Alternative splicing of transposable elements in human breast cancer

BACKGROUND: Diverse molecular mechanisms are being reported in human breast cancer (BC), which can affect the biochemical functions throughout malignant cells development. The microRNAs (miRNAs) are an emerging class of modulators of gene expression with relevant roles in several biological processes, as oncogenic, tumor-suppressive, and metastatic-influencing in BC cells. Recently, a few reports have implied the possible pattern of expression (time oscillation) of miRNAs in time that may be related to molecular changes in mammalian cells. These findings suggest a biological connection among normal and cancer cells, and rhythmic regulation of some miRNAs, but such connection has not yet been studied. In this study, we aimed to identify and compare the rhythmic expression of miRNAs in human breast epithelial normal and cancer cell lines. METHODS: We used cell culture to explore three cell lines, one breast epithelial normal (MCF10A) and two cancer (MCF-7 and MDA-MB-231) cell lines under standard growth conditions in vitro. The cells were synchronized by serum shock (50% horse serum for 2 h), and we collected sample cells (triplicate) for intervals of 4 hours during 48 hours. Collected cells at 12h to 40h (8 time-points) were genome-wide analyzed of miRNA expression using high-throughput Agilent Human miRNA microarray of 2006 human miRNAs. Analysis for identification of rhythmic miRNAs was developed by cosine analysis in R software. RESULTS: We observed diverse oscillation patterns (minimum 6 patterns, i.e. cosine or sine oscillation) of miRNAs in cell lines. Each cell line shows approximately 85 miRNAs with rhythmic oscillation. These also showed distinct phases between cell lines, which could suggest as part of molecular changes in breast normal and cancer cell lines. CONCLUSIONS: Our results suggest that miRNAs may present rhythmic oscillation in the regulation of molecular changes of human breast normal and cancer cells. Citation Format: Chacolla RJ, Trevino VM, Scott SP, Moreno JE. Rhythmic time oscillations of microRNAs in human breast epithelial normal and cancer cell lines. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-03-07.

Tumors display widespread transcriptome alterations, but the full repertoire of isoform-level alternative splicing in cancer is unknown. We developed a long-read (LR) RNA sequencing and analytical platform that identifies and annotates full-length isoforms and infers tumor-specific splicing events. Application of this platform to breast cancer samples identifies thousands of previously unannotated isoforms; ~30% affect protein coding exons and are predicted to alter protein localization and function. We performed extensive cross-validation with -omics datasets to support transcription and translation of novel isoforms. We identified 3059 breast tumor–specific splicing events, including 35 that are significantly associated with patient survival. Of these, 21 are absent from GENCODE and 10 are enriched in specific breast cancer subtypes. Together, our results demonstrate the complexity, cancer subtype specificity, and clinical relevance of previously unidentified isoforms and splicing events in breast cancer that are only annotatable by LR-seq and provide a rich resource of immuno-oncology therapeutic targets.

