The emerging role non-coding RNAs in B cell-related disorders
Cancer Cell International volume 22, Article number: 91 (2022)
Long non-coding RNAs and microRNAs have recently attained much attention regarding their role in the development of B cell lineage as well as participation in the lymphomagenesis. These transcripts have a highly cell type specific signature which endows them the potential to be used as biomarkers for clinical situations. Aberrant expression of several non-coding RNAs has been linked with B cell malignancies and immune related disorders such as rheumatoid arthritis, systemic lupus erythematous, asthma and graft-versus-host disease. Moreover, these transcripts can alter response of immune system to infectious conditions. miR-7, miR-16-1, miR-15a, miR-150, miR-146a, miR-155, miR-212 and miR-132 are among microRNAs whose role in the development of B cell-associated disorders has been investigated. Similarly, SNHG14, MALAT1, CRNDE, AL133346.1, NEAT1, SMAD5-AS1, OR3A4 and some other long non-coding RNAs participate in this process. In the current review, we describe the role of non-coding RNAs in B cell malignancies.
B cells are a subset of immune cells which contribute in the induction of humoral responses. These cells can be sub-classified to three classes based on their ontogeny and anatomic localization. B1 cells are produced from B1 progenitors. B cell progenitor cells of the bone marrow can produce the marginal zone and follicular B cells. Notably, B1 lymphocytes are originated from B1 progenitor cells which reside in the hepatic tissue during the fetal period. These cells preserve their self-renewal capacity after the neonatal time. B2 cells are developed from transitional 2 B cells originating from bone marrow precursors and have sustained output all through the adulthood period . Abnormal development of B cells can result in human disorders including immune deficiency, autoimmunity, or allergy .
B cells are the principal source of antibodies. A typical example of antibodies produced by B1 lymphocytes is the naturally produced antibodies against ABO blood groups . B1 cells can produce IgM antibodies contributing in the maintenance of tissue homeostasis due to their aptitude to bind with reformed self-antigens. These antigens include those produced in the process of cell apoptosis, ischemic damage and oxidative insult in atherosclerosis . Besides, polyreactive IgA antibodies produced by B1 and follicular B cells participate in the mucosal immunity .
In addition, B cells also have an immunomodulatory effect through regulation of immune responses via producing cytokines that impede initiation or progression of immune-related disorders .
Several non-coding RNAs have been demonstrated to be involved in the regulation of function of different classes of B cells, thus contributing in the pathoetiology of related diseases. In fact, three classes of non-coding RNAs, namely long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs) have been vastly investigated in the context of B cell-related disorders. LncRNAs have sizes more than 200 nucleotides, share many features with mRNAs and regulate gene expression at different levels . CircRNAs are a group of transcripts that are produced through 3’-5’ ligation of a single RNA molecule. These transcripts have also regulatory functions on gene expression. They can also produce polypeptides . Finally, miRNAs are transcripts with sizes about 22 nucleotides that suppress expression of mRNAs or degrade them through a base-pairing mechanism .
Through RNA sequencing and de novo transcript assembly methods, Brazão et al. have recognized more than 4500 lncRNAs which are expressed in different phases of development and activation of B cells . Notably, the majority of these transcripts have not been formerly identified, even in the process of commitment of T cells. About one-fifth of these lncRNAs have been found to be either enhancer- or promoter-associated transcripts. Moreover, the B-cell lineage activating transcription factor PAX5 has been shown to directly regulate expression of tens of lncRNAs in pro-B and mature B cells as well as in acute lymphoblastic leukemia (ALL) .
In the current paper, we discuss the effects of non-coding portion of the genome on function of this class of immune cells in different contexts. We also explain the impact of dysregulation of non-coding RNAs in the development of B cell-related disorders, particularly malignant conditions as well as imbalances of immune responses. Identification of the role of these transcripts in these conditions would help in design of targeted therapies for these disorders.
