Showing papers by "Baylor College of Medicine published in 2022"

Curated variation benchmarks for challenging medically relevant autosomal genes

Abstract: The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant benchmark sets, but these exclude nearly 400 medically relevant genes due to their repetitiveness or polymorphic complexity. Here, we characterize 273 of these 395 challenging autosomal genes using a haplotype-resolved whole-genome assembly. This curated benchmark reports over 17,000 single-nucleotide variations, 3,600 insertions and deletions and 200 structural variations each for human genome reference GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically relevant genes, including CBS, CRYAA and KCNE1. When masking these false duplications, variant recall can improve from 8% to 100%. Forming benchmarks from a haplotype-resolved whole-genome assembly may become a prototype for future benchmarks covering the whole genome. Variant detection in problematic genes is facilitated with a curated benchmark.

Rapid Conjugate Appearance of the Giant Ionospheric Lamb Wave Signatures in the Northern Hemisphere After Hunga‐Tonga Volcano Eruptions

Abstract: The explosive eruption of the Hunga-Tonga volcano in the southwest Pacific at 0415UT on 15 January 2022 triggered gigantic atmospheric disturbances with surface air pressure waves propagating around the globe in Lamb mode. In space, concentric traveling ionosphere disturbances (CTIDs) are also observed as a manifestation of air pressure waves in New Zealand ∼0500UT and Australia ∼0630UT. As soon as the air pressure waves reached central Australia ∼0800UT, conjugate CTIDs appeared almost simultaneously in the northern hemispheres through interhemispheric coupling, much earlier than the arrival of the surface air pressure waves to Japan after 1100UT. Combining observations over Australia and Japan between 0800 and 1000UT, both direct and conjugate CTIDs show similar horizontal phase velocities of 320–390 m/s, matching with the dispersion relation of Lamb mode. The arrival of atmospheric Lamb wave to Japan later created in situ CTIDs showing the same Lamb mode characteristics as the earlier conjugate CTIDs.

Pathogenesis of Relapsing Fever.

Abstract: Relapsing fever (RF) is caused by several species of Borrelia; all, except two species, are transmitted to humans by soft (argasid) ticks. The species B. recurrentis is transmitted from one human to another by the body louse, while B. miyamotoi is vectored by hard-bodied ixodid tick species. RF Borrelia have several pathogenic features that facilitate invasion and dissemination in the infected host. In this article we discuss the dynamics of vector acquisition and subsequent transmission of RF Borrelia to their vertebrate hosts. We also review taxonomic challenges for RF Borrelia as new species have been isolated throughout the globe. Moreover, aspects of pathogenesis including symptomology, neurotropism, erythrocyte and platelet adhesion are discussed. We expound on RF Borrelia evasion strategies for innate and adaptive immunity, focusing on the most fundamental pathogenetic attributes, multiphasic antigenic variation. Lastly, we review new and emerging species of RF Borrelia and discuss future directions for this global disease.

Targeting TGF-β for treatment of osteogenesis imperfecta

Abstract: BACKGROUNDCurrently, there is no disease-specific therapy for osteogenesis imperfecta (OI). Preclinical studies demonstrate that excessive TGF-β signaling is a pathogenic mechanism in OI. Here, we evaluated TGF-β signaling in children with OI and conducted a phase I clinical trial of TGF-β inhibition in adults with OI.METHODSHistology and RNA-Seq were performed on bones obtained from children. Gene Ontology (GO) enrichment assay, gene set enrichment analysis (GSEA), and Ingenuity Pathway Analysis (IPA) were used to identify dysregulated pathways. Reverse-phase protein array, Western blot, and IHC were performed to evaluate protein expression. A phase I study of fresolimumab, a TGF-β neutralizing antibody, was conducted in 8 adults with OI. Safety and effects on bone remodeling markers and lumbar spine areal bone mineral density (LS aBMD) were assessed.RESULTSOI bone demonstrated woven structure, increased osteocytes, high turnover, and reduced maturation. SMAD phosphorylation was the most significantly upregulated GO molecular event. GSEA identified the TGF-β pathway as the top activated signaling pathway, and IPA showed that TGF-β1 was the most significant activated upstream regulator mediating the global changes identified in OI bone. Treatment with fresolimumab was well-tolerated and associated with increases in LS aBMD in participants with OI type IV, whereas participants with OI type III and VIII had unchanged or decreased LS aBMD.CONCLUSIONIncreased TGF-β signaling is a driver pathogenic mechanism in OI. Anti-TGF-β therapy could be a potential disease-specific therapy, with dose-dependent effects on bone mass and turnover.TRIAL REGISTRATIONClinicalTrials.gov NCT03064074.FUNDINGBrittle Bone Disorders Consortium (U54AR068069), Clinical Translational Core of Baylor College of Medicine Intellectual and Developmental Disabilities Research Center (P50HD103555) from National Institute of Child Health and Human Development, USDA/ARS (cooperative agreement 58-6250-6-001), and Sanofi Genzyme.

