B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common pediatric cancer and the leading cause of cancer-related death in children worldwide. Despite improvements in treatment regimens, the prognosis remains poor for patients with high risk to relapse and even worse in those who relapse (1). In developed countries, survival rates at 5 years and cure rates are more than 90% and 80%, respectively (2), but significantly lower in developing countries (3, 4). For instance, in Mexico, mortality rate due to BCP-ALL has not been reduced regardless of the use of the same chemotherapy regimens as developed countries (5). Furthermore, approximately 50% of the Mexican children with ALL are classified into the high risk of relapse group and less than 20% are identified as positive for one of the four most common gene rearrangements associated with prognosis (ETV6/RUNX1, TCF3/PBX1, BCR/ABL1, and MLL/AF4) (6, 7). Meanwhile, in developed countries, only one-third of patients are classified as high risk at diagnosis and over 32% of all cases are positive to one of these common translocations (8, 9). Notably, relapses occur in 26.2% of Mexican BCP-ALL pediatric patients and over a half of these relapses occur in the standard risk group, a higher rate than those reported in high-income countries (5, 10). This highlights the necessity of identifying new biomarkers to improve the current clinical and molecular relapse risk stratification in Mexican children with BCP-ALL.

Gene expression profiles have been used to identify new potential genetic biomarkers associated with relapse (11–14), most of them focused on coding RNAs profiles, although these genes represent only 2% of the total transcriptome in a human cell (15). The remaining 98% of transcriptome is represented by non-coding RNAs (ncRNAs) that might carry relevant biological and clinical information. Long non-coding RNAs (lncRNAs) are the largest set of ncRNAs that play roles as gene expression modulators at epigenetic, transcriptional, and post-transcriptional levels. LncRNAs could act as tumor suppressor genes or oncogenes by regulating directly or indirectly the expression of genes involved in cell proliferation, differentiation, apoptosis, metastasis, and multiple biological processes (16–18). In recent years, some of these lncRNAs, as the long intergenic non-protein coding RNAs (lincRNA), have been identified as abnormally expressed in ALL and have been suggested as potential biomarkers to prognosis and molecular classification of this malignancy (16, 19–21). A study exploring the lncRNA landscape of human hematopoiesis and leukemia revealed a dysregulation of the LINC00173 (also known as FLJ42957, MGC148154, MGC148155, and NCRNA00173) in leukemia (22). This gene participates in myeloid progenitor cell proliferation and differentiation processes (22). Additionally, data from diverse solid tumors reveal that LINC00173 acts as a competitive endogenous RNA (ceRNA) and is associated with cancer-related processes and chemoresistance (23–32). In fact, abnormal expression of LINC00173 and its association with poor prognosis has also been reported in those tumors (33–35). For instance, low expression of LINC00173 was associated with worse disease-free survival (DFS) and poor overall survival (OS) in cervical cancer (CC) and esophageal squamous cell carcinoma (ESCC) (26, 33–35). In triple-negative breast cancer, LINC00173 is overexpressed and associated with worse recurrence-free survival (RFS) and OS (25). These findings suggest that LINC00173 plays distinct roles in different cancer types; however, its clinical relevance in ALL has not been investigated. The aim of the present study was to investigate whether LINC00173 is as potential biomarker in BCP-ALL and to explore its expression in other tumor types by using publicly available data in The Cancer Genome Atlas (TCGA) repository.

Over the last decade, the lncRNAs have emerged as potential biomarkers in diverse human diseases. LncRNAs exert diverse roles in human malignancies and have been associated with prognosis and chemoresistance. One of the best examples is HOTAIR, which is abnormally expressed in many cancer types, including acute leukemia, and consistently replicated across different cohorts (17, 40–43). However, information regarding the role of lncRNAs as biomarkers in ALL is still scarce. To investigate whether LINC00173 is a biomarker in ALL, we studied BM of BCP-ALL from Mexican cases and retrieved RNA-seq data from the TARGET repository. Moreover, we explored the expression levels of this lincRNA in different human tumors by using public RNA-seq data that are available in TCGA. We found that LINC00173 expression is significantly reduced in ALL patients in contrast to healthy subjects, together with an association among the expression of this gene with TCF3/PBX1 and poor prognosis in BCP-ALL cases. In addition, an abnormal expression of LINC00173 in many human cancer types and its association with reduced OS were noticed.

