Aspects Of Phenotype Research Articles

The role of transducin β-like 1 X-linked receptor 1 (TBL1XR1) in thyroid hormone metabolism and action in mice.

Transducin β-like 1 X-linked receptor 1 (TBL1XR1) is a WD40 repeat-containing protein and part of the corepressor complex SMRT/NCoR that binds to the thyroid hormone receptor (TR). We recently described a mutation in TBL1XR1 in patients with Pierpont syndrome. A mouse model bearing this Tbl1xr1 mutation (Tbl1xr1Y446C/Y446C ) displays several aspects of the Pierpont phenotype. Although serum thyroid hormone (TH) concentrations were unremarkable in these mice, tissue TH action might be affected due to the role of TBL1XR1 in the SMRT/NCoR corepressor complex. The aim of the present study was to evaluate tissue TH metabolism and action in a variety of tissues of Tbl1xr1Y446C/Y446C mice. We studied the expression of genes involved in TH metabolism and action in tissues of naïve Tbl1xr1Y446C/Y446C mice and wild type (WT) mice. In addition, we measured deiodinase activity in liver (Dio1 and Dio3), kidney (Dio1 and Dio3) and BAT (Dio2). No striking differences were observed in the liver, hypothalamus, muscle and BAT between Tbl1xr1Y446C/Y446C and WT mice. Pituitary TRα1 mRNA expression was lower in Tbl1xr1Y446C/Y446C mice compared to WT, while the mRNA expression of Tshβ and the positively T3-regulated gene Nmb were significantly increased in mutant mice. Interestingly, Mct8 expression was markedly higher in WAT and kidney of mutants, resulting in (subtle) changes in T3-regulated gene expression in both WAT and kidney. In conclusion, mice harboring a mutation in TBL1XR1 display minor changes in cellular TH metabolism and action. TH transport via MCT8 might be affected as the expression is increased in WAT and kidney. The mechanisms involved need to be clarified.

Spectral variables as criteria for selection of soybean genotypes at different vegetative stages

Understanding the association between variables obtained by multispectral imaging, such as plant canopy reflectance at different wavelengths and vegetation indices (VIs), and agronomic traits of interest for soybean is crucial for breeding programs. This approach, associated with the evaluation of the best stage for spectral data collection, can identify easier-to-measure variables to be used in the indirect selection of genotypes for more expensive-to-measure traits or those that are expressed later, resulting in a faster, labor-saving, and large-scale selection process. The hypothesis of this study is the possibility of identifying promising variables for the selection of soybean genotypes through the use of vis and that different times of collection of information regarding reflectance interfere in the selection responses. Thus, our objectives were: i) to estimate heritability (h2) for agronomic traits and VIs; ii) to estimate the gains with direct selection (DS) on the VIs and indirect selection (IS) for the agronomic traits selected by the higher heritability; iii) to estimate correlations between spectral variables, VIs, and agronomic traits; iv) to identify the most promising populations for the evaluated variables; and vi) to identify the most adequate phenological stage for spectral data collection. We installed a field experiment in a randomized block design with four repetitions, 28 F3 soybean populations, and four control treatments. Agronomic traits evaluated were: days to maturity (DM), plant height (PH), first pod insertion height (PIH), number of branches (NB), and grain yield (GY). Spectral collections were performed at the V8 (45 days after emergence), R1 (60 days after emergence) and R5 (80 days after emergence) stages. Correlations between agronomic traits, reflectance at 790 nm (near-infrared), 735 nm (RedEdge), 660 nm (red), 550 nm (green), and 450 nm (blue) wavelengths, and VIs were estimated. The heritability were estimated for agronomic traits and VIs. Our findings reveal that it is possible to select soybean genotypes using spectral variables based on heritability and phenotypic aspects. Enhanced vegetation index (EVI) and soil-adjusted vegetation index (SAVI) have high heritability values (>75%) at V8. It is possible to obtain satisfactory selection gains for agronomic traits, especially GY, based on selection on EVI and SAVI at V8 stage. By this approach, the F3 segregating populations that provided the highest selection gains were P7, P8, P9, P14, P27, and P28. Spectral data collection at V8 stage provided higher h2 for VIs and agronomic traits, while R5 is the most suitable stage for estimating associations between VIs and agronomic traits.

