Shi C, Pamer EG. Monocyte recruitment during infection and inflammation. Nat Rev Immunol. 2011. https://doi.org/10.1038/nri3070.

Article  PubMed  PubMed Central  Google Scholar 

Auffray C, Sieweke MH, Geissmann F. Blood monocytes: development, heterogeneity, and relationship with dendritic cells. Annu Rev Immunol. 2009. https://doi.org/10.1146/annurev.immunol.021908.132557.

Article  PubMed  Google Scholar 

Guilliams M, Ginhoux F, Jakubzick C, Naik SH, Onai N, Schraml BU, Segura E, Tussiwand R, Yona S. Dendritic cells, monocytes and macrophages: a unified nomenclature based on ontogeny. Nat Rev Immunol. 2014. https://doi.org/10.1038/nri3712.

Article  PubMed  PubMed Central  Google Scholar 

Geissmann F, Manz MG, Jung S, Sieweke MH, Merad M, Ley K. Development of monocytes, macrophages, and dendritic cells. Science. 2010. https://doi.org/10.1126/science.1178331.

Article  PubMed  PubMed Central  Google Scholar 

Das A, Sinha M, Datta S, Abas M, Chaffee S, Sen CK, Roy S. Monocyte and macrophage plasticity in tissue repair and regeneration. Am J Pathol. 2015. https://doi.org/10.1016/j.ajpath.2015.06.001.

Article  PubMed  PubMed Central  Google Scholar 

Mosser DM, Edwards JP. Exploring the full spectrum of macrophage activation. Nat Rev Immunol. 2008. https://doi.org/10.1038/nri2448.

Article  PubMed  PubMed Central  Google Scholar 

Gordon S, Martinez FO. Alternative activation of macrophages: mechanism and functions. Immunity. 2010. https://doi.org/10.1016/j.immuni.2010.05.007.

Article  PubMed  PubMed Central  Google Scholar 

Biswas SK, Mantovani A. Macrophage plasticity and interaction with lymphocyte subsets: cancer as a paradigm. Nat Immunol. 2010. https://doi.org/10.1038/ni.1937.

Article  PubMed  Google Scholar 

Murray PJ, Wynn TA. Protective and pathogenic functions of macrophage subsets. Nat Rev Immunol. 2011. https://doi.org/10.1038/nri3073.

Article  PubMed  PubMed Central  Google Scholar 

Wang N, Liang H, Zen K. Molecular mechanisms that influence the macrophage m1–m2 polarization balance. Front Immunol. 2014. https://doi.org/10.3389/fimmu.2014.00614.

Article  PubMed  PubMed Central  Google Scholar 

Huang Z, Luo Q, Yao F, Qing C, Ye J, Deng Y, Li J. Identification of differentially expressed long non-coding RNAs in polarized macrophages. Sci Rep. 2016. https://doi.org/10.1038/srep19705.

Article  PubMed  PubMed Central  Google Scholar 

Nares S, Moutsopoulos NM, Angelov N, Rangel ZG, Munson PJ, Sinha N, Wah SM. Rapid myeloid cell transcriptional and proteomic responses to periodontopathogenic Porphyromonas gingivalis. Am J Pathol. 2009. https://doi.org/10.2353/ajpath.2009.080677.

Article  PubMed  PubMed Central  Google Scholar 

Woollard KJ, Geissmann F. Monocytes in atherosclerosis: subsets and functions. Nat Rev Cardiol. 2010. https://doi.org/10.1038/nrcardio.2009.228.

Article  PubMed  PubMed Central  Google Scholar 

Peranzoni E, Zilio S, Marigo I, Dolcetti L, Zanovello P, Mandruzzato S, Bronte V. Myeloid-derived suppressor cell heterogeneity and subset definition. Curr Opin Immunol. 2010. https://doi.org/10.1016/j.coi.2010.01.021.

Article  PubMed  Google Scholar 

Wynn TA, Chawla A, Pollard JW. Macrophage biology in development, homeostasis and disease. Nature. 2013. https://doi.org/10.1038/nature12034.

Article  PubMed  PubMed Central  Google Scholar 

St Laurent G, Wahlestedt C, Kapranov P. The landscape of long noncoding RNA classification. Trends Genet. 2015. https://doi.org/10.1016/j.tig.2015.03.007.

Article  PubMed  PubMed Central  Google Scholar 

Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet. 2016. https://doi.org/10.1038/nrg.2015.10.