Arginase, an enzyme of the urea cycle, converts L-arginine to L-ornithine, which is the precursor of polyamines that are essential components of cell proliferation. However, Arginine deprivation and Arginase clinical implications in human breast and liver cancers have not been fully elucidated. The objective of the current study was to investigate the potential role of the Arginine degrading enzyme, Arginase, on three cell lines; Luminal A breast cancer (T-47D), TNBC (MDA-MB-231), and HCC cell line, HepG2, respectively. Herein, Arginase was extracted and purified from the beef liver and its specific activity was 0.2 IU/mg protein yielded 49% compared to the crude beef liver Arginase. The purified Arginase is covalently bound via a succinamide propionic acid (SPA) linker to polyethylene glycol (PEG) of molecular weight 5,000 to enhance the half-life time compared to the native enzyme with a maximum specific activity between 37~55℃ and pH 7~9. The potential influence of extracted Peg-Arginase was examined on cell proliferation, clonogenic assays, morphological alteration, and oncogenic signaling pathways of STAT3, β-catenin, and miR-23a. Our data showed that Peg-Arginase treatment displayed a significant inhibition in cell proliferation and viability in a dose-dependent manner in both breast cancer cell lines, but not in HepG2 cells after 48h. Furthermore, mechanistic studies showed that Peg-Arginase induced apoptosis that was associated with cell morphological changes, histone release from fragmented DNA, caspase-3 activation in a dose-dependent manner after 48h, and cell cycle arrest at S and/or G2/M phases. Moreover, Peg-Arginase down-regulated miR-23a, STAT3, β-catenin, cyclin D1, and mutant p53 levels as well as increased p21and Bax, pro-apoptotic signal, in both breast cancer cells as determined by flow cytometry and western blot analysis. In vivo, the effects of native- and Peg-Arginase enzymes were examined on MNU-induced mammary tumors in Albino-Wister rats. Our data showed that 400 IU of native- or peg- Arginase twice per week for two weeks significantly inhibited the growth of MNU-induced mammary tumors by 58.8±4.1 % for peg-Arginase compared to 19.7±3.5 % for native-Arginase. Furthermore, the results also revealed a significant reduction in activities of ALT, AST, and ALP in the Peg-Arginase group compared to MNU untreated or native-Arginase groups, suggesting that Peg-Arginase may eliminate the hepatotoxic effect of the MNU. All in all, our results suggested that the arginine-depleting enzyme, Peg-Arginase, exerted an anticancer effect against both T-47D and MDA-MB-231 breast cancer cell lines through cell proliferation inhibition and apoptosis induction. Citation Format: Asmaa Ali, Omnia Ali, Doaa Othman, Ahmed Sultan. Pegylated arginase isolated from beef liver tissue inhibited cell proliferation, induced apoptosis & inhibits induced mammary tumors in human breast cancer in vitro & in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6332.

Adenoviral vectors with E1A regulated by tumor-specific promoters are selectively cytolytic for breast cancer and melanoma.

Tumors frequently contain a sub-population of cells, referred to as cancer stem cells (CSCs) or tumor-initiating (TI) cells, with the abilities to self-renew and to regenerate all cell types within the tumor. Recent studies suggest that the process of epithelial-mesenchymal transition (EMT) may contribute to generation of CSCs within the tumor. Although alternative splicing has been shown to play a role in the biology of EMT, the occurrence and role of alternative splicing in CSC biology is largely unexplored. Given the role of CSCs in the recurrence and spread of cancer, there is an urgent need to develop new agents that target CSCs. Development of CSC-targeted drugs will be greatly facilitated by biomarkers that can identify CSCs to aid in patient selection and determination of drug response. Analysis of alternative splicing in CSCs may provide valuable new CSC-specific markers. In this study, a TI gene expression signature (Creighton et al, 2009), an EMT gene expression signature (Gupta et al., 2009, Taube et al, 2009) and a Basal B/Luminal breast cancer subtype classifier were used in Support Vector Machine (SVM) analysis of 41 human breast cancer cell lines to identify changes in alternative splicing. We discovered 209 cassette exon splicing events from the union of these 3 classifiers, of which 68 splicing events were concordant. Interestingly, GO and KEGG pathway analysis using these 68 alternatively spliced events demonstrated enrichment of genes encoding key drivers of CSC phenotype, including cell migration, motility, and cell adhesion pathways, as well as extracellular matrix-receptor interactions. SVM analysis of an independent NCI-60 cancer cell line dataset determined that the top 60 exons from the breast cancer cell line training group identified 96% of the CSC-high cell lines and 90% of CSC-low cell lines with high accuracy. To extend the analysis to human tumor samples, we assessed the whole transcriptome data from human breast cancers (81 patients, Lin et al., 2009) using a CSC centroid gene signature model that clustered tumor samples into CSC-high and CSC-low subgroups. Interestingly, a centroid model based on the 68 alternative splicing events similarly identified the CSC-high and CSC-low breast cancers with high accuracy. The CSC-high subgroup contained mostly triple negative breast cancers, known to have increased frequencies of CSC and EMT phenotypes, suggestive of the therapeutic importance of this alternative splicing signature for identification of CSCs in patients. Q-PCR analysis showed that several of the alternative splicing events observed in the CSC-high subgroup were further enriched in tumorspheres grown from human breast cancer cell lines. The CSC-associated alternative splicing signature identified here will be further refined to develop new CSC-specific diagnostic markers to stratify breast cancer patients and monitor response to novel CSC-targeted therapies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-197. doi:1538-7445.AM2012-LB-197

