Circulating tumor cells (CTCs) enter peripheral blood from primary tumors and seed metastases. The genome sequencing of CTCs could offer noninvasive prognosis or even diagnosis, but has been hampered by low single-cell genome coverage of scarce CTCs. Here, we report the use of the recently developed multiple annealing and looping-based amplification cycles for whole-genome amplification of single CTCs from lung cancer patients. We observed characteristic cancer-associated single-nucleotide variations and insertions/deletions in exomes of CTCs. These mutations provided information needed for individualized therapy, such as drug resistance and phenotypic transition, but were heterogeneous from cell to cell. In contrast, every CTC from an individual patient, regardless of the cancer subtypes, exhibited reproducible copy number variation (CNV) patterns, similar to those of the metastatic tumor of the same patient. Interestingly, different patients with the same lung cancer adenocarcinoma (ADC) shared similar CNV patterns in their CTCs. Even more interestingly, patients of smallcell lung cancer have CNV patterns distinctly different from those of ADC patients. Our finding suggests that CNVs at certain genomic loci are selected for the metastasis of cancer. The reproducibility of cancer-specific CNVs offers potential for CTC-based cancer diagnostics.cancer diagnostics | personalized therapy A s a genomic disease, cancer involves a series of changes in the genome, starting from primary tumors, via circulating tumor cells (CTCs), to metastases that cause the majority of mortalities (1-3). These genomic alterations include copy number variations (CNVs), single-nucleotide variations (SNVs), and insertions/deletions (INDELs). Regardless of the concentrated efforts in the past decades, the key driving genomic alterations responsible for metastases are still elusive (1).For noninvasive prognosis and diagnosis of cancer, it is desirable to monitor genomic alterations through the circulatory system. Genetic analyses of cell-free DNA fragments in peripheral blood have been reported (4-6) and recently extended to the whole-genome scale (7-9). However, it may be advantageous to analyze CTCs, as they represent intact functional cancer cells circulating in peripheral blood (10). Although previous studies have shown that CTC counting was able to predict progression and overall survival of cancer patients (11,12), genomic analyses of CTCs could provide more pertinent information for personalized therapy (13). However, it is difficult to probe the genomic changes in DNA obtainable from the small number of captured CTCs. To meet this challenge, a single-cell whole-genome amplification (WGA) method, multiple annealing and loopingbased amplification cycles (MALBAC) (14), has been developed to improve the amplification uniformity across the entire genome over previous methods (15,16), allowing precise determination of CNVs and detection of SNVs with a low false-positive rate in a single cell. Here, we present genomic analyses of CTCs from...
Autophagy is a multistep process in which cytoplasmic components, including invading pathogens, are captured by autophagosomes that subsequently fuse with degradative lysosomes. Negative-strand RNA viruses, including paramyxoviruses, have been shown to alter autophagy, but the molecular mechanisms remain largely unknown. We demonstrate that human parainfluenza virus type 3 (HPIV3) induces incomplete autophagy by blocking autophagosome-lysosome fusion, resulting in increased virus production. The viral phosphoprotein (P) is necessary and sufficient to inhibition autophagosome degradation. P binds to SNAP29 and inhibits its interaction with syntaxin17, thereby preventing these two host SNARE proteins from mediating autophagosome-lysome fusion. Incomplete autophagy and resultant autophagosome accumulation increase extracellular viral production but do not affect viral protein synthesis. These findings highlight how viruses can block autophagosome degradation by disrupting the function of SNARE proteins.
Stress granules (SGs) contain stalled messenger ribonucleoprotein complexes and are related to the regulation of mRNA translation. Picornavirus infection can interfere with the formation of SGs. However, the detailed molecular mechanisms and functions of picornavirus-mediated regulation of SG formation are not clear. Here, we found that the 2A protease of a picornavirus, EV71, induced atypical stress granule (aSG), but not typical stress granule (tSG), formation via cleavage of eIF4GI. Furthermore, 2A was required and sufficient to inhibit tSGs induced by EV71 infection, sodium arsenite, or heat shock. Infection of 2A protease activity-inactivated recombinant EV71 (EV71-2AC110S) failed to induce aSG formation and only induced tSG formation, which is PKR and eIF2α phosphorylation-dependent. By using a Renilla luciferase mRNA reporter system and RNA fluorescence in situ hybridization assay, we found that EV71-induced aSGs were beneficial to viral translation through sequestering only cellular mRNAs, but not viral mRNAs. In addition, we found that the 2A protease of other picornaviruses such as poliovirus and coxsackievirus also induced aSG formation and blocked tSG formation. Taken together, our results demonstrate that, on one hand, EV71 infection induces tSG formation via the PKR-eIF2α pathway, and on the other hand, 2A, but not 3C, blocks tSG formation. Instead, 2A induces aSG formation by cleaving eIF4GI to sequester cellular mRNA but release viral mRNA, thereby facilitating viral translation.
