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PubMed2002

Calpain 10 and genetics of type 2 diabetes.

Positional cloning studies conducted on a region of chromosome 2q providing evidence for linkage to type 2 diabetes implicated genetic variation at the calpain-10 gene (CAPN10) in susceptibility to type 2 diabetes. The variants identified in these studies are located in introns, rather than in coding sequence. It was proposed that the cumulative effects of a combination of variants, rather than variation at a single site, increase the risk of type 2 diabetes. Confirmation of the hypothesis that non-coding sequence variation in CAPN10 affects susceptibility to type 2 diabetes has implications for how we search for susceptibility variants and interpret results of positional cloning studies for complex disorders, and suggests a new pathway in glucose homeostasis. We review the results of follow-up studies on the CAPN10 finding, and consider the issues inherent in conclusively establishing that particular genetic variation affects a complex phenotype.

Calpain↗
PubMed1988

Frequency analysis and topographic mapping of EEG and evoked potentials in epilepsy.

Frequency analysis (spectral analysis) of both EEG and evoked potentials were studied prospectively in 52 patients with complex partial seizures to see if such tests could help localize the epileptic focus. Results were examined in line, bar and topographic head display formats. Asymmetries of fast and slow frequency components were identified in 26/52 patients. The existence and localization of such frequency alterations agreed with the overall results of other tests including the routine EEG, ictal EEG records, thiopental-activated EEG, CT or MRI, positron computed tomography (PET), and neuropsychometric testing. Changes were present in all 5 temporal lobe epilepsy cases that had a focal CT or MRI change, and in a majority (17/33) of cases in which the baseline EEG showed no focal slowing. These changes agreed with the preponderance of evidence in lateralizing the epileptic focus. Overall, EEG and evoked potential frequency analysis and topographic mapping do appear to offer data which are useful and complementary to other available test results, especially when a suspected lesion does not already show up as a defect on the CT scan or as a well-defined EEG slow focus. Considerable care needs to be taken to identify artifacts and normal EEG variants when interpreting these tests.

Adolescent↗
PubMed2025

Calibration of additional computational tools expands ClinGen recommendation options for variant classification with PP3/BP4 criteria.

PURPOSE: We previously developed an approach to calibrate computational tools for clinical variant classification, updating recommendations for the reliable use of variant impact predictors to provide evidence strength up to Strong. A new generation of tools using distinctive approaches has since been released, and these methods must be independently calibrated for clinical application. METHODS: Using our local posterior probability-based calibration and our established data set of ClinVar pathogenic and benign variants, we determined the strength of evidence provided by 3 new tools (AlphaMissense, ESM1b, and VARITY) and calibrated scores meeting each evidence strength. RESULTS: All 3 tools reached the Strong level of evidence for variant pathogenicity and Moderate for benignity, although sometimes for few variants. Compared with previously recommended tools, these yielded at best only modest improvements in the trade-offs between evidence strength and false-positive predictions. CONCLUSION: At calibrated thresholds, 3 new computational predictors provided evidence for variant pathogenicity at similar strength to the 4 previously recommended predictors (and comparable with functional assays for some variants). This calibration broadens the scope of computational tools for application in clinical variant classification. Their new approaches offer promise for future advancement of the field.

Humans↗
PubMed2025

Quantifying evidence for phenotypic specificity (PP4) for syndromic phenotypes: Large-scale integration of rare germline FH variants from diagnostic laboratory testing for HLRCC and renal cancer.

