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1.
J Clin Monit Comput ; 2024 Oct 10.
Article in English | MEDLINE | ID: mdl-39388061

ABSTRACT

Recently, photoplethysmography-based vital parameter measurements have increased in popularity. However, clinical evaluation of these measurements is lacking. The objective of this study was to rigorously evaluate the clinical accuracy and reliability of a novel photoplethysmography-based wristband for measuring key vital parameters-oxygen saturation (SpO2), respiratory rate (RR), and pulse rate (PR)-during heart catheterisations. Vital parameters obtained during heart catheterisations by means of a photoplethysmography-based wristband (CardioWatch 287-2, Corsano Health) were compared to reference measurements performed by a Nellcor fingerclip (SpO2, PR) as well as a 5-lead ECG (RR) (QMAPP Haemodynamic Monitoring module, Fysicon B.V.) by means of correlation coefficients and root means squared error (RMSE). Effects of skin colour and arm hair density were additionally evaluated. In total, 945 samples from a total of 100 patients were included in the analysis. The correlation coefficients and RSME obtained for the difference between reference and photoplethysmography-based wristband measurements were r = 0.815 and 1.6% for SpO2, r = 0.976 and 0.9 brpm for RR, and r = 0.995 and 1.3 bpm for PR. Similar results were obtained across all skin colour and arm hair density subcategories. This study shows that photoplethysmography-based SpO2, RR, and PR measurements can be accurate during heart catheterisations. Future investigations are required to evaluate the wristband's performance under dynamic circumstances as well as over an extended time period. Trial registration: www.clinicaltrials.gov, NCT05566886.

2.
Pain ; 2024 Oct 04.
Article in English | MEDLINE | ID: mdl-39382328

ABSTRACT

ABSTRACT: The 2 tetrodotoxin-resistant (TTXr) voltage-gated sodium channel subtypes NaV1.8 and NaV1.9 are important for peripheral pain signaling. As determinants of sensory neuron excitability, they are essential for the initial transduction of sensory stimuli, the electrogenesis of the action potential, and the release of neurotransmitters from sensory neuron terminals. NaV1.8 and NaV1.9, which are encoded by SCN10A and SCN11A, respectively, are predominantly expressed in pain-sensitive (nociceptive) neurons localized in the dorsal root ganglia (DRG) along the spinal cord and in the trigeminal ganglia. Mutations in these genes cause various pain disorders in humans. Gain-of-function missense variants in SCN10A result in small fiber neuropathy, while distinct SCN11A mutations cause, i. a., congenital insensitivity to pain, episodic pain, painful neuropathy, and cold-induced pain. To determine the impact of loss-of-function of both channels, we generated NaV1.8/NaV1.9 double knockout (DKO) mice using clustered regularly interspaced short palindromic repeats/Cas-mediated gene editing to achieve simultaneous gene disruption. Successful knockout of both channels was verified by whole-cell recordings demonstrating the absence of NaV1.8- and NaV1.9-mediated Na+ currents in NaV1.8/NaV1.9 DKO DRG neurons. Global RNA sequencing identified significant deregulation of C-LTMR marker genes as well as of pain-modulating neuropeptides in NaV1.8/NaV1.9 DKO DRG neurons, which fits to the overall only moderately impaired acute pain behavior observed in DKO mice. Besides addressing the function of both sodium channels in pain perception, we further demonstrate that the null-background is a very valuable tool for investigations on the functional properties of individual human disease-causing variants in NaV1.8 or NaV1.9 in their native physiological environment.

4.
Chem Biomed Imaging ; 2(9): 595-614, 2024 Sep 23.
Article in English | MEDLINE | ID: mdl-39328428

ABSTRACT

Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.

