The cellular architecture and molecular determinants of the zebrafish fusogenic synapse

Myoblast fusion is an indispensable process in skeletal muscle development and regeneration. Studies in Drosophila led to the discovery of the asymmetric fusogenic synapse, in which one cell invades its fusion partner with actin-propelled membrane protrusions to promote fusion. However, the timing and sites of vertebrate myoblast fusion remain elusive. Here, we show that fusion between zebrafish fast muscle cells is mediated by an F-actin-enriched invasive structure. Two cell adhesion molecules, Jam2a and Jam3b, are associated with the actin structure, with Jam2a being the major organizer. The Arp2/3 actin nucleation-promoting factors, WAVE and WASP-but not the bipartite fusogenic proteins, Myomaker or Myomixer-promote the formation of the invasive structure. Moreover, the convergence of fusogen-containing microdomains and the invasive protrusions is a prerequisite for cell membrane fusion. Thus, our study provides unprecedented insights into the cellular architecture and molecular determinants of the asymmetric fusogenic synapse in an intact vertebrate animal.

Repeated Coronavirus Disease 2019 Molecular Testing: Correlation of Severe Acute Respiratory Syndrome Coronavirus 2 Culture With Molecular Assays and Cycle Thresholds

BACKGROUND

Repeated coronavirus disease 2019 (COVID-19) molecular testing can lead to positive test results after negative results and to multiple positive results over time. The association between positive test results and infectious virus is important to quantify.

METHODS

A 2-month cohort of retrospective data and consecutively collected specimens from patients with COVID-19 or patients under investigation were used to understand the correlation between prolonged viral RNA positive test results, cycle threshold (Ct) values and growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in cell culture. Whole-genome sequencing was used to confirm virus genotype in patients with prolonged viral RNA detection. Droplet digital polymerase chain reaction was used to assess the rate of false-negative COVID-19 diagnostic test results.

RESULTS

In 2 months, 29 686 specimens were tested and 2194 patients underwent repeated testing. Virus recovery in cell culture was noted in specimens with a mean Ct value of 18.8 (3.4) for SARS-CoV-2 target genes. Prolonged viral RNA shedding was associated with positive virus growth in culture in specimens collected up to 21 days after the first positive result but mostly in individuals symptomatic at the time of sample collection. Whole-genome sequencing provided evidence the same virus was carried over time. Positive test results following negative results had Ct values >29.5 and were not associated with virus culture. Droplet digital polymerase chain reaction results were positive in 5.6% of negative specimens collected from patients with confirmed or clinically suspected COVID-19.

CONCLUSIONS

Low Ct values in SARS-CoV-2 diagnostic tests were associated with virus growth in cell culture. Symptomatic patients with prolonged viral RNA shedding can also be infectious.

Abstract 604: Accurate identification and prioritization of candidate neoantigens from integrated cancer exome and transcriptome sequencing of FFPE samples

Precise identification and characterization of candidate neoantigens is important for the development of effective cancer vaccines, adoptive T-cell transfer, and prediction of response to checkpoint inhibitors. The candidate tumor neoantigens are actionable only when expressed, however, current prediction methods lack the capacity to evaluate neoantigen expression. Sequencing both DNA and RNA from a patient’s tumor tissue enables identification of mutations and evaluation of their expression leading to accurate identification of putative neoantigens. The purpose of this study was to develop and validate a methodology for co-extraction and sequencing of DNA and RNA from formalin-fixed paraffin-embedded (FFPE) samples to enable a robust neoantigen prediction protocol that integrates whole exome and transcriptome data to identify and prioritize tumor neoantigens for application in immuno-oncology research and clinical trials. In order to prepare high-quality sequencing libraries from FFPE specimens, the tissue was macrodissected to enrich for tumor-specific material, and improve the overall accuracy of next-generation sequencing for detection of somatic alterations. Total DNA and RNA was co-extracted and purified. The DNA was used to prepare whole exome sequencing (WES) libraries, while the co-extracted RNA was ribosome-depleted, and reverse-transcribed to prepare RNA sequencing (RNAseq) libraries. The WES and RNAseq data was then analyzed using a multi-algorithm HLA typing and neoantigen prediction protocol (ImmunoSelect-RTM). ImmunoSelect-R evaluates somatic genomic alterations identified from WES of tumor and matched normal tissue to ensure appropriate prediction of candidate neoantigens. The process of neoantigen prediction was then refined by integration of patient tumor-matched RNAseq data, which allowed for removal of non-expressed putative neoantigens. To further validate the approach, we applied the methodology to a set of experimentally validated neoantigens. In this setting, ImmunoSelect-R correctly classified 18 out of 19 as strong neoantigen candidates, suggesting a sensitivity of greater than 90%. Moreover, in a set of 10 patients, ImmunoSelect-R consistently ranked experimentally validated neoantigens within the top 20% of all neoantigen candidates derived from whole exome sequencing. In summary, our combined tissue processing, macrodissection, co-extraction, and neoantigen prediction methodology is able to identify and prioritize candidate neoantigens. Our approach is unique in combining high-fidelity sequencing (WES) and expression (RNAseq) data to accurately inform the selection of actionable tumor neoantigens for immuno-oncology applications.

