The lymphoid lineage-specific actin-uncapping protein Rltpr is essential for costimulation via CD28 and the development of regulatory T cells.

Although T cell activation can result from signaling via T cell antigen receptor (TCR) alone, physiological T cell responses require costimulation via the coreceptor CD28. Through the use of an N-ethyl-N-nitrosourea-mutagenesis screen, we identified a mutation in Rltpr. We found that Rltpr was a lymphoid cell-specific, actin-uncapping protein essential for costimulation via CD28 and the development of regulatory T cells. Engagement of TCR-CD28 at the immunological synapse resulted in the colocalization of CD28 with both wild-type and mutant Rltpr proteins. However, the connection between CD28 and protein kinase C-θ and Carma1, two key effectors of CD28 costimulation, was abrogated in T cells expressing mutant Rltpr, and CD28 costimulation did not occur in those cells. Our findings provide a more complete model of CD28 costimulation in which Rltpr has a key role.

Vascular Function Recovery Following Saturation Diving.

Background and Objectives: Saturation diving is a technique used in commercial diving. Decompression sickness (DCS) was the main concern of saturation safety, but procedures have evolved over the last 50 years and DCS has become a rare event. New needs have evolved to evaluate the diving and decompression stress to improve the flexibility of the operations (minimum interval between dives, optimal oxygen levels, etc.). We monitored this stress in saturation divers during actual operations. Materials and Methods: The monitoring included the detection of vascular gas emboli (VGE) and the changes in the vascular function measured by flow mediated dilatation (FMD) after final decompression to surface. Monitoring was performed onboard a diving support vessel operating in the North Sea at typical storage depths of 120 and 136 msw. A total of 49 divers signed an informed consent form and participated to the study. Data were collected on divers at surface, before the saturation and during the 9 h following the end of the final decompression. Results: VGE were detected in three divers at very low levels (insignificant), confirming the improvements achieved on saturation decompression procedures. As expected, the FMD showed an impairment of vascular function immediately at the end of the saturation in all divers but the divers fully recovered from these vascular changes in the next 9 following hours, regardless of the initial decompression starting depth. Conclusion: These changes suggest an oxidative/inflammatory dimension to the diving/decompression stress during saturation that will require further monitoring investigations even if the vascular impairement is found to recover fast.

Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B.

The conversion of male germ cell chromatin to a nucleoprotamine structure is fundamental to the life cycle, yet the underlying molecular details remain obscure. Here we show that an essential step is the genome-wide incorporation of TH2B, a histone H2B variant of hitherto unknown function. Using mouse models in which TH2B is depleted or C-terminally modified, we show that TH2B directs the final transformation of dissociating nucleosomes into protamine-packed structures. Depletion of TH2B induces compensatory mechanisms that permit histone removal by up-regulating H2B and programming nucleosome instability through targeted histone modifications, including lysine crotonylation and arginine methylation. Furthermore, after fertilization, TH2B reassembles onto the male genome during protamine-to-histone exchange. Thus, TH2B is a unique histone variant that plays a key role in the histone-to-protamine packing of the male genome and guides genome-wide chromatin transitions that both precede and follow transmission of the male genome to the egg.

ERBB2b mRNA isoform encodes a nuclear variant of the ERBB2 oncogene in breast cancer.

The presence of nuclear ERBB2 receptor-type tyrosine kinase is one of the causes of the resistance to membrane ERBB2-targeted therapy in breast cancers. It has been previously reported that this nuclear location arises through at least two different mechanisms: proteolytic shedding of the extracellular domain of the full-length receptor and translation of the messenger RNA (mRNA)-encoding ERBB2 from internal initiation codons. Here, we report a new mechanism and function where a significant portion of nuclear ERBB2 results from the translation of the variant ERBB2 mRNA under the transcriptional control of a distal promoter that is actively used in breast cancer cells. We show that both membrane ERBB2a and nuclear ERBB2b isoforms are prevalently expressed in breast cancer cell lines and carcinoma samples. The ERBB2b isoform, which is translated from mRNA variant 2, can directly translocate into the nucleus due to the lack of the signal peptide which is required for an intermediate membrane location. Small interfering RNA-mediated gene silencing showed that ERBB2b can repress ERBB2a expression, encoded by variant 1, whereas ERBB2a activates ERBB2b. Nuclear ERBB2 binding to its own promoter was revealed by chromatin immunoprecipitation assay. Altogether, our results provide new insights into the origin and function of nuclear ERBB2 where it can participate at the same time in a positive or a negative feedback autoregulatory loop, dependent on which of its promoters this bona fide transcription factor is acting. They also provide a new understanding for the resistance to therapies targeting the membrane-anchored ERBB2 in breast cancer.

Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation.

Ets1 is a sequence-specific transcription factor that plays an important role during hematopoiesis, and is essential for the transition of CD4(-)/CD8(-) double negative (DN) to CD4(+)/CD8(+) double positive (DP) thymocytes. Using genome-wide and functional approaches, we investigated the binding properties, transcriptional role and chromatin environment of Ets1 during this transition. We found that while Ets1 binding at distal sites was associated with active genes at both DN and DP stages, its enhancer activity was attained at the DP stage, as reflected by levels of the core transcriptional hallmarks H3K4me1/3, RNA Polymerase II and eRNA. This dual, stage-specific ability reflected a switch from non-T hematopoietic toward T-cell specific gene expression programs during the DN-to-DP transition, as indicated by transcriptome analyses of Ets1(-/-) thymic cells. Coincidentally, Ets1 associates more specifically with Runx1 in DN and with TCF1 in DP cells. We also provide evidence that Ets1 predominantly binds distal nucleosome-occupied regions in DN and nucleosome-depleted regions in DP. Finally and importantly, we demonstrate that Ets1 induces chromatin remodeling by displacing H3K4me1-marked nucleosomes. Our results thus provide an original model whereby the ability of a transcription factor to bind nucleosomal DNA changes during differentiation with consequences on its cognate enhancer activity.

A Positive Feed-forward Loop Associating EGR1 and PDGFA Promotes Proliferation and Self-renewal in Glioblastoma Stem Cells.

Glioblastomas are the most common primary brain tumors, highly vascularized, infiltrating, and resistant to current therapies. This cancer leads to a fatal outcome in less than 18 months. The aggressive behavior of glioblastomas, including resistance to current treatments and tumor recurrence, has been attributed to glioma stemlike/progenitor cells. The transcription factor EGR1 (early growth response 1), a member of a zinc finger transcription factor family, has been described as tumor suppressor in gliomas when ectopically overexpressed. Although EGR1 expression in human glioblastomas has been associated with patient survival, its precise location in tumor territories as well as its contribution to glioblastoma progression remain elusive. In the present study, we show that EGR1-expressing cells are more frequent in high grade gliomas where the nuclear expression of EGR1 is restricted to proliferating/progenitor cells. We show in primary cultures of glioma stemlike cells that EGR1 contributes to stemness marker expression and proliferation by orchestrating a PDGFA-dependent growth-stimulatory loop. In addition, we demonstrate that EGR1 acts as a positive regulator of several important genes, including SHH, GLI1, GLI2, and PDGFA, previously linked to the maintenance and proliferation of glioma stemlike cells.

ELOVL5 mutations cause spinocerebellar ataxia 38.

Spinocerebellar ataxias (SCAs) are a heterogeneous group of autosomal-dominant neurodegenerative disorders involving the cerebellum and 23 different genes. We mapped SCA38 to a 56 Mb region on chromosome 6p in a SCA-affected Italian family by whole-genome linkage analysis. Targeted resequencing identified a single missense mutation (c.689G>T [p.Gly230Val]) in ELOVL5. Mutation screening of 456 independent SCA-affected individuals identified the same mutation in two further unrelated Italian families. Haplotyping showed that at least two of the three families shared a common ancestor. One further missense variant (c.214C>G [p.Leu72Val]) was found in a French family. Both missense changes affect conserved amino acids, are predicted to be damaging by multiple bioinformatics tools, and were not identified in ethnically matched controls or within variant databases. ELOVL5 encodes an elongase involved in the synthesis of polyunsaturated fatty acids of the ω3 and ω6 series. Arachidonic acid and docosahexaenoic acid, two final products of the enzyme, were reduced in the serum of affected individuals. Immunohistochemistry on control mice and human brain demonstrated high levels in Purkinje cells. In transfection experiments, subcellular localization of altered ELOVL5 showed a perinuclear distribution with a signal increase in the Golgi compartment, whereas the wild-type showed a widespread signal in the endoplasmic reticulum. SCA38 and SCA34 are examples of SCAs due to mutations in elongase-encoding genes, emphasizing the importance of fatty-acid metabolism in neurological diseases.

