Genetic Investigations Research Articles

Genetic landscape of primary mitochondrial diseases in children and adults using molecular genetics and genomic investigations of mitochondrial and nuclear genome.

Primary mitochondrial diseases (PMD) are one of the most common metabolic genetic disorders. They are due to pathogenic variants in the mitochondrial genome (mtDNA) or nuclear genome (nDNA) that impair mitochondrial function and/or structure. We hypothesize that there isoverlap between PMD and other genetic diseases that are mimicking PMD. For this reason, we performed a retrospective cohort study. All individuals with suspected PMD that underwent molecular genetic and genomic investigations were included. Individuals were grouped for comparison: (1) individuals with mtDNA-PMD; (2) individuals with nDNA-PMD; (3) individuals with other genetic diseases mimicking PMD (non-PMD); (4) individuals without a confirmed genetic diagnosis. 297 individuals fulfilled inclusion criteria. The diagnostic yield of molecular genetics and genomic investigations was 31.3%, including 37% forclinical exome sequencing and 15.8% formitochondrial genome sequencing. We identified 71 individuals with PMD (mtDNA n = 41, nDNA n = 30) and 22 individuals with non-PMD. Adults had higher percentage of mtDNA-PMD compared to children (p-value = 0.00123). There is a statistically significant phenotypic difference between children and adults with PMD. We report a large cohort of individuals with PMD and the diagnostic yield of urine mitochondrial genome sequencing (16.1%). We think liver phenotype might be progressive and shouldbe studied furtherin PMD. Weshowed arelationship between non-PMD genes and their indirect effects on mitochondrial machinery. Differentiation of PMD from non-PMD can be achieved using specific phenotypes as there was a statistically significant difference for muscular, cardiac, and ophthalmologic phenotypes, seizures, hearing loss, peripheral neuropathy in PMD group compared to non-PMDgroup.

Exome Sequencing in Fetuses With Bilateral Renal Agenesis Identified on Second Trimester Ultrasound: ASingle Referral Center Experience.

To determine the exome sequencing results in fetuses with bilateral renal agenesis (BRA). This was a retrospective study of 14 cases with BRA diagnosed on second trimester anatomy ultrasound. All cases underwent invasive prenatal diagnosis. Genetic investigations were performed by chromosomal microarray analysis and trio exome sequencing. Clinical and laboratory data were collected and reviewed for these cases, including maternal demographics, prenatal sonographic findings, molecular sequencing results, and pregnancy outcomes. Pathogenic and likely pathogenic variants in three genes (FRAS1, PBX1, and KMT2D) were detected by exome sequencing in 6 (6/14) cases. One gene (FRAS1) is inherited in an autosomal recessive (AR) manner and two (PBX1and KMT2D) are autosomal dominant (AD); both AD variants were de novo. Only the FRAS1 variants were detected in more than one case. Variants in five cases were believed to be the cause of BRA, and the variants detected in PBX1 and KMT2D were likely the cause of fetal phenotype suggesting that the two genes can present with BRA. The yield of exome sequencing in our series is one third (4/12) after excluding two families with a previous family history. Fraser syndrome, resulting from FRAS1 variants, is the most common cause of genetic BRA identified in this specific cohort. The determination of genetic etiology will be valuable in the possible choices for pregnancy management and risk assessment of recurrence in future pregnancies.

Abstract 4136394: Elucidation of a novel genetic substrate responsible for genetically elusive ring-like arrhythmogenic cardiomyopathy