COVRECON: automated integration of genome- and metabolome-scale network reconstruction and data-driven inverse modeling of metabolic interaction networks.

One central goal of systems biology is to infer biochemical regulations from large-scale OMICS data. Many aspects of cellular physiology and organismal phenotypes can be understood as results of metabolic interaction network dynamics. Previously, we have proposed a convenient mathematical method, which addresses this problem using metabolomics data for the inverse calculation of biochemical Jacobian matrices revealing regulatory checkpoints of biochemical regulations. The proposed algorithms for this inference are limited by two issues: they rely on structural network information that needs to be assembled manually, and they are numerically unstable due to ill-conditioned regression problems for large-scale metabolic networks. To address these problems, we developed a novel regression loss-based inverse Jacobian algorithm, combining metabolomics COVariance and genome-scale metabolic RECONstruction, which allows for a fully automated, algorithmic implementation of the COVRECON workflow. It consists of two parts: (i) Sim-Network and (ii) inverse differential Jacobian evaluation. Sim-Network automatically generates an organism-specific enzyme and reaction dataset from Bigg and KEGG databases, which is then used to reconstruct the Jacobian's structure for a specific metabolomics dataset. Instead of directly solving a regression problem as in the previous workflow, the new inverse differential Jacobian is based on a substantially more robust approach and rates the biochemical interactions according to their relevance from large-scale metabolomics data. The approach is illustrated by in silico stochastic analysis with differently sized metabolic networks from the BioModels database and applied to a real-world example. The characteristics of the COVRECON implementation are that (i) it automatically reconstructs a data-driven superpathway model; (ii) more general network structures can be investigated, and (iii) the new inverse algorithm improves stability, decreases computation time, and extends to large-scale models. The code is available in the website https://bitbucket.org/mosys-univie/covrecon.

Genomic analysis of multiplex consanguineous families reveals causes of neurodevelopmental disorders with epilepsy

IntroductionNeurodevelopmental disorders (NDD) are a diverse group of disorders that affect the development of the nervous system. Epilepsy is a common phenotypic aspect of NDD. MethodsWe recruited eight consanguineous families from Pakistan which segregated recessively inherited NDD with epilepsy. Magnetic Resonance imaging (MRI) and Electroencephalogram (EEG) were completed. Exome sequencing was carried out for selected participants from each family. The exome data were analyzed for exonic and splice-site variants that had allele frequencies of less than 0.01 in public databases. ResultsClinical investigations determined that developmental delay, intellectual disability and seizures were manifested by most patients in early childhood. EEG findings were abnormal in the participants of four families. MRI revealed demyelination orcerebral atrophic changes in multiple participants. We identified four novel homozygous variants including nonsense andmissense variants in OCLN, ALDH7A1, IQSEC2 and COL3A1, segregating with the phenotypes in the participants of four families. Previously reported homozygous variants of CNTNAP2, TRIT1 and NARS1 were found in individuals from three families. Clinical utility was observed in directing treatment in case of patients with an ALDH7A1 variant which included pyridoxine administration and enabling accurate counseling about the natural history and recurrence risk. ConclusionOur results add to the clinical and molecular delineation of very rare NDD with epilepsy. The high success rate of exome sequencing is likely attributable to the expectation of homozygous variants in patients of consanguineous families, and in one case, the availability of positional mapping data that greatly aided the variant prioritization.

Phenotypic and genetic aspects of hereditary ataxia in dogs.

Hereditary ataxias are a large group of neurodegenerative diseases that have cerebellar or spinocerebellar dysfunction as core feature, occurring as an isolated sign or as part of a syndrome. Based on neuropathology, this group of diseases has so far been classified into cerebellar cortical degenerations, spinocerebellar degenerations, cerebellar ataxias without substantial neurodegeneration, canine multiple system degeneration, and episodic ataxia. Several new hereditary ataxia syndromes are described, but most of these diseases have similar clinical signs and unspecific diagnostic findings, wherefore achieving a definitive diagnosis in these dogs is challenging. Eighteen new genetic variants associated with these diseases have been discovered in the last decade, allowing clinicians to reach a definitive diagnosis for most of these conditions, and allowing breeding schemes to adapt to prevent breeding of affected puppies. This review summarizes the current knowledge about hereditary ataxias in dogs, and proposes to add a "multifocal degenerations with predominant (spino)cerebellar component" category regrouping canine multiple system degeneration, new hereditary ataxia syndromes that do not fit in 1 of the previous categories, as well as specific neuroaxonal dystrophies and lysosomal storage diseases that cause major (spino)cerebellar dysfunction.