Transcription-dependent generation of a specialized chromatin structure at the TCRß locus.

V(D)J recombination assembles Ag receptor genes during lymphocyte development. Enhancers at AR loci are known to control V(D)J recombination at associated alleles, in part by increasing chromatin accessibility of the locus, to allow the recombination machinery to gain access to its chromosomal substrates. However, whether there is a specific mechanism to induce chromatin accessibility at AR loci is still unclear. In this article, we highlight a specialized epigenetic marking characterized by high and extended H3K4me3 levels throughout the Dß-Jß-Cß gene segments. We show that extended H3K4 trimethylation at the Tcrb locus depends on RNA polymerase II (Pol II)-mediated transcription. Furthermore, we found that the genomic regions encompassing the two DJCß clusters are highly enriched for Ser(5)-phosphorylated Pol II and short-RNA transcripts, two hallmarks of transcription initiation and early transcription. Of interest, these features are shared with few other tissue-specific genes. We propose that the entire DJCß regions behave as transcription "initiation" platforms, therefore linking a specialized mechanism of Pol II transcription with extended H3K4 trimethylation and highly accessible Dß and Jß gene segments.

Bromodomain-dependent stage-specific male genome programming by Brdt.

Male germ cell differentiation is a highly regulated multistep process initiated by the commitment of progenitor cells into meiosis and characterized by major chromatin reorganizations in haploid spermatids. We report here that a single member of the double bromodomain BET factors, Brdt, is a master regulator of both meiotic divisions and post-meiotic genome repackaging. Upon its activation at the onset of meiosis, Brdt drives and determines the developmental timing of a testis-specific gene expression program. In meiotic and post-meiotic cells, Brdt initiates a genuine histone acetylation-guided programming of the genome by activating essential genes and repressing a 'progenitor cells' gene expression program. At post-meiotic stages, a global chromatin hyperacetylation gives the signal for Brdt's first bromodomain to direct the genome-wide replacement of histones by transition proteins. Brdt is therefore a unique and essential regulator of male germ cell differentiation, which, by using various domains in a developmentally controlled manner, first drives a specific spermatogenic gene expression program, and later controls the tight packaging of the male genome.

H3K4 tri-methylation provides an epigenetic signature of active enhancers.

Combinations of post-translational histone modifications shape the chromatin landscape during cell development in eukaryotes. However, little is known about the modifications exactly delineating functionally engaged regulatory elements. For example, although histone H3 lysine 4 mono-methylation (H3K4me1) indicates the presence of transcriptional gene enhancers, it does not provide clearcut information about their actual position and stage-specific activity. Histone marks were, therefore, studied here at genomic loci differentially expressed in early stages of T-lymphocyte development. The concomitant presence of the three H3K4 methylation states (H3K4me1/2/3) was found to clearly reflect the activity of bona fide T-cell gene enhancers. Globally, gain or loss of H3K4me2/3 at distal genomic regions correlated with, respectively, the induction or the repression of associated genes during T-cell development. In the Tcrb gene enhancer, the H3K4me3-to-H3K4me1 ratio decreases with the enhancer's strength. Lastly, enhancer association of RNA-polymerase II (Pol II) correlated with the presence of H3K4me3 and Pol II accumulation resulted in local increase of H3K4me3. Our results suggest the existence of functional links between Pol II occupancy, H3K4me3 enrichment and enhancer activity.

Histone acetyltransferase cofactor Trrap maintains self-renewal and restricts differentiation of embryonic stem cells.

