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Richard, S.

Publications and source records attributed to Richard, S..

At least 19 recordsLinked to original sources

PRMT7 restricts CD8+ T cells expansion via the NF-κB pathway.

New therapeutics are needed to enhance cytotoxic T lymphocyte (CTL) expansion and effector function for effective tumor control. Here, we show that T cell specific deletion of Prmt7 using CD4-Cre mice increases CD8+ effector differentiation, cytokine secretion, cytolytic activity, and anti-tumor responses. Prmt7 deficiency transcriptionally reprogrammed CD8+ T cells by activating the NF-{kappa}B pathway, boosting proliferation, and elevating effector molecules such as CD25, CD69, and IFN{gamma}. Mechanistically, PRMT7 associated with RelA and restricted its nuclear translocation. To enable therapeutic translation, we developed a PRMT7-targeting PROTAC degrader (MS54). MS54-treated CTLs exhibited NF-{kappa}B pathway activation similar to Prmt7-deficient CTLs. Adoptive transfer of MS54-treated OT-I CTLs significantly improved tumor control in a syngeneic melanoma model. In human CTLs, MS54 enhanced proliferation, activation markers (CD69, CD137), IFN{gamma} production, and cytotoxicity toward melanoma. Together, these findings identify PRMT7 as a negative regulator of CD8+ T cell immunity and highlight MS54 as a promising strategy to improve adoptive T cell therapy.

molecular biology↗

Cholangiocytes' Primary Cilia Regulate DNA Damage Response and Repair

Primary cilia have been considered as tumor-suppressing organelles in cholangiocarcinoma (CCA), though the mechanisms behind their protective role are not fully understood. This study investigates how the loss of primary cilia affects DNA damage response (DDR) and DNA repair processes in CCA. Human cholangiocyte cell lines were used to examine the colocalization of DNA repair proteins at the cilia and assess the impact of experimental deciliation on DNA repair pathways. Deciliation was induced using shRNA knockdown or CRISPR knockout of IFT20, IFT88, and KIF3A, followed by exposure to genotoxic agents such as cisplatin, methyl methanesulfonate (MMS), and irradiation. Cell survival, cell cycle progression, and apoptosis rates were evaluated, while DNA damage was assessed using comet assays and {gamma}H2AX quantification. An in vivo liver-specific knockout model of IFT88 was generated using the Cre/Lox recombination system. Results showed that RAD51 localized at the cilia base, while ATR, PARP1, CHK1 and CHK2 were found within the cilia. Deciliated cells displayed dysregulation in critical DDR pathways. These cells also showed reduced survival and increased S-phase arrest after genotoxic challenges. Enhanced DNA damage was observed via increased {gamma}H2AX signals and comet assay results. An increase in {gamma}H2AX expression was observed in our in vivo model, indicating elevated DNA damage. Additionally, key DDR proteins, such as ATM, p53, and p21, were downregulated in deciliated cells after irradiation. This study underscores the crucial role of primary cilia in regulating DNA repair, suggesting that targeting cilia-related mechanisms could present a novel therapeutic approach for CCA. Key PointsThe results presented delineate the following critical observations: O_LIDNA Damage Response (DDR) and DNA repair proteins localized to primary cilia structures C_LIO_LIDeciliated cells exhibited dysregulated DDR pathways, reduced survival, and S-phase arrest under genotoxic stress C_LIO_LIElevated DNA damage was evident in deciliated cells, with increased {gamma}H2AX signals and comet assay results C_LIO_LIIn vivo IFT88 knockout mice also showed increased {gamma}H2AX expression, indicating heightened DNA damage C_LIO_LIKey DDR proteins (ATM, p53, p21) were downregulated in deciliated cells after irradiation. C_LI