PURPOSE: Hereditary leiomyomatosis and renal cell cancer (HLRCC) is a rare cancer susceptibility syndrome exclusively attributable to pathogenic variants in FH (HGNC:3700). This article quantitatively weights the phenotypic context (PP4/PS4) of such very rare variants in FH. METHODS: We collated clinical diagnostic testing data on germline FH variants from 387 individuals with HLRCC and 1780 individuals with renal cancer and compared the frequency of "very-rare" variants in each phenotypic cohort with 562,295 population controls. We generated pan-gene very rare variant likelihood ratios (PG-VRV-LRs), domain-specific likelihood ratios for missense variants (DS-VRMV-LR) using spatial clustering analysis, and log2.08 likelihood ratios (LLRs) as applicable within the updated American College of Medical Genetics and Genomics/Association for Molecular Pathology variant classification framework. RESULTS: For HLRCC, the PG-VRV-LR was estimated to be 2669.4 (95% CI 1843.4-3881.2, LLR 10.77) for truncating variants and 214.7 (95% CI 185.0-246.9, LLR 7.33) for missense variants. For renal cancer, the PG-VRV-LR was 95.5 (95% CI 48.9-183.0, LLR 6.23) for truncating variants and 5.8 (95% CI 3.5-9.3, LLR 2.39) for missense variants. Clustering analysis in HLRCC cases revealed 3 "hotspot" regions wherein the DS-VRMV-LR increased to 1226.9. CONCLUSION: These data provide quantitative measures for very rare missense and truncating variants in FH, which reflect the differing phenotypic specificity of HLRCC and renal cancer and may be applicable in clinical variant classification.

Humans↗
PubMed2004

Structure/function studies on a S-adenosyl-L-methionine-dependent uroporphyrinogen III C methyltransferase (SUMT), a key regulatory enzyme of tetrapyrrole biosynthesis.

The crystallographic structure of the Pseudomonas denitrificans S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferase (SUMT), which is encoded by the cobA gene, has been solved by molecular replacement to 2.7A resolution. SUMT is a branchpoint enzyme that plays a key role in the biosynthesis of modified tetrapyrroles by controlling flux to compounds such as vitamin B(12) and sirohaem, and catalysing the transformation of uroporphyrinogen III into precorrin-2. The overall topology of the enzyme is similar to that of the SUMT module of sirohaem synthase (CysG) and the cobalt-precorrin-4 methyltransferase CbiF and, as with the latter structures, SUMT has the product S-adenosyl-L-homocysteine bound in the crystal. The roles of a number of residues within the SUMT structure are discussed with respect to their conservation either across the broader family of cobalamin biosynthetic methyltransferases or within the sub-group of SUMT members. The D47N, L49A, F106A, T130A, Y183A and M184A variants of SUMT were generated by mutagenesis of the cobA gene, and tested for SAM binding and enzymatic activity. Of these variants, only D47N and L49A bound the co-substrate S-adenosyl-L-methionine. Consequently, all the mutants were severely restricted in their capacity to synthesise precorrin-2, although both the D47N and L49A variants produced significant quantities of precorrin-1, the monomethylated derivative of uroporphyrinogen III. The activity of these variants is interpreted with respect to the structure of the enzyme.

Amino Acid Sequence↗
PubMed2024

Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data.

The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets are multivariate, and each RBP suffers non-uniform signal-to-noise ratio. To address this, we developed Mudskipper, a versatile computational suite comprising two components: a Dirichlet multinomial mixture model to account for the multivariate nature of ABC datasets and a softmasking approach that identifies and removes non-specific protein-RNA interactions in RBPs with low signal-to-noise ratio. Mudskipper demonstrates superior precision and recall over existing tools on multiplex datasets and supports analysis of repetitive elements and small non-coding RNAs. Our findings unravel splicing outcomes and variant-associated disruptions, enabling higher-throughput investigations into diseases and regulation mediated by RBPs.

RNA-Binding Proteins↗
PubMed1999

Blockade of Ba2+ current through human alpha1E channels by two steroid analogs, (+)-ACN and (+)-ECN.

