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1.
Nat Immunol ; 25(2): 191-193, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38238607
2.
Am J Hum Genet ; 111(2): 393-402, 2024 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-38272031

RESUMEN

Sterile alpha motif domain containing 7 (SAMD7) is a component of the Polycomb repressive complex 1, which inhibits transcription of many genes, including those activated by the transcription factor Cone-Rod Homeobox (CRX). Here we report bi-allelic mutations in SAMD7 as a cause of autosomal-recessive macular dystrophy with or without cone dysfunction. Four of these mutations affect splicing, while another mutation is a missense variant that alters the repressive effect of SAMD7 on CRX-dependent promoter activity, as shown by in vitro assays. Immunostaining of human retinal sections revealed that SAMD7 is localized in the nuclei of both rods and cones, as well as in those of cells belonging to the inner nuclear layer. These results place SAMD7 as a gene crucial for human retinal function and demonstrate a significant difference in the role of SAMD7 between the human and the mouse retina.


Asunto(s)
Anomalías del Ojo , Degeneración Macular , Ratones , Animales , Humanos , Transactivadores/genética , Proteínas de Homeodominio/genética , Retina , Mutación/genética , Degeneración Macular/genética
3.
Clin Genet ; 2024 Jun 11.
Artículo en Inglés | MEDLINE | ID: mdl-38863195

RESUMEN

Biallelic variants in SUMF1 are associated with multiple sulfatase deficiency (MSD), a rare lysosomal storage disorder typically diagnosed in early infancy or childhood, marked by severe neurodegeneration and early mortality. We present clinical and molecular characterisation of three unrelated patients aged 13 to 58 years with milder clinical manifestations due to SUMF1 disease variants, including two adult patients presenting with apparent non-syndromic retinal dystrophy. Whole genome sequencing identified biallelic SUMF1 variants in all three patients; Patient 1 homozygous for a complex allele c.[290G>T;293T>A]; p.[(Gly97Val);(Val98Glu)], Patient 2 homozygous for c.866A>G; p.(Tyr289Cys), and Patient 3 compound heterozygous for c.726-1G>C and p.(Tyr289Cys). Electroretinography indicated a rod-cone dystrophy with additional possible inner retinal dysfunction in all three patients. Biochemical studies confirmed reduced, but not absent, sulfatase enzyme activity in the absence of extra-ocular disease (Patient 1) or only mild systemic disease (Patients 2, 3). These cases are suggestive that non-null SUMF1 genotypes can cause an attenuated clinical phenotype, including retinal dystrophy without systemic complications, in adulthood.

4.
BMC Ophthalmol ; 24(1): 345, 2024 Aug 14.
Artículo en Inglés | MEDLINE | ID: mdl-39143519

RESUMEN

BACKGROUND: Oculocutaneous albinism (OCA) is a genetically heterogeneous condition that is associated with reduced or absent melanin pigment in the skin, hair, and eyes, resulting in reduced vision, high sensitivity to light, and rapid and uncontrolled eye movements. To date, seventeen genes have been associated with OCA including syndromic and non-syndromic forms of the condition. METHODS: Whole exome sequencing (WES) was performed to identify pathogenic variants in nine Pakistani families with OCA, with validation and segregation of candidate variants performed using Sanger sequencing. Furthermore, the pathogenicity of the identified variants was assessed using various in-silico tools and 3D protein structural analysis software. RESULTS: WES identified biallelic variants in three genes explaining the OCA in these families, including four variants in TYR, three in OCA2, and two in HPS1, including two novel variants c.667C > T: p.(Gln223*) in TYR, and c.2009 T > C: p.(Leu670Pro) in HPS1. CONCLUSIONS: Overall, this study adds further knowledge of the genetic basis of OCA in Pakistani communities and facilitates improved management and counselling services for families suffering from severe genetic diseases in Pakistan.


