Structure of the MRAS-SHOC2-PP1C phosphatase complex

RAS-MAPK signalling is fundamental for cell proliferation and is altered in most human cancers1-3. However, our mechanistic understanding of how RAS signals through RAF is still incomplete. Although studies revealed snapshots for autoinhibited and active RAF-MEK1-14-3-3 complexes4, the intermediate steps that lead to RAF activation remain unclear. The MRAS-SHOC2-PP1C holophosphatase dephosphorylates RAF at serine 259, resulting in the partial displacement of 14-3-3 and RAF-RAS association3,5,6. MRAS, SHOC2 and PP1C are mutated in rasopathies-developmental syndromes caused by aberrant MAPK pathway activation6-14-and SHOC2 itself has emerged as potential target in receptor tyrosine kinase (RTK)-RAS-driven tumours15-18. Despite its importance, structural understanding of the SHOC2 holophosphatase is lacking. Here we determine, using X-ray crystallography, the structure of the MRAS-SHOC2-PP1C complex. SHOC2 bridges PP1C and MRAS through its concave surface and enables reciprocal interactions between all three subunits. Biophysical characterization indicates a cooperative assembly driven by the MRAS GTP-bound active state, an observation that is extendible to other RAS isoforms. Our findings support the concept of a RAS-driven and multi-molecular model for RAF activation in which individual RAS-GTP molecules recruit RAF-14-3-3 and SHOC2-PP1C to produce downstream pathway activation. Importantly, we find that rasopathy and cancer mutations reside at protein-protein interfaces within the holophosphatase, resulting in enhanced affinities and function. Collectively, our findings shed light on a fundamental mechanism of RAS biology and on mechanisms of clinically observed enhanced RAS-MAPK signalling, therefore providing the structural basis for therapeutic interventions.

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70-75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70-80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

Conservation of binding properties in protein models

We study the models submitted to round 12 of the Critical Assessment of protein Structure Prediction (CASP) experiment to assess how well the binding properties are conserved when the X-ray structures of the target proteins are replaced by their models. To explore small molecule binding we generate distributions of molecular probes - which are fragment-sized organic molecules of varying size, shape, and polarity - around the protein, and count the number of interactions between each residue and the probes, resulting in a vector of interactions we call a binding fingerprint. The similarity between two fingerprints, one for the X-ray structure and the other for a model of the protein, is determined by calculating the correlation coefficient between the two vectors. The resulting correlation coefficients are shown to correlate with global measures of accuracy established in CASP, and the relationship yields an accuracy threshold that has to be reached for meaningful binding surface conservation. The clusters formed by the probe molecules reliably predict binding hot spots and ligand binding sites in both X-ray structures and reasonably accurate models of the target, but ensembles of models may be needed for assessing the availability of proper binding pockets. We explored ligand docking to the few targets that had bound ligands in the X-ray structure. More targets were available to assess the ability of the models to reproduce protein-protein interactions by docking both the X-ray structures and models to their interaction partners in complexes. It was shown that this application is more difficult than finding small ligand binding sites, and the success rates heavily depend on the local structure in the potential interface. In particular, predicted conformations of flexible loops are frequently incorrect in otherwise highly accurate models, and may prevent predicting correct protein-protein interactions.

Progress toward improved understanding of antibody maturation

Upon encountering an antigen, antibodies mature through various rounds of somatic mutations, resulting in higher affinities and specificities to the particular antigen. We review recent progress in four areas of antibody maturation studies. (1) Next-generation and single-cell sequencing have revolutionized the analysis of antibody repertoires by dramatically increasing the sequences available to study the state and evolution of the immune system. Computational methods, including machine learning tools, have been developed for reconstituting antibody clonal lineages and for general repertoire analysis. (2) The availability of X-ray structures, thermodynamic and kinetic data, and molecular dynamics simulations provide information on the biophysical mechanisms responsible for improved affinity. (3) In addition to improved binding to a specific antigen, providing affinity-independent diversity and self/nonself discrimination are fundamental functions of the immune system. Recent studies, including X-ray structures, yield improved understanding of both mechanisms. (4) Results from in vivo maturation help to develop methods of in vitro maturation to improve antibody properties for therapeutic applications, frequently combining computational and experimental approaches.

Performance and Its Limits in Rigid Body Protein-Protein Docking

The development of fast Fourier transform (FFT) algorithms enabled the sampling of billions of complex conformations and thus revolutionized protein-protein docking. FFT-based methods are now widely available and have been used in hundreds of thousands of docking calculations. Although the methods perform "soft" docking, which allows for some overlap of component proteins, the rigid body assumption clearly introduces limitations on accuracy and reliability. In addition, the method can work only with energy expressions represented by sums of correlation functions. In this paper we use a well-established protein-protein docking benchmark set to evaluate the results of these limitations by focusing on the performance of the docking server ClusPro, which implements one of the best rigid body methods. Furthermore, we explore the theoretical limits of accuracy when using established energy terms for scoring, provide comparison with flexible docking algorithms, and review the historical performance of servers in the CAPRI docking experiment.

