Complex Disease Research Articles

Comparison of the results of active surgical treatment and serial stenting for urolithiasis in pregnant women

Introduction. Renal colic during pregnancy is a common cause of pain in the lower back. Currently, with a diagnosed kidney or ureter stone, the standard treatment is serial drainage of the urine tract using an internal ureter stent, with replacement of the drainage before delivery, followed by surgery to remove the stone after delivery.Objective. To study the effectiveness and safety of ureteroscopic interventions in the treatment of urolithiasis in pregnant women in comparison with the method of serial drainage of the upper urinary tract during gestation followed by surgical treatment of urolithiasis 4 weeks after delivery.Materials & methods. The study group consisted of 119 patients with a confirmed diagnosis of urolothiasis using instrumental diagnostic methods and a gestational age up to and including the 27th week. Two groups were formed based on treatment approaches for urolithiasis: group 1 included 59 patients (49.6%) who underwent surgical removal of the stone; group 2 included 60 patients (50.4%) who underwent internal ureteral stent replacement every 4 – 6 weeks prior to delivery and subsequent ureteroscopy There were no significant differences in age, body mass index, or number of pregnancies between the two groups.Results. The frequency of complete stone removal in groups 1 and 2 was 96.6 and 96.7%, respectively. The median amount of time spent on urolithiasis treatment in groups 1 and 2 was 60 [45; 72] and 97 [54; 105] minutes, respectively (p = 0.002). Migration of the ureteral stent in group 2 was observed in 13.3% of cases (p = 0.05). Among group 1 patients who underwent ureteroscopic intervention aimed at stone removal, the incidence of internal drainage dislocation was 3.4%. Encrustation of the ureteral stent in groups 1 and 2 was observed among 2 (3.4%) and 17 (28.3%) patients, respectively (p < 0.001). The bed-day (median time in days spent in hospital for drainage replacement and time of surgical treatment of urolithiasis) in groups 1 and 2 was four and eight days, respectively (p < 0.05). The frequency of natural childbirth in groups 1 and 2 was 81.35% and 55.0%, respectively (p = 0.002).Conclusion. Urolithiasis among pregnant women is a complex multifactorial disease that affects not only the health of the mother, but also the condition of the developing foetus. It is possible to perform surgical treatment with high efficiency and low complication rate, which improves the quality of life.

Specific gut microbiome's role in skin pigmentation: insights from SCARB1 mutants in Oujiang colour common carp.

Beyond the pivotal roles of the gut microbiome in initiating physiological processes and modulating genetic factors, a query persists: Can a single gene mutation alter the abundance of the gut microbiome community? Not only this, but the intricate impact of gut microbiome composition on skin pigmentation has been largely unexplored. Based on these premises, our study examines the abundance of lipase-producing gut microbes about differential gene expression associated with bile acid synthesis and lipid metabolism-related blood metabolites in red (whole wild) and white (whole white wild and SCARB1-/- mutant) Oujiang colour common carp. Following the disruption of the SCARB1 gene in the resulting mutant fish with white body colour (SCARB1-/-), there is a notable decrease in the abundance of gut microbiomes (Bacillus, Staphylococcus, Pseudomonas, and Serratia) associated with lipase production. This reduction parallels the downregulation seen in wild-type white body colour fish (WW), as contrasting to the wild-type red body colour fish (WR). Meanwhile, in SCARB1-/- fish, there was a downregulation noted not only at the genetic and metabolic levels but also a decrease in lipase-producing bacteria. This consistency with WW contrasts significantly with WR. Similarly, genes involved in the bile acid synthesis pathway, along with blood metabolites related to lipid metabolism, exhibited downregulation in SCARB1-/- fish. The SCARB1 knockout gene blockage led to significant alterations in the gut microbiome, potentially influencing the observed reduction in carotenoid-associated skin pigmentation. Our study emphasizes that skin pigmentation is not only impacted by genetic factors but also by the gut microbiome. Meanwhile, the gut microbiome's adaptability can be rapidly shaped and may be driven by specific single-gene variations.

Connecting genomic and proteomic signatures of amyloid burden in the brain.