Asunto(s)
Albinismo Oculocutáneo , Secuenciación del Exoma , Síndrome de Hermanski-Pudlak , Mutación , Linaje , Humanos , Albinismo Oculocutáneo/genética , Pakistán , Femenino , Masculino , Síndrome de Hermanski-Pudlak/genética , Niño , Adulto , Adolescente , Análisis Mutacional de ADN , Monofenol Monooxigenasa/genética , Preescolar , Proteínas de Transporte de Membrana/genética , Adulto Joven , Proteínas de la Membrana
5.
Biotechnol Lett ; 2024 Jul 27.
Artículo en Inglés | MEDLINE | ID: mdl-39066958

RESUMEN

Klebsiella variicola is a Gram-negative bacterium that is frequently isolated from a wide variety of natural niches. It is a ubiquitous opportunistic pathogen that can cause diverse infections in plants, animals, and humans. It also has significant biotechnological potential. However, due to the lack of efficient genetic tools, the molecular basis contributing to the pathogenesis and beneficial activities of K. variicola remains poorly understood. In this study, we found and characterized a native type I-E CRISPR-Cas system in a recently isolated K. variicola strain KV-1. The system cannot cleave target DNA sequences due to the inactivation of the Cas3 nuclease by a transposable element but retains the activity of the crRNA-guided Cascade binding to the target DNA sequence. A targeting plasmid carrying a mini-CRISPR to encode a crRNA was designed and introduced into the KV-1 strain, which successfully repurposed the native type I-E CRISPR-Cas system to inhibit the expression of the target gene efficiently and specifically. Moreover, by creating a mini-CRISPR to encode multiple crRNAs, multiplex gene repression was achieved by providing a single targeting plasmid. This work provides the first native CRISPR-Cas-based tool for programmable multiplex gene repression in K. variicola, which will facilitate studying the pathogenic mechanism of K. variicola and enable metabolic engineering to produce valuable bioproducts.

6.
Ophthalmic Res ; 67(1): 448-457, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39079514

RESUMEN

INTRODUCTION: The purpose of this project was to explore the current standards of clinical care genetic testing and counseling for patients with inherited retinal diseases (IRDs) from the perspective of leading experts in selected European countries. Also, to gather opinions on current bottlenecks and future solutions to improve patient care. METHODS: On the initiative of the European Vision Institute, a survey questionnaire with 41 questions was designed and sent to experts in the field from ten European countries. Each participant was asked to answer with reference to the situation in their own country. RESULTS: Sixteen questionnaires were collected by November 2023. IRD genetic tests are performed in clinical care settings for 80% or more of tested patients in 9 countries, and the costs of genetic tests in clinical care are covered by the public health service to the extent of 90% or more in 8 countries. The median proportion of patients who are genetically tested, the median rate of genetically solved patients among those who are tested, and the median proportion of patients receiving counseling are 51-70%, 61-80%, and 61-80%, respectively. Improving the education of healthcare professionals who facilitate patient referrals to specialized centers, improving access of patients to more thorough genotyping, and increasing the number of available counselors were the most advocated solutions. CONCLUSION: There is a significant proportion of IRD patients who are not genetically tested, whose genetic testing is inconclusive, or who do not receive counseling. Educational programs, greater availability of state-of-the-art genotyping and genetic counselors could improve healthcare for IRD patients.


Asunto(s)
Pruebas Genéticas , Enfermedades de la Retina , Humanos , Pruebas Genéticas/métodos , Europa (Continente) , Enfermedades de la Retina/genética , Enfermedades de la Retina/diagnóstico , Encuestas y Cuestionarios , Asesoramiento Genético
7.
Neuroimage ; 279: 120325, 2023 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-37579999

