Predicting inhibitor development using a random peptide phage-display library approach in the SIPPET Cohort

Inhibitor development is the most severe complication of hemophilia A care, and is associated with increased morbidity and mortality. The aim of this study was to use a novel IgG epitope mapping method to explore the factor VIII (FVIII)-specific epitope profile in the SIPPET cohort population and to develop an epitope-mapping based inhibitor prediction model. The population consisted of 122 previously untreated patients with severe hemophilia A that were followed-up for 50 days of exposure to FVIII or 3 years, whichever occurred first. Sampling was performed before FVIII treatment and at the end of the follow-up. The outcome was inhibitor development. The FVIII epitope repertoire was assessed by means of a novel random peptide phage-display assay. A LASSO regression model and a random forest model were fitted on post-treatment sample data and validated in pre-treatment sample data. The predictive performance of these models was assessed by the C-statistic and a calibration plot. We identified 27,775 peptides putatively directed against FVIII, which were used as input for the statistical models. The C-statistic of the LASSO and random forest models were good at 0.78 (95%CI: 0.69-0.86) and 0.80 (95%CI: 0.72-0.89). Model calibration of both models was moderately good. Two statistical models, developed on data from a novel random peptide phage display assay, were used to predict inhibitor development before exposure to exogenous FVIII. These models can be used to set up diagnostic tests that predict the risk of inhibitor development before starting treatment with FVIII.

High inter-follicular spatial co-localization of CD8+FOXP3+ with CD4+CD8+ cells predicts favorable outcome in follicular lymphoma

The spatial architecture of the lymphoid tissue in follicular lymphoma (FL) presents unique challenges to studying its immune microenvironment. We investigated the spatial interplay of T cells, macrophages, myeloid cells and natural killer T cells using multispectral immunofluorescence images of diagnostic biopsies of 32 patients. A deep learning-based image analysis pipeline was tailored to the needs of follicular lymphoma spatial histology research, enabling the identification of different immune cells within and outside neoplastic follicles. We analyzed the density and spatial co-localization of immune cells in the inter-follicular and intra-follicular regions of follicular lymphoma. Low inter-follicular density of CD8+FOXP3+ cells and co-localization of CD8+FOXP3+ with CD4+CD8+ cells were significantly associated with relapse (p = 0.0057 and p = 0.0019, respectively) and shorter time to progression after first-line treatment (Logrank p = 0.0097 and log-rank p = 0.0093, respectively). A low inter-follicular density of CD8+FOXP3+ cells is associated with increased risk of relapse independent of follicular lymphoma international prognostic index (FLIPI) (p = 0.038, Hazard ratio (HR) = 0.42 [0.19, 0.95], but not independent of co-localization of CD8+FOXP3+ with CD4+CD8+ cells (p = 0.43). Co-localization of CD8+FOXP3+ with CD4+CD8+ cells is predictors of time to relapse independent of the FLIPI score and density of CD8+FOXP3+ cells (p = 0.027, HR = 0.0019 [7.19 × 10-6 , 0.49], This suggests a potential role of inter-follicular CD8+FOXP3+ and CD4+CD8+ cells in the disease progression of FL, warranting further validation on larger patient cohorts.

Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology

Interferons (IFNs) are key cytokines involved in alerting the immune system to viral infection. After IFN stimulation, cellular transcriptional profile critically changes, leading to the expression of several IFN stimulated genes (ISGs) that exert a wide variety of antiviral activities. Despite many ISGs have been already identified, a comprehensive network of coding and non-coding genes with a central role in IFN-response still needs to be elucidated. We performed a global RNA-Seq transcriptome profile of the HCV permissive human hepatoma cell line Huh7.5 and its parental cell line Huh7, upon IFN treatment, to define a network of genes whose coordinated modulation plays a central role in IFN-response. Our study adds molecular actors, coding and non-coding genes, to the complex molecular network underlying IFN-response and shows how systems biology approaches, such as correlation networks, network's topology and gene ontology analyses can be leveraged to this aim.

ADAM10 hyperactivation acts on piccolo to deplete synaptic vesicle stores in Huntington's disease

Synaptic dysfunction and cognitive decline in Huntington's disease (HD) involve hyperactive A disintegrin and metalloproteinase domain-containing protein 10 (ADAM10). To identify the molecular mechanisms through which ADAM10 is associated with synaptic dysfunction in HD, we performed an immunoaffinity purification-mass spectrometry (IP-MS) study of endogenous ADAM10 in the brains of wild-type and HD mice. We found that proteins implicated in synapse organization, synaptic plasticity, and vesicle and organelles trafficking interact with ADAM10, suggesting that it may act as hub protein at the excitatory synapse. Importantly, the ADAM10 interactome is enriched in presynaptic proteins and ADAM10 co-immunoprecipitates with piccolo (PCLO), a key player in the recycling and maintenance of synaptic vesicles. In contrast, reduced ADAM10/PCLO immunoprecipitation occurs in the HD brain, with decreased density of synaptic vesicles in the reserve and docked pools at the HD presynaptic terminal. Conditional heterozygous deletion of ADAM10 in the forebrain of HD mice reduces active ADAM10 to wild-type level and normalizes ADAM10/PCLO complex formation and synaptic vesicle density and distribution. The results indicate that presynaptic ADAM10 and PCLO are a relevant component of HD pathogenesis.

RUES2 hESCs exhibit MGE-biased neuronal differentiation and muHTT-dependent defective specification hinting at SP1

RUES2 cell lines represent the first collection of isogenic human embryonic stem cells (hESCs) carrying different pathological CAG lengths in the HTT gene. However, their neuronal differentiation potential has yet to be thoroughly evaluated. Here, we report that RUES2 during ventral telencephalic differentiation is biased towards medial ganglionic eminence (MGE). We also show that HD-RUES2 cells exhibit an altered MGE transcriptional signature in addition to recapitulating known HD phenotypes, with reduced expression of the neurodevelopmental regulators NEUROD1 and BDNF and increased cleavage of synaptically enriched N-cadherin. Finally, we identified the transcription factor SP1 as a common potential detrimental co-partner of muHTT by de novo motif discovery analysis on the LGE, MGE, and cortical genes differentially expressed in HD human pluripotent stem cells in our and additional datasets. Taken together, these observations suggest a broad deleterious effect of muHTT in the early phases of neuronal development that may unfold through its altered interaction with SP1.

FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy

Multiple myeloma is a plasma cell neoplasm characterized by the production of unfolded immunoglobulins, which cause endoplasmic reticulum (ER) stress and sensitivity to proteasome inhibition. The genomic landscape of multiple myeloma is characterized by the loss of several genes rarely mutated in other cancers that may underline specific weaknesses of multiple myeloma cells. One of these is FAM46C that is lost in more than 10% of patients with multiple myeloma. We show here that FAM46C is part of a new complex containing the ER-associated protein FNDC3A, which regulates trafficking and secretion and, by impairing autophagy, exacerbates proteostatic stress. Reconstitution of FAM46C in multiple myeloma cells that had lost it induced apoptosis and ER stress. Apoptosis was preceded by an increase of intracellular aggregates, which was not linked to increased translation of IgG mRNA, but rather to impairment of autophagy. Biochemical analysis showed that FAM46C requires interaction with ER bound protein FNDC3A to reside in the cytoplasmic side of the ER. FNDC3A was lost in some multiple myeloma cell lines. Importantly, depletion of FNDC3A increased the fitness of FAM46C-expressing cells and expression of FNDC3A in cells that had lost it recapitulated the effects of FAM46C, inducing aggregates and apoptosis. FAM46C and FNDC3A formed a complex that modulates secretion routes, increasing lysosome exocytosis. The cellular landscape generated by FAM46C/FNDC3A expression predicted sensitivity to sphingosine kinase inhibition. These results suggest that multiple myeloma cells remodel their trafficking machinery to cope with ER stress. SIGNIFICANCE: This study identifies a new multiple myeloma-specific tumor suppressor complex that regulates autophagy and unconventional secretion, highlighting the sensitivity of multiple myeloma cells to the accumulation of protein aggregates.

FOXP1 circular RNA sustains mesenchymal stem cell identity via microRNA inhibition

Stem cell identity and plasticity are controlled by master regulatory genes and complex circuits also involving non-coding RNAs. Circular RNAs (circRNAs) are a class of RNAs generated from protein-coding genes by backsplicing, resulting in stable RNA structures devoid of free 5’ and 3’ ends. Little is known of the mechanisms of action of circRNAs, let alone in stem cell biology. In this study, for the first time, we determined that a circRNA controls mesenchymal stem cell (MSC) identity and differentiation. High-throughput MSC expression profiling from different tissues revealed a large number of expressed circRNAs. Among those, circFOXP1 was enriched in MSCs compared to differentiated mesodermal derivatives. Silencing of circFOXP1 dramatically impaired MSC differentiation in culture and in vivo. Furthermore, we demonstrated a direct interaction between circFOXP1 and miR-17–3p/miR-127–5p, which results in the modulation of non-canonical Wnt and EGFR pathways. Finally, we addressed the interplay between canonical and non-canonical Wnt pathways. Reprogramming to pluripotency of MSCs reduced circFOXP1 and non-canonical Wnt, whereas canonical Wnt was boosted. The opposing effect was observed during generation of MSCs from human pluripotent stem cells. Our results provide unprecedented evidence for a regulatory role for circFOXP1 as a gatekeeper of pivotal stem cell molecular networks.

P2X7 receptor restrains pathogenic Tfh cell generation in systemic lupus erythematosus

T follicular helper cells promote the generation of protective antibodies, but can also foster pathogenic antibodies. The ATP-gated P2X7 receptor selectively limits the expansion of Tfh cells that amplify self-reactive antibodies in systemic lupus erythematosus.

Altered control of T follicular helper (Tfh) cells can lead to generation of autoantibodies and autoimmune manifestations. Signaling pathways that selectively limit pathogenic responses without affecting the protective function of Tfh cells are unknown. Here we show that the ATP-gated ionotropic P2X7 receptor restricts the expansion of aberrant Tfh cells and the generation of self-reactive antibodies in experimental murine lupus, but its activity is dispensable for the expansion of antigen-specific Tfh cells during vaccination. P2X7 stimulation promotes caspase-mediated pyroptosis of Tfh cells and controls the development of pathogenic ICOS⁺ IFN-γ–secreting cells. Circulating Tfh cells from patients with systemic lupus erythematosus (SLE) but not primary antiphospholipid syndrome (PAPS), a nonlupus systemic autoimmune disease, were hyporesponsive to P2X7 stimulation and resistant to P2X7-mediated inhibition of cytokine-driven expansion. These data point to the P2X7 receptor as a checkpoint regulator of Tfh cells; thus, restoring P2X7 activity in SLE patients could selectively limit the progressive amplification of pathogenic autoantibodies, which deteriorate patients’ conditions.

Extracellular MicroRNA Signature of Human Helper T Cell Subsets in Health and Autoimmunity

Upon T cell receptor stimulation, CD4⁺ T helper (Th) lymphocytes release extracellular vesicles (EVs) containing microRNAs. However, no data are available on whether human CD4⁺ T cell subsets release EVs containing different pattern of microRNAs. The present work aimed at filling this gap by assessing the microRNA content in EVs released upon in vitro T cell receptor stimulation of Th1, Th17, and T regulatory (Treg) cells. Our results indicate that EVs released by Treg cells are significantly different compared with those released by the other subsets. In particular, miR-146a-5p, miR-150-5p, and miR-21-5p are enriched, whereas miR-106a-5p, miR-155-5p, and miR-19a-3p are depleted in Treg-derived EVs. The in vitro identified EV-associated microRNA signature was increased in serum of autoimmune patients with psoriasis and returned to healthy levels upon effective treatment with etanercept, a biological drug targeting the TNF pathway and suppressing inflammation. Moreover, Gene Set Enrichment Analysis showed an over-representation of genes relevant for T cell activation, such as CD40L, IRAK1, IRAK2, STAT1, and c-Myb in the list of validated targets of Treg-derived EV miRNAs. At functional level, Treg-derived (but not Th1/Th17-derived) EVs inhibited CD4⁺ T cell proliferation and suppressed two relevant targets of miR-146a-5p: STAT1 and IRAK2. In conclusion, our work identified the miRNAs specifically released by different human CD4⁺ T cell subsets and started to unveil the potential use of their quantity in human serum to mark the pathological elicitation of these cells in vivo and their biological effect in cell to cell communication during the adaptive immune response.

Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR

The high-throughput analysis of microRNAs (miRNAs) circulating within the blood of healthy and diseased individuals is an active area of biomarker research. Whereas quantitative real-time reverse transcription polymerase chain reaction (qPCR)-based methods are widely used, it is yet unresolved how the data should be normalized. Here, we show that a combination of different algorithms results in the identification of candidate reference miRNAs that can be exploited as normalizers, in both discovery and validation phases. Using the methodology considered here, we identify normalizers that are able to reduce nonbiological variation in the data and we present several case studies, to illustrate the relevance in the context of physiological or pathological scenarios. In conclusion, the discovery of stable reference miRNAs from high-throughput studies allows appropriate normalization of focused qPCR assays.

miRiadne: a web tool for consistent integration of miRNA nomenclature

The miRBase is the official miRNA repository which keeps the annotation updated on newly discovered miRNAs: it is also used as a reference for the design of miRNA profiling platforms. Nomenclature ambiguities generated by loosely updated platforms and design errors lead to incompatibilities among platforms, even from the same vendor. Published miRNA lists are thus generated with different profiling platforms that refer to diverse and not updated annotations. This greatly compromises searches, comparisons and analyses that rely on miRNA names only without taking into account the mature sequences, which is particularly critic when such analyses are carried over automatically. In this paper we introduce miRiadne, a web tool to harmonize miRNA nomenclature, which takes into account the original miRBase versions from 10 up to 21, and annotations of 40 common profiling platforms from nine brands that we manually curated. miRiadne uses the miRNA mature sequence to link miRBase versions and/or platforms to prevent nomenclature ambiguities. miRiadne was designed to simplify and support biologists and bioinformaticians in re-annotating their own miRNA lists and/or data sets. As Ariadne helped Theseus in escaping the mythological maze, miRiadne will help the miRNA researcher in escaping the nomenclature maze. miRiadne is freely accessible from the URL http://www.miriadne.org.

Rett syndrome and the urge of novel approaches to study MeCP2 functions and mechanisms of action

Rett syndrome (RTT) is a devastating genetic disorder that worldwide represents the most common genetic cause of severe intellectual disability in females. Most cases are caused by mutations in the X-linked MECP2 gene. Several recent studies have demonstrated that RTT mimicking animal models do not develop an irreversible condition and phenotypic rescue is possible. However, no cure for RTT has been identified so far, and patients are only given symptomatic and supportive treatments. The development of clinical applications imposes a more comprehensive knowledge of MeCP2 functional role(s) and their relevance for RTT pathobiology. Herein, we thoroughly survey the knowledge about MeCP2 structure and functions, highlighting the necessity of identifying more functional domains and the value of molecular genetics. Given that, in our opinion, RTT ultimately is generated by perturbations in gene transcription and so far no genes/pathways have been consistently linked to a dysfunctional MeCP2, we have used higher-level bioinformatic analyses to identify commonly deregulated mechanisms in MeCP2-defective samples. In this review we present our results and discuss the possible value of the utilized approach.

Role of microRNAs and long-non-coding RNAs in CD4(+) T-cell differentiation

CD4(+) T lymphocytes orchestrate adaptive immune responses by differentiating into various subsets of effector T cells such as T-helper 1 (Th1), Th2, Th17, and regulatory T cells. These subsets have been generally described by master transcription factors that dictate the expression of cytokines and receptors, which ultimately define lymphocyte effector functions. However, the view of T-lymphocyte subsets as stable and terminally differentiated lineages has been challenged by increasing evidence of functional plasticity within CD4(+) T-cell subsets, which implies flexible programming of effector functions depending on time and space of T-cell activation. An outstanding question with broad basic and traslational implications relates to the mechanisms, besides transcriptional regulation, which define the plasticity of effector functions. In this study, we discuss the emerging role of regulatory non-coding RNAs in T-cell differentiation and plasticity. Not only microRNAs have been proven to be important for CD4(+) T-cell differentiation, but it is also likely that the overall T-cell functioning is the result of a multilayered network composed by coding RNAs as well as by short and long non-coding RNAs. The integrated study of all the nodes of this network will provide a comprehensive view of the molecular mechanisms underlying T-cell functions in health and disease.

Intracellular modulation, extracellular disposal and serum increase of MiR-150 mark lymphocyte activation

Activated lymphocytes release nano-sized vesicles (exosomes) containing microRNAs that can be monitored in the bloodstream. We asked whether elicitation of immune responses is followed by release of lymphocyte-specific microRNAs. We found that, upon activation in vitro, human and mouse lymphocytes down-modulate intracellular miR-150 and accumulate it in exosomes. In vivo, miR-150 levels increased significantly in serum of humans immunized with flu vaccines and in mice immunized with ovalbumin, and this increase correlated with elevation of antibody titers. Immunization of immune-deficient mice, lacking MHCII, resulted neither in antibody production nor in elevation of circulating miR-150. This study provides proof of concept that serum microRNAs can be detected, with minimally invasive procedure, as biomarkers of vaccination and more in general of adaptive immune responses. Furthermore, the prompt reduction of intracellular level of miR-150, a key regulator of mRNAs critical for lymphocyte differentiation and functions, linked to its release in the external milieu suggests that the selective extracellular disposal of microRNAs can be a rapid way to regulate gene expression during lymphocyte activation.

Inhibition of CCR7/CCL19 axis in lesional skin is a critical event for clinical remission induced by TNF blockade in patients with psoriasis

Despite the evidence that tumor necrosis factor (TNF) inhibitors block TNF and the downstream inflammatory cascade, their primary mechanism of action in inhibiting the self-sustaining pathogenic cycle in psoriasis is not completely understood. This study has the aim to identify early critical events for the resolution of inflammation in skin lesions using anti-TNF therapy. We used a translational approach that correlates gene expression fold change in lesional skin with the Psoriasis Area and Severity Index score decrease induced by TNF blockade after 4 weeks of treatment. Data were validated by immunofluorescence microscopy on skin biopsy specimens. We found that the anti-TNF-modulated genes that mostly associated with the clinical amelioration were Ccr7, its ligand, Ccl19, and dendritic cell maturation genes. Decreased expression of T-cell activation genes and Vegf also associated with the clinical response. More important, the down-regulation of Ccr7 observed at 4 weeks significantly correlated with the clinical remission occurring at later time points. Immunofluorescence microscopy on skin biopsy specimens showed that reduction of CCR7(+) cells and chemokine ligand (CCL) 19 was paralleled by disaggregation of the dermal lymphoid-like tissue. These data show that an early critical event for the clinical remission of psoriasis in response to TNF inhibitors is the inhibition of the CCR7/CCL19 axis and support its role in psoriasis pathogenesis.