Previous work suggests that different neuroactive steroids may exhibit some selectivity in their blocking effects on different high-voltage activated (HVA) Ca2+ currents. At least some of these effects appear to involve direct blocking actions on Ca2+ channels. Thus, direct investigation of the effects of various steroids on cloned Ca2+ channel variants may lead to the development of potent and selective small-molecular weight Ca2+ channel blockers. Here we examine the effects of two steroids on a cloned human alpha1E Ca2+ channel both with and without a beta3 subunit, when expressed in HEK293 cells. One compound, (+)-ACN, has been previously shown to block N-, Q-, and R-subtypes of HVA current without affecting L- and P-type current. The second compound, (+)-ECN, weakly blocks total HVA current in hippocampal neurons. (+)-ECN differs from (+)-ACN in lacking effects on GABA receptors, but shares with (+)-ACN an ability to partially inhibit T current in DRG neurons (Todorovic, S.M., Prakriya, M., Nakashima, Y.M. et al., 1998. Enantioselective blockade of T-type Ca2+ current in adult rat sensory neurons by a steroid lacking GABA-mimetic activity. Mol. Pharmacol. 54, 918-927). (+)-ACN can block 100% of Ba2+ current in HEK cells arising either from the alpha1E subunit (IC50 approximate to 10 microM) or the alpha1Ebeta3 combination (IC50 approximate to 5 microM), while (+)-ECN maximally blocks only about 80% of the alpha1E (10 microM) or alpha1Ebeta3 (16 microM) current. Blockade by (+)-ACN exhibits several differences from blockade by (+)-ECN. (+)-ACN increases the apparent rate of onset of inactivation, particularly for the alpha1E variant, slows recovery from inactivation, and more profoundly shifts the voltage-dependence of current availability for both alpha1E and alpha1Ebeta3 variants than does (+)-ECN. Although the complexity of the normal inactivation kinetics of alpha1E variants makes interpretation of the (+)-ACN-induced kinetic alterations difficult, the results suggest that the two steroids are to some extent acting by distinct mechanisms, and perhaps at different sites.

Animals↗
PubMed2003

The human digastric muscle: patterns and variations with clinical and surgical correlations.

The digastric muscle is located in the suprahyoid region on each side and frequently exhibits two muscular bellies (anterior and posterior) linked by an intermediate tendon. The paired digastric muscles act together either depressing the mandible or elevating the hyoid bone; therefore acting as a single muscle with important physiological roles. In the present study, the digastric muscle has been analyzed bilaterally in 74 adult human cadavers. A computerized morphometrical investigation of the digastric muscles has been performed (Image Pro Plus software package, Media Cybernetics, USA) and the resulting quantitative data have been statistically assessed (SPSS 11.0 for Windows, USA). We hereby propose an original morphological classification that encompasses five types (I-V) for the anterior belly (AB); three types (I-III) for the intermediate tendon (IT); and two types (I-II) for the posterior belly (PB) of the human digastric muscle. In each digastric muscle, the aforementioned anatomical types have been characterized according to the muscular bellies and intermediate tendon. Consequently, as a result of the combinations of those diverse types, individual digastric muscles have been considered as pertaining to distinctive morphological patterns (named from A to J). Cases with absence of either AB or PB have been included in patterns K and L and would be more appropriately defined as monogastric muscles. This innovative classification provides clear-cut anatomical parameters for interpreting morphological variants of the digastric muscle with relevant clinical and surgical correlations.

Adult↗
PubMed2026

Reimagining research papers as interactive and reliable AI agents.