pathology↗

Time-dependent chromatin maturation during 3D spheroid culture improves preclinical modeling of non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is the deadliest cancer worldwide. Therapeutic progress stagnate, highlighting the complexity to replicate NSCLC in preclinical models. Drug discovery studies rely mostly on cancer cells in two-dimension (2D), which poorly predict drug efficacy in patients. There is a growing interest in three-dimensional (3D) preclinical models, such as 3D spheroids, to better model tumor phenotype and improve therapeutic prediction. However, a comprehensive view of 3D culture methods impact on transcriptomes, epigenomes and pharmacological responses and their correlations to NSCLC tumors is still missing. Here, we demonstrate that NSCLC spheroids undergo time-dependent transcriptomic and epigenomic changes, which peak after 3 weeks of culture. While DNA methylome remained stable, chromatin methylation and acetylation marks gained features of advanced NSCLC in a time-dependent manner. Single-cell transcriptomic profiling of spheroids demonstrated that time of 3D culture improved the correlation to NSCLC tumors. Moreover, long-term culture of 3D spheroids increased drug screening predictability, by showing resistance to drugs that failed in NSCLC patients (such as HDAC inhibitors) while demonstrating novel pharmacological vulnerabilities and synergistic interactions (such as combination of PRMT and HDAC inhibitors). Strikingly, reverting 3D spheroids back to 2D culture rapidly reversed transcriptomic, epigenetic and pharmacological signatures acquired after 3 weeks of 3D culture, highlighting the critical impact of cell culture conditions on NSCLC phenotype. Collectively, our findings demonstrate that implementing a time-dependent maturation process into 3D spheroid culture induces chromatin and transcriptomic changes that enhance NSCLC preclinical modeling.

cancer biology↗

Thyroid hormones act as a timer for the postnatal maturation of parvalbumin neurons in mouse neocortex

Thyroid hormones (THs) are required for proper maturation of parvalbumin-expressing GABAergic interneurons in the mouse neocortex, which function is essential to maintain a proper balance between neuronal excitation and inhibition. However, the timeline of this TH action has yet to be elucidated. Here, we used several mouse models expressing dominant negative mutations of the TH nuclear receptor 1 (TR1), to better define the time window during which THs promote the maturation of parvalbumin neurons. The action of THs during the first three postnatal weeks appears to be necessary to initiate the elaboration of a specialized extracellular matrix called the perineuronal net. Transcriptome analysis identified a small set of putative target genes for TR1, which are at the origin of the postnatal remodeling of the repertoire of ions channels and the elaboration of perineuronal nets. These data suggest that THs act as a timer to define the temporal boundaries of the critical period of heightened cortical plasticity, which plays a fundamental role in the development of neuronal circuits. Significance statementThyroid hormones exert a major influence on late neurodevelopment, acting directly on gene expression by binding to nuclear receptors present in all cell types. This study reports the discovery of a direct link between the transcriptional regulation exerted by the thyroid hormones in GABAergic neurons and the timing of the critical period of heightened plasticity. This provides a general framework to understand the pathology associated with altered thyroid hormone signaling.

developmental biology↗

Thyroid hormones maintain parvalbumin neuron functions in mouse neocortex

Parvalbumin-expressing GABAergic interneurons play a key role in maintaining the excitation-inhibition balance in the mammalian neocortex. While postnatal maturation of parvalbumin neurons is highly sensitive to thyroid hormone deficiency, the role of these hormones in mature parvalbumin neurons remains poorly understood. Here, we addressed the possibility that thyroid hormones are also required to maintain the function of mature parvalbumin neurons in the mouse neocortex. To this end, Cre/loxP recombination system was used to express a dominant-negative mutated receptor of thyroid hormones to selectively eliminate thyroid hormone signaling in parvalbumin neurons after the onset of parvalbumin expression. We analyzed the neocortical phenotype of these mice by combining genomics, histology, electrophysiology, sleep recordings and behavioral analysis. In the mutant mice, gene expression analysis revealed a decreased expression of key perineuronal net components. parvalbumin neuron excitability was decreased and mice displayed behavioral hyperactivity and increased susceptibility to epileptic seizures. Additionally, sleep analysis revealed that mutant mice spent more time awake, and had a delayed transition to sleep. Electrophysiological recordings further demonstrated altered gamma oscillations in the somatosensory cortex. The findings of this study underscore that thyroid hormones are essential not only for the differentiation of parvalbumin interneurons, but also for the maintenance of their inhibitory function after the onset of parvalbumin expression. As a consequence, alterations in thyroid hormone signaling, during development or in adulthood, may contribute to the occurrence of neurological and psychiatric disorders involving altered cortical oscillations.