Ventilation-Induced Lung Injury (VILI) in Neonates: Evidence-Based Concepts and Lung-Protective Strategies

Abstract: Supportive care with mechanical ventilation continues to be an essential strategy for managing severe neonatal respiratory failure; however, it is well known to cause and accentuate neonatal lung injury. The pathogenesis of ventilator-induced lung injury (VILI) is multifactorial and complex, resulting predominantly from interactions between ventilator-related factors and patient-related factors. Importantly, VILI is a significant risk factor for developing bronchopulmonary dysplasia (BPD), the most common chronic respiratory morbidity of preterm infants that lacks specific therapies, causes life-long morbidities, and imposes psychosocial and economic burdens. Studies of older children and adults suggest that understanding how and why VILI occurs is essential to developing strategies for mitigating VILI and its consequences. This article reviews the preclinical and clinical evidence on the pathogenesis and pathophysiology of VILI in neonates. We also highlight the evidence behind various lung-protective strategies to guide clinicians in preventing and attenuating VILI and, by extension, BPD in neonates. Further, we provide a snapshot of future directions that may help minimize neonatal VILI.

Cistrome and transcriptome analysis identifies unique androgen receptor (AR) and AR-V7 splice variant chromatin binding and transcriptional activities

Abstract: The constitutively active androgen receptor (AR) splice variant, AR-V7, plays an important role in resistance to androgen deprivation therapy in castration resistant prostate cancer (CRPC). Studies seeking to determine whether AR-V7 is a partial mimic of the AR, or also has unique activities, and whether the AR-V7 cistrome contains unique binding sites have yielded conflicting results. One limitation in many studies has been the low level of AR variant compared to AR. Here, LNCaP and VCaP cell lines in which AR-V7 expression can be induced to match the level of AR, were used to compare the activities of AR and AR-V7. The two AR isoforms shared many targets, but overall had distinct transcriptomes. Optimal induction of novel targets sometimes required more receptor isoform than classical targets such as PSA. The isoforms displayed remarkably different cistromes with numerous differential binding sites. Some of the unique AR-V7 sites were located proximal to the transcription start sites (TSS). A de novo binding motif similar to a half ARE was identified in many AR-V7 preferential sites and, in contrast to conventional half ARE sites that bind AR-V7, FOXA1 was not enriched at these sites. This supports the concept that the AR isoforms have unique actions with the potential to serve as biomarkers or novel therapeutic targets.

Identification of Core Genes and Pathways in Melanoma Metastasis via Bioinformatics Analysis

Abstract: Metastasis is the leading cause of melanoma-related mortality. Current therapies are rarely curative for metastatic melanoma, revealing the urgent need to identify more effective preventive and therapeutic targets. This study aimed to screen the core genes and molecular mechanisms related to melanoma metastasis. A gene expression profile, GSE8401, including 31 primary melanoma and 52 metastatic melanoma clinical samples, was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between melanoma metastases and primary melanoma were screened using GEO2R tool. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analyses of DEGs were performed using the Database for Annotation Visualization and Integrated Discovery (DAVID). The Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape with Molecular Complex Detection (MCODE) plug-in tools were utilized to detect the protein-protein interaction (PPI) network among DEGs. The top 10 genes with the highest degrees of the PPI network were defined as hub genes. In the results, 425 DEGs, including 60 upregulated genes and 365 downregulated genes, were identified. The upregulated genes were enriched in ECM-receptor interactions and the regulation of actin cytoskeleton, while 365 downregulated genes were enriched in amoebiasis, melanogenesis, and ECM-receptor interactions. The defined hub genes included CDK1, COL17A1, EGFR, DSG1, KRT14, FLG, CDH1, DSP, IVL, and KRT5. In addition, the mRNA and protein levels of the hub genes during melanoma metastasis were verified in the TCGA database and paired post- and premetastatic melanoma cells, respectively. Finally, KRT5-specific siRNAs were utilized to reduce the KRT5 expression in melanoma A375 cells. An MTT assay and a colony formation assay showed that KRT5 knockdown significantly promoted the proliferation of A375 cells. A Transwell assay further suggested that KRT5 knockdown significantly increased the cell migration and cell invasion of A375 cells. This bioinformatics study provided a deeper understanding of the molecular mechanisms of melanoma metastasis. The in vitro experiments showed that KRT5 played the inhibitory effects on melanoma metastasis. Therefore, KRT5 may serve important roles in melanoma metastasis.