Here we introduce Paper2Agent, an automated framework that converts research papers into artificial intelligence (AI) agents. Paper2Agent transforms research output from passive artefacts into active systems that accelerate use and discovery. Conventional research papers require readers to understand and adapt the paper's code, data and methods to their work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by converting a paper into an AI agent that functions as a virtual corresponding author, exposing its manuscript, supplementary materials, datasets, code and workflows as active, agent-native knowledge rather than static text. It analyses the paper and codebase using multiple agents to construct a model context protocol (MCP) server, then generates and runs tests to refine and increase robustness of the MCP. These paper MCPs can be connected to a chat agent (such as Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the paper. We demonstrate Paper2Agent's effectiveness through case studies. Paper2Agent created an agent that leveraged AlphaGenome1 to interpret genomic variants and agents based on Scanpy2 and TISSUE (transcript imputation with spatial single-cell uncertainty estimation)3 to conduct single-cell and spatial transcriptomics analyses. We validate that these agents reproduce the results of the original papers and carry out novel user queries. Paper2Agent created multiple agents that collaborate to prioritize a causal gene for psoriasis. By turning static papers into interactive AI agents, Paper2Agent introduces a paradigm for knowledge dissemination and a collaborative ecosystem of AI co-scientists.

Journal Article↗
PubMed1992

The interleukin 2 receptor (IL-2R): the IL-2R alpha subunit alters the function of the IL-2R beta subunit to enhance IL-2 binding and signaling by mechanisms that do not require binding of IL-2 to IL-2R alpha subunit.

Interleukin 2 (IL-2)-mediated signaling through its high-affinity receptor involves a complex interrelationship between IL-2 and two IL-2-binding chains, IL-2R alpha and beta chains. Previously with the reagents available it was difficult to define functional interactions between these two IL-2R subunits involved in IL-2 binding and signal transduction. To extend our understanding of the interplay between the two binding subunits we have done studies with the monoclonal antibody HIEI, which interferes with interaction of IL-2R alpha and beta chains (IL-2R alpha and IL-2R beta, respectively). Furthermore, we used two forms of IL-2, recombinant native IL-2 and F42A, an IL-2 analog (Phe-42----Ala substitution) that binds only to IL-2R beta. Analog F42A manifested 75-100% of the bioactivity of wild-type IL-2. This observation is inconsistent with the strict hierarchical IL-2-binding affinity conversion model previously proposed by Saito and coworkers [Saito Y., Sabe, H., Suzuki, N., Kondo, S., Ogura, T., Shimizu, A. & Honjo, T. (1988) J. Exp. Med. 168, 1563-1572] that predicted an ordered sequence of events in which IL-2 must first bind to IL-2R alpha before its interaction with IL-2R beta. Previous investigations using IL-2 variants were interpreted to show that IL-2R alpha merely acts to concentrate IL-2 to the cell surface and that no other meaningful interaction occurred between IL-2R alpha and IL-2R beta. However, our data are inconsistent with this view. We draw this conclusion on the basis of our observation that antibody HIEI, which reacts with an epitope of IL-2R alpha and interferes with interaction of this chain and IL-2R beta, inhibits the IL-2-dependent proliferative effects mediated by analog F42A. Furthermore, by blocking interaction of IL-2R alpha and IL-2R beta with the antibody HIEI, a decrease in the affinity of radiolabeled analog F42A for IL-2R beta was seen. In our proposed model IL-2R alpha contributes several functions to IL-2-mediated signaling through the high-affinity IL-2R. These functions include concentration of IL-2 within the two-dimensional surface of the plasma membrane as well as alteration of the functional capacity of IL-2R beta, an effect that does not require prior binding of IL-2R to IL-2R alpha. The IL-2R alpha-mediated augmentation of IL-2R beta functions involves affinity conversion of IL-2R beta, increasing its affinity for IL-2, and may involve facilitation of Il-2-mediated signaling after binding of IL-2 to this IL-2R beta.

Amino Acid Sequence↗
PubMed2002

Direct in vivo screening of intrabody libraries constructed on a highly stable single-chain framework.

