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Pax5-dependent contraction of the Igh locus in pro-B cells.The Igh locus, consisting of variable (V), diversity (D), joining (J) and constant (C) gene segments, is in an extended configuration in Pax5-/- pro-B cells, which allows V(D)J recombination to take place only in the proximal domain. In wild-type pro-B cells, all VH genes participate in VH-DJH rearrangements owing to contraction of the Igh locus by looping.
Source publication
The transcription factor Pax5 is essential for commitment of lymphoid progenitors to the B lymphocyte lineage. Pax5 fulfils a dual role by repressing B lineage 'inappropriate' genes and simultaneously activating B lineage-specific genes. This transcriptional reprogramming restricts the broad signaling capacity of uncommitted progenitors to the B ce...
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... 17 . The V H J558 gene family contains half of the 195 V H genes and thus constitutes the largest of the 16 V H gene families, which are spread over a 2.5-megabase region of the Igh locus 51 . The V H J558 genes are located at the distal end of the Igh locus relative to the proximal domain consisting of the D H , J H and C H gene segments 51 (Fig. 4). Analysis of the more proximal V H gene families subsequently showed that the V H -DJ H recombination efficiency in Pax5 -/-pro-B cells progressively increases with decreasing distance of the V H gene from the DJC H domain 52 . Paradoxically, the distal V H J558 genes are just as accessible as the proximal V H 7183 genes in Pax5 ...
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... level beyond that of chromatin accessibility 52 . Indeed, Pax5 is involved in regulating the spa- tial organization of the Igh locus within the nucleus. Pax5 -/-pro-B cells contain the Igh locus in an extended state, which physically separates the distal V H genes from the proximal DJC H domain, thus preventing distal V H -DJ H rearrangements 36 (Fig. 4) (Fig. 4). The recombination of distal V H genes is also specifically impaired in the absence of the histone methyltransferase Ezh2 (ref. 56) . It is therefore conceivable that Pax5 functions as a sequence-specific targeting factor to recruit the Ezh2-containing Polycomb repressive complex 2 (PRC2) to selected regions of the Igh locus, ...
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... that of chromatin accessibility 52 . Indeed, Pax5 is involved in regulating the spa- tial organization of the Igh locus within the nucleus. Pax5 -/-pro-B cells contain the Igh locus in an extended state, which physically separates the distal V H genes from the proximal DJC H domain, thus preventing distal V H -DJ H rearrangements 36 (Fig. 4) (Fig. 4). The recombination of distal V H genes is also specifically impaired in the absence of the histone methyltransferase Ezh2 (ref. 56) . It is therefore conceivable that Pax5 functions as a sequence-specific targeting factor to recruit the Ezh2-containing Polycomb repressive complex 2 (PRC2) to selected regions of the Igh locus, resulting ...
Citations
... For example, within B cells we observe high activity for the TF PAX5. PAX5 is known to play a crucial role in B cell development by guiding the commitment of lymphoid progenitors to the B lymphocyte lineage while simultaneously repressing inappropriate genes and activating B lineage-specific genes [54]. ...
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network Inference (PMF-GRN). Using single-cell expression data, PMF-GRN infers latent factors capturing transcription factor activity and regulatory relationships. Using variational inference allows hyperparameter search for principled model selection and direct comparison to other generative models. We extensively test and benchmark our method using real single-cell datasets and synthetic data. We show that PMF-GRN infers GRNs more accurately than current state-of-the-art single-cell GRN inference methods, offering well-calibrated uncertainty estimates.
... PAX5 is essential for normal B-cell development and maintenance of B-cell lineage identity. Its expression starts at the pre-pro-B cell stage, continues through pre-B and mature B cells, and stops with final B-cell differentiation (7). PAX5 is one of the most frequently mutated genes in sporadic B-ALL cases. ...
