SOX11 transcription factor functional analysis in aggressive MCL

[spa] El linfoma de células del manto (LCM) es un subtipo agresivo de linfoma non Hodgkin asociado a un mal pronóstico y recaídas frecuentes. Recientemente, el factor de transcripción neuronal SOX11 se ha identificado como un marcador muy específico de LCM. SOX11 se encuentra sobreexpresado constantemente en todos los LCM agresivos y en niveles más bajos en un subgrupo de Burkitt linfoma (BL) y leucemia linfoblástica aguda (LLA) aunque no en otros neoplasmas linfoides. SOX11 se encontró exclusivamente sobreexpresado en LMC convencionales y totalmente ausente en células linfoides normales o en pacientes LMC con un curso clínico indolente y una supervivencia prolongada. Aunque la función de SOX11 y sus genes potenciales dianas aún se desconocen, su elevada expresión específica en LCM sugiere que puede ser un elemento importante en la progresión y desarrollo de este tumor. Se han obtenidos dos publicaciones de los estudios que componen esta tesis. En el primer artículo hemos estudiado los mecanismos moleculares responsables de la expresión aberrante de SOX11 en LCM agresivo. El artículo I proporciona una caracterización exhaustiva de los mecanismos epigenéticos que conducen a la desregulación de SOX11 en estas neoplasias linfoides. En general se observó una significativa correlación inversa entre la metilación del promotor de SOX11 y la expresión de dicho gen. Sin embargo, en muchas muestras (células madre embrionarias, ESC, o adultas, células B normales y algunos LCM indolentes, leucemia linfática crónica y linfoma folicular) la expresión de SOX11 se vió reprimida a pesar de su estado no metilado. Estos hallazgos nos sugieren que la expresión de SOX11 no depende exclusivamente del estado de metilación del ADN del gen y nos llevó a estudiar mecanismos epigenéticos alternativos. Hemos observado que la expresión de SOX11 se asocia con la presencia de marcas de activación de las histonas (H3K9/14Ac y H3K4me3) en las células madre embrionarias y algunas neoplasias de células B agresivas. Por el contrario, en las muestras que no expresan SOX11, incluidas las células madre adultas, las células hematopoyéticas normales y diversas neoplasias linfoides, se observó que el promotor de SOX11 mostraba un enriquecimiento en las marcas de silenciamiento H3K9me2 y H3K27me3. El silenciamiento de SOX11 en líneas celulares fue revertido por el inhibidor de la histona deacetilasa (SAHA) pero no por el inhibidor de la ADN metiltransferasa (AZA). Estos datos indican que, como SOX11 no se expresa en las células linfoides normales, no metiladas, lo más probable es que la hipermetilación del ADN en algunos tumores sin expresión de SOX11 sea funcionalmente inerte, y podría estar asociada con la reducción de la plasticidad epigenética en células tumorales. También observamos que la expresión de novo de SOX11 se asocia con las neoplasias linfoides agresivas como el LCM, algunos subtipos de B-LLA y algunos casos de BL siendo este efecto mediado por un “switch” entre inactivación y activación de las modificaciones de las histonas. Además, como SOX11 se expresa fuertemente en las ESC, los datos sugieren que la expresión de SOX11 podría estar asociada con la adquisición de características de la cromatina similares a la de las células madre. En el artículo II nos hemos centrado en identificar las posibles funciones biológicas de SOX11 en LCM. Combinando análisis de microarray de immunopecipitación de cromatina y perfil de expresión diferencial después de silenciar SOX11, hemos identificado genes dianas y programas transcriptionales regulados por SOX11, incluyendo el bloqueo de la diferenciación de la célula B madura, la modulación de ciclo celular, apoptosis y desarrollo de célula madre. PAX5 destacó como uno de los genes diana directos de SOX11 más significativo. El silenciamiento de SOX11 downregula PAX5, induce la expresión de BLIMP1 y promueve el cambio de fenotipo de célula B madura a la diferenciación inicial plasmacítica, tanto en células tumorales primarias