Citation Format: Marián Novak, Sam Angiuoli, Luis A. Diaz, Andrew Georgiadis, Sian Jones, Peter R. Loverso, Sonya Parpart-Li, Maria Sevdali, Victor E. Velculescu, Ellen L. Verner, James White, Theresa Zhang, Mark Sausen. Accurate identification and prioritization of candidate neoantigens from integrated cancer exome and transcriptome sequencing of FFPE samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 604. doi:10.1158/1538-7445.AM2017-604

Abstract A039: Accurate identification and prioritization of candidate neoantigens from cancer exome sequencing

Somatic, nonsynonymous genetic alterations present in cancer can lead to the formation of novel protein sequences and thus production of immunogenic “non-self” neoantigens. Those neoantigens with sufficient expression will be processed and presented on MHC molecules, subsequently inducing a tumor-specific T cell response. Emerging data from clinical studies suggest that neoantigen load and composition is associated with the efficacy of some immunotherapies. As neoantigens play central a role in the cancer-immunity cycle, it is critical to identify the most potent immunogenic neoantigens effectively and accurately. Here we have leveraged highly accurate cancer whole exome (WES) analyses from FFPE tumor tissue with a state-of-the-art analysis protocol to identify and prioritize candidate neoantigens most likely to promote an immune response. ImmunoSelect-R utilizes somatic variants from WES to ensure detection of true somatic peptides and minimize false positives, and provides accurate HLA typing from whole exome sequencing data with >99.9% sensitivity and specificity. When applied to a set of experimentally validated neoantigens, ImmunoSelect correctly classified 18 out of 19 as strong neoantigen candidates, suggesting a sensitivity of greater than 90%. Moreover, in a small set of 10 patients, ImmunoSelect consistently ranked experimentally validated neoantigens within top 20% of all neoantigen candidates derived from whole exome sequencing. In summary, ImmunoSelect is able to identify and prioritize candidate neoantigens from cancer exome sequencing results effectively and accurately, enabling personalized cancer vaccine development, adoptive T-cell transfer, and prediction of response to checkpoint inhibitors

Citation Format: James White, John Simmons, Sam Angiuoli, Mark Sausen, Sian Jones, Lisa Kann, Manish Shukla, Maria Sevdali, Victor Velculescu, Luis Diaz, Theresa Zhang. Accurate identification and prioritization of candidate neoantigens from cancer exome sequencing [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A039.

Abstract 528: Identify and prioritize candidate neoantigens from cancer exome sequencing with unmatched accuracy

Somatic, nonsynonymous genetic alterations present in cancer can lead to the formation of novel protein sequences and thus production of immunogenic “non-self” neoantigens. Some of those neoantigens will be processed, presented on MHC molecules, and induce tumor-specific T cell responses. Because neoantigens play central roles in the cancer-immunity cycle, it is critical to identify the most potent immunogenic neoantigens effectively and accurately.

Combining PGDx's highly accurate cancer exome analyses (CancerXome™) with in silico neoantigen prediction, we have launched ImmunoSelect-R™ that identifies and prioritizes the most relevant mutation-derived neoantigens. To ensure detection of true somatic mutations and prevent false positive mutations from confounding neoantigen identification, ImmunoSelect utilizes CancerXome that delivers unparalleled cancer whole exome sequencing accuracy, achieving 95% sensitivity and 97% positive predictive value at 10% mutant allele frequency with 150x coverage. ImmunoSelect also provides accurate HLA typing from whole exome sequencing with >99.9% sensitivity and specificity. Once exome-based mutations and novel open-reading-frames are identified and HLA genotypes defined, ImmunoSelect utilizes state of art bioinformatics pipelines for prediction and prioritization of the most relevant neoantigens. When applied to a set of experimentally validated neoantigens, ImmunoSelect identified 18 out of 19 of them as being strong neoantigen candidates, suggesting a sensitivity of greater than 90%. Moreover, ImmunoSelect consistently ranked experimentally validated neoantigens within top 20% of all neoantigen candidates derived from whole exome sequencing.