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking

Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template-based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock homology models. The available templates also provided distance restraints that were directly used as input to the server. We show here that such an approach has some advantages. Free docking with template-based restraints using ClusPro reproduced some interfaces suggested by weak or ambiguous templates while not reproducing others, resulting in correct server predicted models. More recently we developed the fully automated ClusPro TBM server that performs template-based modeling and thus can use sequences rather than structures of component proteins as input. The performance of the server, freely available for noncommercial use at https://tbm.cluspro.org, is demonstrated by predicting the protein-protein targets of rounds 38 to 45 of CAPRI.

Template-based modeling by ClusPro in CASP13 and the potential for using co-evolutionary information in docking

As a participant in the joint CASP13-CAPRI46 assessment, the ClusPro server debuted its new template-based modeling functionality. The addition of this feature, called ClusPro TBM, was motivated by the previous CASP-CAPRI assessments and by the proven ability of template-based methods to produce higher-quality models, provided templates are available. In prior assessments, ClusPro submissions consisted of models that were produced via free docking of pre-generated homology models. This method was successful in terms of the number of acceptable predictions across targets; however, analysis of results showed that purely template-based methods produced a substantially higher number of medium-quality models for targets for which there were good templates available. The addition of template-based modeling has expanded ClusPro's ability to produce higher accuracy predictions, primarily for homomeric but also for some heteromeric targets. Here we review the newest additions to the ClusPro web server and discuss examples of CASP-CAPRI targets that continue to drive further development. We also describe ongoing work not yet implemented in the server. This includes the development of methods to improve template-based models and the use of co-evolutionary information for data-assisted free docking.

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

The inhibition of kinases has been pursued by the pharmaceutical industry for over 20 years. While the locations of the sites that bind type II and III inhibitors at or near the adenosine 5'-triphosphate binding sites are well defined, the literature describes 10 different regions that were reported as regulatory hot spots in some kinases and thus are potential target sites for type IV inhibitors. Kinase Atlas is a systematic collection of binding hot spots located at the above ten sites in 4910 structures of 376 distinct kinases available in the Protein Data Bank. The hot spots are identified by FTMap, a computational analogue of experimental fragment screening. Users of Kinase Atlas ( https://kinase-atlas.bu.edu ) may view summarized results for all structures of a particular kinase, such as which binding sites are present and how druggable they are, or they may view hot spot information for a particular kinase structure of interest.

What method to use for protein-protein docking?

A number of well-established servers perform 'free' docking of proteins of known structures. In contrast, template-based docking can start from sequences if structures are available for complexes that are homologous to the target. On the basis of the results of the CAPRI-CASP structure prediction experiments, template-based methods yield more accurate predictions if good templates can be found, but generally fail without such templates. However, free global docking, or focused docking around even poor quality template-based models, can still generate acceptable docked structures in these cases. In accordance with the analysis of a benchmark set, free docking of heterodimers yields acceptable or better predictions in the top 10 models for around 40% of structures. However, it is likely that a combination of template-based and free docking methods can perform better for targets that have template structures available. Another way of improving the reliability of predictions is adding experimental information as restraints, an option built into several docking servers.

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT

Summary

We present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide’s final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor. According to CAPRI peptide docking criteria, an acceptable conformation can often be found among the top-ranking predictions.

Availability and Implementation

The method is available as part of the protein-protein docking server ClusPro at https://peptidock.cluspro.org/nousername.php.

Supplementary information

Supplementary data are available at Bioinformatics online.

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock

Peptide-protein interactions contribute a significant fraction of the protein-protein interactome. Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces. To address this challenge we developed a fragment based high-resolution peptide-protein docking protocol. By streamlining the Rosetta fragment picker for accurate peptide fragment ensemble generation, the PIPER docking algorithm for exhaustive fragment-receptor rigid-body docking and Rosetta FlexPepDock for flexible full-atom refinement of PIPER docked models, we successfully addressed the challenge of accurate and efficient global peptide-protein docking at high-resolution with remarkable accuracy, as validated on a small but representative set of peptide-protein complex structures well resolved by X-ray crystallography. Our approach opens up the way to high-resolution modeling of many more peptide-protein interactions and to the detailed study of peptide-protein association in general. PIPER-FlexPepDock is freely available to the academic community as a server at http://piperfpd.furmanlab.cs.huji.ac.il.