Dissecting lipid droplet biology with coherent Raman scattering microscopy.

Abstract: Lipid droplets (LDs) are lipid-rich organelles universally found in most cells. They serve as a key energy reservoir, actively participate in signal transduction and dynamically communicate with other organelles. LD dysfunction has been associated with a variety of diseases. The content level, composition and mobility of LDs are crucial for their physiological and pathological functions, and these different parameters of LDs are subject to regulation by genetic factors and environmental inputs. Coherent Raman scattering (CRS) microscopy utilizes optical nonlinear processes to probe the intrinsic chemical bond vibration, offering label-free, quantitative imaging of lipids in vivo with high chemical specificity and spatiotemporal resolution. In this Review, we provide an overview over the principle of CRS microscopy and its application in tracking different parameters of LDs in live cells and organisms. We also discuss the use of CRS microscopy in genetic screens to discover lipid regulatory mechanisms and in understanding disease-related lipid pathology.

Decoding the transcriptome of denervated muscle at single‐nucleus resolution

Abstract: Background Skeletal muscle exhibits remarkable plasticity under both physiological and pathological conditions. One major manifestation of this plasticity is muscle atrophy that is an adaptive response to catabolic stimuli. Because the heterogeneous transcriptome responses to catabolism in different types of muscle cells are not fully characterized, we applied single-nucleus RNA sequencing (snRNA-seq) to unveil muscle atrophy related transcriptional changes at single nucleus resolution. Methods Using a sciatic denervation mouse model of muscle atrophy, snRNA-seq was performed to generate single-nucleus transcriptional profiles of the gastrocnemius muscle from normal and denervated mice. Various bioinformatics analyses, including unsupervised clustering, functional enrichment analysis, trajectory analysis, regulon inference, metabolic signature characterization and cell–cell communication prediction, were applied to illustrate the transcriptome changes of the individual cell types. Results A total of 29 539 muscle nuclei (normal vs. denervation: 15 739 vs. 13 800) were classified into 13 nuclear types according to the known cell markers. Among these, the type IIb myonuclei were further divided into two subgroups, which we designated as type IIb1 and type IIb2 myonuclei. In response to denervation, the proportion of type IIb2 myonuclei increased sharply (78.12% vs. 38.45%, P < 0.05). Concomitantly, trajectory analysis revealed that denervated type IIb2 myonuclei clearly deviated away from the normal type IIb2 myonuclei, indicating that this subgroup underwent robust transcriptional reprogramming upon denervation. Signature genes in denervated type IIb2 myonuclei included Runx1, Gadd45a, Igfn1, Robo2, Dlg2, and Sh3d19 (P < 0.001). The gene regulatory network analysis captured a group of atrophy-related regulons (Foxo3, Runx1, Elk4, and Bhlhe40) whose activities were enhanced (P < 0.01), especially in the type IIb2 myonuclei. The metabolic landscape in the myonuclei showed that most of the metabolic pathways were down-regulated by denervation (P < 0.001), while some of the metabolic signalling, such as glutathione metabolism, was specifically activated in the denervated type IIb2 myonulei. We also investigated the transcriptomic alterations in the type I myofibres, muscle stem cells, fibro-adipogenic progenitors, macrophages, endothelial cells and pericytes and characterized their signature responses to denervation. By predicting the cell–cell interactions, we observed that the communications between myofibres and muscle resident cells were diminished by denervation. Conclusions Our results define the myonuclear transition, metabolic remodelling, and gene regulation networks reprogramming associated with denervation-induced muscle atrophy and illustrate the molecular basis of the heterogeneity and plasticity of muscle cells in response to catabolism. These results provide a useful resource for exploring the molecular mechanism of muscle atrophy.

Chemotherapy Coupled to Macrophage Inhibition Induces T-cell and B-cell Infiltration and Durable Regression in Triple-Negative Breast Cancer

