POU2AF1, an amplification target at 11q23, promotes growth of multiple myeloma cells by directly regulating expression of a B-cell maturation factor, TNFRSF17

Three-gene signature revealing the dynamics of lymphocyte infiltration in subchondral bone during osteoarthritis progression

Osteoarthritis (OA), a degenerative joint disorder, has an unclear immune infiltration mechanism in subchondral bone (SCB). Thus, this study aims to discern immune infiltration variations in SCB between early- and late-stages of OA and identify pertinent biomarkers. Utilizing the GSE515188 bulk-seq profile from the Gene Expression Omnibus database, we performed single-sample gene-set enrichment analysis alongside weighted gene co-expression network analysis to identify key cells and immune-related genes (IRGs) involved in SCB at both stages. At the meanwhile, differentially expressed genes (DEGs) were identified in the same dataset and intersected with IRGs to find IR-DEGs. Protein-protein interaction network and enrichment analyses and further gene filtering using LASSO regression led to the discovery of potential biomarkers, which were then validated by ROC curve analysis, single-cell RNA sequencing, qRT-PCR, western blot and immunofluorescence. ScRNA-seq analysis using GSE196678, qRT-PCR, western blot and immunofluorescence results confirmed the upregulation of their expression levels in early-stage OA SCB samples. Our comprehensive analysis revealed lymphocytes infiltration as a major feature in early OA SCB. A total of 13 IR-DEGs were identified, showing significant enrichment in T- or B-cell activation pathways. Three of them (CD247, POU2AF1, and TNFRSF13B) were selected via the LASSO regression analysis, and results from the ROC curve analyses indicated the diagnostic efficacy of these 3 genes as biomarkers. These findings may aid in investigating the mechanisms of SCB immune infiltration in OA, stratifying OA progression, and identifying relevant therapeutic targets.

B-cell hub genes play a cardiovascular pathogenic role of in childhood obesity and Kawasaki disease as revealed by transcriptomics-based analyses

The study aims to explore the central genes that Kawasaki disease (KD) and Obesity (OB) may jointly contribute to coronary artery disease. Investigating single-cell datasets (GSE168732 and GSE163830) from a comprehensive gene expression database, we identified characteristic immune cell subpopulations in KD and OB. B cells emerged as the common immune cell characteristic subgroup in both conditions. Subsequently, we analyzed RNA sequencing datasets (GSE18606 and GSE87493) to identify genes associated with B-cell subpopulations in KD and OB. Lastly, a genome-wide association study and Mendelian randomization were conducted to substantiate the causal impact of these core genes on myocardial infarction. Quantitative real-time PCR (qRT-PCR) to validate the expression levels of hub genes in KD and OB. The overlapping characteristic genes of B cell clusters in both KD and OB yielded 70 shared characteristic genes. PPI analysis led to the discovery of eleven key genes that significantly contribute to the crosstalk. Employing receiver operating characteristic analysis, we evaluated the specificity and sensitivity of these core genes and scored them using Cytoscape software. The inverse variance weighting analysis suggested an association between TNFRSF17 and myocardial infarction risk, with an odds ratio of 0.9995 (95% CI = 0.9990-1.0000, p = 0.049). By employing a single-cell combined transcriptome data analysis, we successfully pinpointed central genes associated with both KD and OB. The implications of these findings extend to shedding light on the increased risk of coronary artery disease resulting from the co-occurrence of OB and KD.

The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities

Multiple myeloma (MM) is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, MM remains incurable, and better risk stratification as well as new therapies are therefore highly needed. The proteome of MM has not been systematically assessed before and holds the potential to uncover insight into disease biology and improved prognostication in addition to genetic and transcriptomic studies. Here we provide a comprehensive multiomics analysis including deep tandem mass tag-based quantitative global (phospho)proteomics, RNA sequencing, and nanopore DNA sequencing of 138 primary patient-derived plasma cell malignancies encompassing treatment-naive MM, plasma cell leukemia and the premalignancy monoclonal gammopathy of undetermined significance, as well as healthy controls. We found that the (phospho)proteome of malignant plasma cells are highly deregulated as compared with healthy plasma cells and is both defined by chromosomal alterations as well as posttranscriptional regulation. A prognostic protein signature was identified that is associated with aggressive disease independent of established risk factors in MM. Integration with functional genetics and single-cell RNA sequencing revealed general and genetic subtype-specific deregulated proteins and pathways in plasma cell malignancies that include potential targets for (immuno)therapies. Our study demonstrates the potential of proteogenomics in cancer and provides an easily accessible resource for investigating protein regulation and new therapeutic approaches in MM.

A novel iTreg-related signature for prognostic prediction in lung adenocarcinoma

Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer. Most patients are diagnosed at an advanced stage, therefore it is crucial to identify novel prognostic biomarkers for LUAD. As important regulatory cells, inducible regulatory T cells (iTregs) play a vital role in immune suppression and are important for the maintenance of immune homeostasis. This study explored the prognostic value and therapeutic effects of iTreg-related genes in LUAD. Data for LUAD patients, including immune infiltration data, RNA sequencing data, and clinical features, were acquired from The Cancer Genome Atlas, Gene Expression Omnibus, and Tumor Immune Single-cell Hub 2 databases. Immune-related subgroups with different infiltration patterns and iTreg-related genes were identified through univariate and multivariate Cox regression analyses and weighted correlation network analysis. Functional enrichment analyses were performed to explore the underlying mechanisms of iTreg-related genes. A prognostic risk signature was constructed using Cox regression analysis with the least absolute shrinkage and selection operator penalty. The ESTIMATE algorithm was applied to determine the immune status of LUAD patients. We applied the constructed signature to predict chemosensitivity and performed single-cell RNA sequencing analysis. The infiltration of iTregs was identified as an independent factor for predicting patient outcomes. We constructed a prognostic signature based on seven iTreg-related genes (GIMAP5, SLA, MS4A7, ZNF366, POU2AF1, MRPL12, and COL5A1), which was applied to subdivide patients into high- and low-risk subgroups. Our results revealed that patients in the iTreg-related low-risk subgroup had a better prognosis and possibly greater sensitivity to traditional chemotherapy. Our study provides a novel iTreg-related signature to elucidate the mechanisms underlying LUAD prognosis and promote individualized chemotherapy treatment.

The Role of the Transcriptional Coactivator BOB.1/OBF.1 in Adaptive Immunity

BOB.1/OBF.1 is a transcriptional coactivator involved in octamer-dependent transcription. Thereby, BOB.1/OBF.1 is involved in the transcriptional regulation of genes important for lymphocyte physiology. BOB.1/OBF.1-deficient mice reveal multiple B- and T-cell developmental defects. The most prominent defect of these mice is the complete absence of germinal centers (GCs) resulting in severely impaired T-cell-dependent immune responses. In humans, BOB.1/OBF.1 is associated with several autoimmune and inflammatory diseases but also linked to liquid and solid tumors. Although its role for B-cell development is relatively well understood, its exact role for the GC reaction and T-cell biology has long been unclear. Here, the contribution of BOB.1/OBF.1 for B-cell maturation is summarized, and recent findings regarding its function in GC B- as well as in various T-cell populations are discussed. Finally, a detailed perspective on how BOB.1/OBF.1 contributes to different pathologies is provided.