Our findings related to the underexpression of LINC00173 in BCP-ALL cases in contrast to healthy subjects point this gene as a probable biomarker for BCP-ALL, as has been suggested for NSCLC diagnosis (44). However, the molecular function of LINC00173 in ALL and its clinical relevance have not been explored. In an lncRNA expression portrait of hematopoiesis and leukemia reported by Schwarzer et al. (22), it was identified that LINC00173 belongs to a unique fingerprint non-coding RNA of mature granulocytes. Furthermore, the authors demonstrated that this lincRNA is an early regulator of granulopoiesis and myeloid differentiation. It was documented that LINC00173 controls the myeloid progenitor proliferation, as well as the differentiation and maturation of granulocytes (22). By using RNA immunoprecipitation and qRT-PCR techniques, studies in two different cell lines revealed that LINC00173 interacts with the Enhancer of zeste homolog 2 gene (a central component of the Polycomb repressor complex 2 subunit), to silence a set of stemness genes, and suppresses alternative cell fates (22). By knocking down LINC00173 in human CD34+ hematopoietic stem and progenitor cells, it was demonstrated that this lincRNA modifies the methylation patterns at the promoter regions of a set of stem cell genes, which include HOXA7, HOXA9, HOXA10, and SYDE1. All these genes are involved in hematopoiesis and cancer (45–48). Localization studies showed that LINC00173 is found within the nucleus, as the non-coding RNAs X-inactivating XIST and MALAT1 (22). Hence, the downregulation of LINC00173 might inhibit hematopoietic cell differentiation or promote proliferation in ALL cells. The restoration of its expression in pre-B ALL could have potential therapeutic implications as has been reported for other downregulated lincRNAs in ALL, including RP11-446E9 and linc-PINT, in which their induced expression promotes tumor suppressor phenotypes and reduces cell proliferation and migration in ALL cell lines (49, 50). We cannot discount the fact that our results could be explained by the differences in the cell lineage composition between normal hematopoietic cells and B-ALL rather than a potential biological role of LINC00173 in BCP-ALL (22, 51, 52). Further studies are needed to determine whether LINC00173 underexpression contributes to the development of ALL.

Additionally, our work presents the first report showing an association between LINC00173 and the TCF3/PBX1 fusion gene. It has been reported that some lncRNAs are differentially expressed in the presence of certain rearrangements in ALL, highly predicting the cytogenetic abnormality (53–55). For instance, in the MLL/AF4 ALL subtype, BARL-2 and BARL-6 were found to be overexpressed, which correlated with worse OS and poor responsiveness to prednisone treatment (56). However, at the present time, there are no reports evaluating the expression of LINC00173 in ALL molecular subtypes. According to the described role of LINC00173 in myelopoiesis, it has been reported that TCF3/PBX1 can also block myeloid differentiation and stimulates proliferation (57). Moreover, it has been shown that TCF3/PBX1 negatively regulates the expression of genes involved in differentiation and cell cycle regulation processes (58). These findings could explain our results regarding the reduced OS observed in BCP-ALL cases carrying TCF3/PBX1 and displaying underexpression of LINC00173. Furthermore, we discovered that the BCR/ABL1 molecular subtype expressed the highest levels of LINC00173. According to these data, we observed that LINC00173 is highly expressed in the K562 cell line (BCR/ABL1-positive); furthermore, a high expression of LINC00173 has also been reported in the Philadelphia chromosome-like (Ph-like) subtype (59). In vitro and in vivo experiments have shown that LINC00173 represses the expression of the EF2 target, sphingosine kinase 1 (SPHK1), suppressing cell proliferation and promoting apoptosis (32). To note, SPHK1 is an upregulated BRC/ABL1 subtype of ALL (60). More experimental studies should be carried out to decipher the molecular mechanisms involving LINC00173 and BCR/ABL1 and their clinical significance in ALL. We cannot discard a direct interaction among LINC00173 and BCR/ABL1 in BCP-ALL, since it is widely known that certain proteins involved in cancer favor tumor progression through modulation of lncRNA expression (61). Although the multivariate analysis adjusted by variables with prognostic significance (age, WCB, hyperdiploidy, and common fusion genes) suggested that LINC00173 is an independent biomarker ( Table 2 ), the role of other potential confounding factors, such as the poor prognosis phenotype Ph-like (data not available to both cohorts) that occurs at different frequencies between populations, should be discarded (62).

