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Abstract Background Long INterspersed Element-1 (LINE-1) is an autonomous retroelement able to “copy-and-paste” itself into new loci of the host genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p, a nucleic acid chaperone, and ORF2p, a protein with endonuclease and reverse transcriptase activity. Both proteins bind LINE-1 mRNA in cis and are necessary for retrotransposition. While LINE-1 transcription is usually repressed in most healthy somatic cells through a plethora of mechanisms, ORF1p expression has been observed in nearly 50% of tumors, and new LINE-1 insertions have been documented in a similar fraction of tumors, including prostate cancer. Results Here, we utilized RNA ImmunoPrecipitation (RIP) and the L1EM analysis software to identify ORF1p bound RNA in prostate cancer cells. We identified LINE-1 loci that were expressed in parental androgen sensitive and androgen independent clonal derivatives. In all androgen independent cells, we found higher levels of LINE-1 RNA, as well as unique expression patterns of LINE-1 loci. Interestingly, we observed that ORF1p bound many non-LINE-1 mRNA in all prostate cancer cell lines evaluated, and polyA RNA, and RNA localized in p-bodies were especially enriched. Furthermore, the expression levels of RNAs identified in our ORF1p RIP correlated with RNAs expressed in LINE-1 positive tumors from The Cancer Genome Atlas (TCGA). Conclusion Our results show a significant remodeling of LINE-1 loci expression in androgen independent cell lines when compared to parental androgen dependent cells. Additionally, we found that ORF1p bound a significant amount of non-LINE-1 mRNA, and that the enriched ORF1p bound mRNAs are also amplified in LINE-1 expressing TCGA prostate tumors, indicating the biological relevance of our findings to prostate cancer.

Abstract Background Long interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types of human cancers are characterized by L1 promoter hypomethylation, L1 transcription, L1 ORF1p protein expression, and somatic L1 retrotransposition. ORF2p encodes the endonuclease and reverse transcriptase activities required for L1 retrotransposition. Its expression is poorly characterized in human tissues and cell lines. Results We report mass spectrometry-based tumor proteome profiling studies wherein ORF2p eludes detection. To test whether ORF2p could be detected with specific reagents, we developed and validated five rabbit monoclonal antibodies with immunoreactivity for specific epitopes on the protein. These reagents readily detect ectopic ORF2p expressed from bicistronic L1 constructs. However, endogenous ORF2p is not detected in human tumor samples or cell lines by western blot, immunoprecipitation, or immunohistochemistry despite high levels of ORF1p expression. Moreover, we report endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, wherein we similarly fail to detect ORF2p. These samples include primary tumors harboring hundreds of somatically acquired L1 insertions. The new data are available via ProteomeXchange with identifier PXD013743. Conclusions Although somatic retrotransposition provides unequivocal genetic evidence for the expression of ORF2p in human cancers, we are unable to directly measure its presence using several standard methods. Experimental systems have previously indicated an unequal stoichiometry between ORF1p and ORF2p, but in vivo, the expression of these two proteins may be more strikingly uncoupled. These findings are consistent with observations that ORF2p is not tolerable for cell growth.

