Methylation risk scores are associated with a collection of phenotypes within electronic health record systems

Inference of clinical phenotypes is a fundamental task in precision medicine, and has therefore been heavily investigated in recent years in the context of electronic health records (EHR) using a large arsenal of machine learning techniques, as well as in the context of genetics using polygenic risk scores (PRS). In this work, we considered the epigenetic analog of PRS, methylation risk scores (MRS), a linear combination of methylation states. We measured methylation across a large cohort (n = 831) of diverse samples in the UCLA Health biobank, for which both genetic and complete EHR data are available. We constructed MRS for 607 phenotypes spanning diagnoses, clinical lab tests, and medication prescriptions. When added to a baseline set of predictive features, MRS significantly improved the imputation of 139 outcomes, whereas the PRS improved only 22 (median improvement for methylation 10.74%, 141.52%, and 15.46% in medications, labs, and diagnosis codes, respectively, whereas genotypes only improved the labs at a median increase of 18.42%). We added significant MRS to state-of-the-art EHR imputation methods that leverage the entire set of medical records, and found that including MRS as a medical feature in the algorithm significantly improves EHR imputation in 37% of lab tests examined (median R² increase 47.6%). Finally, we replicated several MRS in multiple external studies of methylation (minimum p-value of 2.72 × 10⁻⁷) and replicated 22 of 30 tested MRS internally in two separate cohorts of different ethnicity. Our publicly available results and weights show promise for methylation risk scores as clinical and scientific tools.

Robust Mendelian randomization in the presence of residual population stratification, batch effects and horizontal pleiotropy

Mendelian Randomization (MR) studies are threatened by population stratification, batch effects, and horizontal pleiotropy. Although a variety of methods have been proposed to mitigate those problems, residual biases may still remain, leading to highly statistically significant false positives in large databases. Here we describe a suite of sensitivity analysis tools that enables investigators to quantify the robustness of their findings against such validity threats. Specifically, we propose the routine reporting of sensitivity statistics that reveal the minimal strength of violations necessary to explain away the MR results. We further provide intuitive displays of the robustness of the MR estimate to any degree of violation, and formal bounds on the worst-case bias caused by violations multiple times stronger than observed variables. We demonstrate how these tools can aid researchers in distinguishing robust from fragile findings by examining the effect of body mass index on diastolic blood pressure and Townsend deprivation index.

Bladder Cancer Immunotherapy by BCG Is Associated with a Significantly Reduced Risk of Alzheimer's Disease and Parkinson's Disease

Bacillus Calmette–Guerin (BCG) is a live attenuated form of Mycobacterium bovis that was developed 100 years ago as a vaccine against tuberculosis (TB) and has been used ever since to vaccinate children globally. It has also been used as the first-line treatment in patients with nonmuscle invasive bladder cancer (NMIBC), through repeated intravesical applications. Numerous studies have shown that BCG induces off-target immune effects in various pathologies. Accumulating data argue for the critical role of the immune system in the course of neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). In this study, we tested whether repeated exposure to BCG during the treatment of NMIBC is associated with the risk of developing AD and PD. We presented a multi-center retrospective cohort study with patient data collected between 2000 and 2019 that included 12,185 bladder cancer (BC) patients, of which 2301 BCG-treated patients met all inclusion criteria, with a follow-up of 3.5 to 7 years. We considered the diagnosis date of AD and nonvascular dementia cases for BC patients. The BC patients were partitioned into those who underwent a transurethral resection of the bladder tumor followed by BCG therapy, and a disjoint group that had not received such treatment. By applying Cox proportional hazards (PH) regression and competing for risk analyses, we found that BCG treatment was associated with a significantly reduced risk of developing AD, especially in the population aged 75 years or older. The older population (≥75 years, 1578 BCG treated, and 5147 controls) showed a hazard ratio (HR) of 0.726 (95% CI: 0.529–0.996; p-value = 0.0473). While in a hospital-based cohort, BCG treatment resulted in an HR of 0.416 (95% CI: 0.203–0.853; p-value = 0.017), indicating a 58% lower risk of developing AD. The risk of developing PD showed the same trend with a 28% reduction in BCG-treated patients, while no BCG beneficial effect was observed for other age-related events such as Type 2 diabetes (T2D) and stroke. We attributed BCG’s beneficial effect on neurodegenerative diseases to a possible activation of long-term nonspecific immune effects. We proposed a prospective study in elderly people for testing intradermic BCG inoculation as a potential protective agent against AD and PD.