Background: Arrhythmogenic cardiomyopathy (ACM) is a genetic heart disease characterized by fibrofatty replacement of ventricular myocardium. Arrhythmogenic left ventricular (LV) cardiomyopathy (ALVC) is a phenotypic variant of ACM predominantly involving the LV. Mutations in genes encoding for desmosome proteins and filamin C have been implicated in ALVC, especially in the setting of a ring-like late gadolinium enhancement (LGE) imaging pattern. Objective: To identify the underlying genetic substrate responsible for genetically elusive ring-like ALVC in a patient with seemingly sporadic/recessive disease. Methods: A 38-year-old male was referred for genetic investigation to determine the underlying genetic substrate responsible for his ALVC phenotype. The patient fulfilled both electrocardiographic (low voltage in the limb leads and anterolateral T-wave inversions) and imaging (>1 segment of subepicardial LGE) criteria for ALVC. Additionally, the patient experienced unexplained episodes of tachycardia, shakiness, sweating, and nausea prompting concern for an underlying neuromuscular disease. Genome sequencing (GS) was performed on DNA isolated from the affected patient and both of his unaffected parents. Variants were filtered assuming either a sporadic de novo occurrence or an autosomal recessive inheritance pattern. Results: GS identified compound heterozygous GNPTAB variants in the affected patient. A previously reported maternally derived p.Leu257Leu (c.771G>A) variant involving the last nucleotide of exon 7 of the GNPTAB gene and a novel paternally inherited Lys834fs*5 frame-shift variant were identified. The p.Leu257Leu variant has been reported to cause aberrant splicing and exon skipping of the GNPTAB mRNA transcript. Pathogenic variants in the GNPTAB encoded N-acetylglucosamine-1 (GlcNAc)-phosphotransferase subunits alpha/beta cause mucolipidosis type III, a rare recessive lysosomal storage disease characterized by coarse facial features, developmental delay, short stature, skeletal deformities, and cardiac involvement including valvular thickening and cardiomyopathy. Conclusions: Here, using a genome sequencing trio analysis we identified a compound heterozygous GNPTAB pathogenic variants as the underlying genetic substrate in a patient with ring-like ALVC and concomitant neuromuscular disease manifestation. Genome sequencing may identify the genetic etiology responsible for an otherwise undifferentiated diagnosis of cardiomyopathy.

Patellae as a source of DNA in forensic and archaeological analysis.

Analysing genetic material from skeletonised human remains has become valuable in forensic and archaeological contexts. While the petrous bone is often preferred for DNA extraction, its availability is not guaranteed, and because of destructive sampling, it is not frequently used in forensic cases. This study explores the potential of patellae as an alternative source of bone material for genetic investigations. Forty-five patellae were sampled from a post-World War II mass grave and an archaeological Christian cemetery dated from the 13th to 19th centuries. A full demineralisation extraction method was used to obtain the DNA, and real-time PCR quantification was used to determine the quantity and quality of DNA. To evaluate the suitability of patellae for forensic and archaeological analyses, short tandem repeat (STR) typing was performed using the ESI17 Fast PCR amplification kit (Promega). To explore the difference in DNA yield, DNA degradation and STR typing success between the post-World War II and archaeological patellae, statistical analysis was performed. The results revealed significantly higher DNA yield and STR typing success in WWII patellae and higher degradation of DNA in archaeological patellae, highlighting the impact of environmental exposure time on genetic material preservation. Almost all WWII patellae achieved a high success rate in STR typing with full profiles generated. More than half of the archaeological patellae showed high STR typing performance and highly informative partial profiles were obtained, indicating the suitability of patellae not only for forensic purposes but also for archaeological genetic analyses.

Lithium - Fifteen Years Later.

