Gene Next-generation Sequencing Research Articles

Transcriptomic Profiling in Low-Risk Thyroid Cancer Induced by Microwave Ablation.

Peripheral blood mononuclear cells (PBMCs) serve as the immune system's primary transportation hub outside of the affected ablated tissue. This study aims to explore the transcriptomic profiling of the immune response in PBMCs induced by microwave ablation (MWA) in low-risk thyroid cancer. For eight patients diagnosed with low-risk thyroid cancer, 10 ml of peripheral venous blood was collected before MWA as well as one day and one month after MWA. mRNA was extracted from PBMCs for transcriptome next-generation gene sequencing and qRT-PCR analyses. The plasma samples were used for chemokine detection purposes. One day and one month after MWA, there were significant changes in GSEA, particularly in the NF-kappa B-TNFα pathway, inflammatory response, and early and late estrogen response. Common changes in differently expressed genes resulted in a significant downregulation of tumor-promoting genes (BCL3, NR6A1, and PFKFB3). One day after low-risk thyroid cancer MWA, GO enrichment analysis mainly revealed processes related to oxygen transport and other pathways. One month after MWA, GO enrichment analysis mainly revealed regulation of toll-like receptor signaling and other pathways. Furthermore, inflammation-related cytokines and regulatory genes, as well as tumor-promoting cytokines and regulatory genes, were downregulated after MWA. This study presents a comprehensive profile of the systemic immune response induced by thermal ablation for treating low-risk thyroid cancer. More significantly, this study provides valuable insight into potential references for systemic antitumor immunity of ablation against low-risk thyroid cancer. This trial is registered with ChiCTR1900024544.

Characterization of treatment resistance and viral kinetics in the setting of single- versus dual-active monoclonal antibodies against SARS-CoV-2.

Monoclonal antibodies (mAbs) represent a crucial antiviral strategy for SARS-CoV-2 infection, but it is unclear whether combination mAbs offer a benefit over single-active mAb treatment. Amubarvimab and romlusevimab significantly reduced the risk of hospitalizations or death in the ACTIV-2/A5401 trial. Certain SARS-CoV-2 variants are intrinsically resistant against romlusevimab, leading to only single-active mAb therapy with amubarvimab in these variants. We evaluated virologic outcomes in individuals treated with single- versus dual-active mAbs. Participants were non-hospitalized adults at higher risk of clinical progression randomized to amubarvimab plus romlusevimab or placebo. Quantitative SARS-CoV-2 RNA levels and targeted S gene next-generation sequencing was performed on anterior nasal samples. We compared viral load kinetics and resistance emergence between individuals treated with effective single- versus dual-active mAbs depending on the infecting variant. Study participants receiving single- and dual-active mAbs had similar demographics, baseline nasal viral load, symptom score, and symptom duration. Compared to single-active mAb, treatment with dual-active mAbs led to faster viral load decline at study day 3 (p < 0.001) and day 7 (p < 0.01). Treatment-emergent resistance mutations were more likely to be detected after amubarvimab plus romlusevimab treatment than placebo (2.6% vs 0%, P < 0.001), and more frequently detected in the setting of single-active compared to dual-active mAb treatment (7.2% vs 1.1%, p < 0.01). Single-active and dual-active mAb treatment resulted in similar decrease in rates of hospitalizations or death. Compared to single-active mAb therapy, dual-active mAbs led to similar clinical outcomes, but significantly faster viral load decline and a lower risk of emergent resistance.

Implementation of a High-Accuracy Targeted Gene Expression Panel for Clinical Care

This study describes the validation of a clinical RNA expression panel with evaluation of concordance between gene copy gain by a next generation sequencing (NGS) assay and high gene expression by an RNA expression panel. The RNA Salah Targeted Expression Panel (RNA STEP) was designed with input from oncologists to include 204 genes with utility for clinical trial prescreening and therapy selection. RNA STEP was validated with the nanoString platform using remnant FFPE-derived RNA from 102 patients previously tested with a validated clinical NGS panel. The repeatability, reproducibility, and concordance of RNA STEP results with NGS results were evaluated. RNA STEP demonstrated high repeatability and reproducibility with excellent correlation (r > 0.97, p < 0.0001) for all comparisons. Comparison of RNA STEP high gene expression (log2 ratio ≥ 2) versus NGS DNA-based gene copy number gain (copies ≥ 5) for 38 mutually covered genes revealed an accuracy of 93.0% with a positive percentage agreement (PPA) of 69.4% and negative percentage agreement (NPA) of 93.8%. Moderate correlation was observed between platforms (r = 0.53, p < 0.0001). Concordance between high gene expression and gene copy number gain varied by specific gene and some genes had higher accuracy between assays. Clinical implementation of RNA STEP provides gene expression data complementary to NGS and offers a tool for prescreening patients for clinical trials.