Central role of lung macrophages in SARS-CoV-2 physiopathology: a cross-model single-cell RNA-seq perspective

Cytokine storms are considered a driving factor in coronavirus disease 2019 (COVID-19) severity. However, the triggering and resolution of this cytokine production, as well as the link between this phenomenon and infected cells, are still poorly understood. In this study, a cross-species scRNA-seq analysis showed that cytokine-producing macrophages together with pneumocytes were found to be the main contributors of viral transcripts in both Syrian hamsters and African green monkeys. Whatever the cell type, viral read-bearing cells show an apoptotic phenotype. A comparison of SARS-CoV-2 entry receptor candidates showed that Fc receptors are better correlated with infected cells than ACE2, NRP1, or AXL. Although both species show similar interferon responses, differences in adaptive immunity were highlighted. Lastly, Fc receptor and cytokine upregulation in M1 macrophages was found to correlate with a comprehensive interferon response. Based on these results, we propose a model in which lung macrophages play a central role in COVID-19 severity through antibody-dependent enhancement.

Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias

Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies that have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mutations in MM. Instead, these agents target pathways critical for PC biology yet largely dispensable for malignant or normal cells of most other lineages. Here we systematically characterized the lineage-preferential molecular dependencies of MM through genome-scale clustered regularly interspaced short palindromic repeats (CRISPR) studies in 19 MM versus hundreds of non-MM lines and identified 116 genes whose disruption more significantly affects MM cell fitness compared with other malignancies. These genes, some known, others not previously linked to MM, encode transcription factors, chromatin modifiers, endoplasmic reticulum components, metabolic regulators or signaling molecules. Most of these genes are not among the top amplified, overexpressed or mutated in MM. Functional genomics approaches thus define new therapeutic targets in MM not readily identifiable by standard genomic, transcriptional or epigenetic profiling analyses.

Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

Multiple myeloma (MM) is a highly refractory hematologic cancer. Targeted immunotherapy has shown promise in MM but remains hindered by the challenge of identifying specific yet broadly representative tumor markers. We analyzed 53 bone marrow (BM) aspirates from 41 MM patients using an unbiased, high-throughput pipeline for therapeutic target discovery via single-cell transcriptomic profiling, yielding 38 MM marker genes encoding cell-surface proteins and 15 encoding intracellular proteins. Of these, 20 candidate genes were highlighted that are not yet under clinical study, 11 of which were previously uncharacterized as therapeutic targets. The findings were cross-validated using bulk RNA sequencing, flow cytometry, and proteomic mass spectrometry of MM cell lines and patient BM, demonstrating high overall concordance across data types. Independent discovery using bulk RNA sequencing reiterated top candidates, further affirming the ability of single-cell transcriptomics to accurately capture marker expression despite limitations in sample size or sequencing depth. Target dynamics and heterogeneity were further examined using both transcriptomic and immuno-imaging methods. In summary, this study presents a robust and broadly applicable strategy for identifying tumor markers to better inform the development of targeted cancer therapy.

SIGNIFICANCE

Single-cell transcriptomic profiling and multiomic cross-validation to uncover therapeutic targets identifies 38 myeloma marker genes, including 11 transcribing surface proteins with previously uncharacterized potential for targeted antitumor therapy.

Ectopic lymphoid structures in the aged lacrimal glands

Aging is a complex biological process in which many organs are pathologically affected. We previously reported that aged C57BL/6J had increased lacrimal gland (LG) lymphoid infiltrates that suggest ectopic lymphoid structures. However, these ectopic lymphoid structures have not been fully investigated. Using C57BL/6J mice of different ages, we analyzed the transcriptome of aged murine LGs and characterized the B and T cell populations. Age-related changes in the LG include increased differentially expressed genes associated with B and T cell activation, germinal center formation, and infiltration by marginal zone-like B cells. We also identified an age-related increase in B1+ cells and CD19+B220+ cells. B220+CD19+ cells were GL7+ (germinal center-like) and marginal zone-like and progressively increased with age. There was an upregulation of transcripts related to T follicular helper cells, and the number of these cells also increased as mice aged. Compared to a mouse model of Sjögren syndrome, aged LGs have similar transcriptome responses but also unique ones. And lastly, the ectopic lymphoid structures in aged LGs are not exclusive to a specific mouse background as aged diverse outbred mice also have immune infiltration. Altogether, this study identifies a profound change in the immune landscape of aged LGs where B cells become predominant. Further studies are necessary to investigate the specific function of these B cells during the aged LGs.

Prolyl-tRNA synthetase as a novel therapeutic target in multiple myeloma

Multiple myeloma (MM) is a plasma cell malignancy characterised by aberrant production of immunoglobulins requiring survival mechanisms to adapt to proteotoxic stress. We here show that glutamyl-prolyl-tRNA synthetase (GluProRS) inhibition constitutes a novel therapeutic target. Genomic data suggest that GluProRS promotes disease progression and is associated with poor prognosis, while downregulation in MM cells triggers apoptosis. We developed NCP26, a novel ATP-competitive ProRS inhibitor that demonstrates significant anti-tumour activity in multiple in vitro and in vivo systems and overcomes metabolic adaptation observed with other inhibitor chemotypes. We demonstrate a complex phenotypic response involving protein quality control mechanisms that centers around the ribosome as an integrating hub. Using systems approaches, we identified multiple downregulated proline-rich motif-containing proteins as downstream effectors. These include CD138, transcription factors such as MYC, and transcription factor 3 (TCF3), which we establish as a novel determinant in MM pathobiology through functional and genomic validation. Our preclinical data therefore provide evidence that blockade of prolyl-aminoacylation evokes a complex pro-apoptotic response beyond the canonical integrated stress response and establish a framework for its evaluation in a clinical setting.

Identification of Tumor Microenvironment and DNA Methylation-Related Prognostic Signature for Predicting Clinical Outcomes and Therapeutic Responses in Cervical Cancer

Background: Tumor microenvironment (TME) has been reported to have a strong association with tumor progression and therapeutic outcome, and epigenetic modifications such as DNA methylation can affect TMB and play an indispensable role in tumorigenesis. However, the potential mechanisms of TME and DNA methylation remain unclear in cervical cancer (CC).

Methods: The immune and stromal scores of TME were generated by the ESTIMATE algorithm for CC patients in The Cancer Genome Atlas (TCGA) database. The TME and DNA methylation-related genes were identified by the integrative analysis of DNA promoter methylation and gene expression. The least absolute shrinkage and selection operator (LASSO) Cox regression was performed 1,000 times to further identify a nine-gene TME and DNA methylation-related prognostic signature. The signature was further validated in Gene Expression Omnibus (GEO) dataset. Then, the identified signature was integrated with the Federation International of Gynecology and Obstetrics (FIGO) stage to establish a composite prognostic nomogram.

Results: CC patients with high immunity levels have better survival than those with low immunity levels. Both in the training and validation datasets, the risk score of the signature was an independent prognosis factor. The composite nomogram showed higher accuracy of prognosis and greater net benefits than the FIGO stage and the signature. The high-risk group had a significantly higher fraction of genome altered than the low-risk group. Eleven genes were significantly different in mutation frequencies between the high- and low-risk groups. Interestingly, patients with mutant TTN had better overall survival (OS) than those with wild type. Patients in the low-risk group had significantly higher tumor mutational burden (TMB) than those in the high-risk group. Taken together, the results of TMB, immunophenoscore (IPS), and tumor immune dysfunction and exclusion (TIDE) score suggested that patients in the low-risk group may have greater immunotherapy benefits. Finally, four drugs (panobinostat, lenvatinib, everolimus, and temsirolimus) were found to have potential therapeutic implications for patients with a high-risk score.