neuroscience↗

Fine-tuning Rpb4 phosphorylation modulates Rpb4/7 stoichiometry within yeast RNA polymerase II and regulates gene expression

RNA polymerase II (RNAPII) consists of 12 subunits, including Rpb4 and Rpb7, which form a heterodimeric stalk domain. In yeast, assembly of Rpb4/7 with the 10-subunit "core" is substoichiometric. Aside from its role in transcription, Rpb4/7 also binds to mRNAs co-transcriptionally (mRNA imprinting), exits the nucleus together with the mRNA, and modulates subsequent cytoplasmic processes like translation and degradation. However, the mechanisms underlying Rpb4/7 functions and its association with RNAPII remain poorly understood. In this study, we identify five phosphorylation sites in Rpb4 that regulate various steps of mRNA and snoRNA biogenesis, including transcription elongation and the polyadenylation step. We also provide evidence that the kinase Hrr25 and the phosphatase Fcp1, known to target the carboxyl-terminal domain (CTD) of Rpb1 and participate in processes at gene 3'-ends, coordinate Rpb4 phosphorylation. Inefficient Rpb4 phosphorylation leads to increased Rpb4 association with RNAPII, particularly at gene 3'-ends, suggesting that Rpb4-P promotes stalk dissociation from RNAPII either before or during transcription termination. Collectively, our findings underscore the pivotal role of dynamic Rpb4 phosphorylation in regulating Rpb4/7 stoichiometry as well as transcription elongation and termination, with an impact on mRNA imprinting.

molecular biology↗

LETHAL COVID-19 ASSOCIATES WITH RAAS-INDUCED INFLAMMATION FOR MULTIPLE ORGAN DAMAGE INCLUDING MEDIASTINAL LYMPH NODES

Lethal COVID-19 outcomes are most often attributed to classic cytokine storm and attendant excessive immune signaling. We re-visit this question using RNA sequencing in nasopharyngeal and 40 autopsy samples from COVID-19-positive and negative individuals. In nasal swabs, the top 100 genes which significantly correlated with COVID-19 viral load, include many canonical innate immune genes. However, 22 much less studied "non-canonical" genes are found and despite the absence of viral transcripts, subsets of these are upregulated in heart, lung, kidney, and liver, but not mediastinal lymph nodes. An important regulatory potential emerges for the non-canonical genes for over-activating the renin-angiotensin-activation-system (RAAS) pathway, resembling this phenomenon in hereditary angioedema (HAE) and its overlapping multiple features with lethal COVID-19 infections. Specifically, RAAS overactivation links increased fibrin deposition, leaky vessels, thrombotic tendency, and initiating the PANoptosis death pathway, as suggested in heart, lung, and especially mediastinal lymph nodes, with a tightly associated mitochondrial dysfunction linked to immune responses. For mediastinal lymph nodes, immunohistochemistry studies validate the transcriptomic findings showing abnormal architecture, excess fibrin and collagen deposition, and pathogenic fibroblasts. Further, our findings overlap findings in SARS-CoV-2 infected hamsters, C57BL/6 and BALB/c mouse models, and importantly peripheral blood mononuclear cell (PBMC) and whole blood samples from COVID-19 patients infected with early variants and later SARS-CoV-2 strains. We thus present cytokine storm in lethal COVID-19 disease as an interplay between upstream immune gene signaling producing downstream RAAS overactivation with resultant severe organ damage, especially compromising mediastinal lymph node function.

immunology↗

Opposing Strain Directions on Adjacent Left Ventricular Segments Predict Fibrotic Remodeling after Acute Myocardial Infarction