B-cell acute lymphoblastic leukemia (B-ALL) is one of the most common childhood cancers worldwide. Although most cases are sporadic, some familial forms, inherited as autosomal dominant traits with incomplete penetrance, have been described over the last few years. Germline pathogenic variants in transcription factors such as PAX5, IKZF1, and ETV6 have been identified as causal in familial forms. The proband was a 7-year-old Mexican girl diagnosed with high-risk B-ALL at five years and 11 months of age. Family history showed that the proband’s mother had high-risk B-ALL at 16 months of age. She received chemotherapy and was discharged at nine years of age without any evidence of recurrence of leukemia. The proband’s father was outside the family nucleus, but no history of leukemia or cancer was present up to the last contact with the mother. We performed exome sequencing on the proband and the proband’s mother and identified the PAX5 variant NM_016734.3:c.963del: p.(Ala322LeufsTer11), located in the transactivation domain of the PAX5 protein. The variant was classified as probably pathogenic according to the ACMG criteria. To the best of our knowledge, this is the first Mexican family with an inherited increased risk of childhood B-ALL caused by a novel germline pathogenic variant of PAX5. Identifying individuals with a hereditary predisposition to cancer is essential for modern oncological practice. Individuals at high risk of leukemia would benefit from hematopoietic stem cell transplantation, but family members carrying the pathogenic variant should be excluded as hematopoietic stem cell donors.
... The top two predicted transcription factors were PAX5 and NRF2 (Fig. 6A). PAX5 encodes the B cell lineage-specific activator protein expressed exclusively in B lymphocyte lineage and is unlikely to be mitigating ferroptosis in breast epithelial cells (29). NRF2 protects against oxidative and electrophilic stress (30). ...
The TP53 tumor suppressor gene is mutated early in most of the patients with triple-negative breast cancer (TNBC). The most frequent TP53 alterations are missense mutations that contribute to tumor aggressiveness. Here, we used an autochthonous somatic TNBC mouse model, in which mutant p53 can be toggled on and off genetically while leaving the tumor microenvironment intact and wild-type for p53 to identify physiological dependencies on mutant p53. In TNBCs that develop in this model, deletion of two different hotspot p53R172H and p53R245W mutants triggers ferroptosis in vivo, a cell death mechanism involving iron-dependent lipid peroxidation. Mutant p53 protects cells from ferroptosis inducers, and ferroptosis inhibitors reverse the effects of mutant p53 loss in vivo. Single-cell transcriptomic data revealed that mutant p53 protects cells from undergoing ferroptosis through NRF2-dependent regulation of Mgst3 and Prdx6 , which encode two glutathione-dependent peroxidases that detoxify lipid peroxides. Thus, mutant p53 protects TNBCs from ferroptotic death.
... Notably, the transcription factor Pax5 plays crucial roles during the development and maturation of B cells (5,6). Homozygous Pax5 mutation in mice inhibits B cell development at early pro-B cell stage and impairs the expression of maturation marker genes, such as CD19, CD25, and BP-1 (7). ...
In mammals, the transcription factor Pax5 is a key regulator of B cell development and maturation and specifically expressed in naive/mature B cells but repressed upon B cell activation. Despite the long-standing proposal that Pax5 repression is essential for proper B cell activation, the underlying mechanisms remain largely elusive. In this study, we used a teleost model to elucidate the mechanisms governing Pax5 repression during B cell activation. Treatment with lipopolysaccharide (LPS) and chitosan oligosaccharide (COS) significantly enhanced the antibody secreting ability and phagocytic capacity of IgM⁺ B cells in large yellow croaker (Larimichthys crocea), coinciding with upregulated expression of activation-related genes, such as Bcl6, Blimp1, and sIgM, and downregulated expression of Pax5. Intriguingly, two CpG islands were identified within the promoter region of Pax5. Both CpG islands exhibited hypomethylation in naive/mature B cells, while CpG island1 was specifically transited into hypermethylation upon B cell activation. Furthermore, treatment with DNA methylation inhibitor 5-aza-2’-deoxycytidine (AZA) prevented the hypermethylation of CpG island1, and concomitantly impaired the downregulation of Pax5 and activation of B cells. Finally, through in vitro methylation experiments, we demonstrated that DNA methylation exerts an inhibitory effect on promoter activities of Pax5. Taken together, our findings unveil a novel mechanism underlying Pax5 repression during B cell activation, thus promoting the understanding of B cell activation process.