Alzheimer's disease (AD) has a high heritable component characteristic of complex diseases, yet many of the genetic risk factors remain unknown. We combined genome-wide association studies (GWAS) on amyloid endophenotypes measured in cerebrospinal fluid (CSF) and positron emission tomography (PET) as surrogates of amyloid pathology, which may be helpful to understand the underlying biology of the disease. We performed a meta-analysis of GWAS of CSF Aβ42 and PET measures combining six independent cohorts (n=2,076). Due to the opposite effect direction of Aβ phenotypes in CSF and PET measures, only genetic signals in the opposite direction were considered for analysis (n=376,599). Polygenic risk scores (PRS) were calculated and evaluated for AD status and amyloid endophenotypes. We then searched the CSF proteome signature of brain amyloidosis using SOMAscan proteomic data (Ace cohort, n=1,008) and connected it with GWAS results of loci modulating amyloidosis. Finally, we compared our results with a large meta-analysis using publicly available datasets in CSF (n=13,409) and PET (n=13,116). This combined approach enabled the identification of overlapping genes and proteins associated with amyloid burden and the assessment of their biological significance using enrichment analyses. After filtering the meta-GWAS, we observed genome-wide significance in the rs429358- APOE locus and nine suggestive hits were annotated. We replicated the APOE loci using the large CSF-PET meta-GWAS and identified multiple AD-associated genes as well as the novel GADL1 locus. Additionally, we found a significant association between the AD PRS and amyloid levels, whereas no significant association was found between any Aβ PRS with AD risk. CSF SOMAscan analysis identified 1,387 FDR-significant proteins associated with CSF Aβ42 levels. The overlap among GWAS loci and proteins associated with amyloid burden was very poor (n=35). The enrichment analysis of overlapping hits strongly suggested several signalling pathways connecting amyloidosis with the anchored component of the plasma membrane, synapse physiology and mental disorders that were replicated in the large CSF-PET meta-analysis. The strategy of combining CSF and PET amyloid endophenotypes GWAS with CSF proteome analyses might be effective for identifying signals associated with the AD pathological process and elucidate causative molecular mechanisms behind the amyloid mobilization in AD.

The goldmine of GWAS summary statistics: a systematic review of methods and tools

Genome-wide association studies (GWAS) have revolutionized our understanding of the genetic architecture of complex traits and diseases. GWAS summary statistics have become essential tools for various genetic analyses, including meta-analysis, fine-mapping, and risk prediction. However, the increasing number of GWAS summary statistics and the diversity of software tools available for their analysis can make it challenging for researchers to select the most appropriate tools for their specific needs. This systematic review aims to provide a comprehensive overview of the currently available software tools and databases for GWAS summary statistics analysis. We conducted a comprehensive literature search to identify relevant software tools and databases. We categorized the tools and databases by their functionality, including data management, quality control, single-trait analysis, and multiple-trait analysis. We also compared the tools and databases based on their features, limitations, and user-friendliness. Our review identified a total of 305 functioning software tools and databases dedicated to GWAS summary statistics, each with unique strengths and limitations. We provide descriptions of the key features of each tool and database, including their input/output formats, data types, and computational requirements. We also discuss the overall usability and applicability of each tool for different research scenarios. This comprehensive review will serve as a valuable resource for researchers who are interested in using GWAS summary statistics to investigate the genetic basis of complex traits and diseases. By providing a detailed overview of the available tools and databases, we aim to facilitate informed tool selection and maximize the effectiveness of GWAS summary statistics analysis.

Congenital heart disease: Epidemiological, genetic and evolutive profil.

