The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.

Although gene discovery in neuropsychiatric disorders, including autism spectrum disorder, intellectual disability, epilepsy, schizophrenia, and Tourette disorder, has accelerated, resulting in a large number of molecular clues, it has proven difficult to generate specific hypotheses without the corresponding datasets at the protein complex and functional pathway level. Here, we describe one path forward-an initiative aimed at mapping the physical and genetic interaction networks of these conditions and then using these maps to connect the genomic data to neurobiology and, ultimately, the clinic. These efforts will include a team of geneticists, structural biologists, neurobiologists, systems biologists, and clinicians, leveraging a wide array of experimental approaches and creating a collaborative infrastructure necessary for long-term investigation. This initiative will ultimately intersect with parallel studies that focus on other diseases, as there is a significant overlap with genes implicated in cancer, infectious disease, and congenital heart defects.

Charting the metabolic biogeography of the colorectum in cancer: challenging the right sided versus left sided classification.

OBJECTIVE: Colorectal cancer (CRC) is conventionally classified as right sided, left sided, and rectal cancer. Clinicopathological, molecular features and risk factors do not change abruptly along the colorectum, and variations exist even within the refined subsites, which may contribute to inconsistencies in the identification of clinically relevant CRC biomarkers. We generated a CRC metabolome map to describe the association between metabolites, diagnostic and survival heterogeneity in cancers of different subsites of the colorectum. DESIGN: Utilizing 372 patient-matched tumor and normal mucosa tissues, liquid chromatography-mass spectrometry was applied to examine metabolomic profiles along seven subsites of the colorectum: cecum (n = 63), ascending colon (n = 44), transverse colon (n = 32), descending colon (n = 28), sigmoid colon (n = 75), rectosigmoid colon (n = 38), and rectum (n = 92). RESULTS: 39 and 70 significantly altered metabolites (including bile acids, lysophosphatidylcholines and lysophosphatidylethanolamines) among tumors and normal mucosa, respectively, showed inter-subsite metabolic heterogeneity between CRC subsites. Gradual changes in metabolite abundances with significantly linear trends from cecum to rectum were observed: 23 tumor-specific metabolites, 30 normal mucosa-specific metabolites, and 15 metabolites in both tumor and normal mucosa, had concentration gradients across the colorectum, and is disease status dependent. The metabolites that showed a linear trend included bile acids, amino acids, lysophosphatidylcholines, and lysophosphatidylethanolamines. Comparison of tumors to patient-matched normal mucosa revealed metabolite changes exclusive to each subsite, thereby further highlighting differences in cancer metabolism across the 7 subsites of the colorectum. Furthermore, metabolites associated with survival were different and unique to each subsite. Finally, an interactive and publicly accessible CRC metabolome database was designed to enable access and utilization of this rich data resource ( https://colorectal-cancer-metabolome.com/yale-university ). CONCLUSIONS: Gradual changes exist in metabolite abundances from the cecum to the rectum. The association between patient survival and distinct metabolites with anatomic subsite of the colorectum, reveals differences between cancers across the colorectum. These inter-subsite metabolic heterogeneities enrich the current understanding and substantiate previous studies that have challenged the conventional classification of right-sided, left-sided, and rectal cancers, by identifying specific metabolites that offer new biological insights into CRC subsite heterogeneity. The database designed in this study will enable researchers to delve into granular information on the CRC metabolome, which until now has not been available.

cGMP inhibition of type 3 phosphodiesterase is the major mechanism by which C-type natriuretic peptide activates CFTR in the shark rectal gland.

