Variable Expression Research Articles

Split Hand-Foot Malformations-Unveiling Unique Molecular Diagnosis From a Brazilian Cohort.

Split hand-foot malformation (SHFM) is a congenital limb malformation affecting primarily the central rays of the hands and/or feet, with variable expressivity, incomplete penetrance and syndromic forms. It is genetically heterogeneous, including point mutations and structural variants in different loci. Five individuals with SHFM were clinically evaluated in a Tertiary Center in Brazil: four of them presented additional, nonskeletal findings, including one individual with split foot, hand syndactyly, and ectodermal findings. Structural variants and point mutations in genes associated with SHFM were identified in all individuals. Our results highlight genetic heterogeneity observed in this group of skeletal disorders, alongside incomplete penetrance, a challenging task imposed on genetic counseling. Of note, an individual harboring a recurrent heterozygous variant in MAP3K20 presented a phenotype reminiscent of TP63-related disorders, contrary to the one recently reported in the literature with prominent facial dysmorphisms, expanding the phenotypic spectrum of this newly recognized syndromic form of SHFM.

Two Novel Biallelic Variants in the FARSA Gene: The First Italian Case and a Literature Review

Background/Objectives: The FARSA gene encodes for the catalytic α subunit of Cytoplasmic phenylalanine-tRNA synthetase (FARS1), an essential enzyme for protein biosynthesis in transferring its amino acid component to tRNAs. Biallelic pathogenic variants have been associated with a multisystemic condition, characterized by variable expressivity and incomplete penetrance. Here, we report the case of an 11 year-old girl presenting interstitial lung disease, supratentorial leukoencephalopathy with brain cysts, hepatic dysfunction, hypoalbuminemia, skin and joint hyperlaxity, growth retardation, and dysmorphic features. In addition, our patient also developed two clinical features never reported before: hypergammaglobulinemia and myopic chorioretinitis. Methods: NGS analysis of the patient’s skin-derived DNA revealed two novel biallelic variants in FARSA gene (NM_004461.3) never described before: the maternal nonsense variant, c.799C>T [p.(Gln267Ter)], and the paternal missense variant, c.737T>C [p.(Met246Thr)], both predicted as deleterious. Results: From a therapeutic perspective, this young girl has been enrolled in a clinical trial with Nintedanib, in order to treat the severe pulmonary fibrosis, with interesting initial results. Conclusions: Our findings expand the clinical and molecular spectrum of the FARSA-related phenotype and introduce new cues on lung fibrosis treatment in pediatric age.

Identifying key factors for recurrence of genetic disorder: insights from Indian families with multiple affected children.

This study investigates the factors contributing to the recurrence of severe genetic conditions in multiple children of the same couple, focusing on a cohort of 26 families who had more than one child affected by the same genetic disorder. Conducted at a genetic clinic in India, the study employed a qualitative methodology guided by COREQ guidelines, using semi-structured interviews to explore the interplay of individual beliefs, healthcare provider practices, and systemic healthcare inefficiencies. The interviews were transcribed and analyzed using a combination of content analysis and grounded theory, which allowed for the identification of recurrent themes and emerging ideas. The study found that strong religious and cultural beliefs often led families to disregard medical advice, contributing to the recurrence of genetic conditions. Additionally, significant gaps in healthcare provider knowledge and inadequate reproductive counseling were identified as critical barriers to timely diagnosis and prevention of recurrence. Another major theme was the inherent complexities of genetic diseases and genetic testing, where variable expression of conditions, delayed symptom onset, and limitations of genetic tests themselves often prevented early diagnosis and intervention. This research highlights the need for improved genetic literacy among healthcare providers, culturally sensitive counseling, and better integration of genetic services into the broader healthcare system. By addressing these barriers, the risk of recurrence can be significantly reduced, improving patient outcomes and family well-being. This study is one of the few in India to analyze such factors and underscore the critical need for targeted interventions at multiple levels.

A molecular and immunohistochemical study of 37 cases of ovarian Sertoli-Leydig cell tumor.

