bims-myxlip Biomed News
on Myxoid liposarcoma
Issue of 2021–01–03
fourteen papers selected by
Laura Mannarino
  1. Targeting Tumor-Associated Macrophages in the Pediatric Sarcoma Tumor Microenvironment.
  2. Mithramycin A radiosensitizes EWS:Fli1+ Ewing sarcoma cells by inhibiting double strand break repair.
  3. The Lipid Metabolic Landscape of Cancers and New Therapeutic Perspectives.
  4. Systemic inflammation response index (SIRI) as a predictive factor for overall survival in advanced soft tissue sarcoma treated with eribulin.
  5. Trabectedin Plus Radiotherapy for Advanced Soft-Tissue Sarcoma: Experience in Forty Patients Treated at a Sarcoma Reference Center.
  6. Prospects for NK Cell Therapy of Sarcoma.
  7. The chromatin remodeler ALC1 underlies resistance to PARP inhibitor treatment.
  8. MiR-144-3p Targets FoxO1 to Reduce Its Regulation of Adiponectin and Promote Adipogenesis.
  9. Human macrophages stimulate expression of inflammatory mediators in adipocytes; effects of second-generation antipsychotics and glucocorticoids on cellular cross-talk.
  10. T lymphocytes related biomarkers for predicting immunotherapy efficacy in non-small cell lung cancer.
  11. Tumor-Associated Macrophages in Tumor Immunity.
  12. MultiPaths: a python framework for analyzing multi-layer biological networks using diffusion algorithms.
  13. SATB1-mediated chromatin landscape in T cells.
  14. Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data.
  1. Front Oncol. 2020 ;10 581107
    Targeting Tumor-Associated Macrophages in the Pediatric Sarcoma Tumor Microenvironment.
    Jane Koo, Masanori Hayashi, Michael R Verneris, Alisa B Lee-Sherick.
      For many pediatric sarcoma patients, multi-modal therapy including chemotherapy, radiation, and surgery is sufficient to cure their disease. However, event-free and overall survival rates for patients with more advanced disease are grim, necessitating the development of novel therapeutic approaches. Within many pediatric sarcomas, the normal immune response, including recognition and destruction of cancer cells, is lost due to the highly immune suppressive tumor microenvironment (TME). In this setting, tumor cells evade immune detection and capitalize on the immune suppressed microenvironment, leading to unchecked proliferation and metastasis. Recent preclinical and clinical approaches are aimed at understanding this immune suppressive microenvironment and employing cancer immunotherapy in an attempt to overcome this, by renewing the ability of the immune system to recognize and destroy cancer cells. While there are several factors that drive the attenuation of immune responses in the sarcoma TME, one of the most remarkable are tumor associated macrophage (TAMs). TAMs suppress immune cytolytic function, promote tumor growth and metastases, and are generally associated with a poor prognosis in most pediatric sarcoma subtypes. In this review, we summarize the mechanisms underlying TAM-facilitated immune evasion and tumorigenesis and discuss the potential therapeutic application of TAM-focused drugs in the treatment of pediatric sarcomas.
    Keywords:  efferocytosis; immunotherapy; pediatric sarcoma; tumor microenvironment; tumor-associated macrophage
    DOI:  https://doi.org/10.3389/fonc.2020.581107
  2. Int J Radiat Oncol Biol Phys. 2020 Dec 26. pii: S0360-3016(20)34656-3. [Epub ahead of print]
    Mithramycin A radiosensitizes EWS:Fli1+ Ewing sarcoma cells by inhibiting double strand break repair.
    Mei Yun Lin, Timothy A Damron, Megan E Oest, Jason A Horton.
       PURPOSE: The oncogenic EWS:Fli1 fusion protein is a key transcriptional mediator of Ewing sarcoma initiation, progression, and therapeutic resistance. Mithramycin A (MithA) is a potent and specific inhibitor of transcription mediated by the EWS:Fli1. We tested the hypothesis that pretreatment with MithA could selectively radiosensitize EWS:Fli1+ tumor cells by altering the transcriptional response to radiation injury.
    METHODS: A panel of four EWS:Fli1+ and three EWS:Fli1- Ewing sarcoma cell lines and one non-tumor cell line were subjected to MithA dose-response viability assays to determine the relative potency of MithA in cells possessing or lacking the EWS:Fli1 fusion. Radiosensitization by MithA was evaluated by clonogenic survival assays in vitro and in a murine xenograft model. DNA damage was evaluated by comet assay and γ-H2Ax flow cytometry. Immunoblotting, flow cytometry and RT-qPCR were used to evaluate DNA damage-induced signaling and repair processes, and apoptosis .