RESUMEN

Observational studies consistently disclose brain imaging-derived phenotypes (IDPs) as critical markers for early diagnosis of both brain disorders and cardiovascular diseases. However, it remains unclear about the shared genetic landscape between brain IDPs and the risk of brain disorders and cardiovascular diseases, restricting the applications of potential diagnostic techniques through brain IDPs. Here, we reported genetic correlations and putative causal relationships between 921 brain IDPs, 20 brain disorders and six cardiovascular diseases by leveraging their large-scale genome-wide association study (GWAS) summary statistics. Applications of Mendelian randomization (MR) identified significant putative causal effects of multiple region-specific brain IDPs in relation to the increased risks for amyotrophic lateral sclerosis (ALS), major depressive disorder (MDD), autism spectrum disorder (ASD) and schizophrenia (SCZ). We also found brain IDPs specifically from temporal lobe as a putatively causal consequence of hypertension. The genome-wide colocalization analysis identified three genomic regions in which MDD, ASD and SCZ colocalized with the brain IDPs, and two novel SNPs to be associated with ASD, SCZ, and multiple brain IDPs. Furthermore, we identified a list of candidate genes involved in the shared genetics underlying pairs of brain IDPs and MDD, ASD, SCZ, ALS and hypertension. Our results provide novel insights into the genetic relationships between brain disorders and cardiovascular diseases and brain IDP, which may server as clues for using brain IDPs to predict risks of diseases.


Asunto(s)
Esclerosis Amiotrófica Lateral , Trastorno del Espectro Autista , Encefalopatías , Enfermedades Cardiovasculares , Trastorno Depresivo Mayor , Hipertensión , Humanos , Trastorno Depresivo Mayor/diagnóstico por imagen , Trastorno Depresivo Mayor/genética , Enfermedades Cardiovasculares/diagnóstico por imagen , Enfermedades Cardiovasculares/genética , Estudio de Asociación del Genoma Completo/métodos , Trastorno del Espectro Autista/diagnóstico por imagen , Trastorno del Espectro Autista/genética , Análisis de la Aleatorización Mendeliana/métodos , Fenotipo , Encefalopatías/diagnóstico por imagen , Encefalopatías/genética , Neuroimagen
8.
Eur Radiol ; 33(4): 2965-2974, 2023 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-36418622

RESUMEN

OBJECTIVES: Recent studies have revealed the change of molecular subtypes in breast cancer (BC) after neoadjuvant therapy (NAT). This study aims to construct a non-invasive model for predicting molecular subtype alteration in breast cancer after NAT. METHODS: Eighty-two estrogen receptor (ER)-negative/ human epidermal growth factor receptor 2 (HER2)-negative or ER-low-positive/HER2-negative breast cancer patients who underwent NAT and completed baseline MRI were retrospectively recruited between July 2010 and November 2020. Subtype alteration was observed in 21 cases after NAT. A 2D-DenseUNet machine-learning model was built to perform automatic segmentation of breast cancer. 851 radiomic features were extracted from each MRI sequence (T2-weighted imaging, ADC, DCE, and contrast-enhanced T1-weighted imaging), both in the manual and auto-segmentation masks. All samples were divided into a training set (n = 66) and a test set (n = 16). XGBoost model with 5-fold cross-validation was performed to predict molecular subtype alterations in breast cancer patients after NAT. The predictive ability of these models was subsequently evaluated by the AUC of the ROC curve, sensitivity, and specificity. RESULTS: A model consisting of three radiomics features from the manual segmentation of multi-sequence MRI achieved favorable predictive efficacy in identifying molecular subtype alteration in BC after NAT (cross-validation set: AUC = 0.908, independent test set: AUC = 0.864); whereas an automatic segmentation approach of BC lesions on the DCE sequence produced good segmentation results (Dice similarity coefficient = 0.720). CONCLUSIONS: A machine learning model based on baseline MRI is proven useful for predicting molecular subtype alterations in breast cancer after NAT. KEY POINTS: • Machine learning models using MRI-based radiomics signature have the ability to predict molecular subtype alterations in breast cancer after neoadjuvant therapy, which subsequently affect treatment protocols. • The application of deep learning in the automatic segmentation of breast cancer lesions from MRI images shows the potential to replace manual segmentation..