Automated identification of clinical features from sparsely annotated 3-dimensional medical imaging

One of the core challenges in applying machine learning and artificial intelligence to medicine is the limited availability of annotated medical data. Unlike in other applications of machine learning, where an abundance of labeled data is available, the labeling and annotation of medical data and images require a major effort of manual work by expert clinicians who do not have the time to annotate manually. In this work, we propose a new deep learning technique (SLIVER-net), to predict clinical features from 3-dimensional volumes using a limited number of manually annotated examples. SLIVER-net is based on transfer learning, where we borrow information about the structure and parameters of the network from publicly available large datasets. Since public volume data are scarce, we use 2D images and account for the 3-dimensional structure using a novel deep learning method which tiles the volume scans, and then adds layers that leverage the 3D structure. In order to illustrate its utility, we apply SLIVER-net to predict risk factors for progression of age-related macular degeneration (AMD), a leading cause of blindness, from optical coherence tomography (OCT) volumes acquired from multiple sites. SLIVER-net successfully predicts these factors despite being trained with a relatively small number of annotated volumes (hundreds) and only dozens of positive training examples. Our empirical evaluation demonstrates that SLIVER-net significantly outperforms standard state-of-the-art deep learning techniques used for medical volumes, and its performance is generalizable as it was validated on an external testing set. In a direct comparison with a clinician panel, we find that SLIVER-net also outperforms junior specialists, and identifies AMD progression risk factors similarly to expert retina specialists.

A machine learning algorithm to increase COVID-19 inpatient diagnostic capacity

Worldwide, testing capacity for SARS-CoV-2 is limited and bottlenecks in the scale up of polymerase chain reaction (PCR-based testing exist. Our aim was to develop and evaluate a machine learning algorithm to diagnose COVID-19 in the inpatient setting. The algorithm was based on basic demographic and laboratory features to serve as a screening tool at hospitals where testing is scarce or unavailable. We used retrospectively collected data from the UCLA Health System in Los Angeles, California. We included all emergency room or inpatient cases receiving SARS-CoV-2 PCR testing who also had a set of ancillary laboratory features (n = 1,455) between 1 March 2020 and 24 May 2020. We tested seven machine learning models and used a combination of those models for the final diagnostic classification. In the test set (n = 392), our combined model had an area under the receiver operator curve of 0.91 (95% confidence interval 0.87-0.96). The model achieved a sensitivity of 0.93 (95% CI 0.85-0.98), specificity of 0.64 (95% CI 0.58-0.69). We found that our machine learning algorithm had excellent diagnostic metrics compared to SARS-CoV-2 PCR. This ensemble machine learning algorithm to diagnose COVID-19 has the potential to be used as a screening tool in hospital settings where PCR testing is scarce or unavailable.

Benchmarking of computational error-correction methods for next-generation sequencing data

BACKGROUND

Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequencing technologies in clinical tools. Computational error correction promises to eliminate sequencing errors, but the relative accuracy of error correction algorithms remains unknown.

RESULTS

In this paper, we evaluate the ability of error correction algorithms to fix errors across different types of datasets that contain various levels of heterogeneity. We highlight the advantages and limitations of computational error correction techniques across different domains of biology, including immunogenomics and virology. To demonstrate the efficacy of our technique, we apply the UMI-based high-fidelity sequencing protocol to eliminate sequencing errors from both simulated data and the raw reads. We then perform a realistic evaluation of error-correction methods.

CONCLUSIONS

In terms of accuracy, we find that method performance varies substantially across different types of datasets with no single method performing best on all types of examined data. Finally, we also identify the techniques that offer a good balance between precision and sensitivity.

Systematic benchmarking of omics computational tools

Computational omics methods packaged as software have become essential to modern biological research. The increasing dependence of scientists on these powerful software tools creates a need for systematic assessment of these methods, known as benchmarking. Adopting a standardized benchmarking practice could help researchers who use omics data to better leverage recent technological innovations. Our review summarizes benchmarking practices from 25 recent studies and discusses the challenges, advantages, and limitations of benchmarking across various domains of biology. We also propose principles that can make computational biology benchmarking studies more sustainable and reproducible, ultimately increasing the transparency of biomedical data and results.

Benchmarking studies are important for comprehensively understanding and evaluating different computational omics methods. Here, the authors review practices from 25 recent studies and propose principles to improve the quality of benchmarking studies.

Comparison of pQCT parameters between ulna and radius in retired elite gymnasts: the skeletal benefits associated with long-term gymnastics are bone- and site-specific

OBJECTIVES

To compare the skeletal benefits associated with gymnastics between ulna and radius.

METHODS

19 retired artistic gymnasts, aged 18-36 years, were compared to 24 sedentary women. Bone mineral content (BMC), total and cortical bone area (ToA, CoA), trabecular and cortical volumetric density (TrD, CoD) and cortical thickness (CoTh) were measured by pQCT at the 4% and 66% forearm.

RESULTS

At the 4% site, BMC and ToA were more than twice greater at the radius than ulna whereas at the 66% site, BMC, ToA, CoA, CoTh and SSIpol were 20 to 51% greater at the ulna than radius in both groups (p<0.0001). At the 4% site, the skeletal benefits in BMC of the retired gymnasts over the non-gymnasts were 1.9 times greater at the radius than ulna (p<0.001), with enlarged bone size at the distal radius only. In contrast, the skeletal benefits at the 66% site were twice greater at the ulna than radius for BMC and CoA (p<0.01).