Abstract: Immunosuppressive elements within the tumor microenvironment, such as tumor-associated macrophages (TAM), can present a barrier to successful antitumor responses by cytolytic T cells. Here we employed preclinical syngeneic p53 null mouse models of triple-negative breast cancer (TNBC) to develop a treatment regimen that harnessed the immunostimulatory effects of low-dose cyclophosphamide coupled with the pharmacologic inhibition of TAMs using either a small-molecule CSF1R inhibitor or an anti-CSF1R antibody. This therapeutic combination was effective in treating several highly aggressive TNBC murine mammary tumor and lung metastasis models. Single-cell RNA sequencing characterized tumor-infiltrating lymphocytes including Th cells and antigen-presenting B cells that were highly enriched in responders to combination therapy. In one model that exhibited long-term posttreatment tumor regression, high-dimensional imaging techniques identified the close spatial localization of B220+/CD86+-activated B cells and CD4+ T cells in tertiary lymphoid structures that were present up to 6 weeks posttreatment. The transcriptional and metabolic heterogeneity of TAMs was also characterized in two closely related claudin-low/mesenchymal subtype tumor models with differential treatment responses. A murine TAM signature derived from the T12 model was highly conserved in human claudin-low breast cancers, and high expression of the TAM signature correlated with reduced overall survival in patients with breast cancer. This TAM signature may help identify human patients with claudin-low breast cancer that will benefit from the combination of cyclophosphamide and anti-CSF1R therapy. These studies illustrate the complexity of the tumor immune microenvironment and highlight different immune responses that result from rational immunotherapy combinations.Immunostimulatory chemotherapy combined with pharmacologic inhibition of TAMs results in durable treatment responses elicited by Th cells and B cells in claudin-low TNBC models.

Papilledema and hypervitaminosis A after elexacaftor/tezacaftor/ivacaftor for cystic fibrosis

