[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-seo-330143-105":3,"detail-sidebar-cat-0-en-105":81,"doc-detail-330143-en":130},{"code":4,"msg":5,"data":6},0,"ok",{"site_id":7,"language":8,"slug":9,"title":10,"keywords":11,"description":12,"schema_data":13,"social_meta":74,"head_meta":76,"extra_data":78,"updated_unix":80},105,"en","locus-specific-line-1-expression-in-clinical-ovarian-cancer-specimens-at-the-single-cell-level","Locus‑specific LINE‑1 expression in clinical ovarian cancer specimens at the single‑cell level","","Long interspersed nuclear elements (LINE‑1/L1) can copy within genomes, and L1 activity is often increased in cancers. This study identifies locus-specific L1 expression using 3′ single-cell RNA sequencing in high-grade serous ovarian carcinoma (HGSOC) samples from 11 patients before and after neoadjuvant chemotherapy, and in fallopian tube samples from five healthy women. L1 expression was primarily observed in cancer cells and also in cancer-associated fibroblasts, with similar levels pre- and post-treatment. L1 activity inversely correlated with MYC target gene expression, supporting MYC as an L1 suppressor.",{"@graph":14,"@context":73},[15,34,56],{"@type":16,"itemListElement":17},"BreadcrumbList",[18,23,27,31],{"item":19,"name":20,"@type":21,"position":22},"https://docshare.wps.com","Home","ListItem",1,{"item":24,"name":25,"@type":21,"position":26},"https://docshare.wps.com/document/","Document",2,{"item":28,"name":29,"@type":21,"position":30},"https://docshare.wps.com/document/research-report/","Research & Report",3,{"item":32,"name":10,"@type":21,"position":33},"https://docshare.wps.com/document/locus-specific-line-1-expression-in-clinical-ovarian-cancer-specimens-at-the-single-cell-level/330143/",4,{"url":32,"name":10,"@type":35,"image":36,"author":41,"headline":10,"publisher":44,"fileFormat":47,"inLanguage":8,"description":12,"dateModified":48,"datePublished":49,"encodingFormat":47,"isAccessibleForFree":50,"interactionStatistic":51},"DigitalDocument",{"url":37,"@type":38,"width":39,"height":40},"https://docshare.wps.com/thumbnails/locus-specific-line-1-expression-in-clinical-ovarian-cancer-specimens-at-the-single-cell-level/330143.png","ImageObject",300,407,{"name":42,"@type":43},"Patrick","Person",{"url":19,"name":45,"@type":46},"DocShare","Organization","application/pdf","2026-10-23","2026-09-21",true,{"@type":52,"interactionType":53,"userInteractionCount":55},"InteractionCounter",{"@type":54},"ViewAction",6,{"@type":57,"mainEntity":58},"FAQPage",[59,65,69],{"name":60,"@type":61,"acceptedAnswer":62},"Why is locus-specific LINE‑1 expression hard to measure in single-cell RNA-seq?","Question",{"text":63,"@type":64},"L1 elements are repetitive, so reads are difficult to align unambiguously to individual loci. The study addresses this by quantifying reads mapping to 1 kb downstream windows of specific L1 loci.","Answer",{"name":66,"@type":61,"acceptedAnswer":67},"Where did the study detect LINE‑1 expression in ovarian cancer samples?",{"text":68,"@type":64},"L1 expression was mainly found in cancer cells, but it was also detected in other cell types, including cancer-associated fibroblasts.",{"name":70,"@type":61,"acceptedAnswer":71},"How did chemotherapy affect LINE‑1 activity and what gene association was found?",{"text":72,"@type":64},"L1 transcriptional activity appeared similar in samples collected before and after neoadjuvant chemotherapy. LINE‑1 activity was negatively associated with MYC target gene expression, consistent with MYC acting as an L1 suppressor.","https://schema.org",{"og:url":32,"og:type":75,"og:title":10,"og:site_name":45,"og:description":12},"article",{"robots":77,"canonical":32},"index,follow",{"doc_id":79,"site_id":7},330143,1789996357,{"code":4,"msg":82,"data":83},"success",[84,88,92,96,101,105,110,114,119,122,126],{"id":22,"doc_module":4,"doc_module_name":25,"category_name":85,"show_sort_weight":86,"slug":87},"Story & Novel",90,"story-novel",{"id":26,"doc_module":4,"doc_module_name":25,"category_name":89,"show_sort_weight":90,"slug":91},"Literature",80,"literature",{"id":33,"doc_module":4,"doc_module_name":25,"category_name":93,"show_sort_weight":94,"slug":95},"Exam",70,"exam",{"id":97,"doc_module":4,"doc_module_name":25,"category_name":98,"show_sort_weight":99,"slug":100},5,"Comic",60,"comic",{"id":55,"doc_module":4,"doc_module_name":25,"category_name":102,"show_sort_weight":103,"slug":104},"Technology",50,"technology",{"id":106,"doc_module":4,"doc_module_name":25,"category_name":107,"show_sort_weight":108,"slug":109},7,"Healthcare",40,"healthcare",{"id":111,"doc_module":4,"doc_module_name":25,"category_name":29,"show_sort_weight":112,"slug":113},8,30,"research-report",{"id":115,"doc_module":4,"doc_module_name":25,"category_name":116,"show_sort_weight":117,"slug":118},9,"Religion & Spirituality",20,"religion-spirituality",{"id":117,"doc_module":4,"doc_module_name":25,"category_name":120,"show_sort_weight":117,"slug":121},"World Cup","world-cup",{"id":123,"doc_module":4,"doc_module_name":25,"category_name":124,"show_sort_weight":123,"slug":125},10,"Lifestyle","lifestyle",{"id":127,"doc_module":4,"doc_module_name":25,"category_name":128,"show_sort_weight":97,"slug":129},19,"General","general",{"code":4,"msg":82,"data":131},{"doc_id":79,"user_id":132,"nickname":42,"user_avatar":133,"doc_module":4,"category_id":111,"category_name":29,"doc_title":10,"doc_description":12,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":55,"is_deleted":4,"is_public":22,"is_downloadable":22,"audit_status":22,"page_count":139,"language":140,"language_code":8,"site_id":7,"html_lang":8,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":12,"update_tm":144,"read_time":145,"preview_page_count":4},549758146520,"https://ap-avatar.wpscdn.com/avatar/80002397d8c0411e94?