CONCLUSION

Whereas the skeletal benefits associated with long-term gymnastics were greater at the radius than ulna in the distal forearm, the reverse was found in the proximal forearm, suggesting both bones should be analysed when investigating forearm strength.

Vector Transmission of Xylella fastidiosa to Dormant Grape

Homalodisca coagulata (Say) is a sharpshooter leafhopper vector of the bacterial plant pathogen Xylella fastidiosa. Introduced into California about 15 years ago, this insect triggered recent outbreaks of Pierce's disease of grapevine in the state. H. coagulata has been observed feeding on dormant grapevines during the winter, raising the possibility of X. fastidiosa transmission during that season. We tested whether H. coagulata can acquire X. fastidiosa from and inoculate the bacterium to dormant grape (Vitis vinifera) in the laboratory and in the field. Usually, >90% of H. coagulata survived on dormant plants in the laboratory and field. Field experiments showed that H. coagulata can inoculate X. fastidiosa into dormant plants, yet field acquisition experiments did not result in transmission. Transmission to dormant plants during the winter is a potential problem in California vineyards adjacent to citrus groves or other habitats with large overwintering populations of H. coagulata. Because dormant plants have positive root pressure, our findings provide evidence that X. fastidiosa transmission does not require negative pressure in plant xylem to be inoculated into plants.

Leptin directly regulates bone cell function in vitro and reduces bone fragility in vivo

Fat mass is an important determinant of bone density, but the mechanism of this relationship is uncertain. Leptin, as a circulating peptide of adipocyte origin, is a potential contributor to this relationship. Recently it was shown that intracerebroventricular administration of leptin is associated with bone loss, suggesting that obesity should be associated with low bone mass, the opposite of what is actually found. Since leptin originates in the periphery, an examination of its direct effects on bone is necessary to address this major discrepancy. Leptin (>10(-11) m) increased proliferation of isolated fetal rat osteoblasts comparably with IGF-I, and these cells expressed the signalling form of the leptin receptor. In mouse bone marrow cultures, leptin (>or=10(-11) m) inhibited osteoclastogenesis, but it had no effect on bone resorption in two assays of mature osteoclasts. Systemic administration of leptin to adult male mice (20 injections of 43 micro g/day over 4 weeks) reduced bone fragility (increased work to fracture by 27% and displacement to fracture by 21%, P<0.001). Changes in tibial histomorphometry were not statistically significant apart from an increase in growth plate thickness in animals receiving leptin. Leptin stimulated proliferation of isolated chondrocytes, and these cells also expressed the signalling form of the leptin receptor. It is concluded that the direct bone effects of leptin tend to reduce bone fragility and could contribute to the high bone mass and low fracture rates of obesity. When administered systemically, the direct actions of leptin outweigh its centrally mediated effects on bone, the latter possibly being mediated by leptin's regulation of insulin sensitivity.

CD34+ cells from mobilized peripheral blood retain fetal bone marrow repopulating capacity within the Thy-1+ subset following cell division ex vivo

Ex vivo cell cycling of hematopoietic stem cells (HSC), a subset of primitive hematopoietic progenitors (PHP) with engrafting capacity, is required for transduction with retroviral vectors and to increase transplantable HSC numbers. However, induction of division of HSC ex vivo also may lead to differentiation and loss of in vivo marrow repopulating potential. We evaluated mobilized peripheral blood (MPB) PHP for maintenance of stem cell function after ex vivo culture under conditions that we show can induce cycling of a majority of PHP with minimal differentiation. The following methods were combined: cell labeling with the division tracking dye carboxyfluorescein-diacetate succinimidylester (CFSE), analysis of primitive cell surface marker expression, an ex vivo PHP assay, and an in vivo marrow repopulating assay. MPB-purified CD34+ Thy-1+ cells were labeled with CFSE dye and cultured for 112 hours in serum-deprived medium in the presence of the cytokine combinations of thrombopoietin (TPO), flt3 ligand (FL), and c-kit ligand (KL), or TPO, FL, and interleukin 6 (IL-6). Both cytokine combinations supported division of greater than 95% of cells within 112 hours with an average 2.1-fold (TPO, FL, KL) or 1.3-fold (TPO, FL, IL-6) increase in total cell numbers. An average of 21.6% (TPO, FL, KL) and 27.4% (TPO, FL, IL-6) of the divided cells still expressed the Thy-1 marker after 112 hours. Functional assays were performed to compare cultured and uncultured cells. CD34+ Thy-1+ CFSElo (post division) cells showed maintenance of cobblestone area-forming cell (CAFC) frequency (a mean of 1/9.0) relative to the starting population of uncultured CD34+ Thy-1+ cells (a mean of 1/8.4). In contrast, CD34+ cells that had lost Thy-1 expression during culture (CD34+ Thy-1 CFSElo) showed a mean 5.8-fold reduction in CAFC frequency (a mean of 1/52.5). Only the Thy-1-expressing fraction of cells post culture could engraft in vivo in the SCID-hu bone assay. Because the majority of HSC functional activity post culture was found in the CD34+ Thy-1+ fraction, we focused on this fraction for subsequent analysis. CFSE labeling allows segregation and purification by flow cytometry of cells having undergone discrete numbers of divisions during culture. Very few cells that divided more than four times in culture still expressed Thy-1. Cells that retained expression of Thy-1 during culture retained CAFC activity relative to fresh CD34+ Thy-1+ cells, after undergoing at least two divisions. CAFC frequency decreased after four divisions in culture with TPO, FL, and KL or after three divisions in TPO, FL, and IL-6. We then compared populations of Thy-1+ cells that had undergone sequential numbers of divisions in culture for their ability to engraft in the SCID-hu bone assay. Engrafting ability was retained throughout four divisions in both cytokine combinations. These data demonstrate that primitive MPB CD34+ cells maintain HSC function coincident with Thy-1 expression while undergoing two to four divisions under these culture conditions. Essentially all CD34+ Thy-1+ cells divided under the conditions tested, promoting susceptibility to retroviral transduction.