The in vitro perfused rectal gland of the dogfish shark (Squalus acanthias) and filter-grown monolayers of primary cultures of shark rectal gland (SRG) epithelial cells were used to analyze the signal transduction pathway by which C-type natriuretic peptide (CNP) stimulates chloride secretion. CNP binds to natriuretic receptors in the basolateral membrane, elevates cellular cGMP, and opens cystic fibrosis transmembrane conductance regulator (CFTR) chloride channels in the apical membrane. CNP-provoked chloride secretion was completely inhibitable by the nonspecific protein kinase inhibitor staurosporine and the PKA inhibitor H89 but insensitive to H8, an inhibitor of type I and II isoforms of cGMP-dependent protein kinase (cGKI and cGKII). CNP-induced secretion could not be mimicked by nonhydrolyzable cGMP analogs added alone or in combination with the protein kinase C activator phorbolester, arguing against a role for cGK or for cGMP-induced PKC signaling. We failed to detect a dogfish ortholog of cGKII by molecular cloning and affinity chromatography. However, inhibitors of the cGMP-inhibitable isoform of phosphodiesterase (PDE3) including milrinone, amrinone, and cilostamide but not inhibitors of other PDE isoenzymes mimicked the effect of CNP on chloride secretion in perfused glands and monolayers. CNP raised cGMP and cAMP levels in the SRG epithelial cells. This rise in cAMP as well as the CNP and amrinone-provoked chloride secretion, but not the rise in cGMP, was almost completely blocked by the Gαi-coupled adenylyl cyclase inhibitor somatostatin, arguing against a role for cGMP cross-activation of PKA in CNP action. These data provide molecular, functional, and pharmacological evidence for a CNP/cGMP/PDE3/cAMP/PKA signaling cascade coupled to CFTR in the SRG.

A foundational atlas of autism protein interactions reveals molecular convergence.

Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification. A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions.

Hemoglobin normalization outperforms other methods for standardizing dried blood spot metabolomics: A comparative study.

Dried blood spot (DBS) metabolomics has numerous applications in newborn health screening, exposomics, and biomonitoring of environmental chemicals in pregnant women and the elderly. However, accurate metabolite quantification is hindered by several challenges: notably the "hematocrit effect" and unknown blood-spotting volumes. Different techniques have been employed to overcome these issues but there is no consensus on the optimal normalization method for DBS metabolomics, and in some cases no normalization is used. We compared five normalization methods (hemoglobin (Hb), specific gravity (SG), protein, spot weight, potassium (K+)) to unnormalized data, and assessed sex-related differences in the DBS metabolome in 21 adults (group 1, n = 10 males, n = 11 females). The performance of each normalization method was evaluated using multiple criteria: (a) reduction of intragroup variation (pooled median absolute deviation, pooled estimate of variance, pooled coefficient of variation, NMDS and principal component analysis), (b) effect on differential metabolic analysis (dendrogram, heatmap, p-value distribution), and (c) influence on classification accuracy (partial least squares discriminant analysis, sparse partial least squares discriminant analysis error rates, receiver operating curve, random forest out of bag error rate). Our results revealed that Hb normalization outperformed all the other methods based on the three criteria and 13 different parameters; the performance of Hb was further demonstrated in an independent group of DBS from 18 neonates (group 2, n = 9 males, n = 9 females). Furthermore, we showed that SG and Hb are correlated in adults (rs = 0.86, p < 0.001), and validated this relationship in an independent group of 18 neonates and infants (group 3) (rs = 0.84, p < 0.001). Using the equation, SG = -0.4814Hb2 + 2.44Hb + 0.005, SG can be used as a surrogate for normalization by Hb. This is the first comparative study to concurrently evaluate multiple normalization methods for DBS metabolomics which will serve as a robust methodological platform for future environmental epidemiological studies.

Multi-omic analysis reveals metabolic pathways that characterize right-sided colon cancer liver metastasis.

There are well demonstrated differences in tumor cell metabolism between right sided (RCC) and left sided (LCC) colon cancer, which could underlie the robust differences observed in their clinical behavior, particularly in metastatic disease. As such, we utilized liquid chromatography-mass spectrometry to perform an untargeted metabolomics analysis comparing frozen liver metastasis (LM) biobank samples derived from patients with RCC (N = 32) and LCC (N = 58) to further elucidate the unique biology of each. We also performed an untargeted RNA-seq and subsequent network analysis on samples derived from an overlapping subset of patients (RCC: N = 10; LCC: N = 18). Our biobank redemonstrates the inferior survival of patients with RCC-derived LM (P = 0.04), a well-established finding. Our metabolomic results demonstrate increased reactive oxygen species associated metabolites and bile acids in RCC. Conversely, carnitines, indicators of fatty acid oxidation, are relatively increased in LCC. The transcriptomic analysis implicates increased MEK-ERK, PI3K-AKT and Transcription Growth Factor Beta signaling in RCC LM. Our multi-omic analysis reveals several key differences in cellular physiology which taken together may be relevant to clinical differences in tumor behavior between RCC and LCC liver metastasis.

