Meeting (Dobogokő, Hungary, April 2009) on the need for a paradigm shift in recognizing and naming HAdVs in the future. An ad hoc committee then met to formulate the principles of the new approach. Recommendations 1 through 4 originated during the open-floor discussion and were discussed by the committee; recommendations 5 and 6 were developed by the authors to avoid conflicting claims and to deal with recombinants. These were reaffirmed at an NIH-sponsored and user-driven workshop of the Human Adenovirus Working Group, which met at NCBI (Bethesda, MD) on February 3, 2011. “Type” will succeed “serotype,” reflecting the prevalence of genome sequence data usage; type is already in usage per International Committee on Taxonomy of Viruses (ICTV) definitions. Previously named HAdVs will transition to the new format; e.g., “serotype HAdV-C1” will become “type HAdV-C1,” where the letter “C” indicates the adenovirus species (currently species A through G). Each adenovirus type will have a unique, consecutively assigned number; i.e., there will not be an HAdV-D54 and an HAdV-C54. Acceptance of a new type will require analysis of the complete genome sequence, including phylogenomics. Serum neutralization will continue to be used as an additional criterion, per the ICTV definition. This should be by actual serum neutralization and hemagglutination inhibition, rather than by imputed derivation by limited DNA sequencing of the epitopes. Naming priority will follow the order in which genome sequence data are released in the public sequence databases. Adherence to the Bermuda principles, whereby sequences are released as soon as possible, will be encouraged (see http://www.ornl.gov/sci/techresources/Human_Genome/publicat/hgn/v7n6/19intern.shtml). Recombination is an accepted feature of HAdV evolution and will be accommodated. Recombinants will be classified as novel types if there are sufficient genomic, biological, or pathogenic differences from related types. Until a new recombinant genome is peer-reviewed and published, a provisional standardized name that reflects critical serological markers and similarities to established types in species, penton base, and serology-based motifs in hexon and fiber, plus the year and place of isolation, will be used for the recombinant. Thus, the provisional name for HAdV-D53 is HAdV-D/Hannover/[unique identifier]/2005/P37/H22/F8. “P” refers to the penton base, “H” to the hexon loop 1 region, and “F” to the fiber knob; numbers refer to the established type with the highest level of nucleotide identity in the respective regions. The unique identifier is a lab designation or strain name, e.g., 2005-IAI-1 for HAdV-D53 isolate 1 and 2005-IAI-2 for HAdV-D53 isolate 2 should both genomes be deposited in GenBank. Discoverers of “candidate” novel HAdV types should submit a FASTA file with the genome nucleotide sequence and the “evidence” to vog.hin.mln.ibcn@semoneg with the subject line “Human Adenovirus Working Group.” This file will be forwarded with submitter information removed to the NIH Human Adenovirus Working Group for a rapid, preliminary, confidential data review to coordinate the assignment of type number. This is not meant as a peer review but will prevent multiple genomes being assigned the same type number. Detailed information, including contact information for the working group members and current recommendations on typing parameters, may be found at http://hadvwg.gmu.edu. HAdV typing criteria are being refined, and input from the community is appreciated. Revisions to the criteria used in establishing HAdV types must avoid compromising the stability and utility of the current system while accommodating changes in technology that reflect the nature of the data available. The effective replacement of serology by DNA sequencing and bioinformatics has recently been observed with the characterization of HAdV-G52, HAdV-D53, HAdV-D54, HAdV-B55, and HAdV-D56. These advances set the scene for the recognition of new HAdV types in the future.

Computational Analysis of Two Species C Human Adenoviruses Provides Evidence of a Novel Virus

ABSTRACT Human adenovirus C (HAdV-C) species are a common cause of respiratory infections and can occasionally produce severe clinical manifestations. A deeper understanding of the variation and evolution in species HAdV-C is especially important since these viruses, including HAdV-C6, are used as gene delivery vectors for human gene therapy and in other biotechnological applications. Here, the full-genome analysis of the prototype HAdV-C6 and a recently identified virus provisionally termed HAdV-C57 are reported. Although the genomes of all species HAdV-C members are very similar to each other, the E3 region, hexon and fiber (ten proteins total) present a wide range of identity values at the amino acid level. Studies of these viruses in comparison to the other three HAdV-C prototypes (1, 2, and 5) comprise a comprehensive analysis of the diversity and conservation within HAdV-C species. HAdV-C6 contains a recombination event within the constant region of the hexon gene. HAdV-C57 is a recombinant virus with a fiber gene nearly identical to HAdV-C6 and a unique hexon distinguished by its loop 2 motif.

Partial dislocation of laser in situ keratomileusis flap by air bag injury.

PURPOSE A patient developed significant corneal complications from air bag deployment, 17 months after laser in situ keratomileusis (LASIK). METHODS Case report, slit-lamp microscopy, and review of the medical literature. RESULTS A 37-year-old woman underwent bilateral LASIK with resultant 20/20 uncorrected visual acuity. Seventeen months later, she sustained facial and ocular injuries from air bag deployment during a motor vehicle accident. Examination revealed bilateral corneal abrasions, partial dislocation of the right corneal LASIK flap, and a hyphema in the right eye. The LASIK flap was realigned, but recovery was complicated by a slowly healing epithelial defect and flap edema. One month following the injury, epithelial ingrowth beneath the LASIK flap was noted. Surgical elevation of the flap and removal of the epithelial ingrowth was performed. Eight months later, epithelial ingrowth was absent and the visual acuity was 20/40. Residual irregular astigmatism necessitated rigid gas permeable contact lens fitting to achieve 20/20 visual acuity. CONCLUSIONS Air bags may cause significant ocular trauma. The wound healing response of LASIK allows corneal flap separation from its stromal bed for an indeterminate time after surgery. Discussion of the possible risk of corneal trauma as part of informed consent prior to LASIK may be appropriate.