Contribution of miRNAs in the regulation of B cell functions and related disorders
Several miRNAs have been found to affect function of B cells. This process has been mostly evaluated in the context of immune-related disorders and cancers. For instance, miR-7 has been shown to influence expression of PTEN in B cells. Expression of this miRNA has been increased in MRLlpr/lpr mouse model of lupus. Treatment with miR-7 antagomir has decreased disease manifestations in these animals. miR-7-related inhibition of PTEN/AKT signaling has enhanced differentiation of B cells into plasmablasts/plasma cells. Moreover, miR-7 silencing has reduced spontaneous formation of germinal center and normalized B cell subtype fractions in the spleen. In addition, miR-7 antagomir has decreased phosphorylation of STAT3 and IL-21 synthesis. Taken together, miR-7 has an important role in regulation of PTEN expression and functions of B cells .
Tan et al. have assessed miRNA profiles of naïve, germinal center and memory B cells. They have reported elevation of numerous miRNAs in germinal center B cells. miR-17-5p, miR-106a and miR-181b have been among mostly up-regulated miRNAs in these cells. miR-150 has been a miRNA with high expression in all three B-cell subsets. However, its expression has been found to be lower in germinal center B cells compared with naïve and memory B cells. Notably, expressions of miR-17-5p, miR-106a and miR-181b have been gradually decreased from the dark to the light zone of germinal center. Expression of miR-150 has been inversely correlated with c-Myb and Survivin levels in tonsil tissues, implying potential inhibition of these genes by miR-150 .
Several other miRNAs have been found to affect pathogenesis of diffuse large B-cell lymphoma (DLBC). A number of miRNAs have been shown to be dysregulated in these patients. For instance, expression of miR-16–1 has been found to be significantly lower in DLBC patients compared to controls in a single study . Another study has shown differential expression of miR-197 in DLBCL versus controls. While expression levels of miR-197 have not been correlated with clinicopathologic parameters such as international prognostic index, down-regulation of this miRNA has been associated with disease progression in patients treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone. Down-regulation of miR-197 levels could predict shorter progression-free survival in this subgroup of patients as well as non-germinal center B-like subgroup. Cell line studies have shown that miR-197 can enhance doxorubicin-associated apoptosis in SUDHL9 cells but not in OCI-Ly1 cells .
Another study in the context of sepsis has shown up-regulation of miR-19a in B cells. Moreover, in vitro studies have confirmed over-expression of this miRNA in activated B cells. Expression of CD22 has been initially increased but afterwards reduced. Notably, up-regulation of miR-19a has led to activation of BCR signaling, whereas up-regulation of CD22 has resulted in the attenuation of the effects of miR-19a and enhanced its expression. Taken together, miR-19a and CD22 contribute in establishment of a feedback circuit for B cell responses in sepsis, which can be considered as a putative target for re-establishment of immune homeostasis .
miR-30a is another miRNA that participates in the activation of B cells. This miRNA can specifically bind the 3'-UTR of Lyn transcript to inhibit its expression. miR-30a expression has been found to be elevated in B cells of patients with systemic lupus erythematous (SLE) compared with controls. Moreover, its levels have been negatively correlated with Lyn levels in B cells. Up-regulation of miR-30a has promoted proliferation of B cells and release of IgG antibodies. Thus, up-regulation of miR-30a can reduce Lyn levels in B cells, indicating its role in induction of B cell hyperactivity in SLE .
miR-155 is an example of miRNAs whose functions have been evaluated in different contexts such as rheumatoid arthritis , DLBC and non-Hodgkin lymphoma  as well as chronic psychological stress . In B cell malignancies, higher levels of miR-155 have been correlated with the presence of B symptoms, involvement of extranodal sites, and high ECOG score .
Figure 1 depicts the impacts of miRNAs on regulation of their target genes in the context of DLBCL.