This study provides an analysis of 37 ovarian Sertoli-Leydig cell tumors (SLCT), focusing on their morphological, immunohistochemical, and molecular features. The cohort was comprised of 9 well-differentiated, 25 moderately differentiated, and 3 poorly differentiated tumors. The immunohistochemical analysis was performed with 28 markers, including diagnostic markers and markers with possible predictive significance. The results showed high expression of sex cord markers (FOXL2, SF1, inhibin A, CD99, calretinin, ER, PR, AR), and variable expression of other markers such as CKAE1/3 (83%), CAIX (14%), and MUC4 (1%). Loss of PTEN expression was present in 14% of cases, and CTLA4 expression was seen in 43% of cases. All tumors were MMR proficient and HER2 and PD-L1 negative. The molecular analysis showed DICER1 mutations in 54.5% of cases, and a FOXL2 mutation in 6% of tumors. In addition, we detected 2 cases with TERT promoter mutation. RNA NGS sequencing identified significant differences in mRNA expression between DICER1MUT and DICER1WT tumors. The DICER1WT tumors showed increased expression of PRKCA, HNF1A, LDLR, and MAP2K5. On the contrary, the DICER1MUT cases showed increased expression of CDK6, NOTCH2, and FGFR2. The results of our study show that SLCTs exhibit distinct molecular features based on their degree of differentiation. We have confirmed that DICER1 mutations are characteristic of moderately and poorly differentiated SLCTs, while well-differentiated SLCTs may represent a distinct entity. DICER1MUT and DICER1WT tumors showed different mRNA expression profiles. The FOXL2 mutation is less common in these tumors and is mutually exclusive with the DICER1 mutation.

Locational marginal pricing of energy in pipeline transport of natural gas and hydrogen with carbon offset incentives

We propose an optimization formulation for locational pricing of energy transported through a pipeline network that carries mixtures of natural gas and hydrogen from distributed sources to consumers. The objective includes the economic value provided by the pipeline to consumers of energy and suppliers of natural gas and green hydrogen, as well as incentives to lower carbon emissions by consuming the latter instead of the former. The optimization is subject to the physics of gas flow and mixing in the pipeline network as well as engineering limits. In addition to formulating this mathematical program, we synthesize the Lagrangian and derive analytical expressions for the dual variables. We propose that the dual solution can be used to derive locational marginal prices of natural gas, hydrogen, and energy, as well as the decarbonization premium paid by consumers that receive hydrogen. We derive several properties of solutions obtained using the proposed market mechanism, and demonstrate them using case studies for standard 8-node and 40-node pipeline test networks. Finally, we show that optimization-based analysis of the type proposed here is critical for making sound decisions about economic policy and infrastructure expansion for blending green hydrogen into existing natural gas pipelines.

Epigenetics of cardiomyopathies: the next frontier.

Cardiomyopathies (CMP) are a diverse group of myocardial diseases that cause structural, functional, and pathological changes to the heart. Alterations at the molecular level associated with the clinical phenotype and progression of CMPs cannot be solely explained by the genetic mutations, even in inherited cardiomyopathies. Epigenetics and environmental factors are likely to significantly modify the clinical manifestations of CMPs, resulting in variable clinical expression and different age-related penetrance. This review examines the role of dysfunctional DNA methylation, histone modifications, chromatin remodelling, and noncoding RNAs in the development and exacerbation of CMPs, highlighting their potential as diagnostic markers and therapeutic targets, including the use of histone deacetylase inhibitors. Additionally, it explores how environmental exposures can influence epigenetic changes and potentially be used for preventive strategies and personalized care in CMP patients. Monozygotic twin studies and intergenerational studies are discussed as valuable tools for understanding the interplay between genetics, epigenetics, and environmental factors. Lastly, this review addresses current challenges and future perspectives, such as the need for greater specificity in epigenetic therapies, minimizing off-target effects, and investigating sex differences in CMP research and treatment.