Congenital heart disease is a heterogeneous group of malformations and one of the most common causes of mortality in children. The aim of this study was to investigate the clinical, genetic and evolutive characteristics of congenital heart disease. A retrospective, descriptive study was carried out between 2020 and 2023 at the pediatrics and neonatology department of Mongi Slim university hospital of Tunis. All children with confirmed congenital heart disease were included. Forty-five patients were included, representing 5.7‰ of all admissions. The sex ratio was 1.4. A prenatal diagnosis of congenital heart disease was established in 9% of cases. The median age at the time of discovery was 18 days. The initial symptomatology was respiratory distress in 64% of cases. The main reasons for performing a cardiac ultrasound were heart murmur in 38% followed by polymalformative assessment in 27% of cases. Most of the cardiopathies were atrial septal defects (42%) and ventricular septal defects (40%). Cyanotic heart diseases represented 29% of cases, conotruncal ones 13% and ductodependent ones 16%. Congenital heart disease was associated with a genetic anomaly in 53% of patients, including 15 cases of trisomy 21 and four Di-George syndromes. The treatment was mainly medical (38%), associated with surgery in 5 cases. Death occurred in nine patients, representing a mortality rate of 20%. Efforts still need to be made to improve pre- and post-natal diagnosis and ensure rapid treatment in order to reduce morbidity and mortality in our country.

A case report of human infection with avian influenza H10N3 with a complex respiratory disease history

BackgroundOn March 16th 2024, the first case of Human infection with avian influenza H10N3 since the end of the global COVID-19 Pandemic was reported in Kunming, China. To enhance comprehension of the source of infection and risk factors of the H10N3 virus infection, this case report summarizes the clinical features, epidemiological investigation, and laboratory test results. Provides recommendations for the prevention and control of Human infection with avian influenza H10N3.Case presentationA 51-year-old male with a history of COVID-19 infection and a smoking habit of 30 years, worked in livestock breeding and was exposed to sick and dead poultry before falling ill with fever and chills on 28th February 2024. A week later, he was diagnosed with severe pneumonia, influenza, and respiratory failure by the Third People's Hospital of Kunming(KM-TPH). He was discharged on 17th April and none of his 6 close contacts showed any symptoms of illness. Environmental samples taken from the epidemic spot revealed that peacock feces tested positive for avian influenza sub-type H9 and waterfowl specimens showed positive results for avian influenza sub-type H5. Gene sequencing conducted on positive specimens from the patient's respiratory tract by the Chinese Centre for Disease Control and Prevention (CCDC) showed a high degree of similarity (98.6–99.5%) with the strain responsible for the second global case of human infected with H10N3 (reported from Zhejiang, China 2022).ConclusionsAccording to the available epidemiological information, there is limited evidence to suggest that H10N3 viruses are excessively lethal. However, adaptive site mutations have been observed in the H10N3 isoform of mammals. While it is unlikely that the H10N3 virus will spread among humans, the possibility of additional cases cannot be entirely ruled out. Symptoms of human infection with H10N3 avian influenza are similar to those of common respiratory infections, which may result in them being overlooked during initial clinical consultations. Therefore, it is essential to improve surveillance of the H10 sub-type of avian influenza and to increase the awareness of hospital-related workers of cases of pneumonia of unknown origin.

Proteome-wide association studies using summary pQTL data of three tissues identified 30 risk genes of Alzheimer's disease dementia.

Proteome-wide association study (PWAS) integrating proteomic data with genome-wide association study (GWAS) summary data is a powerful tool for studying Alzheimer's disease (AD) dementia. Existing PWAS analyses of AD often rely on the availability of individual-level proteomic and genetic data of a reference panel. Leveraging summary protein quantitative trait loci (pQTL) reference data of multiple AD-relevant tissues is expected to improve PWAS findings of AD dementia. We conducted PWAS of AD dementia by integrating publicly available summary pQTL data of brain, cerebrospinal fluid (CSF), and plasma tissues, with the latest GWAS summary data of AD dementia. For each target protein per tissue, we employed our recently published OTTERS tool to obtain omnibus PWAS p-value, to test whether the genetically regulated protein abundance in the corresponding tissue is associated with AD dementia. Protein-protein interactions and enriched pathways of identified significant PWAS risk genes were analyzed by STRING. The potential causal effects of these PWAS risk genes were assessed by probabilistic Mendelian randomization analyses. We identified 30 unique significant PWAS risk genes for AD dementia, including 11 for brain, 9 for CSF, and 16 for plasma tissues. Four of these were shared by at least two tissues, and gene MAPK3 was found in all three tissues. We found that 11 of these PWAS risk genes were associated with AD or AD pathological hall marks as shown in GWAS Catalog; 18 of these were detected by transcriptome-wide association studies (TWAS); and 25 of these, including 8 out of 9 novel genes, were interconnected within a protein-protein interaction network involving the well-known AD risk gene APOE . Especially, these PWAS risk genes were enriched in immune response, glial cell proliferation, and high-density lipoprotein particle clearance pathways. Mediated causal effects were validated for 13 PWAS risk genes (43.3%). Our findings provide novel insights into the genetic mechanisms of AD dementia in brain, CSF, and plasma tissues, and targets for developing therapeutic interventions. We also demonstrated the effectiveness of integrating summary pQTL and GWAS data for mapping risk genes of complex human diseases.