Peptide-protein interactions are crucial components of various important biological processes in living cells. High-resolution structural information of such interactions provides insight about the underlying biophysical principles governing the interactions, and a starting point for their targeted manipulations. Accurate docking algorithms can help fill the gap between the vast number of these interactions and the small number of experimentally solved structures. However, the accuracies of the existing protocols have been limited, in particular for ab initio docking when no information about the peptide beyond its sequence is available. Here we introduce PIPER-FlexPepDock, a fragment-based global docking protocol for high-resolution modeling of peptide-protein interactions. Integration of accurate and efficient representation of the peptide using fragment ensembles, their fast and exhaustive rigid-body docking, and their subsequent accurate flexible refinement, enables peptide-protein docking of remarkable accuracy. The validation on a representative benchmark set of crystallographically solved high-resolution peptide-protein complexes demonstrates significantly improved performance over all existing docking protocols. This opens up the way to the modeling of many more peptide-protein interactions, and to a more detailed study of peptide-protein association in general.

The ClusPro web server for protein-protein docking

The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds

Energy evaluation using fast Fourier transforms (FFTs) enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods, efficient acceleration is achieved only in either the translational or the rotational subspace. Developing an efficient and accurate docking method that expands FFT-based sampling to five rotational coordinates is an extensively studied but still unsolved problem. The algorithm presented here retains the accuracy of earlier methods but yields at least 10-fold speedup. The improvement is due to two innovations. First, the search space is treated as the product manifold [Formula: see text], where [Formula: see text] is the rotation group representing the space of the rotating ligand, and [Formula: see text] is the space spanned by the two Euler angles that define the orientation of the vector from the center of the fixed receptor toward the center of the ligand. This representation enables the use of efficient FFT methods developed for [Formula: see text] Second, we select the centers of highly populated clusters of docked structures, rather than the lowest energy conformations, as predictions of the complex, and hence there is no need for very high accuracy in energy evaluation. Therefore, it is sufficient to use a limited number of spherical basis functions in the Fourier space, which increases the efficiency of sampling while retaining the accuracy of docking results. A major advantage of the method is that, in contrast to classical approaches, increasing the number of correlation function terms is computationally inexpensive, which enables using complex energy functions for scoring.

Bioaccumulation and speciation of selenium in fish and insects collected from a mountaintop removal coal mining-impacted stream in West Virginia

A major contaminant of concern for mountaintop removal/valley fill (MTR/VF) coal mining is selenium (Se), an essential micronutrient that can be toxic to fish. Creek chubs (Semotilus atromaculatus), green sunfish (Lepomis cyanellus), and composite insect samples were collected in March-July, 2011-2013 at two sites within the Mud River, West Virginia. One site (MR7) receives MTR/VF coal mining effluent, while the reference site (LFMR) does not. MR7 water had significantly higher concentrations of soluble Se (p < 0.01) and conductivity (p < 0.005) compared to LFMR. MR7 whole insects contained significantly higher concentrations of Se compared to LFMR insects (p < 0.001). MR7 creek chubs had significantly higher Se in fillets, liver, and ovary tissues compared to LFMR samples (p < 0.0001, p < 0.0001, and p < 0.02, respectively). MR7 green sunfish fillets contained significantly higher Se (p < 0.0001). Histological examination showed LFMR creek chub gills contained a typical amount of parasitic infestations; however MR7 gills contained minimal to no visible parasites. X-ray absorption spectroscopic analyses revealed that MR7 whole insects and creek chub tissues primarily contained organic Se and selenite. These two species of Mud River fish were shown to specifically accumulate Se differently in tissues compartments. Tissue-specific concentrations of Se may be useful in determining potential reproductive consequences of Se exposure in wild fish populations.

The CLRX.1/NOD24 (NLRP2P) pseudogene codes a functional negative regulator of NF-κB, pyrin-only protein 4

Pseudogenes are duplicated yet defunct copies of functional parent genes. However, some pseudogenes have gained or retained function. In this study, we consider a functional role for the NLRP2-related, higher primate-specific, processed pseudogene NLRP2P, which is closely related to Pyrin-only protein 2 (POP2/PYDC2), a regulator of nuclear factor-κB (NF-κB) and the inflammasome. The NLRP2P open-reading frame on chromosome X has features consistent with a processed pseudogene (retrotransposon), yet encodes a 45-amino-acid, Pyrin-domain-related protein. The open-reading frame of NLRP2P shares 80% identity with POP2 and is under purifying selection across Old World primates. Although widely expressed, NLRP2P messenger RNA is upregulated by lipopolysaccharide in human monocytic cells. Functionally, NLRP2P impairs NF-κB p65 transactivation by reducing activating phosphorylation of RelA/p65. Reminiscent of POP2, NLRP2P reduces production of the NF-κB-dependent cytokines tumor necrosis factor alpha and interleukin (IL)-6 following toll-like receptor stimulation. In contrast to POP2, NLRP2P fails to inhibit the ASC-dependent NLRP3 inflammasome. In addition, beyond regulating cytokine production, NLRP2P has a potential role in cell cycle regulation and cell death. Collectively, our findings suggest that NLRP2P is a resurrected processed pseudogene that regulates NF-κB RelA/p65 activity and thus represents the newest member of the POP family, POP4.