DARC (aka Duffy), a chemokine receptor, is expressed on erythrocytes and endothelial cells in blood vessels. It has been linked to inhibition of tumor metastasis, through blockade of tumor cell invasion into vessels, and to regulation of plasma levels of some cytokines which influence leukocyte egress from blood into tissues. The Duffy null (Fy-) phenotype, in which DARC is not expressed on red blood cells, is especially prevalent among people of West African descent. These populations are also highly susceptible to aggressive subtypes of breast and prostate cancers with higher rates of metastases. There is limited evidence, from a Chinese study, that the Fy- phenotype may be associated with increased breast cancer (BrCa) invasiveness and lower rates of survival. However, little is known about how the presence or absence of DARC expression may affect breast cancer metastases and overall survival among African-American and European- American women. Our lab is investigating whether Fy- phenotypes could be associated with increased BrCa metastasis by genotyping the Fy- (null and weak) alleles and assessing DARC gene expression in breast and lymphoblast cells using qPCR and Immunofluorescence (IF). Because there are two isoforms of DARC and the Fy- SNP is located in the promoter of one and the 5′UTR of the other, it is plausible that the alternate isoform is specific to these cell types and may still be expressed. Here we present data from the preliminary stages of this project; including characterizing Duffy alleles in our cell line models. We have genotyped the 3 known DARC polymorphisms that result in Fy- (and weak) erythrocyte phenotypes in breast cancer and lymphoblast cell lines. Specifically, we validated that HAPMAP Yoruba lines are homozygous for the -541T>C point mutation Fy- allele (rs2814778) and half of the African-American lines are heterozygous while the remaining are homozygous for the Fy- allele and the CEPH-European lines do not have the Fy- allele. Our breast cancer (BrCa) lines are derived from tumors of varying molecular subtypes, isolated from African-American women. We show that these BrCa lines are homozygous for the Fy- allele and yet still express the DARC protein. The specific isoform expressed in these cells (DARC-2) may not be the same as used to phenotype the Fy- status in erythrocytes (DARC-1). This suggests that a Fy- genotype may still have some tissue specific expression of DARC-2 in epithelial cells. Therefore, we will also show whether these SNPs correspond with expression of the DARC gene in HAPMAP lymphoblasts and delineate which isoform is being expressed in both cell types. In conclusion, we hypothesize that Fy- status as determined in endothelial and erythrocytes, in people of African descent may remove the metastatic protection of DARC and alternate expression of DARC-2 on epithelial cells may increase the rate of metastases in these populations. Currently, we are analyzing clinical samples (blood and breast tissues) from local breast cancer patients for Fy- status and will determine if this correlates with metastatic disease. In addition, biochemical experiments will be conducted to determine whether DARC-related chemokines are in higher prevalence in the Fy- patients, how the isoforms differ in their affinity to the chemokine ligands and whether this is associated with specific breast cancer subtypes. Citation Format: Melissa Davis, Rupa Hire, Jonathan Swanson, Kauthar Mumin, Michele Monteil, Michele Lou. Investigating correlations of DARC underexpression (Duffy Null phenotypes) with increased breast cancer lymph node metastasis. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr C69. doi:10.1158/1538-7755.DISP13-C69