QIGTD: identifying critical genes in the evolution of lung adenocarcinoma with tensor decomposition

BackgroundIdentifying critical genes is important for understanding the pathogenesis of complex diseases. Traditional studies typically comparing the change of biomecules between normal and disease samples or detecting important vertices from a single static biomolecular network, which often overlook the dynamic changes that occur between different disease stages. However, investigating temporal changes in biomolecular networks and identifying critical genes is critical for understanding the occurrence and development of diseases.MethodsA novel method called Quantifying Importance of Genes with Tensor Decomposition (QIGTD) was proposed in this study. It first constructs a time series network by integrating both the intra and inter temporal network information, which preserving connections between networks at adjacent stages according to the local similarities. A tensor is employed to describe the connections of this time series network, and a 3-order tensor decomposition method was proposed to capture both the topological information of each network snapshot and the time series characteristics of the whole network. QIGTD is also a learning-free and efficient method that can be applied to datasets with a small number of samples.ResultsThe effectiveness of QIGTD was evaluated using lung adenocarcinoma (LUAD) datasets and three state-of-the-art methods: T-degree, T-closeness, and T-betweenness were employed as benchmark methods. Numerical experimental results demonstrate that QIGTD outperforms these methods in terms of the indices of both precision and mAP. Notably, out of the top 50 genes, 29 have been verified to be highly related to LUAD according to the DisGeNET Database, and 36 are significantly enriched in LUAD related Gene Ontology (GO) terms, including nuclear division, mitotic nuclear division, chromosome segregation, organelle fission, and mitotic sister chromatid segregation.ConclusionIn conclusion, QIGTD effectively captures the temporal changes in gene networks and identifies critical genes. It provides a valuable tool for studying temporal dynamics in biological networks and can aid in understanding the underlying mechanisms of diseases such as LUAD.

Extracting regulatory active chromatin footprint from cell-free DNA

Cell-free DNA (cfDNA) has emerged as a pivotal player in precision medicine, revolutionizing the diagnostic and therapeutic landscape. While its clinical applications have significantly increased in recent years, current cfDNA assays have limited ability to identify the active transcriptional programs that govern complex disease phenotypes and capture the heterogeneity of the disease. To address these limitations, we have developed a non-invasive platform to enrich and examine the active chromatin fragments (cfDNAac) in peripheral blood. The deconvolution of the cfDNAac signal from traditional nucleosomal chromatin fragments (cfDNAnuc) yields a catalog of features linking these circulating chromatin signals in blood to specific regulatory elements across the genome, including enhancers, promoters, and highly transcribed genes, mirroring the epigenetic data from the ENCODE project. Notably, these cfDNAac counts correlate strongly with RNA polymerase II activity and exhibit distinct expression patterns for known circadian genes. Additionally, cfDNAac signals across gene bodies and promoters show strong correlations with whole blood gene expression levels defined by GTEx. This study illustrates the utility of cfDNAac analysis for investigating epigenomics and gene expression, underscoring its potential for a wide range of clinical applications in precision medicine.