Contribution of lncRNAs in the regulation of B cell functions and related disorders
Impacts of lncRNAs on B cell functions have been investigated in malignancies, particularly DLBCL. SNHG14 has been shown to be elevated in DLBCL. Its silencing has decreased proliferation, migration and epithelial to mesenchymal transition (EMT) features in these cells. From a mechanistical point of view, SNHG14 could sponge miR-5590-3p and subsequently enhance expression of ZEB1. Moreover, ZEB1 could activate transcriptional of SNHG14 and PD-L1 to increase immune evasion in these cells. Cumulatively, SNHG14/miR-5590-3p/ZEB1 axis can promote progression of DLBCL and immune evasion in a positive feedback loop. This axis can regulate PD-1/PD-L1 checkpoint .
Another study has shown up-regulation of MALAT1, PD-L1 and CD8 in DLBCL tissues, parallel with down-regulation of miR-195. Mechanistically, MALAT1 has been shown to sponge miR-195 to influence PD-L1 levels. MALAT1 silencing has enhanced miR-195 levels and reduced PD-L1 levels. Moreover, MALAT1 silencing has suppressed proliferation, migratory potential and immune escape aptitude of DLBCL cells while increasing their apoptosis. MALAT1 silencing has also inhibited EMT features through modulation of Ras/ERK signaling .
NEAT1 is another lncRNA whose expression has been enhanced in DLBCL tissues and cell lines parallel with up-regulation of GLI1 and down-regulation of miR-34b-5p. NEAT1 silencing or miR-34b-5p up-regulation could inhibit proliferation and enhance apoptosis of these cells. In fact, NEAT1 acts as a competing endogenous RNA (ceRNA) to regulate expression the miR-34b-5p/GLI1 axis. Besides, MYC has been shown to modulate NEAT1 expression through directly binding to promoter of NEAT1 . Figure 2 shows the interactions between lncRNAs and miRNAs in the context of DLBCL.
CRNDE has been shown to be up-regulated in the bone marrow of B-cell precursor acute lymphoblastic leukemia patients and related cell lines. CRNDE silencing has decreased cell proliferation and enhanced cell apoptosis in these cells. Functionally, CRNDE could bind with to miR-345-5p and down-regulate its expression, thus affecting expression of CREB. Notably, in vivo studies have shown that CRNDE silencing increases survival of mice models of this type of leukemia .
In addition to this type of studies, expression patterns of lncRNAs have been compared between cancer cells and non-cancerous controls using high throughput methods. For instance, Cuadros et al. have reported differential expression of 48 lncRNAs between pediatric B-ALL and normal bone marrow specimens. They have recognized AL133346.1/CCN2 as the most relevant lncRNA/mRNA pair in this type of malignancy. Expression of AL133346.1/CCN2 pair has been enhanced in B-ALL specimens .
Expression of PTTG3P has been shown to be up-regulated in samples obtained from patients with IgA nephropathy compared with normal samples. Notably, expression of PTTG3P in urine samples has been correlated with expression of PTTG3P in intra-renal samples of IgA nephropathy cases. Up-regulation of PTTG3P has stimulated B cell growth and increased expressions of cyclin D1 and ki-67. In addition, its up-regulation of PTTG3P has led to induction of IL-1β and IL-8 release. PTTG3P up-regulation could suppress expression of miR-383 in B cells. Taken together, PTTG3P could increase B cell growth and IL-1β and IL-8 release through influencing expression of miR-383. Through this effect, PTTG3P contributes in the pathogenesis of IgA nephropathy .
Expression of lncRNA RP11-530C5.1 has been shown to be higher in relapsing MS patients, compared to remitting MS patients and healthy subjects, whereas expression of AL928742.12 has been decreased. Notably, expression levels of RP11-530C5.1 and AL928742.12 have been correlated with PAWR and IGHA2 levels, respectively .
Table 2 shows the impact of lncRNAs in B cell functions.
Contribution of circRNAs in the regulation of B cell-related disorders
The impact of circRNAs on B cell functions has been mostly assessed in the context of DLBCL. For instance, circ_OTUD7A expression has been found to be increased in DLBCL. Its silencing has suppressed proliferation and metastasis of DLBCL, induce cell cycle arrest and enhance their apoptosis. Mechanistically, circ_OTUD7A acts as a sponge for miR-431-5p and miR-431-5p to further regulate expression of FOXP1 .