Variations in the effect of incarceration on community gonorrhoea rates, Guilford County, North Carolina, 2005-2006

Community incarceration rates have been shown to be associated with rates of HIV and sexually transmitted diseases (STDs). Mechanisms underlying this association include transmission by recently released inmates and community disruption resulting from the absence of incarcerated individuals. We studied the 2006 rates of gonorrhoea at the census tract level in Guilford County, North Carolina (NC) with the previous year's incarceration rates as the exposure of interest. We replicated an analysis conducted in Durham, NC, but unlike in Durham found no meaningful association. When terms were added to the model to allow for a non-linear effect, incarceration levels were associated with rates of gonorrhoea (P < 0.05), indicating the effect of incarceration on gonorrhoea rates differs based on the level of incarceration. Using a spatial model, we found evidence that the association varies across the county. The association between incarceration and gonorrhoea varies by the rate of incarceration and geographically.

A hundred years of the hepatotrophic controversy

Venous blood returning from the splanchnic viscera has liver-supporting (hepatotrophic) qualities not found to the same degree in other kinds of arterial or venous blood. The effects of portal blood have been noted in animals with two livers (or a differential portal blood supply to different regions of one liver) to include hypertrophy, glycogen storage, hyperplasia, capacity for regeneration, increase of several synthetic functions, and maintenance of normal structure. The main splanchnic venous hepatotrophic factors are endogenous hormones of which the single most important is insulin. Thus, the foregoing portal hepatotrophic effects are largely eliminated with the diabetes produced by alloxan or total pancreatectomy. The injury of portacaval shunt is caused by the diversion of the hormones around the liver. Accordingly, the atrophy, injury to the organelles, and loss of the capacity for cell renewal is minimized if insulin is infused into the portally deprived liver. In these and other experiments, exogenous glucagon alone or the addition of glucagon to insulin has had no effect, but this may be because of the masking presence of gut glucagon and other hormonal or non-hormonal substances in our models. At present, the effects on the liver of exogenous insulin, glucagon, epidermal growth factor, and numerous other hormones are being determined by their intraportal infusion into eviscerated dogs in which other endogenous splanchnic factors have been eliminated.

Portacaval shunt for glycogen storage disease and hyperlipidaemia

Complete portacaval shunt was used to treat 10 patients with glycogen storage disease. A favourable effect was noted on body growth and a number of metabolic abnormalities. More recently, continous night feedings with an intermittently placed gastric tube or through a gastrostomy has been shown to be helpful either before or after portacaval shunts. Such alimentation techniques may eliminate the need for shunts in some patients and be of adjuvant benefit in others. Portacaval shunt was also used for three children who had homozygous Type II hyperlipidaemia. Substantial reductions in serum cholesterol concentration were observed, as well as resorption of xanthomas. Reversal of some cardiovascular lesions has been documented. The benefits of portacaval shunt in these disorders is probably due to the change in the hormone climate of the liver and the whole organism brought about by diversion of the hormone-rich splanchnic venous blood around the liver.

Variation in the progression of diabetic nephropathy according to racial origin

BACKGROUND

In the United Kingdom, diabetic nephropathy is a leading cause of end-stage renal disease. There is a higher incidence amongst subjects of Indo-Asian and African-Caribbean origin compared with Caucasians that is not wholly explained by the differences in the prevalence of diabetes. Therefore, we postulated that this observation could be related to variations in the rate of progression of renal disease according to racial origin.

METHODS

We conducted a retrospective case-note review of 1684 adult attendees of the diabetes clinic. Forty-five patients were found with renal impairment (serum creatinine > or = 170 micromol/l) due to diabetic nephropathy. The patients were of Indo-Asian (n=10), African-Caribbean (n=11), and Caucasian (n=24) origin. Progression of nephropathy was assessed by analysing (i) the doubling of serum creatinine through construction of Kaplan-Meier curves and (ii) the slope (beta) of the rate of change in serum creatinine using linear regression analysis in relation to demographic variables, putative risk factors for nephropathy and antihypertensive drug therapy.

RESULTS

There were no statistically significant differences between systolic and diastolic blood pressure, glycaemic control, smoking habit, baseline proteinuria, and usage of angiotensin-converting enzyme inhibitors between the three groups. The proportion of patients doubling their creatinine was significantly higher in the Indo-Asian compared with the African-Caribbean and Caucasian groups (100, 45 and 50%; P=0.025 respectively). In addition, the mean (95% CI) of beta (micromol/l/month) was highest in the Indo-Asian (5.36 (2.21-8.52)) compared with the African-Caribbean (3.14 (0.82-5.46)) and Caucasian (2.22 (1.31-3.14)) groups (P=0.035). The mean ranks of beta were highest in the Indo-Asian group (P=0.038) after adjusting for marginal differences in blood pressure age, gender, baseline proteinuria, anti-hypertensive treatment, and smoking habit.