    RESULTS: We found that MithA alone could potently and selectively inhibited the growth of EWS:Fli1+ tumor cells, but not cells lacking this fusion. Pretreatment with MithA for 24 hours before irradiation significantly reduced clonogenic survival in vitro and delayed tumor regrowth in vivo prolonging survival of EWS:Fli1+ tumor-bearing mice. While MithA did not increase the level of DNA double-strand breaks (DSBs), mechanistic studies revealed that MithA pretreatment selectively inhibited DNA DSB repair through downregulation of EWS:Fli1-mediated transcription, leading to tumor cell death by apoptosis.
    CONCLUSIONS: Our data indicate that MithA is an effective radiosensitizer of EWS:Fli1+ tumors and may achieve better local control at lower doses of radiation.
    Keywords:  DNA Repair; Ewing sarcoma; Mithramycin A; Radiosensitization; Radiotherapy
    DOI:  https://doi.org/10.1016/j.ijrobp.2020.12.010
  3. Front Oncol. 2020 ;10 605154
    The Lipid Metabolic Landscape of Cancers and New Therapeutic Perspectives.
    Wenjun Wang, Ling Bai, Wei Li, Jiuwei Cui.
      Lipid metabolism reprograming, as a hallmark of malignancy, has received renewed interest in recent years in such areas as energy sources, cell membrane components, and signaling molecules involved in the rapid tumor growth and the adaptation to the tumor microenvironment. Lipid metabolism deregulation in cancer involves multiple aspects, including an increased lipid uptake, endogenous de novo fatty acid synthesis, fatty acid oxidation, and cholesterol accumulation, thereby promoting tumor growth and progression. Recent advances in the understanding of specific metabolic alterations in cancer reveal novel pathogenesis mechanisms and a growing number of drugs targeting lipid metabolism have been applied in anti-tumor therapy. Thus, this review discusses the lipid metabolic landscape of cancers and the interplay with oncogenic signaling, and summarizes potential therapeutic targets to improve the therapeutic efficiency in cancer patients, in order to provide more reference and thinking for the treatment of lipid metabolism of cancer patients.
    Keywords:  cancer; cancer metabolism; cholesterol; fatty acid catabolism; fatty acid synthesis; lipid uptake; tumor microenvironment
    DOI:  https://doi.org/10.3389/fonc.2020.605154
  4. J Orthop Sci. 2020 Dec 29. pii: S0949-2658(20)30346-8. [Epub ahead of print]
    Systemic inflammation response index (SIRI) as a predictive factor for overall survival in advanced soft tissue sarcoma treated with eribulin.
    Hiroshi Kobayashi, Tomotake Okuma, Koichi Okajima, Yuki Ishibashi, Liuzhe Zhang, Toshihide Hirai, Takahiro Ohki, Masachika Ikegami, Ryoko Sawada, Yusuke Shinoda, Toru Akiyama, Takahiro Goto, Sakae Tanaka.
       BACKGROUND: Eribulin is a tubulin and microtubule-targeting drug that has clinical benefit in overall survival (OS) for patients with advanced soft tissue sarcoma. Eribulin's efficacy has been confirmed in several clinical trials, although no clinically useful biomarkers have been identified. We therefore sought to clarify the predictive factor of eribulin treatment, while focusing on systemic inflammation and immune response values.
    METHODS: This study included 33 advanced STS patients treated with eribulin between March 2016 and September 2019. We evaluated the associations of clinical factors influencing the efficacy of eribulin treatment and systemic inflammatory and immune response, including the neutrophil-to-lymphocyte ratio (NLR), the platelet-to-lymphocyte ratio (PLR), the lymphocyte-to-monocyte ratio (LMR), the systemic inflammation response index (SIRI), and the prognostic nutrition index (PNI), with progression-free survival (PFS) and OS using the Kaplan-Meier method and log-rank test.
    RESULTS: NLR, LMR, PLR, SIRI, and PNI were unassociated with PFS. Compared with patients with SIRI <1.5, those with an SIRI ≥1.5 had a significantly shorter OS [median OS 15 months (95% confidence interval [CI] 8-not reached) vs. 7 months (95% CI 3-14), P = 0.04]. Moreover, the PFS tended to be shorter for patients with SIRI ≥1.5 who received chemotherapy after eribulin treatment than in those with SIRI >1.5 [median PFS 92.5 days (95% CI 27-204) vs. 133 days (95% CI 36-507), P = 0.08].