The 75th anniversary of introducing lithium into modern psychiatry is recognized, attested by the 1949 paper of John Cade. About this event, my editorial in the special 2010 issue of Neuropsychobiology was titled "Lithium: Sixty Years Thereafter". Since then, fifteen more years have brought further information about lithium. This paper makes a narrative review of the most important articles published in this period. The selected key literature of 2010-2024 addressed lithium prophylactic efficacy in bipolar disorder (BD), including pediatric, recurrent depression, and lithium augmentation of antidepressants in treatment-resistant depression (TRD). Novel data have been obtained for lithium adverse effects (kidney, thyroid) and beneficial outcomes of long-term lithium administration (anti-suicidal, neuroprotective, antiviral, and others). The results on the mechanisms of lithium action covered genetic investigations of the ConLiGen, and in vitro studies with induced pluripotent stem cells and lymphoblastoid cell lines. The underutilization of lithium nowadays was emphasized, and the ways to overcome it were considered. Lithium remains the choice drug for recurrence prevention in BD, also in adolescents, and a significant option for augmentation of antidepressants in TRD. The adverse side effects should be carefully followed and managed according to current guidelines. There are also beneficial lithium impacts, of which anti-suicidal and anti-dementia seem the most important. Most of the results of neurobiological studies on lithium mechanisms may be related to lithium response and some (e.g. immunomodulatory) to the pathogenesis of BD. Better education about lithium could make more patients the beneficiary of this drug.

Previously defined variants of uncertain significance may play an important role in epilepsy and interactions between certain variants may become pathogenic.

Epilepsy is a chronic neurological disorder related to various etiologies, and the prevalence of active epilepsy is estimated to be between 4 and 10 per 1000 individuals having a significant role in genetic mutations. Next-Generation Sequencing (NGS) panels are utilized for genetic testing, but a substantial proportion of the results remain uncertain and are not considered directly causative of epilepsy. This study aimed to reevaluate pediatric patients diagnosed with epilepsy who underwent genetic investigation using NGS panels, focusing on inconclusive variant findings or multiple variants of uncertain significance (VUSs). A subgroup of pediatric patients aged 0-25 years, diagnosed with epilepsy, who underwent genetic investigation with an NGS epilepsy panel at the Child Neurology Unit, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, between 2018 and 2022 through Invitae, was reevaluated. Patients with inconclusive variant findings or multiple VUSs in their test results were included. Genetic data were analyzed to identify potentially pathogenic variants and frequent genetic combinations. Two unrelated potentially pathogenic variants were identified in the SCN9A and QARS1 genes. A frequent genetic combination, RANBP2&RYR3, was also observed among other combinations. The RANBP2 gene consistently co-occurred with RYR3 variants in uncertain results, suggesting potential pathogenicity. Analysis of unaffected parents' data revealed certain combinations inherited from different parents, suggesting specific gene combinations as possible risk factors for the disease. This study highlights the importance of reevaluating genetic data from pediatric epilepsy patients with inconclusive variant findings or multiple VUSs. Identification of potentially pathogenic variants and frequent genetic combinations, such as RANBP2&RYR3, could aid in understanding the genetic basis of epilepsy and identifying potential hotspots. We have performed a retrospective analysis on a subpopulation of pediatric patients diagnosed with epilepsy. We found that specific genetic variants were repeatable, indicating their potential pathogenicity to the disease.

Ethical, Legal and Social Implications (ELSI) Regarding Forensic Genetic Investigations (FGIs)

Ethical, Legal and Social Implications (ELSI) Regarding Forensic Genetic Investigations (FGIs)

Case report: A CLCN1 complex variant mutation in exon 15 in a mixed-breed dog with hereditary myotonia

At 4 months of age, a male dog was presented with a complaint of a stiff gait following a startle response. Neurological examination revealed no deficits, but clinical myotonia was easily induced upon requesting the patient to jump. Additionally, myotonia of the upper lip muscles was observed upon manipulation. Hereditary myotonia was suspected, and electromyography confirmed the presence of myotonic potentials. Genetic testing of the myotonic patient identified a complex of mutations, including c.[1636_1639 delins AACGGG] and c.[1644 A>T], both located in exon 15 of the CLCN1 gene leading to the formation of a premature stop codon. Genetic investigations of the mother and four littermates revealed that, except for one littermate who was wild type, all others carried a copy of the mutated gene. To the best of the authors' knowledge, these mutations have not been previously reported.

Prevalence and Genetic Variation Investigation of the Pseudorabies Virus in Southwest China.