Denovo glomerulonephritis associated with IgA anti-GBM alloantibodies after kidney transplantation in Alport syndrome: A case report with diagnostic implications

Alport syndrome (AS) is a hereditary disorder caused by pathogenic variants in COL4A3, COL4A4, or COL4A5 genes expressing α3, α4, and α5 chains of basement membrane type IV collagen (COL4). The triple-helical α3α4α5(IV) protomer is a major component of the mature glomerular basement membrane (GBM) whose defective formation in AS leads to structural GBM disruption and kidney dysfunction, often resulting in kidney replacement therapy. A genetically intact renal graft exposes the immune system to a non-tolerized α3α4α5(IV) component and an alloimmune response eventually ensues. So far, only IgG alloantibodies reacting against COL4 have been reported in AS alloimmune responses. Here, we report alloimmune glomerulonephritis mediated by IgA antibodies against the non-collagenous C-terminal domain 1 of the α5(IV) chain in a patient with autosomal recessive AS following a second kidney transplantation. The patient presented a not previously described biallelic variant in the COL4A4 gene. Immunological, diagnostic, and clinical implications are discussed.

Advances in pathogenesis research and challenges in treatment development for acute myeloid leukemia.

Acute myeloid leukemia (AML) develops when hematopoietic stem cells acquire chromosomal and genetic abnormalities, transforming into leukemia stem cells (LSCs) and further gaining driver mutations. Advances in genomic analysis have identified numerous new gene mutations involved in AML development. Recent research has shown that individuals with germline mutations in genes like DDX41 and CEBPA develop AML upon acquiring additional somatic mutations, and the latest WHO classification separates AML with such mutations into distinct disease groups. LSCs are regulated by different metabolic processes than normal stem cells, contributing to drug resistance and relapse. LSCs rely on oxidative phosphorylation (OXPHOS) metabolism for energy production, and venetoclax inhibits this process, affecting LSCs. Resistant LSCs show enhanced glycolysis, which suggests that targeting both OXPHOS and glycolysis is crucial. While targeted therapies like FLT3, BCL-2, and IDH inhibitors have shown efficacy, resistance remains an issue, highlighting the need for new treatment strategies. CAR-T cell therapy is an emerging immunotherapy that shows particular promise for targeting CD123 and CLL-1, with acceptable toxicity. Future developments in CAR-T cell therapy and other immunotherapies are anticipated to improve AML treatment outcomes.

The effects of Cannabis sativa and cannabinoids on the inhibition of pancreatic lipase – An enzyme involved in obesity

IntroductionObesity is a chronic noncommunicable disease characterized by excessive body fat that can have negative health consequences. Obesity is a complex disease caused by a combination of genetic, environmental, and lifestyle factors. It is characterized by a discrepancy between caloric intake and expenditure. Obesity increases the risk of acquiring major chronic diseases, including heart disease, stroke, cancer, and Type 2 diabetes mellitus (T2DM). Currently, the inhibition of pancreatic lipases (PL) is a promising pharmacological therapy for obesity and weight management. In this study, the inhibition of pancreatic lipase by Cannabis sativa (C. sativa) plant extract and cannabinoids was investigated. MethodsThe inhibitory effect was assessed using p-nitrophenyl butyrate (pNPB), and the results were obtained by calculating the percentage relative activity and assessed using one-way analysis of variance (ANOVA). Kinetic studies and spectroscopy techniques were used to evaluate the mode of inhibition. Diet-induced; and diabetic rat models were studied to evaluate the direct effects of C. sativa extract on PL activity. ResultsKinetic analyses showed that the plant extracts inhibited pancreatic lipase, with tetrahydrocannabinol (THC) and cannabinol (CBN) being the potential cause of the inhibition noted for the C. sativa plant extract. CBN and THC inhibited the pancreatic lipase activity in a competitive manner, with the lowest residual enzyme activity of 52 % observed at a 10 μg/mL concentration of CBN and 39 % inhibition at a 25 μg/mL concentration of THC. Circular dichroism (CD) spectroscopy revealed that the inhibitors caused a change in the enzyme's secondary structure. At low concentrations, THC showed potential for synergistic inhibition with orlistat. C.sativa treatment in an in vivo rat model confirmed its inhibitory effects on pancreatic lipase activity. ConclusionThe findings in this study provided insight into the use of cannabinoids as pancreatic lipase inhibitors and the possibility of using these compounds to develop new pharmacological treatments for obesity.