CONCLUSIONS

In this small cohort of type 2 diabetic subjects with established renal disease, the rate of decline in renal function is accelerated in Indo-Asian subjects. This observation could be related to differences in renoprotection from antihypertensive therapy.

Electrocautery as a factor in seroma formation following mastectomy

BACKGROUND

Electrocautery has been postulated as a factor in the risk of seroma formation after mastectomy.

METHODS

Eighty consecutive mastectomies in 74 patients were randomly assigned to dissection of the mastectomy flaps with either scalpel (n = 38) or electrocautery (n = 42). Total volume of fluid output through drains and aspirated from seromas was recorded. Other factors investigated included the type of drain utilized, estimated blood loss, and complications.

RESULTS

Seromas developed in 16 wounds in the electrocautery group compared with 5 in the scalpel group (38% and 13%, respectively; P = 0.01). Other factors with an independent risk for seroma included use of Jackson-Pratt drains compared with Blake drains (P = 0.006), and lower estimated blood loss (P = 0.006). No differences in characteristics of patients or in other complications were noted.

CONCLUSIONS

Use of electrocautery to create skin flaps in mastectomy reduced blood loss but increased the rate of seroma formation.

Clinicopathological features of Zimbabwean patients with sustained proteinuria

OBJECTIVE

To describe clinico-pathological features of patients admitted with significant proteinuria.

DESIGN

Hospital based prospective survey conducted from 1982 to 1987.

SETTING

Paediatric and medical wards at both tertiary referral hospitals in Harare.

SUBJECTS

119 patients who presented with significant proteinuria were investigated.

RESULTS

Of the primary nephritides, diffuse mesangial proliferative glomerulonephritis was the most common finding (25/119); IgM was the dominant or sole immunoglobulin identified in 17/25. Minor glomerular abnormalities were common (19/119); there were 11 patients with minimal change disease and this number accounted for 42% of the children aged three to 12 years who were nephrotic. This incidence is higher than previously reported from Africa. Diffuse membranous nephropathy was frequent (18/119); hepatitis B surface antigen was present in only five of these patients. Focal sclerosing glomerulo-sclerosis was as frequent as diffuse membranous nephropathy (18/119) and appeared to be idiopathic. Diffuse mesangiocapillary glomerulonephritis (membranoproliferative) was present in 15/119 patients; no causal association was made.

CONCLUSION

The pattern of primary glomerulonephritis is described from 1982 to 1987. We describe a slightly higher number of patients with minimal change disease and minor glomerular abnormalities than previously reported and a surprisingly small number of patients with diffuse endocapillary glomerulonephritis. In common with other African series, no patient with IgA nephropathy was found.

Breast cancer in elderly women: presentation, survival, and treatment options

Recent data suggest that breast cancer in elderly women does not present as more advanced disease, nor is survival significantly inferior to that in younger women. Unfortunately, until recently, older women have been excluded from clinical trials that have determined survival benefit in both screening and treatment modalities. Unless co-morbid conditions adversely affect one's life expectancy or tolerance to therapy, older women should be treated with standard surgical procedures (including breast conservation, if so desired) for early-stage disease, as outcome is comparable to that in younger patients. Adjuvant tamoxifen therapy has proven survival benefit in women over 70 years of age with estrogen receptor-positive tumors and should be considered in all women with tumors greater than 1 cm in size. Older women may experience more chemotherapy-related toxicities. However, for those with a significant risk of recurrence due to tumor size or lymph node status, chemotherapy can be safely administered when factors such as age-related decline in creatinine clearance and co-morbid conditions are considered. Hormonal therapy (tamoxifen) is usually the first-line treatment option over chemotherapy for metastatic disease in the elderly unless the patient has an estrogen receptor-negative tumor, visceral-dominant disease, or significant disease-related symptoms. In the latter settings, chemotherapy can provide improved or more rapid response proportions but does not affect long-term survival.

The current role of prophylactic mastectomy

Prophylactic mastectomy has a role in preventing breast cancer in the woman at high risk. The rare indications for this operation are based on genetic and histologic factors that affect relative or cumulative risk. Evaluation of women at high risk must draw on multidisciplinary expertise, including genetic counseling. If prophylactic mastectomy is recommended, skin-sparing total mastectomy (not subcutaneous) with autogenous tissue reconstruction is the preferred approach.

Inflammatory breast cancer

Multimodal therapy with induction chemotherapy has improved significantly local disease control and overall survival in patients with IBC. This is now considered standard therapy for patients with this disease. Although survival has been improved, well over 50% of these patients will succumb to this disease. Ongoing and future investigations may better define the optimal approach for local control, the optimal duration of maintenance chemotherapy, and the possible role of biologic response modifiers and growth factors in further improving the outcome for patients with this disease.

