Pericentromeric satellite lncRNAs are induced in cancer-associated fibroblasts and regulate their functions in lung tumorigenesis

Abstract

The abnormal tumor microenvironment (TME) often dictates the therapeutic response of cancer to chemo- and immuno-therapy. Aberrant expression of pericentromeric satellite repeats has been reported for epithelial cancers, including lung cancer. However, the transcription of tandemly repetitive elements in stromal cells of the TME has been unappreciated, limiting the optimal use of satellite transcripts as biomarkers or anti-cancer targets. We found that transcription of pericentromeric satellite DNA (satDNA) in mouse and human lung adenocarcinoma was observed in cancer-associated fibroblasts (CAFs). In vivo, lung fibroblasts expressed pericentromeric satellite repeats HS2/HS3 specifically in tumors. In vitro, transcription of satDNA was induced in lung fibroblasts in response to TGFβ, IL1α, matrix stiffness, direct contact with tumor cells and treatment with chemotherapeutic drugs. Single-cell transcriptome analysis of human lung adenocarcinoma confirmed that CAFs were the cell type with the highest number of satellite transcripts. Human HS2/HS3 pericentromeric transcripts were detected in the nucleus, cytoplasm, extracellularly and co-localized with extracellular vesicles in situ in human biopsies and activated fibroblasts in vitro. The transcripts were transmitted into recipient cells and entered their nuclei. Knock-down of satellite transcripts in human lung fibroblasts attenuated cellular senescence and blocked the formation of an inflammatory CAFs phenotype which resulted in the inhibition of their pro-tumorigenic functions. In sum, our data suggest that satellite long non-coding (lnc) RNAs are induced in CAFs, regulate expression of inflammatory genes and can be secreted from the cells, which potentially might present a new element of cell-cell communication in the TME.

Overexpression of Pericentromeric HSAT2 DNA Increases Expression of EMT Markers in Human Epithelial Cancer Cell Lines

“…Despite the initial ideas about transcriptionally silent pericentromeres, we know now that the DNA of all HSAT families (HSAT1-3) can be transcribed in a cell under certain circumstances (stress, malignization, cancer-associated polarization, differentiation, senescence, oogenesis, and embryogenesis) [ 19 , 25 , 41 , 42 , 43 ]. In cancer cells, HSAT DNA and RNA contribute to genetic instability [ 20 , 44 , 45 , 46 , 47 ].…”

“…In tumors as a whole, pericentromeric transcripts transcribed in microenvironment cells (e.g., fibroblasts) can increase drug resistance, provoke inflammation, activate the innate immune system, etc. [ 19 , 26 , 27 , 41 ]. HSAT transcription is correlated with poor prognosis and lower survival [ 26 , 48 , 49 ] and is more prominent in advanced tumors [ 19 ].…”

“…We report here that the sequence of the previously identified transcript is tandemly repeated on nine chromosomes (1, 2, 7, 9, 10, 16, 17, 22, and Y). Despite our previous description of it as human satellite III or human satellite 2/3 (HS2/HS3) transcript [ 13 , 17 , 19 , 27 ], a detailed analysis of its genomic localization and annotation in the T2T-CHM13 assembly revealed that the sequence belonged to the HSAT2 (human satellite 2) family of TR DNA. Unexpectedly the transcript DNA was found on both strands of HSAT2 arrays.…”

“…Earlier, we detected HS2/HS3 transcription in human preovulatory oocytes [ 17 , 18 ], some cancer cell lines, and senescent and cancer-associated fibroblasts [ 13 , 19 ]. At that time, mapping the sequence onto human chromosomes and analysis of adjacent chromosomal regions was complicated because pericentromeric and centromeric TR DNA sequences remained almost entirely missing from the assembled human reference genome for the past 20 years [ 20 ].…”

“…The plasmid overexpressing HS2/HS3 was then used for functional studies on cancer cells. Transcription of TR DNA of human pericentromeric satellites was demonstrated in solid tumors and in hematological malignancies [ 19 , 25 , 26 , 27 ], where it was transcribed by cancer cells [ 25 ] and/or by microenvironment cells [ 19 , 27 ]. The association of HS2/HS3 transcription with a poor prognosis has been demonstrated [ 26 ].…”