5.
Cell Rep ; 43(9): 114750, 2024 Sep 24.
Article in English | MEDLINE | ID: mdl-39283743

ABSTRACT

Mir483 is a conserved and highly expressed microRNA in placental mammals, embedded within the Igf2 gene. Its expression is dysregulated in a number of human diseases, including metabolic disorders and certain cancers. Here, we investigate the developmental regulation and function of Mir483 in vivo. We find that Mir483 expression is dependent on Igf2 transcription and the regulation of the Igf2/H19 imprinting control region. Transgenic Mir483 overexpression in utero causes fetal, but not placental, growth restriction through insulin-like growth factor 1 (IGF1) and IGF2 and also causes cardiovascular defects leading to fetal death. Overexpression of Mir483 post-natally results in growth stunting through IGF1 repression, increased hepatic lipid production, and excessive adiposity. IGF1 infusion rescues the post-natal growth restriction. Our findings provide insights into the function of Mir483 as a growth suppressor and metabolic regulator and suggest that it evolved within the INS-IGF2-H19 transcriptional region to limit excessive tissue growth through repression of IGF signaling.


Subject(s)
Insulin-Like Growth Factor II , Insulin-Like Growth Factor I , MicroRNAs , Animals , MicroRNAs/metabolism , MicroRNAs/genetics , Insulin-Like Growth Factor II/metabolism , Insulin-Like Growth Factor II/genetics , Insulin-Like Growth Factor I/metabolism , Insulin-Like Growth Factor I/genetics , Mice , Female , Pregnancy , Gene Expression Regulation, Developmental , Mice, Transgenic , Humans , Genomic Imprinting , Fetal Growth Retardation/metabolism , Fetal Growth Retardation/genetics , Fetal Growth Retardation/pathology , Mice, Inbred C57BL , RNA, Long Noncoding
6.
Int J Mol Sci ; 25(18)2024 Sep 10.
Article in English | MEDLINE | ID: mdl-39337287

ABSTRACT

Goats are natural hosts of Mycobacterium (M.) bovis, and affected herds can be the cause of significant economic losses. Similarites in disease course and lesions of M. bovis infections in goats and M. tuberculosis in humans make goats good models for human tuberculosis. The aim of this investigation was to characterize M. bovis challenge models in goats. For this, goats were endobronchially inoculated with three doses of M. bovis or culture medium. Clinical signs, shedding, and immune responses were monitored until 146 days post inoculation (dpi). At necropsy, lesions were examined by computed tomography, histology, and bacteriological culture. Infected goats did not develop clinical signs. M. bovis was cultured from feces, but never from nasal swabs. IGRAs were positive from 28 dpi onwards, antibodies at 140 dpi, and SICCT at 146 dpi. The increase in CD25+, IFN-γ+, and IFN-γ-releasing T-cell subpopulations was time-related, but not dose-dependent. All infected goats developed paucibacillary granulomas in the lungs and regional lymph nodes. M. bovis was regularly cultured. Dose-dependent effects included the size of pulmonary lesions, caverns, intestinal lesions, and early generalization in the high-dose group. In summary, reproducible challenge models with dose-dependent differences in lesions were established, which may serve for testing vaccines for veterinary or medical use.


Subject(s)
Disease Models, Animal , Goats , Mycobacterium bovis , Tuberculosis , Animals , Mycobacterium bovis/pathogenicity , Tuberculosis/microbiology , Tuberculosis/veterinary , Tuberculosis/pathology , Tuberculosis/immunology , Goat Diseases/microbiology , Lung/microbiology , Lung/pathology , Feces/microbiology , Interferon-gamma/metabolism
7.
Leukemia ; 2024 Sep 04.
Article in English | MEDLINE | ID: mdl-39232206

ABSTRACT

Pediatric acute lymphoblastic leukemia (ALL) is marked by low mutational load at initial diagnosis, which increases at relapse. To determine which processes are active in (relapsed) ALL and how they behave during disease progression before and after therapy, we performed whole genome sequencing on 97 tumor samples of 29 multiply relapsed ALL patients. Mutational load increased upon relapse in 28 patients and upon every subsequent relapse in 22 patients. In addition to two clock-like mutational processes, we identified UV-like damage, APOBEC activity, reactive oxygen species, thiopurine-associated damage and an unknown therapy component as drivers of mutagenesis. Mutational processes often affected patients over longer time periods, but could also occur in isolated events, suggesting the requirement of additional triggers. Thiopurine exposure was the most prominent source of new mutations in relapse, affecting over half of the studied patients in first and/or later relapse and causing potential relapse-driving mutations in multiple patients. Our data demonstrate that multiple mutational processes frequently act in parallel as prominent secondary drivers with dynamic activity during ALL development and progression.