BackgroundDespite similar levels of coronary occlusion and standard of care management, the occurrence of scarring over adaptive heart repair following acute myocardial infarction (AMI) remains unpredictable. Recent studies indicate that mechanical cues may modulate the transcriptional programs involved in tissue repair, possibly explaining why ventricular mechanical dyssynchrony an independent predictor of post-infarction outcome. ObjectiveOur study aimed to investigate the relationship between mechanical cues and the outcome of post-myocardial infarction heart remodeling by live imaging. Specifically, we examined the impact of individual variability of myocardial dyssynchrony, characterized by a divergent direction of injured left ventricle wall movement next to live tissue, on the formation of a large scar, dilation of the left ventricle, and loss of pumping function. MethodsWe assessed the location and degree of regional systolic and diastolic dyssynchrony using transthoracic echocardiography coupled with speckle tracking imaging. Specifically, we measured the difference in absolute strain values between adjacent regions of the left ventricle at 5 days following the induction of a standard experimental infarction in female C57Bl6 mice. Three weeks later, transthoracic echocardiography was repeated to analyze the mass and global function of the left ventricle right before termination. We then examined the size of the scar in matched mid-sections of the left ventricle circumferential segments from each mouse using histomorphometry. Finally, we evaluated the potential impact on transcriptional tissue repair programs using spatial transcriptomic analysis on representative hearts with either adaptive or fibrotic post-infarction heart remodeling. ResultsWe analyzed all 96 systolic and diastolic strain-related parameters in the same 48 regions of the left ventricle in all mice, with echocardiographic and histological sections following the same orientation. Stepwise analysis of the live imaging data revealed that a combination of 8 regional strain parameters could predict fibrotic remodeling (Area under the ROC curve= 0.8290). We observed that scarring remodeling was associated with opposing trends of systolic and diastolic circumferential strain % delta values on adjacent regions at day 5, while adaptive remodeling at day 28 occurred when the trend followed the direction of control (sham) hearts. Cluster analysis of gene transcripts and speckle tracking assessment on representative hearts with adaptive or fibrotic post-infarction remodeling indicated a correlation between regional post-infarction dyssynchrony and the transcriptional program. Adrenergic receptors, including Adra1, Trpc3, and Myh7, were found to be linked to specific regional dyssynchrony values and scarring remodeling. ConclusionOur study demonstrates the potential of regional strain parameters obtained through live imaging in predicting fibrotic remodeling following myocardial infarction. Furthermore, our findings suggest a link between regional post-infarction dyssynchrony and the transcriptional program. These results highlight the potential applicability of our approach in clinical settings and provide insights for future personalization of therapeutic strategies.

physiology↗

Fungal antigenic variation using mosaicism and reassortment of subtelomeric genes' repertoires, potentially mediated by DNA triplexes

Surface antigenic variation is crucial for major pathogens that infect humans, e.g. Plasmodium 1, Trypanosoma 2, Giardia 3. In order to escape the immune system, they exploit various mechanisms in order to modify or exchange the protein that is exposed on the cell surface, at the genetic, expressional, and/or epigenetic level 4. Understanding these mechanisms is important to better prevent and fight the deadly diseases caused. However, those used by the fungus Pneumocystis jirovecii that causes life-threatening pneumonia in immunocompromised individuals remain poorly understood. Here, though this fungus is currently not cultivable 5, our detailed analysis of the subtelomeric sequence motifs and genes encoding surface proteins suggest that the system involves mediation of homologous recombinations during meiosis by DNA triplexes. This leads to the reassortment of the repertoire of ca. 80 non-expressed genes present in each strain, from which single genes are retrieved for mutually exclusive expression within subpopulations of cells 6. The recombinations generates also constantly new mosaic genes. Dispersion of the new alleles and repertoires, supposedly by healthy carrier individuals, appears very efficient because identical alleles are observed in patients from all over the world. Our observations reveal a unique strategy of antigenic variation allowing colonization of the non-sterile niche corresponding to lungs of healthy humans. They also highlight the possible role in genome rearrangements of small imperfect mirror sequences forming DNA triplexes 7. Such mirror sequences are widespread in eukaryotic genomes 8, as well as in HIV virus 9, but remain poorly understood so far.

microbiology↗

Inhibition of Type I PRMTs Reforms Muscle Stem Cell Identity Enhancing their Therapeutic Capacity