de LCM como en un modelo en vitro. Nuestros resultados sugieren que SOX11 contribuye al desarrollo tumoral mediante la modulación del programa de diferenciación terminal de célula B en LCM. Además, hemos demostrado la habilidad tumorigénica de SOX11 en vivo mediante un modelo de xenotrasplante de LCM en ratones CB17-SCID. La reducción significativa del crecimiento tumoral de las células con expresión de SOX11 silenciada comparada con el crecimiento de células de LCM con elevados niveles de expresión de SOX11 de los xenotrasplantes, demuestra la implicación de la expresión de SOX11 en el comportamiento agresivo de este linfoma. En conclusión, nuestros resultados demuestran que SOX11 puede actuar como oncogén en LCM.[eng] Mantle cell lymphoma (MCL) is an aggressive subtype of non-Hodgkin lymphomas associated with poor prognosis and frequent relapses. Recently, the neuronal transcription factor SOX11 has been identified as a very specific biomarker for MCL. SOX11 is constantly overexpressed in virtually all aggressive MCLs, and at lower levels in a subgroup of Burkitt lymphoma and acute lymphoblastic leukemia but not in other lymphoid neoplasms. SOX11 was found exclusively overexpressed in conventional MCL and totally absent in normal lymphoid cells or in MCL patients with indolent clinical course and prolonged survival. Although SOX11 function and potential target genes in lymphoid cells are poorly known, the highly specific expression in aggressive MCL suggests that it may be an important element in the development and progression of this tumor. Two publications resulted from our studies and compose this thesis. In paper I, we have studied the molecular mechanisms leading to the aberrant expression of SOX11 in aggressive MCL. MCL is one of the lymphoid neoplasms with highest number of genetic aberrations but none involving the SOX11 genomic region at chromosome 2p25. As no chromosomal changes affecting SOX11 locus were identified in MCL, we hypothesized that epigenetic events could lead to SOX11 aberrant overexpression. We performed a comprehensive SOX11 gene expression and epigenetic studies. We observed that SOX11 expression was associated with unmehtylated DNA and presence of activating histone marks (H3K9/14Ac and H3K4me3) in embryonic stem cells and some aggressive B-cell neoplasms, including MCL. Conversely, the loss of SOX11 expression in adult stem cells, normal hematopoietic cells and other lymphoid neoplasms was associated with the presence of silencing histone marks H3K9me2 and H3K27me3 with or without simultaneous DNA methylation. We concluded that the pathogenic role of SOX11 is associated with its de novo expression in some aggressive lymphoid malignancies, which is mediated by a shift from inactivating to activating histone modifications. In paper II, we have focused on uncovering putative biological functions of SOX11 in aggressive MCL. Using chromatin immunoprecipitation microarray analysis combined with gene expression profiling upon SOX11 knockdown, we identified target genes and transcriptional programs regulated by SOX11 including the block of mature B-cell differentiation, modulation of cell cycle, apoptosis, and stem cell development. PAX5 stood out as one of the major SOX11 direct target genes. SOX11 silencing downregulates PAX5, induces BLIMP1 expression, and promotes the shift from a mature B-cell into the initial plasmacytic differentiation phenotype in both MCL primary tumor cells and an in vitro model. Our results suggested that SOX11 contributes to tumor development by altering the terminal B-cell differentiation program of MCL cells. Moreover, we have demonstrated the tumorigenic ability of SOX11 in vivo, using a xenotransplant model of MCL in CB17-SCID mice. The significant reduction on tumor growth of the SOX11-silenced cells compared to the growth of control MCL cells in the xenograft experiments highlighted the implication of SOX11 expression in the aggressive behavior of this lymphoma. Overall our results demonstrated that SOX11 can act as oncogene in MCL