Does a young woman living with a smoker or taking a job working in a smoky bar have a greater chance of developing breast cancer? Some scientists believe that such situations can indeed raise a woman’s risk of developing breast cancer before the age of 50. Because epidemiological and toxicological studies show that women’s breast tissue may be especially sensitive to exposure to carcinogens prior to first pregnancy, these researchers contend that public education should be directed at alerting adolescents and young women to the potential risk. However, not everyone in the international public health community agrees that the evidence to date supports a link between passive smoking and breast cancer, and some say that women are being alarmed unnecessarily. This disagreement has sparked debate that is sometimes heated. The stakes are high because breast cancer is the most common cancer in women in industrialized countries, according to the WHO. It is the leading cancer killer of nonsmoking women, and second only to lung cancer deaths among women who smoke. Among the researchers interviewed for this article who disagree that there is enough evidence to link secondhand smoke (SHS) with breast cancer, the majority call the evidence to date “suggestive but not sufficient,” as the Surgeon General’s 2006 report, The Health Consequences of Involuntary Exposure to Tobacco Smoke, put it. That characterization is based largely on the fact that the research considered when the Surgeon General’s report was being amassed did not clearly link even active smoking to breast cancer. Researchers in this camp do, however, stress that ongoing campaigns to prohibit smoking in public will protect the whole of society against the wide variety of ills proven to be caused by SHS. These include lung cancer, cardiovascular disease, and sudden infant death syndrome, among others. A smaller group contends that the question of whether or not SHS causes breast cancer is a political issue with the potential to compromise the scientific process. “A premature decision about causality could jeopardize the credibility of the entire review process and all of the other, established effects of secondhand smoke,” says Michael Thun, national vice president of epidemiology and surveillance research for the American Cancer Society. Adds Valerie Beral, director of the University of Oxford Cancer Research UK Epidemiology Unit, “To prematurely come to conclusions about the causation when there is a big division in the scientific community . . . is bad science.” Thun debated the subject in a series of public forums held in conjunction with scientific meetings. Taking the opposing view was Kenneth C. Johnson, a research scientist with the Public Health Agency of Canada, who was one of the first scientists to discern a potential link. During the debates, Johnson pointed out there are about the same number of studies linking breast cancer to passive smoking as there were linking lung cancer to SHS in 1986, when the Surgeon General concluded that passive smoking caused lung cancer. Johnson also says that more of the breast cancer studies are statistically significant, and that the estimated risk for breast cancer is higher.

<i>FOXP3</i> is not mutated in human melanoma

The pro-proliferative effect of interferon-γ in breast cancer cell lines is dependent on stimulation of ASCT2-mediated glutamine cellular uptake

Four breast cancer cell lines (MCF-7, BT-549, MDA-MB-231 and T-47D) and four ovarian cancer cell lines (1A9/A2780, ES-2, MES-OV and OVCAR-3) were selected for taxane resistance by exposing cells to either docetaxel or paclitaxel in the presence of the P-glycoprotein inhibitor, PSC-833 (valspodar, 2 μM). All of these co-selected variants are MDR1/ABCB1(-), and the resistance to taxanes is not transporter-mediated. We have previously reported elevated class III β-tubulin (TUBB3), reduced BRCA1, elevated CDKN1A (p21), and altered epithelial-mesenchymal transition (EMT) genes in the majority of the non-MDR1 taxane variants. Inhibitors of apoptosis (IAP) proteins directly bind and inhibit several caspases, and may play a critical role in determining cell fate after exposure to chemotherapeutic agents. In this study, we profiled the expression of IAP proteins and found elevated content in this panel of taxane-resistant human breast and ovarian cancer cell lines. In both the paclitaxel- (TP) and docetaxel-selected (TxTP) ovarian cancer cell lines we observed significantly overexpressed cIAP1 (BIRC2), cIAP2 (BIRC3), XIAP (BIRC4), and Livin (BIRC7) relative to parental cell lines. Expression of cIAP2 was undetectable in OVCAR-3 and its taxane resistant cell lines, OVCAR-3/TP20 and OVCAR-3/TxTP5. Elevated cIAP1 and XIAP levels were detected in the human breast cancer variant BT-549/TxTP50, and Livin was overexpressed in all taxane-resistant breast cancer cell models. Survivin (BIRC5) is highly expressed in cancers and has been associated with taxane resistance via its effects on apoptosis and the cell cycle. We observed reduced Survivin content in the majority of the variants established in our laboratory except for the ovarian ES-2/TP80 cell line where we found slightly elevated expression resulting from paclitaxel selection relative to its parental control. In addition to these alterations in IAP content, we observed elevated Bcl-2 in ovarian (MES-OV/TP40 and MES-OV/TxTP50) and breast (MCF-7/TxTP50, BT-549/TxTP50, and MDA231/TxTP50) cancer cell lines at the transcript level by rt-PCR and confirmed by immunoblotting. Specific gene silencing by RNAi and treatment with small molecule inhibitors will test the functional significance of IAP alterations in these models of taxane resistance. Citation Format: George E. Duran, Anamaria Brozovic, Francisco J. Martinez, E Brian Francisco, Yan C. Wang, Branimir I. Sikic. Overexpression of inhibitors of apoptosis (IAP) family members in human breast and ovarian cancer models of non-MDR1 taxane resistance. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 901. doi:10.1158/1538-7445.AM2013-901

