To study the multistep process of cervical cancer development, we analyzed 128 frozen cervical samples spanning normalcy, increasingly severe cervical intraepithelial neoplasia (CIN1-CIN3), and cervical cancer (CxCa) from multiple perspectives, revealing a cascade of progressive changes. Compared with normal tissue, expression of many DNA replication/repair and cell proliferation genes was increased in CIN1/ CIN2 lesions and further sustained in CIN3, consistent with high-risk human papillomavirus (HPV)-induced tumor suppressor inactivation. The CIN3-to-CxCa transition showed metabolic shifts, including decreased expression of mitochondrial electron transport complex components and ribosomal protein genes. Significantly, despite clinical, epidemiological, and animal model results linking estrogen and estrogen receptor alpha (ERα) to CxCa, ERα expression declined >15-fold from normalcy to cancer, showing the strongest inverse correlation of any gene with the increasing expression of p16, a marker for HPV-linked cancers. This drop in ERα in CIN and tumor cells was confirmed at the protein level. However, ERα expression in stromal cells continued throughout CxCa development. Our further studies localized stromal ERα to FSP1+, CD34+, SMA− precursor fibrocytes adjacent to normal and precancerous CIN epithelium, and FSP1−, CD34−, SMA+ activated fibroblasts in CxCas. Moreover, rank correlations with ERα mRNA identified IL-8, CXCL12, CXCL14, their receptors, and other angiogenesis and immune cell infiltration and inflammatory factors as candidates for ERα-induced stroma-tumor signaling pathways. The results indicate that estrogen signaling in cervical cancer has dramatic differences from ERα+ breast cancers, and imply that estrogen signaling increasingly proceeds indirectly through ERα in tumor-associated stromal fibroblasts.cervical cancer | HPV | estrogen | tumor microenvironment | stroma G lobally, cervical cancer (CxCa) is the second most common cancer in women, with >500,000 new cases each year, half of which are ultimately fatal (1). In the developed world, routine CxCa screening for abnormal cervical cytology, human papillomavirus (HPV), or both (2) has strongly reduced CxCa incidence, demonstrating the value of recognizing and removing early neoplasms (3). Such screening programs present a rare opportunity to study the sequential molecular changes in the development of a human cancer (4).CxCa development is related to infection with high-risk oncogenic HPVs, most prominently HPV16 and HPV18 (5-7). HPV oncoproteins E6 and E7 are best known for blocking tumor suppressor functions of p53 and Rb, respectively, but have numerous additional interaction partners (8-13). Most cervical HPV infections are cleared (14), but in a fraction of cases persistent infections lead to increasingly severe grades of dysplasia (cervical intraepithelial neoplasia grades 1, 2, and 3; CIN1, CIN2, CIN3) and ultimately to invasive cancer. Although the key steps of the carcinogenic process, HPV infection, progression to precancer, and invas...

Positive-strand RNA viruses, the largest genetic class of viruses, include numerous important pathogens such as Zika virus. These viruses replicate their RNA genomes in novel, membrane-bounded mini-organelles, but the organization of viral proteins and RNAs in these compartments has been largely unknown. We used cryo-electron tomography to reveal many previously unrecognized features of Flock house nodavirus (FHV) RNA replication compartments. These spherular invaginations of outer mitochondrial membranes are packed with electron-dense RNA fibrils and their volumes are closely correlated with RNA replication template length. Each spherule’s necked aperture is crowned by a striking cupped ring structure containing multifunctional FHV RNA replication protein A. Subtomogram averaging of these crowns revealed twelve-fold symmetry, concentric flanking protrusions, and a central electron density. Many crowns were associated with long cytoplasmic fibrils, likely to be exported progeny RNA. These results provide new mechanistic insights into positive-strand RNA virus replication compartment structure, assembly, function and control.DOI: http://dx.doi.org/10.7554/eLife.25940.001