Epigenetic Activation of SOX11 in Lymphoid Neoplasms by Histone Modifications

Recent studies have shown aberrant expression of SOX11 in various types of aggressive B-cell neoplasms. To elucidate the molecular mechanisms leading to such deregulation, we performed a comprehensive SOX11 gene expression and epigenetic study in stem cells, normal hematopoietic cells and different lymphoid neoplasms. We observed that SOX11 expression is associated with unmethylated DNA and presence of activating histone marks (H3K9/14Ac and H3K4me3) in embryonic stem cells and some aggressive B-cell neoplasms. In contrast, adult stem cells, normal hematopoietic cells and other lymphoid neoplasms do not express SOX11. Such repression was associated with silencing histone marks H3K9me2 and H3K27me3. The SOX11 promoter of non-malignant cells was consistently unmethylated whereas lymphoid neoplasms with silenced SOX11 tended to acquire DNA hypermethylation. SOX11 silencing in cell lines was reversed by the histone deacetylase inhibitor SAHA but not by the DNA methyltransferase inhibitor AZA. These data indicate that, although DNA hypermethylation of SOX11 is frequent in lymphoid neoplasms, it seems to be functionally inert, as SOX11 is already silenced in the hematopoietic system. In contrast, the pathogenic role of SOX11 is associated with its de novo expression in some aggressive lymphoid malignancies, which is mediated by a shift from inactivating to activating histone modifications