Chromatin states are believed to play a key role in distinct patterns of gene expression essential for self-renewal and pluripotency of embryonic stem cells (ESCs); however, the genes governing the establishment and propagation of the chromatin signature characteristic of pluripotent cells are poorly understood. Here, we show that conditional deletion of the histone acetyltransferase cofactor Trrap in mouse ESCs triggers unscheduled differentiation associated with loss of histone acetylation, condensation of chromatin into distinct foci (heterochromatization), and uncoupling of H3K4 dimethylation and H3K27 trimethylation. Trrap loss results in downregulation of stemness master genes Nanog, Oct4, and Sox2 and marked upregulation of specific differentiation markers from the three germ layers. Chromatin immunoprecipitation-sequencing analysis of genome-wide binding revealed a significant overlap between Oct4 and Trrap binding in ESCs but not in differentiated mouse embryonic fibroblasts, further supporting a functional interaction between Trrap and Oct4 in the maintenance of stemness. Remarkably, failure to downregulate Trrap prevents differentiation of ESCs, suggesting that downregulation of Trrap may be a critical step guiding transcriptional reprogramming and differentiation of ESCs. These findings establish Trrap as a critical part of the mechanism that restricts differentiation and promotes the maintenance of key features of ESCs.

Attentional costs and failures in air traffic control notifications.

Large display screens are common in supervisory tasks, meaning that alerts are often perceived in peripheral vision. Five air traffic control notification designs were evaluated in their ability to capture attention during an ongoing supervisory task, as well as their impact on the primary task. A range of performance measures, eye-tracking and subjective reports showed that colour, even animated, was less effective than movement, and notifications sometimes went unnoticed. Designs that drew attention to the notified aircraft by a pulsating box, concentric circles or the opacity of the background resulted in faster perception and no missed notifications. However, the latter two designs were intrusive and impaired primary task performance, while the simpler animated box captured attention without an overhead cognitive cost. These results highlight the need for a holistic approach to evaluation, achieving a balance between the benefits for one aspect of performance against the potential costs for another. Practitioner summary: We performed a holistic examination of air traffic control notification designs regarding their ability to capture attention during an ongoing supervisory task. The combination of performance, eye-tracking and subjective measurements demonstrated that the best design achieved a balance between attentional power and the overhead cognitive cost to primary task performance.

Review of saturation decompression procedures used in commercial diving.

Introduction: This is a review of commercial heliox saturation decompression procedures. The scope does not include compression, storage depth or bell excursion dive procedures. The objectives are to: identify the sources of the procedures; trace their evolution; describe the current practice; and detect relevant trends. Methods: Eleven international commercial diving companies provided their diving manuals for review under a confidentiality agreement. Results: Modern commercial diving saturation procedures are derived from a small number of original procedures (United States Navy, Comex, and NORSOK). In the absence of relevant scientific studies since the late 80's, the companies have empirically adapted these procedures according to their needs and experience. Such adaptation has caused differences in decompression rates shallower than 60 msw, decompression rest stops and the decision to decompress linearly or stepwise. Nevertheless, the decompression procedures present a remarkable homogeneity in chamber PO2 and daily decompression rates when deeper than 60 msw. The companies have also developed common rules of good practice; no final decompression should start with an initial ascending excursion; a minimum hold is required before starting a final decompression after an excursion dive. Recommendation is made for the divers to exercise during decompression. Conclusions: We observed a trend towards harmonisation within the companies that enforce international procedures, and, between companies through cooperation inside the committees of the industry associations.

Evaluation of North Sea saturation procedures through divers monitoring.

