PMID- 38419051 OWN - NLM STAT- MEDLINE DCOM- 20240301 LR - 20240304 IS - 1423-0127 (Electronic) IS - 1021-7770 (Print) IS - 1021-7770 (Linking) VI - 31 IP - 1 DP - 2024 Feb 28 TI - Integration of transcription regulation and functional genomic data reveals lncRNA SNHG6's role in hematopoietic differentiation and leukemia. PG - 27 LID - 10.1186/s12929-024-01015-8 [doi] LID - 27 AB - BACKGROUND: Long non-coding RNAs (lncRNAs) are pivotal players in cellular processes, and their unique cell-type specific expression patterns render them attractive biomarkers and therapeutic targets. Yet, the functional roles of most lncRNAs remain enigmatic. To address the need to identify new druggable lncRNAs, we developed a comprehensive approach integrating transcription factor binding data with other genetic features to generate a machine learning model, which we have called INFLAMeR (Identifying Novel Functional LncRNAs with Advanced Machine Learning Resources). METHODS: INFLAMeR was trained on high-throughput CRISPR interference (CRISPRi) screens across seven cell lines, and the algorithm was based on 71 genetic features. To validate the predictions, we selected candidate lncRNAs in the human K562 leukemia cell line and determined the impact of their knockdown (KD) on cell proliferation and chemotherapeutic drug response. We further performed transcriptomic analysis for candidate genes. Based on these findings, we assessed the lncRNA small nucleolar RNA host gene 6 (SNHG6) for its role in myeloid differentiation. Finally, we established a mouse K562 leukemia xenograft model to determine whether SNHG6 KD attenuates tumor growth in vivo. RESULTS: The INFLAMeR model successfully reconstituted CRISPRi screening data and predicted functional lncRNAs that were previously overlooked. Intensive cell-based and transcriptomic validation of nearly fifty genes in K562 revealed cell type-specific functionality for 85% of the predicted lncRNAs. In this respect, our cell-based and transcriptomic analyses predicted a role for SNHG6 in hematopoiesis and leukemia. Consistent with its predicted role in hematopoietic differentiation, SNHG6 transcription is regulated by hematopoiesis-associated transcription factors. SNHG6 KD reduced the proliferation of leukemia cells and sensitized them to differentiation. Treatment of K562 leukemic cells with hemin and PMA, respectively, demonstrated that SNHG6 inhibits red blood cell differentiation but strongly promotes megakaryocyte differentiation. Using a xenograft mouse model, we demonstrate that SNHG6 KD attenuated tumor growth in vivo. CONCLUSIONS: Our approach not only improved the identification and characterization of functional lncRNAs through genomic approaches in a cell type-specific manner, but also identified new lncRNAs with roles in hematopoiesis and leukemia. Such approaches can be readily applied to identify novel targets for precision medicine. CI - (c) 2024. The Author(s). FAU - Hazan, Joshua M AU - Hazan JM AD - Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. FAU - Amador, Raziel AU - Amador R AD - Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain. AD - Universitat de Barcelona (UB), Barcelona, Catalonia, Spain. FAU - Ali-Nasser, Tahleel AU - Ali-Nasser T AD - Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. FAU - Lahav, Tamar AU - Lahav T AD - Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. FAU - Shotan, Stav Roni AU - Shotan SR AD - Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. FAU - Steinberg, Miryam AU - Steinberg M AD - Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. FAU - Cohen, Ziv AU - Cohen Z AD - Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. AD - The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. FAU - Aran, Dvir AU - Aran D AD - Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. AD - The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. FAU - Meiri, David AU - Meiri D AD - Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. FAU - Assaraf, Yehuda G AU - Assaraf YG AD - The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. FAU - Guigo, Roderic AU - Guigo R AD - Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain. AD - Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain. FAU - Bester, Assaf C AU - Bester AC AUID- ORCID: 0000-0002-5490-2187 AD - Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel. bestera@technion.ac.il. LA - eng GR - ‎2228/19‎/Israel Science Foundation/ GR - ‎20230069‎/Israel Cancer Association/ GR - 2020095/Israel Cancer Association/ PT - Journal Article DEP - 20240228 PL - England TA - J Biomed Sci JT - Journal of biomedical science JID - 9421567 RN - 0 (RNA, Long Noncoding) RN - 0 (long non-coding RNA SNHG6, human) SB - IM MH - Animals MH - Humans MH - Mice MH - Cell Differentiation/genetics MH - Cell Line, Tumor MH - Cell Proliferation/genetics MH - Gene Expression Regulation, Neoplastic MH - Genomics MH - *Leukemia/genetics MH - *RNA, Long Noncoding/genetics/metabolism PMC - PMC10900714 OTO - NOTNLM OT - CRISPR screening OT - Gene regulation OT - Hematopoiesis. OT - Machine learning OT - lncRNA COIS- The authors declare no competing interests. EDAT- 2024/02/29 00:42 MHDA- 2024/03/01 06:43 PMCR- 2024/02/28 CRDT- 2024/02/28 23:47 PHST- 2023/07/21 00:00 [received] PHST- 2024/02/22 00:00 [accepted] PHST- 2024/03/01 06:43 [medline] PHST- 2024/02/29 00:42 [pubmed] PHST- 2024/02/28 23:47 [entrez] PHST- 2024/02/28 00:00 [pmc-release] AID - 10.1186/s12929-024-01015-8 [pii] AID - 1015 [pii] AID - 10.1186/s12929-024-01015-8 [doi] PST - epublish SO - J Biomed Sci. 2024 Feb 28;31(1):27. doi: 10.1186/s12929-024-01015-8.