1675-P: Reproductive and Intergenerational Impacts of Metformin

Recent data suggest that metformin can influence male reproductive health, directly or indirectly. Lastly, an epidemiologic cohort study demonstrated an association between preconceptional use of metformin in men and genital birthdefects in their offsprings. Given the need to test these associations in the absence of complex genetic and environmental factors in humans, we assessed the impact of metformin on both male reproductive health and health of offspring in C57/BL6J mice. Male mice age 8 weeks were treated with low fat (10% fat) or high fat (60% fat) diet to induce obesity; after two weeks, mice were randomized to continued dietary treatment, with or without metformin 350 mg/kg/day (n=8/group). After 12 weeks of treatment, metabolic status was assessed by glucose and insulin tolerance tests; as expected, metformin improved insulin sensitivity (21% improvement vs. HFD, p=0.008) despite no significant difference in body weight or glucose tolerance. To determine effect of male metformin treatment on reproductive success, HFD and HFD-MET males were bred with 6-8 week old females. Breeding was successful for 87.5% of HFD males, as compared with 37.5% for HFD-MET males (P=0.038). In both groups, insulin resistance (HOMA-IR) was strongly correlated with body weight (HFD: r=0.86, P=0.006; HFD-MET: r=0.92, P=0.001). However insulin resistance was inversely correlated with successful pregnancy rates only in HFD-MET mice (HFD: r=-0.3, P=0.21; HFD-MET: r=-0.68, P=0.04), suggesting that insulin sensitivity is a stronger and more significant determinant of fertility in metformin treated mice. Thus, we hypothesize that metformin may have dual impact on male reproductive health, with both beneficial increases in insulin sensitivity and potential adverse impact to reduce fertility. Additional studies are in progress to determine impact of male metformin treatment on hormonal and germ cell aspects of male reproductive health and offspring developmental phenotypes. Disclosure B.Ozturk: None. R.Ferraz-bannitz: None. V.Efthymiou: None. L.Poulos: None. V.Navarrete: None. M.Patti: Consultant; MBX Biosciences, AstraZeneca, Hanmi Pharm. Co., Ltd., Other Relationship; Fractyl Health, Inc. Funding National Institutes of Health (R01DK106193)

Cholesterol, Amyloid Beta, Fructose, and LPS Influence ROS and ATP Concentrations and the Phagocytic Capacity of HMC3 Human Microglia Cell Line.

Research has found that genes specific to microglia are among the strongest risk factors for Alzheimer's disease (AD) and that microglia are critically involved in the etiology of AD. Thus, microglia are an important therapeutic target for novel approaches to the treatment of AD. High-throughput in vitro models to screen molecules for their effectiveness in reversing the pathogenic, pro-inflammatory microglia phenotype are needed. In this study, we used a multi-stimulant approach to test the usefulness of the human microglia cell 3 (HMC3) cell line, immortalized from a human fetal brain-derived primary microglia culture, in duplicating critical aspects of the dysfunctional microglia phenotype. HMC3 microglia were treated with cholesterol (Chol), amyloid beta oligomers (AβO), lipopolysaccharide (LPS), and fructose individually and in combination. HMC3 microglia demonstrated changes in morphology consistent with activation when treated with the combination of Chol + AβO + fructose + LPS. Multiple treatments increased the cellular content of Chol and cholesteryl esters (CE), but only the combination treatment of Chol + AβO + fructose + LPS increased mitochondrial Chol content. Microglia treated with combinations containing Chol + AβO had lower apolipoprotein E (ApoE) secretion, with the combination of Chol + AβO + fructose + LPS having the strongest effect. Combination treatment with Chol + AβO + fructose + LPS also induced APOE and TNF-α expression, reduced ATP production, increased reactive oxygen species (ROS) concentration, and reduced phagocytosis events. These findings suggest that HMC3 microglia treated with the combination of Chol + AβO + fructose + LPS may be a useful high-throughput screening model amenable to testing on 96-well plates to test potential therapeutics to improve microglial function in the context of AD.