... SupirFactor distinguishes activation between myeloid (monocytes and DCs) and lymphocytic (B, NK, and T cells) lineages (Fig. 5E). The framework also recovers known celltype-specific regulators along the myeloid lineage, monocytes and DCs, (KLF1) [51], B cells (PAX5, SMAD5) [52,53], NK cells (ARNT) [54], CD4 T cells (IRF1, RUNX3) [55,56], and CD8 T cells (NR4A1) [57]. We show that SupirFactor infers cell-type-specific differential mTF activation and TF activation among distinct cell types that correspond with known biological processes and protein activity for multiple key cell types. ...
Background
Modeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of genome-wide transcription factor activity (TFA) making it difficult to separate covariance and regulatory interactions. Inference of regulatory interactions and TFA requires aggregation of complementary evidence. Estimating TFA explicitly is problematic as it disconnects GRN inference and TFA estimation and is unable to account for, for example, contextual transcription factor-transcription factor interactions, and other higher order features. Deep-learning offers a potential solution, as it can model complex interactions and higher-order latent features, although does not provide interpretable models and latent features.
Results
We propose a novel autoencoder-based framework, StrUcture Primed Inference of Regulation using latent Factor ACTivity (SupirFactor) for modeling, and a metric, explained relative variance (ERV), for interpretation of GRNs. We evaluate SupirFactor with ERV in a wide set of contexts. Compared to current state-of-the-art GRN inference methods, SupirFactor performs favorably. We evaluate latent feature activity as an estimate of TFA and biological function in S. cerevisiae as well as in peripheral blood mononuclear cells (PBMC).
Conclusion
Here we present a framework for structure-primed inference and interpretation of GRNs, SupirFactor, demonstrating interpretability using ERV in multiple biological and experimental settings. SupirFactor enables TFA estimation and pathway analysis using latent factor activity, demonstrated here on two large-scale single-cell datasets, modeling S. cerevisiae and PBMC. We find that the SupirFactor model facilitates biological analysis acquiring novel functional and regulatory insight.
... We also defined three subtypes of B cells in our dataset, including naïve B cells, memory B cells and plasma cells, and observed a clear developmental trajectory from naïve through memory B cells to plasma cells through pseudotime analysis (Supplementary Fig. 4d). Binding motif for PAX5, a deciding factor for B cell specification, was enriched in naïve and memory B cells 53,54 . Motifs for POU2F2 and IRF4 were highly enriched in plasma cells ( Supplementary Fig. 4b) 50,55 . ...
Seminoma is the most common malignant solid tumor in 14 to 44 year-old men. However, its molecular features and tumor microenvironment (TME) is largely unexplored. Here, we perform a series of studies via genomics profiling (single cell multi-omics and spatial transcriptomics) and functional examination using seminoma samples and a seminoma cell line. We identify key gene expression programs share between seminoma and primordial germ cells, and further characterize the functions of TFAP2C in promoting tumor invasion and migration. We also identify 15 immune cell subtypes in TME, and find that subtypes with exhaustion features were located closer to the tumor region through combined spatial transcriptome analysis. Furthermore, we identify key pathways and genes that may facilitate seminoma disseminating beyond the seminiferous tubules. These findings advance our knowledge of seminoma tumorigenesis and produce a multi-omics atlas of in situ human seminoma microenvironment, which could help discover potential therapy targets for seminoma.
... These oncoproteins often harbor domains of transcription factors (TFs) (e.g., ETV6::RUNX1, TCF3::PBX1, PAX5::ETV6, and PAX5::ELN) (Coyaud et al., 2010;Familiades et al., 2009;Mullighan et al., 2007). For instance, the TF PAX5, known to play an important role in the transcriptional regulatory networks (TNRs) of early B cells, the definitive B cell commitment, and the plasticity of committed B cells (Cobaleda et al., 2007a(Cobaleda et al., , 2007b, was also shown to promote leukemogenesis once translocated in mouse models (Jamrog et al., 2018;Jurado et al., 2022;Smeenk et al., 2017). Thus, it is widely thought that recurrent chromosomal translocations can act as a first oncogenic event in the early steps of B-ALL initiation, though the precise mechanisms at play are yet ill-known. ...
