%0 Journal Article %J bioRxiv %D 2023 %T Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load. %A Avadhanula, Vasanthi %A Creighton, Chad J %A Ferlic-Stark, Laura %A Sucgang, Richard %A Zhang, Yiqun %A Nagaraj, Divya %A Nicholson, Erin G %A Rajan, Anubama %A Menon, Vipin Kumar %A Harshavardhan Doddapaneni %A Donna M Muzny %A Ginger A Metcalf %A Cregeen, Sara Joan Javornik %A Hoffman, Kristi Louise %A Richard A Gibbs %A Petrosino, Joseph %A Piedra, Pedro A %X

Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.

%B bioRxiv %8 2023 May 25 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/37292999?dopt=Abstract %R 10.1101/2023.05.24.542181 %0 Journal Article %J Sci Rep %D 2021 %T Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors. %A Chen, Fengju %A Zhang, Yiqun %A Sucgang, Richard %A Ramani, Sasirekha %A Corry, David %A Kheradmand, Farrah %A Creighton, Chad J %K A549 Cells %K Bronchi %K COVID-19 %K Epithelial Cells %K Host Microbial Interactions %K Humans %K Immunity %K Lung Neoplasms %K SARS-CoV-2 %K Transcription, Genetic %K Transcriptome %K Virus Replication %X

A deeper understanding of the molecular biology of SARS-CoV-2 infection, including the host response to the virus, is urgently needed. Commonalities exist between the host immune response to viral infections and cancer. Here, we defined transcriptional signatures of SARS-CoV-2 infection involving hundreds of genes common across lung adenocarcinoma cell lines (A549, Calu-3) and normal human bronchial epithelial cells (NHBE), with additional signatures being specific to one or both adenocarcinoma lines. Cross-examining eight transcriptomic databases, we found that host transcriptional responses of lung adenocarcinoma cells to SARS-CoV-2 infection shared broad similarities with host responses to multiple viruses across different model systems and patient samples. Furthermore, these SARS-CoV-2 transcriptional signatures were manifested within specific subsets of human cancer, involving ~ 20% of cases across a wide range of histopathological types. These cancer subsets show immune cell infiltration and inflammation and involve pathways linked to the SARS-CoV-2 response, such as immune checkpoint, IL-6, type II interferon signaling, and NF-κB. The cell line data represented immune responses activated specifically within the cancer cells of the tumor. Common genes and pathways implicated as part of the viral host response point to therapeutic strategies that may apply to both SARS-CoV-2 and cancer.

%B Sci Rep %V 11 %P 2459 %8 2021 Jan 28 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/33510359?dopt=Abstract %R 10.1038/s41598-021-82221-4 %0 Journal Article %J PLoS One %D 2021 %T Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. %A Harshavardhan Doddapaneni %A Cregeen, Sara Javornik %A Sucgang, Richard %A Meng, Qingchang %A Xiang Qin %A Avadhanula, Vasanthi %A Chao, Hsu %A Menon, Vipin %A Nicholson, Erin %A Henke, David %A Piedra, Felipe-Andres %A Rajan, Anubama %A Momin, Zeineen %A Kottapalli, Kavya %A Hoffman, Kristi L %A Fritz J Sedlazeck %A Ginger A Metcalf %A Piedra, Pedro A %A Donna M Muzny %A Petrosino, Joseph F %A Richard A Gibbs %K COVID-19 %K DNA, Complementary %K Gene Frequency %K Genetic Variation %K Genome, Viral %K Humans %K Open Reading Frames %K Real-Time Polymerase Chain Reaction %K RNA, Viral %K SARS-CoV-2 %K Sequence Analysis, DNA %K Viral Load %X

The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

%B PLoS One %V 16 %P e0244468 %8 2021 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/34432798?dopt=Abstract %R 10.1371/journal.pone.0244468 %0 Journal Article %J bioRxiv %D 2020 %T Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. %A Harshavardhan Doddapaneni %A Cregeen, Sara Javornik %A Sucgang, Richard %A Meng, Qingchang %A Xiang Qin %A Avadhanula, Vasanthi %A Chao, Hsu %A Menon, Vipin %A Nicholson, Erin %A Henke, David %A Piedra, Felipe-Andres %A Rajan, Anubama %A Momin, Zeineen %A Kottapalli, Kavya %A Hoffman, Kristi L %A Fritz J Sedlazeck %A Ginger A Metcalf %A Piedra, Pedro A %A Donna M Muzny %A Petrosino, Joseph F %A Richard A Gibbs %X