BACKGROUND: Saturation diving is a standard method of intervention for commercial diving during offshore operations. Current saturation procedures achieve a high level of safety with regards to decompression sickness but still put the divers under multiple stressors: 1) Environmental stress (long confinement, heat/cold, dense gases, high oxygen levels), 2) Work stress (muscular fatigue, psychological pressure, breathing equipment, etc.), 3) venous gas emboli associated with decompression, 4) Inflammation related to oxidative stress and microparticles. We present the results of a saturation divers monitoring campaign performed in the North Sea Danish sector, on the Tyra field, during 2022. The study was supported by TotalEnergies, the field operator, and performed by Boskalis Subsea Services, the diving contractor, onboard the diving support vessel Boka Atlantis. The objective was twofold: document the level of diving stress during saturation operations in the Danish sector, and compare the performances of two saturation procedures, the Boskalis and the NORSOK procedures. MATERIALS AND METHODS: Fourteen divers volunteered for the study. The monitoring package include weight and temperature measurements, psychomotor tests (objective evaluation) and questionnaires (subjective evaluation), Doppler bubble detection and bioimpedance. The results were presented in a radar diagram that provides a general view of the situation. RESULTS: The data were analysed along 3 dimensions: work and environmental, desaturation bubbles, oxidative stress and inflammation. The results showed little or no variations from the reference values. No bubbles were detected after excursion dives and the final decompression, except for two divers with a grade 1 after arriving at surface. No statistical difference could be found between the Boskalis and the NORSOK saturation procedures. CONCLUSIONS: At a depth of 40-50 msw corresponding to the Danish sector, the two saturation procedures monitored induce no or little stress to the divers. The divers know how to manage their diet, equilibrate their hydration and pace their effort. Data available on divers' post saturation period show a recovery over the 24-48 hours following the end of the decompression. Further research should focus on diving deeper than 100 msw where a greater stress can be anticipated.

Divergent transcription is associated with promoters of transcriptional regulators.

BACKGROUND: Divergent transcription is a wide-spread phenomenon in mammals. For instance, short bidirectional transcripts are a hallmark of active promoters, while longer transcripts can be detected antisense from active genes in conditions where the RNA degradation machinery is inhibited. Moreover, many described long non-coding RNAs (lncRNAs) are transcribed antisense from coding gene promoters. However, the general significance of divergent lncRNA/mRNA gene pair transcription is still poorly understood. Here, we used strand-specific RNA-seq with high sequencing depth to thoroughly identify antisense transcripts from coding gene promoters in primary mouse tissues. RESULTS: We found that a substantial fraction of coding-gene promoters sustain divergent transcription of long non-coding RNA (lncRNA)/mRNA gene pairs. Strikingly, upstream antisense transcription is significantly associated with genes related to transcriptional regulation and development. Their promoters share several characteristics with those of transcriptional developmental genes, including very large CpG islands, high degree of conservation and epigenetic regulation in ES cells. In-depth analysis revealed a unique GC skew profile at these promoter regions, while the associated coding genes were found to have large first exons, two genomic features that might enforce bidirectional transcription. Finally, genes associated with antisense transcription harbor specific H3K79me2 epigenetic marking and RNA polymerase II enrichment profiles linked to an intensified rate of early transcriptional elongation. CONCLUSIONS: We concluded that promoters of a class of transcription regulators are characterized by a specialized transcriptional control mechanism, which is directly coupled to relaxed bidirectional transcription.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

BACKGROUND: Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. RESULTS: We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information and is a productive avenue in generating new hypotheses. The second objective of InteractomeBrowser is to fill the gap between interaction databases and dynamic modeling. It is thus compatible with the network analysis software Cytoscape and with the Gene Interaction Network simulation software (GINsim). We provide examples underlying the benefits of this visualization tool for large gene set analysis related to thymocyte differentiation. CONCLUSIONS: The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at: http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis.

A review of accelerated decompression from heliox saturation in commercial diving emergencies.

INTRODUCTION: Saturation diving is a specialised method of intervention in offshore commercial diving. Emergencies may require the crew to be evacuated from the diving support vessel. Because saturation divers generally need several days to reach surface, the emergency evacuation of divers is based on dedicated hyperbaric rescue systems. There are still potential situations for which these systems cannot be used or deployed, and where an emergency decompression provides an alternative solution. METHODS: Our objective was to describe historical cases and assess the benefit of emergency decompressions, with the collection of data from the authors' direct experience and networks, providing witness or first-hand information. RESULTS: We documented three cases of emergency decompression following bell evacuations, and six cases of accelerated decompression performed in the chamber or hyperbaric rescue chamber. Review of these cases showed: 1) the complicated nature of such emergencies that make decisions difficult; 2) the variety of solutions implemented; and 3) the surprisingly safe and successful outcomes of several operations. Analysis of the accelerated decompression occurrences allowed derivation of the options used; upward initial excursion, increased chamber partial pressure of oxygen associated to increased ascent rates, and inert gas switching. We identified four published procedures for accelerated decompression. CONCLUSIONS: Despite modern hyperbaric rescue systems, accelerated decompression remains an essential tool in case of emergency. The diving industry needs clear guidance on what can be achieved, depending on the saturation depth and the level of emergency.