Asunto(s)
Neoplasias de la Mama , Humanos , Femenino , Neoplasias de la Mama/diagnóstico por imagen , Neoplasias de la Mama/terapia , Neoplasias de la Mama/patología , Estudios Retrospectivos , Terapia Neoadyuvante/métodos , Imagen por Resonancia Magnética/métodos , Aprendizaje Automático
9.
J Med Genet ; 59(12): 1151-1164, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-35764379

RESUMEN

BACKGROUND: The 100 000 Genomes Project (100K) recruited National Health Service patients with eligible rare diseases and cancer between 2016 and 2018. PanelApp virtual gene panels were applied to whole genome sequencing data according to Human Phenotyping Ontology (HPO) terms entered by recruiting clinicians to guide focused analysis. METHODS: We developed a reverse phenotyping strategy to identify 100K participants with pathogenic variants in nine prioritised disease genes (BBS1, BBS10, ALMS1, OFD1, DYNC2H1, WDR34, NPHP1, TMEM67, CEP290), representative of the full phenotypic spectrum of multisystemic primary ciliopathies. We mapped genotype data 'backwards' onto available clinical data to assess potential matches against phenotypes. Participants with novel molecular diagnoses and key clinical features compatible with the identified disease gene were reported to recruiting clinicians. RESULTS: We identified 62 reportable molecular diagnoses with variants in these nine ciliopathy genes. Forty-four have been reported by 100K, 5 were previously unreported and 13 are new diagnoses. We identified 11 participants with unreportable, novel molecular diagnoses, who lacked key clinical features to justify reporting to recruiting clinicians. Two participants had likely pathogenic structural variants and one a deep intronic predicted splice variant. These variants would not be prioritised for review by standard 100K diagnostic pipelines. CONCLUSION: Reverse phenotyping improves the rate of successful molecular diagnosis for unsolved 100K participants with primary ciliopathies. Previous analyses likely missed these diagnoses because incomplete HPO term entry led to incorrect gene panel choice, meaning that pathogenic variants were not prioritised. Better phenotyping data are therefore essential for accurate variant interpretation and improved patient benefit.


Asunto(s)
Síndrome de Bardet-Biedl , Ciliopatías , Humanos , Antígenos de Neoplasias , Síndrome de Bardet-Biedl/genética , Proteínas Portadoras/genética , Proteínas de Ciclo Celular/genética , Ciliopatías/diagnóstico , Ciliopatías/genética , Proteínas del Citoesqueleto/genética , Genotipo , Proteínas Asociadas a Microtúbulos/genética , Fenotipo , Medicina Estatal , Genoma Humano
10.
Genet Med ; 24(3): 631-644, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-34906488

RESUMEN

PURPOSE: We previously defined biallelic HYAL2 variants causing a novel disorder in 2 families, involving orofacial clefting, facial dysmorphism, congenital heart disease, and ocular abnormalities, with Hyal2 knockout mice displaying similar phenotypes. In this study, we better define the phenotype and pathologic disease mechanism. METHODS: Clinical and genomic investigations were undertaken alongside molecular studies, including immunoblotting and immunofluorescence analyses of variant/wild-type human HYAL2 expressed in mouse fibroblasts, and in silico modeling of putative pathogenic variants. RESULTS: Ten newly identified individuals with this condition were investigated, and they were associated with 9 novel pathogenic variants. Clinical studies defined genotype-phenotype correlations and confirmed a recognizable craniofacial phenotype in addition to myopia, cleft lip/palate, and congenital cardiac anomalies as the most consistent manifestations of the condition. In silico modeling of missense variants identified likely deleterious effects on protein folding. Consistent with this, functional studies indicated that these variants cause protein instability and a concomitant cell surface absence of HYAL2 protein. CONCLUSION: These studies confirm an association between HYAL2 alterations and syndromic cleft lip/palate, provide experimental evidence for the pathogenicity of missense alleles, enable further insights into the pathomolecular basis of the disease, and delineate the core and variable clinical outcomes of the condition.