Characterization of multidrug and heavy metal resistance of carbapenemases producing Klebsiella pneumoniae from poultry samples in Bangladesh.

Resistance to multiple drugs in Klebsiella pneumoniae (KPN) is an important issue in human and animal medicine. KPN phenotypic and genotypic aspects in poultry samples have not been comprehensively explored in Bangladesh. This research focused on the prevalence of antibiotic resistance and the characterization of KPN in Bangladeshi poultry isolates using both phenotypic and genotypic approaches. A total of 32 poultry samples were randomly obtained from a commercial poultry farm in Narsingdi, Bangladesh, and 43.90% (18/41) of the isolates were confirmed to be KPN, whereas all isolates were biofilm producers. The antibiotic sensitivity test revealed the most remarkable (100%) antibiotic resistance level against Ampicillin, Doxycycline and Tetracycline while remaining susceptible to Doripenem, Meropenem, Cefoxitin and Polymyxin B. Resistance to Nalidixic acid, Nitrofurantoin, Trimethoprim, Levofloxacin, Ciprofloxacin, Cefuroxime and Chloramphenicol ranges from 18% to 70%. Minimum inhibitory concentrations for carbapenem-resistant KPN ranged from 128 to 512mg/mL for Meropenem, Imipenem, Gentamycin and Ciprofloxacin, respectively. [Correction added on 15 June 2023, after first online publication: 512 g/mL was corrected to 512 mg/mL in the preceding sentence]. Carbapenemase-producing KPN isolates harboured a single or multiple β-lactamase genes, blaSIM-1 , blaIMP-4 and blaOXA-48 as well as one ESBL gene (blaTEM ) and plasmid-mediated quinolone resistance gene (qnrB). Furthermore, Cr and Co outperformed Cu and Zn in antibacterial effectiveness. The results of this investigation showed that the high prevalence of multidrug-resistant pathogenic KPN in our chosen geographic location had displayed sensitivity to FOX/PB/Cr/Co, which might be regarded as an alternate treatment to reduce pressure of use on carbapenems.

Imprinting in an interspecific brood parasitic bird.

Many animals learn to recognize conspecifics after an early experience with them through sexual imprinting. For brood parasitic birds, it is not possible to develop conspecific recognition using cues provided by their foster parents. One solution is that a unique species-specific signal triggers the learning of additional aspects of the conspecific's phenotype. It has been proposed that for brood parasitic cowbirds, this signal is an innate vocalization, the chatter. This vocalization might act in a cross-modal learning process through which juveniles that listen to the song learn to recognize the visual characteristics of the song's producer. We trained two groups of juvenile shiny cowbirds (Molothrus bonariensis). In one group, individuals listened to the chatter or a heterospecific call while they observed a stuffed model of the corresponding species. In the other group, individuals listened to the call of one species (cowbird or heterospecific) while they observed the stuffed model of the other species. In the preference test, juveniles chose the model associated with the chatter, regardless of whether the model was a cowbird or a heterospecific. These results show how the auditory system through a species-specific signal can lead to cross-modal learning of visual cues allowing conspecific recognition in brood parasitic cowbirds.

Phenotypic and Biomechanical Characteristics of Human Fetal Neural Progenitor Cells Exposed to Pesticide Compounds