B cell acute lymphoblastic leukemia (B-ALL) is a multistep disease characterized by the hierarchical acquisition of genetic alterations. However, the question of how a primary oncogene reprograms stem cell–like properties in committed B cells and leads to a preneoplastic population remains unclear. Here, we used the PAX5::ELN oncogenic model to demonstrate a causal link between the differentiation blockade, the self-renewal, and the emergence of preleukemic stem cells (pre-LSCs). We show that PAX5::ELN disrupts the differentiation of preleukemic cells by enforcing the IL7r/JAK-STAT pathway. This disruption is associated with the induction of rare and quiescent pre-LSCs that sustain the leukemia-initiating activity, as assessed using the H2B-GFP model. Integration of transcriptomic and chromatin accessibility data reveals that those quiescent pre-LSCs lose B cell identity and reactivate an immature molecular program, reminiscent of human B-ALL chemo-resistant cells. Finally, our transcriptional regulatory network reveals the transcription factor EGR1 as a strong candidate to control quiescence/resistance of PAX5::ELN pre-LSCs as well as of blasts from human B-ALL.
... Our results suggest that TF activity estimation could elucidate cell type specific regulatory mechanisms that would be missed by looking only at the expression level of TFs. For example, PAX5 is a well-known central regulator in B cell development, controlling their identity and function throughout the process of B lymphopoiesis ( 80 ) and EOMES plays a crucial role in NK cell maturation and functionality and its expression is observed across all stages of NK cell development ( 81 ,82 ). However, the expression of both PAX5 and EOMES is only captured in around 6.7% of B and 10.3% of NK cells in the analyzed PBMC dataset, respectively. ...
Gene regulation plays a critical role in the cellular processes that underlie human health and disease. The regulatory relationship between transcription factors (TFs), key regulators of gene expression, and their target genes, the so called TF regulons, can be coupled with computational algorithms to estimate the activity of TFs. However, to interpret these findings accurately, regulons of high reliability and coverage are needed. In this study, we present and evaluate a collection of regulons created using the CollecTRI meta-resource containing signed TF-gene interactions for 1186 TFs. In this context, we introduce a workflow to integrate information from multiple resources and assign the sign of regulation to TF-gene interactions that could be applied to other comprehensive knowledge bases. We find that the signed CollecTRI-derived regulons outperform other public collections of regulatory interactions in accurately inferring changes in TF activities in perturbation experiments. Furthermore, we showcase the value of the regulons by examining TF activity profiles in three different cancer types and exploring TF activities at the level of single-cells. Overall, the CollecTRI-derived TF regulons enable the accurate and comprehensive estimation of TF activities and thereby help to interpret transcriptomics data.
... In the midnightblue module, the large proportion of B cell-related genes (at least 44) among the differentially expressed protein-coding genes (n = 84) was striking. These B cell signature genes were involved in various B cell functions, such as antigen processing and presentation [HLA-DOA, HLA-DOB] [23], B cell receptor signaling [BANK1 [24], BLK [25], BLNK [26], CD19 [27], CD22 [28], CD72 [29], CD79A, CD79B [30], MS4A1 [31], NIBAN3 (also known as BCNP1) [32]], Fc receptors [FCRLA, FCRL1, FCRL2], transcription factor [E2F5 [33], EBF1 [34], LINC00926 [35], PAX5 [36], POU2AF1 [37], SPIB [38]], and other B cell functions including development, differentiation, migration, and others [COBLL1, CXCR5, FAM30A, TNFRSF13B]. Additionally, there were numerous genes of unknown function [e.g., AFF3, CORO2B, GNG7, OSBPL10, P2RX5, and SYNPO] that are known to be expressed in B cells based on expression data from The Human Protein Atlas [19] or from the validated B cell signature reported by Henning et. ...