Asunto(s)
Labio Leporino , Fisura del Paladar , Alelos , Animales , Moléculas de Adhesión Celular/genética , Labio Leporino/genética , Fisura del Paladar/genética , Proteínas Ligadas a GPI/genética , Estudios de Asociación Genética , Humanos , Hialuronoglucosaminidasa/genética , Ratones , Fenotipo
11.
PLoS Genet ; 14(8): e1007504, 2018 08.
Artículo en Inglés | MEDLINE | ID: mdl-30157172

RESUMEN

We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post fertilization. The depressed electroretinogram (ERG) cone response and cone spectral sensitivity of 5 dpf KO zebrafish and reduced eye size, retinal thickness, and expression of rod and cone opsins could be rescued by injection of wild type CLCC1 mRNA. Clcc1+/- KO mice showed decreased ERGs and photoreceptor number. Together these results strongly suggest that intracellular chloride transport by CLCC1 is a critical process in maintaining retinal integrity, and CLCC1 is crucial for survival and function of retinal cells.


Asunto(s)
Canales de Cloruro/genética , Mutación Missense , Retinitis Pigmentosa/genética , Animales , Pueblo Asiatico/genética , Línea Celular , Canales de Cloruro/metabolismo , Citoplasma/metabolismo , Proteínas del Ojo/genética , Proteínas del Ojo/metabolismo , Células HEK293 , Homocigoto , Humanos , Ratones , Ratones Noqueados , Pakistán , Retina/metabolismo , Células Fotorreceptoras Retinianas Conos/metabolismo , Células Fotorreceptoras Retinianas Bastones/metabolismo , Retinitis Pigmentosa/diagnóstico , Pez Cebra/genética , Pez Cebra/metabolismo
12.
Ann Hum Genet ; 83(6): 477-482, 2019 11.
Artículo en Inglés | MEDLINE | ID: mdl-31173343

RESUMEN

Ciliopathies are a clinically and genetically heterogeneous group of disorders often exhibiting phenotypic overlap and caused by abnormalities in the structure or function of cellular cilia. As such, a precise molecular diagnosis is important for guiding clinical management and genetic counseling. In the present study, two Pakistani families comprising individuals with overlapping clinical features suggestive of a ciliopathy syndrome, including intellectual disability, obesity, congenital retinal dystrophy, and hypogonadism (in males), were investigated clinically and genetically. Whole-exome sequencing identified the likely causes of disease as a novel homozygous frameshift mutation (NM_152384.2: c.196delA; p.(Arg66Glufs*12); family 1) in BBS5, and a nonsense mutation (NM_019892.5:c.1879C>T; p.Gln627*; family 2) in INPP5E, previously reported in an extended Pakistani family with MORM syndrome. Our findings expand the molecular spectrum associated with BBS5 mutations in Pakistan and provide further supportive evidence that the INPP5E mutation is a common cause of ciliopathy in Northern Pakistan, likely representing a regional founder mutation. This study also highlights the value of genomic studies in Pakistan for families affected by rare heterogeneous developmental disorders and where clinical phenotyping may be limited by geographical and financial constraints. The identification of the spectrum and frequency of disease-causing variants within this setting enables the development of population-specific genetic testing strategies targeting variants common to the local population and improving health care outcomes.