Recently, messenger RNAs in eukaryotes have shown to associate with antisense (AS) transcript partners that are often referred to as long noncoding RNAs (lncRNAs) whose function is largely unknown. Here, we have identified a natural AS transcript for tyrosine kinase containing immunoglobulin and epidermal growth factor homology domain-1 (tie-1), tie-1AS lncRNA in zebrafish, mouse, and humans. In embryonic zebrafish, tie-1AS lncRNA transcript is expressed temporally and spatially in vivo with its native target, the tie-1 coding transcript and in additional locations (ear and brain). The tie-1AS lncRNA selectively binds tie-1 mRNA in vivo and regulates tie-1 transcript levels, resulting in specific defects in endothelial cell con- IntroductionOver the past few years, intensive unbiased analysis of transcriptome species has revealed that eukaryotic genomes contain a variety of RNA species. RNA molecules are essentially classified into 2 types, protein coding and nonprotein coding. The protein-coding transcripts or messenger RNA (mRNA) account for only approximately 2.3% of the human genome. 1 The majority of transcription appears to be nonprotein coding or noncoding, and the function of these noncoding transcripts is largely unknown. 2 Of the noncoding RNAs, the regulatory short noncoding RNAs, such as microRNAs, are well studied. The long noncoding RNAs (lncRNAs), which compose the largest portion of the mammalian noncoding transcriptome, are the least understood, especially its function. 3,4 lncRNAs are oriented in sense or antisense (AS) direction with respect to a protein coding locus, and located in intronic or intergenic regions. 5 In humans and mice, 61% to 72% of all transcribed regions possess lncRNAs in AS orientation, 2,6 and AS lncRNA transcripts play important roles in pathogenesis. For instance, the BACE1-AS transcript was elevated in subjects with Alzheimer disease and in amyloid precursor protein transgenic mice. 7 A growing body of evidence suggests that lncRNAs for most critical physiologic processes will be identified. Angiogenesis, the development of new vasculature from existing vasculature, is one of the fundamental developmental physiologic processes regulated in a developing vertebrate embryo. 8 Here, we identify a natural AS transcript for tyrosine kinase containing immunoglobulin and epidermal growth factor homology domain-1 (tie-1), tie-1AS lncRNA in zebrafish, mouse, and humans. tie-1 is a cell-surface tyrosine kinase receptor for angiopoietin ligands that is known to play a role in vascular development in vertebrates. [9][10][11][12] In embryonic zebrafish, tie-1AS lncRNA transcript is expressed temporally and spatially in vivo with its native target, the tie-1 coding transcript, and in additional locations (ear and brain). Its expression is controlled by a 3-kb genomic fragment in the 3Ј region of tie-1, and the bioinformatic predicted hybrid structure between tie-1:tie-1AS was detected in vivo. Capped or uncapped tie-1AS lncRNA selectively binds tie-1 mRNA in vivo and regulates tie-1...

No abstract

For positive-strand RNA [(+)RNA] viruses, the major target for antiviral therapies is genomic RNA replication, which occurs at poorly understood membrane-bound viral RNA replication complexes. Recent cryoelectron microscopy (cryo-EM) of nodavirus RNA replication complexes revealed that the viral double-stranded RNA replication template is coiled inside a 30- to 90-nm invagination of the outer mitochondrial membrane, whose necked aperture to the cytoplasm is gated by a 12-fold symmetric, 35-nm diameter “crown” complex that contains multifunctional viral RNA replication protein A. Here we report optimizing cryo-EM tomography and image processing to improve crown resolution from 33 to 8.5 Å. This resolves the crown into 12 distinct vertical segments, each with 3 major subdomains: A membrane-connected basal lobe and an apical lobe that together comprise the ∼19-nm-diameter central turret, and a leg emerging from the basal lobe that connects to the membrane at ∼35-nm diameter. Despite widely varying replication vesicle diameters, the resulting two rings of membrane interaction sites constrain the vesicle neck to a highly uniform shape. Labeling protein A with a His-tag that binds 5-nm Ni-nanogold allowed cryo-EM tomography mapping of the C terminus of protein A to the apical lobe, which correlates well with the predicted structure of the C-proximal polymerase domain of protein A. These and other results indicate that the crown contains 12 copies of protein A arranged basally to apically in an N-to-C orientation. Moreover, the apical polymerase localization has significant mechanistic implications for template RNA recruitment and (−) and (+)RNA synthesis.