Abstract: Although most patients with papilledema in an ophthalmic practice have idiopathic intracranial hypertension (IIH), papilledema and increased intracranial pressure (ICP) will sometimes have an identifiable cause. Cystic fibrosis (CF) is a multisystem disorder that frequently causes pancreatic insufficiency and intestinal malabsorption. Individuals with CF are prone to fat-soluble vitamin deficiencies and are often on chronic supplementation. Elevated ICP can develop in CF patients if excessive supplementation leads to hypervitaminosis A, a known cause of intracranial hypertension.1Eid NS Shoemaker LR Samiec TD. Vitamin A in cystic fibrosis: case report and review of the literature.J Pediatr Gastroenterol Nutr. 1990; 10: 265-269Crossref PubMed Scopus (26) Google Scholar Recently, CF therapy has been revolutionized by cystic fibrosis transmembrane conductance regulator (CFTR) modulators, which in addition to improving respiratory function improve pancreatic function and reduce malabsorption.2Rosenfeld M Cunningham S Harris WT et al.An open-label extension study of ivacaftor in children with CF and a CFTR gating mutation initiating treatment at age 2–5 years (KLIMB).J. Cyst Fibros. 2019; 18: 838-843Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar Increased absorption of fat-soluble vitamins could lead to vitamin toxicity. Here we describe two 12-year-old girls who shortly after beginning therapy with the new combination CFTR modulator elexacaftor/ivacaftor/tezacaftor (Trikafta; Vertex Pharmaceuticals Inc, Boston, Mass.) developed papilledema and other symptoms of increased ICP as well as mildly elevated serum retinol (the major circulating form of vitamin A). Patient 1 was a 12-year-old girl with CF referred for papilledema. She was diagnosed with CF at age 11 years with the F∆508 and c.274 G>A mutations and was noted to have severe pancreatic insufficiency and severely depressed serum retinol (<6 µg/dL; normal for age is 20–50 µg/dL). She began taking pancreatic enzyme replacement and 2 AquADEKs multivitamins (Actavis Pharma, Dublin, Ireland) per day for a daily total of 18,167 IU vitamin A, 1,453 IU in retinoid form. The patient's growth remained poor, and her serum retinol increased slowly, reaching 16 µg/dL 8 months after the CF diagnosis. Ten months after the diagnosis, the patient's AquADEK dosage was doubled to 4 tablets per day, and 14 months after the diagnosis, serum retinol had increased to 23 µg/dL. At this time, the patient was begun on elexacaftor/tezacaftor/ivacaftor at standard dosage (two 100 mg elexacaftor, 50 mg tezacaftor, and 75 mg ivacaftor tablets per morning and one 150 mg ivacaftor tablet per evening). Liver enzymes were persistently elevated from CF-associated liver disease but did not increase during CFTR modulator therapy. After 2 months on elexacaftor/tezacaftor/ivacaftor, the patient reported a severe headache with nausea, and 1 month later she was found to have bilateral optic disc edema during a routine eye examination. The patient reported intermittent blurry vision, and her best corrected visual acuity (BCVA) was 20/25 OU. The anterior segment was unremarkable, and both pupils were equal, round, and reactive to light with no relative afferent pupillary defect. Funduscopy showed grade 3+ disc edema bilaterally. Magnetic resonance imaging (MRI) of the brain and orbits and magnetic resonance venography (MRV) were unremarkable besides protruding optic nerve heads on MRI. Lumbar puncture showed an elevated opening pressure of 40 cm H2O and normal cerebrospinal fluid (CSF) consistency. For papilledema owing to presumed IIH, the patient was prescribed acetazolamide 750 mg/day. Two weeks later, the patient had grade 4 disc edema OU with optical coherence tomography (OCT) revealing severely increased global retinal nerve fibre layer thickness (RNFL), 347 µm OD and 307 µm OS (Fig. 1). Automated perimetry showed superior and inferior arcuate visual field defects bilaterally. The patient's acetazolamide was increased to 1000 mg/day. One month after the diagnosis of papilledema, the patient's serum retinol was measured as 58 µg/dL, mildly elevated and substantially higher than previous values. In all vitamin A laboratory determinations, retinyl palmitate, another circulating form of vitamin A, was less than 0.02 mg/L (normal). Because of a concern that hypervitaminosis A might be the cause of her increased ICP, the patient's multivitamin dosage was reduced to 2 tablets per day. Two months after the diagnosis of papilledema, the patient was found to have continued but reduced optic disc swelling, grade 2 bilaterally, with RNFL thickness 192 µm OD and 186 µm OS. BCVA remained 20/25 bilaterally. For continued resolution of her papilledema, the patient was maintained on the same dose of acetazolamide. Patient 2 was a 12-year-old girl with CF referred for papilledema. She was diagnosed at age 11 years with the FΔ508 and G551D mutations and was found to have moderate pancreatic insufficiency. Although vitamin D levels at diagnosis were low, serum retinol was 45 µg/dL, near the upper limit of normal. The patient was prescribed pancreatic enzyme replacement and began taking a daily multivitamin containing 1,440 IU retinoid vitamin A. One month after the diagnosis, the patient was started on the CFTR potentiator ivacaftor. Throughout treatment, the patient struggled to gain weight, and her pancreatic enzyme supplementation was repeatedly increased. Thirteen months after her CF diagnosis, the patient's ivacaftor was replaced with elexacaftor/tezacaftor/ivacaftor at standard dosage. The patient subsequently reported an increase in appetite and gained several pounds over the next month. At this time, she also replaced her daily pediatric multivitamin with 2 AquADEKs multivitamin tablets per day, representing a marginal increase of her retinoid vitamin A supplementation to 1,453 IU/day. Liver enzymes remained within normal ranges throughout therapy. Two months after beginning elexacaftor/tezacaftor/ivacaftor, the patient was found to have bilateral disc edema. She noted mild bitemporal headaches beginning after initiation of elexacaftor/tezacaftor/ivacaftor and endorsed bilateral nonpulsatile tinnitus but denied other symptoms. Visual acuity was 20/20 bilaterally. The pupils and anterior segments were normal. Funduscopy revealed grade 2 disc edema bilaterally, and OCT showed bilaterally increased global RNFL thickness, 168 µm OD and 163 µm OS (Fig. 2). MRI and MRV were unremarkable, and lumbar puncture showed an elevated opening pressure of 55 cm H2O with normal CSF. Over concern that elevated ICP might be an adverse effect of elexacaftor/tezacaftor/ivacaftor or a result of hypervitaminosis A, elexacaftor/tezacaftor/ivacaftor and all multivitamins were discontinued. However, serum retinol was measured as 48 µg/dL (within normal range). For papilledema owing to possible IIH, the patient was prescribed acetazolamide 500 mg/day. Four weeks later, the patient's headaches had resolved, and her visual acuity was unchanged. Automated perimetry revealed a few points of reduced sensitivity bilaterally. Funduscopy showed trace optic disc edema in each eye, and OCT yielded RNFL measurements (145 µm OD, 147 µm OS) that were elevated but below previous values. For continued resolution of the papilledema, acetazolamide was increased to 1000 mg/day. Seven weeks after the papilledema diagnosis, the patient's serum retinol was now found to be mildly elevated (57 µg/dL) despite her no longer receiving any vitamin A supplementation. Fifteen weeks after the diagnosis, the patient was noted to have no optic disc edema on funduscopy and nearly normal RNFL thickness (112 µm OD, 113 µm OS). However, serum retinol had further increased to 60 µg/dL. In all vitamin A laboratory determinations, retinyl palmitate was less than 0.02 mg/L. Here we present two 12-year-old females with CF who developed both papilledema and mild hypervitaminosis A within a few months of starting elexacaftor/tezacaftor/ivacaftor. We believe that this therapy increased the absorption of our patients’ supplemental vitamin A, causing a state of relative vitamin A excess that then led to intracranial hypertension with papilledema. Elexacaftor/tezacaftor/ivacaftor is a recently approved combination of 3 CFTR modulators approved for CF patients 12 years of age and older with a F∆508 mutation.3Hoy SM. Elexacaftor/ivacaftor/tezacaftor: first approval.Drugs. 