Single-chain Fv antibody fragments (scFv) represent a convenient antibody format for intracellular expression in eukaryotic or prokaryotic cells. These so-called intrabodies have great potential in functional genomics as a tool to study the function of newly identified proteins in vivo, for example by binding-induced modulation of their activity or by blocking interactions with other proteins. However, the intracellular expression and activity of many single-chain Fvs are limited by their instability and folding efficiency in the reducing intracellular environment, where the highly conserved intrachain disulfide bonds do not form. In the present work, we used an in vivo selection system to isolate novel antigen-binding intrabodies. We screened two intrabody libraries carrying a randomized third hypervariable loop onto the heavy chain of a stable framework, which had been further optimized by random mutagenesis for better behavior in the selection system, and we biophysically characterized the selected variants to interpret the outcome of the selection. Our results show that single-framework intrabody libraries can be directly screened in vivo to rapidly select antigen-specific intrabodies.

Amino Acid Sequence↗
PubMed2005

Mutation screen of the membrane-type frizzled-related protein (MFRP) gene in patients with inherited retinal degenerations.

MFRP is a member of the frizzled-related protein family and contains a cysteine-rich domain essential for Wnt binding and signaling. MFRP is highly expressed in the retinal pigment epithelial cells of the eye. A splice donor mutation in the mouse ortholog of Mfrp is responsible for photoreceptor degeneration in the rd6 mouse. For these reasons, we investigated MFRP as a candidate gene for a phenotype associated with mutations. We screened 152 patients with inherited retinal degenerations including retinitis pigmentosa, Leber congenital amaurosis and Stargardt macular dystrophy. We identified five polymorphisms in the 5' untranslated region, four missense changes, six isocoding variants and four intronic changes. None of the sequence variants were interpreted as pathogenic.

5' Untranslated Regions↗
PubMed2006

Implications of small effect sizes of individual genetic variants on the design and interpretation of genetic association studies of complex diseases.

Accumulated evidence from searching for candidate gene-disease associations of complex diseases can offer some insights as the field moves toward discovery-oriented approaches with massive genome-wide testing. Meta-analyses of 50 non-human lymphocyte antigen gene-disease associations with documented overall statistical significance (752 studies) show summary odds ratios with a median of 1.43 (interquartile range, 1.28-1.65). Many different biases may operate in this field, for both single studies and meta-analyses, and these biases could invalidate some of these seemingly "validated" associations. Studies with a sample size of >500 show a median odds ratio of only 1.15. The median sample size required to detect the observed summary effects in each population addressed in the 752 studies is estimated to be 3,535 (interquartile range, 1,936-9,119 for cases and controls combined). These estimates are steeply inflated in the presence of modest bias. Population heterogeneity, as well as gene-gene and gene-environment interactions, could steeply increase these estimates and may be difficult to address even by very large biobanks and observational cohorts. The one visible solution is for a large number of teams to join forces on the same research platforms. These collaborative studies ideally should be designed up front to also assess more complex gene-gene and gene-environment interactions.

Alleles↗
PubMed2026

Immune dysregulatory disorders: perspective from solving a diagnostic odyssey.

PURPOSE OF REVIEW: Inborn errors of immunity (IEIs), once considered rare disorders characterized primarily by recurrent infections, are now recognized as a rapidly expanding group of diseases encompassing autoimmunity, autoinflammation, allergy, malignancy, and immune dysregulation. Advances in next-generation sequencing, functional immunology, and systems biology have revealed overlap between traditionally distinct disease categories and highlighted the complexity of genotype-phenotype relationships. RECENT FINDINGS: While this evolution has led to the discovery of hundreds of previously unrecognized disorders, it has also challenged conventional diagnostic paradigms and demonstrated how patients may have care spread across multiple specialties, without a clear medical home. These discoveries have also highlighted ongoing challenges translating scientific findings to the clinic including difficulties in accessing genomic testing, interpretation of variants of uncertain significance, impacts of incomplete penetrance and somatic mosaicism, and limited availability of specialized functional assays. Emerging computational approaches, including artificial intelligence, offer opportunities to accelerate diagnosis but cannot replace comprehensive clinical evaluation or longitudinal physician-patient relationships. SUMMARY: This perspective examines how the diagnostic odyssey for immune dysregulatory disorders has evolved, side-by-side with the changing framework for diagnosing rare immune diseases. We propose an integrated approach combining clinical phenotyping, genomics, functional validation, and multidisciplinary expertise to unite ongoing discovery between clinicians and scientists, diagnostics, and patient outcomes.

diagnostic odyssey↗
PubMed1985

Inherited thermostability variants of seven enzymes in a Japanese population.