Prostate cancer invasion is promoted by the miR-96-5p-induced NDRG1 deficiency through NF-κB regulation.

The N-myc downstream-regulated gene 1 (NDRG1) has been discovered as a significant gene in the progression of cancers. However, the regulatory mechanism of NDRG1 remained obscure in prostate cancer (PCa). The miR-96-5p and NDRG1 expression levels were evaluated in PCa cell lines, and prostate tissues, and validated in public databases by real-time polymerase chain reaction, western blot analysis, and immunohistochemistry. The function of miR-96-5p and NDRG1 were investigated by scratch assay and transwell assays in vitro, and mouse xenograft assay in vivo. The candidate pathway regulated by NDRG1 was conducted by the next-generation gene sequencing technique. Immunofluorescence and luciferase assays were used to detect the relation between miR-96-5p, NDRG1, and NF-kB pathway. Overexpressing NDRG1 suppresses the migration, invasion, and epithelial-mesenchymal transition (EMT) in vitro, and inhibits metastasis in vivo. Moreover, miR-96-5p contributes to NDRG1 deficiency and promotes PCa cell migration and invasion. Furthermore, NDRG1 loss activates the NF-kB pathway, which stimulates p65 and IKBa phosphorylation and induces EMT in PCa. MiR-96-5p promotes the migration and invasion of PCa by targeting NDRG1 and regulating the NF-kB pathway.

Impacts of Groundwater Pumping on Subterranean Microbial Communities in a Deep Aquifer Associated with an Accretionary Prism.

Accretionary prisms are composed mainly of ancient marine sediment scraped from the subducting oceanic plate at convergent plate boundaries. Anoxic groundwater is stored in deep aquifers associated with accretionary prisms and can be collected via deep wells. We investigated how such groundwater pumping affects the microbial community in a deep aquifer. Groundwater samples were collected from a deep well drilled down to 1500 m every six months (five times in total) after completion of deep well construction and the start of groundwater pumping. Next-generation sequencing and clone-library analyses of 16S rRNA genes were used to describe the subterranean microbial communities in the samples. The archaea: the prokaryote ratio in groundwater increased significantly from 1 to 7% (0 and 7 months after initiating groundwater pumping) to 59 to 72% (13, 19, and 26 months after initiating groundwater pumping), and dominant prokaryotes changed from fermentative bacteria to sulfate-reducing archaea. The optimal growth temperature of the sulfate-reducing archaea, estimated based on the guanine-plus-cytosine contents of their 16S rRNA genes, was 48-52 °C, which agreed well with the groundwater temperature at the deep-well outflow. Our results indicated that, in deep aquifers, groundwater pumping enhances groundwater flow, and the supply of sulfate-containing seawater activates the metabolism of thermophilic sulfate-reducing archaea.

Genetic determinants of global developmental delay and intellectual disability in Ukrainian children

BackgroundGlobal developmental delay or intellectual disability usually accompanies various genetic disorders as a part of the syndrome, which may include seizures, autism spectrum disorder and multiple congenital abnormalities. Next-generation sequencing (NGS) techniques have improved the identification of pathogenic variants and genes related to developmental delay. This study aimed to evaluate the yield of whole exome sequencing (WES) and neurodevelopmental disorder gene panel sequencing in a pediatric cohort from Ukraine. Additionally, the study computationally predicted the effect of variants of uncertain significance (VUS) based on recently published genetic data from the country’s healthy population.MethodsThe study retrospectively analyzed WES or gene panel sequencing findings of 417 children with global developmental delay, intellectual disability, and/or other symptoms. Variants of uncertain significance were annotated using CADD-Phred and SIFT prediction scores, and their frequency in the healthy population of Ukraine was estimated.ResultsA definitive molecular diagnosis was established in 66 (15.8%) of the individuals. WES diagnosed 22 out of 37 cases (59.4%), while the neurodevelopmental gene panel identified 44 definitive diagnoses among the 380 tested patients (12.1%). Non-diagnostic findings (VUS and carrier) were reported in 350 (83.2%) individuals. The most frequently diagnosed conditions were developmental and epileptic encephalopathies associated with severe epilepsy and GDD/ID (associated genes ARX, CDKL5, STXBP1, KCNQ2, SCN2A, KCNT1, KCNA2). Additionally, we annotated 221 VUS classified as potentially damaging, AD or X-linked, potentially increasing the diagnostic yield by 30%, but 18 of these variants were present in the healthy population of Ukraine.ConclusionsThis is the first comprehensive study on genetic causes of GDD/ID conducted in Ukraine. This study provides the first comprehensive investigation of the genetic causes of GDD/ID in Ukraine. It presents a substantial dataset of diagnosed genetic conditions associated with GDD/ID. The results support the utilization of NGS gene panels and WES as first-line diagnostic tools for GDD/ID cases, particularly in resource-limited settings. A comprehensive approach to resolving VUS, including computational effect prediction, population frequency analysis, and phenotype assessment, can aid in further reclassification of deleterious VUS and guide further testing in families.