Cloning and sequence analysis of the rat augmenter of liver regeneration (ALR) gene: expression of biologically active recombinant ALR and demonstration of tissue distribution

A full-length cDNA clone encoding a purified augmenter of liver regeneration (ALR) factor prepared from the cytosol of weanling rat livers was isolated. The 1.2-kb cDNA included a 299-bp 5' untranslated region, a 375-bp coding region, and a 550-bp 3' untranslated region. It encoded a protein consisting of 125 amino acids. The molecular weight of ALR calculated from the cDNA was 15,081, which is consistent with the size estimated by SDS/PAGE under reducing conditions. The molecular weight of the purified native ALR estimated by SDS/PAGE under nonreducing conditions was approximately 30,000; thus ALR apparently has a homodimeric structure. The recombinant ALR produced by expression of the cDNA in COS cells was tested in vivo in the canine Eck fistula model and found to have potency equivalent to the purified native ALR. The 125-aa sequence deduced from the rat ALR cDNA shows 50% homology to the amino acid sequence of the gene for oxidative phosphorylation and vegetative growth in the yeast Saccharomyces cerevisiae.

Small-for-size liver transplanted into larger recipient: a model of hepatic regeneration

Orthotopic liver transplantation was performed in 60 recipient rats weighing 200 to 250 gm. Sixty rats of the same strain were used as liver donors, 30 weighing 100 to 140 gm (small for size) and the other 30 weighing 200 to 250 gm (same size). After 1, 2, 3, 4, 7 and 14 days (n = 5 each) DNA synthesis, nuclear thymidine labeling and mitoses were increased in both the small-for-size and same-size groups, but significantly more in the former. These changes were maximal after 48 to 72 hr, similar to but later than the well-known regeneration response after partial hepatectomy, which peaks at 24 hr in rats. Indirect indexes of regeneration of the transplanted livers also were measured: plasma or serum ornithine decarboxylase; insulin and glucagon serum levels; estradiol and testosterone serum levels (and their nuclear and cytosolic receptors); and transforming growth factor-beta, c-Ha-ras and c-jun mRNA expressions. With the small-for-size transplantation, these followed the same delayed pattern as the direct regeneration parameters. The small livers gradually increased in size over the course of 1 to 2 wk and achieved a volume equal to that of the liver originally present in the recipient. In contrast, no significant liver weight gain occurred in the transplanted livers from same-size donors despite the evidence of regeneration by direct indexes, but not by most of the surrogate parameters, including ornithine decarboxylase.

Functional imprinting and epigenetic modification of the human SNRPN gene

The SNRPN gene encodes a small nuclear ribonucleoprotein subunit, SmN, thought to be involved in splicing of pre-mRNA. A closely related protein, SmB/B', is constitutively expressed in all tissues except the brain, where SmN is predominantly expressed. The mouse homolog of the SNRPN gene has been shown to be functionally imprinted in mouse brain, being expressed only from the paternally derived chromosome. SNRPN has been mapped to human chromosome 15q11-q13 within the shortest region of deletion overlap for the Prader-Willi syndrome. We have now demonstrated functional imprinting of the human SNRPN gene using reverse transcription followed by the polymerase chain reaction (RT-PCR). No expression was observed in cultured skin fibroblasts of Prader-Willi patients, but was found in all Angelman patients and normal controls examined. We have also demonstrated a parent-specific DNA methylation imprint within intron 5 of the SNRPN gene, which suggests an epigenetic mechanism by which parent-specific expression of this gene might be inherited. Our findings indicate that SNRPN is expressed only from the paternally derived chromosome 15 in humans and therefore may fulfill one major criterion for being involved in the pathogenesis of the Prader-Willi syndrome.

Clinical features and natural history of central cavitary necrosis

Central cavitary necrosis (CCN) is an unusual complication of acute pancreatitis in which the necrosis is confined almost entirely to the pancreatic parenchyma and there is little if any extrapancreatic necrosis. In our experience with 10 patients with CCN, clinical features suggested that the episodes of acute pancreatitis were initially severe, with high Ranson scores (mean, 4.2; range, 1-6), development of systemic complications, computed tomography (CT) grade of D or E by the Balthazar-Ranson scoring system, need for intensive care unit admission in 8 of 10 patients, and mean length of hospitalization of 56 days (range, 28-153 days). However, the incidence of infection was low (20%) and mortality was also low (10%). Factors that help explain a favorable prognosis were low APACHE-II scores at admission and at 48 h, absence of shock, paucity of extrapancreatic necrosis, and rapid resolution of clinical toxicity prior to the diagnosis of CCN by CT scan at a mean of 19.8 days (range, 9-63 days) after the onset of symptoms. Surgical debridement is indicated for complications such as secondary infection and ongoing pain. In the absence of complications, an attempt should be made to treat CCN medically.