Conclusions: Our findings highlight that the TME and DNA methylation-related prognostic signature can accurately predict the prognosis of CC and may be important for stratified management of patients and precision targeted therapy.

Mono a Mano: ZBP1’s Love–Hate Relationship with the Kissing Virus

Z-DNA binding protein (ZBP1) very much represents the nuclear option. By initiating inflammatory cell death (ICD), ZBP1 activates host defenses to destroy infectious threats. ZBP1 is also able to induce noninflammatory regulated cell death via apoptosis (RCD). ZBP1 senses the presence of left-handed Z-DNA and Z-RNA (ZNA), including that formed by expression of endogenous retroelements. Viruses such as the Epstein–Barr “kissing virus” inhibit ICD, RCD and other cell death signaling pathways to produce persistent infection. EBV undergoes lytic replication in plasma cells, which maintain detectable levels of basal ZBP1 expression, leading us to suggest a new role for ZBP1 in maintaining EBV latency, one of benefit for both host and virus. We provide an overview of the pathways that are involved in establishing latent infection, including those regulated by MYC and NF-κB. We describe and provide a synthesis of the evidence supporting a role for ZNA in these pathways, highlighting the positive and negative selection of ZNA forming sequences in the EBV genome that underscores the coadaptation of host and virus. Instead of a fight to the death, a state of détente now exists where persistent infection by the virus is tolerated by the host, while disease outcomes such as death, autoimmunity and cancer are minimized. Based on these new insights, we propose actionable therapeutic approaches to unhost EBV.

Identification of Signature Genes in the PD-1 Relative Gastric Cancer Using a Combined Analysis of Gene Expression and Methylation Data

BACKGROUND

The morbidity and mortality rates for gastric cancer (GC) rank second among all cancers, indicating the serious threat it poses to human health, as well as human life. This study aims to identify the pathways and genes as well as investigate the molecular mechanisms of tumor-related genes in gastric cancer (GC).

METHOD

We compared differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in gastric cancer and normal tissue samples using The Cancer Genome Atlas (TCGA) data. The Kyoto Encyclopedia of Gene and Genome (KEGG) and the Gene Ontology (GO) enrichment analysis' pathway annotations were conducted on DMGs and DEGs using a clusterProfiler R package to identify the important functions, as well as the biological processes and pathways involved. The intersection of the two was chosen and defined as differentially methylated and expressed genes (DMEGs). For DMEGs, we used the principal component analysis (PCA) to differentiate gastric cancer from adjacent samples. The linear discriminant analysis method was applied to categorize the samples using DMEGs methylation data and DMEGs expression profiles data and was validated using the leave-one-out cross-validation (LOOCV) method. We plotted the ROC curve for the classification and calculated the AUC (area under the ROC curve) value for a more intuitive view of the classification effect. We also used the NetworkAnalyst 3.0 tool to analyze DMEGs, using DrugBank to acquire information on protein-drug interactions and generate a network map of gene-drug interactions.

RESULTS

We identified a total of 971 DMGs in 188 PD-1 negative and 187 PD-1 positive gastric cancer samples obtained from TCGA. The KEGG and GO enrichment analysis showed the involvement of the regulation of ion transmembrane transport, collagen-containing extracellular matrix, cell-cell junction, and peptidase regulator activity. We simultaneously obtained 1,189 DEGs, out of which 986 were downregulated, while 203 were upregulated in tumors. The enriched analysis of the GO's and KEGG's pathways indicated that the most significant pathways included an intestinal immune network for IgA production, Staphylococcus aureus infection, cytokine-cytokine receptor interaction, and viral protein interaction with cytokine and cytokine receptor, which have previously been linked with gastric cancer. The compound DB01830 can bind well to the active site of the LCK protein and shows good stability, thus making it a potential inhibitor of the LCK protein. To observe the relationship between DMEGs' expression and prognosis, we observed 10 genes, among which were TRIM29, TSPAN8, EOMES, PPP1R16B, SELL, PCED1B, IYD, JPH1, CEACAM5, and RP11-44K6.2. Their high expressions were related to high risks. Besides, those genes were validated in different internal and external validation sets.

CONCLUSION

These results may provide potential molecular biological therapy for PD-1 negative gastric cancer.

Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues

While the chicken (Gallus gallus) is the most consumed agricultural animal worldwide, the chicken transcriptome remains understudied. We have characterized the transcriptome of 10 cell and tissue types from the chicken using RNA-seq, spanning intestinal tissues (ileum, jejunum, proximal cecum), immune cells (B cells, bursa, macrophages, monocytes, spleen T cells, thymus), and reproductive tissue (ovary). We detected 17,872 genes and 24,812 transcripts across all cell and tissue types, representing 73% and 63% of the current gene annotation, respectively. Further quantification of RNA transcript biotypes revealed protein-coding and lncRNAs specific to an individual cell/tissue type. Each cell/tissue type also has an average of around 1.2 isoforms per gene, however, they all have at least one gene with at least 11 isoforms. Differential expression analysis revealed a large number of differentially expressed genes between tissues of the same category (immune and intestinal). Many of these differentially expressed genes in immune cells were involved in cellular processes relating to differentiation and cell metabolism as well as basic functions of immune cells such as cell adhesion and signal transduction. The differential expressed genes of the different segments of the chicken intestine (jejunum, ileum, proximal cecum) correlated to the metabolic processes in nutrient digestion and absorption. These data should provide a valuable resource in understanding the chicken genome.

Characterization of GECPAR, a noncoding RNA that regulates the transcriptional program of diffuse large B-cell lymphoma

Enhancers are regulatory regions of DNA, which play a key role in cell-type specific differentiation and development. Most active enhancers are transcribed into enhancer RNA (eRNA) that can regulate transcription of target genes by means of in cis as well as in trans action. eRNA stabilize contacts between distal genomic regions and mediate the interaction of DNA with master transcription factors. Here, we characterized an enhancer eRNA, GECPAR (germinal center proliferative adapter RNA), which is specifically transcribed in normal and neoplastic germinal center B cells from the super-enhancer of POU2AF1, a key regulatory gene of the germinal center reaction. Using diffuse large B-cell lymphoma cell line models, we demonstrated the tumor suppressor activity of GECPAR, which is mediated via its transcriptional regulation of proliferation and differentiation genes, particularly MYC and the Wnt pathway.

Profiling B cell immunodominance after SARS-CoV-2 infection reveals antibody evolution to non-neutralizing viral targets

Dissecting the evolution of memory B cells (MBCs) against SARS-CoV-2 is critical for understanding antibody recall upon secondary exposure. Here, we used single-cell sequencing to profile SARS-CoV-2-reactive B cells in 38 COVID-19 patients. Using oligo-tagged antigen baits, we isolated B cells specific to the SARS-CoV-2 spike, nucleoprotein (NP), open reading frame 8 (ORF8), and endemic human coronavirus (HCoV) spike proteins. SARS-CoV-2 spike-specific cells were enriched in the memory compartment of acutely infected and convalescent patients several months post symptom onset. With severe acute infection, substantial populations of endemic HCoV-reactive antibody-secreting cells were identified and possessed highly mutated variable genes, signifying preexisting immunity. Finally, MBCs exhibited pronounced maturation to NP and ORF8 over time, especially in older patients. Monoclonal antibodies against these targets were non-neutralizing and non-protective in vivo. These findings reveal antibody adaptation to non-neutralizing intracellular antigens during infection, emphasizing the importance of vaccination for inducing neutralizing spike-specific MBCs.