In 2022, a significant PRV outbreak in a southwestern China pig farm led to a high incidence of sow abortion. A serological analysis using gE antigen-based ELISA revealed a high prevalence (69.30%) of PRV gE antibodies among the affected pigs, with a significant variation across different pig populations (1.11-76.12%). We collected additional 5552 pig serum samples and 580 pig cerebrospinal fluid (CSF) samples from various pig farms in Southwest China between 2022 and 2024. The seropositive rates for PRV gE antibodies ranged from 2.36% and 8.65% in the serum samples, while the positive detection rates for the PRV gE gene in the cerebrospinal fluid samples, as determined by PCR, were between 1.06% and 2.36%. The PCR analysis and sequencing of the PRV gB, gC, gE, and TK genes from eight randomly selected samples identified two distinct strains, CQ1 and CQ2. CQ1's gC gene showed similarity to the vaccine strain Bartha, while the other genes aligned with Chinese classical strains, suggesting its potential genetic recombination. CQ2 aligned with the Chinese classical strain SC. Although the overall PRV infection in Southwest China's pig farms is relatively low, occasional outbreaks with high positivity rates are observed. These findings highlight the necessity for increased surveillance and stringent control measures to safeguard the swine industry.

Genetic investigations in cerebral palsy.

https://onlinelibrary.wiley.com/doi/10.1111/dmcn.16080

Intragenic duplication disrupting the reading frame of MFSD8 in Small Swiss Hounds with neuronal ceroid lipofuscinosis.

Neuronal ceroid lipofuscinosis (NCL) represents a heterogenous group of lysosomal storage diseases resulting in progressive neurodegeneration. We investigated two Small Swiss Hound littermates that showed progressive ataxia and loss of cognitive functions and vision starting around the age of 12 months. Both dogs had to be euthanized a few months after the onset of disease owing to the severity of their clinical signs. Pathological investigation of one affected dog revealed cerebral and cerebellar atrophy with cytoplasmic accumulation of autofluorescent material in degenerating neurons. The clinical signs in combination with the characteristic histopathology led to a tentative diagnosis of NCL. In the subsequent genetic investigation, the genome of one affected dog was sequenced. This revealed a duplication of 18 819 bp within the MFSD8 gene. The duplication breakpoints were located in intron 3 and exon 12 of the gene and were predicted to disrupt the reading frame. Both affected dogs carried the duplication in a homozygous state and there was perfect cosegregation of the genotypes with the phenotype in a large pedigree, consistent with autosomal recessive inheritance. MFSD8 loss-of-function variants are a known cause of NCL7 in human patients, dogs and other mammalian species. The existing knowledge on MFSD8 together with the experimental data strongly suggests that the identified intragenic MFSD8 duplication caused the disease in the Small Swiss Hounds. These results allow their diagnosis to be refined to NCL7 and enable genetic testing in the breed to avoid further unintentional carrier × carrier matings.

Population Genetic Investigation of Hypophthalmichthys nobilis in the Yangtze River Basin Based on RAD Sequencing Data.

The Bighead carp (Hypophthalmichthys nobilis), a primary freshwater aquaculture species in China, faces challenges due to over-exploitation and environmental changes. We leveraged RAD-seq to perform a comprehensive population genetic analysis on 14 H. nobilis populations sampled from the Yangtze River (13 populations) and the Marseilles Reach of the Illinois River (one population). Analysis of genetic diversity showed that different parameters demonstrated varied inferences, and notably, Zhongxian (ZX2), Wanhzou (WZ2), Yangzhou hatchery (YZYZ), Yangzhou (YZ), and Taihu (TH) populations showed apparent heterozygote deficiency. Linkage disequilibrium (LD) analysis exhibited a trend of higher linkage disequilibrium in populations from the upper reaches of the Yangtze River, followed by those from the middle reaches and then those from the lower reaches. Additionally, the reconstructed polygenetic tree and PCA plot clustered all populations into 2 major subgroups, while the results of structure analysis indicated 4 ancestors. The pairwise FST values ranged from 0 to 0.5530. Among these, high FST values (0.1931-0.5530) were only observed between populations WZ2, YZ, YZYZ, and the remaining 11 populations. Furthermore, genetic bottlenecks were observed in all populations 20-30 thousand years ago. Overall, the research offers insights essential for genetic management practices for sustainable aquaculture and biodiversity conservation of bighead carp.