Déanann an t-alt seo machnamh ar na bealaí éagsúla inar cuireadh téacsanna i nGàidhlig na hAlban i láthair i leabhair agus in irisleabhair Ghaeilge ó thús an fichiú haois. Cé go bhfuil dlúthbhaint ag Gaeilge na hÉireann agus Gàidhlig na hAlban lena chéile, tá sé sách doiléir a mhéid is féidir le léitheoirí na Gaeilge an Ghàidhlig scríofa a thuiscint. Uaireanta clúdaíonn an t-idéalachas ‘pan-Ghaelach’ tuairimí ar an ábhar, rud a fhágann go bhfuil cleamhnas teangeolaíoch samhalta ann (nó cleamhnas bunaithe ar dhóchas). I bhfianaise na neamhchinnteachta seo, is féidir roinnt straitéisí éagsúla chun téacsanna Gaelacha na hAlban a chur i láthair a aithint, agus is féidir a rá go bhfuil siad seo ag brath ar thuiscintí neamh-chomhoiriúnacha ar mhéid na comh-intuigtheachta idir an dá theanga. Uaireanta cuirtear buntéacs i nGàidhlig na hAlban gan aon nótaí míniúcháin leis; uaireanta soláthraítear aistriúchán go Gaeilge nó aistriúchán go Béarla; uaireanta ní thugtar ach aistriúchán Gaeilge, gan an bunleagan. Go háirithe maidir le téacsanna próis (a bhíonn níos faide de ghnáth) is minic nach soláthraítear an buntéacs Gàidhlig. Is féidir na straitéisí éagsúla foilseacháin seo a fheiceáil, mar shampla, sa chaoi a gcaitheann eagarthóirí agus criticeoirí éagsúla le filíocht an nuafhile iomráitigh Albanaigh Somhairle MacGill-Eain. Tríd is tríd, is cosúil gurb é an buntéacs in éineacht le haistriúchán Gaeilge an réiteach is praiticiúla, cé gur fearr a chinntiú go dtugtar tosaíocht iomchuí don bhunthéacs, mar shampla tríd an aistriúchán a chur i gcló iodálach nó faoi bhun an bhuntéacs. Deacracht bhunúsach is ea laige na nasc cultúrtha idir Éire agus Albain Ghaelach, ionas gur beag an deis atá ag léitheoirí na Gaeilge dul i dtaithí ar Ghàidhlig na hAlban. Ina theannta sin, le céad bliain anuas tá an bhearna teanga idir an dá chineál ag leathnú, mar gheall ar phróisis éagsúla nuachóirithe agus caighdeánaithe. Cé go raibh tionscnaimh chultúrtha éagsúla ann chun an dá phobal teanga a nascadh, is beag tionchar buan a bhí acu seo.

This series provides clinicians with strategies and tools to interpret and integrate evidence from published research in their care of patients. The 2 key principles for applying all the articles in this series to patient care relate to the value-laden nature of clinical decisions and to the hierarchy of evidence postulated by evidence-based medicine. Clinicians need to be able to distinguish high from low quality in primary studies, systematic reviews, practice guidelines, and other integrative research focused on management recommendations. An evidence-based practitioner must also understand the patient's circumstances or predicament; identify knowledge gaps and frame questions to fill those gaps; conduct an efficient literature search; critically appraise the research evidence; and apply that evidence to patient care. However, treatment judgments often reflect clinician or societal values concerning whether intervention benefits are worth the cost. Many unanswered questions concerning how to elicit preferences and how to incorporate them in clinical encounters constitute an enormously challenging frontier for evidence-based medicine. Time limitation remains the biggest obstacle to evidence-based practice but clinicians should seek evidence from as high in the appropriate hierarchy of evidence as possible, and every clinical decision should be geared toward the particular circumstances of the patient. [ABSTRACT FROM AUTHOR]

Clinicians rely on knowledge about the clinical manifestations of disease to make clinical diagnoses. Before using research on the frequency of clinical features found in patients with a disease, clinicians should appraise the evidence for its validity, results, and applicability. For validity, 4 issues are important-how the diagnoses were verified, how the study sample relates to all patients with the disease, how the clinical findings were sought, and how the clinical findings were characterized. Ideally, investigators will verify the presence of disease in study patients using credible criteria that are independent of the clinical manifestations under study. Also, ideally the study patients will represent the full spectrum of the disease, undergo a thorough and consistent search for clinical findings, and these findings will be well characterized in nature and timing. The main results of these studies are expressed as the number and percentages of patients with each manifestation. Confidence intervals can describe the precision of these frequencies. Most clinical findings occur with only intermediate frequency, and since these frequencies are equivalent to diagnostic sensitivities, this means that the absence of a single finding is rarely powerful enough to exclude the disease. Before acting on the evidence, clinicians should consider whether it applies to their own patients and whether it has been superseded by new developments. Detailed knowledge of the clinical manifestations of disease should increase clinicians' ability to raise diagnostic hypotheses, select differential diagnoses, and verify final diagnoses. JAMA. 2000;284:869-875 [ABSTRACT FROM AUTHOR]