The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

%B bioRxiv %8 2020 Jul 27 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/32766579?dopt=Abstract %R 10.1101/2020.07.27.223495 %0 Journal Article %J bioRxiv %D 2020 %T Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals. %A Harshavardhan Doddapaneni %A Cregeen, Sara Javornik %A Sucgang, Richard %A Meng, Qingchang %A Xiang Qin %A Avadhanula, Vasanthi %A Chao, Hsu %A Menon, Vipin %A Nicholson, Erin %A Henke, David %A Piedra, Felipe-Andres %A Rajan, Anubama %A Momin, Zeineen %A Kottapalli, Kavya %A Hoffman, Kristi L %A Fritz J Sedlazeck %A Ginger A Metcalf %A Piedra, Pedro A %A Donna M Muzny %A Petrosino, Joseph F %A Richard A Gibbs %X

The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

%B bioRxiv %8 2020 Dec 11 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/33330863?dopt=Abstract %R 10.1101/2020.12.11.421057 %0 Journal Article %J Curr Biol %D 2015 %T Genomic signatures of cooperation and conflict in the social amoeba. %A Ostrowski, Elizabeth A %A Shen, Yufeng %A Tian, Xiangjun %A Sucgang, Richard %A Jiang, Huaiyang %A Qu, Jiaxin %A Katoh-Kurasawa, Mariko %A Brock, Debra A %A Dinh, Christopher %A Lara-Garduno, Fremiet %A Lee, Sandra L %A Kovar, Christie L %A Dinh, Huyen H %A Korchina, Viktoriya %A Jackson, Laronda %A Patil, Shobha %A Han, Yi %A Chaboub, Lesley %A Shaulsky, Gad %A Muzny, Donna M %A Worley, Kim C %A Gibbs, Richard A %A Richards, Stephen %A Kuspa, Adam %A Strassmann, Joan E %A Queller, David C %K Dictyostelium %K Evolution, Molecular %K Genome, Protozoan %K Genomics %K Polymorphism, Genetic %K Selection, Genetic %X

Cooperative systems are susceptible to invasion by selfish individuals that profit from receiving the social benefits but fail to contribute. These so-called "cheaters" can have a fitness advantage in the laboratory, but it is unclear whether cheating provides an important selective advantage in nature. We used a population genomic approach to examine the history of genes involved in cheating behaviors in the social amoeba Dictyostelium discoideum, testing whether these genes experience rapid evolutionary change as a result of conflict over spore-stalk fate. Candidate genes and surrounding regions showed elevated polymorphism, unusual patterns of linkage disequilibrium, and lower levels of population differentiation, but they did not show greater between-species divergence. The signatures were most consistent with frequency-dependent selection acting to maintain multiple alleles, suggesting that conflict may lead to stalemate rather than an escalating arms race. Our results reveal the evolutionary dynamics of cooperation and cheating and underscore how sequence-based approaches can be used to elucidate the history of conflicts that are difficult to observe directly.

%B Curr Biol %V 25 %P 1661-5 %8 2015 Jun 15 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/26051890?dopt=Abstract %R 10.1016/j.cub.2015.04.059 %0 Journal Article %J Nucleic Acids Res %D 2003 %T Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. %A Sucgang, Richard %A Chen, Guokai %A Liu, Wen %A Lindsay, Ryan %A Lu, Jing %A Muzny, Donna %A Shaulsky, Gad %A Loomis, William %A Gibbs, Richard %A Kuspa, Adam %K Animals %K Chromosome Mapping %K Dictyostelium %K DNA, Protozoan %K In Situ Hybridization, Fluorescence %K Molecular Sequence Data %K Plasmids %K RNA, Ribosomal %K Sequence Analysis, DNA %X

Ribosomal RNAs (rRNAs) are encoded by multicopy families of identical genes. In Dictyostelium and other protists, the rDNA is carried on extrachromosomal palindromic elements that comprise up to 20% of the nuclear DNA. We present the sequence of the 88 kb Dictyostelium rDNA element, noting that the rRNA genes are likely to be the only transcribed regions. By interrogating a library of ordered YAC clones, we provide evidence for a chromosomal copy of the rDNA on chromosome 4. This locus may provide master copies for the stable transmission of the extrachromosomal elements. The extrachromosomal elements were also found to form chromosome-sized clusters of DNA within nuclei of nocodazole-treated cells arrested in mitosis. These clusters resemble true chromosomes and may allow the efficient segregation of the rDNA during mitosis. These rDNA clusters may also explain the cytological observations of a seventh chromosome in this organism.

%B Nucleic Acids Res %V 31 %P 2361-8 %8 2003 May 01 %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/12711681?dopt=Abstract %R 10.1093/nar/gkg348