Identification of the key genes and pathways involved in B cells in primary Sjögren' s syndrome

Primary Sjögren’ s syndrome (pSS) is a relatively common autoimmune disease, which mainly involves the exocrine glands, causing dry eye, dryness of mouth, fatigue and pain in the joints, thus severely affecting the normal lives of patients. B cell populations are considered to play an important role in their pathogenesis and pSS patients are generally characterized by exhibiting biological signs of B cell activation. Moreover, another important characterized change in the peripheral blood of pSS patients is found to be the decreased number of circulating memory B cells. However, the mechanisms underlying the B cell activation and the decreased level of circulating memory B cells in pSS patients are still unclear. Therefore, we identified key genes and pathways involved in B cells in pSS through a combination of several bioinformatic approaches including Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and weighted gene co-expression network analysis (WGCNA) using gene expression data of pSS patients and controls from an open database Gene Expression Omnibus (GEO). The results may provide some novel insights into the pathogenesis of pSS. Moreover, we constructed and validated a diagnostic model for pSS by using the expression patterns of these key genes, which may assist clinicians in diagnosing pSS.

The landscape and driver potential of site-specific hotspots across cancer genomes

Large sets of whole cancer genomes make it possible to study mutation hotspots genome-wide. Here we detect, categorize, and characterize site-specific hotspots using 2279 whole cancer genomes from the Pan-Cancer Analysis of Whole Genomes project and provide a resource of annotated hotspots genome-wide. We investigate the excess of hotspots in both protein-coding and gene regulatory regions and develop measures of positive selection and functional impact for individual hotspots. Using cancer allele fractions, expression aberrations, mutational signatures, and a variety of genomic features, such as potential gain or loss of transcription factor binding sites, we annotate and prioritize all highly mutated hotspots. Genome-wide we find more high-frequency SNV and indel hotspots than expected given mutational background models. Protein-coding regions are generally enriched for SNV hotspots compared to other regions. Gene regulatory hotspots show enrichment of potential same-patient second-hit missense mutations, consistent with enrichment of hotspot driver mutations compared to singletons. For protein-coding regions, splice-sites, promoters, and enhancers, we see an excess of hotspots associated with cancer genes. Interestingly, missense hotspot mutations in tumor suppressors are associated with elevated expression, suggesting localized amino-acid changes with functional impact. For individual non-coding hotspots, only a small number show clear signs of positive selection, including known sites in the TERT promoter and the 5' UTR of TP53. Most of the new candidates have few mutations and limited driver evidence. However, a hotspot in an enhancer of the oncogene POU2AF1, which may create a transcription factor binding site, presents multiple lines of driver-consistent evidence.

CRISPR-based screens uncover determinants of immunotherapy response in multiple myeloma

Cancer cells commonly develop resistance to immunotherapy by loss of antigen expression. Combinatorial treatments that increase levels of the target antigen on the surface of cancer cells have the potential to restore efficacy to immunotherapy. Here, we use our CRISPR interference- and CRISPR activation-based functional genomics platform to systematically identify pathways controlling cell surface expression of the multiple myeloma immunotherapy antigen B-cell maturation antigen (BCMA). We discovered that pharmacologic inhibition of HDAC7 and the Sec61 complex increased cell surface BCMA, including in primary patient cells. Pharmacologic Sec61 inhibition enhanced the antimyeloma efficacy of a BCMA-targeted antibody-drug conjugate. A CRISPR interference chimeric antigen receptor T cells (CAR-T cells) coculture screen enabled us to identify both antigen-dependent and antigen-independent mechanisms controlling response of myeloma cells to BCMA-targeted CAR-T cells. Thus, our study shows the potential of CRISPR screens to uncover mechanisms controlling response of cancer cells to immunotherapy and to suggest potential combination therapies.

NF2 and Canonical Hippo-YAP Pathway Define Distinct Tumor Subsets Characterized by Different Immune Deficiency and Treatment Implications in Human Pleural Mesothelioma

Simple Summary

It is a long-held notion that loss-of-function mutations in negative regulators of the Hippo-YAP pathway, such as NF2, LATS1/2, have a similar potential to promote nuclear YAP activity, which is thought to play an essential role in the pathogenesis of MPM. Whether loss-of-function in these individual regulators uniformly affects the Hippo-YAP activity and contributes to a similar disease phenotype has not yet been revealed in MPM. Surprisingly and interestingly, we found in this study that loss-of-function in the upstream regulator NF2 of the Hippo pathway is linked to the aberrant activation of Hippo-YAP-independent signaling. More importantly, our work showed NF2 loss-of-function and dysregulated Hippo-YAP pathway define distinct MPM subsets that differ in molecular features, therapeutic implications, patients’ prognosis, and in particular, infiltrative immune signatures. Our findings in this study may be instrumental for the precise management of immunotherapy and/or targeted therapy for MPM patients.

Abstract

(1) Inactivation of the tumor suppressor NF2 is believed to play a major role in the pathogenesis of malignant pleural mesothelioma (MPM) by deregulating the Hippo-YAP signaling pathway. However, NF2 has functions beyond regulation of the Hippo pathway, raising the possibility that NF2 contributes to MPM via Hippo-independent mechanisms. (2) We performed weighted gene co-expression analysis (WGCNA) in transcriptomic and proteomic datasets obtained from The Cancer Gene Atlas (TCGA) MPM cohort to identify clusters of co-expressed genes highly correlated with NF2 and phospho (p)-YAP protein, surrogate markers of active Hippo signaling and YAP inactivation. The potential targets are experimentally validated using a cell viability assay. (3) MPM tumors with NF2 loss-of-function are not associated with changes in p-YAP level nor YAP/TAZ activity score, but are characterized by a deficient B-cell receptor (BCR) signaling pathway. Conversely, MPM tumors with YAP activation display exhausted CD8 T-cell-mediated immunity together with significantly upregulated PD-L1, which is validated in an independent MPM cohort, suggesting a potential benefit of immune-checkpoint inhibitors (ICI) in this patient subset. In support of this, mutations in core Hippo signaling components including LATS2, but not NF2, are independently associated with better overall survival in response to ICI in patients. Additionally, based on cancer cell line models, we show that MPM cells with a high Hippo-YAP activity are particularly sensitive to inhibitors of BCR-ABL/SRC, stratifying a unique MPM patient subset that may benefit from BCR-ABL/SRC therapies. Furthermore, we observe that NF2 physically interacts with a considerable number of proteins that are not involved in the canonical Hippo-YAP pathway, providing a possible explanation for its Hippo-independent role in MPM. Finally, survival analyses show that YAP/TAZ scores together with p-YAP protein level, but not NF2, predict the prognosis of MPM patients. (4) NF2 loss-of-function and dysregulated Hippo-YAP pathway define distinct MPM subsets that differ in their molecular features and prognosis, which has important clinical implications for precision oncology in MPM patients.

Cerebrospinal fluid cells immune landscape in multiple sclerosis

Background

Multiple Sclerosis (MS) is a potentially devastating autoimmune neurological disorder, which characteristically induces demyelination of white matter in the brain and spinal cord.

Methods

In this study, three characteristics of the central nervous system (CNS) immune microenvironment occurring during MS onset were explored; immune cell proportion alteration, differential gene expression profile, and related pathways. The raw data of two independent datasets were obtained from the ArrayExpress database; E-MTAB-69, which was used as a derivation cohort, and E-MTAB-2374 which was used as a validation cohort. Differentially expressed genes (DEGs) were identified by the false discovery rate (FDR) value of < 0.05 and |log2 (Fold Change)|> 1, for further analysis. Then, functional enrichment analyses were performed to explore the pathways associated with MS onset. The gene expression profiles were analyzed using CIBERSORT to identify the immune type alterations involved in MS disease.