Prognostic factors in sterile pancreatic necrosis

Although the overall mortality in sterile pancreatic necrosis is low, patients who experience systemic complications may have a higher mortality. To study the impact of systemic complications and other factors on survival, possible prognostic factors were evaluated among 26 patients who experienced at least one systemic complication. Mortality was 38%. Factors that correlated with a fatal outcome were high Ranson's scores during the first 48 hours (P = 0.01), high APACHE-II scores at admission (P = 0.04) and at 48 hours (P = 0.03), shock (P < 0.001), renal insufficiency (P < 0.05), multiple systemic complications (P < 0.001), and high body mass index (P = 0.01). Most systemic complications occurred during the first 2 weeks of illness. Logistic regression analysis showed that shock was the best predictor of a fatal outcome. Patients with favorable prognostic factors survived whether treated medically or surgically, whereas those with unfavorable factors had a fatal outcome whether treated medically or surgically. It is concluded that patients with severe sterile necrosis have a high mortality rate and that shock and other prognostic factors identify which patients are most likely to have a fatal outcome.

Obesity as a predictor of severity in acute pancreatitis

In order to determine whether the presence of obesity, defined as increased body mass index, would serve as a predictor of severity in acute pancreatitis, we have reviewed the medical records of 27 patients with severe acute pancreatitis. All patients had at least four positive Ranson's signs; all but three patients had at least five Ranson's signs. When the 13 patients with a fatal outcome were compared with the 14 who lived, neither obesity nor respiratory failure was an independent predictor of death. However, when the 27 patients were analyzed on the basis of whether they were obese (15 patients) or not obese (12 patients), obesity was an independent predictor of respiratory failure. Obesity was not a predictor of renal failure, pancreatic necrosis, or need for surgery. We suggest that obese patients with severe acute pancreatitis require close monitoring for the development of respiratory failure.

Studies on mechanisms of augmentation of liver regeneration by cyclosporine and FK 506

Evidence could not be found of immune modulation of liver regeneration. The powerful immunosuppressive drug FK 506, which augments the response after partial hepatectomy in normal rats, had the same effect in T cell-deficient nude rats. The cytotoxicity of natural killer cells in treated nude rats was not significantly changed by FK 506 therapy. However, the serum of FK 506-treated nude rats increased hepatocyte proliferation when added to third-party hepatocyte cultures, suggesting that FK 506 had induced a serum growth factor in the nude rats or had suppressed an inhibitory factor. A hypothesis was advanced that FK 506 (and cyclosporine) affects hepatic growth by nonimmunological pathways.

Cyclosporine and liver regeneration studied by in vivo 31P nuclear magnetic resonance spectroscopy

The changes in fructose-1-phosphate (F-1-P), intracellular pH, and ATP content of the liver after a fructose challenge were investigated noninvasively in vivo using phosphorus-31 nuclear magnetic resonance spectroscopy of dog liver four days after a portacaval shunt (PCS) with or without portal venous infusion of cyclosporin (CsA). The F-1-P metabolism was slower in PCS dogs (N = 2) as compared to either the normal (N = 2) or PCS + CsA-treated dogs (N = 3) (P less than 0.05). The intracellular pH temporarily decreased from 7.3 +/- 0.05 to 7.0 +/- 0.05 during the fructose challenge. The regenerative indexes were increased in the PCS + CsA group (P less than 0.01). These data obtained in vivo using 31P-NMR spectroscopy in the liver following a portacaval shunt, suggest that: (1) the energy status of the liver and the metabolic response to fructose are reduced in PCS compared to normal animals and (2) CsA treatment enhances the regenerative response of the liver and prevents the reduction in hepatic function associated with portacaval shunting.

Selected topics on FK 506, with special references to rescue of extrahepatic whole organ grafts, transplantation of "forbidden organs," side effects, mechanisms, and practical pharmacokinetics

FK 506 is a superior immunosuppressive agent that should improve the grafting of organs that already are part of our every day transplant practices, as well as those which are presently impractical. Immune intervention for serious autoimmune diseases also should be a more attractive option with this drug. Lessons are still being learned about dosage and what determines safe dose schedules. At a basic level, the study of FK 506 and its comparison to CyA may have shed light on mechanisms and characteristics of the whole class of so-called macrolide immunosuppresants and their cytosolic binding sites.