8.
Cells ; 13(16)2024 Aug 19.
Article in English | MEDLINE | ID: mdl-39195266

ABSTRACT

The mononuclear phagocyte system includes monocytes, macrophages, some dendritic cells, and multinuclear giant cells. These cell populations display marked heterogeneity depending on their differentiation from embryonic and bone marrow hematopoietic progenitors, tissue location, and activation. They contribute to tissue homeostasis by interacting with local and systemic immune and non-immune cells through trophic, clearance, and cytocidal functions. During evolution, they contributed to the innate host defense before effector mechanisms of specific adaptive immunity emerged. Mouse macrophages appear at mid-gestation and are distributed throughout the embryo to facilitate organogenesis and clear cells undergoing programmed cell death. Yolk sac, AGM, and fetal liver-derived tissue-resident macrophages persist throughout postnatal and adult life, supplemented by bone marrow-derived blood monocytes, as required after injury and infection. Nobel awards to Elie Metchnikoff and Paul Ehrlich in 1908 drew attention to cellular phagocytic and humoral immunity, respectively. In 2011, prizes were awarded to Jules Hoffmann and Bruce Beutler for contributions to innate immunity and to Ralph Steinman for the discovery of dendritic cells and their role in antigen presentation to T lymphocytes. We trace milestones in the history of mononuclear phagocyte research from the perspective of Nobel awards bearing directly and indirectly on their role in cellular immunity.


Subject(s)
Immunity, Cellular , Nobel Prize , Phagocytes , Animals , Humans , Dendritic Cells/immunology , History, 20th Century , History, 21st Century , Immunity, Innate , Macrophages/immunology , Mononuclear Phagocyte System/immunology , Nobel Prize/history , Phagocytes/immunology
9.
Palliat Med Rep ; 5(1): 306-315, 2024.
Article in English | MEDLINE | ID: mdl-39144133

ABSTRACT

Background: The Surprise Question (SQ) is a common method aimed at identifying frail patients who need serious illness conversations to integrate a palliative approach. However, little is known about whether the SQ identifies patients on hemodialysis who perceive that they are declining or have low health-related quality of life (HRQoL)-important aspects when considering the need for serious illness conversations. Objective: To explore how nurses and physicians' responses to the SQ are associated with patients' self-reported HRQoL. Design: Cross-sectional study. Subjects: In total, 282 patients on hemodialysis were included. Measurements: One nurse and one physician responded to the SQ for each patient. The patient-reported HRQoL was measured with the RAND 36-Item Health Survey 1.0 (RAND-36) and the EuroQual vertical visual analogue scale (EQ-VAS) from the EuroQual-5 Dimension Questionnaire (EQ-5D). Results: Nurses' responses "no, not surprised" to the SQ were associated with patient-reported worsened health compared to one year ago (RAND-36), and lower perceived overall health (EQ-VAS). Physicians' responses "no, not surprised" were associated with lower overall health and lower physical functioning. Patient-reported pain, general health, fatigue, and emotional and social aspects were not associated with responses to the SQ. Conclusions: The findings indicate that the SQ identifies patients on hemodialysis who report low overall health and low physical functioning. However, the SQ did not identify patients who reported pain, emotional problems, or fatigue, which are also important aspects to consider in identifying needs for serious illness conversations, symptom management, and to be able to integrate a palliative approach.