Article  PubMed  Google Scholar 

Ma L, Bajic VB, Zhang Z. On the classification of long non-coding RNAs. RNA Biol. 2013. https://doi.org/10.4161/rna.24604.

Article  PubMed  PubMed Central  Google Scholar 

Engreitz JM, Ollikainen N, Guttman M. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol. 2016. https://doi.org/10.1038/nrm.2016.126.

Article  PubMed  Google Scholar 

Labonte AC, Tosello-Trampont AC, Hahn YS. The role of macrophage polarization in infectious and inflammatory diseases. Mol Cells. 2014. https://doi.org/10.14348/molcells.2014.2374.

Article  PubMed  PubMed Central  Google Scholar 

Braga TT, Agudelo JS, Camara NO. Macrophages during the fibrotic process: M2 as friend and foe. Front Immunol. 2015. https://doi.org/10.3389/fimmu.2015.00602.

Article  PubMed  PubMed Central  Google Scholar 

Ruffell B, Coussens LM. Macrophages and therapeutic resistance in cancer. Cancer Cell. 2015. https://doi.org/10.1016/j.ccell.2015.02.015.

Article  PubMed  PubMed Central  Google Scholar 

Funes SC, Rios M, Escobar-Vera J, Kalergis AM. Implications of macrophage polarization in autoimmunity. Immunology. 2018. https://doi.org/10.1111/imm.12910.

Article  PubMed  PubMed Central  Google Scholar 

Leitinger N, Schulman IG. Phenotypic polarization of macrophages in atherosclerosis. Arterioscler Thromb Vasc Biol. 2013;33:1120–6. https://doi.org/10.1161/ATVBAHA.112.300173.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yihao L, Minmin S, Xingfeng H, Yizhi C, Pengyi L, Fanlu L, Siyi Z, Chenlei W, Qian Z, Zhiwei X, Jiancheng W, Baofa S, Baiyong S. LncRNA-PACERR induces pro-tumour macrophages via interacting with miR-671-3p and m6A-reader IGF2BP2 in pancreatic ductal adenocarcinoma. J Hematol Oncol. 2022. https://doi.org/10.1186/s13045-022-01272-w.

Article  Google Scholar 

Tian X, Wu Y, Yang Y, Wang J, Niu M, Gao S, Qin T, Bao D. Long noncoding RNA LINC00662 promotes M2 macrophage polarization and hepatocellular carcinoma progression via activating Wnt/b-catenin signaling. Mol Oncol. 2020. https://doi.org/10.1002/1878-0261.12606.

Article  PubMed  PubMed Central  Google Scholar 

Fordham JB, Naqvi AR, Nares S. Regulation of miR-24, miR-30b, and miR-142-3p during macrophage and dendritic cell differentiation potentiates innate immunity. J Leukoc Biol. 2015. https://doi.org/10.1189/jlb.1A1014-519RR.

Article  PubMed  PubMed Central  Google Scholar 

Naqvi AR, Fordham B, Nares S. miR-24, miR-30b, and miR-142-3p regulate phagocytosis in myeloid inflammatory cells. J Immunol. 2015. https://doi.org/10.4049/jimmunol.

Article  PubMed  Google Scholar 

Naqvi AR, Fordham B, Ganesh B, Nares S. miR-24, miR-30b and miR-142-3p interfere with antigen processing and presentation by primary macrophages and dendritic cells. Sci Rep. 2016. https://doi.org/10.1038/srep32925.

Article  PubMed  PubMed Central  Google Scholar 

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet J. 2011. https://doi.org/10.14806/ej.17.1.200.

Article  Google Scholar 

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012. https://doi.org/10.1038/nmeth.1923.

Article  PubMed  PubMed Central  Google Scholar 

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013. https://doi.org/10.1186/gb-2013-14-4-r36.

Article  PubMed  PubMed Central  Google Scholar 

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015. https://doi.org/10.1038/nbt.3122.

Article  PubMed  PubMed Central  Google Scholar 

Frazee CA, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol. 2015. https://doi.org/10.1038/nbt.3172.

Article  PubMed  PubMed Central  Google Scholar 

Lei K, Yong Z, Zhi-Qiang ZY, Xiao-Qiao L, Shu-Qi Z, Liping W, Ge G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007. https://doi.org/10.1093/nar/gkm391.

Article  Google Scholar 

Liang S, Haitao L, Dechao B, Guoguang Z, Kuntao Y, Changhai Z, Yuanning L, Runsheng C, Yi Z. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 2013. https://doi.org/10.1093/nar/gkt646.

Article  PubMed  PubMed Central