Biomechanical restoration of metastatic cancer-induced peri-acetabular bone defects by ablation-osteoplasty-reinforcement-internal fixation technique (AORIF): To screw or not to screw?

BACKGROUND: Minimally invasive percutaneous polymethyl methacrylate cement augmentation procedures offer numerous clinical advantages for patients with periacetabular osteolytic metastatic bone defects in contrast to open reconstructive procedures that are associated with many complications. Several techniques, such as Ablation-Osteoplasty-Reinforcement-Internal Fixation (AORIF), cementoplasty alone, and screw fixation alone are currently used. There is no consensus on optimal skeletal reinforcement of diseased bones. The purpose of this study was to determine the most effective technique of percutaneous acetabular augmentation for joint preservation, with respect to resilience on cyclic loading and fracture pattern at maximal load to failure. METHODS: Five cohorts of hemipelvis composite bones with uniform periacetabular defects and various types of reinforcement techniques were utilized to simulate osteolytic metastasis in the weight bearing dome of the acetabulum. Five groups of hemipelves underwent finite element analysis and biomechanical testing for load to failure, energy absorption to failure, stress relaxation on cyclic loading, and fracture locations. RESULTS: The combination of screws and bone cement augmentation demonstrated significant higher energy absorption than the cement or screw only groups (p < 0.05), and better protection of acetabulum from displaced intraarticular fractures than the screws alone oror cement only groups (p < 0.05). Resilience to cyclic loading was higheest in the screw with cement fixation group than the screw only repair (p < 0.01), though not the cement fixation only group. INTERPRETATION: These data support the hypothesis that cementoplasty combined with screw augmentation such as the AORIF technique provides the best protection of acetabulum from massive metastatic cancer-induced acetabular fractures compared to augmentation with screws or cement alone.

Investigation of Whole Spine MRI in the Emergency Department at Two Large Tertiary Care Academic Medical Centers in the United States.

RATIONALE AND OBJECTIVES: The impact of emergent whole spine magnetic resonance imaging (WS-MRI) on patient management has not been extensively studied to date. Here, we explore indications, results, and outcomes associated with WS-MRI performed through the emergency departments (EDs) of 2 large tertiary care, academic medical centers in the Northeastern United States. We hypothesize that given a relatively low barrier to entry, coupled with lack of appropriateness guidelines, a sizeable proportion of WS-MRI studies performed emergently do not result in spine findings necessitating inpatient admission for immediate treatment. MATERIALS AND METHODS: We retrospectively studied 335 adult patients (≥18 years) who underwent WS-MRI through the ED between 2016 and 2019. The demographic data collected included, age, sex, chief complaint, history of spine disease, and date and type of last spine imaging prior to ED presentation. Data compiled from the time of ED visit included WS-MRI result and patient disposition, including reason for hospital admission, by which patients were categorized into groups to allow for ease of comparisons. Hypergeometric tests were used to determine statistically significant associations between random discrete variables. RESULTS: Trauma was the most frequent chief complaint, comprising 35% (n = 117) of all presentations, followed by pain (25%, n = 84), motor deficit (16%, n = 55), sensory disturbance (12%, n = 41), bowel, and/or bladder dysfunction (9%, n = 30), and subjective or objective fevers with suspicion for spine infection (2%, n = 8). The largest proportion of WS-MRI studies revealed degenerative disc disease (DDD) as the principal result (41%, n = 139). 52% of all patients were either discharged directly from the ED (41%) or admitted for a non-spine issue after WS-MRI (11%); of these numbers, 61% underwent WS-MRI and no other imaging study in the ED. In patients who presented with a chief complaint of pain, DDD was often the principal WS-MRI finding (54%), albeit this association was not statistically significant. DDD, nonetheless, was positively associated with a discharge from the ED (P <0.001). Trauma was positively associated with fracture or ligamentous/soft tissue injury (P <0.001) on WS-MRI and hospital admission for a spine issue (P <0.01). CONCLUSION: That just under half of patients in our study were admitted for spine-related pathology suggests that WS-MRI is valuable in the emergent setting. At the same time, however, that over half of patients were not subsequently admitted for a spine-related issue points to the possibility of further refining which patients would benefit most from WS-MRI. WS-MRI may be less helpful in patients presenting with pain, though may be higher-yield in those with trauma, motor deficits, and bowel/bladder complaints. Although MRI is highly sensitive in ruling out emergent central nervous system pathology, given the resource-intensive nature of the test, it is prudent to carefully select which patients should undergo emergent WS-MRI, especially in instances when more cost-effective, alternative diagnostic approaches, including detailed neurological exam, computed tomography, or localized/targeted MRI, are possible.