    CONCLUSIONS: High SIRI values may predict poorer overall survival and the efficacy of subsequent drugs after eribulin treatment among patients with advanced soft tissue sarcoma.
    DOI:  https://doi.org/10.1016/j.jos.2020.11.006
  5. Cancers (Basel). 2020 Dec 12. pii: E3740. [Epub ahead of print]12(12):
    Trabectedin Plus Radiotherapy for Advanced Soft-Tissue Sarcoma: Experience in Forty Patients Treated at a Sarcoma Reference Center.
    Nadia Hindi, Irene Carrasco García, Alberto Sánchez-Camacho, Antonio Gutierrez, Javier Peinado, Inmaculada Rincón, Johanna Benedetti, Pilar Sancho, Paloma Santos, Paloma Sánchez-Bustos, David Marcilla, Victor Encinas, Sara Chacon, Cristobal Muñoz-Casares, David Moura, Javier Martin-Broto.
      Symptomatic control and tumoral shrinkage is an unmet need in advanced soft-tissue sarcoma (STS) patients beyond first-line. The combination of trabectedin and radiotherapy showed activity in a recently reported clinical trial in this setting. This retrospective series aims to analyze our experience with the same regimen in the real-life setting. We retrospectively reviewed advanced sarcoma patients treated with trabectedin concomitantly with radiotherapy with palliative intent. Growth-modulation index (GMI) was calculated as a surrogate of efficacy. Forty metastatic patients were analyzed. According to RECIST, there was one (2.5%) complete response, 12 (30%) partial responses, 18 (45%) disease stabilizations, and nine (22.5%) progressions. After a median follow-up of 15 months (range 2-38), median progression-free survival (PFS) and overall survival (OS) were 7.5 months (95% CI 2.8-12.2) and 23.5 months (95% CI 1.1-45.8), respectively. Median GMI was 1.42 (range 0.19-23.76), and in 16 (53%) patients, it was >1.33. In patients with GMI >1.33, median OS was significantly longer than in those with GMI 0-1.33 (median OS 52.1 months (95% CI not reached) vs. 8.9 months (95% CI 6.3-11.6), p = 0.028). The combination of trabectedin plus radiotherapy is an active therapeutic option in patients with advanced STS, especially when tumor shrinkage for symptomatic relief is needed.
    Keywords:  advanced soft-tissue sarcoma; growth-modulation index; palliative therapy; trabectedin plus radiotherapy
    DOI:  https://doi.org/10.3390/cancers12123740
  6. Cancers (Basel). 2020 Dec 11. pii: E3719. [Epub ahead of print]12(12):
    Prospects for NK Cell Therapy of Sarcoma.
    Mieszko Lachota, Marianna Vincenti, Magdalena Winiarska, Kjetil Boye, Radosław Zagożdżon, Karl-Johan Malmberg.
      Natural killer (NK) cells are innate lymphoid cells with potent antitumor activity. One of the most NK cell cytotoxicity-sensitive tumor types is sarcoma, an aggressive mesenchyme-derived neoplasm. While a combination of radical surgery and radio- and chemotherapy can successfully control local disease, patients with advanced sarcomas remain refractory to current treatment regimens, calling for novel therapeutic strategies. There is accumulating evidence for NK cell-mediated immunosurveillance of sarcoma cells during all stages of the disease, highlighting the potential of using NK cells as a therapeutic tool. However, sarcomas display multiple immunoevasion mechanisms that can suppress NK cell function leading to an uncontrolled tumor outgrowth. Here, we review the current evidence for NK cells' role in immune surveillance of sarcoma during disease initiation, promotion, progression, and metastasis, as well as the molecular mechanisms behind sarcoma-mediated NK cell suppression. Further, we apply this basic understanding of NK-sarcoma crosstalk in order to identify and summarize the most promising candidates for NK cell-based sarcoma immunotherapy.
    Keywords:  Natural Killer (NK) cells; adoptive cell therapy; cancer; cell-mediated cytotoxicity; chimeric antigen receptor (CAR); immunotherapy; sarcoma; solid tumors; tumor microenvironment (TME)
    DOI:  https://doi.org/10.3390/cancers12123719
  7. Sci Adv. 2020 Dec;pii: eabb8626. [Epub ahead of print]6(51):
    The chromatin remodeler ALC1 underlies resistance to PARP inhibitor treatment.