In summary, ImmunoSelect is able to identify and prioritize candidate neoantigens from cancer exome sequencing results effectively and accurately, enabling personalized cancer vaccine development, adoptive T-cell transfer, and prediction of response to checkpoint inhibitors

Citation Format: James White, Sam Angiuoli, Mark Sausen, Sian Jones, Lisa Kann, Manish Shukla, Maria Sevdali, Victor Velculescu, Luis Diaz, Theresa Zhang. Identify and prioritize candidate neoantigens from cancer exome sequencing with unmatched accuracy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 528.

Human congenital myopathy actin mutants cause myopathy and alter Z-disc structure in Drosophila flight muscle

Over 190 mutations in the human skeletal muscle α-actin gene, ACTA1 cause congenital actin myopathies. We transgenically expressed six different mutant actins, G15R, I136M, D154N, V163L, V163M and D292V in Drosophila indirect flight muscles and investigated their effects in flies that express one wild type and one mutant actin copy. All the flies were flightless, and the IFMs showed incomplete Z-discs, disorganised actin filaments and 'zebra bodies'. No differences in levels of sarcomeric protein expression were observed, but tropomodulin staining was somewhat disrupted in D164N, V163L, G15R and V163M heterozygotes. A single copy of D292V mutant actin rescued the hypercontractile phenotypes caused by TnI and TnT mutants, suggesting that the D292V mutation interferes with thin filament regulation. Our results show that expression of actin mutations homologous to those in humans in the indirect flight muscles of Drosophila disrupt sarcomere organisation, with somewhat similar phenotypes to those observed in humans. Using Drosophila to study actin mutations may help aid our understanding of congential myopathies caused by actin mutations.

Neuromuscular control of a single twitch muscle in wild type and mutant Drosophila, measured with an ergometer

How do deficits in neuronal growth, aging or synaptic function affect the final, mechanical output of a single muscle twitch? We address this in vivo (indeed in situ) with a novel ergometer that records the output of a large specialised muscle, the Drosophila jump muscle. Here, we describe in detail the ergometer, its construction and use. We evaluated the ergometer by showing that adult fly jump muscle output varies little between 3 h and 7 days; but newly eclosed flies produce only 65%. In a mutant with little octopamine (Tbetah), jump muscle performance is reduced by 28%. The initial responses of synaptic growth mutants (highwire and spinster) do not differ from wild type, as expected on the homeostatic hypothesis. However, responses in highwire mutations gradually decline following repeated stimuli, suggesting physiological as well as anatomical abnormalities. We conclude that the assay is robust, sensitive and reliable with a good throughput.

Comparison of the manual Mycobacteria Growth Indicator tube and the Etest with the method of proportion for susceptibility testing of Mycobacterium tuberculosis

BACKGROUND

Clinical microbiology laboratories should provide reliable results on susceptibility testing of Mycobacterium tuberculosis to different agents.

METHODS

The manual Mycobacteria Growth Indicator Tube (MGIT) and Etest were compared to the method of proportion (MOP) for susceptibility testing of 88 clinical isolates of M. tuberculosis against isoniazid (INH), rifampin (RIF), streptomycin (STR) and ethambutol (EMB). Isolates were recovered from different patients and were identified at species level by PCR and hybridization.

RESULTS

Resistance to INH was detected in 20.5, 29.5 and 12.5% of the isolates, followed by STR resistance (19.3, 26.1 and 1.1%), RIF (9.1, 4.5 and 5.7%) and EMB (2.3, 11.4 and 2.3%) by the MOP, MGIT and Etest, respectively. Sensitivity of the manual MGIT ranged from 37.5% for RIF resistance to 100% for EMB, while Etest sensitivity ranged from 5.9% for STR to 62.5% for RIF.

CONCLUSIONS

MOP remains the method of choice, with the manual MGIT showing superior sensitivity at detecting resistance to INH, STR and EMB compared to the Etest.

Sensitivity of the Cobas Amplicor system for detection of Mycobacterium tuberculosis in respiratory and extrapulmonary specimens

The Cobas Amplicor PCR system (CA-PCR) was compared with culture and staining for acid-fast bacilli (AFB) for the early detection of Mycobacterium tuberculosis in respiratory clinical specimens and otherwise normal sterile body fluids. The sensitivity, specificity and positive and negative predictive values of CA-PCR were determined with AFB-positive and AFB-negative specimens. The sensitivity of CA-PCR ranged from 73.6% to 100% for AFB-positive samples, while sputa collected after bronchoscopy were the most useful specimens, with 70% sensitivity and 98.6% specificity among the AFB-negative samples.