Abstract 5038: Validation of a comprehensive next-generation sequencing liquid biopsy assay for clinical diagnostics and clinical trial applications

Abstract Liquid biopsy next generation sequencing (NGS) provides a powerful non-invasive approach to detect solid tumor derived somatic variants in a massively parallel manner. Liquid biopsy NGS has rapidly become an invaluable choice of testing technologies for clinical utility where invasive tissue biopsy is inaccessible and/or inadequate for molecular characterization. We present here a targeted NGS gene panel assay designed and validated specifically for liquid biopsy characterization. The assay was designed to test cell free DNA and cell free RNA from blood plasma for detection of single nucleotide variants (SNV), insertion/deletion (Indel), copy number variants (CNV), and gene fusions present in 52 most commonly mutated genes in cancers. The validation was performed to assess assay accuracy, specificity, sensitivity, repeatability, and reproducibility, with including pre-characterized reference controls, retrospective plasma samples from cancer patients, and prospectively-collected clinic blood specimen. Triplicates were included and testing was performed at different times and by different operators to assess the assay precision. Over 100 clinic blood specimens were collected in Streck cfDNA tubes from multiple trial centers, including treatment naïve phase III-IV patients with solid tumor (lung cancer, breast cancer, brain cancer, prostate cancer, kidney cancer, melanoma, etc) as well as heathy donors, processed within 7 days for plasma separation and total nucleotide acid (TNA) extraction, and assessed by the NGS assay for mutation detection. The identified mutations and wild-types were verified with orthogonal ddPCR. Assay sensitivity as low as 0.1% for SNV and Indel, 1.3 fold change for CNV, and 10 copies for gene fusion were observed, with near-perfect assay specificity (&amp;gt;99.99%) at these sensitivity levels. In conclusion, a targeted NGS liquid biopsy assay was analytically validated under medical oversight, with a demonstrated rigor of the test by its high sensitivity/specificity and robust reproducibility. The validated assay has been utilized for clinical diagnostics and to support research and development efforts in clinical trials. Citation Format: Xin-Xing Tan, Tricia Peters, Meredith Berry, Kimberly Barber, Kristyn Jeter, Brigitte Lovell, Paula Elizondo, Yanglong Mou, Brad Thomas, Heng Xie, Jiannan Guo. Validation of a comprehensive next-generation sequencing liquid biopsy assay for clinical diagnostics and clinical trial applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5038.

Genetic inheritance in tandem: Non-syndromic autosomal recessive congenital ichthyosis with beta-thalassaemia: A rare coincidence

Ichthyosis belongs to the group of Mendelian disorders of cornification. Congenital ichthyosis is inherited as an autosomal recessive trait, so it is also known as autosomal recessive congenital ichthyosis (ARCI). ARCI is classified into two types: syndromic and non-syndromic ARCI. Non-syndromic ARCIs include lamellar ichthyosis, congenital ichthyosiform erythroderma and Harlequin ichthyosis. Syndromic-ARCI is associated with multisystemic involvement, which includes Netherton syndrome, Chanarin-Dorfman disease and others. Other systemic diseases associated with ichthyosis include Gaucher disease type II and hypothyroidism. Chanarin-Dorfman and Gaucher disease-II are additionally associated with hepatosplenomegaly (HSM) and anaemia. We describe a child of congenital ichthyosis with HSM and anaemia thought to be syndromic-ARCI, but diagnosed for beta-thalassaemia (b-thal) concurrently. An infant presented with peeling skin along with absent sweating since birth and recent onset paleness of the body. Examination revealed Ichthyosis (Lamellar-variant), severe pallor and HSM, raising the possibility of Chanarin-Dorfman syndrome and Gaucher’s disease. The investigation revealed an Erlenmeyer flask deformity of the knee, but no Gaucher’s cells were found in the bone marrow. In the absence of lipid vacuoles leaden leukocytes (Jordan’s anomaly), Chanarin-Dorfman disease was also ruled out. Haemoglobin (Hb) high-performance liquid chromatography revealed β-thal major, and both parents were traits, giving us the diagnosis, which was further confirmed by the next-generation gene sequencing for clinical exomes. This report was to highlight non-syndromic ARCI involving the CYP4F22 gene variant, which is a rare finding, and the association of such ichthyosis with β-thal major was an unexpected result. Genetic counselling was provided to the parents in light of the autosomal recessive nature of both diseases. Genes of congenital ichthyosis and β-thal were unrelated, but simultaneous expressions of two autosomal-recessive diseases together are it merely by chance or a new entity.