Avoiding Limb-Length Discrepancy with Reconstruction of a Massive Tibial Defect Using a Bone Allograft and a Minimally Invasive Lengthening System in a Pediatric Patient: A Case Report.

CASE: A 7-year-old boy was found to have Ewing sarcoma of the left tibia. The sarcoma was resected, and the defect was reconstructed using a humeral head allograft and intramedullary limb-lengthening nail. CONCLUSIONS: Limb-salvage reconstruction in children can be complicated by the sacrifice of epiphyseal plates and limb-length discrepancies and thus requires techniques tailored to each case.

Intracellular Staphylococcus aureus in bone and joint infections: A mechanism of disease recurrence, inflammation, and bone and cartilage destruction.

Bone and joint infections are devastating afflictions. Although medical interventions and advents have improved their care, bone and joint infections still portend dismal outcomes. Indeed, bone and joint infections are associated with extremely high mortality and morbidity rates and, generally, occur secondary to the aggressive pathogen Staphylococcus aureus. The consequences of bone and joint infections are further compounded by the fact that although they are aggressively treated, they frequently recur and result in massive bone and articular cartilage loss. Here, we review the literature and chronicle the fact that the fundamental cellular components of the musculoskeletal system can be internally infected with Staphylococcus aureus, which explains the ready recurrence of bone and joint infections even after extensive administration of antibiotic therapy and debridement and offer potential treatment solutions for further study. Moreover, we review the ramifications of intracellular infection and expound that the massive bone and articular cartilage loss is caused by the sustained proinflammatory state induced by infection and offer potential combination therapies for further study to protect bone and cartilage.

Re-appraising the potential of naringin for natural, novel orthopedic biotherapies.

Naringin is a naturally occurring flavonoid found in plants of the Citrus genus that has historically been used in traditional Chinese medical regimens for the treatment of osteoporosis. Naringin modulates signaling through numerous molecular pathways critical to musculoskeletal development, cellular differentiation, and inflammation. Administration of naringin increases in vitro expression of bone morphogenetic proteins (BMPs) and activation of the Wnt/ß-catenin and extracellular signal-related kinase (Erk) pathways, thereby promoting osteoblastic proliferation and differentiation from stem cell precursors for bone formation. Naringin also inhibits osteoclastogenesis by both modifying RANK/RANKL interactions and inducing apoptosis in osteoclasts in vitro. In addition, naringin acts on the estrogen receptor in bone to mimic the native bone-preserving effects of estrogen, with few systemic side effects on other estrogen-sensitive tissues. The efficacy of naringin therapy in reducing the osteolysis characteristic of common musculoskeletal pathologies such as osteoporosis, degenerative joint disease, and osteomyelitis, as well as inflammatory conditions affecting bone such as diabetes mellitus, has been extensively demonstrated in vitro and in animal models. Naringin thus represents a naturally abundant, cost-efficient agent whose potential for use in novel musculoskeletal biotherapies warrants re-visiting and further exploration through human studies. Here, we review the cellular mechanisms of action that have been elucidated regarding the action of naringin on bone resident cells and the bone microenvironment, in vivo evidence of naringin's osteostimulative and chondroprotective properties in the setting of osteolytic bone disease, and current limitations in the development of naringin-containing translational therapies for common musculoskeletal conditions.

De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis.

We previously established the contribution of de novo damaging sequence variants to Tourette disorder (TD) through whole-exome sequencing of 511 trios. Here, we sequence an additional 291 TD trios and analyze the combined set of 802 trios. We observe an overrepresentation of de novo damaging variants in simplex, but not multiplex, families; we identify a high-confidence TD risk gene, CELSR3 (cadherin EGF LAG seven-pass G-type receptor 3); we find that the genes mutated in TD patients are enriched for those related to cell polarity, suggesting a common pathway underlying pathobiology; and we confirm a statistically significant excess of de novo copy number variants in TD. Finally, we identify significant overlap of de novo sequence variants between TD and obsessive-compulsive disorder and de novo copy number variants between TD and autism spectrum disorder, consistent with shared genetic risk.