10.
Dis Model Mech ; 17(8)2024 Aug 01.
Article in English | MEDLINE | ID: mdl-39114912

ABSTRACT

The Bacillus Calmette-Guérin (BCG) vaccine is the oldest cancer immunotherapeutic agent in use. Despite its effectiveness, its initial mechanisms of action remain largely unknown. Here, we elucidate the earliest cellular mechanisms involved in BCG-induced tumor clearance. We developed a fast preclinical in vivo assay to visualize in real time and at single-cell resolution the initial interactions among bladder cancer cells, BCG and innate immunity using the zebrafish xenograft model. We show that BCG induced the recruitment and polarization of macrophages towards a pro-inflammatory phenotype, accompanied by induction of the inflammatory cytokines tnfa, il1b and il6 in the tumor microenvironment. Macrophages directly induced apoptosis of human cancer cells through zebrafish TNF signaling. Macrophages were crucial for this response as their depletion completely abrogated the BCG-induced phenotype. Contrary to the general concept that macrophage anti-tumoral activities mostly rely on stimulating an effective adaptive response, we demonstrate that macrophages alone can induce tumor apoptosis and clearance. Thus, our results revealed an additional step to the BCG-induced tumor immunity model, while providing proof-of-concept experiments demonstrating the potential of this unique model to test innate immunomodulators.


Subject(s)
Apoptosis , BCG Vaccine , Macrophages , Signal Transduction , Urinary Bladder Neoplasms , Zebrafish , Urinary Bladder Neoplasms/pathology , Urinary Bladder Neoplasms/drug therapy , Urinary Bladder Neoplasms/immunology , Animals , Macrophages/metabolism , Macrophages/drug effects , BCG Vaccine/pharmacology , BCG Vaccine/therapeutic use , Signal Transduction/drug effects , Humans , Cell Line, Tumor , Apoptosis/drug effects , Tumor Necrosis Factor-alpha/metabolism , Tumor Microenvironment
11.
Med Microbiol Immunol ; 213(1): 17, 2024 Aug 02.
Article in English | MEDLINE | ID: mdl-39093331

ABSTRACT

Carl Flügge is best known for the promotion of studies demonstrating the transmission of all manner of infections, but particularly tuberculosis, by coughed droplets. But it is seldom recognised that Flügge was also influential in a number of other fields comprising the practice of hygiene. One-hundred years following his death in 1923, we review literature related to the studies of Flügge and his colleagues and students and illustrate the particular emphasis he laid upon the environment within which disease and its transmission might be fostered or prevented, embracing and studying aspects essential to the health of any community ranging from fundamental microbiology in the laboratory to subjects as disparate as housing, clean water supply, nutrition, sanitation, socio-economic circumstances and climate. Very early in his career he promoted breast feeding for the prevention of seasonal gastro-enteritis and later the sheltering of cough as a means of preventing the transmission of infected respiratory droplets, not only as regards tuberculosis, but also concerning all manner of other respiratory infections. By the time of Flügge's death the complexification of available scientific methodologies comprising hygiene made it difficult for any individual to comprehend and study the wide range of hygiene-related subjects such as Flügge did. Carl Flügge was one of the last holistic hygienists and an originator of the study of environmental health as a pillar of hygiene.


Subject(s)
Hygiene , Humans , History, 20th Century , Hygiene/history , Communicable Diseases/transmission , Communicable Diseases/history
12.
Front Cell Dev Biol ; 12: 1426043, 2024.
Article in English | MEDLINE | ID: mdl-39119041

ABSTRACT

Exact three-dimensional (3D) structural information of developing organoids is key for optimising organoid generation and for studying experimental outcomes in organoid models. We set up a 3D imaging technique and studied complexly arranged native and experimentally challenged cardioids of two stages of remodelling. The imaging technique we employed is S-HREM (Scanning High Resolution Episcopic Microscopy), a variant of HREM, which captures multiple images of subsequently exposed surfaces of resin blocks and automatically combines them to large sized digital volume data of voxels sizes below 1 µm3. We provide precise volumetric information of the examined specimens and their single components and comparisons between stages in terms of volume and micro- and macroanatomic structure. We describe the 3D arrangement and lining of different types of cavities and their changes between day 10 and day 14 and map the various cell types to their precise spatial and structural environment. Exemplarily, we conducted semiautomatic counts of nuclei. In cryo-injured cardioids, we examined the extension and composition of the injured areas. Our results demonstrate the high quality and the great potential of digital volume data produced with S-HREM. It also provides sound metric and structural information, which assists production of native and experimentally challenged left ventricle cardioids and interpretation of their structural remodelling.