Results

After verification, the proportion of five types of immune cells (plasma cells, monocytes, macrophage M2, neutrophils and eosinophils) in cerebrospinal fluid (CSF) were revealed to be significantly altered in MS cases compared to the control group. Thus, the complement and coagulation cascades and the systemic lupus erythematosus (SLE) pathways may play critical roles in MS. We identified NLRP3, LILRB2, C1QB, CD86, C1QA, CSF1R, IL1B and TLR2 as eight core genes correlated with MS.

Conclusions

Our study identified the change in the CNS immune microenvironment of MS cases by analysis of the in silico data using CIBERSORT. Our data may assist in providing directions for further research as to the molecular mechanisms of MS and provide future potential therapeutic targets in treatment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02804-7.

Evaluation of Cytotoxicity and α-Glucosidase Inhibitory Activity of Amide and Polyamino-Derivatives of Lupane Triterpenoids

A series of two new and twenty earlier synthesized branched extra-amino-triterpenoids obtained by the direct coupling of betulinic/betulonic acids with polymethylenpolyamines, or by the cyanoethylation of lupane type alcohols, oximes, amines, and amides with the following reduction were evaluated for cytotoxicity toward the NCI-60 cancer cell line panel, α-glucosidase inhibitory, and antimicrobial activities. Lupane carboxamides, conjugates with diaminopropane, triethylenetetramine, and branched C3-cyanoethylated polyamine methyl betulonate showed high cytotoxic activity against most of the tested cancer cell lines with GI50 that ranged from 1.09 to 54.40 µM. Betulonic acid C28-conjugate with triethylenetetramine and C3,C28-bis-aminopropoxy-betulin were found to be potent micromolar inhibitors of yeast α-glucosidase and to simultaneously inhibit the endosomal reticulum α-glucosidase, rendering them as potentially capable to suppress tumor invasiveness and neovascularization, in addition to the direct cytotoxicity. Plausible mechanisms of cytotoxic action and underlying disrupted molecular pathways were elucidated with CellMinner pattern analysis and Gene Ontology enrichment analysis, according to which the lead compounds exert multi-target antiproliferative activity associated with oxidative stress induction and chromatin structure alteration. The betulonic acid diethylentriamine conjugate showed partial activity against methicillin-resistant S. aureus and the fungi C. neoformans. These results show that triterpenic polyamines, being analogs of steroidal squalamine and trodusquemine, are important substances for the search of new drugs with anticancer, antidiabetic, and antimicrobial activities.

Transcriptomic and Proteomic Analysis of Clear Cell Foci (CCF) in the Human Non-Cirrhotic Liver Identifies Several Differentially Expressed Genes and Proteins with Functions in Cancer Cell Biology and Glycogen Metabolism

Clear cell foci (CCF) of the liver are considered to be pre-neoplastic lesions of hepatocellular adenomas and carcinomas. They are hallmarked by glycogen overload and activation of AKT (v-akt murine thymoma viral oncogene homolog)/mTOR (mammalian target of rapamycin)-signaling. Here, we report the transcriptome and proteome of CCF extracted from human liver biopsies by laser capture microdissection. We found 14 genes and 22 proteins differentially expressed in CCF and the majority of these were expressed at lower levels in CCF. Using immunohistochemistry, the reduced expressions of STBD1 (starch-binding domain-containing protein 1), USP28 (ubiquitin-specific peptidase 28), monad/WDR92 (WD repeat domain 92), CYB5B (Cytochrome b5 type B), and HSPE1 (10 kDa heat shock protein, mitochondrial) were validated in CCF in independent specimens. Knockout of Stbd1, the gene coding for Starch-binding domain-containing protein 1, in mice did not have a significant effect on liver glycogen levels, indicating that additional factors are required for glycogen overload in CCF. Usp28 knockout mice did not show changes in glycogen storage in diethylnitrosamine-induced liver carcinoma, demonstrating that CCF are distinct from this type of cancer model, despite the decreased USP28 expression. Moreover, our data indicates that decreased USP28 expression is a novel factor contributing to the pre-neoplastic character of CCF. In summary, our work identifies several novel and unexpected candidates that are differentially expressed in CCF and that have functions in glycogen metabolism and tumorigenesis.

Identification of four genes associated with cutaneous metastatic melanoma

Background

Cutaneous melanoma is an aggressive cancer with increasing incidence and mortality rates worldwide. Metastasis is one of the primary elements that influence the prognosis of patients with cutaneous melanoma. This study aims to clarify the potential mechanism underlying the low survival rate of metastatic melanoma and to search for novel target genes to improve the survival rate of patients with metastatic tumors.

Methods

Gene expression dataset and clinical data were downloaded from The Cancer Genome Atlas portal. Differentially expressed genes (DEGs) were identified, and their functions were studied through gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Survival and multivariate Cox regression analyses were used to screen out candidate genes that could affect the prognosis of patients with metastatic melanoma.

Results

After a series of comprehensive statistical analysis, 464 DEGs were identified between primary tumor tissues and metastatic tissues. Survival and multivariate Cox regression analyses revealed four vital genes, namely, POU2AF1, ITGAL, CXCR2P1, and MZB1, that affect the prognosis of patients with metastatic melanoma.

Conclusion

This study provides a new direction for studying the pathogenesis of metastatic melanoma. The genes related to cutaneous metastatic melanoma that affect the overall survival time of patients were identified.

Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database

Background

Clear cell renal cell carcinoma (ccRCC) is the most common pathological subtype of renal cell carcinoma. Bioinformatics analyses were used to screen candidate genes associated with the prognosis and microenvironment of ccRCC and elucidate the underlying molecular mechanisms of action.

Methods

The gene expression profiles and clinical data of ccRCC patients were downloaded from The Cancer Genome Atlas database. The ESTIMATE algorithm was used to compute the immune and stromal scores of patients. Based on the median immune/stromal scores, all patients were sorted into low‐ and high‐immune/stromal score groups. Differentially expressed genes (DEGs) were extracted from high‐ versus low‐immune/stromal score groups and were described using functional annotations and protein‒protein interaction (PPI) network.

Results

Patients in the high‐immune/stromal score group had poorer survival outcome. In total, 95 DEGs (48 upregulated and 47 downregulated genes) were screened from the gene expression profiles of patients with high immune and stromal scores. The genes were primarily involved in six signaling pathways. Among the 95 DEGs, 43 were markedly related to overall survival of patients. The PPI network identified the top 10 hub genes—CD19, CD79A, IL10, IGLL5, POU2AF1, CCL19, AMBP, CCL18, CCL21, and IGJ—and four modules. Enrichment analyses revealed that the genes in the most important module were involved in the B‐cell receptor signaling pathway.

Conclusion

This study mainly revealed the relationship between the ccRCC microenvironment and prognosis of patients. These results also increase the understanding of how gene expression patterns can impact the prognosis and development of ccRCC by modulating the tumor microenvironment. The results could contribute to the search for ccRCC biomarkers and therapeutic targets.

Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer

Extensive transcriptional alterations are observed in cancer, many of which activate core biological processes established in unicellular organisms or suppress differentiation pathways formed in metazoans. Through rigorous, integrative analysis of genomics data from a range of solid tumors, we show many transcriptional changes in tumors are tied to mutations disrupting regulatory interactions between unicellular and multicellular genes within human gene regulatory networks (GRNs). Recurrent point mutations were enriched in regulator genes linking unicellular and multicellular subnetworks, while copy-number alterations affected downstream target genes in distinctly unicellular and multicellular regions of the GRN. Our results depict drivers of tumourigenesis as genes that created key regulatory links during the evolution of early multicellular life, whose dysfunction creates widespread dysregulation of primitive elements of the GRN. Several genes we identified as important in this process were associated with drug response, demonstrating the potential clinical value of our approach.

Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer

Extensive transcriptional alterations are observed in cancer, many of which activate core biological processes established in unicellular organisms or suppress differentiation pathways formed in metazoans. Through rigorous, integrative analysis of genomics data from a range of solid tumors, we show many transcriptional changes in tumors are tied to mutations disrupting regulatory interactions between unicellular and multicellular genes within human gene regulatory networks (GRNs). Recurrent point mutations were enriched in regulator genes linking unicellular and multicellular subnetworks, while copy-number alterations affected downstream target genes in distinctly unicellular and multicellular regions of the GRN. Our results depict drivers of tumourigenesis as genes that created key regulatory links during the evolution of early multicellular life, whose dysfunction creates widespread dysregulation of primitive elements of the GRN. Several genes we identified as important in this process were associated with drug response, demonstrating the potential clinical value of our approach.

Cancers arise when harmful changes happen in the genetic information of certain cells. These ‘mutations’ are different from person to person, but overall, they disrupt healthy cells in similar ways. In particular, cancer cells tend to lose features that help cells work together in the body. Researchers have suggested that cancers may emerge when cells stop being able to cooperate with each other as part of an organism.

Our bodies still rely on old genes that were present in our earliest, single-cell ancestors. However, we also have newer genes that evolved when the organisms in our lineage started to have more than one cell. A complex network of signals exists to ensure that both sets of genes work together smoothly, and previous studies have suggested that cancers may appear when this delicate balance is disrupted.

To address this question, Trigos et al. have now used a computational approach to analyse different types of tumours from over 9,000 patients. This showed that, in cancer, many mutations disrupt the genes that coordinate old and new genes. These mutations were usually small, punctual changes in the genetic sequence. However, large modifications, such as an entire gene being deleted or repeated, took place more often in the old or the new genes themselves. Therefore, different classes of mutations have specific roles when disrupting how old and new genes work in cancer.

While certain genes highlighted during this analysis were already known to be associated with cancer, others were not – including genes present during the evolution of the earliest animals on Earth. Looking more closely into how these genes can cause disease may help us better understand and fight cancer.

A Jurkat 76 based triple parameter reporter system to evaluate TCR functions and adoptive T cell strategies

Adoptive T cell therapy using TCR transgenic autologous T cells has shown great potential for the treatment of tumor patients. Thorough characterization of genetically reprogrammed T cells is necessary to optimize treatment success. Here, we describe the generation of triple parameter reporter T cells based on the Jurkat 76 T cell line for the evaluation of TCR and chimeric antigen receptor functions as well as adoptive T cell strategies. This Jurkat subline is devoid of endogenous TCR alpha and TCR beta chains, thereby circumventing the problem of TCR miss-pairing and unexpected specificities. The resultant reporter cells allow simultaneous determination of the activity of the transcription factors NF-κB, NFAT and AP-1 that play key roles in T cell activation. Human TCRs directed against tumor and virus antigens were introduced and reporter responses were determined using tumor cell lines endogenously expressing the antigens of interest or via addition of antigenic peptides. Finally, we demonstrate that coexpression of adhesion molecules like CD2 and CD226 as well as CD28 chimeric receptors represents an effective strategy to augment the response of TCR-transgenic reporters to cells presenting cognate antigens.

Whole-exome and transcriptome sequencing of refractory diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. Although rituximab therapy improves clinical outcome, some patients develop resistant DLBCL; however, the genetic alterations in these patients are not well documented. To identify the genetic background of refractory DLBCL, we conducted whole-exome sequencing and transcriptome sequencing for six patients with refractory and seven with responsive DLBCL. The average numbers of pathogenic somatic single nucleotide variants and indels in coding regions were 71 in refractory patients (range 28–120) and 38 (range 19–66) in responsive patients. Missense mutations of TP53 were exclusive in 50% (3/6) of refractory patients and involved the DNA-binding domain of TP53. All missense mutations of TP53 were accompanied by copy number deletions. RAB11FIP5, PRKCB, PRDM15, FNBP4, AHR, CEP128, BRE, DHX16, MYO6, and NMT1 mutations were recurrent in refractory patients. MYD88, B2M, SORCS3, and WDFY3 mutations were more frequent in refractory patients than in responsive patients. REL–BCL11A fusion was found in two refractory patients; one had both fusion and copy number gain. Recurrent copy gains of POU2AF1, SLC1A4, REL11, FANCL, CACNA1D, TRRAP, and CUX1 with significantly increased average expression were found in refractory patients. The expression profile revealed enriched gene sets associated with treatment resistance, including oxidative phosphorylation and ATP-binding cassette transporters. In conclusion, this study integrated both genomic and transcriptomic alterations associated with refractory DLBCL and found several treatment-resistance alterations that may contribute to refractoriness.

Transcriptome analysis of CD34+ cells from myelodysplastic syndrome patients

The myelodysplastic syndrome (MDS) represents a heterogeneous group of clonal hematologic stem cell disorders with the characteristic of ineffective hematopoiesis leading to low blood counts, and a risk of progression to acute myeloid leukemia (AML). To understand specific molecular characteristics of different MDS subtypes with del(5q), we analyzed the gene expression profiles of CD34+ cells from MDS patients of different databases and its enriched pathways. 44 genes, such as MME and RAG1, and eight related pathways were identified to be commonly changed, indicating their conserved roles in MDS development. Additionally, U43604 was identified to be specifically changed in three subtypes with del(5q), including refractory anemia (RA), refractory anemia with ringed sideroblasts (RARS) and refractory anemia with excess blasts (RAEB). C10orf10 and CD79B were specifically changed in RA patients with del(5q), while POU2AF1 were in RARS patients with del(5q). We also analyzed specific pathways of MDS subtypes, such as "Glycosaminoglycan biosynthesis-chondroitin sulfate" which was specific identified in RARS patients. Importantly, those findings can be validated well using another MDS database. Taken together, our analysis identified specific genes and pathways associated with different MDS subtypes with del(5q).

The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies

Plasma cells (PC) represent the heterogeneous final stage of the B cells (BC) differentiation process. To characterize the transition of BC into PC, transcriptomes from human naïve BC were compared to those of three functionally-different subsets of human in vivo-generated PC: i) tonsil PC, mainly consisting of early PC; ii) PC released to the blood after a potent booster-immunization (mostly cycling plasmablasts); and, iii) bone marrow CD138⁺ PC that represent highly mature PC and include the long-lived PC compartment. This transcriptional transition involves subsets of genes related to key processes for PC maturation: the already known protein processing, apoptosis and homeostasis, and of new discovery including histones, macromolecule assembly, zinc-finger transcription factors and neuromodulation. This human PC signature is partially reproduced in vitro and is conserved in mouse. Moreover, the present study identifies genes that define PC subtypes (e.g., proliferation-associated genes for circulating PC and transcriptional-related genes for tonsil and bone marrow PC) and proposes some putative transcriptional regulators of the human PC signatures (e.g., OCT/POU, XBP1/CREB, E2F, among others). Finally, we also identified a restricted imbalance of the present PC transcriptional program in monoclonal gammopathies that correlated with PC malignancy.