Prevalence of Obesity among Polish Primary Care Population Considered Healthy.

Obesity is a complex disease with numerous health complications, influenced by factors such as genetics, lifestyle, mental health, societal impact, economic status, comorbidities, and treatments. This multicenter study included adults aged ≥35 years referred to a CVD prevention program, where sociodemographic data, anthropometric examinations, laboratory tests, and HLPCQ responses were collected. The study analyzed 1044 patients with a mean age of 47.9 years. Among them, 22.2% (232 patients) were diagnosed with obesity. These patients exhibited higher blood pressure, non-HDL cholesterol, triglycerides, and glucose levels (all p < 0.001). A comparative analysis showed that obese patients had significantly lower scores in healthy dietary choices, dietary harm avoidance, daily routine, organized physical exercise, and overall HLPCQ scores. These results indicate that individuals considered healthy were actually living with obesity and its associated complications. Consequently, family physicians should proactively identify patients at risk of obesity using existing programs. The Polish healthcare system urgently needs systemic solutions, including effective health promotion and the creation of obesity prevention programs at an early stage of adult life. These measures are essential to address the growing obesity epidemic and improve public health outcomes.

EIF1AX mutation in thyroid nodules: a histopathologic analysis of 56 cases in the context of institutional practices.

EIF1AX mutation has been identified as a driver mutation for papillary thyroid carcinoma (PTC) by The Cancer Genome Atlas (TCGA) study. Subsequent studies confirmed this mutation in PTC and Anaplastic Thyroid Carcinoma (ATC) but also reported EIF1AX mutation in Follicular nodular disease (FND) and benign thyroid nodules. In this study, we review thyroid nodules with EIF1AX mutation from two institutions: a tertiary care hospital (YNHH, n = 22) and a major cancer referral center (MSKCC, n = 34) and report the varying histomorphology in the context of additional genetic abnormalities and institutional practices. Pathology diagnoses were reviewed according to the WHO 5th edition and correlated with the type of EIF1AX mutation and additional concurrent molecular alterations, if any. Most cases were splice site type mutations. Cases consisted of 9 FND, 7 follicular (FA) or oncocytic adenomas (OA), 2 non-invasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP) and 38 follicular-cell derived thyroid carcinomas. Of 8 cases with isolated EIF1AX mutation, 7 were FND, FA or OA (88%) and one was an oncocytic carcinoma (12%). Of 12 cases with EIF1AX and one additional molecular alteration, 9 (75%) were FND, FA or OA, 2 (17%) were NIFTPs and one (8%) was a poorly differentiated thyroid carcinoma. All 36 cases with EIF1AX mutation and molecular alterations were malignant (100%) and included TP53 and TERT promoter mutations associated with ATC (n = 8) and high-grade follicular cell-derived non-anaplastic carcinoma (HGC, n = 2). Isolated EIF1AX mutation was noted only in thyroid nodules seen at YNHH and were predominantly encountered in benign thyroid nodules including FND. Accumulation of additional genetic abnormalities appears to be progressively associated with malignant tumors.

Targeted therapies for vascular malformations.

Targeted medical therapies for the treatment of vascular malformations is an exciting and evolving area of research. As the identification of specific causative genetic mutations involved in vascular malformations becomes more accessible and inexpensive, the development of targeted therapies to address these genetic anomalies becomes all the more enticing. It is an excellent example of the potential of translational research where basic science discoveries are translated to clinical practise from 'bench to bedside'. In this mini-review we aim to synopsise some of the recent studies published in this area with specific focus on the paediatric population. We also aim to highlight the growing demand for future research in the field to elucidate further the optimum duration of treatments, strategies for discontinuation, potential for combination of therapies and the effects of prolonged use of these medications.

Capturing biomarkers associated with Alzheimer disease subtypes using data distribution characteristics.