13.
Behav Brain Res ; 471: 115136, 2024 08 05.
Article in English | MEDLINE | ID: mdl-38971431

ABSTRACT

Gestational exposure to valproic acid (VPA) is a risk factor for autism spectrum disorder (ASD). Rodents exposed to VPA in utero display common features of ASD, including volumetric dysregulation in higher-order cognitive regions like the medial prefrontal cortex (mPFC), the anterior cingulate cortex (ACC), and the hippocampus. Exercise has been shown in elderly populations to boost cognition and to buffer against brain volume losses with age. This study employed an adolescent treadmill exercise intervention to facilitate cognitive flexibility and regional brain volume regulation in rats exposed to VPA during gestation. It was found that exercise improved performance on extra-dimensional shifts of attention on a set-shifting task, which is indicative of improved cognitive flexibility. Exercise decreased frontal cortex volume in females, whereas in males exercise increased the ventral hippocampus. These findings suggest that aerobic exercise may be an effective intervention to counteract the altered development of prefrontal and hippocampal regions often observed in ASD.


Subject(s)
Disease Models, Animal , Physical Conditioning, Animal , Animals , Male , Female , Physical Conditioning, Animal/physiology , Valproic Acid/pharmacology , Cognition/physiology , Rats , Pregnancy , Hippocampus , Prefrontal Cortex/physiopathology , Autistic Disorder/physiopathology , Autistic Disorder/therapy , Prenatal Exposure Delayed Effects/physiopathology , Brain/physiopathology , Autism Spectrum Disorder/physiopathology , Autism Spectrum Disorder/therapy
14.
medRxiv ; 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-39072024

ABSTRACT

Aging increases the risk of neurodegeneration, cognitive decline, and Alzheimer's disease (AD). Currently no means exist to measure neuronal cell death during life or to prevent it. Here we show that cross-sectional measures of human plasma proteins released from dying/damaged neurons (ubiquitin C-terminal hydrolase-L1/UCH-L1 and neurofilament light/NfL) become exponentially higher from age 2-85; UCH-L1 rises faster in females. Glial fibrillary acidic protein (GFAP) concentrations, indicating astrogliosis/inflammation, increase exponentially after age 40. Treatment with human granulocyte-macrophage colony-stimulating factor (GM-CSF/sargramostim) halted neuronal cell death, as evidenced by reduced plasma UCH-L1 concentrations, in AD participants to levels equivalent to those of five-year-old healthy controls. The ability of GM-CSF treatment to reduce neuronal apoptosis was confirmed in a rat model of AD. These findings suggest that the exponential increase in neurodegeneration with age, accelerated by neuroinflammation, may underlie the contribution of aging to cognitive decline and AD and can be halted by GM-CSF/sargramostim treatment.

15.
Clin Kidney J ; 17(7): sfae141, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38989279

ABSTRACT

Background: The use of diuretics in patients on haemodialysis (HD) is thought to maintain diuresis. However, this assumption and the optimal dose are based on little scientific evidence, and associations with clinical outcomes are unclear. Methods: We reported international variations in diuretic use and loop diuretic dose across 27 759 HD patients with dialysis vintage <1 year in the Dialysis Outcomes and Practice Patterns Study phases 2-5 (2002-2015), a prospective cohort study. Doses of torsemide (4:1) and bumetanide (80:1) were converted to oral furosemide-equivalent doses. Adjusted Cox, logistic and linear regressions were used to investigate the association of diuretic use and dose with outcomes. Results: Diuretic utilization varied widely by country at vintage <3 months, ranging from >80% in Germany and Sweden to <35% in the USA, at a median dose ranging from 400-500 mg/day in Germany and Sweden to <100 mg/day in Japan and the USA. Neither diuretic use nor higher doses were associated with a lower risk of all-cause mortality, a higher risk of hospitalization for fracture or elevated parathyroid hormone levels, but the prescription of higher doses (>200 mg/day) was associated with a higher risk of all-cause hospitalization. Conclusions: Substantial international differences exist in diuretic prescriptions, with use and doses much higher in some European countries than the USA. The prescription and higher doses of loop diuretics was not associated with improved outcomes.