Circulating hepatitis B surface antigen particles carry hepatocellular microRNAs

Hepatitis B virus (HBV) produces high quantities of subviral surface antigen particles (HBsAg) which circulate in the blood outnumbering virions of about 1\10(3-6) times. In individuals coinfected with the defective hepatitis Delta virus (HDV) the small HDV-RNA-genome and Delta antigen circulate as ribonucleoprotein complexes within HBsAg subviral particles. We addressed the question whether subviral HBsAg particles may carry in the same way cellular microRNAs (miRNAs) which are released into the bloodstream within different subcellular forms such as exosomes and microvescicles. Circulating HBsAg particles were isolated from sera of 11 HBsAg carriers by selective immunoprecipitation with monoclonal anti-HBs-IgG, total RNA was extracted and human miRNAs were screened by TaqMan real-time quantitative PCR Arrays. Thirty-nine human miRNAs were found to be significantly associated with the immunoprecipitated HBsAg, as determined by both comparative DDCT analysis and non-parametric tests (Mann-Whitney, p<0.05) with respect to controls. Moreover immunoprecipitated HBsAg particles contained Ago2 protein that could be revealed in ELISA only after 0.5% NP40. HBsAg associated miRNAs were liver-specific (most frequent = miR-27a, miR-30b, miR-122, miR-126 and miR-145) as well as immune regulatory (most frequent = miR-106b and miR-223). Computationally predicted target genes of HBsAg-associated miRNAs highlighted molecular pathways dealing with host-pathogen. The finding that HBsAg particles carry selective pools of hepatocellular miRNAs opens new avenues of research to disentangle the complex interactions between host and HBV and provides a non invasive tool to study the physiopathology of liver epigenetics.

Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output

The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. Nucleosome number in cells was considered fixed, but recently aging yeast and mammalian cells were shown to contain fewer nucleosomes. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker, and variant histones, and a correspondingly reduced number of nucleosomes, possibly because HMGB1 facilitates nucleosome assembly. Yeast nhp6 mutants lacking Nhp6a and -b proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and affects the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform and can be modelled assuming that different nucleosomal sites compete for available histones. Sites with a high propensity to occupation are almost always packaged into nucleosomes both in wild type and nucleosome-depleted cells; nucleosomes on sites with low propensity to occupation are disproportionately lost in nucleosome-depleted cells. We suggest that variation in nucleosome number, by affecting nucleosomal occupancy both genomewide and gene-specifically, constitutes a novel layer of epigenetic regulation.

Subcellular localization of the cyclin dependent kinase inhibitor Sic1 is modulated by the carbon source in budding yeast

The cyclin dependent kinase inhibitor Sic1 and the cyclin Clb5 are essential regulators of the cyclin dependent kinase Cdc28 during the G1 to S transition in budding yeast. Yeast enters S phase after ubiquitin-mediated degradation of Sic1, an event triggered by Cln1, 2-Cdc28 mediated phosphorylation. We recently showed that Sic1 is involved in carbon source modulation of the critical cell size required to enter S phase. Here we show that the amount and sub-cellular localization of Sic1 are also carbon source-modulated. We identify a bipartite nuclear localization sequence responsible for nuclear localization of Sic1 and for correct cell cycle progression in a carbon-source dependent manner. Similarly to Cip/Kip proteins-Sic1 mammalian counterparts-Sic1 facilitates nuclear accumulation of its cognate cyclin, since cytoplasmic building-up of Clb5 is observed upon switching off expression of the SIC1 gene. Our data indicate a previously unrecognized inhibitor/activator dual role for Sic1 and put it among key molecules whose activity is regulated by their nuclear-cytoplasmic localization.

Glucose modulation of cell size in yeast

Saccharomyces cerevisiae cells grown in glucose have larger average size than cells grown in ethanol. Besides, yeast must reach a carbon source-modulated critical cell size in order to enter S phase at Start. This control is of outmost physiological relevance, since it allows us to coordinate cell growth with cell cycle progression and it is responsible for cell size homeostasis. The cell sizer mechanism requires the overcoming of two sequential thresholds, involving Cln3 and Far1, and Clb5,6 and Sic1, respectively. When both thresholds are non-functional, carbon source modulation of cell size at Start is completely abolished. Since inactivation of extracellular glucose sensing through deletion of either the GPR1 or the GPA2 gene causes a marked, but partial, reduction in the ability to modulate cell size and protein content at Start, it is proposed that both extracellular and intracellular glucose signalling is required for properly setting the cell sizer in glucose media.

A cell sizer network involving Cln3 and Far1 controls entrance into S phase in the mitotic cycle of budding yeast

Saccharomyces cerevisiae must reach a carbon source-modulated critical cell size, protein content per cell at the onset of DNA replication (Ps), in order to enter S phase. Cells grown in glucose are larger than cells grown in ethanol. Here, we show that an increased level of the cyclin-dependent inhibitor Far1 increases cell size, whereas far1Δ cells start bud emergence and DNA replication at a smaller size than wild type. Cln3Δ, far1Δ, and strains overexpressing Far1 do not delay budding during an ethanol glucose shift-up as wild type does. Together, these findings indicate that Cln3 has to overcome Far1 to trigger Cln–Cdc28 activation, which then turns on SBF- and MBF-dependent transcription. We show that a second threshold is required together with the Cln3/Far1 threshold for carbon source modulation of Ps. A new molecular network accounting for the setting of Ps is proposed.