Hydration status during commercial saturation diving measured by bioimpedance and urine specific gravity.

Excessive fluid loss triggered by hyperbaric pressure, water immersion and hot water suits causes saturation divers to be at risk of dehydration. Dehydration is associated with reductions in mental and physical performance, resulting in less effective work and an increased risk of work-related accidents. In this study we examined the hydration status of 11 male divers over 19 days of a commercial saturation diving campaign to a working depth of 74 m, using two non-invasive methods: Bioelectrical impedance analysis (BIA) and urine specific gravity (USG). Measurements were made daily before and after bell runs, and the BIA data was used to calculated total body water (TBW). We found that BIA and USG were weakly negatively correlated, probably reflecting differences in what they measure. TBW was significantly increased after bell runs for all divers, but more so for bellmen than for in-water divers. There were no progressing changes in TBW over the 19-day study period, indicating that the divers' routines were sufficient for maintaining their hydration levels on short and long term.

[Production of knowledge using data collected by associations of patients: The fibromyalgia example]. / Production de savoirs à partir de données collectées par les associations de malades - L'exemple de la fibromyalgie.

To respond to the social challenge of medical knowledge democratisation, numerous initiatives have been developed: information, training or consultation of patients or research applications funded by associations of patients. Only a few numbers of collaborations are initiated by the persons directly involved (patients and relatives) or fulfill association research need. We have adopted and tested such an approach with the French fibromyalgia association (Fibromyalgie France). Our work demonstrates the interest to use data collected by associations of patients to answer to their questioning or to rise further relevant research questions. Such participative approach will have a pertinent and significant impact on the knowledge of diseases and on the development of collaborative actions of research, providing a better answer to patient needs, while being methodologically rigorous.

TITLE: Production de savoirs à partir de données collectées par les associations de malades - L'exemple de la fibromyalgie. ABSTRACT: Pour répondre au défi sociétal de démocratisation de l'accès à la connaissance, différentes initiatives de recherches participatives se développent : actions d'information, de formation ou de consultation des citoyens ou par l'intermédiaire de demandes de financement par des chercheurs auprès des associations. Cependant, peu des collaborations chercheurs-malades sont à l'initiative des personnes concernées, les patients et leurs familles. Nous avons adopté et testé cette démarche à la demande et en coopération avec l'association Fibromyalgie France.

Peripheral T-cell lymphoma gene expression profiling and potential therapeutic exploitations.

Peripheral T-cell lymphomas constitute a heterogeneous group with regard to diagnosis, treatment and prognosis. Efforts have been made to combine novel techniques with cytology and immunochemistry in order to more precisely define these entities. Molecular profiling has contributed to novel insights in the biology of T-cell lymphoma. Regarding anaplastic large cell lymphoma, low expression T-cell receptor signalling and high STAT3 target signatures have been associated with the ALK-positive subgroup. Gene expression profiling differentiates angioblastic T-cell lymphoma from other T-cell malignancies, suggests that the normal counterpart of lymphoma cells are follicular helper T cells, and supports the involvement of vascular endothelial growth factor deregulation in its physiopathology. In peripheral T-cell lymphoma unspecified, gene profiling suggests the normal counterpart of tumour cells are activated CD4(+) or CD8(+) T-lymphocytes, delineates prognostic groups depending on the proliferative signature, and suggests therapeutic options aimed at regulating nuclear factor-kappaB and platelet-derived growth factor receptor-alpha phosphorylation. Gene expression profiling of primary cutaneous T cell lymphomas highlighted the importance of abnormal methylation patterns, suggested a pivotal role for JUNB/AP-1, and defined a predictive model for response to interferon-alpha. In conclusion, gene expression profiling is beginning to change the pathological classification, the prognosis profiles and the therapeutic approach in T-cell lymphomas.