16.
J Am Coll Cardiol ; 84(4): 354-364, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39019530

ABSTRACT

BACKGROUND: ARTESiA (Apixaban for the Reduction of Thrombo-Embolism in Patients With Device-Detected Sub-Clinical Atrial Fibrillation) demonstrated that apixaban, compared with aspirin, significantly reduced stroke and systemic embolism (SE) but increased major bleeding in patients with subclinical atrial fibrillation. OBJECTIVES: To help inform decision making, the authors evaluated the efficacy and safety of apixaban according to baseline CHA2DS2-VASc score. METHODS: We performed a subgroup analysis according to baseline CHA2DS2-VASc score and assessed both the relative and absolute differences in stroke/SE and major bleeding. RESULTS: Baseline CHA2DS2-VASc scores were <4 in 1,578 (39.4%) patients, 4 in 1,349 (33.6%), and >4 in 1,085 (27.0%). For patients with CHA2DS2-VASc >4, the rate of stroke was 0.98%/year with apixaban and 2.25%/year with aspirin; compared with aspirin, apixaban prevented 1.28 (95% CI: 0.43-2.12) strokes/SE per 100 patient-years and caused 0.68 (95% CI: -0.23 to 1.57) major bleeds. For CHA2DS2-VASc <4, the stroke/SE rate was 0.85%/year with apixaban and 0.97%/year with aspirin. Apixaban prevented 0.12 (95% CI: -0.38 to 0.62) strokes/SE per 100 patient-years and caused 0.33 (95% CI: -0.27 to 0.92) major bleeds. For patients with CHA2DS2-VASc =4, apixaban prevented 0.32 (95% CI: -0.16 to 0.79) strokes/SE per 100 patient-years and caused 0.28 (95% CI: -0.30 to 0.86) major bleeds. CONCLUSIONS: One in 4 patients in ARTESiA with subclinical atrial fibrillation had a CHA2DS2-VASc score >4 and a stroke/SE risk of 2.2% per year. For these patients, the benefits of treatment with apixaban in preventing stroke/SE are greater than the risks. The opposite is true for patients with CHA2DS2-VASc score <4. A substantial intermediate group (CHA2DS2-VASc =4) exists in which patient preferences will inform treatment decisions. (Apixaban for the Reduction of Thrombo-Embolism in Patients With Device-Detected Sub-Clinical Atrial Fibrillation; NCT01938248).


Subject(s)
Aspirin , Atrial Fibrillation , Factor Xa Inhibitors , Pyrazoles , Pyridones , Stroke , Humans , Atrial Fibrillation/drug therapy , Atrial Fibrillation/complications , Pyrazoles/therapeutic use , Pyridones/therapeutic use , Pyridones/adverse effects , Pyridones/administration & dosage , Aspirin/therapeutic use , Male , Female , Aged , Middle Aged , Stroke/prevention & control , Stroke/etiology , Stroke/epidemiology , Factor Xa Inhibitors/therapeutic use , Risk Assessment/methods , Hemorrhage/chemically induced , Hemorrhage/epidemiology
17.
HLA ; 103(6): e15543, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38837862