Background
While many women with rheumatoid arthritis (RA) improve during pregnancy and others worsen, there are no biomarkers to predict this improvement or worsening. In our unique RA pregnancy cohort that includes a pre-pregnancy baseline, we have examined pre-pregnancy gene co-expression networks to identify differences between women with RA who subsequently improve during pregnancy and those who worsen.
Methods
Blood samples were collected before pregnancy (T0) from 19 women with RA and 13 healthy women enrolled in our prospective pregnancy cohort. RA improvement/worsening between T0 and 3rd trimester was assessed by changes in the Clinical Disease Activity Index (CDAI). Pre-pregnancy expression profiles were examined by RNA sequencing and differential gene expression analysis. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules correlated with the improvement/worsening of RA during pregnancy and to assess their functional relevance.
Results
Of the 19 women with RA, 14 improved during pregnancy (RAimproved) while 5 worsened (RAworsened). At the T0 baseline, however, the mean CDAI was similar between the two groups. WGCNA identified one co-expression module related to B cell function that was significantly correlated with the worsening of RA during pregnancy and was significantly enriched in genes differentially expressed between the RAimproved and RAworsened groups. A neutrophil-related expression signature was also identified in the RAimproved group at the T0 baseline.
Conclusion
The pre-pregnancy gene expression signatures identified represent potential biomarkers to predict the subsequent improvement/worsening of RA during pregnancy, which has important implications for the personalized treatment of RA during pregnancy.
... Among the responders, we observed the activation of the PAX5 network in the immune regions adjacent (spatial gene expression clusters in direct contact) (Additional file 4: Fig. S3) to tumor clusters (Fig. 3A, Additional file 5: Fig. S4), while FOS and JUN modules are highly active in CAFs surrounding the tumor spots ( Fig. 3B, C, Additional file 5: Fig. S4). PAX5 is a transcription factor that is central to B cell differentiation [28,29]. The PAX5 activity, which was investigated in immune-enriched or CAF-enriched regions only, co-localizes with spots showing high expression of the genes CD19, CD22, CD79A, and CIITA (B cell markers) (Fig. 3D), relative to spots corresponding to HCC or CAF clusters confirming that this is an essential factor for B cell lineage activation and maturation. ...
Background
Novel immunotherapy combination therapies have improved outcomes for patients with hepatocellular carcinoma (HCC), but responses are limited to a subset of patients. Little is known about the inter- and intra-tumor heterogeneity in cellular signaling networks within the HCC tumor microenvironment (TME) that underlie responses to modern systemic therapy.
Methods
We applied spatial transcriptomics (ST) profiling to characterize the tumor microenvironment in HCC resection specimens from a prospective clinical trial of neoadjuvant cabozantinib, a multi-tyrosine kinase inhibitor that primarily blocks VEGF, and nivolumab, a PD-1 inhibitor in which 5 out of 15 patients were found to have a pathologic response at the time of resection.
Results
ST profiling demonstrated that the TME of responding tumors was enriched for immune cells and cancer-associated fibroblasts (CAF) with pro-inflammatory signaling relative to the non-responders. The enriched cancer-immune interactions in responding tumors are characterized by activation of the PAX5 module, a known regulator of B cell maturation, which colocalized with spots with increased B cell marker expression suggesting strong activity of these cells. HCC-CAF interactions were also enriched in the responding tumors and were associated with extracellular matrix (ECM) remodeling as there was high activation of FOS and JUN in CAFs adjacent to the tumor. The ECM remodeling is consistent with proliferative fibrosis in association with immune-mediated tumor regression. Among the patients with major pathologic responses, a single patient experienced early HCC recurrence. ST analysis of this clinical outlier demonstrated marked tumor heterogeneity, with a distinctive immune-poor tumor region that resembles the non-responding TME across patients and was characterized by HCC-CAF interactions and expression of cancer stem cell markers, potentially mediating early tumor immune escape and recurrence in this patient.
Conclusions
These data show that responses to modern systemic therapy in HCC are associated with distinctive molecular and cellular landscapes and provide new targets to enhance and prolong responses to systemic therapy in HCC.