In skeletal muscle, muscle stem cells (MuSC) are the main cells responsible for regeneration upon injury. In diseased skeletal muscle, it would be therapeutically advantageous to replace defective MuSCs, or rejuvenate them with drugs to enhance their self-renewal and ensure long-term regenerative potential. One limitation of the replacement approach has been the inability to efficiently expand MuSCs ex vivo, while maintaining their stemness and engraftment abilities. Herein, we show that inhibition of type I protein arginine methyltransferases (PRMTs) with MS023 increases the proliferative capacity of ex vivo cultured MuSCs. Single cell RNA sequencing (scRNAseq) of ex vivo cultured MuSCs revealed the emergence of subpopulations in MS023-treated cells which are defined by elevated Pax7 expression and markers of MuSC quiescence, both features of enhanced self-renewal. Furthermore, the scRNAseq identified MS023-specific subpopulations to be metabolically altered with upregulated glycolysis and oxidative phosphorylation (OxPhos). Transplantation of MuSCs treated with MS023 had a better ability to repopulate the MuSC niche and contributed efficiently to muscle regeneration following injury. Interestingly, the preclinical mouse model of Duchenne muscular dystrophy had increased grip strength with MS023 treatment. Our findings show that inhibition of type I PRMTs increased the proliferation capabilities of MuSCs with altered cellular metabolism, while maintaining their stem-like properties such as self-renewal and engraftment potential.

molecular biology↗

Brown adipocytes local response to thyroid hormone is required for adaptive thermogenesis in adult male mice

Thyroid hormone (T3) and its nuclear receptors (TR) are important regulators of energy expenditure and adaptive thermogenesis, notably through their action in the brown adipose tissue (BAT). However, T3 acts in many other peripheral and central tissues which are also involved in energy expenditure. The general picture of how T3 regulates BAT thermogenesis is currently not fully established, notably due to the absence of extensive omics analyses and the lack of specific mice model. Here, we first used transcriptome and cistrome analyses to establish the list of T3/TR direct target genes in brown adipocytes. We then developed a novel model of transgenic mice, in which T3-signaling is specifically suppressed in brown adipocytes at adult stage. We addressed the capacity of these mice to mount a thermogenic response when challenged by either a cold exposure or a high-fat diet, and analyzed the associated changes in BAT transcriptome. We conclude that T3 plays a crucial role in the thermogenic response of the BAT, controlling the expression of genes involved in lipid and glucose metabolism and regulating BAT proliferation. The resulting picture provides an unprecedented view on the pathways by which T3 activates energy expenditure through an efficient adaptive thermogenesis in the BAT. Significance StatementThyroid hormones (TH) increase energy expenditure by regulating the expression of target genes in many metabolic tissues. Among them, brown adipose tissue (BAT) dissipates biochemical energy into heat production to notably prevent hypothermia during cold exposure. Hypothyroid mice display inefficient BAT thermogenesis suggesting that TH are crucial for this process. Here, we eliminated TH signaling specifically in brown adipocytes and expose the mice to different physiological stressors. We showed that TH signaling is crucial for BAT thermogenesis as it controls the expression of genes involved in proliferation and in the metabolism of lipids and glucose, the main energy resources for BAT thermogenesis. This study provides an unprecedented view on the pathways by which T3 activates energy expenditure the BAT.

genomics↗

Post-vaccination Omicron infections induce broader immunity across antigenic space than prototype mRNA COVID-19 booster vaccination or primary infection

The rapid emergence of new SARS-CoV-2 variants challenges vaccination strategies. Here, we measured antigenic diversity among variants and interpreted neutralizing antibody responses following single and multiple exposures in longitudinal infection and vaccine cohorts. Antigenic cartography using primary infection antisera showed that BA.2, BA.4/BA.5, and BA.2.12.1 are distinct from BA.1 and closer to the Beta cluster. Three doses of an mRNA COVID-19 vaccine increased breadth to BA.1 more than to BA.4/BA.5 or BA.2.12.1. Omicron BA.1 post-vaccination infection elicited antibody landscapes characterized by broader immunity across antigenic space than three doses alone, although with less breadth than expected to BA.2.12.1 and BA.4/BA.5. Those with Omicron BA.1 infection after two or three vaccinations had similar neutralizing titer magnitude and antigenic breadth. Accounting for antigenic differences among variants of concern when interpreting neutralizing antibody titers aids understanding of complex patterns in humoral immunity and informs selection of future COVID-19 vaccine strains.

microbiology↗

Crest maturation at the cardiomyocyte surface contributes to a new late postnatal development stage that controls the diastolic function of the adult heart