. Furthermore, we found that N L478A is also defective in virus growth. To our knowledge, we are the first to use a paramyxovirus to identify a precise amino acid within N that is critical for N-RNA and P interaction but not for N 0 -P interaction for the formation of inclusion bodies, which appear to be bona fide sites of RNA synthesis. Human parainfluenza virus type 3 (HPIV3) is a cytoplasmic, enveloped virus with a nonsegmented negative-strand (NNS) RNA genome that is classified in the Paramyxoviridae family, in the order Mononegavirales. It can cause severe respiratory tract diseases such as bronchiolitis, pneumonia, and croup in infants and young children (1). However, currently no valid antiviral therapy or vaccine is available. Thus, further exploration of its replication mechanism will be helpful in the development of novel therapeutic approaches. The RNA genome of HPIV3 consists of 15,462 nucleotides and is encapsidated by the nucleoprotein (N; 68 kDa) to form a helical nucleocapsid containing N-RNA that has the characteristic herringbone-like structure also observed in other Paramyxoviridae members (2-6). This N-RNA complex serves as a template to interact with the RNA-dependent RNA polymerase (RdRp) complex consisting of a large protein (L; 255 kDa) and a phosphoprotein (P; 90 kDa) cofactor; interaction between N-RNA and RdRp forms an active ribonucleoprotein (RNP) complex that is necessary for transcription and replication (2, 7) to generate six monocistronic mRNAs and an antigenome intermediate. P mRNA encodes a basic protein, designated C, via the translation of a ϩ1 open reading frame of P mRNA, which is responsible for inhibiting viral RNA synthesis as well as counteracting the host interferon signaling pathway (8, 9). A synergic association between the L-P and N-RNA templates would therefore determine the ability of the RNA polymerase complex to transcribe or replicate.Pairs of paramyxoviruses, such as HPIV3 and Sendai virus and canine distemper virus and measles virus, share about 50% nucleotide identity, despite the low level of sequence similarity among known paramyxovirus N genes by sequence comparisons (10)(11)(12). N consists of two major domains that are chemically opposite in nature: a highly conserved N-terminal core (about 80% of the sequence), which forms a globular body, and a hypervariable Cterminal tail (about 20% of the sequence), which extends from the N-terminal body (13). The N terminus contains all of the necessary components for N self-assembly and RNA binding to form N-RNA complex (14-16). Structural assays of the N-RNA complex of some NNS RNA viruses revealed that the RNA is sequestered between the N-and C-terminal lobes of the N-RNA complex (17, 18). The C terminus is mainly responsible for the binding of the N-RNA complex to P (3,(19)(20)(21). Thus, the C terminus is required for the binding of the N-RNA template to the RNA polymerase complex for viral RNA synthesis (22,23). Studies of the nucleocapsid of Sendai virus showed that deletion of the C-terminal fragment abroga...
Typical stress granules (tSGs) are stalled translation pre-initiation complex aggregations in the cytoplasm, and their formation is a common consequence of translation initiation inhibition under stress. We previously found that 2A protease of picornaviruses blocks tSG formation and induces atypical SG formation, but the molecular mechanism by which 2A inhibits tSG formation remains unclear. Here, we found that eukaryotic translation initiation factor 4 gamma1 (eIF4GI) is critical for tSG formation by interacting with Ras-GTPase-activating protein SH3-domain-binding protein (G3BP), and this interaction is mediated by aa 182–203 of eIF4GI and the RNA-binding domain of G3BP. Upon eIF4GI-G3BP interaction, eIF4GI can assemble into tSGs and rescue tSG formation. Finally, we found that 2A or L protein of picornaviruses blocks tSG formation by disrupting eIF4GI-G3BP interaction. Our findings provide the first evidence that eIF4GI-G3BP interaction is indispensable for tSG formation, and 2A or L protein of picornaviruses interferes eIF4GI-G3BP interaction, thereby blocking tSG formation.
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