Oxidative/Nitrosative Stress and Brain Involvement in Sepsis: A Relationship Supported by Immunohistochemistry

Background and Objectives: A large amount of recent evidence suggests that cellular inability to consume oxygen could play a notable part in promoting sepsis as a consequence of mitochondrial dysfunction and oxidative stress. The latter could, in fact, represent a fundamental stage in the evolution of the “natural history” of sepsis. Following a study previously conducted by the same working group on heart samples, the present research project aims to evaluate, through an immunohistochemical study, the existence and/or extent of oxidative stress in the brains of subjects who died due to sepsis and define, after reviewing the literature, its contribution to the septic process to support the use of medications aimed at correcting redox anomalies in the management of septic patients. Materials and Methods: 10 cases of subjects who died in healthcare facilities with ante-mortem clinical-laboratory signs that allowed the diagnosis of septic shock were selected as case studies, and 1 case of a subject who died immediately following a road traffic accident was used as a negative control. Samples of the cerebral cortex were then taken, fixed in formalin, and subjected to sections on which an immunohistochemical study was performed using anti-NOX-2, NT, iNOS, and 8-OHdG antibodies. Results: The results emerging from the present study demonstrate that despite a variable expressivity for the NT, iNOS, and NOX2 markers, the brain samples demonstrated univocal and high positivity for the 8-OHdG marker. Conclusions: This would allow us to hypothesize how, regardless of the mechanism of production of ROS and NOS (iNOS or NOX2 mediated) and the pathophysiological mechanisms that are triggered during sepsis, oxidative damage to DNA represents the event to which this whole process leads and, in fact, in the literature, is directly correlated to sepsis-dependent mortality. Neurons, conversely, appear to be more sensitive to oxidative stress because of a low number of protective or scavenger molecules (catalase, glutathione peroxidase, GSH, or vitamin E). Therefore, despite reduced production, the manifestation of the damage remains high. This evidence, together with that of the previous study, can only support the introduction of substances with an antioxidant function in the guidelines for the treatment of sepsis.

Multilineage Pituitary Neuroendocrine Tumors Expressing TPIT and SF1: A Clinicopathological Series of Six Tumors.

Tumors of adenohypophysial hormone-secreting cells, now classified as pituitary neuroendocrine tumors (PitNETs), have been subclassified based on cell differentiation. Normal adenohypophysial cells have three lineages of differentiation driven by the transcription factors PIT1, TPIT, and SF1 which are responsible for the regulation of hormone gene expression; PIT1 drives expression of GH, PRL, and TSH, TPIT is required for POMC expression that gives rise to ACTH, and SF1 is the transcription factor responsible for FSH and LH expression. The vast majority of PitNETs follow these three lineage differentiation pathways but rare PitNETs show either no lineage differentiation or express biomarkers of more than one lineage. The recent WHO classification continued the terminology "plurihormonal" for tumors that have features of more than one lineage but a better term is "multilineage" since some tumors may express more than one lineage-specific transcription factor without the hormones that are driven by those factors. Recent data indicate that tumors with expression of PIT1 and SF1 are the most common multilineage PitNETs. Here we report the existence of rare PitNETs that express TPIT and SF1. The 6 patients (5 female, 1 male; mean age 54.8years; range 35-84years) represent less than 1% of patients in our series of PitNETs. Most patients had clinically silent tumors with no evidence of hormone excess and variable degrees of hypopituitarism; two had Cushing disease. All patients had macrotumors with a mean tumor size of 2.46cm (range 1.1-5.0cm). Crooke's hyaline change was identified in the nontumorous adenohypophysis of the two patients with Cushing disease. The mean Ki67 labeling index was 2.91% (range 2.03-3.94%). All tumors were negative for PIT1 and PIT1-lineage hormones (GH, PRL, and TSH). TPIT was focal in one tumor, and the remaining tumors had diffuse reactivity in more than 50% of tumor cells. SF1 expression was focal in 5 tumors and diffuse in one. Three tumors had variable expression of at least one gonadotropin (FSH or LH). GATA3 was expressed in two tumors. Variable ER-alpha expression was noted in three tumors. CAM5.2 was positive in all tumors. With the exception of two tumors causing Cushing disease, p27 expression was intact. Our study confirms that multilineage PitNETs expressing TPIT and SF1 occur but are extremely rare; they can be clinically non-functional or can cause Cushing disease. Irrespective of functional status of a PitNET, routine application of pituitary transcription factors is warranted to identify these tumors. Data on the molecular correlates and clinical significance are still needed for these rare multilineage PitNETs.

Identifying spatially variable genes by projecting to morphologically relevant curves.