Late-onset Alzheimer disease (AD) is a highly complex disease with multiple subtypes, as demonstrated by its disparate risk factors, pathological manifestations, and clinical traits. Discovery of biomarkers to diagnose specific AD subtypes is a key step towards understanding biological mechanisms underlying this enigmatic disease, generating candidate drug targets, and selecting participants for drug trials. Popular statistical methods for evaluating candidate biomarkers, fold change (FC) and area under the receiver operating characteristic curve (AUC), were designed for homogeneous data and we demonstrate the inherent weaknesses of these approaches when used to evaluate subtypes representing less than half of the diseased cases. We introduce a unique evaluation metric that is based on the distribution of the values, rather than the magnitude of the values, to identify analytes that are associated with a subset of the diseased cases, thereby revealing potential biomarkers for subtypes. Our approach, Bimodality Coefficient Difference (BCD), computes the difference between the degrees of bimodality for the cases and controls. We demonstrate the effectiveness of our approach with large-scale synthetic data trials containing nearly perfect subtypes. In order to reveal novel AD biomarkers for heterogeneous subtypes, we applied BCD to gene expression data for 8,650 genes for 176 AD cases and 187 controls. Our results confirm the utility of BCD for identifying subtypes of heterogeneous diseases.

Limited fasciectomy with versus without autologous adipose tissue grafting for treatment of Dupuytren’s contracture (REMEDY): study protocol for a multicentre randomised controlled trial

BackgroundDupuytren’s contracture is a hereditary disorder which causes progressive fibrosis of the palmar aponeurosis of the hand, resulting in digital flexion contractures of the affected rays. Limited fasciectomy is a standard surgical treatment for Dupuytren’s, and the one with the lowest recurrence rate; however, the recurrence is still relatively high (2–39%). Adipose-derived stem cells have been shown to inhibit Dupuytren’s myofibroblasts proliferation and contractility in vitro, as well as to improve scar quality and skin regeneration in different types of surgeries. Autologous adipose tissue grafting has already been investigated as an adjuvant treatment to percutaneous needle fasciotomy for Dupuytren’s contracture with good results, but it was only recently associated with limited fasciectomy. The purpose of REMEDY trial is to investigate if limited fasciectomy with autologous adipose tissue grafting would decrease recurrence compared to limited fasciectomy alone.MethodsThe REMEDY trial is a multi-centre open-label randomised controlled trial (RCT) with 1:1 allocation ratio. Participants (n = 150) will be randomised into two groups, limited fasciectomy with autologous adipose tissue grafting versus limited fasciectomy alone. The primary outcome is the recurrence of Dupuytren’s contracture on any of the treated rays at 2 years postoperatively. The secondary outcomes are recurrence at 3 and 5 years, scar quality, complications, occurrence of algodystrophy (complex regional pain syndrome), patient-reported hand function, and hypodermal adipose tissue loss at 1 year postoperatively in a small subset of patients.DiscussionThe REMEDY trial is one of the first studies investigating limited fasciectomy associated with autologous adipose tissue grafting for Dupuytren’s contracture, and, to our knowledge, the first one investigating long-term outcomes of this treatment. It will provide insight into possible benefits of combining adipose tissue grafting with limited fasciectomy, such as lower recurrence rate and improvement of scar quality.Trial registrationClinicalTrials.gov NCT05067764, June 13, 2022.

Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing

High-throughput sequencing technologies have increasingly led to discovery of disease-causing genetic variants, primarily in postnatal multi-cell DNA samples. However, applying these technologies to preimplantation genetic testing (PGT) in nuclear or mitochondrial DNA from single or few-cells biopsied from in vitro fertilised (IVF) embryos is challenging. PGT aims to select IVF embryos without genetic abnormalities. Although genotyping-by-sequencing (GBS)-based haplotyping methods enabled PGT for monogenic disorders (PGT-M), structural rearrangements (PGT-SR), and aneuploidies (PGT-A), they are labour intensive, only partially cover the genome and are troublesome for difficult loci and consanguineous couples. Here, we devise a simple, scalable and universal whole genome sequencing haplarithmisis-based approach enabling all forms of PGT in a single assay. In a comparison to state-of-the-art GBS-based PGT for nuclear DNA, shallow sequencing-based PGT, and PCR-based PGT for mitochondrial DNA, our approach alleviates technical limitations by decreasing whole genome amplification artifacts by 68.4%, increasing breadth of coverage by at least 4-fold, and reducing wet-lab turn-around-time by ~2.5-fold. Importantly, this method enables trio-based PGT-A for aneuploidy origin, an approach we coin PGT-AO, detects translocation breakpoints, and nuclear and mitochondrial single nucleotide variants and indels in base-resolution.