Thrombopoietin, flt3, and kit ligands together suppress apoptosis of human mobilized CD34+ cells and recruit primitive CD34+ Thy-1+ cells into rapid division

Various combinations of cytokines have profoundly different effects on inhibition of apoptosis and stimulation of self-renewal division of hematopoietic stem cells (HSC) in short-term, ex vivo culture. Our goal was to quantitate expansion of cells with a primitive CD34+ Thy-1+ phenotype, as well as cell cycling, division history, differentiation, and apoptosis of CD34+ cells enriched from normal donor mobilized peripheral blood (MPB) cells. The balance of these parameters determines the net number of transplantable HSC produced in ex vivo cultures. Comparing several different combinations of cytokines added to 90-hour cultures of MPB CD34 cells, thrombopoietin (TPO), flt3 ligand (FL), and c-kit ligand (KL) gave the best result, with the lowest percentage of apoptotic cells and a mean 1.2-fold increase in the number of CD34+ Thy-1+ cells. A combination of interleukin 3 (IL-3), interleukin 6 (IL-6), and leukemia inhibitory factor (LIF) gave the worst outcome, including a decrease of CD34+ Thy-1+ cell number to a mean of 30% of the starting cell number. Cell division history was tracked using the dye 5-(and 6-) carboxyfluorescein diacetate succinimidyl ester (CFSE). Division of CD34+ Thy-1+ cells was faster and more synchronous in TPO, FL, and KL than in IL-3, IL-6, and LIF, which left a significant proportion of CD34+ cells undivided. Such detailed analyses of short-term, ex vivo cultures generated "replication scores," which allowed prediction of a sixfold improvement of the efficiency of gene transduction of primitive hematopoietic progenitors from MPB, using TPO, FL, and KL to replace IL-3, IL-6, and LIF. Analysis of retroviral transduction efficiency confirmed the increase of transgene expression from MPB primitive hematopoietic progenitors assayed after stromal culture was fivefold, validating the usefulness of multiparameter analysis of short-term cultures for survival and replication of CD34+ Thy-1+ cells.

Thrombopoietin, kit ligand, and flk2/flt3 ligand together induce increased numbers of primitive hematopoietic progenitors from human CD34+Thy-1+Lin- cells with preserved ability to engraft SCID-hu bone

CD34(+)Thy-1(+)Lin- cells are enriched for primitive hematopoietic progenitor cells (PHP), as defined by the cobblestone area-forming cell (CAFC) assay, and for bone marrow (BM) repopulating hematopoietic stem cells (HSC), as defined by the in vivo SCID-hu bone assay. We evaluated the effects of different cytokine combinations on BM-derived PKH26-labeled CD34(+)Thy-1(+)Lin- cells in 6-day stroma-free cultures. Nearly all (>95%) of the CD34(+)Thy-1(+)Lin- cells divided by day 6 when cultured in thrombopoietin (TPO), c-kit ligand (KL), and flk2/flt3 ligand (FL). The resulting CD34(hi) PKHlo (postdivision) cell population retained a high CAFC frequency, a mean 3.2-fold increase of CAFC numbers, as well as a capacity for in vivo marrow repopulation similar to freshly isolated CD34(+)Thy-1(+)Lin- cells. Initial cell division of the majority of cells occurred between day 2 and day 4, with minimal loss of CD34 and Thy-1 expression. In contrast, cultures containing interleukin-3 (IL-3), IL-6, and leukemia inhibitory factor contained a mean of 75% of undivided cells at day 6. These CD34(hi) PKHhi cells retained a high frequency of CAFC, whereas the small population of CD34(hi) PKHlo postdivision cells contained a decreased frequency of CAFC. These data suggest that use of a combination of TPO, KL, and FL for short-term culture of CD34(+)Thy-1(+)Lin- cells increases the number of postdivision PHP, measured as CAFC, while preserving the capacity for in vivo engraftment.