2019; 79: 2001-2007Crossref PubMed Scopus (30) Google Scholar Reported adverse effects include elevated liver enzymes and cataracts;4Safety and Possible Side Effects | TRIKAFTA (elexacaftor/tezacaftor/ivacaftor and ivacaftor). www.trikafta.com/safety-side-effects [accessed September 21, 2020].Google Scholar we found no prior reports of increased ICP. Although such work has not been done on elexacaftor/tezacaftor/ivacaftor, evidence indicates that monotherapy with ivacaftor substantially improves intestinal absorption in CF patients through a variety of means, including reversal of pancreatic insufficiency,2Rosenfeld M Cunningham S Harris WT et al.An open-label extension study of ivacaftor in children with CF and a CFTR gating mutation initiating treatment at age 2–5 years (KLIMB).J. Cyst Fibros. 2019; 18: 838-843Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar increased intestinal pH,5Gelfond D Heltshe S Ma C et al.Impact of CFTR modulation on intestinal pH, motility, and clinical outcomes in patients with cystic fibrosis and the G551D mutation.Clin Transl Gastroenterol. 2017; 8: e81Crossref PubMed Scopus (57) Google Scholar and decreased inflammation.6Stallings VA Sainath N Oberle M Bertolaso C Schall JI. Energy balance and mechanisms of weight gain with ivacaftor treatment of cystic fibrosis gating mutations.J Pediatr. 2018; 201 (229–37.e4)Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar Recently, Sommerburg et al.7Sommerburg O Hämmerling S Schneider SP et al.CFTR modulator therapy with lumacaftor/ivacaftor alters plasma concentrations of lipid-soluble vitamins A and E in patients with cystic fibrosis.Antioxidants. 2021; 10: 483Crossref PubMed Scopus (5) Google Scholar found that therapy with lumacaftor/ivacaftor significantly increased patients’ serum vitamin A levels, indicating that improved intestinal function includes increased absorption of vitamin A. It is not surprising that our patients, both of whom were pancreatic insufficient and previously had poor weight gain, would experience improved intestinal absorption on elexacaftor/tezacaftor/ivacaftor. Increased absorption of vitamin A clearly would explain the retinol measurements of patient 1, in whom a previously slow rise in serum retinol accelerated markedly after elexacaftor/tezacaftor/ivacaftor was begun. (Retinol more than doubled over 4 months, increasing from 23 to 58 µg/dL.) The second case is more puzzling because this patient showed elevated serum retinol only after the diagnosis of papilledema. Despite her measured serum retinol of 48 µg/dL, we believe that patient 2 was already in a vitamin A overloaded state at the papilledema diagnosis. The patient's vitamin A supplementation and CFTR modulators were both stopped at that time, and vitamin A intake from a normal diet alone is insufficient to explain the subsequent development of hypervitaminosis, as indicated by consecutive elevated retinol values of 57 and 60 µg/dL. Given this discrepancy, it seems likely that the retinol measurement of 48 µg/dL for patient 2 was inaccurate. Vitamin A studies are prone to inconsistencies that may be owing to imprecise measurement techniques, variable sample collection, and incomplete protection of samples from light.8Libien J Kupersmith M Blaner W et al.Role of vitamin A metabolism in IIH: results from the idiopathic intracranial hypertension treatment trial.J Neurol Sci. 2017; 372: 78-84Abstract Full Text Full Text PDF PubMed Scopus (18) Google Scholar Although our samples were drawn from fasting patients and were analyzed via high-performance liquid chromatography, the standard for fat-soluble vitamin measurement,9Greaves RF Woollard GA Hoad KE et al.Laboratory medicine best practice guideline: vitamins A, E and the carotenoids in blood.Clin Biochem Rev. 2014; 35: 81-113PubMed Google Scholar we cannot be sure that all aspects of sample collection and storage were adequate. It is also possible that the patient's liver, the principal storage site for vitamin A, was just saturated with vitamin A by the papilledema diagnosis, with a delayed spike in serum retinol occurring as the liver later released increasing amounts of retinol. This seems plausible because the liver maintains stable serum retinol over a wide range of hepatic levels such that serum retinol correlates with hepatic vitamin A stores only when they are at extremes10Conaway HH Henning P Lerner UH. Vitamin A metabolism, action, and role in skeletal homeostasis.Endocr Rev. 2013; 34: 766-797Crossref PubMed Scopus (93) Google Scholar and because there are prior reports of a delayed peak in serum retinol after excessive vitamin A ingestion.11Lam HS Chow CM Poon WT et al.Risk of vitamin A toxicity from candy-like chewable vitamin supplements for children.Pediatrics. 2006; 118: 820-824Crossref PubMed Scopus (41) Google Scholar Our patient's maximum serum retinol levels of 58 and 60 µg/dL are only mildly elevated and typically would be considered unlikely to cause toxicity. However, there appears to be substantial variability in the minimum toxic level of vitamin A, and there are reports of children with CF developing toxicity with relatively mild hypervitaminosis A,1Eid NS Shoemaker LR Samiec TD. Vitamin A in cystic fibrosis: case report and review of the literature.J Pediatr Gastroenterol Nutr. 1990; 10: 265-269Crossref PubMed Scopus (26) Google Scholar,12Safi KH Filbrun AG Nasr SZ. Hypervitaminosis A causing hypercalcemia in cystic fibrosis. case report and focused review.Ann Am Thorac Soc. 2014; 11: 1244-1247Crossref PubMed Scopus (9) Google Scholar suggesting that such individuals may be more vulnerable to toxicity. Given such cases and the known link between vitamin A and intracranial hypertension, we believe that our patients developed increased ICP owing to a relative hypervitaminosis A. Although serum retinol in patient 2 was measured as normal at the papilledema diagnosis, we suspect that this measurement was inaccurate or that there were short-term increases in serum retinoids over the previous months that led to intracranial hypertension. Although improved vitamin absorption certainly would be a benefit of CFTR modulator therapy, it would mean that patients on these drugs may require adjustment of pancreatic enzyme and vitamin supplementation and lend additional importance to monitoring fat-soluble vitamin levels. We cannot exclude the possibility that elexacaftor/ivacaftor/tezacaftor caused papilledema as a direct adverse effect. However, we found no suggestion of this on the basis of its mechanism of action or prior reports in the literature. The authors have no proprietary or commercial interest in any materials discussed in this article.