Unraveling the Genetic Puzzle: Could MAP3K7 Be a Candidate Gene for RASopathies? Case Presentation.

Noonan Syndrome (NS) diagnosis is challenging due to diverse clinical manifestations. Here, our case report highlights MAP3K7's novel role in NS. A 10.4-year-old female patient presented with short stature and suggestive clinical findings of RASopathy. Despite atypical facial features, the patient met two major diagnostic criteria of Van der Burgt.Initial genetic testing for known NS-associated genes did not find any variants. Later, whole exome sequencing (WES) discovered a unique de novo heterozygous variant (c.65C>A, p.(P22H)) in the MAP3K7. This variant, categorized as a variant of uncertain significance (VUS) by the American College of Medical Genetics and Genomics (ACMG) criteria, raised questions about its potential role in NS. The patient's clinical presentation deviated from classical manifestations of MAP3K7-associated syndromes, underscoring the genetic and molecular mechanisms' complexity. Notably, this is the first case reported to associate MAP3K7 variants with NS, advancing knowledge of the condition's genetic causes. Despite challenges in NS diagnosis, proper management, including recombinant growth hormone therapy, is crucial for optimizing growth potential. The case underscores MAP3K7 as a potential candidate gene for NS, and more functional genetic investigations are required to clarify the delicate interaction between genetic abnormalities, the RAS/MAPK pathway, and clinical manifestations observed in NS cases.

Expanding the genetic spectrum of hereditary motor sensory neuropathies in Pakistan

BackgroundHereditary motor and sensory neuropathy (HMSN) refers to a group of inherited progressive peripheral neuropathies characterized by reduced nerve conduction velocity with chronic segmental demyelination and/or axonal degeneration. HMSN is highly clinically and genetically heterogeneous with multiple inheritance patterns and phenotypic overlap with other inherited neuropathies and neurodegenerative diseases. Due to this high complexity and genetic heterogeneity, this study aimed to elucidate the genetic causes of HMSN in Pakistani families using Whole Exome Sequencing (WES) for variant identification and Sanger sequencing for validation and segregation analysis, facilitating accurate clinical diagnosis.MethodsFamilies from Khyber Pakhtunkhwa with at least two members showing HMSN symptoms, who had not previously undergone genetic analysis, were included. Referrals for genetic investigations were based on clinical features suggestive of HMSN by local neurologists. WES was performed on affected individuals from each family, with Sanger sequencing used to validate and analyze the segregation of identified variants among family members. Clinical data including age of onset were assessed for variability among affected individuals, and the success rate of genetic diagnosis was compared with existing literature using proportional differences and Cohen’s h.ResultsWES identified homozygous pathogenic variants in GDAP1 (c.310 + 4 A > G, p.?), SETX (c.5948_5949del, p.(Asn1984Profs*30), IGHMBP2 (c.1591 C > A, p.(Pro531Thr) and NARS1 (c.1633 C > T, p.(Arg545Cys) as causative for HMSN in five out of nine families, consistent with an autosomal recessive inheritance pattern. Additionally, in families with HMSN, a SETX variant was found to cause cerebellar ataxia, while a NARS1 variant was linked to intellectual disability. Based on American College of Medical Genetics and Genomics criteria, the GDAP1 variant is classified as a variant of uncertain significance, while variants in SETX and IGHMBP2 are classified as pathogenic, and the NARS1 variant is classified as likely pathogenic. The age of onset ranged from 1 to 15 years (Mean = 5.13, SD = 3.61), and a genetic diagnosis was achieved in 55.56% of families with HMSN, with small effect sizes compared to previous studies.ConclusionsThis study expands the molecular genetic spectrum of HMSN and HMSN plus type neuropathies in Pakistan and facilitates accurate diagnosis, genetic counseling, and clinical management for affected families.