Germline variation in the 3'-untranslated region of the POU2AF1 gene is associated with susceptibility to lymphoma

Genetic variations in certain genes may alter the susceptibility to lymphoma. We searched electronic databases and selected candidate single-nucleotide polymorphisms (SNPs) located within 3'-untranslated regions (3'-UTRs) that might affect miRNA-binding ability in the 50 most dysregulated genes in lymphoma for further study. We found that rs1042752-located in the 3'-UTR of POU2AF1, which plays a vital role in lymphomagenesis-was significantly associated with lymphoma risk in a case-control study with 793 patients and 939 controls. Compared with individuals with the rs1042752TT genotype, those with the rs1042752CC genotype had a higher risk of lymphoma (OR = 2.14, 95% CI: 1.55-2.95, P < 0.001), even in stratified analysis for non-Hodgkin lymphoma (OR = 4.58, 95% CI: 2.38-8.81, P < 0.001), B-cell lymphoma (OR = 4.89, 95% CI: 2.46-9.73, P < 0.001), T-cell lymphoma (OR = 4.20, 95% CI: 1.76-10.05, P = 0.001), and Hodgkin lymphoma (OR = 3.62, 95% CI: 1.25-10.46, P = 0.018). Similar results were also observed in a recessive genetic model. Database findings suggested that rs1042752 might affect the interaction of POU2AF1 mRNA with hsa-miR-633. Functional assays confirmed that rs1042752C altered the binding site of hsa-miR-633 and increased POU2AF1 expression in Ramos, HuT 102, and Jurkat E6-1 cell lines. These findings demonstrate for the first time that functional polymorphism in the 3'-UTR of POU2AF1 is associated with susceptibility, and that SNP interaction with hsa-miR-633 affects gene expression and increases the risk of lymphoma.

TCR-based therapy for multiple myeloma and other B-cell malignancies targeting intracellular transcription factor BOB1

Immunotherapy for hematological malignancies or solid tumors by administration of monoclonal antibodies or T cells engineered to express chimeric antigen receptors or T-cell receptors (TCRs) has demonstrated clinical efficacy. However, antigen-loss tumor escape variants and the absence of currently targeted antigens on several malignancies hamper the widespread application of immunotherapy. We have isolated a TCR targeting a peptide of the intracellular B cell-specific transcription factor BOB1 presented in the context of HLA-B*07:02. TCR gene transfer installed BOB1 specificity and reactivity onto recipient T cells. TCR-transduced T cells efficiently lysed primary B-cell leukemia, mantle cell lymphoma, and multiple myeloma in vitro. We also observed recognition and lysis of healthy BOB1-expressing B cells. In addition, strong BOB1-specific proliferation could be demonstrated for TCR-modified T cells upon antigen encounter. Furthermore, clear in vivo antitumor reactivity was observed of BOB1-specific TCR-engineered T cells in a xenograft mouse model of established multiple myeloma. Absence of reactivity toward a broad panel of BOB1^- but HLA-B*07:02⁺ nonhematopoietic and hematopoietic cells indicated no off-target toxicity. Therefore, administration of BOB1-specific TCR-engineered T cells may provide novel cellular treatment options to patients with B-cell malignancies, including multiple myeloma.

Transcriptome Analysis of B Cell Immune Functions in Periodontitis: Mucosal Tissue Responses to the Oral Microbiome in Aging

Evidence has shown activation of T and B cells in gingival tissues in experimental models and in humans diagnosed with periodontitis. The results of this adaptive immune response are noted both locally and systemically with antigenic specificity for an array of oral bacteria, including periodontopathic species, e.g., Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans. It has been recognized through epidemiological studies and clinical observations that the prevalence of periodontitis increases with age. This report describes our studies evaluating gingival tissue transcriptomes in humans and specifically exploiting the use of a non-human primate model of naturally occurring periodontitis to delineate gingival mucosal tissue gene expression profiles focusing on cells/genes critical for the development of humoral adaptive immune responses. Patterns of B cell and plasmacyte genes were altered in aging healthy gingival tissues. Substantial increases in a large number of genes reflecting antigen-dependent activation, B cell activation, B cell proliferation, and B cell differentiation/maturation were observed in periodontitis in adults and aged animals. Finally, evaluation of the relationship of these gene expression patterns with those of various tissue destructive molecules (MMP2, MMP9, CTSK, TNFα, and RANKL) showed a greater frequency of positive correlations in healthy tissues versus periodontitis tissues, with only MMP9 correlations similar between the two tissue types. These results are consistent with B cell response activities in healthy tissues potentially contributing to muting the effects of the tissue destructive biomolecules, whereas with periodontitis this relationship is adversely affected and enabling a progression of tissue destructive events.

Effects of smoking cessation on gene expression in human leukocytes of chronic smoker

OBJECTIVE

The risks of cigarette smoking concerning higher systemic disease mortality are lessened by smoking cessation.

METHODS

Microarray analysis compared the expression profiles of smokers who were successful and not successful at smoking cessation, with the goal of identifying genes that might serve as potential biomarkers or that might be valuable in elucidating distinct biological mechanisms. The mRNAs were isolated and compared from peripheral leukocytes of six smokers who were successful in cessation and six smokers who failed in smoking cessation.

RESULTS

Two hundred ninety nine genes displayed significantly different expression; 196 genes were up-regulated and 103 genes were down-regulated in the success group compared to the failure group. Twenty four of these genes were identified with biological processes including immunity, cytoskeleton and cell growth/cycle. Real-time PCR confirmed the differential gene expression. The mRNA levels of HEPACAM family member 2 (HEPACAM2) and tropomodulin 1 (TMOD1) were significantly more expressed in the success group, while the mRNA ubiquitin specific peptides 18 (USP18) were significantly less expressed in the success group compared to the failure group.

CONCLUSION

The results suggest that smoking cessation can modulate cell adhesion and immune response by regulating expression levels of genes, especially HEPACAM2, TMOD1 and USP18, which have an important relationship with smoking cessation.

Regulatory roles of the tumor necrosis factor receptor BCMA

B cell maturation antigen (BCMA) is a tumor necrosis family receptor (TNFR) member that is predominantly expressed on terminally differentiated B cells and, upon binding to its ligands B cell activator of the TNF family (BAFF) and a proliferation inducing ligand (APRIL), delivers pro-survival cell signals. Thus, BCMA is mostly known for its functional activity in mediating the survival of plasma cells that maintain long-term humoral immunity. The expression of BCMA has also been linked to a number of cancers, autoimmune disorders, and infectious diseases that suggest additional roles for BCMA activity. Despite recent advances in our understanding of the roles for the related TNFR members BAFF-R and transmembrane activator and calcium-modulator and cyclophilin ligand interactor (TACI), the signaling pathway used by BCMA for mediating plasma cell survival as well as its putative function in certain disease states are not well understood. By examining the expression, regulation, and signaling targets of BCMA, we may gain further insight into this receptor and how it operates within cells in both health and disease. This information is important for identifying new therapeutic targets that may be relevant in treating diseases that involve the BAFF/APRIL cytokine network.