Populations of Xylella fastidiosa in Plants Required for Transmission by an Efficient Vector

ABSTRACT Xylella fastidiosa, a xylem-limited bacterium that causes Pierce's disease (PD) of grapevine and other diseases, is transmitted efficiently by xylem-feeding leafhoppers. Acquisition of a PD strain of X. fastidiosa by the blue-green sharpshooter (BGSS) from five plant host species-grapevine (Vitis vinifera), Himalayan blackberry (Rubus discolor), California mugwort (Artemisia douglasiana), watergrass (Echinochloa crus-galli), and Bermuda grass (Cynodon dactylon)-was tested at various time intervals after vector inoculation. The minimum incubation periods in plant hosts before BGSS acquired X. fastidiosa were 4, 22, 29, and 25 days for grapevine, blackberry, mugwort, and watergrass, respectively. There were no transmissions by vectors or recoveries of X. fastidiosa by culturing from Bermuda grass in 133 attempts, including 80 attempts with the green sharpshooter, Draeculacephala minerva. The first acquisitions and subsequent transmissions by BGSS occurred after X. fastidiosa multiplied to a population of about 10(4) CFU/g of stem tissue. Higher populations of bacteria in plants resulted in higher rates of transmission. In grapevine, the rate of transmission increased over time (4.5% in the first 10 days to 55% after day 25) as the maximum number of viable CFU of X. fas-tidiosa recovered by culturing also increased (from 5 x 10(5) CFU/g during the first 10 days to 5 x 10(8) after day 25).

Glycosaminoglycans of the uterine and vaginal cul-de-sac tissue in the brushtail possum (Trichosurus vulpecula)

Live-captured feral brushtail possums (Trichosurus vulpecula) received slow-release progestagen implants for 16 days after removal of pouch young. At the time of implant removal one group was injected intramuscularly with pregnant mare serum gonadotrophin (PMSG, 2 I.U. kg-1 in 0.2 mL saline) and another group received an equivalent volume of sterile saline. Animals from each group were killed on Days 0, 3, 4, 5 or 6 after implant removal (PMSG, n = 4 per day; saline controls, n = 3 per day). The uterus and vaginal cul-de-sac were excised and tissue was analysed for glycosaminoglycans (GAGs) and keratan sulfate content. GAG concentration increased progressively over the six-day period following implant removal. Mean uterine GAG concentrations were significantly higher than those in vaginal cul-de-sac from Day 3 to Day 6 in PMSG-treated and saline-treated animals following progestagen implant removal (P < 0.05). Keratan sulfate concentrations showed a similar response--concentrations were higher in uterine tissue than in vaginal cul-de-sac tissue and PMSG-treated animals showed a greater response than did saline controls in the uterine tissue, but the same response in cul-de-sac tissue (P < 0.05 for all groups). The progressive increase in GAG concentrations of reproductive tract tissue following removal of the progesterone implant is indicative of hormonal stimulation and suggests that GAGs may have a supportive role in gamete and embryo nutrition and growth in the brushtail possum.

The interaction of calmodulin with clathrin-coated vesicles, triskelions, and light chains. Localization of a binding site

The binding of clathrin-coated vesicles, clathrin triskelions, and free clathrin light chains to calmodulin-Sepharose was compared. When isolated from bovine brain, all three components bound to calmodulin-Sepharose in the presence of calcium and could be eluted by its removal. In contrast, coated vesicles and triskelions isolated from bovine adrenal gland did not bind to calmodulin-Sepharose, although the free light chains from adrenal gland bound as effectively as those from brain. As distinct isoforms of the clathrin light chains are expressed by brain and adrenal gland, these results implicate the clathrin light chains as the calmodulin-binding component of coated vesicles and triskelions. Furthermore, the insertion sequences found in the neuron-specific isoforms, although not necessary for the binding of free clathrin light chains to calmodulin, must facilitate the interaction of heavy chain-associated light chains with calmodulin. Recombinant mutants of LCa, with deletions spanning the entire sequence, were tested for binding to calmodulin-Sepharose. Those mutants retaining structural integrity, as assessed by the binding of a panel of monoclonal antibodies, exhibited varying amounts of calmodulin binding activity. However, deletion of the carboxyl-terminal 20 residues abolished calmodulin interaction. Thus, the carboxyl terminus of LCa appears to constitute a calmodulin-binding site. Peptides corresponding to the carboxyl terminus of LCa or LCb inhibited the interaction of the light chains with calmodulin, suggesting that this region forms the calmodulin-binding site of both LCa and LCb. The carboxyl-terminal peptides of LCa and LCb inhibited the interaction of light chains with calmodulin approximately 10-fold less effectively than a calmodulin-binding peptide derived from smooth muscle myosin light chain kinase, but much more effectively than a calmodulin-binding peptide derived from adenylate cyclase. This comparison places the clathrin light chain-calmodulin interaction within the physiological range seen for other calmodulin-binding proteins.