SOX11 transcription factor functional analysis in aggressive MCL

Mantle cell lymphoma (MCL) is an aggressive subtype of non-Hodgkin lymphomas associated with poor prognosis and frequent relapses. Recently, the neuronal transcription factor SOX11 has been identified as a very specific biomarker for MCL. SOX11 is constantly overexpressed in virtually all aggressive MCLs, and at lower levels in a subgroup of Burkitt lymphoma and acute lymphoblastic leukemia but not in other lymphoid neoplasms. SOX11 was found exclusively overexpressed in conventional MCL and totally absent in normal lymphoid cells or in MCL patients with indolent clinical course and prolonged survival. Although SOX11 function and potential target genes in lymphoid cells are poorly known, the highly specific expression in aggressive MCL suggests that it may be an important element in the development and progression of this tumor. Two publications resulted from our studies and compose this thesis. In paper I, we have studied the molecular mechanisms leading to the aberrant expression of SOX11 in aggressive MCL. MCL is one of the lymphoid neoplasms with highest number of genetic aberrations but none involving the SOX11 genomic region at chromosome 2p25. As no chromosomal changes affecting SOX11 locus were identified in MCL, we hypothesized that epigenetic events could lead to SOX11 aberrant overexpression. We performed a comprehensive SOX11 gene expression and epigenetic studies. We observed that SOX11 expression was associated with unmehtylated DNA and presence of activating histone marks (H3K9/14Ac and H3K4me3) in embryonic stem cells and some aggressive B-cell neoplasms, including MCL. Conversely, the loss of SOX11 expression in adult stem cells, normal hematopoietic cells and other lymphoid neoplasms was associated with the presence of silencing histone marks H3K9me2 and H3K27me3 with or without simultaneous DNA methylation. We concluded that the pathogenic role of SOX11 is associated with its de novo expression in some aggressive lymphoid malignancies, which is mediated by a shift from inactivating to activating histone modifications. In paper II, we have focused on uncovering putative biological functions of SOX11 in aggressive MCL. Using chromatin immunoprecipitation microarray analysis combined with gene expression profiling upon SOX11 knockdown, we identified target genes and transcriptional programs regulated by SOX11 including the block of mature B-cell differentiation, modulation of cell cycle, apoptosis, and stem cell development. PAX5 stood out as one of the major SOX11 direct target genes. SOX11 silencing downregulates PAX5, induces BLIMP1 expression, and promotes the shift from a mature B-cell into the initial plasmacytic differentiation phenotype in both MCL primary tumor cells and an in vitro model. Our results suggested that SOX11 contributes to tumor development by altering the terminal B-cell differentiation program of MCL cells. Moreover, we have demonstrated the tumorigenic ability of SOX11 in vivo, using a xenotransplant model of MCL in CB17-SCID mice. The significant reduction on tumor growth of the SOX11-silenced cells compared to the growth of control MCL cells in the xenograft experiments highlighted the implication of SOX11 expression in the aggressive behavior of this lymphoma. Overall our results demonstrated that SOX11 can act as oncogene in MCL.El linfoma de células del manto (LCM) es un subtipo agresivo de linfoma non Hodgkin asociado a un mal pronóstico y recaídas frecuentes. Recientemente, el factor de transcripción neuronal SOX11 se ha identificado como un marcador muy específico de LCM. SOX11 se encuentra sobreexpresado constantemente en todos los LCM agresivos y en niveles más bajos en un subgrupo de Burkitt linfoma (BL) y leucemia linfoblástica aguda (LLA) aunque no en otros neoplasmas linfoides. SOX11 se encontró exclusivamente sobreexpresado en LMC convencionales y totalmente ausente en células linfoides normales o en pacientes LMC con un curso clínico indolente y una supervivencia prolongada. Aunque la función de SOX11 y sus genes potenciales dianas aún se desconocen, su elevada expresión específica en LCM sugiere que puede ser un elemento importante en la progresión y desarrollo de este tumor. Se han obtenidos dos publicaciones de los estudios que componen esta tesis. En el primer artículo hemos estudiado los mecanismos moleculares responsables de la expresión aberrante de SOX11 en LCM agresivo. El artículo I proporciona una caracterización exhaustiva de los mecanismos epigenéticos que conducen a la desregulación de SOX11 en estas neoplasias linfoides. En general se observó una significativa correlación inversa entre la metilación del promotor de SOX11 y la expresión de dicho gen. Sin embargo, en muchas muestras (células madre embrionarias, ESC, o adultas, células B normales y algunos LCM indolentes, leucemia linfática crónica y linfoma folicular) la expresión de SOX11 se vió reprimida a pesar de su estado no metilado. Estos hallazgos nos sugieren que la expresión de SOX11 no depende exclusivamente del estado de metilación del ADN del gen y nos llevó a estudiar mecanismos epigenéticos alternativos. Hemos observado que la expresión de SOX11 se asocia con la presencia de marcas de activación de las histonas (H3K9/14Ac y H3K4me3) en las células madre embrionarias y algunas neoplasias de células B agresivas. Por el contrario, en las muestras que no expresan SOX11, incluidas las células madre adultas, las células hematopoyéticas normales y diversas neoplasias linfoides, se observó que el promotor de SOX11 mostraba un enriquecimiento en las marcas de silenciamiento H3K9me2 y H3K27me3. El silenciamiento de SOX11 en líneas celulares fue revertido por el inhibidor de la histona deacetilasa (SAHA) pero no por el inhibidor de la ADN metiltransferasa (AZA). Estos datos indican que, como SOX11 no se expresa en las células linfoides normales, no metiladas, lo más probable es que la hipermetilación del ADN en algunos tumores sin expresión de SOX11 sea funcionalmente inerte, y podría estar asociada con la reducción de la plasticidad epigenética en células tumorales. También observamos que la expresión de novo de SOX11 se asocia con las neoplasias linfoides agresivas como el LCM, algunos subtipos de B-LLA y algunos casos de BL siendo este efecto mediado por un “switch” entre inactivación y activación de las modificaciones de las histonas. Además, como SOX11 se expresa fuertemente en las ESC, los datos sugieren que la expresión de SOX11 podría estar asociada con la adquisición de características de la cromatina similares a la de las células madre. En el artículo II nos hemos centrado en identificar las posibles funciones biológicas de SOX11 en LCM. Combinando análisis de microarray de immunopecipitación de cromatina y perfil de expresión diferencial después de silenciar SOX11, hemos identificado genes dianas y programas transcriptionales regulados por SOX11, incluyendo el bloqueo de la diferenciación de la célula B madura, la modulación de ciclo celular, apoptosis y desarrollo de célula madre. PAX5 destacó como uno de los genes diana directos de SOX11 más significativo. El silenciamiento de SOX11 downregula PAX5, induce la expresión de BLIMP1 y promueve el cambio de fenotipo de célula B madura a la diferenciación inicial plasmacítica, tanto en células tumorales primarias de LCM como en un modelo en vitro. Nuestros resultados sugieren que SOX11 contribuye al desarrollo tumoral mediante la modulación del programa de diferenciación terminal de célula B en LCM. Además, hemos demostrado la habilidad tumorigénica de SOX11 en vivo mediante un modelo de xenotrasplante de LCM en ratones CB17-SCID. La reducción significativa del crecimiento tumoral de las células con expresión de SOX11 silenciada comparada con el crecimiento de células de LCM con elevados niveles de expresión de SOX11 de los xenotrasplantes, demuestra la implicación de la expresión de SOX11 en el comportamiento agresivo de este linfoma. En conclusión, nuestros resultados demuestran que SOX11 puede actuar como oncogén en LCM