MDM2 and MDM4 are heterodimeric, non-redundant oncoproteins that potently inhibit the p53 tumor suppressor protein. MDM2 and MDM4 also enhance the tumorigenicity of breast cancer cells in in vitro and in vivo models and are overexpressed in primary human breast cancers. Prior studies have characterized Estrogen Receptor Alpha (ERα/ESR1) as a regulator of MDM2 expression and an MDM2- and p53-interacting protein. However, similar crosstalk between ERα and MDM4 has not been investigated. Moreover, signaling pathways that mediate the overexpression of MDM4 in human breast cancer remain to be elucidated. Using the Cancer Genome Atlas (TCGA) breast invasive carcinoma patient cohort, we have analyzed correlations between ERα status and MDM4 and MDM2 expression in primary, treatment-naïve, invasive breast carcinoma samples. We report that the expression of MDM4 and MDM2 is elevated in primary human breast cancers of luminal A/B subtypes and associates with ERα-positive disease, independently of p53 mutation status. Furthermore, in cell culture models, ERα positively regulates MDM4 and MDM2 expression via p53-independent mechanisms, and these effects can be blocked by the clinically-relevant endocrine therapies fulvestrant and tamoxifen. Additionally, ERα also positively regulates p53 expression. Lastly, we report that endogenous MDM4 negatively regulates ERα expression and forms a protein complex with ERα in breast cancer cell lines and primary human breast tumor tissue. This suggests direct signaling crosstalk and negative feedback loops between ERα and MDM4 expression in breast cancer cells. Collectively, these novel findings implicate ERα as a central component of the p53-MDM2-MDM4 signaling axis in human breast cancer.

Breast cancer (BCa) and prostate cancer (PCa) are both hormone driven cancers with similar etiology and tumor microenvironment inflammation promotes BCa and PCa progression. Interleukin-1 (IL-1) is an inflammatory cytokine present in the tumor microenvironment and IL-1 is elevated in BCa and PCa patient tumor and/or blood serum and correlates with poor prognosis. We have shown that IL-1 represses the BCa and PCa therapeutic targets, Estrogen Receptor Alpha (ERa) and Androgen Receptor (AR), respectively, in PCa and BCa cell lines; yet the cells remain viable. Thus, IL-1 may promote treatment resistance and disease progression. The pro-survival protein Sequestome-1 (SQSMT1/p62) is also upregulated in both BCa and PCa cell lines exposed to IL-1, suggesting that BCa and PCa cells have evolved a shared response to IL-1 and hormone receptor loss. RNA sequencing of an IL-1-treated PCa cell line revealed an IL-1-modulated gene suite predicted to confer AR-independent tumorigenicity. We performed RT-qPCR in PCa cell lines for several select genes to confirm the RNA sequencing results and given the similar etiology and IL-1 regulation of ERa, AR, and p62 expression in BCa and PCa cell lines, we presumed that our select genes would be similarly regulated by IL-1 in BCa cells. However, outside of ERa, AR, and p62 expression, our select genes did not show similar IL-1 regulation in BCa cell lines, suggesting that IL-1 regulates a unique set of genes that could contribute to ERa-independent tumorigenicity in BCa cells. Therefore, to identify a BCa-specific IL-1-modulated gene suite, we performed RNA sequencing on an IL-1-treated ERα+ BCa cell line and compared gene expression changes with 1) basal gene expression in an ERa- BCa cell line and 2) our IL-1-modulated PCa-specific gene suite. Our bioinformatics analysis revealed pathways that are predicted to promote ERa-independent tumorigenicity in BCa cells and investigations are underway to demonstrate the functional significance of our gene expression data. Taken together, our studies provide insight into the mechanistic function of IL-1 in PCa and BCa resistance to hormone receptor-targeted therapies and tumor progression. Citation Format: Afshan Fathima Nawas, Mohammed Kanchwala, Shayna Thomas-Jardin, Vanessa Anunobi, Ally Wong, Chao Xing, Nikki Delk. Identification of Interleukin-1 (IL-1) induced gene expression pattern in breast cancer (BCa) cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3444.