Biomineralization of struvite by Shewanella oneidensis MR-1 for phosphorus recovery: Cr(VI) effect and behavior

Abstract: Bacterial mineralization of struvite from wastewaters is one of the promising approaches to recover phosphorus. However, the information about whether and how the heavy metal Cr(VI) affect the bacterial mineralization system is still lack. Here a model microbe Shewanella oneidensis MR-1 was used to induce struvite mineralization in simulated Cr(VI)-bearing wastewaters and the composition, morphology, and Cr content of precipitates were characterized by a wide range of techniques. Our results reveal that the yield of struvite and Mg transformation efficiency are almost not affected by the concomitant Cr(VI), but pitting and roughening of struvite surfaces are observed. Meanwhile, the struvite mineralized from model wastewaters with 0.1 or 0.2 mM Cr(VI) can meet the regulatory standard of Cr content as fertilizer. Strain MR-1 can not only create an alkaline environment for struvite precipitation, but also completely reduce Cr(VI) to Cr(III), helping to form soluble organo-Cr(III) complexes in the supernatant, hence significantly reducing the Cr content in struvite. And the loaded Cr(III) exists in the form of amorphous Cr(III) species (e.g., Cr(OH)3) on the struvite surface instead of the crystal lattice substitution in abiotic case. Current results serve as a guidance for further development of struvite biomineralization and P recovery from Cr(VI)-containing wastewaters.

Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain

Abstract: Single-cell spatial transcriptomics (sc-ST) holds the promise to elucidate architectural aspects of complex tissues. Such analyses require modeling cell types in sc-ST datasets through their integration with single-cell RNA-seq datasets. However, this integration, is nontrivial since the two technologies differ widely in the number of profiled genes, and the datasets often do not share many marker genes for given cell types. We developed a neural network model, spatial transcriptomics cell-types assignment using neural networks (STANN), to overcome these challenges. Analysis of STANN's predicted cell types in mouse olfactory bulb (MOB) sc-ST data delineated MOB architecture beyond its morphological layer-based conventional description. We find that cell-type proportions remain consistent within individual morphological layers but vary significantly between layers. Notably, even within a layer, cellular colocalization patterns and intercellular communication mechanisms show high spatial variations. These observations imply a refinement of major cell types into subtypes characterized by spatially localized gene regulatory networks and receptor-ligand usage.