Various forms of pesticides have been reported to be among the environmental toxicants, which are detrimental to human health. The active ingredients of these formulations can enter the human body through air, food, or water. Epidemiological studies suggest that these compounds strongly affect the developing brain in fetal and infant stages due to their ability to breach the underdeveloped blood–brain barrier. Since neural progenitor stem cells (NPCs) in the developing brain are the most vulnerable to these compounds, the mechanisms by which NPCs experience toxicity upon exposure to these chemicals must be investigated. Here, we assessed the viability of human fetal NPCs in 2D cultures in the presence of the active ingredients of six widely used pesticides using Live/Dead® and Hoechst staining. The IC50 values ranged from 4.1–201 μM. A significant drop in cell viability with increasing toxicant concentration (p < 0.01) was noted, with the order of toxicity being malathion < 4-aminopyridine < methoprene < prallethrin < temephos < pyriproxyfen. Changes in cellular biomechanical characteristics (Young’s modulus, tether force, membrane tension, and tether radius) were quantified using atomic force microscopy, whereas cell migration was elucidated over 48 h using a customized wound-healing assay. The Young’s modulus of fetal NPCs exposed to IC50/2 doses of these compounds was reduced by 38–70% and that of those exposed to IC50 doses was reduced by 71–80% (p < 0.001 vs. controls for both; p < 0.01 for IC50 vs. IC50/2 for each compound). Similar patterns were noted for tether forces and membrane tension in fetal NPCs. NPC migration was found to be compound type- and dose-dependent. These results attest to the significant detrimental effects of these compounds on various aspects of the human fetal NPC phenotype, and the utility of cell mechanics as a marker to assess developmental neurotoxicity.

Glucagon-like Peptide 1 Receptor Agonists for the Treatment of Polycystic Ovary Syndrome: A Systematic Review and Meta-analysis of Randomized Controlled Trials

Background: Since the Polycystic Ovary Syndrome (PCOS) phenotype might change at different points in a person's life, individualized diagnosis and treatment are required. Since glucagon-like peptide 1 (GLP-1) receptor agonists (RA) improve insulin sensitivity and reduce the risk of cardiovascular disease, they offer a unique opportunity to treat many comorbid diseases and phenotypic aspects of (PCOS) all at once.
 Methods: The PICO framework—which includes the terms "participants," "intervention," "control," and "outcome"—formed the basis for the search parameters. The appropriate research publications were identified by searching many databases, including Web of Sciences, PubMed, Scopus and PRISMA flow chart was constructed. RevMan 5.4 was utilized for the meta-analysis, while RoB-2.0 was employed for quality control.
 Results: After following PRISMA, 14 research articles were included in the present systematic review and meta-analysis. GLP-1 RAs alone or in combination gave good results when compared with control/placebo/other drugs. In the meta-analysis, GLP-1 RA was compared to control (Metformin, a comparative drug, a placebo, and other treatments) for Menestral frequency rate (MFR), Free Androgen Index (FAI), Homeostasis Model Assessment-estimated Insulin Resistance (HOMA-IR), and Total Testosterone (Total T). The results showed that GLP-1 RA had a statistically significant effect on MFR and Total T, indicating that the intervention was more effective than the control group but had no effect on FAI and HOMA-IR, suggesting that both GLP-1 RA and the control group were equally effective. When the quality assessment was done, 7 studies had low risk of bias, and 7 had some concerns, while no study had a high risk of bias.
 Conclusion: GLP-1 RAs may be suitable for obese patients with PCOS, particularly those with insulin resistance. However, as 7 studies had questions about randomization. There has to be more high-quality studies conducted on GLP-1 RAs to determine their effectiveness for PCOS in women.

Modeling Duchenne Muscular Dystrophy Cardiomyopathy with Patients' Induced Pluripotent Stem-Cell-Derived Cardiomyocytes.

Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle degenerative disease caused by mutations in the dystrophin gene, resulting in death by the end of the third decade of life at the latest. A key aspect of the DMD clinical phenotype is dilated cardiomyopathy, affecting virtually all patients by the end of the second decade of life. Furthermore, despite respiratory complications still being the leading cause of death, with advancements in medical care in recent years, cardiac involvement has become an increasing cause of mortality. Over the years, extensive research has been conducted using different DMD animal models, including the mdx mouse. While these models present certain important similarities to human DMD patients, they also have some differences which pose a challenge to researchers. The development of somatic cell reprograming technology has enabled generation of human induced pluripotent stem cells (hiPSCs) which can be differentiated into different cell types. This technology provides a potentially endless pool of human cells for research. Furthermore, hiPSCs can be generated from patients, thus providing patient-specific cells and enabling research tailored to different mutations. DMD cardiac involvement has been shown in animal models to include changes in gene expression of different proteins, abnormal cellular Ca2+ handling, and other aberrations. To gain a better understanding of the disease mechanisms, it is imperative to validate these findings in human cells. Furthermore, with the recent advancements in gene-editing technology, hiPSCs provide a valuable platform for research and development of new therapies including the possibility of regenerative medicine. In this article, we review the DMD cardiac-related research performed so far using human hiPSCs-derived cardiomyocytes (hiPSC-CMs) carrying DMD mutations.