Eight active transglutaminases (TGs) (TGs 1-7 and factor XIIIa) are expressed in mammals, of which TGs 1-3 (Kim et al. 1999) 1 and 6 (Hadjivassilou et al. 2008) are present in human brain. The major reaction thus far attributed to the cerebral TGs is transamidation. In this reaction the carboxamide moiety of a Q residue [-C(O)NH 2 ] is converted to a substituted carboxamide [-C(O)NHR] by nucleophilic attack of an amine [RNH 2 ] such as various mono-, di-, and polyamines or the e amino group of a K residue (Lorand and Graham 2003). Of the possible transamidation linkages, theisopeptide linkage formed between Q and K resides, is the most commonly studied. GGEL bonds occur both within and between polypeptide chains, and thereby contribute to the formation of stable soluble and insoluble polymers. TGs also cross-link proteins via bis-c-glutamylpolyamine bridges between Q residues (Piacentini et al. 1988). These linkages are formed by two successive transamidations: the first utilizes a free polyamine to generate a c-glutamylpolyamine residue, which becomes the amine-bearing substrate for a second transamidation. bis-c-Glutamylpolyamine cross-links are formed at least as frequently as those involving GGEL -dependent enzymes that catalyze a variety of modifications of glutaminyl (Q) residues. In the brain, these modifications include the covalent attachment of a number of amine-bearing compounds, including lysyl (K) residues and polyamines, which serve to either regulate enzyme activity or attach the TG substrates to biological matrices. Aberrant TG activity is thought to contribute to Alzheimer disease, Parkinson disease, Huntington disease, and supranuclear palsy. Strategies designed to interfere with TG activity have some benefit in animal models of Huntington and Parkinson diseases. The following review summarizes the involvement of TGs in neurodegenerative diseases and discusses the possible use of selective inhibitors as therapeutic agents in these diseases.

High-risk human papillomaviruses (HPVs) infect epithelial cells and are causally associated with cervical cancer, but HPV infection is not sufficient for carcinogenesis. Previously, we reported that estrogen signaling in the stromal tumor microenvironment is associated with cervical cancer maintenance and progression. We have now determined how HPV oncogenes and estrogen treatment affect genome-wide host gene expression in laser-captured regions of the cervical epithelium and stroma of untreated or estrogen-treated nontransgenic and HPV-transgenic mice. HPV oncogene expression in the cervical epithelium elicited significant gene-expression changes in the proximal stromal compartment, and estrogen treatment uniquely affected gene expression in the cervical microenvironment of HPV-transgenic mice compared with nontransgenic mice. Several potential estrogen-induced paracrine-acting factors were identified in the expression profile of the cervical tumor microenvironment. The microenvironment of estrogen-treated HPV-transgenic mice was significantly enriched for chemokine/cytokine activity and inflammatory and immune functions associated with carcinogenesis. This inflammatory signature included several proangiogenic CXCR2 receptor ligands. A subset of the same CXCR2 ligands was likewise increased in cocultures of early-passage cells from human cervical samples, with levels highest in cocultures of cervical fibroblasts and cancer-derived epithelial cells. Our studies demonstrate that high-risk HPV oncogenes profoundly reprogram the tumor microenvironment independently of and synergistically with estrogen. These observations illuminate important means by which HPVs can cause cancer through alterations in the tumor microenvironment.

No abstract