Is hepatic lipogenesis fundamental for NAFLD/NASH? A focus on the nuclear receptor coactivator PGC-1β

Non-alcoholic fatty liver diseases are the hepatic manifestation of metabolic syndrome. According to the classical pattern of NAFLD progression, de novo fatty acid synthesis has been incriminated in NAFLD progression. However, this hypothesis has been challenged by the re-evaluation of NAFLD development mechanisms together with the description of the role of lipogenic genes in NAFLD and with the recent observation that PGC-1β, a nuclear receptor/transcription factor coactivator involved in the transcriptional regulation of lipogenesis, displays protective effects against NAFLD/NASH progression. In this review, we focus on the implication of lipogenesis and triglycerides synthesis on the development of non-alcoholic fatty liver diseases and discuss the involvement of these pathways in the protective role of PGC-1β toward these hepatic manifestations

PGC-1β Induces Susceptibility To Acetaminophen-Driven Acute Liver Failure

Acetaminophen (APAP) is a worldwide commonly used painkiller drug. However, high doses of APAP can lead to acute hepatic failure and, in some cases, death. Previous studies indicated that different factors, including life-style and metabolic diseases, could predispose to the risk of APAP-induced liver failure. However, the molecular process that could favor APAP hepatotoxicity remains understood. Here, we reported that a short-term high fat-enriched diet worsens APAP-induced liver damage, by promoting liver accumulation of lipids that induces the activation of peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1β). Therefore, we challenged mice with hepatic-specific PGC-1β overexpression on a chow diet with a subtoxic dose of APAP and we found that PGC-1β overexpression renders the liver more sensitive to APAP damage, mainly due to intense oxidative stress, finally ending up with liver necrosis and mice death. Overall, our results indicated that during high fat feeding, PGC-1β adversely influences the ability of the liver to overcome APAP toxicity by orchestrating different metabolic pathways that finally lead to fatal outcome

A New Ensemble Method for Detecting Anomalies in Gene Expression Matrices

One of the main problems in the analysis of real data is often related to the presence of anomalies. Namely, anomalous cases can both spoil the resulting analysis and contain valuable information at the same time. In both cases, the ability to detect these occurrences is very important. In the biomedical field, a correct identification of outliers could allow the development of new biological hypotheses that are not considered when looking at experimental biological data. In this work, we address the problem of detecting outliers in gene expression data, focusing on microarray analysis. We propose an ensemble approach for detecting anomalies in gene expression matrices based on the use of Hierarchical Clustering and Robust Principal Component Analysis, which allows us to derive a novel pseudo-mathematical classification of anomalies

Prognostic value of lesion dissemination in doxorubicin, bleomycin, vinblastine, and dacarbazine‐treated, interimPET‐negative classical Hodgkin Lymphoma patients: A radio‐genomic study

International audienceWe evaluated the prognostic role of the largest distance between two lesions (Dmax), defined by positron emission tomography (PET) in a retrospective cohort of newly diagnosed classical Hodgkin Lymphoma (cHL) patients. We also explored the molecular bases underlying Dmax through a gene expression analysis of diagnostic biopsies. We included patients diagnosed with cHL from 2007 to 2020, initially treated with ABVD, with available baseline PET for review, and with at least two FDG avid lesions. Patients with available RNA from diagnostic biopsy were eligible for gene expression analysis. Dmax was deduced from the three-dimensional coordinates of the baseline metabolic tumor volume (MTV) and its effect on progression free survival (PFS) was evaluated. Gene expression profiles were correlated with Dmax and analyzed using CIBERSORTx algorithm to perform deconvolution. The study was conducted on 155 eligible cHL patients. Using its median value of 20 cm, Dmax was the only variable independently associated with PFS (HR = 2.70, 95% CI 1.1-6.63, pValue = 0.03) in multivariate analysis of PFS for all patients and for those with early complete metabolic response (iPET-). Among patients with iPET-low Dmax was associated with a 4-year PFS of 90% (95% CI 82.0-98.9) significantly better compared to high Dmax (4-year PFS 72.4%, 95% CI 61.9-84.6). From the analysis of gene expression profiles differences in Dmax were mostly associated with variations in the expression of microenvironmental components. In conclusion our results support tumor dissemination measured through Dmax as novel prognostic factor for cHL patients treated with ABVD