Phenotypic and genotypic aspects of sorbitol-negative Escherichia coli isolated from cattle

Escherichia coli especially sorbitol-negative serogroups such as O157 that produces Shiga toxin (STEC) is involved in food poisoning with severity ranging from individual cases into outbreaks that threaten human and animal health. This study aimed to evaluate phenotypic and genotypic aspects of sorbitol-negative E.coli isolated from different sources. A total of 420 samples were collected from fecal swabs and raw milk of cattle from various locations in Kafr Elsheikh government, Egypt. The prevalence of E. coli isolates was 9.3% (39/420) as was determined by bacterial culturing. The phenotype of these isolates was serologically and molecularly determined, and the results showed an overall prevalence of E. coli O157 of 23% (9/39) with a high incidence in fecal swabs samples. The multidrug resistance (MDR) phenotype as detected by antibiotic sensitivity test and confirmed by PCR revealed resistance to amoxicillin, clavulanic acid, vancomycin, ampicillin, and sulbactam with the detection of blaTEM and blaSHV MDR genes in 9 and 2 isolates, respectively. Virulence genes (stx1, stx2, eaeA) were also detected in 1, 9, 6 isolates, respectively. With these results, we could conclude that E. coli O157 was identified in not only cattle fecal swab samples but also in their milk and subsequently this could threaten animal and human health.

Advances in the Co-Host Immune Response to Multisystem Inflammatory Syndrome and Kawasaki Disease in Children with AI-Guided Features

Purpose: To explore the role of artificial intelligence in the immune response mechanism of children with multi-system inflammatory syndrome and Kawasaki disease. Methods: To search the domestic and foreign literatures about the immune response mechanism of these two diseases, and analyze the literatures according to the characteristics of artificial intelligence. Results: AI analysis showed that the two kinds of children's syndrome were concentrated in the cytokine storm centered on il-15/IL15RA, which confirmed that the two diseases had the same initial immune pathway, but the differences in immune phenotype, cytokine, cell count and other aspects suggested that KD and MIS-C were two different diseases. Conclusion: It shows the applicability of AI in this research direction, and points out the limitations of the current research scope and samples. The difference between the results of KD and MIS-C research guides the direction of future research. Accurate and comprehensive laboratory indicators and parameters can be applied to artificial intelligence and provide basis for diagnosis and treatment of diseases. As the number of infected people increases, the problem of sample limitation in the current work can also be improved.

Abstract 178: Establishment of patient-derived organoid of breast cancer

Abstract A patient-derived organoid (PDO) is an in vitro three-dimensional model which shows similar features in phenotypic and genetic aspects with primary tissue from patients. PDOs are useful for preclinical studies including drug sensitivity tests of tumors from individual patients as well as development of novel targeted agents. Collectively, PDOs are recently introduced as an emerging platform for personalized medicine. We obtained a total of 100 surgical specimens from 100 patients with breast cancer at the Yonsei Cancer Center, Severance Hospital, Seoul, Korea. One of the tissue specimens was acquired from a breast cancer patient-derived xenograft model. We dissociated the tissues and isolated breast cancer primary tumor cells from the samples, and then the cells were cultured in basement membrane-like matrix in 3D manner with growth medium with supplements. We defined successful establishment of PDOs as continuous growth after 3 passaging. Among all 100 cases, 32 cases failed to culture or passage, however, 41 cases were successfully cultured over 3 passages. In addition, the remaining 27 cases are still in progress of establishment. Success rate of PDO was 68% (68/100). Subtypes of primary tumors of the PDO were 33.8% (23/68) of luminal A, 26.5% (18/68) of luminal B, 26.5% (18/68) of triple-negative, 5.9% (4/68) of triple-positive and 7.4% (5/68) of HER2-enriched. Success rates of each subtype were 69.7% (23/33) of luminal A, 72.0% (18/25) of luminal B, 66.7% (18/27) of triple-negative, 66.7% (4/6) of triple-positive and 55.6% (5/9) of HER2-enriched. Pathologic evaluation using immunohistochemistry revealed that PDOs showed similar morphologic and immunohistochemical features with primary tumors. The selective sensitivity of PARP inhibitor, olaparib, was confirmed in PDOs harboring mutant BRCA1/2 compared with BRCA1/2 wild-type PDOs. Overall, PDOs can be used as a real-time platform for drug sensitivity and screening analyses, and a robust tool for preclinical studies in breast cancer. Citation Format: Won-Ji Ryu, Shinyoung Park, Jeong Dong Lee, Yumi Hwang, Seongyeon Jo, Kweon Tae Yong, Ja Seung Koo, Min Hwan Kim, Joo Hyuk Sohn, Hyung Seok Park. Establishment of patient-derived organoid of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 178.