    Szilvia Juhász, Rebecca Smith, Tamás Schauer, Dóra Spekhardt, Hasan Mamar, Siham Zentout, Catherine Chapuis, Sébastien Huet, Gyula Timinszky.
      Poly(ADP-ribose) polymerase (PARP) inhibitors are used in the treatment of BRCA-deficient cancers, with treatments currently extending toward other homologous recombination defective tumors. In a genome-wide CRISPR knockout screen with olaparib, we identify ALC1 (Amplified in Liver Cancer 1)-a cancer-relevant poly(ADP-ribose)-regulated chromatin remodeling enzyme-as a key modulator of sensitivity to PARP inhibitor. We found that ALC1 can remove inactive PARP1 indirectly through binding to PARylated chromatin. Consequently, ALC1 deficiency enhances trapping of inhibited PARP1, which then impairs the binding of both nonhomologous end-joining and homologous recombination repair factors to DNA lesions. We also establish that ALC1 overexpression, a common feature in multiple tumor types, reduces the sensitivity of BRCA-deficient cells to PARP inhibitors. Together, we conclude that ALC1-dependent PARP1 mobilization is a key step underlying PARP inhibitor resistance.
    DOI:  https://doi.org/10.1126/sciadv.abb8626
  8. Front Genet. 2020 ;11 603144
    MiR-144-3p Targets FoxO1 to Reduce Its Regulation of Adiponectin and Promote Adipogenesis.
    Weimin Lin, Yonghang Tang, Yuelei Zhao, Jindi Zhao, Lifan Zhang, Wei Wei, Jie Chen.
      MicroRNAs (miRNAs), as a series of important short-chain non-coding RNAs, play an important post-transcriptional role in many biological activities, including adipogenesis. miR-144 is significantly upregulated in type II diabetes (T2D), and is considered to be an important biomarker for T2D. However, although the occurrence of T2D is inextricably linked to adipogenesis, whether miR-144 directly regulates adipogenesis remains to be further explored. In this paper, we demonstrate that miR-144 has a higher expression level in a porcine high backfat group, and it has a significant positive effect on promoting the differentiation of pre-adipocytes. FoxO1 is a target gene of miR-144, and inhibits the differentiation of pre-adipocytes. On the other hand, we demonstrate that FoxO1 can bind to the AdipoQ gene promoter, then regulate the AdipoQ expression by binding to the FoxO1 binding site in the AdipoQ promoter -1,499 to -1,489 bp and -1,238 to -1,228 bp regions, especially the -1,499 to -1,489 bp region. Meanwhile, miR-144 and FoxO1 co-expressional research has also shown that both factors regulate adipogenesis. To sum up, our research indicates that miR-144 targets FoxO1, thus reducing its expression and inhibiting its promotional effect on adiponectin, thereby alleviating the inhibitory effect of adiponectin on adipogenesis.
    Keywords:  FoxO1; adipogenesis; adiponectin; miR-144-3p; miRNAs
    DOI:  https://doi.org/10.3389/fgene.2020.603144
  9. Psychoneuroendocrinology. 2020 Dec 11. pii: S0306-4530(20)30494-7. [Epub ahead of print]125 105071
    Human macrophages stimulate expression of inflammatory mediators in adipocytes; effects of second-generation antipsychotics and glucocorticoids on cellular cross-talk.
    Assel Sarsenbayeva, Priya Dipta, Martin Lundqvist, Kristina E Almby, Boaz Tirosh, Giada Di Nunzio, Jan W Eriksson, Maria J Pereira.
       OBJECTIVE: Adipose tissue inflammation and distorted macrophage-adipocyte communication are positively associated with metabolic disturbances. Some pharmacological agents, such as second-generation antipsychotics (SGAs) and synthetic glucocorticoid (GC) dexamethasone, tend to induce adverse metabolic side effects and the underlying mechanisms are not fully understood. Our work aimed to study whether SGAs and dexamethasone affect macrophage phenotype and macrophage-adipocyte communication on gene expression level. We selected the model involving THP-1-derived macrophages, polarized into M0, M1, and M2 phenotypes, and primary human mature subcutaneous adipocytes.