Asunto(s)
Ciliopatías/diagnóstico , Ciliopatías/genética , Proteínas del Citoesqueleto/genética , Mutación , Proteínas de Unión a Fosfato/genética , Monoéster Fosfórico Hidrolasas/genética , Adolescente , Adulto , Niño , Preescolar , Análisis Mutacional de ADN , Femenino , Efecto Fundador , Estudios de Asociación Genética/métodos , Predisposición Genética a la Enfermedad , Humanos , Lactante , Masculino , Persona de Mediana Edad , Pakistán , Linaje , Adulto Joven
14.
Nucleic Acids Res ; 45(19): 11437-11448, 2017 Nov 02.
Artículo en Inglés | MEDLINE | ID: mdl-28981683

RESUMEN

The speed at which a molecular motor operates is critically important for the survival of a virus or an organism but very little is known about the underlying mechanisms. Tailed bacteriophage T4 employs one of the fastest and most powerful packaging motors, a pentamer of gp17 that translocates DNA at a rate of up to ∼2000-bp/s. We hypothesize, guided by structural and genetic analyses, that a unique hydrophobic environment in the catalytic space of gp17-adenosine triphosphatase (ATPase) determines the rate at which the 'lytic water' molecule is activated and OH- nucleophile is generated, in turn determining the speed of the motor. We tested this hypothesis by identifying two hydrophobic amino acids, M195 and F259, in the catalytic space of gp17-ATPase that are in a position to modulate motor speed. Combinatorial mutagenesis demonstrated that hydrophobic substitutions were tolerated but polar or charged substitutions resulted in null or cold-sensitive/small-plaque phenotypes. Quantitative biochemical and single-molecule analyses showed that the mutant motors exhibited 1.8- to 2.5-fold lower rate of ATP hydrolysis, 2.5- to 4.5-fold lower DNA packaging velocity, and required an activator protein, gp16 for rapid firing of ATPases. These studies uncover a speed control mechanism that might allow selection of motors with optimal performance for organisms' survival.


Asunto(s)
Adenosina Trifosfatasas/metabolismo , Bacteriófago T4/metabolismo , Empaquetamiento del ADN , ADN Viral/metabolismo , Proteínas Virales/metabolismo , Adenosina Trifosfatasas/genética , Adenosina Trifosfato/metabolismo , Aminoácidos/química , Aminoácidos/genética , Aminoácidos/metabolismo , Bacteriófago T4/genética , Sitios de Unión/genética , Dominio Catalítico/genética , ADN Viral/química , ADN Viral/genética , Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Hidrólisis , Modelos Moleculares , Mutación , Dominios Proteicos , Proteínas Virales/química , Proteínas Virales/genética , Ensamble de Virus/genética
15.
BMC Med Genet ; 19(1): 160, 2018 09 10.
Artículo en Inglés | MEDLINE | ID: mdl-30200890

RESUMEN

BACKGROUND: Autosomal recessive anophthalmia and microphthalmia are rare developmental eye defects occurring during early fetal development. Syndromic and non-syndromic forms of anophthalmia and microphthalmia demonstrate extensive genetic and allelic heterogeneity. To date, disease mutations have been identified in 29 causative genes associated with anophthalmia and microphthalmia, with autosomal dominant, autosomal recessive and X-linked inheritance patterns described. Biallelic ALDH1A3 gene variants are the leading genetic causes of autosomal recessive anophthalmia and microphthalmia in countries with frequent parental consanguinity. METHODS: This study describes genetic investigations in two consanguineous Pakistani families with a total of seven affected individuals with bilateral non-syndromic clinical anophthalmia. RESULTS: Using whole exome and Sanger sequencing, we identified two novel homozygous ALDH1A3 sequence variants as likely responsible for the condition in each family; missense mutation [NM_000693.3:c.1240G > C, p.Gly414Arg; Chr15:101447332G > C (GRCh37)] in exon 11 (family 1), and, a frameshift mutation [NM_000693.3:c.172dup, p.Glu58Glyfs*5; Chr15:101425544dup (GRCh37)] in exon 2 predicted to result in protein truncation (family 2). CONCLUSIONS: This study expands the molecular spectrum of pathogenic ALDH1A3 variants associated with anophthalmia and microphthalmia, and provides further insight of the key role of the ALDH1A3 in human eye development.