Mutations of the CK2 phosphorylation site of Sic1 affect cell size and S-Cdk kinase activity in Saccharomyces cerevisiae

By sequence analysis we found an amino acid stretch centred on Serine201 matching a stringent CK2 consensus site within the C-terminal, inhibitory domain of Sic1. Here we show by direct mass spectrometry analysis that Sic1, but not a mutant protein whose CK2 phospho-acceptor site has been mutated to alanine, Sic1S201A, is actually phosphorylated in vitro by CK2 on Serine 201. Mutation of Serine 201 alters the coordination between growth and cell cycle progression. A significant increase of average protein content and of the average protein content at the onset of DNA synthesis is observed for exponentially growing cells harbouring the Sic1S201A protein. A strong reduction of the same parameters is observed in cells harbouring Sic1S201E. The deregulated coordination between cell size and cell cycle is also apparent at the level of S-Cdk activity.

Checking cell size in budding yeast: a systems biology approach

The regulation of cell cycle progression via the attainment of a critical cell size is a conserved feature from simpler unicellular organisms to mammalian cells that is obtaining much attention recently. Genome wide analysis of Saccharomyces cerevisiae deletion strains, genetic epistasis, DNA microarray analysis have recently revealed an increasingly complex network of cell size modulation mechanisms. A systems biology-based approach, that is needed to structure the underlying complexity of cell cycle regulatory mechanisms, is described.

First Report of Phakopsora pachyrhizi, the Causal Organism of Soybean Rust in the Province of Misiones, Argentina

In April 2002, Phakopsora pachyrhizi Sydow was observed for the first time in L. N. Alem, in the Province of Misiones, Argentina. Misiones is nearly surrounded by Paraguay and Brazil, where P. pachyrhizi was discovered recently (2) and where it is a serious disease (3). Symptoms were observed on leaves in the upper half of plants at the R6 stage in a soybean research field trial. Symptoms included reddish-brown lesions on leaves especially on the abaxial surface, and uredinias were observed in the lesions with a 10× lens. Leaf defoliation was observed due to the disease after the R5 stage, and the enviroment (high humidity and air temperatures) was particularly conducive to the disease. The field trial area was 2,500 m² and included soybean genotypes of maturity groups V to IX. Symptoms were detected in the later maturity groups. Field trials were surrounded by kudzu (Pueraria sp.), which is a common weed introduced in South America as a forage plant by Asian farmers, and it was reported as the main host of this pathogen in Paraguay (2). To confirm the identity of the pathogen, leaf samples from the middle part of plants were collected and sent to the Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD. Samples were analyzed using a real-time polymerase chain reaction assay (1). Identification of P. pachyrhizi was confirmed the last week of May, 2002 (R. Frederick, personal communication). The soybean production area in Misiones is a small area in Argentina lying 600 km northeast of the main soybean area in the north central part of the country. SENASA (Servicio Nacional de Sanidad Vegetal [Nacional Service of Plant Health]) and SAGPYA (Secretary of Agriculture) were formally informed about these results on June 19, 2002. A program to assess the risk of disease spread is under development. References: (1) R. D. Frederick et al. Phytopathology 92:217, 2002. (2) W. Morel Paiva. AnaisII Congresso Brasilero de Soja e Mercosoja. Foz de Iguazu, Brazil, 2002. (3) T. Yorinori. Anais II Congresso Brasilero de Soja e Mercosoja. Foz de Iguazu, Brazil, 2002.

Laparoscopy in pancreatic and hepatobiliary cancer

Laparoscopic techniques can be used for diagnosis, staging, and therapeutic procedures, both palliative or curative. Laparoscopy needs to be used in the context of algorithms of evaluation and management that consider the natural history and biology of the diseases at stake, concepts of evidence-based decisions, cost-effectiveness, quality of life, expertise available, and the philosophy of involved institutions. Accurate staging facilitates the selection of patients for resection, for neoadjuvant therapy, and selective planning for best palliation. The therapeutic role of advanced laparoscopic or laparoscopic assisted procedures is likely to increase (biliary bypass, gastro-jejunostomy, liver resections, cryosurgery, radiofrequency ablation, etc.). The place of laparoscopy in staging and treatment, however, has to be critically and continuously reviewed in the context of new developments in diagnostic imaging techniques, endoscopic procedures, and advances in oncology.

Management of hilar cholangiocarcinoma: comparison of an American and a Japanese experience

OBJECTIVE

To compare the experience and outcome in the management of hilar cholangiocarcinoma at one American and one Japanese medical center.

SUMMARY BACKGROUND DATA

Controversies surround the issues of extent of resection for hilar cholangiocarcinoma and whether the histopathology of such cancers are similar between patients treated in America and in Japan.

METHODS

Records were reviewed of 100 patients treated between 1980 and 1995 at the Lahey Clinic in the United States, and of 155 patients treated between 1977 and 1995 at Nagoya University Hospital in Japan. Selected pathologic slides of resected cancers were exchanged between the two institutions and reviewed for diagnostic concordance.

RESULTS

In the Lahey cohort, there were 25 resections, 53 cases of surgical exploration with biliary bypass or intubation, and 22 cases of percutaneous transhepatic biliary drainage or endoscopic biliary drainage without surgery. In the Nagoya cohort, the respective figures were 122, 10, and 23. The overall 5-year survival rate of all patients treated (surgical and nonsurgical) during the study periods was 7% in the Lahey cohort and 16% in the Nagoya cohort. The overall 10-year survival rates were 0% and 12%, respectively. In patients who underwent resection with negative margins, the 5- and 10-year survival rates were 43% and 0% for the Lahey cohort and 25% and 18% for the Nagoya cohort. The surgical death rate for patients undergoing resection was 4% for Lahey patients and 8% for Nagoya patients. Of the patients who underwent resection, en bloc caudate lobectomy was performed in 8% of the Lahey patients and 89% of the Nagoya patients. Histopathologic examination of resected cancers showed that the Nagoya patients had a higher stage of disease than the Lahey patients.

CONCLUSIONS

In both Lahey and Nagoya patients, survival was most favorable when resection of hilar cholangiocarcinoma was accomplished with margin-negative resections. Combined bile duct and liver resection with caudate lobectomy contributed to a higher margin-negative resection rate in the Nagoya cohort.

Thyroid cancer

The management of patients with thyroid cancer can be optimized by developing multidisciplinary groups of highly specialized individuals. The completeness of surgery and its morbidity are mostly surgeon-dependent. Similarly, the decisions regarding selection of adjuvant treatments, doses, follow-up schemes, and so forth require depth of knowledge and understanding of the disease; its variables; factors that govern its course; and the values, limitations, and side effects of alternative therapies.