The link between rheumatic disorders and inborn errors of immunity.

Inborn errors of immunity (IEIs) are immunological disorders characterized by variable susceptibility to infections, immune dysregulation and/or malignancies, as a consequence of damaging germline variants in single genes. Though initially identified among patients with unusual, severe or recurrent infections, non-infectious manifestations and especially immune dysregulation in the form of autoimmunity or autoinflammation can be the first or dominant phenotypic aspect of IEIs. An increasing number of IEIs causing autoimmunity or autoinflammation, including rheumatic disease have been reported over the last decade. Despite their rarity, identification of those disorders provided insight into the pathomechanisms of immune dysregulation, which may be relevant for understanding the pathogenesis of systemic rheumatic disorders. In this review, we present novel IEIs primarily causing autoimmunity or autoinflammation along with their pathogenic mechanisms. In addition, we explore the likely pathophysiological and clinical relevance of IEIs in systemic rheumatic disorders.

Investigating the genetic basis of vertebrate dispersal combining RNA-seq, RAD-seq and quantitative genetics.

Although animal dispersal is known to play key roles in ecological and evolutionary processes such as colonization, population extinction and local adaptation, little is known about its genetic basis, particularly in vertebrates. Untapping the genetic basis of dispersal should deepen our understanding of how dispersal behaviour evolves, the molecular mechanisms that regulate it and link it to other phenotypic aspects in order to form the so-called dispersal syndromes. Here, we comprehensively combined quantitative genetics, genome-wide sequencing and transcriptome sequencing to investigate the genetic basis of natal dispersal in a known ecological and evolutionary model of vertebrate dispersal: the common lizard, Zootoca vivipara. Our study supports the heritability of dispersal in semi-natural populations, with less variation attributable to maternal and natal environment effects. In addition, we found an association between natal dispersal and both variation in the carbonic anhydrase (CA10) gene, and in the expression of several genes (TGFB2, SLC6A4, NOS1) involved in central nervous system functioning. These findings suggest that neurotransmitters (serotonin and nitric oxide) are involved in the regulation of dispersal and shaping dispersal syndromes. Several genes from the circadian clock (CRY2, KCTD21) were also differentially expressed between disperser and resident lizards, supporting that the circadian rhythm, known to be involved in long-distance migration in other taxa, might affect dispersal as well. Since neuronal and circadian pathways are relatively well conserved across vertebrates, our results are likely to be generalisable, and we therefore encourage future studies to further investigate the role of these pathways in shaping dispersal in vertebrates.