Spatial transcriptomics enables high-resolution gene expression measurements while preserving the two-dimensional spatial organization of the sample. A common objective in spatial transcriptomics data analysis is to identify spatially variable genes within predefined cell types or regions within the tissue. However, these regions are often implicitly one-dimensional, making standard two-dimensional coordinate-based methods less effective as they overlook the underlying tissue organization. Here we introduce a methodology grounded in spectral graph theory to elucidate a one-dimensional curve that effectively approximates the spatial coordinates of the examined sample. This curve is then used to establish a new coordinate system that better reflects tissue morphology. We then develop a generalized additive model (GAM) to detect genes with variable expression in the new morphologically relevant coordinate system. Our approach directly models gene counts, thereby eliminating the need for normalization or transformations to satisfy normality assumptions. We demonstrate improved performance relative to current methods based on hypothesis testing, while also accurately estimating gene expression patterns and precisely identifying spatial loci where deviations from constant expression are observed. We validate our approach through extensive simulations and by analyzing experimental data from multiple platforms such as Slide-seq and MERFISH.

The interaction between a piezoelectric screw dislocation and collinear rigid lines in one-dimensional hexagonal quasicrystals

The interaction between a piezoelectric screw dislocation and collinear rigid lines in one-dimensional (1D) hexagonal quasicrystals (QCs) under anti-plane mechanical and in-plane electrical loading is analysed. Two idealized electrical assumptions, namely electrically conductive and dielectric, are considered. By using Muskhelishvilid’s complex transformation method, the explicit expressions for the field variables, the singularity of the field variables at the line tip and the force on the dislocation are obtained for a single rigid line. Based on the generalized Peach–Koehler formula, the generalized stress intensity factors and image force on dislocations in piezoelectric quasicrystal (PQC) are obtained. It is evident that the existence of phason field has an effect on image force.

Fetal Presentation of MYRF-Related Cardiac Urogenital Syndrome: An Emerging and Challenging Prenatal Diagnosis.

MYRF-related cardiac-urogenital syndrome (MYRF-CUGS) is a rare condition associated with heterozygous MYRF variants. The description of MYRF-CUGS phenotype is mostly based on postnatal cases and 36 affected individuals have been published so far. We aim now to delineate the prenatal phenotype of MYRF-CUGS by reporting clinical data from fetuses and neonates with a pathogenic MYRF variant. Detailed radiographic, pathological, clinical, and molecular data from 12 prenatal cases were collected through an international collaborative study. Adding the five fetuses previously published, we were able to study a cohort of 17 cases. Main ultrasound-accessible manifestations of MYRF-CUGS include congenital heart defects (13/17, 76%), congenital diaphragmatic hernia (10/17, 59%) and disorders of sexual differentiation in 46, XY fetuses (7/14; 50%). Postnatal examination and/or autopsy data highlighted additional birth defects and neurological findings with a large spectrum of severity. Molecular results revealed ten previously unpublished variants, one missense and nine predicted truncating variants (three frameshift, three nonsense and three splice site variants). We report the first prenatal cohort of MYRF-CUGS, allowing us to further characterize the variable expressivity of this rare disorder in fetuses. Severe congenital anomalies with a poor prognosis are more frequent than previously described in postnatal cases. Our data suggest that MYRF-CUGS is characterized by a recurrent recognizable malformative association, accessible to prenatal diagnosis, with a significant intrafamilial phenotypic variability making genetic counseling challenging.

The dynamic transcriptome reveals response patterns to black shank disease in tobacco (Nicotiana tabacum L.)

Black shank disease, caused by Phytophthora nicotianae, is one of the major causes of yield loss in tobacco production. The present study aimed to explore the dynamic transcriptome in tobacco genotypes resistant or susceptible to black shank disease and to understand the defense response of tobacco to P. nicotianae infection. Roots and stems were sampled from two resistant and two susceptible materials at 0, 12, 24, 48, and 72 h post infection and used in RNA-sequencing. Conventional approaches that identify differentially expressed genes are not the best way for handling the complex datasets, so a new method that calculates the standard deviation among samples was applied to identify transcripts with variable expression levels in roots and stems of the four materials at different time points. Of the total of 229,501 transcripts, 7,261 were found to be variable transcripts, with many of them annotated to be related to defense responses against pathogen infection. These variable transcripts showed expression patterns that varied significantly between roots and stems as well as between the resistant and the susceptible materials. Several transcripts were identified to be potential candidates for further functional characterization. Our findings provide invaluable insights into the dynamic transcriptome in defense responses of tobacco against P. nicotianae infection.