Hepatic malignancies

The battle against malignancies of the liver is far from over, although tremendous strides have been made in the past decade, such as improved diagnostic capabilities, safe surgical resection, availability of safe nonsurgical ablative modalities, multimodality therapy, and aggressive approach to recurrent disease. Even after the best attempts at curative treatment, recurrence of primary and secondary malignancies of the liver continues to be the cause of demise for more than 70% of treated patients. The battle continues in the laboratories, where investigations are focused on delineating the pathophysiology of cancer on the molecular and genetic levels and mapping the patterns of cancer emergence and spread. The new millennium holds promise for formulating therapies that may improve disease-free survival for patients with malignancies of the liver.

Multidisciplinary considerations for patients with cancer of the pancreas or biliary tract

The past century has been nearly all of the growth in knowledge about the anatomy and pathophysiology associated with cancers of the pancreas and surrounding biliary structures. Through advances in imaging technology, endoscopic practice, improvement in surgical technique and perioperative care, anesthesia advances, and a better appreciation for the usefulness of adjuvant chemotherapy and radiation therapy, physicians can offer patients some hope for long-term survival and a better quality of life when they are faced with these devastating tumors. Although surgical intervention is the "last best hope" for these patients, advances in the nonoperative disciplines will be required for substantial further improvement in patient outcomes.

Options and strategies for the management of choledocholithiasis

The introduction of laparoscopic techniques for the management of biliary stone disease has expanded the therapeutic choices for surgeons confronted with choledocholithiasis. As new strategies emerge, the treatment of cholelithiasis and choledocholithiasis remains controversial. This paper discusses the options available for the treatment of common bile duct stones. Diagnostic and therapeutic algorithms are proposed. The treatment of these patients must be individualized, taking into consideration the condition of the patient, associated diseases, secondary complications of the gallstones, and the surgical expertise and resources of the institution.

The acute abdomen. An overview and algorithms

The diagnosis and management of the patient with an acute abdomen remains one of the most difficult challenges for the surgeon. A thorough understanding of the anatomy and physiology of the abdomen are essential to properly generate a differential diagnosis and to formulate a treatment plan. While recent advances in technology can be extremely helpful in certain situations, they cannot replace a physician's clinical judgment based upon a good history and physical examination. This article provides a general overview of the evaluation of the patient with an acute abdomen. It will also suggest algorithms to consider in the diagnosis and treatment of these patients.

Gastroduodenal polyps in familial adenomatous polyposis

BACKGROUND

Malignant degeneration of gastroduodenal polyps has been noted in patients with familial adenomatous polyposis. To evaluate this problem further, patients with familial adenomatous polyposis were contacted and offered upper gastrointestinal tract endoscopy.

METHODS

A prospective endoscopic examination was performed in 42 patients.

RESULTS

The median age of patients at endoscopy was 35 years. The duration of known familial adenomatous polyposis at the time of endoscopy was 8 years. Polyps were visualized in 21 patients (50%). Gastric polyps were seen in 14 patients (33%), duodenal polyps were seen in 11 patients (26%), and ampullary polyps were seen in 7 patients (17%). Nine patients (43%) had polyps in more than one site. Adenomatous change was noted in 73% of duodenal lesions and in only 14% of gastric polyps. Surgical intervention was required in four patients; one patient had an early ampullary carcinoma, and three patients had severe dysplasia involving the duodenum or ampulla. All four patients had undergone a previous screening examination, results of which were normal in three patients. Compared with other patients, these four patients were older (median age, 58 years; p = 0.02) and had a longer duration of disease (median duration, 25 years; p = 0.002).

CONCLUSIONS

All patients with familial adenomatous polyposis require lifelong endoscopic surveillance to detect malignant degeneration, which may appear later in life.

Long-term results of pylorus-preserving pancreatoduodenectomy for chronic pancreatitis

OBJECTIVE

To assess the long-term outcome of patients following pylorus-preserving pancreatoduodenectomy (PPPD) for chronic pancreatitis.

DESIGN

Retrospective study with mean follow-up of 63 months (range, 1 month to 13.7 years).

SETTING

Tertiary referral hospital.

PATIENTS

Records of all patients who underwent PPPD for chronic pancreatitis at Lahey Clinic were reviewed. All patients who were alive were contacted by telephone. In cases where patients had died, information was gathered from family members and hospital records.

RESULTS

Forty-five patients underwent PPPD for disabling chronic pancreatitis. The mean preoperative duration of pain was 50 months, with 32 patients (70%) requiring daily narcotics. In one patient resection of the portal vein was required. One patient died within 30 days of the operation. Forty-one patients (92%) had improvement of pain at 5 years. The mean pain score (on a scale of 0 to 10) was 9.2 preoperatively and 1.5, 0.8, 1.1, and 1.1 at 6 months, 1 year, 2 years, and 5 years, respectively. Thirty-three patients (74%) had a postoperative weight gain to an average of 92% of their pre-illness weight. New-onset diabetes occurred in six patients (14%) by 6 months and in 21 patients (46%) by 5 years. Hypoglycemia was the cause of death in one patient who underwent total pancreatectomy. Four patients died of causes unrelated to PPPD. Marginal ulcers occurred in five patients (10%). Nine patients required late operations.

CONCLUSIONS

In selected patients, resection of the head of the pancreas achieves long-term pain improvement in over 90% of cases. The early development of diabetes mellitus is infrequent, but over longer follow-up periods it reaches prevalence rates similar to those described in patients who have not undergone resection. Weight gain in this group was superior to that previously reported for our patients who underwent "standard Whipple" operation for chronic pancreatitis.

Malignant obstructive jaundice. Evaluation and management

A large number of laboratory tests, radiologic studies, and endoscopic techniques are available for the evaluation of the jaundiced patient. Similarly, the therapeutic options have increased with the development and improvement of endoscopic, percutaneous, and laparoscopic procedures, and the morbidity and mortality rates associated with open surgery have decreased. The challenge is to select, on an individual basis, the most efficient and cost-effective evaluation as well as the management with the lowest morbidity and mortality rates and the best short- and long-term goals.