_k=1775819394049821470","[www. nature.com/scientificreports](www. nature.com/scientificreports)  \nOPEN  \nLocus‑specific LINE‑1 expression in clinical ovarian cancer specimens at the single‑cell level  \nAnna Perkiö1, Barun Pradhan1,5,6, Fatih Genc1, Anna Pirttikoski1, Sanna Pikkusaari1, Erdogan Pekcan Erkan1,7, Matias Marin Falco1, Kaisa Huhtinen1,2, Sara Narva3, Johanna Hynninen3, Liisa Kauppi1* & Anna Vähärautio1,4*  \nLong interspersed nuclear elements (LINE‑1s/L1s) are a group of retrotransposons that can copy themselves within a genome. In humans, it isthe most successful transposon in nucleotide content. L1 expression is generally mild in normal human tissues, but the activity has been shown to increase significantly in many cancers. Few studies have examined L1 expression at single‑cell resolution, thus it is undetermined whether L1 reactivation occurs solely in malignant cells within tumors.  \nOne of the cancer types with frequent L1 activity is high‑grade serous ovarian carcinoma (HGSOC) . Here, we identified locus‑specific L1 expression with 3′ single‑cell RNA sequencing in pre‑ and post‑ chemotherapy HGSOC sample pairs from 11 patients, and in fallopian tube samples from five healthy women. Although L1 expression quantification with the chosen technique was challenging duetothe repetitive nature of the element, we found evidence of L1 expression primarily in cancer cells, but also in other cell types, e.g. cancer‑associated fibroblasts. The expression levels were similar in samples taken before and after neoadjuvant chemotherapy, indicating that L1 transcriptional activity was  \nunaffected by clinical platinum‑taxane treatment. Furthermore, L1 activity was negatively associated with the expression of MYC target genes, a finding that supports earlier literature of MYC being an L1 suppressor.  \nTransposons, also referred to as “jumping genes”, are DNA elements that can change their location within a genome. They were first discovered in maize by Barbara McClintock in the 1950s1, but since then, they have been found in nearly all eukaryotic genomes sequenced2. In total, transposons make up around even 90 percent of the genome of certain plants3, and 50 percent of the human genome4. However, currently only one type of transposon, namely long interspersed nuclear element-1 (LINE-1, or L1 for short) is still capable of moving independently within the human genome, thanks to its self-encoded transposition machinery5. Furthermore, L1 is the most successful transposon in terms of nucleotide content, covering at least 17% of the human genome4.  \nL1s are repressed in most normal adult tissues6,7. However, recent studies have shown L1 activity to also occur in normal epithelia8,9. Nevertheless, L1 activity is significantly higher in many cancers, especially in those of epithelial origin6,8,9. One of these cancer types is ovarian cancer10–12.  \nL1 activity can be investigated by assessing different stages ofthe L1 element’s life cycle, for instance, by studying new L1 insertions, mRNA or ORF1 protein expression. To date, most studies of L1 transcription are based on bulk RNA-seq on tissue samples or cell lines12, 13; a few single-cell level protocols have only just recently been applied9, 14, 15. Therefore, a standard workflow for this type of analysis is lacking. From a biological standpoint, it is currently unclear whether L1 expression detected in tumor samples originates purely from cancer cells, or whether the microenvironment of the tumor also shows L1 activity.  \nIn this study, we aimed to identify L1 expression at the locus-specific level, based on 3′ single-cell RNAsequencing (scRNA-seq), and to further compare this to L1 expression detected in bulk RNA. Our data consisted  \n1Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland. 2Institute of Biomedicine and FICAN West Cancer Centre, University of Turku and Turku University Hospital, 20521 Turku, Finland. 3Department of","cbCaipWPT3JIiB9n","https://ap.wps.com/l/cbCaipWPT3JIiB9n","pdf",2391663,14,"English","# Introduction\n## Background on transposons and LINE‑1 activity\n## Rationale and aims of the study\n# Results\n## Quantification strategy for locus-specific L1 expression\n## Observed sparsity of L1 activity in single cells","[{\"question\":\"Why is locus-specific LINE‑1 expression hard to measure in single-cell RNA-seq?\",\"answer\":\"L1 elements are repetitive, so reads are difficult to align unambiguously to individual loci. The study addresses this by quantifying reads mapping to 1 kb downstream windows of specific L1 loci.\"},{\"question\":\"Where did the study detect LINE‑1 expression in ovarian cancer samples?\",\"answer\":\"L1 expression was mainly found in cancer cells, but it was also detected in other cell types, including cancer-associated fibroblasts.\"},{\"question\":\"How did chemotherapy affect LINE‑1 activity and what gene association was found?\",\"answer\":\"L1 transcriptional activity appeared similar in samples collected before and after neoadjuvant chemotherapy. LINE‑1 activity was negatively associated with MYC target gene expression, consistent with MYC acting as an L1 suppressor.\"}]","Locus‑specific LINE‑1 expression in clinical ovarian cancer specimens at the single‑cell level | PDF",1789987403,35]