Novel MIP gene mutation causes autosomal-dominant congenital cataract.

To identify disease-causative mutations in families with congenital cataract. Two Chinese families with autosomal-dominant congenital cataract (ADCC) were recruited and underwent comprehensive eye examinations. Gene panel next-generation sequencing of common pathogenic genes of congenital cataract was performed in the proband of each family. Sanger sequencing was used to valid the candidate gene mutations and sequence the other family members for co-segregation analysis. The effect of sequence changes on protein structure and function was predicted through bioinformatics analysis. Major intrinsic protein (MIP)-wildtype and MIP-G29R plasmids were constructed and microinjected into zebrafish single-cell stage embryos. Zebrafish embryonic lens phenotypes were screened using confocal microscopy. A novel heterozygous mutation (c.85G>A; p.G29R) in the MIP gene was identified in the proband of one family. A known heterozygous mutation (c.97C>T; p.R33C; rs864309693) in MIP was found in the proband of another family. In-silico prediction indicated that the novel mutation might affect the MIP protein function. Zebrafish embryonic lens was uniformly transparent in both wild-type PCS2+MIP and mutant PCS2+MIP. Two missense mutations in the MIP gene in Chinese cataract families are identified, and one of which is novel. These findings expand the genetic spectrum of MIP mutations associated with cataracts. The functional studies suggest that the novel MIP mutation might not be a gain-of-function but a loss-of-function mutation.

Identification of novel pathogenic variants of CUBN in patients with isolated proteinuria.

Although proteinuria is long recognized as an independent risk factor for progressive chronic kidney diseases, not all forms of proteinuria are detrimental to kidney function, one of which is isolated proteinuria caused by cubilin (CUBN)-specific mutations. CUBN encodes an endocytic receptor, initially found to be responsible for the Imerslund-Gräsbeck syndrome (IGS; OMIM #261100) characterized by a combined phenotype of megaloblastic anemia and proteinuria. After analyzing their clinical and pathological characterizations, next-generation sequencing for renal disease genes or whole-exome sequencing (WES) was performed on four patients with non-progressive isolated proteinuria. CUBN biallelic pathogenic variants were identified and further analyzed by cDNA-PCR sequencing, immunohistochemistry, minigene assay, and multiple in silico prediction tools, including 3D protein modeling. Here, we present four patients with isolated proteinuria caused by CUBN C-terminal biallelic pathogenic variants, all of which showed no typical IGS symptoms, such as anemia and vitamin B12 deficiency. Their urine protein levels fluctuated between +~++ and estimated glomerular filtration rate (eGFR) were normal or slightly higher. Mild mesangial hypercellularity was found in three children's renal biopsies. A homozygous splice-site variant of CUBN (c.6821+3 (IVS44) A>G) was proven to result in the exon 44 skipping and premature translation termination by cDNA sequencing and immunohistochemistry. Compound heterozygous mutations were identified among the other three children, including another novel splice-site variant (c.10764+1 (IVS66) G>A) causing the retention of first 4 nucleotides in intron 66 by minigene assay, two unreported missense mutations (c.4907G>A (p.R1636Q); c. 9095 A>G (p.Y3032C)), and two reported missense mutations in China (c.8938G>A (p.D2980N); c. 9287T>C (p.L3096P)), locating behind the vitamin B12-binding domain, affecting CUB11, CUB16, CUB22, CUB23, and CUB27 domains, respectively. These results demonstrate that above CUBN mutations may cause non-progressive and isolated proteinuria, expanding the variant spectrum of CUBN and benefiting our understanding of proteinuria and renal function.

Comprehensive insights into the differences of fungal communities at taxonomic and functional levels in stony coral Acropora intermedia under a natural bleaching event