BackgroundThe function and regulatory mechanism of FBXO43 in breast cancer (BC) are still unclear. Here, we intended to determine the role and mechanism of FBXO43 in BC.MethodsFBXO43 expression in BC was evaluated by analysis of The Cancer Genome Atlas (TCGA). RT-qPCR and western blotting were utilized to detect FBXO43 expression in BC cell lines. Lentivirus was applied to downregulate FBXO43 in human BC cells. Proliferation assays were performed to evaluate the proliferative ability of BC cells. The apoptosis and cell cycle analysis of BC cells were analyzed by flow cytometry. Cell migration and invasion were investigated via Transwell assays. The function of FBXO43 in vivo was evaluated by constructing a xenograft mouse model. The proteins that might interact with FBXO43 in BC were identified by mass spectrometry, bioinformatics analysis, and co-immunoprecipitation (Co-IP) assays. Finally, rescue experiments were conducted to validate the recovery effects of the proteins interacting with FBXO43.ResultsFBXO43 was highly expressed in BC and was significantly downregulated after FBXO43 knockdown. The proliferation, migration, and invasion of BC cells were inhibited, and cell apoptosis was induced by FBXO43 knockdown. In addition, an in vivo experiment indicated that FBXO43 knockdown could inhibit the cell growth of BC. The results of the Co-IP assay showed that FBXO43 interacted with PCNA. Further rescue experiments confirmed that overexpression of PCNA significantly reversed the effects of FBXO43 knockdown on BC cells.ConclusionDownregulation of FBXO43 inhibits the tumor growth of BC by limiting its interaction with PCNA. FBXO43 might be a new potential oncogene and a therapeutic target for BC.

Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, ParasiTE, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.

BackgroundThe biological functions of transposable element (TE)-derived transcripts during physiological development, disease development, and progression have been previously reported. However, research on locus-specific TE-derived transcript expression in various human cell types remains limited.MethodsWe processed 2596 publicly available human long-read RNA-sequencing (LR RNA-seq) datasets covering 21 organs and 71 cell lines in both healthy individuals and diseased patients with various conditions to compile this TE-derived transcript annotation. We established a pipeline for assembling transcripts containing TE sequences to measure transcriptionally active TE-derived transcripts in diverse tissues and cell types. Next, we applied our TE annotation to the Genotype-Tissue Expression (GTEx) single-cell RNA-sequencing (scRNA-seq) data from eight tissues.ResultsWe constructed the first transcriptom6e-based TE annotation using massive amounts of human LR RNA-seq data for use as a comprehensive reference to detect locus-specific TE-derived transcripts. Our annotation showed better detection accuracy for TE-derived transcripts than the RepeatMasker and GENCODE nonTE gene annotations. This annotation enabled the identification of novel TE-derived transcripts and their isoforms. We also identified alternative transcription end sites for long noncoding genes and confirmed previously annotated TE-nonTE gene fusion transcripts. Next, we applied our TE-derived transcript annotation to public scRNA-seq data from various human tissues and identified several cell-type-specific TE-derived transcripts in a locus-specific manner.ConclusionsWe generated a comprehensive, TE-derived transcript annotation using large-scale, LR RNA-seq data. Researchers can use our TE reference annotation to analyze active TE transcripts and their splicing isoforms in specific transcriptome datasets and to detect de novo TE transcripts. The discovery of cell-type-specific TE-derived transcripts may help explain mechanisms underlying the maintenance of cellular identity and provide new insights into the pathological mechanisms of various diseases.Supplementary InformationThe online version contains supplementary material available at 10.1186/s44342-025-00048-1.