The Prostate Cancer Androgen Receptor Cistrome in African American Men Associates with Upregulation of Lipid Metabolism and Immune Response

Abstract: African-American (AA) men are more likely to be diagnosed with and die from prostate cancer than European American (EA) men. Despite the central role of the androgen receptor (AR) transcription factor in prostate cancer, little is known about the contribution of epigenetics to observed racial disparities. We performed AR chromatin immunoprecipitation sequencing on primary prostate tumors from AA and EA men, finding that sites with greater AR binding intensity in AA relative to EA prostate cancer are enriched for lipid metabolism and immune response genes. Integration with transcriptomic and metabolomic data demonstrated coinciding upregulation of lipid metabolism gene expression and increased lipid levels in AA prostate cancer. In a metastatic prostate cancer cohort, upregulated lipid metabolism associated with poor prognosis. These findings offer the first insights into ancestry-specific differences in the prostate cancer AR cistrome. The data suggest a model whereby increased androgen signaling may contribute to higher levels of lipid metabolism, immune response, and cytokine signaling in AA prostate tumors. Given the association of upregulated lipogenesis with prostate cancer progression, our study provides a plausible biological explanation for the higher incidence and aggressiveness of prostate cancer observed in AA men.With immunotherapies and inhibitors of metabolic enzymes in clinical development, the altered lipid metabolism and immune response in African-American men provides potential therapeutic opportunities to attenuate racial disparities in prostate cancer.

Single-Cell Analysis Unveils the Role of the Tumor Immune Microenvironment and Notch Signaling in Dormant Minimal Residual Disease

Abstract: Abstract Tumor dormancy is a stage in which residual cancer cells remain inactive, but regrowth of dormant cancer cells contributes to recurrence. The complex ecosystem in cancer that promotes cell survival and the factors that eventually overcome growth constraints and result in proliferation remain to be fully elucidated. Doing so may provide new insights and help identify novel strategies to prolong cancer dormancy and prevent disease recurrence. To dissect the molecular pathways and the microenvironments involved in regulation of dormancy, we utilized a novel immunocompetent transgenic model to study minimal residual disease and relapse. This model revealed a significant reorganization of cancer cell structures, stroma, and immune cells, with cancer cells showing dormant cell signatures. Single-cell RNA sequencing uncovered remodeling of myeloid and lymphoid compartments. In addition, the Jagged-1/Notch signaling pathway was shown to regulate many aspects of tumorigenesis, including stem cell development, epithelial-to-mesenchymal transition, and immune cell homeostasis during minimal residual disease. Treatment with an anti–Jagged-1 antibody inhibited the Jagged-1/Notch signaling pathway in tumor cells and the microenvironment, delaying tumor recurrence. These findings uncover a cascade of regulatory changes in the microenvironment during dormancy and identify a therapeutic strategy to undercut these changes. Significance: Single-cell RNA-sequencing analysis reveals dormancy-associated changes in immune and stromal cells and demonstrates a rationale to pursue Jagged-1/Notch pathway inhibition as a viable therapeutic strategy to reduce disease recurrence.

Advancing Equity in Academic Medicine Through Holistic Review for Faculty Recruitment and Retention

Abstract: The Association of American Medical Colleges (AAMC) in 2007 developed the Holistic Review Framework for medical school admissions to increase mission-aligned student diversity. This approach balances an applicant's experiences, attributes, and metrics during the screening, interview, and selection processes. Faculty recruitment provides its own set of challenges, and there is persistent underrepresentation of certain racial and ethnic minority groups and women in faculty and leadership positions in U.S. academic health centers (AHCs). In 2019, the AAMC initiated a pilot program to adapt and implement the framework for use in faculty recruitment at AHCs. In this Invited Commentary, the authors describe the pilot implementation of the Holistic Review Framework for Faculty Recruitment and Retention and share lessons learned to date. Although the pilot proceeded during 2020, institutional implementation was impacted by the COVID-19 pandemic and racial justice movement. Pilot institutions encountered hiring freezes, reductions in funding, and restrictions on in-person meetings due to COVID-19 that resulted in both barriers and opportunities in implementing the framework. Renewed commitment to racial justice was associated with increased momentum and urgency for the implementation of faculty holistic review at the majority of pilot institutions. Common themes from the pilot leads' experiences included the importance of achieving "buy in," having a dedicated implementation team, and being explicit about core values. Other themes included the importance of adaptability and flexibility to meet the needs of different institutions and mission areas. The faculty holistic review framework has shown promise as an approach to advancing faculty diversity goals. The pilot institutions will continue to share best practices, track outcomes, implement quality improvement, and disseminate findings to assist other institutions and health care communities with their endeavors to recruit and retain diverse faculty.