ABSTRACT

The MHC class I region contains crucial genes for the innate and adaptive immune response, playing a key role in susceptibility to many autoimmune and infectious diseases. Genome-wide association studies have identified numerous disease-associated SNPs within this region. However, these associations do not fully capture the immune-biological relevance of specific HLA alleles. HLA imputation techniques may leverage available SNP arrays by predicting allele genotypes based on the linkage disequilibrium between SNPs and specific HLA alleles. Successful imputation requires diverse and large reference panels, especially for admixed populations. This study employed a bioinformatics approach to call SNPs and HLA alleles in multi-ethnic samples from the 1000 genomes (1KG) dataset and admixed individuals from Brazil (SABE), utilising 30X whole-genome sequencing data. Using HIBAG, we created three reference panels: 1KG (n = 2504), SABE (n = 1171), and the full model (n = 3675) encompassing all samples. In extensive cross-validation of these reference panels, the multi-ethnic 1KG reference exhibited overall superior performance than the reference with only Brazilian samples. However, the best results were achieved with the full model. Additionally, we expanded the scope of imputation by developing reference panels for non-classical, MICA, MICB and HLA-H genes, previously unavailable for multi-ethnic populations. Validation in an independent Brazilian dataset showcased the superiority of our reference panels over the Michigan Imputation Server, particularly in predicting HLA-B alleles among Brazilians. Our investigations underscored the need to enhance or adapt reference panels to encompass the target population's genetic diversity, emphasising the significance of multiethnic references for accurate imputation across different populations.


Subject(s)
Alleles , Ethnicity , Gene Frequency , Polymorphism, Single Nucleotide , Humans , Brazil , Ethnicity/genetics , HLA Antigens/genetics , Linkage Disequilibrium , Genome-Wide Association Study/methods , Genotype , Genetics, Population/methods , Histocompatibility Antigens Class I/genetics , Computational Biology/methods
18.
mBio ; 15(7): e0080524, 2024 Jul 17.
Article in English | MEDLINE | ID: mdl-38912775

ABSTRACT

Piperaquine (PPQ) is widely used in combination with dihydroartemisinin as a first-line treatment against malaria. Multiple genetic drivers of PPQ resistance have been reported, including mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and increased copies of plasmepsin II/III (pm2/3). We generated a cross between a Cambodia-derived multidrug-resistant KEL1/PLA1 lineage isolate (KH004) and a drug-susceptible Malawian parasite (Mal31). Mal31 harbors a wild-type (3D7-like) pfcrt allele and a single copy of pm2/3, while KH004 has a chloroquine-resistant (Dd2-like) pfcrt allele with an additional G367C substitution and multiple copies of pm2/3. We recovered 104 unique recombinant parasites and examined a targeted set of progeny representing all possible combinations of variants at pfcrt and pm2/3. We performed a detailed analysis of competitive fitness and a range of PPQ susceptibility phenotypes with these progenies, including PPQ survival assay, area under the dose response curve, and a limited point IC50. We find that inheritance of the KH004 pfcrt allele is required for reduced PPQ sensitivity, whereas copy number variation in pm2/3 further decreases susceptibility but does not confer resistance in the absence of additional mutations in pfcrt. A deep investigation of genotype-phenotype relationships demonstrates that progeny clones from experimental crosses can be used to understand the relative contributions of pfcrt, pm2/3, and parasite genetic background to a range of PPQ-related traits. Additionally, we find that the resistance phenotype associated with parasites inheriting the G367C substitution in pfcrt is consistent with previously validated PPQ resistance mutations in this transporter.IMPORTANCEResistance to piperaquine, used in combination with dihydroartemisinin, has emerged in Cambodia and threatens to spread to other malaria-endemic regions. Understanding the causal mutations of drug resistance and their impact on parasite fitness is critical for surveillance and intervention and can also reveal new avenues to limiting the evolution and spread of drug resistance. An experimental genetic cross is a powerful tool for pinpointing the genetic determinants of key drug resistance and fitness phenotypes and has the distinct advantage of quantifying the effects of naturally evolved genetic variation. Our study was strengthened since the full range of copies of KH004 pm2/3 was inherited among the progeny clones, allowing us to directly test the role of the pm2/3 copy number on resistance-related phenotypes in the context of a unique pfcrt allele. Our multigene model suggests an important role for both loci in the evolution of this multidrug-resistant parasite lineage.