Previous studies have reported the correlations between bacterial communities and coral bleaching, but the knowledge of fungal roles in coral bleaching is still limited. In this study, the taxonomic and functional diversities of fungi in unbleached, partly bleached and bleached stony coral Acropora intermedia were investigated through the ITS-rRNA gene next-generation sequencing. An unexpected diversity of successfully classified fungi (a total of 167 fungal genera) was revealed in this study, and the partly bleached coral samples gained the highest fungal diversity, followed by bleached and unbleached coral samples. Among these fungi, 122 genera (nearly 73.2%) were rarely found in corals in previous studies, such as Calostoma and Morchella, which gave us a more comprehensive understanding of coral-associated fungi. Positively correlated fungal genera (Calostoma, Corticium, Derxomyces, Fusicolla, Penicillium and Vishniacozyma) and negative correlated fungal genera (Blastobotrys, Exophiala and Dacryopinax) with the coral bleaching were both detected. It was found that a series of fungal genera, dominant by Apiotrichum, a source of opportunistic infections, was significantly enriched; while another fungal group majoring in Fusicolla, a probiotic fungus, was distinctly depressed in the bleached coral. It was also noteworthy that the abundance of pathogenic fungi, including Fusarium, Didymella and Trichosporon showed a rising trend; while the saprotrophic fungi, including Tricladium, Botryotrichum and Scleropezicula demostrated a declining trend as the bleaching deteriorating. The rising of pathogenic fungi and the declining of saprotrophic fungi revealed the basic rules of fungal community transitions in the coral bleaching, but the mechanism of coral-associated fungal interactions still lacks further investigation. Overall, this is an investigation focused on the differences of fungal communities at taxonomic and functional levels in stony coral A. intermedia under different bleaching statuses, which provides a better comprehension of the correlations between fungal communities and the coral bleaching.

The tongue microbiome of young patients with chronic kidney disease and their healthy mothers.

Oral microbiome plays a crucial role in the incidence and development of oral diseases. An altered intestinal microbiome has been reported in adults with chronic kidney disease (CKD). This study aimed to characterize the tongue microbiome of young patients with CKD compared to their healthy mothers to identify the influence of CKD-associated factors on resilient tongue ecosystem. Thirty patients with CKD (mean age, 14.2 years; 16 males and 14 females) and generalized gingivitis were included in the study. Swabs of the posterior tongue were collected from the patients and 21 mothers (mean age 40.8 years). Next-generation sequencing of 16S rDNA genes was employed to quantitatively characterize microbial communities. The bacterial communities were similar in terms of richness and diversity between patients and mothers (p > 0.05). In patients with CKD, 5 core phyla, 20 core genera, and 12 core species were identified. The tongue microbiome of the study participants showed no relevant CKD-associated differences compared to their mothers and appears to be a highly preserved niche in the oral cavity. Differences observed in the abundance of individual species in this study could be attributed to the age rather than CKD, even after a mean disease duration of 11 years. CKD and its associated metabolic changes appear to have no detectable impact on the resilient tongue microbiome observed in young patients.

Skin Microbial Community Associated to Strawberry Disease in Farmed Rainbow Trout (Oncorhynchus mykiss Walbaum, 1792).

Aquaculture plays a crucial role in addressing the growing global demand for food. However, diseases associated with intensive aquaculture practices, especially those affecting the skin, can present significant challenges to both fish health and the industry as a whole. Strawberry disease (SD), also known as red-mark syndrome, is a persistent and non-lethal skin condition observed in Rainbow Trout (Oncorhynchus mykiss) in the United States and various European countries. SD is a nonlethal skin condition of an unclear etiology that affects rainbow trout reared in freshwater close to the harvest period. We used a RNA-based approach to examine active microbiota in the SD skin lesions and compared to non-injured skin. Our results, based on using 16S rRNA gene next-generation sequencing, showed that the skin microbiota was dominated by the phyla Firmicutes, Proteobacteria, and Actinobacteria. The comparisons of the skin microbiota between injured and non-injured samples showed differences in the alpha diversity (Fisher index) and beta diversity metrics (ANOSIM). At the genus level, both Pseudomonas and Candidatus Midichloria were highlighted as the most abundant taxa detected in samples obtained from fish affected with strawberry diseases. In contrast, the most abundant taxa in non-injured skin were Escherichia-Shigella, Streptococcus, and Pseudoalteromonas. In conclusion, our study on SD revealed distinct differences in the microbiota composition between skin lesions and non-injured skin. This is the first description of microbiota associated with SD-injured skin samples using an RNA approach.

Concurrent &lt;i&gt;THRB&lt;/i&gt; and &lt;i&gt;DUOX2&lt;/i&gt; variants in a patient detected via newborn screening for congenital hypothyroidism: a case of resistance to thyroid hormone

Concurrent &lt;i&gt;THRB&lt;/i&gt; and &lt;i&gt;DUOX2&lt;/i&gt; variants in a patient detected via newborn screening for congenital hypothyroidism: a case of resistance to thyroid hormone

Detection of zoonotic Cryptosporidium spp. in small wild rodents using amplicon-based next-generation sequencing