Biliary tract complications of laparoscopic cholecystectomy are detected more frequently with routine intraoperative cholangiography

Controversy over whether intraoperative cholangiography (IOC) should be done routinely has intensified since the advent of laparoscopic cholecystectomy (LC). As yet, no study has demonstrated a clear benefit to its use, although their have been suggestions in the literature that routine use may confer an advantage to detection of injuries. One-hundred seventy-seven biliary tract complications occurring secondary to LC were identified from the combined data of seven institutions. The goal of this retrospective study was to examine the impact of IOC on the occurrence, recognition, and correction of such complications. The complications identified include 39 cystic duct leaks, 69 major ductal leaks or strictures, and 69 major ductal transection or excision injuries. Whether IOC was performed was known in 157 (88%) patients with 53 patients definitely having and 104 not having an IOC. Data concerning IOC were unavailable in 20 cases. More injuries were detected intraoperatively in the group having IOC (P < 0.001). Conversion of the LC to a laparotomy, often for repair of the injury, occurred more commonly in the group having a correctly interpreted IOC (P < 0.001). Conversion resulted in detection of injuries sooner, resulting in fewer operative procedures to correct the injury (P < 0.001). A transecting injury was prevented in at least seven patients when no visualization of the proximal biliary tree was documented by IOC. These partial ductal incisions were treated by t-tube placement. Incorrect interpretation of the IOC occurred in at least eight patients, with no identification of the proximal biliary tree in six.(ABSTRACT TRUNCATED AT 250 WORDS)

Occult well differentiated thyroid carcinoma presenting as cervical node disease

Records of 92 patients with differentiated thyroid carcinoma presenting as cervical adenopathy without a palpable mass were reviewed to identify prognostic factors and to evaluate therapy. Patients were treated between 1940 and 1990 and were observed for 3 to 48 years (median 18 years). Follow-up data were obtained by chart review, correspondence, and telephone contact. Among the group, 20 patients had unilateral and 72 bilateral thyroid lobectomy, with node dissection in 77. Thyroid hormone was used in 50 patients and radioactive iodine in 20. Patients were younger than the overall population of patients with differentiated thyroid carcinoma, with more men and more multifocal thyroid disease. Risk group defined by age and sex was the most important determinant of survival. All women 50 years of age or younger and all men 40 or younger (low risk group) survived independent of the type of initial operation or use of thyroid-stimulating hormone suppression or radioactive iodine. Of the low-risk patients, 16% had recurrent disease but were treated successfully with surgery or radioactive iodine; 28% of the older patients (high risk) died of disease. A trend for better survival was noted in high risk patients undergoing bilateral thyroidectomy and in patients receiving thyroid suppression. Of the high risk patients, 26% had recurrent disease, with a 71% mortality rate. Age and sex are the primary determinants of survival. Therapy should be based on risk factors. Low risk patients should have conservative thyroid surgery and modified or limited node dissection.(ABSTRACT TRUNCATED AT 250 WORDS)

Ductal carcinoma in situ of the male breast

BACKGROUND

Ductal carcinoma in situ (DCIS) of the male breast is an uncommon disease, accounting for approximately 7% of all male breast carcinomas. Compared with invasive carcinomas of the breast, the prognosis associated with DCIS in men is excellent; however, clinical features, pathology, and treatment of this disease are not well defined in the literature.

METHODS

Records of 23 men with carcinoma of the breast treated at the Lahey Clinic from 1968 to 1991 were reviewed, revealing 4 patients with pure DCIS (17%). The reported management of DCIS in women is discussed in comparison with that of DCIS in men.

RESULTS

Of the four patients with DCIS, the presenting complaint was a retroareolar mass in three patients and a bloody nipple discharge in one patient. The pathologic subtype was papillary in one patient and intracystic papillary in three patients. Two patients were treated with partial mastectomy alone. Disease recurred locally as DCIS in both patients, requiring mastectomy at 30 and 108 months. No lymph node metastases were found in the three patients who underwent axillary dissection. All four patients were alive without disease at 133, 120, 36, and 32 months of follow-up, respectively.

CONCLUSIONS

Although the sample size was small, our patients and a review of the literature suggest that most DCIS in men is of the papillary type and that mastectomy without axillary dissection is the preferred treatment.

Bile duct injuries. Spectrum, mechanisms of injury, and their prevention

Bile duct injuries remain a relatively uncommon but potentially devastating complication of both open procedures and laparoscopic procedures. They may present immediately after a given operation or take years to be recognized. Despite the best intentions of the surgeon, many of these injuries are imminently preventable. Recent advances in laparoscopic procedures have served to remind us of lessons learned from the prelaparoscopic era with respect to injuries of the bile ducts. To conduct any operation safely on or near the biliary system, the surgeon should be familiar with the anatomy and its variations, the nature of the pathologic processes that may enhance the likelihood of causing harm, and, most important, his or her own limitations and the limitations of the system with which he or she has to work.

Biliary reconstruction

The success of the initial repair after bile duct injury is critical to the long-term patency and function of the biliary tract. Dissection of the hilar plate, obtaining adequate width of the hepatic duct opening, and accurate mucosa-to-mucosa anastomosis are essential to achieving satisfactory reconstruction of the biliary tract. The plan of treatment for bile duct injuries should be tailored to the individual patient based on the type, level, and extent of the injury, the timing of diagnosis, the overall status of the patient, and the available expertise. The goal of therapy is not necessarily to avoid surgery but to achieve the best long-term results in the most cost-effective manner and with the least morbidity and mortality. A coordinated multidisciplinary approach to the diagnosis and treatment of patients with biliary injuries is now the standard.

Techniques of laparoscopic cholecystectomy. The difficult operation

Laparoscopic cholecystectomy has settled as the treatment of choice for patients with gallstone disease. Injury to the bile ducts, still the main drawback of the technique, is decreasing progressively with better understanding of the mechanisms of injury and adequate training. With the expansion of indications for laparoscopic cholecystectomy, more difficult operations are being performed. Adequate understanding of the obstacles that may arise during the laparoscopic procedure as well as knowledge of specific maneuvers to deal with the difficult operation are important for the success and safety of the procedure.