Analysis of genotype effects and inter-individual variability in iPSC-derived trisomy 21 neural progenitor cells.

Trisomy of human chromosome 21 (T21) gives rise to Down syndrome (DS), the most frequent live-born autosomal aneuploidy. T21 triggers genome-wide transcriptomic alterations that result in multiple atypical phenotypes with highly variable penetrance and expressivity in individuals with DS. Many of these phenotypes, including atypical neurodevelopment, emerge prenatally. To enable in vitro analyses of the cellular and molecular mechanisms leading to the neurological alterations associated with T21, we created and characterized a panel of genomically diverse T21 and euploid induced pluripotent stem cells (iPSCs). We subsequently differentiated these iPSCs to generate a panel of neural progenitor cells (NPCs). Alongside characterizing genotype effects from T21, we found that T21 NPCs showed inter-individual variability in growth rates, oxidative stress, senescence characteristics, and gene and protein expression. Pathway enrichment analyses of T21 NPCs identified vesicular transport, DNA repair, and cellular response to stress pathways. These results demonstrate T21-associated variability at the cellular level and suggest that cell lines from individuals with DS should not solely be analyzed as a homogenous population. Examining large cohorts of genetically diverse samples may more fully reveal the effects of aneuploidy on transcriptomic and phenotypic characteristics in T21 cell types. A panel of genomically diverse T21 and euploid induced pluripotent stem cells (iPSCs) were created and subsequently differentiated into neural progenitor cells (NPCs). T21 NPCs showed reduced growth, increased oxidative stress, and inter-individual variability in gene and protein expression. This inter-individual variability suggests that studies with large cohorts of genetically diverse T21 samples may more fully reveal the effects of aneuploidy.

Bidirectional Risk Modulator and Modifier Variant of Dilated and Hypertrophic Cardiomyopathy in BAG3

The genetic factors that modulate the reduced penetrance and variable expressivity of heritable dilated cardiomyopathy (DCM) are largely unknown. BAG3 genetic variants have been implicated in both DCM and hypertrophic cardiomyopathy (HCM), nominating BAG3 as a gene that harbors potential modifier variants in DCM. To interrogate the clinical traits and diseases associated with BAG3 coding variation. This was a cross-sectional study in the Penn Medicine BioBank (PMBB) enrolling patients of the University of Pennsylvania Health System's clinical practice sites from 2014 to 2023. Whole-exome sequencing (WES) was linked to electronic health record (EHR) data to associate BAG3 coding variants with EHR phenotypes. This was a health care population-based study including individuals of European and African genetic ancestry in the PMBB with WES linked to EHR phenotypes, with replication studies in BioVU, UK Biobank, MyCode, and DCM Precision Medicine Study. Carrier status for BAG3 coding variants. Association of BAG3 coding variation with clinical diagnoses, echocardiographic traits, and longitudinal outcomes. In PMBB (n = 43 731; median [IQR] age, 65 [50-76] years; 21 907 female [50.1%]), among 30 324 European and 11 198 African individuals, the common C151R variant was associated with decreased risk for DCM (odds ratio [OR], 0.85; 95% CI, 0.78-0.92) and simultaneous increased risk for HCM (OR, 1.59; 95% CI, 1.25-2.02), which was confirmed in the replication cohorts. C151R carriers exhibited improved longitudinal outcomes compared with noncarriers as assessed by age at death (hazard ratio [HR], 0.85; 95% CI, 0.74-0.96; median [IQR] age, 71.8 [63.1-80.7] in carriers and 70.3 [61.6-79.2] in noncarriers) and heart transplant (HR, 0.81; 95% CI, 0.66-0.99; median [IQR] age, 56.7 [46.1-63.1] in carriers and 55.6 [45.2-62.9] in noncarriers). C151R was associated with reduced risk of DCM (OR, 0.42; 95% CI, 0.24-0.74) and heart failure (OR, 0.27; 95% CI, 0.14-0.50) among individuals harboring truncating TTN variants in exons with high cardiac expression (n = 358). BAG3 C151R was identified as a bidirectional modulator of risk along the DCM-HCM spectrum, as well as an important genetic modifier variant in TTN-mediated DCM. This work expands on the understanding of the etiology and penetrance of DCM, suggesting that BAG3 C151R is an important genetic modifier variant contributing to the variable expressivity of DCM, warranting further exploration of its mechanisms and of genetic modifiers in DCM more broadly.