Rodents may serve as reservoirs of zoonotic species of Cryptosporidium; however, data from molecular surveys in support of this hypothesis are still scarce. In this study, we screened faeces and rectal content from murid and cricetid rodents (N = 58) caught around three farms in Zealand, Denmark, for Cryptosporidium spp. by amplicon-based next-generation sequencing (NGS) of ribosomal genes. Selected samples were further examined using nested conventional PCR targeting SSU rRNA, gp60, and actin genes. Cryptosporidium-specific DNA was identified in 40/58 (69%) samples, and in 12 (30%) of the 40 positive animals, mixed cryptosporidial infections were observed. Cryptosporidium ditrichi was the species most commonly identified, found in 28 (48%) of the animals. Cryptosporidium parvum was identified in 4 (7%) of the animals, all of which were co-infected with C. ditrichi. The present study is the first to utilize NGS-based screening for Cryptosporidium species in wild rodents. Moreover, it is the first study to provide molecular data on Cryptosporidium in rodents sampled in Denmark and to detect DNA of C. ditrichi in Mus musculus, Myodes glareolus, and Microtus agrestis. The NGS approach was successfully applied to yield new knowledge, and the results showed that zoonotic species of Cryptosporidium are common in murid and cricetid rodents in Zealand, Denmark.

Detection and Characterization of Electrogenic Bacteria from Soils.

Soil microbial fuel cells (SMFCs) are bioelectrical devices powered by the oxidation of organic and inorganic compounds due to microbial activity. Seven soils were randomly selected from Bergen Community College or areas nearby, located in the state of New Jersey, USA, were used to screen for the presence of electrogenic bacteria. SMFCs were incubated at 35-37 °C. Electricity generation and electrogenic bacteria were determined using an application developed for cellular phones. Of the seven samples, five generated electricity and enriched electrogenic bacteria. Average electrical output for the seven SMFCs was 155 microwatts with the start-up time ranging from 1 to 11 days. The highest output and electrogenic bacterial numbers were found with SMFC-B1 with 143 microwatts and 2.99 × 109 electrogenic bacteria after 15 days. Optimal electrical output and electrogenic bacterial numbers ranged from 1 to 21 days. Microbial DNA was extracted from the top and bottom of the anode of SMFC-B1 using the ZR Soil Microbe DNA MiniPrep Protocol followed by PCR amplification of 16S rRNA V3-V4 region. Next-generation sequencing of 16S rRNA genes generated an average of 58 k sequences. BLAST analysis of the anode bacterial community in SMFC-B1 demonstrated that the predominant bacterial phylum was Bacillota of the class Clostridia (50%). However, bacteria belonging to the phylum Pseudomonadota (15%) such as Magnetospirillum sp. and Methylocaldum gracile were also part of the predominant electrogenic bacterial community in the anode. Unidentified uncultured bacteria accounted for 35% of the predominant bacterial community. Bioelectrical devices such as MFCs provide sustainable and clean alternatives to future applications for electricity generation, waste treatment, and biosensors.

Blastocystis genetic diversity in animal and human samples from different departments of Colombia using complete sequencing of the 18S rRNA gene (SSU rRNA) by Oxford Nanopore Technologies (ONT)

Blastocystis is an intestinal microeukaryote that has raised attention due to its wide distribution in animals and humans. The risk of zoonotic circulation primarily arises from close contact with infected animals. Therefore, the following study aimed to evaluate the diversity and frequency of Blastocystis subtypes in Colombian human and animal samples using complete sequencing of the 18S rRNA gene. For this purpose, 341 human stool samples and 277 animal fecal samples (from cattle, sheep, goat, pigs, cats, and dogs), were collected from different Colombian regions and analyzed using PCR-based detection and full-length 18S SSU rRNA gene Next-Generation Sequencing (NGS). Among the 618 samples from both hosts, humans and animals, the results revealed widespread Blastocystis frequency, with 48.09% (n = 164) in humans and 31.4% (n = 87) detection in animals. Dogs, cats, sheep, pigs, and wild animals tested positive, aligning with global prevalence patterns. Also, 29 human samples and 23 animal samples were sequenced using ONT technology from which 11 long-read unique sequences were generated and cluster with their compared reference sequences. The subtype distribution varied within hosts, detecting ST1 and ST3 in both human and animal samples. Subtypes ST5, ST10, ST14, ST15, ST21, ST24, ST25 and ST26 were limited to animals hosts, some of which are considered to have zoonotic potential. On the other hand, ST2 was found exclusively in human samples from Bolivar region. Mixed infections occurred in both animal and humans, 60.86% and 27.58% respectively. Moreover, to our knowledge, this is the first study in Colombia identifying ST15 in pigs and ST25 in sheep. The subtypes (STs) identified in this study indicate that certain animals may serve as reservoirs with the potential for zoonotic transmission. The identification of zoonotic subtypes highlights the use of Next Generation Sequencing as the depth and resolution of the sequences increases providing insights into STs of medical and veterinarian significance. It also reveals the coexistence of diverse subtypes among hosts. Further research is essential for understanding transmission dynamics, health implications, and detection strategies for Blastocystis occurrence in animals and humans, mainly associated to the role of animals as reservoirs and their close interaction with humans.