Subject(s)
Antimalarials , Aspartic Acid Endopeptidases , Drug Resistance , Membrane Transport Proteins , Plasmodium falciparum , Protozoan Proteins , Quinolines , Plasmodium falciparum/genetics , Plasmodium falciparum/drug effects , Protozoan Proteins/genetics , Protozoan Proteins/metabolism , Drug Resistance/genetics , Antimalarials/pharmacology , Quinolines/pharmacology , Aspartic Acid Endopeptidases/genetics , Aspartic Acid Endopeptidases/metabolism , Membrane Transport Proteins/genetics , Malaria, Falciparum/parasitology , Malaria, Falciparum/drug therapy , Humans , Alleles , Cambodia , Mutation , Piperazines
19.
Proc Natl Acad Sci U S A ; 121(25): e2312499121, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38857395

ABSTRACT

Ex vivo expansion of human CD34+ hematopoietic stem and progenitor cells remains a challenge due to rapid differentiation after detachment from the bone marrow niche. In this study, we assessed the capacity of an inducible fusion protein to enable sustained ex vivo proliferation of hematopoietic precursors and their capacity to differentiate into functional phagocytes. We fused the coding sequences of an FK506-Binding Protein 12 (FKBP12)-derived destabilization domain (DD) to the myeloid/lymphoid lineage leukemia/eleven nineteen leukemia (MLL-ENL) fusion gene to generate the fusion protein DD-MLL-ENL and retrovirally expressed the protein switch in human CD34+ progenitors. Using Shield1, a chemical inhibitor of DD fusion protein degradation, we established large-scale and long-term expansion of late monocytic precursors. Upon Shield1 removal, the cells lost self-renewal capacity and spontaneously differentiated, even after 2.5 y of continuous ex vivo expansion. In the absence of Shield1, stimulation with IFN-γ, LPS, and GM-CSF triggered terminal differentiation. Gene expression analysis of the obtained phagocytes revealed marked similarity with naïve monocytes. In functional assays, the novel phagocytes migrated toward CCL2, attached to VCAM-1 under shear stress, produced reactive oxygen species, and engulfed bacterial particles, cellular particles, and apoptotic cells. Finally, we demonstrated Fcγ receptor recognition and phagocytosis of opsonized lymphoma cells in an antibody-dependent manner. Overall, we have established an engineered protein that, as a single factor, is useful for large-scale ex vivo production of human phagocytes. Such adjustable proteins have the potential to be applied as molecular tools to produce functional immune cells for experimental cell-based approaches.


Subject(s)
Cell Differentiation , Phagocytes , Humans , Phagocytes/metabolism , Hematopoietic Stem Cells/metabolism , Oncogene Proteins, Fusion/genetics , Oncogene Proteins, Fusion/metabolism , Recombinant Fusion Proteins/metabolism , Recombinant Fusion Proteins/genetics , Myeloid-Lymphoid Leukemia Protein/metabolism , Myeloid-Lymphoid Leukemia Protein/genetics , Leukemia/genetics , Leukemia/pathology , Leukemia/metabolism , Protein Engineering/methods , Phagocytosis
20.
Biophys Rep (N Y) ; 4(2): 100157, 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38795740

ABSTRACT

T1 mapping is a quantitative method to characterize tissues with magnetic resonance imaging in a quick and efficient manner. It utilizes the relaxation rate of protons to depict the underlying structures within the imaging frame. While T1-mapping techniques are used with some frequency in areas such as cardiac imaging, their application for understanding malignancies and identifying tumor structures has yet to be thoroughly investigated. Utilizing a saturation recovery method to acquire T1 maps for two different tumor models has revealed that longitudinal relaxation mapping is sensitive enough to distinguish between normal and malignant tissue. This is seen even with decreased signal/noise ratios using small voxel sizes to obtain high-resolution images. In both tumor models, it was revealed that relaxation mapping recorded significantly different relaxation values between regions encapsulating the tumor, muscle, kidney, or spleen, as well as between the cell lines themselves. This indicates a potential future application of relaxation mapping as a method to fingerprint various stages of tumor development and may prove a useful measure to identify micro-metastases.


Subject(s)
Magnetic Resonance Imaging , Magnetic Resonance Imaging/methods , Animals , Mice , Cell Line, Tumor , Humans , Neoplasms/diagnostic imaging , Neoplasms/pathology , Neoplasms/diagnosis , Signal-To-Noise Ratio
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