The role of master regulators in the metabolic/transcriptional coupling in breast carcinomas

Metabolic transformations have been reported as involved in neoplasms survival. This suggests a role of metabolic pathways as potential cancer pharmacological targets. Modulating tumor's energy production pathways may become a substantial research area for cancer treatment. The significant role of metabolic deregulation as inducing transcriptional instabilities and consequently whole-system failure, is thus of foremost importance. By using a data integration approach that combines experimental evidence for high-throughput genome wide gene expression, a non-equilibrium thermodynamics analysis, nonlinear correlation networks as well as database mining, we were able to outline the role that transcription factors MEF2C and MNDA may have as main master regulators in primary breast cancer phenomenology, as well as the possible interrelationship between malignancy and metabolic dysfunction. The present findings are supported by the analysis of 1191 whole genome gene expression experiments, as well as probabilistic inference of gene regulatory networks, and non-equilibrium thermodynamics of such data. Other evidence sources include pathway enrichment and gene set enrichment analyses, as well as motif comparison with a comprehensive gene regulatory network (of homologue genes) in Arabidopsis thaliana. Our key finding is that the non-equilibrium free energies provide a realistic description of transcription factor activation that when supplemented with gene regulatory networks made us able to find deregulated pathways. These analyses also suggest a novel potential role of transcription factor energetics at the onset of primary tumor development. Results are important in the molecular systems biology of cancer field, since deregulation and coupling mechanisms between metabolic activity and transcriptional regulation can be better understood by taking into account the way that master regulators respond to physicochemical constraints imposed by different phenotypic conditions.

Chromosome 11q23.1 is an unstable region in B-cell tumor cell lines

Chromosome 11q23 region is a frequent target of chromosome aberrations in B-cell lymphoid tumors. Here, we present the cytogenetic and molecular characterization of an amplification affecting 11q23.1 in four cell lines derived from B-cell lymphoid tumors. A minimal common region of amplification of 330 kb was identified in three cell lines using Affymetrix Human Mapping 250K arrays. When analyzed with three BAC clones, the amplifications appeared different at cytogenetic level in each cell line. Possibly affected transcripts were evaluated using tiling arrays, and validated by real time PCR. Since no effect of the amplification at the local transcription level was observed, it is possible that 11q23 amplification might mainly represent the effect of unstable chromosomal region.

High resolution genome-wide analysis of chromosomal alterations in Burkitt's lymphoma

Additional chromosomal abnormalities are currently detected in Burkitt's lymphoma. They play major roles in the progression of BL and in prognosis. The genes involved remain elusive. A whole-genome oligonucleotide array CGH analysis correlated with karyotype and FISH was performed in a set of 27 Burkitt's lymphoma-derived cell lines and primary tumors. More than half of the 145 CNAs<2 Mb were mapped to Mendelian CNVs, including GSTT1, glutathione s-transferase and BIRC6, an anti-apoptotic protein, possibly predisposing to some cancers. Somatic cell line-specific CNVs localized to the IG locus were consistently observed with the 244 K aCGH platform. Among 136 CNAs >2 Mb, gains were found in 1q (12/27), 13q (7/27), 7q (6/27), 8q(4/27), 2p (3/27), 11q (2/27) and 15q (2/27). Losses were found in 3p (5/27), 4p (4/27), 4q (4/27), 9p (4/27), 13q (4/27), 6p (3/27), 17p (3/27), 6q (2/27),11pterp13 (2/27) and 14q12q21.3 (2/27). Twenty one minimal critical regions (MCR), (range 0.04–71.36 Mb), were delineated in tumors and cell lines. Three MCRs were localized to 1q. The proximal one was mapped to 1q21.1q25.2 with a 6.3 Mb amplicon (1q21.1q21.3) harboring BCA2 and PIAS3. In the other 2 MCRs, 1q32.1 and 1q44, MDM4 and AKT3 appeared as possible drivers of these gains respectively. The 13q31.3q32.1 <89.58–96.81> MCR contained an amplicon and ABCC4 might be the driver of this amplicon. The 40 Kb 2p16.1 <60.96–61> MCR was the smallest gained MCR and specifically encompassed the REL oncogene which is already implicated in B cell lymphomas. The most frequently deleted MCR was 3p14.1 <60.43–60.53> that removed the fifth exon of FHIT. Further investigations which combined gene expression and functional studies are essential to understand the lymphomagenesis mechanism and for the development of more effective, targeted therapeutic strategies.

Pleiotropic anti-myeloma activity of ITF2357: inhibition of interleukin-6 receptor signaling and repression of miR-19a and miR-19b

BACKGROUND

The histone deacetylase inhibitor ITF2357 has potent cytotoxic activity in multiple myeloma in vitro and has entered clinical trials for this disease.

DESIGN AND METHODS

In order to gain an overall view of the activity of ITF2357 and identify specific pathways that may be modulated by the drug, we performed gene expression profiling of the KMS18 multiple myeloma cell line treated with the drug. The modulation of several genes and their biological consequence were verified in a panel of multiple myeloma cell lines and cells freshly isolated from patients by using polymerase chain reaction analysis and western blotting.

RESULTS

Out of 38,500 human genes, we identified 140 and 574 up-regulated genes and 102 and 556 down-modulated genes at 2 and 6 h, respectively, with a significant presence of genes related to transcription regulation at 2 h and to cell cycling and apoptosis at 6 h. Several of the identified genes are particularly relevant to the biology of multiple myeloma and it was confirmed that ITF2357 also modulated their encoded proteins in different multiple myeloma cell lines. In particular, ITF2357 down-modulated the interleukin-6 receptor alpha (CD126) transcript and protein in both cell lines and freshly isolated patients' cells, whereas it did not significantly modify interleukin-6 receptor beta (CD130) expression. The decrease in CD126 expression was accompanied by decreased signaling by interleukin-6 receptor, as measured by STAT3 phosphorylation in the presence and absence of inter-leukin-6. Finally, the drug significantly down-modulated the MIRHG1 transcript and its associated microRNA, miR-19a and miR-19b, known to have oncogenic activity in multiple myeloma.

CONCLUSIONS

ITF2357 inhibits several signaling pathways involved in myeloma cell growth and survival.

Chromosome 8q23.3 and 11q23.1 variants modify colorectal cancer risk in Lynch syndrome

BACKGROUND & AIMS

Recent genome-wide association studies have identified common low-risk variants for colorectal cancer (CRC). To assess whether these influence CRC risk in the Lynch syndrome, we genotyped these variants in a large series of proven mutation carriers.

METHODS

We studied 675 individuals from 127 different families from the Dutch Lynch syndrome Registry whose mutation carrier status was known. We genotyped 8q24.21, 8q23.3, 10p14, 11q23.1, 15q13.3, and 18q21.1 variants in carriers of a mismatch repair gene mutation. Univariate and multivariate analysis was used to analyse the association between the presence of a risk variant and CRC risk.

RESULTS

A significant association was found between CRC risk and rs16892766 (8q23.3) and rs3802842 (11q23.1). For rs16892766, possession of the C-allele was associated with an elevated risk of CRC in a dose-dependent fashion, with homozygosity for CC being associated with a 2.16-fold increased risk. For rs3802842, the increased risk of CRC associated with the C-allele was only found among female carriers, while CRC risk was substantially higher among homozygous (hazard ratio [HR] 3.08) than among heterozygous carriers of the C-allele (HR 1.49). In an additive model of both variants, the risk was significantly associated with the number of risk alleles (HR 1.60 for carriers of 2 or more risk alleles). The effects were stronger in female carriers than in male carriers.

CONCLUSION

We have identified 2 loci that are significantly associated with CRC risk in Lynch syndrome families. These modifiers may be helpful in identifying high-risk individuals who require more intensive surveillance.

TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database

Background

As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data.

Methodology

We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%). We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/). User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs) or associated with a set of functional terms.

Conclusions/Significance

As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.