Another study has shown that up-regulation of circCFL1 in DLBCL cells leads to reduction of miR-107 levels and subsequent up-regulation of HMGB1 in these cells. Functional studies have revealed that circCFL1 could directly bind with miR-107 and release HMGB1 from inhibitory effects of this miRNA. Up-regulation of circCFL1 increases migration and proliferation of DLBCL cells .
Circ-APC is another circRNA which is produced from APC and suppress proliferation of DLBCL cells through decreasing activity of Wnt/β-catenin pathway. This effect is exerted through its interaction with TET1 and miR-888 .
The impact of circRNAs has also been investigated on progression of leukemia. For instance, circ_0132266 has been shown to be down-regulated in chronic lymphocytic leukemia. This down-regulation has lead to enhancement of viability of these cells via influencing activity of miR-337-3p/PML axis . Table 3 shows the effects of circRNAs in the pathogenesis of B cell-related disorders.
Accumulating evidence suggest the role of non-coding RNAs in the development of normal B cells as well as lymphomagenesis. Since they are have a highly cell type specific signature, these transcripts have been suggested as potential biomarkers for diverse clinical situations .
LncRNAs particularly those related with p53 or MYC pathways have also applications as therapeutic targets . These transcripts could act as sponges for miRNAs, thus influencing expressions of their target genes. SNHG14/miR-5590-3p, MALAT1/miR-195, CRNDE/miR-345-5p, NEAT1/miR-34b-5p, SMAD5-AS1/miR-135b-5p, PTTG3P/miR-383, SNHG8/ miR-335-5p, PCAT1/miR-508-3p, SBF2-AS1/miR-494-3p, SNHG14/ miR-152-3p and LINC00908/miR-671-5p are among lncRNA/miRNA axes which are involved in the regulation of B cells. Ras/ERK, Wnt/β-catenin pathway, NF-κB/ERK, PI3K/mTOR, BCR, TNF, IL-11/STAT3, IFN-I, Notch2, MAPK/ERK, PI3K/AKT and glucocorticoid response pathways are among pathways that are regulated by lncRNAs in this context.
CircRNAs that regulate function of B cells are mostly associated with Wnt/β-catenin signaling pathway. They can also serve as sponges for miRNA. For instance, circ_OTUD7A/miR-431-5p, circCFL1/miR-107, circ-APC/miR-888, circ_0132266/miR-337-3p, circ_0005774/miR-192-5p, circ_0009910/miR-5195-3p and circ-CBFB/miR-607 are among important circRNA/miRNA axes in regulation of proliferation of B cells.
Finally, miRNAs that are involved in the pathogenesis of B cell-related disorders can modulate NF-κB, TGF-β, BCR, TAK1/IKKα-IKKβ/IκBα and MAPK/p65 signaling pathways.
Cumulatively, different classes of non-coding RNAs interact with each other to modulate function of B cells. Notably, non-coding RNAs have also interactions with immune check point proteins in the context of B cell disorders.
The observed interaction between non-coding RNAs and immune check point proteins suggests the importance of these transcripts as targets for immunotherapeutic approaches. Moreover, several lncRNAs, circRNAs and miRNAs have been found to affect proliferation of B cells, thus being involved in the pathogenesis of B cell-related disorders, particularly malignant disorders. The observed correlations between expression levels of these transcripts and clinic-pathological parameters further emphasize their role in the carcinogenic processes.
Understanding the impact of non-coding RNAs in B cell-related malignancies would provide new avenues for targeted therapies.
Availability of data and materials
The analyzed data sets generated during the study are available from the corresponding author on reasonable request.
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This study was financially supported by Grant from Medical School of Shahid Beheshti University of Medical Sciences.
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Ghafouri-Fard, S., Khoshbakht, T., Hussen, B.M. et al. The emerging role non-coding RNAs in B cell-related disorders. Cancer Cell Int 22, 91 (2022). https://doi.org/10.1186/s12935-022-02521-1