Asunto(s)
Aldehído Oxidorreductasas/genética , Anoftalmos/genética , Genes Recesivos/genética , Microftalmía/genética , Mutación/genética , Consanguinidad , Exoma/genética , Exones/genética , Femenino , Humanos , Masculino , Linaje , Análisis de Secuencia de ADN/métodos
17.
ACS Sens ; 9(4): 2066-2074, 2024 04 26.
Artículo en Inglés | MEDLINE | ID: mdl-38627252

RESUMEN

In microfluidics, water droplets are often used as independent biochemical microreactor units, enabling the implementation of massively parallel screening assays where only a few of the reacting water droplets yield a positive result. However, sampling the product of these few successful reactions is an unsolved challenge. One possible solution is to use acoustic tweezers, which are lab-free, easily miniaturized, and biocompatible manipulation tools, and existing acoustic tweezers manipulating particles or cells, and water droplet manipulation in oil with an acoustic tweezer is absent. The first challenge in attempting to recover a few water droplets from a large batch is the selective manipulation of water droplets in an oil system. In this paper, we trap and manipulate single water droplets in oil using integrated single-beam (focused beam/vortex beam) acoustic tweezers for the first time. We find that water droplets with a diameter smaller than half a wavelength are trapped by acoustic vortices, while larger ones are better captured by focused acoustic beams. It is the first step to extract the target water droplet microreactors (positive ones) in an oil system and analyze their content. Compared to previous techniques, such as fluorescence-activated cell sorting (FACS), our technique is sparse, meaning that the sampling time is proportional to the number of droplets required and very insensitive to the total number of microreactors, making it well suited for large-scale screening assays.


Asunto(s)
Acústica , Aceites , Agua , Agua/química , Aceites/química , Técnicas Analíticas Microfluídicas/instrumentación , Técnicas Analíticas Microfluídicas/métodos , Tamaño de la Partícula
18.
Comput Biol Med ; 173: 108365, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38537563

RESUMEN

BACKGROUND: Most of the methods using digital pathological image for predicting Hepatocellular carcinoma (HCC) prognosis have not considered paracancerous tissue microenvironment (PTME), which are potentially important for tumour initiation and metastasis. This study aimed to identify roles of image features of PTME in predicting prognosis and tumour recurrence of HCC patients. METHODS: We collected whole slide images (WSIs) of 146 HCC patients from Sun Yat-sen Memorial Hospital (SYSM dataset). For each WSI, five types of regions of interests (ROIs) in PTME and tumours were manually annotated. These ROIs were used to construct a Lasso Cox survival model for predicting the prognosis of HCC patients. To make the model broadly useful, we established a deep learning method to automatically segment WSIs, and further used it to construct a prognosis prediction model. This model was tested by the samples of 225 HCC patients from the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC). RESULTS: In predicting prognosis of the HCC patients, using the image features of manually annotated ROIs in PTME achieved C-index 0.668 in the SYSM testing dataset, which is higher than the C-index 0.648 reached by the model only using image features of tumours. Integrating ROIs of PTME and tumours achieved C-index 0.693 in the SYSM testing dataset. The model using automatically segmented ROIs of PTME and tumours achieved C-index of 0.665 (95% CI: 0.556-0.774) in the TCGA-LIHC samples, which is better than the widely used methods, WSISA (0.567), DeepGraphSurv (0.593), and SeTranSurv (0.642). Finally, we found the Texture SumAverage Skew HV on immune cell infiltration and Texture related features on desmoplastic reaction are the most important features of PTME in predicting HCC prognosis. We additionally used the model in prediction HCC recurrence for patients from SYSM-training, SYSM-testing, and TCGA-LIHC datasets, indicating the important roles of PTME in the prediction. CONCLUSIONS: Our results indicate image features of PTME is critical for improving the prognosis prediction of HCC. Moreover, the image features related with immune cell infiltration and desmoplastic reaction of PTME are the most important factors associated with prognosis of HCC.