Pylorus-preserving pancreatoduodenectomy. Is it an adequate cancer operation

OBJECTIVE

To assess the adequacy of pylorus-preserving pancreatoduodenectomy (PPPD) as a definitive surgical treatment for primary malignant diseases of the periampullary region.

DESIGN

Retrospective review of the clinical records of patients undergoing PPPD for malignant diseases of the periampullary region. Median and 5-year actuarial survival by type and stage of cancer were determined. Survival data from this study were compared with those of patients undergoing a conventional Whipple operation.

SETTING

Lahey Clinic, Burlington, Mass.

STUDY PARTICIPANTS

One hundred six patients undergoing PPPD for primary malignant disease of the periampullary region between November 1979 and June 1992.

INTERVENTION

Pylorus-preserving pancreatoduodenectomy was performed with curative intent in the 106 patients. Ninety-five patients underwent proximal pancreatectomy; 11 patients, total pancreatectomy. Resection of the portal vein was performed in 10 patients.

MAIN OUTCOME MEASURE

Long-term survival following PPPD was analyzed with respect to the type and stage of cancer. Median follow-up was 30 months (range, 6 to 156 months).

RESULTS

Five-year actuarial survival rates were 45.4% for patients with ampullary adenocarcinoma; 6.6%, with pancreatic ductal adenocarcinoma; 33.3%, with distal bile duct adenocarcinoma; 75%, with pancreatic islet cell adenocarcinoma; and 0%, with pancreatic cystadenocarcinoma. An early cancer stage was associated with more favorable survival for ampullary and distal bile duct adenocarcinomas. For pancreatic ductal adenocarcinoma only, tumors less than 2 cm were associated with better survival. Duodenal resection margins were free of disease in all patients, while peripancreatic and retroperitoneal extension of the tumor was found in 20%.

CONCLUSION

For patients with periampullary malignant disease, long-term survival following PPPD is similar to that following a conventional Whipple operation. The potential benefits of hemigastrectomy with perigastric lymphadenectomy are frequently obviated by the presence of positive margins and lymph nodes elsewhere, ie, in the retroperitoneum. We advocate PPPD as the procedure of choice for locally resectable malignant disease of the periampullary region, provided the duodenal margin is viable and tumor free.

Characteristics of biliary tract complications during laparoscopic cholecystectomy: a multi-institutional study

We collected the records of 81 patients with biliary tract injuries occurring during laparoscopic cholecystectomy (LC) who were referred to 3 referral centers during a 33-month (May 1990 to March 1993) period. All records were reviewed to provide data concerning the anatomy of the lesion induced, method of injury, timing of injury detection, role of intraoperative cholangiography (IOC), methods of treatment, and outcome of these injuries. Injuries were classified by our own method as follows: (1) cystic duct leaks (n = 15), (2) bile leaks and/or ductal strictures (n = 27), and (3) ductal transections or excisions (n = 39). Peak occurrence by quarter of the year was 4th quarter, 1990 (Lahey), and 3rd quarter, 1991 (Mason), and 1st quarter, 1992 (Mayo). The majority (62%) of the injuries were recognized after LC. At the time of LC, 31 of 81 (38%) injuries were recognized and converted to open procedures. Data regarding IOC were available in 63 of 81 (78%) cases. In patients in whom IOC was not performed, 14 of 38 (37%) operations were converted; if an IOC was obtained and interpreted correctly, 13 of 21 (62%) operations were converted. Primary repair was attempted in 11 leaks and/or strictures, but 36% required additional treatment. Primary repair was used in six transections or excisions, and 17% have required further intervention. In patients who had biliary-enteric bypass (BEB) performed outside (17) versus at the referral institution (29), 94% (16 patients) versus 0%, respectively, required additional operative (e.g., revision of a hepaticojejunostomy) or nonoperative (e.g., radiologic or endoscopic stenting or balloon dilation) procedures. When used as initial therapy or after a primary ductal repair, stents (with or without balloon dilation) resolved 100% of simple cystic duct leaks and 91% of leaks and/or strictures. In conclusion, the peak incidence of LC-related biliary injuries appears to have passed. A completed and correctly interpreted IOC increases the chance of detection of biliary injuries intraoperatively and should assist surgeons who use routine IOC. Nonsurgical techniques allow treatment of most simple cystic duct leaks, major ductal leaks and/or strictures, and postoperative BEB strictures, although follow-up is limited. The poor results of pre-referral BEB is not surprising since all of these patients were selected for referral because their treatments had not been successful.

Bile duct injury during laparoscopic cholecystectomy: mechanism of injury, prevention, and management

Although several studies have shown a low incidence of bile duct injuries during laparoscopic cholecystectomy, concerns remain because of the sustained increase in the number of referrals for biliary reconstruction after the procedure. Twenty-one patients have been referred to our institution because of major bile duct injuries after laparoscopic cholecystectomy. The injury was recognized during the laparoscopic procedure in only 6 of the 21 (29%). Nineteen patients underwent hepaticojejunostomy at least once, one patient required hepaticojejunostomy and repair of a choledochoduodenal fistula, and one patient needed repair of a biliary colonic fistula. Hepaticojejunostomy above the bifurcation was required in 10 patients (50%), at the bifurcation in 3, and below the bifurcation in 7. Nine of the eleven patients in whom the initial repair was performed at the local hospital presented with early stricture (median 7 months). The common denominator of the development of bile duct injuries during laparoscopic cholecystectomy is the failure to identify the structures of the triangle of Calot. Specific steps during laparoscopic cholecystectomy to avoid bile duct injuries are described. Expertise in hepatobiliary surgery appears to optimize results of biliary reconstruction.

Acute relapsing pancreatitis as a complication of papillary stenosis after endoscopic sphincterotomy

Endoscopic sphincterotomy has proven to be a safe alternative to surgery for selected types of biliary disease. Despite a relatively low morbidity, postprocedure complications are well described. This report presents an experience with three patients in whom acute relapsing pancreatitis developed as a possible complication of papillary stenosis after endoscopic sphincterotomy. None of the patients had a previous history of elevations in serum amylase levels before endoscopic sphincterotomy. After procedure, pancreatitis and subsequently acute relapsing pancreatitis with documented stricture of the pancreatic duct orifice developed in all three patients. After surgical transduodenal sphincteroplasty, no new episodes of acute relapsing pancreatitis occurred.