18F-FDG PET/CT Cannot Substitute Endoscopy in the Staging of Gastrointestinal Involvement in Mantle Cell Lymphoma. A Retrospective Multi-Center Cohort Analysis

The detection of gastrointestinal (GI) involvement in Mantle Cell Lymphoma is often underestimated and may have an impact on outcome and clinical management. We aimed to evaluate whether baseline 18F-FDG PET/CT presents comparable results to endoscopic biopsy in the diagnosis of GI localizations. In our retrospective cohort of 79 patients, sensitivity and specificity of 18F-FDG PET/CT were low for the stomach, with a fair concordance (k = 0.32), while higher concordance with pathologic results (k = 0.65) was detected in the colorectal tract. Thus, gastric biopsy remains helpful in the staging of MCL despite 18F-FDG PET/CT, while colonoscopy could be omitted in asymptomatic patients. The validation of our data in prospective cohorts is desirabl

A Digital Gene-Expression Signature Supports Mediastinal Gray Zone Lymphoma Stratification within Classical Hodgkin or Primary Mediastinal B-Cell Lymphoma

Mediastinal non-Hodgkin Lymphomas with intermediate features between Primary Mediastinal Large B-cell Lymphoma (PMBCL) and classical Hodgkin Lymphoma (cHL) - also known as mediastinal Gray Zone Lymphomas (mGZL) - represent a unique, diagnostically challenging entity (Khoury et al., Leukemia 2022). They typically exhibit discordant morpho-phenotypical characteristics between cHL and PMBCL, a high rate of diagnostic reclassification and consequent poor therapeutic outcomes. While a comprehensive biological picture of this entity remains to be fully deciphered, recent gene expression profiling of mGZL confirmed their molecular straddling between cHL and PMBCL (Pittaluga et al., Blood Cancer Discov., 2020; Sarkozy et al., BLOOD ADVANCES, 2020). However, the diagnosis of mGZL is still challenging and largely based on the satisfaction of morphological and immunophenotypic criteria. Therefore, there is an urgent need of practical tools exploiting deeper molecular traits of mGZL to facilitate their pathological boundaries between cHL or PMBCL and selection of proper treatment. We applied CIBERSORTx (Newman et al., Nat. Biotechnol., 2019) to public Gene Expression Profiling (GEP) data of a training set comprising 50 cHL (GSE17920) and 31 PMBCL (GSE11318). Such approach purified GEP of both tumor and microenvironment (TME) origin, followed by a Nonnegative Matrix Factorization (NMF)-based selection of 2,913 genes with high discriminating capacity between the two lymphoma subtypes. After a fine-tuned feature selection, a final signature of 168 genes was verified on the training cohort, tested in silico on an independent series of 34 cHL (GSE17920) and 20 PMBCL (GSE87371), and finally validated by NanoString technology on a real-life (RL) cohort including ten cHL and twelve PMBCL to which were added ten mGZL samples. Although we initially gathered 20 GZL, only the mediastinal were included in the study (n=14). Finally, we selected only the ten mGZL that successfully passed Quality Control. The signature produced a successful clustering of cHL or PMBCL cases in all the series analyzed from different technology platforms. Notably, the mGZL broke down into the two clusters, either cHL or PMBCL subtypes on a transcriptomic ground (Figure 1). Moreover, to assess the specificity of the signature in categorizing mGZL within the cHL/PMBCL spectrum, we tested it on ten Follicular Lymphoma samples which, as expected, segregated in a stand-alone subgroup. In conclusion, we provided a proof of concept of a NanoString-based gene signature enabling a transcriptomic stratification of mGZL, adding up to their morpho-phenotypical categorization. If validated on larger cohorts, our approach might prompt the design of a useful molecular assay easily transferable to routine clinical practice