Peptide sequences from the hypervariable regions of two monoclonal anti-idiotypic antibodies against the thyrotropin (TSH) receptor are similar to TSH and inhibit TSH-increased cAMP production in FRTL-5 thyroid cells

Monoclonal antibodies, D2 and 4G11, selected by the autoantiidiotypic approach following injection of thyrotropin (TSH) into mice, mimic TSH in binding to receptors on thyroid membranes. Based on TSH receptor transfection studies, D2 and 4G11 show unequivocal specificity for the TSH receptor. To see if the complementary determining regions (CDRs) of these antibodies share any primary sequence similarities to regions of TSH critical for receptor binding, we deduced the primary structure of the variable regions of D2 and 4G11 by sequencing the immunoglobulin mRNA. We found that CDR1 of 4G11K and CDR2 of D2 mu show sequence similarity to regions of TSH alpha and TSH beta that had been previously implicated in the interaction of the hormone with its receptor. We tested the inhibitory effects of synthetic peptides from D2 mu-CDR2 and 4G11K-CDR1 on the binding of the corresponding antibodies to rat thyroid FRTL-5 cells and found an EC50 of 0.1 and 1 microM, respectively. TSH-derived peptides with similarity to D2 mu-CDR2 and 4G11K-CDR1 showed a significant but lesser effect on the binding of 4G11 or D2 to thyroid cells. Additionally, we tested the effects of the CDR peptides and TSH-derived peptides on TSH-stimulated cAMP production in FRTL-5 cells and found that D2 mu-CDR2 and 4G11K-CDR1 inhibited this activity, D2 mu-CDR2 most strongly (EC50 10 microM). Thus, linear sequences from the CDRs of these autoantiidiotypic antibodies with similarity to sequences from both subunits of TSH appear to interact with the TSH receptor. These data support previous studies indicating the complexity of the interaction between TSH and its receptor and advance earlier findings that such immunologic approaches are useful in dissecting receptor-ligand interactions.

Clathrin light chains: arrays of protein motifs that regulate coated-vesicle dynamics

Polymerization of clathrin triskelions into clathrin coats and subsequent disassembly by the heat shock protein hsc70 control receptor-mediated pathways of intracellular transport. The clathrin light chains are major regulatory elements in these processes. These polypeptides consist of linear arrays of functional domains with distinctive sequence motifs. Comparison of unicellular and multicellular eukaryotes reveals differences in the numbers of clathrin light chains and in the functional domains they contain.

The calcium-binding site of clathrin light chains

Clathrin light chains are calcium-binding proteins (Mooibroek, M. J., Michiel, D. F., and Wang, J. H. (1987) J. Biol. Chem. 262, 25-28) and clathrin assembly can be modulated by calcium in vitro. Thus, intracellular calcium may play a regulatory role in the function of clathrin-coated vesicles. The structural basis for calcium's influence on clathrin-mediated processes has been defined using recombinant deletion mutants and isolated fragments of the light chains. A single calcium-binding site, formed by residues 85-96, is present in both mammalian light chains (LCa and LCb) and in the single yeast light chain. This sequence has structural similarity to the calcium-binding EF-hand loops of calmodulin and related proteins. In mammalian light chains, the calcium-binding sequence is flanked by domains that regulate clathrin assembly and disassembly.

Uncoating protein (hsc70) binds a conformationally labile domain of clathrin light chain LCa to stimulate ATP hydrolysis

Uncoating of clathrin-coated vesicles is mediated by the heat shock cognate protein, hsc70, and requires clathrin light chains (LCa and LCb) and ATP hydrolysis. We demonstrate that purified light chains and synthetic peptides derived from their sequences bind hsc70 to stimulate ATP hydrolysis. LCa is more effective than LCb in stimulating hsc70 ATPase and in inhibiting clathrin uncoating by hsc70. These differences correlate with high sequence divergence in the proline- and glycine-rich region (residues 47-71) that forms the hsc70 binding site. For LCa, but not LCb, this region undergoes reversible conformational changes upon perturbation of the ionic strength or the calcium ion concentration. Our results show that LCa is more important for interactions with hsc70 than is LCb and suggest a model in which the LCa conformation regulates coated vesicle uncoating.

Blindness in a dog with IgA-forming myeloma

A 9-year-old dog with a 2-month history of weight loss and a 1-week history of blindness had an IgA-forming myeloma. Seemingly, the blindness was a result of bilaterally detached retinas. The dog also had leukopenia, anemia, hypoalbuminemia, hyperglobulinemia, and proteinuria as well as lytic lesions in the cervical portion of the spine and high IgA concentrations in serum and urine. Evaluation of aspirates from the subretinal spaces revealed lymphocytes in a proteinaceous fluid. Histologically, retinal lesions consisted of vascular endothelial cell damage and intraretinal cysts and hemorrhages.