Asunto(s)
Carcinoma Hepatocelular , Neoplasias Hepáticas , Humanos , Carcinoma Hepatocelular/diagnóstico por imagen , Neoplasias Hepáticas/diagnóstico por imagen , Hospitales , Microambiente Tumoral
19.
J Adv Res ; 2024 Jun 09.
Artículo en Inglés | MEDLINE | ID: mdl-38862035

RESUMEN

INTRODUCTION: Frailty Index (FI) is a common measure of frailty, which has been advocated as a routine clinical test by many guidelines. The genetic and phenotypic relationships of FI with cardiovascular indicators (CIs) and behavioral characteristics (BCs) are unclear, which has hampered ability to monitor FI using easily collected data. OBJECTIVES: This study is designed to investigate the genetic and phenotypic associations of frailty with CIs and BCs, and further to construct a model to predict FI. METHOD: Genetic relationships of FI with 288 CIs and 90 BCs were assessed by the cross-trait LD score regression (LDSC) and Mendelian randomization (MR). The phenotypic data of these CIs and BCs were integrated with a machine-learning model to predict FI of individuals in UK-biobank. The relationships of the predicted FI with risks of type 2 diabetes (T2D) and neurodegenerative diseases were tested by the Kaplan-Meier estimator and Cox proportional hazards model. RESULTS: MR revealed putative causal effects of seven CIs and eight BCs on FI. These CIs and BCs were integrated to establish a model for predicting FI. The predicted FI is significantly correlated with the observed FI (Pearson correlation coefficient = 0.660, P-value = 4.96 × 10-62). The prediction model indicated "usual walking pace" contributes the most to prediction. Patients who were predicted with high FI are in significantly higher risk of T2D (HR = 2.635, P < 2 × 10-16) and neurodegenerative diseases (HR = 2.307, P = 1.62 × 10-3) than other patients. CONCLUSION: This study supports associations of FI with CIs and BCs from genetic and phenotypic perspectives. The model that is developed by integrating easily collected CIs and BCs data in predicting FI has the potential to monitor disease risk.

20.
Front Oncol ; 14: 1382878, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39165684

RESUMEN

Background: Prolonged postoperative hospital stay following gastric cancer (GC) surgery is an important risk factor affecting patients' mood and increasing complications. We aimed to develop a nomogram to predict risk factors associated with prolonged postoperative length of stay (PLOS) in patients undergoing gastric cancer resection. Methods: Data were collected from 404 patients. The least absolute shrinkage and selection operator (LASSO) was used for variable screening, and a nomogram was designed. The nomogram performance was evaluated by the area under the receiver operating characteristic curve (AUC). The consistency between the predicted and actual values was evaluated via a calibration map, and the clinical application value was evaluated via decision curve analysis (DCA) and clinical impact curve analysis (CICA). Results: A total of 404 patients were included in this study. Among these patients, 287 were assigned to the training cohort, and 117 were assigned to the validation cohort. According to the PLOS quartile distance, 103 patients were defined as having prolonged PLOS. LASSO regression and logistic multivariate analysis revealed that 4 clinical characteristics, the neutrophil-lymphocyte ratio (NLR) on postoperative day one, the NLR on postoperative day three, the preoperative prognostic nutrition index and the first time anal exhaust was performed, were associated with the PLOS and were included in the construction of the nomogram. The AUC of the nomogram prediction model was 0.990 for the training set and 0.983 for the validation set. The calibration curve indicated good correlation between the predicted results and the actual results. The Hosmer-Lemeshow test revealed that the P values for the training and validation sets were 0.444 and 0.607, respectively, indicating that the model had good goodness of fit. The decision curve analysis and clinical impact curve of this model showed good clinical practicability for both cohorts. Conclusion: We explored the risk factors for prolonged PLOS in GC patients via the enhanced recovery after surgery (ERAS) program and developed a predictive model. The designed nomogram is expected to be an accurate and personalized tool for predicting the risk and prognosis of PLOS in GC patients via ERAS measures.

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