Comprehensive Transcriptomic Analysis Reveals Defense-Related Genes and Pathways of Rice Plants in Response to Fall Armyworm (Spodoptera frugiperda) Infestation.

Rice (Oryza sativa L.) serves as a substitute for bread and is a staple food for half of the world's population, but it is heavily affected by insect pests. The fall armyworm (Spodoptera frugiperda) is a highly destructive pest, threatening rice and other crops in tropical regions. Despite its significance, little is known about the molecular mechanisms underlying rice's response to fall armyworm infestation. In this study, we used transcriptome analysis to explore the global changes in gene expression in rice leaves during a 1 h and 12 h fall armyworm feeding. The results reveal 2695 and 6264 differentially expressed genes (DEGs) at 1 and 12 h post-infestation, respectively. Gene Ontology (GO) and KEGG enrichment analyses provide insights into biological processes and pathways affected by fall armyworm feeding. Key genes associated with hormone regulation, defense metabolic pathways, and antioxidant and detoxification processes were upregulated, suggesting the involvement of jasmonic acid (JA) signaling, salicylic acid biosynthesis pathways, auxin response, and heat shock proteins in defense during 1 h and 12 h after fall armyworm infestation. Similarly, key genes involved in transcriptional regulation and defense mechanisms reveal the activation of calmodulins, transcription factors (TFs), and genes related to secondary metabolite biosynthesis. Additionally, MYB, WRKY, and ethylene-responsive factors (ERFs) are identified as crucial TF families in rice's defense response. This study provides a comprehensive understanding of the molecular dynamics in rice responding to fall armyworm infestation, offering valuable insights for developing pest-resistant rice varieties and enhancing global food security. The identified genes and pathways provide an extensive array of genomic resources that can be used for further genetic investigation into rice herbivore resistance. This also suggests that rice plants may have evolved strategies against herbivorous insects. It also lays the groundwork for novel pest-resistance techniques for rice.

Uncovering underlying cause for heart failure in a 51-year-old woman with fibromuscular dysplasia

Abstract Introduction/Objective Arrhythmogenic cardiomyopathy is a rare disorder characterized by the replacement of the myocardium with fibroadipose tissue, usually affecting the right ventricle and rarely affecting the left. Methods/Case Report We present the case of a 51-year-old woman with past medical history including fibromuscular dysplasia of the internal carotid arteries and suspected ischemic cardiomyopathy with reduced ejection fraction awaiting heart transplant. The patient suffered a spontaneous coronary artery dissection eight years prior, which was the inciting factor that led to the decline in her cardiac function. After transplant, gross examination of the explanted heart showed a moderate amount of epicardial fat and visible intramural ventricular adipose tissue deposits in the myocardium. On histology, both the right and left ventricle walls showed extensive microscopic fatty infiltration along with focal involvement of the interventricular septum. These findings supported the final diagnosis of arrhythmogenic cardiomyopathy of the right and left ventricle, as well as involvement of the interventricular septum making this case especially rare. There were no signs of infarct or ischemic damage, contrary to what was expected given her diagnosis of ischemic cardiomyopathy. Results (if a Case Study enter NA) NA Conclusion The pathological work-up of this case shed light on the true nature of the patient’s cardiomyopathy and has prompted further genetic testing, as arrhythmogenic cardiomyopathy can be caused by several different genetic mutations. In addition to this work-up, a thorough literature review was performed looking for connections between arrhythmogenic cardiomyopathy and fibromuscular dysplasia, as arrhythmogenic cardiomyopathy is not often seen in this setting. Although no direct connection between the two was uncovered, it was found in the literature that a polymorphism in the Phosphatase and Actin Regulator 1 (PHACTR1) gene has been identified as a genetic component of fibromuscular dysplasia. This variant has been linked to spontaneous coronary artery dissection, which our patient experienced at the young age of 43. This could prompt further genetic investigation into her fibromuscular dysplasia in addition to the genetic work up already being done for her arrhythmogenic cardiomyopathy. This case highlights how rare etiologies can be uncovered through diligent histological analysis, and how further analysis using laboratory techniques such as genetic testing can help patients understand the full breadth of their conditions.