The Potential of Intertwining Gene Diagnostics and Surgery for Mitral Valve Prolapse

Mitral valve prolapse (MVP) is common among heart valve disease patients, causing severe mitral regurgitation (MR). Although complications such as cardiac arrhythmias and sudden cardiac death are rare, the high prevalence of the condition leads to a significant number of such events. Through next-generation gene sequencing approaches, predisposing genetic components have been shown to play a crucial role in the development of MVP. After the discovery of the X-linked inheritance of filamin A, autosomal inherited genes were identified. In addition, the study of sporadic MVP identified several genes, including DZIP1, TNS1, LMCD1, GLIS1, PTPRJ, FLYWCH, and MMP2. The early screening of these genetic predispositions may help to determine the patient population at risk for severe complications of MVP and impact the timing of reconstructive surgery. Surgical mitral valve repair is an effective treatment option for MVP, resulting in excellent short- and long-term outcomes. Repair rates in excess of 95% and low complication rates have been consistently reported for minimally invasive mitral valve repair performed in high-volume centers. We therefore conceptualize a potential preventive surgical strategy for the treatment of MVP in patients with genetic predisposition, which is currently not considered in guideline recommendations. Further genetic studies on MVP pathology and large prospective clinical trials will be required to support such an approach.

Application Gene Variation Detection before and after Hematopoietic Stem Cell Transplantation to Predict the Relapse of Hematopoietic Neoplasm Patients after Transplantation: Retrospective Data from a Single Center in China

Objective: To evaluate the changes of gene variation in patients with hematological neoplasms at the time of diagnosis and after allogeneic hematopoietic stem cell transplantation (allo-HSCT), and the relationship between gene mutation and recurrence after transplantation. Methods: 76 patients with hematological neoplasms were analyzed retrospectively, including 69 acute myeloid leukemia, 21 acute lymphoblastic leukemia, 5 myelodysplastic syndrome, 1 mixed acute leukemia and 1 chronic myelomonocytic leukemia. The median age was 37 (7-63) years, with 52 males and 45 females. Among 97 patients, 21 were matched sibling donor HSCT (MDS-HSCT), 14 were matched unrelated donor HSCT (MUS-HSCT), and 62 were haploidentical HSCT (haplo-HSCT). There were 88 cases of myeloablative conditioning regimen and 9 cases of non-myeloablative conditioning regimen. All patients underwent next generation sequencing (NGS) of hematological neoplasms variation genes at the time of diagnosis and 28 days after transplantation. Results: Primary and Secondary variations were detected in 89 of 97 patients during diagnosis. Common variations include CEBPA (18/97), NRAS (13/97), FLT3 (12/97), DNMT3A (11/97), TP53 (9/97), etc. After transplantation, only 29 patients had primary and Secondary variations, including ABCB1 (30/97), CYP2C19 (13/97); The number of other variations did not exceed 3 cases. The above NGS detection results suggest that the number of primary and Secondary variations after transplantation is significantly reduced (p=0.019), and ABCB1 and CYP2C19 are the main variation forms. The membrane related protein encoded by ABCB1 is a member of the ATP binding cassette (ABC) transporter superfamily, and CYP2C19 is a drug metabolizing enzyme, both of which are involved in drug metabolism. Single Nucleotide Polymorphisms (SNP) variations were detected in 52 of 97 patients at diagnosis, and GATA2 (27/97) and TET2 (25/97) variations were the most common variation forms. SNP variations of GATA2 and TET2 increased significantly after transplantation, 59/97 and 54/97 respectively. The increase of GATA2/TET2 double variation was more significant after transplantation (19/97 vs. 46/97, P&amp;lt;0.001). The increased variation frequency of GATA2 and TET2 after transplantation may be related to the mixed chimerism at the early stage of transplantation, which needs to be observed for a long time. Furthermore, we analyzed the relationship between gene variation and recurrence of 97 patients with hematological neoplasms at the time of diagnosis and after allo-HSCT. Eleven of 97 patients recurred after transplantation. The single factor competitive risk model showed that the presence of primary and Secondary variations after transplantation was an independent risk factor for recurrence (P=0.017) (Figure 1). The primary and secondary variations before transplantation, SNP variations before and after transplantation had no effect on recurrence after transplantation. The schemes of transplantation in 29 patients with primary and secondary variations after transplantation were analyzed, including 9 cases of MSD-HSCT, 14 cases of haplo-HSCT, and 6 cases of MUD-HSCT. It suggests that relative donors are more likely to have primary and secondary variations related to diseases. We used Fisher's Exact Test to analyze the relationship between ASXL1, TP53, GATA2, RUNX1 and other high-risk variations at the time of diagnosis/after transplantation and recurrence, and did not find that the presence of these gene variations would increase the risk of recurrence after transplantation. Conclusion: The NGS gene variation detection before and after transplantation can predict the recurrence after transplantation. Large samples and long-term monitoring are also needed to find a more accurate variation pattern to predict the recurrence of hematological neoplasms after transplantation.