Exposure to nonanoic acid alters small intestinal neuroendocrine tumor phenotype

BackgroundSmall intestinal neuroendocrine tumors (SI-NET) are highly differentiated and genetically stable malignant tumors, yet they often present with advanced metastatic spread at the time of diagnosis. In contrast to many other types of malignant tumors, primary SI-NET are often asymptomatic and typically smaller in size compared to adjacent lymph node metastases. This study explores the hypothesis that stimulating the chemosensing olfactory receptor 51E1 (OR51E1) decreases SI-NET proliferation suggesting a mechanism that explains a difference in proliferative rate based on tumor location.MethodsClinical data was used to address difference in tumor size depending on location. A SI-NET tissue microarray was used to evaluate expression of OR51E1 and olfactory marker protein (OMP). Primary cultured tumor cells from 5 patients were utilized to determine the effect of OR51E1 agonist nonanoic acid on metabolic activity. The SI-NET cell line GOT1 was used to determine effects of nonanoic acid on the transcriptome as well as long-term effects of nonanoic acid exposure with regards to cell proliferation, serotonin secretion, alterations of the cell-cycle and morphology.ResultsTumor size differed significantly based on location. OR51E1 and OMP were generally expressed in SI-NET. Primary SI-NET cells responded to nonanoic acid with a dose dependent altered metabolic activity and this was replicated in the GOT1 cell line but not in the MCF10A control cell line. Nonanoic acid treatment in GOT1 cells upregulated transcripts related to neuroendocrine differentiation and hormone secretion. Long-term nonanoic acid treatment of GOT1 cells decreased proliferation, induced senescence, and altered cell morphology.ConclusionOur results raise the possibility that exposure of intraluminal metabolites could represent a mechanism determining aspects of the SI-NET tumor phenotype. However, we could not causally link the observed effects of nonanoic acid exposure to the OR51E1 receptor.

Genome-sequence, annotation and phylogenetic insights of the lactic acid bacterium Limosilactobacillus fermentum strain LAB1 obtained from the dairy beverage borhani

Limosilactobacillus fermentum is a promising probiotic with several documented health benefits. LAB1 is an antagonistic L. fermentum strain isolated from borhani, a traditional South Asian beverage prepared from dairy and plant ingredients. Here, I present the genome sequence of the L. fermentum LAB1 strain, its annotation, and phylogenetic features. The 2.01 Mb genome with a G+C content of 51.9% was assembled into 221 contigs and predicted to have 1,913 protein-coding genes, 98 pseudo genes, 7 rRNAs, 60 tRNAs, and 1 CRISPR array. As much as 91.1% of the coding sequences could be assigned to known functional genes. Determination of average nucleotide identity (ANI) of the genome sequence revealed 99.37% identity to that of the type strain ATCC 14931. Its 16S rRNA gene sequence extracted from the genome sequence showed close phylogenetic association with several L. fermentum strains. The genome sequence is expected to provide useful insights with regard to the phenotypic, metabolic and beneficial aspects of this lactic acid bacterium.

The Josephin domain (JD) containing proteins are predicted to bind to the same interactors: Implications for spinocerebellar ataxia type 3 (SCA3) studies using Drosophila melanogaster mutants.

Spinocerebellar ataxia type 3, also known as Machado-Joseph disease (SCA3/ MJD), is the most frequent polyglutamine (polyQ) neurodegenerative disorder. It is caused by a pathogenic expansion of the polyQ tract, located at the C-terminal region of the protein encoded by the ATXN3 gene. This gene codes for a deubiquitinating enzyme (DUB) that belongs to a gene family, that in humans is composed by three more genes (ATXN3L, JOSD1, and JOSD2), that define two gene lineages (the ATXN3 and the Josephins). These proteins have in common the N-terminal catalytic domain (Josephin domain, JD), that in Josephins is the only domain present. In ATXN3 knock-out mouse and nematode models, the SCA3 neurodegeneration phenotype is not, however, reproduced, suggesting that in the genome of these species there are other genes that are able to compensate for the lack of ATXN3. Moreover, in mutant Drosophila melanogaster, where the only JD protein is coded by a Josephin-like gene, expression of the expanded human ATXN3 gene reproduces multiple aspects of the SCA3 phenotype, in contrast with the results of the expression of the wild type human form. In order to explain these findings, phylogenetic, as well as, protein-protein docking inferences are here performed. Here we show multiple losses of JD containing genes across the animal kingdom, suggesting partial functional redundancy of these genes. Accordingly, we predict that the JD is essential for binding with ataxin-3 and proteins of the Josephin lineages, and that D. melanogaster mutants are a good model of SCA3 despite the absence of a gene from the ATXN3 lineage. The molecular recognition regions of the ataxin-3 binding and those predicted for the Josephins are, however, different. We also report different binding regions between the two ataxin-3 forms (wild-type (wt) and expanded (exp)). The interactors that show an increase in the interaction strength with exp ataxin-3, are enriched in extrinsic components of mitochondrial outer membrane and endoplasmatic reticulum membrane. On the other hand, the group of interactors that show a decrease in the interaction strength with exp ataxin-3 is significantly enriched in extrinsic component of cytoplasm.