The frequency of inherited variations in thermostability was investigated in a series of seven enzymes in a Japanese population. Among a total of 5930 determinations, nine variants were encountered. In each instance one parent exhibited a similar finding. It is suggested that this procedure should detect a high proportion of the variants of these enzymes characterized by amino acid substitutions not altering molecular charge. Failure to detect more such thermostability variants is interpreted to mean that electrophoresis not only detects amino acid substitutions altering molecular charge but also a considerable proportion of those that do not alter charge.

Adenylate Kinase↗
PubMed1989

Circle of Willis in newborns: color Doppler imaging of 53 healthy full-term infants.

To establish the usual pattern of flow in the circle of Willis in newborns, the authors scanned 53 healthy full-term infants within 3 days of birth with color Doppler imaging. All examinations were performed and images interpreted by the same experienced individuals. The basilar, internal carotid (ICA), and anterior and middle cerebral arteries were seen in all infants. Vertebral, posterior cerebral, superior cerebellar, and posterior communicating (PCoA) arteries were seen in most infants. PCoA flow was from the ICA toward the posterior cerebral artery in 73 (98.6%) of the 74 vessels that were seen. Flow in the anterior communicating artery was seen in six infants, indicating dependence of an anterior cerebral artery on contralateral ICA perfusion. Two pitfalls involving the distal portion of the ICA were noted: This vessel could be confused with the proximal portion of the anterior cerebral artery or cavernous sinus if real-time images were not interpreted carefully. Variant patterns of flow included tortuous basilar arteries (n = 2), reversed PCoA flow (n = 1), and inferior angulation of the proximal portions of the anterior cerebral arteries (n = 2). Color Doppler imaging allows a detailed analysis of the circle of Willis in newborns and detection of some anatomic variations.

Cerebral Arteries↗
PubMed2026

Expanding the Genomic Spectrum of NHLRC2-Associated FINCA Disease: Integrated Bioinformatic Characterization of a Novel Deep Intronic Variant Predicted to Activate a Pseudoexon.

NHLRC2-associated FINCA disease is an ultra-rare autosomal recessive multisystem disorder caused by biallelic pathogenic variants in NHLRC2. Its mutational spectrum and genotype-phenotype correlations remain incompletely defined, and the contribution of non-coding variants is poorly understood. Here, we report a male infant with a severe FINCA-like phenotype, including early-onset hemolytic anemia, pulmonary involvement, neurodevelopmental impairment, growth failure, recurrent infections, and fatal progression at 8.5 months. Whole-genome sequencing identified a compound heterozygous NHLRC2 genotype comprising the previously reported pathogenic missense variant c.442G>T (p.Asp148Tyr) and a novel deep intronic variant, c.331+6863A>G. Segregation analysis confirmed inheritance from different parents. Integrated genomic and splicing analysis predicted that c.331+6863A>G creates a strong cryptic donor splice site and supports pseudoexon inclusion. Reconstruction of the predicted aberrant transcript indicated premature termination and potential susceptibility to nonsense-mediated mRNA decay. To our knowledge, this is the first reported deep intronic NHLRC2 variant predicted to activate pseudoexon inclusion. Although experimental validation was unavailable, convergent clinical, segregation, population, and computational evidence supports c.331+6863A>G as the most plausible second disease-associated allele. This case expands the genomic spectrum of NHLRC2-associated FINCA disease and highlights the diagnostic value of phenotype-driven whole-genome sequencing.

Humans↗