Cell blebbing novel therapeutic possibilities to counter metastasis.

Cells constantly reshape there plasma membrane and cytoskeleton during physiological and pathological processes (Hagmann et al. in J Cell Biochem 73:488-499, 1999). Cell blebbing, the formation of bulges or protrusions on the cell membrane, is related to mechanical stress, changes in intracellular pressure, chemical signals, or genetic anomalies. These membrane bulges interfere with the force balance of actin filaments, microtubules, and intermediate filaments, the basic components of the cytoskeleton (Charras in J Microsc 231:466-478,2008). In the past, these blebs with circular structures were considered apoptotic markers (Blaser et al. in Dev Cell 11:613-627,2006). Cell blebbing activates phagocytes and promotes the rapid removal of intrinsic compartments. However, recent studies have revealed that blebbing is associated with dynamic cell reorganization and alters the movement of cells in-vivo and in-vitro (Charras and Paluch in Nat Rev Mol Cell Biol 9:730-736,2008). During tumor progression, blebbing promotes invasion of cancer cells into blood, and lymphatic vessels, facilitating tumor progression and metastasis (Weems et al. in Nature 615:517-525,2023). Blebbing is a dominant feature of tumor cells generally absent in normal cells. Restricting tumor blebbing reduces anoikis resistance (survival in suspension) (Weems et al. in Nature 615:517-525,2023). Hence, therapeutic intervention with targeting blebbing could be highly selective for proliferating pro-metastatic tumor cells, providing a novel therapeutic pathway for tumor metastasis with minimal side effects. Here, we review the association between cell blebbing and tumor cells, to uncover new research directions and strategies for metastatic cancer therapy. Finaly, we aim to identify the druggable targets of metastatic cancer in relation to cell blebbing.

Proteomic networks and related genetic variants associated with smoking and chronic obstructive pulmonary disease

BackgroundStudies have identified individual blood biomarkers associated with chronic obstructive pulmonary disease (COPD) and related phenotypes. However, complex diseases such as COPD typically involve changes in multiple molecules with interconnections that may not be captured when considering single molecular features.MethodsLeveraging proteomic data from 3,173 COPDGene Non-Hispanic White (NHW) and African American (AA) participants, we applied sparse multiple canonical correlation network analysis (SmCCNet) to 4,776 proteins assayed on the SomaScan v4.0 platform to derive sparse networks of proteins associated with current vs. former smoking status, airflow obstruction, and emphysema quantitated from high-resolution computed tomography scans. We then used NetSHy, a dimension reduction technique leveraging network topology, to produce summary scores of each proteomic network, referred to as NetSHy scores. We next performed a genome-wide association study (GWAS) to identify variants associated with the NetSHy scores, or network quantitative trait loci (nQTLs). Finally, we evaluated the replicability of the networks in an independent cohort, SPIROMICS.ResultsWe identified networks of 13 to 104 proteins for each phenotype and exposure in NHW and AA, and the derived NetSHy scores significantly associated with the variable of interests. Networks included known (sRAGE, ALPP, MIP1) and novel molecules (CA10, CPB1, HIS3, PXDN) and interactions involved in COPD pathogenesis. We observed 7 nQTL loci associated with NetSHy scores, 4 of which remained after conditional analysis. Networks for smoking status and emphysema, but not airflow obstruction, demonstrated a high degree of replicability across race groups and cohorts.ConclusionsIn this work, we apply state-of-the-art molecular network generation and summarization approaches to proteomic data from COPDGene participants to uncover protein networks associated with COPD phenotypes. We further identify genetic associations with networks. This work discovers protein networks containing known and novel proteins and protein interactions associated with clinically relevant COPD phenotypes across race groups and cohorts.