RATIONALEIn addition to its typical rod-shape, the mammalian adult cardiomyocyte (CM) harbors a unique lateral membrane surface architecture with periodic crests, relying on the presence of subsarcolemmal mitochondria (SSM) the role of which is still unknown. OBJECTIVETo investigate the development and functional role of CM crests during the postnatal period. METHODS AND RESULTSElectron/confocal microscopy and western-blot of left ventricular tissues from rat hearts indicated a late CM surface crest maturation, between postnatal day 20 (P20) and P60, as shown by substantial SSM swelling and increased claudin-5 cell surface expression. The P20-P60 postnatal stage also correlates with an ultimate maturation of the T-Tubules and the intercalated disk. At the cellular level, we identified an atypical CM hypertrophy characterized by an increase in long- and short-axes without myofibril addition and with sarcomere lateral stretching, indicative of lateral stretch-based CM hypertrophy. We confirmed the P20-P60 hypertrophy at the organ level by echocardiography but also demonstrated a transcriptomic program after P20 targeting all the cardiac cell populations. At the functional level, using Doppler echocardiography, we found that the P20-P60 period is specifically dedicated to the improvement of relaxation. Mechanistically, using CM-specific knock-out mice, we identified ephrin-B1 as a determinant of CM crest maturation after P20 controlling lateral CM stretch-hypertrophy and relaxation. Interestingly, while young adult Efnb1CMspe-/- mice essentially show a relaxation impairment with exercise intolerance, they progressively switch toward heart failure with 100% KO mice dying after 13 months. CONCLUSIONSThis study highlights a new late P20-P60 postnatal developmental stage of the heart in rodents during which the CM surface crests mature through an ephrin-B1-dependant mechanism and regulate the diastolic function. Moreover, we demonstrate for the first time that the CM crest architecture is cardioprotective.

cell biology↗

PRMT7 ablation stimulates anti-tumor immunity and sensitizes melanoma to immune checkpoint blockade

Despite the success of immune checkpoint inhibitor (ICI) therapy in different cancers, resistance and relapses are frequent. Thus, combination therapies are expected to enhance response rates and overcome resistance to ICIs. Herein, we report that combining protein arginine methyltransferase 7 (PRMT7) inhibition with ICIs triggers a strong anti-tumor T cell immunity and restrains tumor growth in vivo by increasing tumor immune cell infiltration. Consistently, TCGA database analysis showed an inverse correlation between PRMT7 expression and T cell infiltration in human melanomas. Mechanistically, we show that PRMT7 has a two-prong effect on melanoma tumor immunity. On one hand, it serves as a coactivator of IRF-1 for PD-L1 expression by upregulating promoter H4R3me2s levels in melanoma cells. Next, PRMT7 prevents repetitive element expression to avoid intracellular dsRNA accumulation or viral mimicry. PRMT7 deletion resulted in increased endogenous retroviral elements (ERVs), dsRNA, and genes implicated in interferon activation, antigen presentation and chemokine signaling. Our findings identify PRMT7 as factor used by melanoma to evade anti-tumor immunity and define the therapeutic potential of PRMT7 alone or in combination with PD-(L)1 blockade to enhance ICI efficiency.

immunology↗

Arginine Methylation Regulates SARS-CoV-2 Nucleocapsid Protein Function and Viral Replication

Viral proteins are known to be methylated by host protein arginine methyltransferases (PRMTs) playing critical roles during viral infections. Herein, we show that PRMT1 methylates SARS-CoV-2 nucleocapsid (N) protein at residues R95 and R177 within RGG/RG sequences. Arginine methylation of N protein was confirmed by immunoblotting viral proteins extracted from SARS-CoV-2 virions isolated by cell culture. We demonstrate that arginine methylation of N protein is required for its RNA binding capacity, since treatment with a type I PRMT inhibitor (MS023) or substitution of R95K or R177K inhibited interaction with the 5-UTR of the SARS-CoV-2 genomic RNA. We defined the N interactome in HEK293 cells with or without MS023 treatment and identified PRMT1 and many of its RGG/RG substrates including the known interactor, G3BP1, and other components of stress granules (SG). Methylation of N protein at R95 regulates another function namely its property to suppress the formation of SGs. MS023 treatment or R95K substitution blocked N-mediated suppression of SGs. Also, the co-expression of methylarginine reader TDRD3 quenched N-mediated suppression of SGs in a dose-dependent manner. Finally, pre-treatment of VeroE6 cells with MS023 significantly reduced SARS-CoV-2 replication. With type I PRMT inhibitors being in clinical trials for cancer treatment, inhibiting arginine methylation to target the later stages of the viral life cycle such as viral genome packaging and assembly of virions may be an additional therapeutic application of these drugs.