A Comparative Analysis of Models for AAV-Mediated Gene Therapy for Inherited Retinal Diseases.

Inherited retinal diseases (IRDs) represent a diverse group of genetic disorders leading to progressive degeneration of the retina due to mutations in over 280 genes. This review focuses on the various methodologies for the preclinical characterization and evaluation of adeno-associated virus (AAV)-mediated gene therapy as a potential treatment option for IRDs, particularly focusing on gene therapies targeting mutations, such as those in the RPE65 and FAM161A genes. AAV vectors, such as AAV2 and AAV5, have been utilized to deliver therapeutic genes, showing promise in preserving vision and enhancing photoreceptor function in animal models. Despite their advantages-including high production efficiency, low pathogenicity, and minimal immunogenicity-AAV-mediated therapies face limitations such as immune responses beyond the retina, vector size constraints, and challenges in large-scale manufacturing. This review systematically compares different experimental models used to investigate AAV-mediated therapies, such as mouse models, human retinal explants (HREs), and induced pluripotent stem cell (iPSC)-derived retinal organoids. Mouse models are advantageous for genetic manipulation and detailed investigations of disease mechanisms; however, anatomical differences between mice and humans may limit the translational applicability of results. HREs offer valuable insights into human retinal pathophysiology but face challenges such as tissue degradation and lack of systemic physiological effects. Retinal organoids, on the other hand, provide a robust platform that closely mimics human retinal development, thereby enabling more comprehensive studies on disease mechanisms and therapeutic strategies, including AAV-based interventions. Specific outcomes targeted in these studies include vision preservation and functional improvements of retinas damaged by genetic mutations. This review highlights the strengths and weaknesses of each experimental model and advocates for their combined use in developing targeted gene therapies for IRDs. As research advances, optimizing AAV vector design and delivery methods will be critical for enhancing therapeutic efficacy and improving clinical outcomes for patients with IRDs.

BEACH domain-containing protein SPIRRIG facilitates microtubule cytoskeleton-associated trichome morphogenesis in Arabidopsis.

Our studies reveal the involvement of SPI in cytoskeleton-associated trichome morphogenesis, expanding the roles of SPI in regulating plant epidermal celldevelopment. Acquisition of distinct shapes is crucial for cells to perform their biological functions in multicellular organisms. Trichomes are specialized epidermal cells of plant aerial parts, offering an excellent paradigm for dissecting the underlying regulatory mechanism of plant cell shape development at the single-cell level. SPIRRIG (SPI) that encodes a BEACH domain-containing protein was initially identified to regulate trichome branch extension, but the possible pathway(s) through which SPI regulates trichome morphogenesis remain unclear. Here, we report that SPI facilitates microtubule-associated regulation on trichome branching in Arabidopsis. Functional loss of SPI results in trichome morphogenesis hyper-sensitive to the microtubule-disrupting drug oryzalin, implying SPI may mediate microtubule stability during trichome development. Accordingly, spi mutant has less-branched trichomes. Detailed live-cell imaging showed that the spatio-temporal microtubule organization during trichome morphogenesis is aberrant in spi mutants. Further genetic investigation indicated that SPI may cooperate with ZWICHEL (ZWI) to modulate microtubule dynamics during trichome morphogenesis. ZWI encodes a kinesin-like calmodulin-binding protein (KCBP), whose distribution is necessary for the proper microtubule organization in trichomes, and zwi mutants produce less-branched trichomes as well. Trichome branching is further inhibited in spi-3 zwi-101 double mutants compared to either of the single mutant. Moreover, we found SPI could co-localize with the MYTH4 domain of ZWI. Taken together, our results expand the role of SPI in regulating trichome morphogenesis and also reveal a molecular and genetic pathway in plant cell shape formation control.