Studies of possible antiidiotypic control mechanisms in Graves' disease

Serum from 55 patients with active Graves' disease and 55 patients who had received successful treatment (in whom the disease was inactive) were examined for the presence of possible antiidiotypic antibodies with an enzyme-linked immunosorbent assay (ELISA) for anti-F(ab')2. Murine IgG monoclonal antibodies (Mabs) against human thyroid-stimulating hormone (TSH) and human TSH receptors were also used as antigens in parallel ELISA assays. Patients with active and patients with inactive Graves' disease showed elevations of IgG anti-F(ab')2 antibodies when compared with normal controls. Similarly, both active and inactive Graves' disease sera showed higher levels of IgG anti-LE4, a mouse Mab to human TSH, than was seen with normal controls. However, F(ab')2 isolated from sera reacting with LE4 in the ELISA did not inhibit binding of the LE4 Mab with labeled TSH in a fluid phase competition assay. Patients with inactive Graves' disease showed higher ELISA reactivity with two different murine anti-TSH receptor Mabs than was recorded with either active Graves' or normal controls. A rough inverse correlation was noted between strongly positive ELISA reactions against these two Mabs with anti-TSH receptor specificity and the ability of immunoglobulins from inactive Graves' sera to stimulate increases in cyclic adenosine monophosphate (cAMP) in the normal rat thyroid cell line assay. Untreated Graves' sera showing high cAMP release only rarely showed elevated ELISA reactivity against Mabs with anti-TSH receptor activity.

Monoclonal antibodies to the thyrotropin receptor raised by an autoantiidiotypic protocol and their relationship to monoclonal autoantibodies from Graves' patients

Monoclonal antibodies that bind to the TSH receptor were obtained by an autoantiidiotypic approach in which immunization of BALB/c mice was performed with mixtures of bovine (b) and human (h) TSH. Two of 28 positive wells were selected for cloning and characterization: D2 and 4G11. Their antiidiotypic character was evidenced by TSH-inhibitable binding to affinity-purified polyclonal anti-TSH. The specificity of D2 and 4G11 for the hormone-binding region of the TSH receptor was demonstrated by several findings: 1) they inhibited the binding of [125I]iodo-bTSH to receptor in a dose-dependent manner; 2) their binding to partially purified thyroid plasma membranes could be completely inhibited by bTSH and hTSH; and 3) they inhibited the TSH-dependent growth and adenylate cyclase stimulation in FRTL-5 cells in a dose-dependent manner. By Western blot analysis of bovine thyroid membranes, D2 bound to a polypeptide of 188,000-195,000 mol wt under nonreducing conditions and 54,000-59,000 mol wt after treatment of membranes with beta-mercaptoethanol; the 4G11 epitope was undetectable. Scatchard analysis of the binding of 125I-labeled antibodies to receptor showed that 4G11 bound to a single site with a Kd of 5.7 X 10(-9) M, whereas D2 showed complex binding characterized by high affinity (Kd = 1.74 X 10(-11) M) and low affinity (Kd = 1.3 X 10(-8) M) sites. Binding studies in which D2 and 4G11 competed with each other for the TSH receptor showed mutual but unequal inhibition. The data suggest that portions of the D2 and 4G11 epitopes overlap, but that there is a high affinity binding site(s) for D2 for which 4G11 competes less effectively. The binding of D2 and 4G11 to TSH receptor was inhibited by monoclonal antibodies secreted by Graves' heterohybridomas, showing that D2 and 4G11 share characteristics with autoantibodies of Graves' disease and lending support to the hypothesis that idiotypic network interactions may play a role in the pathogenesis of Graves' disease.

Identification of the phosphorylation sites of clathrin light chain LCb

Clathrin light chains, LCa and LCb, are products of two closely related genes whose mRNAs undergo differential splicing to result in at least four different light chain isoforms. The physiological significance of clathrin light chain diversity remains unclear. To date, the only evidence for a functional distinction of LCa and LCb is the preferential phosphorylation of LCb, which takes place at serine residues and is mediated by coated vesicle-associated casein kinase II. As a first step toward determining the function of light chain diversity, we have mapped the in vitro phosphorylation sites on LCb. We use [32P]ATP to phosphorylate LCb within coated vesicles, followed by sequencing of 32P-labeled chymotryptic peptides thereof, to identify serine residues at positions 11 and 13 as the phosphorylation sites. We find that phosphorylation of LCb within coated vesicles can be inhibited by four monoclonal antibodies specific for different epitopes of the clathrin light chains.

Chronic obstructive pulmonary disease in a dog

Chronic obstructive pulmonary disease was diagnosed in a 3-year-old Basset Hound that was referred to the hospital because of respiratory distress. Results of radiography, bronchoscopy, and pulmonary function tests indicated lung hyperinflation, airflow restriction, and loss of elastic recoil of the lungs. Because of the poor response to treatment, the dog was euthanatized. Postmortem findings revealed emphysema, bronchiectasis, and bronchitis, which comprise chronic obstructive pulmonary disease.