molecular biology↗

Patient Similarity Network of Newly Diagnosed Multiple Myeloma Identifies Patient Sub-groups with Distinct Genetic Features and Clinical Implications

The remarkable genetic heterogeneity of Multiple Myeloma (MM) poses a significant challenge for proper prognostication and clinical management of patients. Accurate dissection of the genetic and molecular landscape of the disease and the robust identification of homogeneous classes of patients are essential steps to reliable risk stratification and the development of novel precision medicine strategies. Here we introduce MM-PSN, the first multi-omics Patient Similarity Network of newly diagnosed MM. MM-PSN has enabled the identification of three broad patient groups and twelve distinct sub-groups defined by five data types generated from genomic and transcriptomic patient profiling of 655 patients. The MM-PSN classification uncovered novel associations between distinct MM hallmarks with significant prognostic implications and allowed further refinement of risk stratification. Our analysis revealed that gain of 1q is the most important single lesion conferring high risk of relapse, and its association with an MMSET translocation is the most significant determinant of poor outcome. We developed a classifier and validated these results in an independent dataset of 559 pts. Our findings suggest that gain of 1q should be incorporated in routine staging systems and risk assessment tools. The MM-PSN classifier is available as a free resource to allow for an easy implementation in most clinical settings.

cancer biology↗

Numerous post-translational modifications of RNA polymerase II subunit Rpb4 link transcription to post-transcriptional mechanisms

Rpb4/7 binds RNA Polymerase II (Pol II) transcripts co-transcriptionally and accompanies them throughout their lives. By virtue of its capacity to interact with key regulators (e.g., Pol II, eIF3, Pat1) both temporarily and spatially, Rpb4/7 regulates the major stages of the mRNA lifecycle. Here we show that Rpb4/7 can undergo over 100 combinations of post-translational modifications (PTMs). Remarkably, the Rpb4/7 PTMs repertoire changes as the mRNA/Rpb4/7 complex progresses from one stage to the next. A mutagenesis approach in residues that undergo PTMs suggests that temporal Rpb4 PTMs regulate its interactions with key regulators of gene expression that control transcriptional and post-transcriptional stages. Moreover, one mutant type specifically affects mRNA synthesis despite its normal association with Pol II, whereas the other affects both mRNA synthesis and decay; both types disrupt the balance between mRNA synthesis and decay ( mRNA buffering) and the cells capacity to respond to the environment. Taken together, we propose that temporal Rpb4/7 PTMs are involved in cross talks among the various stages of the mRNA lifecycle.

molecular biology↗

Long term outcomes of Everolimus therapy in de novo liver transplantation: a systematic review and meta-analysis of randomized controlled trials

BackgroundRisk of nephrotoxicity in liver transplant patients on calcineurin inhibitors (CnIs) is a concern. Several controlled trials reported benefit of Everolimus (EVR) in minimizing this risk when combined with a reduced CnIs dose.\n\nObjectiveTo systematically review the efficacy and safety of EVR, alone or with reduced CnI dose, as compared to CnI alone post liver transplantation.\n\nMethodsWe searched MEDLINE, Scopus and the Cochrane Library for randomized controlled trials (RCTs) comparing EVR and CnI based regimens post liver transplanation. Assessment of studies and data extraction was undertaken independently.\n\nResultsEight studies were selected describing 769 patients. Cockcroft-Gault GFR (CG-GFR) was significantly higher at one (p=0.05), 3 & 5 years (p=0.030) in patients receiving EVR as compared to those receiving CnI therapy. The composite end point of efficacy failure was similar between the two arms after 1, 3 & 5 years of study. Higher number of patients discontinued EVR due to adverse effects in one year, however no difference was noted after 3 & 5 years. A higher rates of proteinuria, peripheral edema and incisional hernia were noted in patients on EVR.\n\nConclusionThe analysis confirms non-inferiority of EVR and reduced CnI combination. Patients on the combination regimen had better renal function compared to standard CnI therapy.

immunology↗