Pure wild forest reindeer (Rangifer tarandus fennicus) or hybrids? A whole-genome sequencing approach to solve the taxonomical status

AbstractIn Finland, the geographic distribution of domestic reindeer (Rangifer tarandus tarandus) and Finnish wild forest reindeer (Rangifer tarandus fennicus) partly overlap in the vicinity of the southern border of the reindeer herding area. Additionally, domestic reindeer are occasionally kept as pets within the distribution range of the wild forest reindeer. Hybridisation of these two subspecies is one of the major threats for the wild forest reindeer population. Concerns about potential hybridisation served as the catalyst also for this study, which we aimed to clarify the taxonomic status of presumed wild forest reindeer individuals intended as founder individuals for a reintroduction project. To do this, we resequenced genomes of four Rangifer tarandus individuals with unknown taxonomical status and investigated their ancestries by comparing the genomic data with the existing resequenced data of the Finnish domestic reindeer and Finnish wild forest reindeer. The genetic relationship investigations indicated that all individuals we analysed were pure wild forest reindeer, making them suitable as founder individuals for the reintroduction project. Thus, our study provided critical knowledge for practical conservation action, where it was essential to recognise each individual’s origin. In the future, it will also offer novel insights into the spread of native wild forest reindeer to new geographic regions in Finland. For subsequent studies, additional resequenced genomic data of Rangifer individuals will be needed to develop an ancestry information marker panel of single nucleotide polymorphisms for rapid and cost-effective identification of hybrid individuals of these subspecies.

Comprehensive mutational profiling identifies new driver events in cutaneous leiomyosarcoma.

Cutaneous leiomyosarcoma (cLMS) is a rare soft tissue neoplasm, showing smooth muscle differentiation, that arises from the mesenchymal cells of the dermis. To-date, genetic investigation of these tumours has involved studies with small sample sizes and limited analyses that identified recurrent somatic mutations in RB1 and TP53, copy number gain of MYCOD and IGF1R, and copy number loss of PTEN. To better understand the molecular pathogenesis of cLMS, we comprehensively explored the mutational landscape of these rare tumours to identify candidate driver events. In this retrospective, multi-institutional study, we performed whole-exome sequencing and RNA sequencing on 38 cases of cLMS. TP53 and RB1 were identified as significantly mutated, thus, represent validated driver genes of cLMS. COSMIC mutational signatures SBS7a/b and DBS1 were recurrent, thus, ultraviolet light exposure may be an aetiological factor driving cLMS. Analysis of significantly recurrent somatic copy number alterations, which represent candidate driver events, found focal (<10Mb) deletions encompassing TP53 and KDM6B, and amplifications encompassing ZMYM2, MYOCD, MAP2K4 and NCOR1. A larger (24 Mb) recurrent deletion encompassing CYLD was also identified as significant. Significantly recurrent broad copy number alterations, involving at least half of a chromosome arm, included deletions of 6p/q, 10p/q, 11q, 12q, 13q and 16p/q, and amplification of 15q. Notably PTEN is located on 10q, RB1 on 13q and IGFR1 on 15q. Fusion gene analysis identified recurrent CRTC1/3::MAML2 fusions, as well as many novel fusions in individual samples. Our analysis of the largest number of cLMS cases to-date highlights the importance of large cohort sizes and the exploration beyond small targeted gene panels when performing molecular analyses, as it allowed a comprehensive exploration of the mutational landscape of these tumours and identification of novel candidate driver events. It also uniquely afforded the opportunity to compare the molecular phenotype of cLMS with LMS of other tissue types, such as uterine and soft tissue LMS. Given that molecular profiling has resulted in the development of novel targeted treatment approaches for uterine and soft tissue LMS, our study now allows the same opportunities to become available for patients with cLMS.