    METHODS: Abdominal subcutaneous adipose tissue needle biopsies were obtained from 6 healthy subjects (4F/2M; age: 22-64 yr; BMI: 21.7-27.6 kg/m2) followed by isolation of mature adipocytes. THP-1-human monocytic cell line was used for the study. THP-1 monocytes were differentiated and polarized into M0 (naïve), M1 (classically activated), and M2 (alternatively activated) macrophages. During and after polarization the macrophages were treated for 24 h without (control) or with therapeutic and supra-therapeutic concentrations of olanzapine (0.2 µM and 2.0 µM), aripiprazole (1.0 µM and 10 µM) and its active metabolite dehydroaripiprazole (0.4 µM and 4.0 µM). Isolated mature human adipocytes were co-incubated with THP-1-derived polarized macrophages pre-treated with SGAs after their polarization. Adipocytes and macrophages were collected before and after co-culture for mRNA expression analysis of genes involved in inflammation.
    RESULTS: Co-incubation of mature human adipocytes with human macrophages, regardless of polarization, resulted in a marked induction of pro-inflammatory cytokines in adipocytes, including IL1B, IL6, TNFA, and IL10. Remarkably, it did not affect the expression of adipokines and genes involved in the regulation of energy, lipid, and glucose metabolism in adipocytes. Dexamethasone markedly reduced gene expression of pro-inflammatory cytokines in macrophages and prevented macrophage-induced inflammatory response in adipocytes. In contrast, SGAs did not affect macrophage-adipocyte communication and had a minute anti-inflammatory effect in macrophages at supra-therapeutic concentrations. Interestingly, the adipocytes co-incubated with M1 macrophages pre-treated with dexamethasone and SGAs particularly the supra-therapeutic concentration of olanzapine, reduced expression of LPL, LIPE, AKT1, and SLC2A4, suggesting that the expression of metabolic genes in adipocytes was dependent on the presence of pro-inflammatory M1 macrophages.
    CONCLUSION: Together, these data suggest that macrophages induce expression of pro-inflammatory genes in human subcutaneous adipocytes without affecting the expression of adipokines or genes involved in energy regulation. Furthermore, our findings demonstrated that SGAs and dexamethasone had a mild effect on macrophage-adipocyte communication in M1 macrophage phenotype.
    Keywords:  Adipose tissue; Glucocorticoids; Inflammation; Macrophages; Second-generation antipsychotics
    DOI:  https://doi.org/10.1016/j.psyneuen.2020.105071
  10. Oncol Lett. 2021 Feb;21(2): 89
    T lymphocytes related biomarkers for predicting immunotherapy efficacy in non-small cell lung cancer.
    Xiaoying Wei, Ling Gu, Wei Heng.
      The immune environment is a determinant of whether patients with cancer can benefit from immunotherapy. Immune checkpoint inhibitors (ICIs) have improved the prognosis of patients with different types of malignancies and have initiated a transformation in tumor therapy. However, some patients cannot achieve a long-term response and several patients even have no response to ICIs therapy. Thus, potential biomarkers that can effectively predict the efficacy of ICIs are essential for their clinical application and for the selection of patients. The accuracy of well-known biomarkers, such as expression of programmed cell death ligand 1 and tumor mutational burden, remains controversial. One of the critical factors for immune responses in the tumor microenvironment is tumor antigen-specific T cell. The density and distribution of tumor-infiltrating lymphocytes, T cells activation and T lymphocytes phenotypes in peripheral blood and serum cytokines have been observed in different types of solid cancer. Although the association with immunotherapy prognosis is in dispute, the prospect of T cell-related biomarkers is encouraged. The present review discusses whether these factors are associated with clinical outcomes of patients with non-small cell lung cancer. The association between several serum cytokines and ICIs therapy efficacy is also discussed.
    Keywords:  biomarkers; cytokines; immunotherapy; lymphocytes; non-small cell lung cancer
    DOI:  https://doi.org/10.3892/ol.2020.12350
  11. Front Immunol. 2020 ;11 583084
    Tumor-Associated Macrophages in Tumor Immunity.
    Yueyun Pan, Yinda Yu, Xiaojian Wang, Ting Zhang.
      Tumor-associated macrophages (TAMs) represent one of the main tumor-infiltrating immune cell types and are generally categorized into either of two functionally contrasting subtypes, namely classical activated M1 macrophages and alternatively activated M2 macrophages. The former typically exerts anti-tumor functions, including directly mediate cytotoxicity and antibody-dependent cell-mediated cytotoxicity (ADCC) to kill tumor cells; the latter can promote the occurrence and metastasis of tumor cells, inhibit T cell-mediated anti-tumor immune response, promote tumor angiogenesis, and lead to tumor progression. Both M1 and M2 macrophages have high degree of plasticity and thus can be converted into each other upon tumor microenvironment changes or therapeutic interventions. As the relationship between TAMs and malignant tumors becoming clearer, TAMs have become a promising target for developing new cancer treatment. In this review, we summarize the origin and types of TAMs, TAMs interaction with tumors and tumor microenvironment, and up-to-date treatment strategies targeting TAMs.