Along with our BCP-ALL findings, we detected an abnormal expression of LINC00173 in many human cancer types and an association with reduced OS. Since LINC00173 was either under- or overexpressed in all human cancer types deposited in TCGA, it is likely that this gene could act as an oncogene and a tumor suppressor gene by controlling relevant processes in cancer. For example, the LINC00173 silencing in ESCC cell lines induces an increased cell proliferation and cell cycle alteration (33). Likewise, other studies have shown that LINC00173 is associated with cancer-related processes including proliferation, migration, invasion, metastasis, inhibition of apoptosis, and chemoresistance (23–32). According to these reports, our pathway enrichment analysis showed that overexpression of LINC00173 correlates with the expression of genes involved in several cancer-related pathways along with immune response (alpha interferon, gamma interferon, cytokine-related, and integrin) pathways. Interestingly, we found that underexpression of LINC00173 was associated with an enrichment of pathways related to increased cell proliferation, which is in agreement with our findings regarding DFS and OS. Emerging data show the complex role of LINC00173 in cancer. For instance, it is known that the locus of this lincRNA is located into a region co-occupied by RUNX1 transcription factor (63) and that LINC00173 recruits the polycomb group of proteins leading to the condensation of chromatin (64). In CC, the underexpression of LINC00173 increases miR-182-5p and decreases FBXW7 expression, enhancing proliferation and invasion (26, 34). In NSCLC, LINC00173 induces miR-182-5p accumulation and increases proliferation, migration, and apoptosis inhibition via the AGER/NF-κB axis (26). Notably, miR-182-5p overexpression at the end of induction therapy for leukemia increases short-term relapses and death (65). The knowledge that LINC00173 is abnormally expressed in most human cancer types exhibits this lincRNA as a relevant gene in the oncogenesis process; thus, we need to delve into the molecular mechanisms involving LINC00173 in human malignancies. Otherwise, our findings in the Mexican cohort that were not validated in TARGET could be due to our small sample size, which, in addition to the molecular heterogeneity of ALL, might influence the statistical power of the present study. Furthermore, since we did not discard BM samples based on blast percentage, the lincRNA of normal hematopoietic cells, especially those previously associated with myeloid differentiation, could act as a confounding factor. Nevertheless, the association between LINC00173 and TCF3/PBX1 was noteworthy. LINC00173 expression has been correlated with poor prognosis in many human solid cancers, supporting the potential role of this gene in ALL as a risk predictor of poor outcome. Thus, to gain a better understanding of the role of LINC00173 as a biomarker associated with relapse and death in children with ALL in our population, issues such as the sample size, sorting of ALL cells, and validation in an independent cohort should be considered. Additionally, functional studies are needed to clarify both LINC00173 and TCF3/PBX1, and LINC00173 and BCR/ABL associations.

This analysis revealed that LINC00173 expression is dysregulated in BCP-ALL and multiple cancer types, suggesting that this gene plays a relevant role in general processes of cancer. In addition, the association between LINC00173, TCF3/PBX1, and BCR/ABL1 fusion genes in ALL needs to be further investigated to decipher the molecular mechanisms involved in relapse and death. More studies involving multi-ethnic cohorts are needed to endorse the value of LINC00173 as a peripheral blood biomarker to identify BCP-ALL cases with poor prognosis and with chemoresistance, and/or to determine its potential use in targeted therapy.

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .

The National Scientific Research and Ethics Committees of the Mexican Institute of Social Security approved the protocol: R-2013-785-068. Written informed consent to participate in this study was provided by the participants’ legal guardian/next of kin.

Conceptualization: SJ-M and DM-H. Methodology: DM-H, DB-L, JN-E, and VB-M. Formal Analysis: DM-H, DB-L, FB-A, and JN-E. Investigation: DM-H, DB-L, JN-E, and SJ-M. Resources: VB-M, EJ-H, MO-M, FG-C, AM-S, JF-L, JM-T, JP-G, MV-A, JT-N, GH-E, RE-E, MLG-R, RS-H, MP-S, LF-V, LM-P, DD-R, MM-R, OS-R, HV-R, AH-M, JM-A, and SJ-M. Writing—Original Draft Preparation: DM-H and SJ-M. Writing—Review and Editing: SJ-M and JM-A. Supervision: SJ-M. Funding Acquisition: SJ-M and JN-E. All authors contributed to the article and approved the submitted version.

This work was supported by the Consejo Nacional de Ciencia y Tecnología (CONACyT; grant numbers Investigación en Fronteras de la Ciencia (IFC)-2016–01–2119; FORDECYT PRONACES 2019-02-303019) and by the National Institute of Genomic Medicine (19/2019/I). The funding body had no role in the design of the study; collection, analysis, and interpretation of the data; or preparation of the manuscript. DM-H and DB-L received a fellowship by Consejo Nacional de Ciencia y Tecnología CONACyT (CVU 858577 and 737534, respectively).

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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