Characterization of a bioeffective monoclonal antibody against thyrotropin beta-subunit

To describe a region of the TSH molecule participating in binding to receptor, a monoclonal antibody specific for a TSH epitope shared by beta-subunits of bovine (b), ovine (o), and human (h) TSH was obtained by immunization with mixtures of purified bTSH and hTSH. RIAs showed that the antibody also bound the beta-subunits of bLH, oLH, hLH, and hCG, but not the beta-subunits of porcine LH and TSH. Preincubation of [125I]iodo-bTSH with the antibody completely inhibited binding of the hormone to the TSH receptor of bovine thyroid membrane preparations at pH 7.4 in 50 mM NaCl (ED50 = 10 nM). The antibody also inhibited TSH-induced mitogenesis of FRTL-5 cells (ED50 = 50 nM). We conclude that the antibody binds to a site on the bTSH molecule that participates in high affinity binding of hormone to physiological TSH receptor. The target epitope includes a conserved structural determinant in beta-subunits of the glycoprotein hormones as well as a feature that allows discrimination of porcine hormones from those of bovine, ovine, and human origin.

Response of pups to modified-live canine parvovirus component in a combination vaccine

Twenty-eight pups from a general pet population were vaccinated for canine parvovirus (CPV) with a combination vaccine every 3 weeks until the pups were 11 to 16 weeks old. Canine parvovirus antibody titers were measured by serum neutralization before each vaccination and greater than or equal to 2 weeks after the final vaccination. Eighteen pups that initially were seronegative for CPV seroconverted after 1 to 3 doses of modified-live virus CPV vaccine administered when the pups were between 8 and 16 weeks old; 16 of 18 seroconverted after the 1st dose. Of 10 pups that were seropositive for CPV at initial examination, 7 did not develop protective titers after 3 doses of vaccine, with the last dose given when the pups were 14 to 16 weeks old. Maternally derived antibody was the primary cause of vaccination failure.

Ventricular preexcitation in seven dogs and nine cats

Ventricular preexcitation was diagnosed in 6 dogs and 7 cats examined because of weakness, syncope, or congestive heart failure, and as an incidental finding in 1 dog and 2 cats. Reciprocating tachycardias were documented in 8 of the cases. Six of the cats had a pathologic diagnosis of primary cardiomyopathy. Two of the dogs had an associated congenital heart defect. Reciprocating tachycardias were controlled in 4 cases with digoxin, in 2 cases with propranolol, and in 1 case with quinidine. Conduction through the accessory pathway was altered by quinidine (2 cases), digoxin, and propranolol (1 case each), resulting in a lengthened P-R interval and more normal QRS complex configuration.

Immobilized cholinesterase to detect airborne concentrations of hexamethylene diisocyanate (HDI)

A sensitive personal passive dosimeter, based on an enzymatic reaction, was developed to monitor exposure to airborne concentrations of hexamethylene diisocyanate (HDI), used in the production of polyurethanes. Dosimeters were prepared by adsorption of butyryl- or acetylcholinesterase on sheets of polystyrene. Exposure of enzyme-coated strips to vapors of isocyanates demonstrated their great sensitivity to HDI. Dosimeters detected workplace exposure levels of 5 ppb (NIOSH recommended threshold limit value) within 12 min. Dosimeters responded to higher concentrations of toluene diisocyanate (TDI). Interference by TDI and other anticholinesterase agents is unlikely as they would not be expected to be present in the same industrial workplace.

Patent ductus arteriosus with pulmonary hypertension in the dog

The clinical, physiologic, and pathologic manifestations of patent ductus arteriosus (PDA) with pulmonary hypertension (right to left type PDA) were studied in 5 dogs. Cyanosis, hindlimb collapse, low-intensity heart murmurs, and splitting of the 2nd heart sound were prominent clinical findings. Secondary polycythemia was a feature in 3 dogs. Electrocardiography revealed marked frontal plane right axis deviation in all dogs. Radiographic findings in all dogs consisted of an enlarged right ventricle and main pulmonary artery segment, with a hypovascular pulmonary pattern. A wide descending aorta was evident in 4 dogs. Pulmonary arteriography revealed blunt, tortuous secondary and tertiary vessels. Blood flow through the PDA was from right to left in 4 dogs and bidirectional in 1. Necropsy of 1 dog revealed extensive pulmonary arterial disease characterized by fibromuscular intimal proliferation. Surgical correction was contraindicated, and medical therapy was not required in the 4 dogs retained by the owners as pets. Due to the persisting congenital heart defect and the real and potential sequelae, the prognosis is guarded.

Traumatically induced bullous lung lesions in the dog: a radiographic report of three cases

Three dogs with automobile-induced trauma had radiographic evidence of multiple bullous pulmonary lesions. Two of these dogs were subsequently reexamined, and resolution of their lesions was demonstrated radiographically.