    Keywords:  immunosuppression; regulation; tumor microenvironment; tumor therapy; tumor-associated macrophages
    DOI:  https://doi.org/10.3389/fimmu.2020.583084
  12. Bioinformatics. 2020 Dec 26. pii: btaa1069. [Epub ahead of print]
    MultiPaths: a python framework for analyzing multi-layer biological networks using diffusion algorithms.
    Josep Marín-Llaó, Sarah Mubeen, Alexandre Perera-Lluna, Martin Hofmann-Apitius, Sergio Picart-Armada, Daniel Domingo-Fernández.
       SUMMARY: High-throughput screening yields vast amounts of biological data which can be highly challenging to interpret. In response, knowledge-driven approaches emerged as possible solutions to analyze large datasets by leveraging prior knowledge of biomolecular interactions represented in the form of biological networks. Nonetheless, given their size and complexity, their manual investigation quickly becomes impractical. Thus, computational approaches, such as diffusion algorithms, are often employed to interpret and contextualize the results of high-throughput experiments. Here, we present MultiPaths, a framework consisting of two independent Python packages for network analysis. While the first package, DiffuPy, comprises numerous commonly used diffusion algorithms applicable to any generic network, the second, DiffuPath, enables the application of these algorithms on multi-layer biological networks. To facilitate its usability, the framework includes a command line interface, reproducible examples, and documentation. To demonstrate the framework, we conducted several diffusion experiments on three independent multi-omics datasets over disparate networks generated from pathway databases, thus, highlighting the ability of multi-layer networks to integrate multiple modalities. Finally, the results of these experiments demonstrate how the generation of harmonized networks from disparate databases can improve predictive performance with respect to individual resources.
    AVAILABILITY: DiffuPy and DiffuPath are publicly available under the Apache License 2.0 at https://github.com/multipaths.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa1069
  13. Nucleus. 2020 Dec;11(1): 117-131
    SATB1-mediated chromatin landscape in T cells.
    Tomas Zelenka, Charalampos Spilianakis.
      The regulatory circuits that define developmental decisions of thymocytes are still incompletely resolved. SATB1 protein is predominantly expressed at the CD4+CD8+cell stage exerting its broad transcription regulation potential with both activatory and repressive roles. A series of post-translational modifications and the presence of potential SATB1 protein isoforms indicate the complexity of its regulatory potential. The most apparent mechanism of its involvement in gene expression regulation is via the orchestration of long-range chromatin loops between genes and their regulatory elements. Multiple SATB1 perturbations in mice uncovered a link to autoimmune diseases while clinical investigations on cancer research uncovered that SATB1 has a promoting role in several types of cancer and can be used as a prognostic biomarker. SATB1 is a multivalent tissue-specific factor with a broad and yet undetermined regulatory potential. Future investigations on this protein could further uncover T cell-specific regulatory pathways and link them to (patho)physiology.
    Keywords:  CD4 cells; SATB1; T cell receptor; autoimmunity; cancer; chromatin organization; nuclear matrix; phase separation; thymocytes
    DOI:  https://doi.org/10.1080/19491034.2020.1775037
  14. Genome Res. 2020 Dec 21.
    Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data.
    Wanqing Shao, Ting Wang.
      Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized cell type-specific gene expression analysis. However, effective scRNA-seq quantification tools tailored for TEs are lacking, limiting our ability to dissect TE expression dynamics at single-cell resolution. To address this issue, we established a TE expression quantification pipeline that is compatible with scRNA-seq data generated across multiple technology platforms. We constructed TE-containing ncRNA references using bulk RNA-seq data and showed that quantifying TE expression at the transcript level effectively reduces noise. As proof of principle, we applied this strategy to mouse embryonic stem cells and successfully captured the expression profile of endogenous retroviruses in single cells. We further expanded our analysis to scRNA-seq data from early stages of mouse embryogenesis. Our results illustrated the dynamic TE expression at preimplantation stages and revealed 146 TE-containing ncRNA transcripts with substantial tissue specificity during gastrulation and early organogenesis.
    DOI:  https://doi.org/10.1101/gr.265173.120
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