Novel Biomarkers for Assessing Clinical Severity in Hereditary Spherocytosis - Application of Routine and Advanced Diagnostic Tests

Background: Hereditary spherocytosis (HS) is caused by pathogenic variants in genes encoding red blood cell (RBC) cytoskeletal and (trans)membrane proteins. This ultimately leads to instability of the RBC membrane and subsequent membrane loss, resulting in the transformation of the biconcave RBC into a poorly deformable spherocyte, which is susceptible to premature splenic clearance. The diagnosis of HS has substantially improved over the last years and new advanced techniques have been established, including osmotic gradient ektacytometry, eosin-5'-maleimide (EMA) binding test and next-generation sequencing (NGS). However, there is little knowledge on the applicability of these diagnostic outcome parameters as biomarkers for clinical severity in HS. Aim: To explore possible correlations between established and novel diagnostic outcome parameters and clinical severity in a well-defined cohort of HS patients. Methods: This monocenter retrospective cohort study involves patients diagnosed with HS upon referral to our department between 2012 and 2023. Clinical characteristics, routine and advanced diagnostic laboratory parameters, and genotype were evaluated. Clinical severity was classified as previously described, based on parameters such as hemoglobin, reticulocyte percentage and bilirubin 1. The following laboratory tests were included: routine hematological parameters (Cel-Dyn Sapphire or Alinity hq), EMA binding test, osmotic fragility test (OFT) and osmotic gradient ektacytometry (osmoscan, Lorrca MaxSis). The latter technique was also explored for other parameters than the commonly used EI max, O hyper and O min. NGS gene panel analysis was used for molecular diagnosis. Differences between groups were determined using either Chi-squared test, unpaired t-test or Mann-Whitney U test and correlations using point-biserial, Pearson's or Spearman's test via GraphPad Prism. Results: Eighty-two non-splenectomized patients were included. Thirty-five of these (42.7%) were classified as mild, and forty-seven as moderate-severe (57.3%)). Demographic characteristics nor genotype differed significantly, albeit SPTB variants occurred more frequently in the moderate-severe group (15 vs. 4 in the mild group). Expectedly, both reticulocyte count and EI max correlated with clinical severity. RBC distribution width (RDW) correlated moderately, suggesting greater RBC heterogeneity (r=0.606, p&amp;lt;0.0001) is associated with a more severe clinical phenotype. Similarly, EMA binding test results correlated with clinical severity (r=0.390, p&amp;lt;0.001), indicating more pronounced membrane loss in clinically more severe patients. We further evaluated three novel osmoscan parameters ( Figure 1): EI O290, the elongation index (EI) at physiologic isotonicity, which correlated with clinical severity (r=-0.500, p&amp;lt;0.0001), and also with EI max (r=0.856, p&amp;lt;0.0001). The O min-width and O max-width, defined as the difference in osmolality between the intersection points of y=EI min or EI max +/- 0.05 and the osmoscan curve. Thisassesses the effect of changes in osmolality on EI min or EI max, respectively. O min-width correlated with RDW (r-0.439, p&amp;lt;0.0001), OFT results (N=30, r=0.671, p&amp;lt;0.0001) and clinical severity (r=0.390, p&amp;lt;0.001). O max-width correlated with clinical severity (r=-0.375, p&amp;lt;0.001) and strongly with percentage of hyperchromic cells (N=76, r=-0.751, p&amp;lt;0.0001), yet weakly with RDW (-0.273, p&amp;lt;0.05). All significant correlations with clinical severity are displayed in Figure 2. Conclusion: In this study, a number of routine and advanceddiagnostic laboratory parameters were found to correlate with clinical severity in HS. O min-width and O max-width are novel osmoscan-derived biomarkers that correlated with RDW, hyperchromic cells (O max-width), OFT results (O min-width) and clinical severity. EI O290, another novel osmoscan-derived biomarker, also correlated with clinical severity, although not stronger than EI max and AUC. The biomarkers identified in this study, together with patient-reported outcome measures (PROMs), could be used to revise the previously established severity classification system and thereby aid in stratifying clinical severity and subsequent clinical decision-making.