Thermogenesis from intravenous medium-chain triglycerides

Eighteen hospitalized patients dependent on total parenteral nutrition (TPN) were randomly enrolled into a prospective study comparing intravenous long-chain triglycerides (LCT) with a physical mixture of 75% medium-chain triglycerides (MCT) and 25% LCT. The TPN was given continuously as amino acids and glucose over 5 days with the respective lipid emulsion given intermittently during each day for 10 hr. Indirect calorimetry was measured on each patient before the lipid emulsion was administered in the morning and again 10 hr later near the end of the lipid infusion, on days 1, 3, and 5. Resting energy expenditure, VO2, VCO2, and calculated fat oxidation were shown to increase during MCT infusion but not during LCT administration, (resting energy expenditure 899 +/- 37 to 1085 +/- 40, compared with 978 +/- 23 to 976 +/- 39, kcal/m2 body surface area [BSA]/day, respectively, p less than 0.0002; VO2: 129.9 +/- 5.2 to 157.2 +/- 5.9, compared with 140.9 +/- 3.6 to 141.2 +/- 5.9 ml O2/min/m2 BSA, respectively, p less than 0.0005; and VCO2: 110.7 +/- 4.4 to 127.5 +/- 4.3, compared with 118.3 +/- 2.8 to 118.0 +/- 5.3, ml CO2/min/m2 BSA, respectively, p less than 0.0076; calculated fat oxidation 10.7 +/- 1.5 to 19.3 +/- 2.4, compared with 20.0 +/- 2.7 to 20.0 +/- 3.6, kcal/m2 BSA/hr, respectively, p less than 0.014). Respiratory quotient tended to fall with lipid infusion but did not change statistically. Body temperatures were unaltered by either fat infusion. It is concluded that TPN consisting of MCT causes an increased thermogenesis, most likely through increased fat oxidation, reflective of MCT's property as an obligate fuel. The increased thermogenesis occurs without an increase in body temperature.

Hepatotrophic effects of FK506 in dogs

Portacaval shunt (Eck fistula) in dogs causes hepatocyte atrophy and organelle disruption, as well as tripling of hepatocyte mitoses. After submitting dogs to this procedure, FK506 was infused into the tied-off left portal vein. The size, anatomic quality, and replication of hepatocytes were enhanced in the portion of liver infused with FK506, with a significant spillover effect in the noninfused portion. These hepatotrophic qualities of FK506 may explain part of FK506's efficacy for the treatment of chronic liver rejection. Also, the observations support a trial with this drug for the treatment of autoimmune liver diseases because, in addition to turning off the immunologic genesis of such disorders, repair and regeneration of the damaged liver may be augmented. Finally, these hepatrophic qualities are part of an emerging spectrum of biologic effects caused by drugs that may modulate the enzyme cis-trans peptidyl-prolyl isomerase (PPIase), the principal constituent of the cytosolic binding sites of FK506, repatomycin, cyclosporine, and presumably other immunosuppressive drugs as yet undiscovered.

Disseminated, nonmeningeal gastrointestinal cryptococcal infection in an HIV-negative patient

Gastrointestinal cryptococcosis is extremely rare, especially in patients with no involvement of the central nervous system. We describe a 63-yr-old man undergoing prednisone therapy for chronic hepatitis and cirrhosis who presented with peritonitis, colitis, and skin lesions. Pathological studies revealed necrosis and numerous cryptococcal organisms in the colon, omentum, and skin, and cultures yielded Cryptococcus neoformans. The patient died of multisystem organ failure following emergency exploratory surgery performed when he had onset of symptoms of a bowel perforation after an endoscopic biopsy. Clinicians should be aware that gastrointestinal cryptococcosis can occur in the absence of infection of the central nervous system or lungs, and that it may affect relatively healthy patients who are immunocompromised because of splenectomy, chronic liver disease, or steroid therapy.

Pain insensitivity in schizophrenia. Case report and review of the literature

We describe a schizophrenic man whose lack of pain and related objective signs of a perforated small bowel led to a delay in diagnosis and surgical intervention. A review of the literature suggests that both psychodynamic and specific biologic factors can produce atypical presentations in psychotic patients with illnesses in which pain is characteristically a prominent presenting symptom. While research into the cause of altered pain perception in psychotic patients is continuing, clinicians should maintain a high index of suspicion of serious medical illness when evaluating such patients.

The hepatotropic influence of cyclosporine

The effect of cyclosporine on liver regeneration has been investigated in 25 dogs that underwent an end-to-side portacaval shunt (Eck fistula) followed by 4 days continuous infusion of the drug into the left branch of the portal vein. Three different cyclosporine infusion rates were used: 0.06, 0.6, and 4.0 mg/kg/day. Control animals received the intravenous vehicle of cyclosporine at the same rate as the treated animals; a second control group received insulin, 0.42 units/kg/day. Hepatocyte 3H-thymidine-labeled mitoses (index of hyperplasia) and hepatocyte volume (index of hypertrophy) were studied in the left (infused) and right (control) lobes in each animal. Cyclosporine vehicle had no measurable effect on hepatocytes that suffered typical atrophy and moderate increase in mitotic index after the Eck fistula. Cyclosporine infusion stimulated cell renewal significantly and restored hepatocyte size in the infused lobes with a dose-response relation. Similar positive effects were observed in the right (nonperfused) lobes, although they were less than those in the left (infused) lobes. This was because of an unmistakable spillover of cyclosporine from the infused lobes, especially in the large-dose group. No sign of hepatotoxicity was detected at any cyclosporine infusion rate. Cyclosporine has a remarkable hepatotropic effect that may be helpful in the context of liver transplantation.