Abstract 4120375: Penetrance and Phenotype Conversion Rate of Genetic Hypertrophic Cardiomyopathy in an Academic Biobank

Introduction: Hypertrophic cardiomyopathy (HCM) is an autosomal dominant condition with incomplete penetrance and variable expressivity. Given the increasing prevalence of sequencing and current guidelines on secondary finding disclosure, HCM P/LP alleles are increasingly being returned to patients who undergo genetic testing for other reasons. Whether individuals carrying P/LP HCM variants discovered in a genome-first context have progressive endophenotypes indicative of HCM remains poorly understood. Methods: To evaluate the penetrance and phenotype conversion rate of adults with P/LP HCM variants, we leveraged the Massachusetts General Brigham Biobank (MGBB), which consists of 36,417 participants with genotyping array and clinical data. Primary images of the earliest and latest TTE studies were reviewed for measurements of the posterior wall (PW), interventricular septum (IVS), and left ventricular morphology. Phenotype-positive (P+) status was defined by a PW or IVS thickness of at least 13 mm. Results: P/LP HCM variants were identified in 42 (0.1%) individuals with mean (SD) age 50.0 (16.6) years and 21 (50%) female sex. The most common HCM variants were in MYBPC3 (44%) and MYH7 (40%), followed by TNNI3(7%), MYL3 (7%), and TNNT2 (2%). Among the 42 genotype-positive (G+) individuals in MGBB, 17 (40%) had pre-existing HCM diagnoses prior to genomic return of results (gRoR). In contrast, 25 (60%) G+ individuals lacked a prior HCM diagnosis, among whom gRoR prompted TTE studies in 13 patients, revealing evidence of HCM in 9 individuals. Among the 42 G+ patients, 25 (58%) patients had completed at least two TTE studies, with a median [IQR] of 6 [3-9] TTE studies per patient, across a span of 10 [7-15] years follow-up. At the time of first TTE, 16 (64%) patients were P+ while 9 (36%) were P-. No G+, P- individuals converted to P+ over 10 years follow-up, nor was there any significant change in IVS or PW thickness. In contrast, individuals who were P+ at the initial TTE exhibited thickening PW (25% increase, CI 97.5% of 6 to 44) and IVS (26% increase, CI 97.5% of 4 to 49) over 8 years follow-up. Conclusion: In a genome-first approach, we identified 42 individuals in the MGBB with a P/LP HCM variant, among whom 60% lacked a prior clinical diagnosis of HCM. Targeted phenotyping revealed that nearly half of this newly identified group were P+. Over a median of 10 years follow-up, we observed a 0% phenotype conversion rate among G+, P- adult carriers of HCM variants.

Cell-type-specific splicing of transcription regulators and Ptbp1 by Rbfox1/2/3 in the developing neocortex.

How master splicing regulators crosstalk with each other and to what extent transcription regulators are differentially spliced remain unclear in the developing brain. Here, cell-type-specific RNA-Seq analyses of the developing neocortex uncover variable expression of the Rbfox1/2/3 genes and enriched splicing events in transcription regulators, altering protein isoforms or inducing nonsense-mediated mRNA decay. Transient expression of Rbfox proteins in radial glial progenitors induces neuronal splicing events preferentially in transcription regulators such as Meis2 and Tead1 Surprisingly, Rbfox proteins promote the inclusion of a mammal-specific alternative exon and a previously undescribed poison exon in Ptbp1 Simultaneous ablation of Rbfox1/2/3 in the neocortex downregulates neuronal isoforms and disrupts radial neuronal migration. Furthermore, the progenitor isoform of Meis2 promotes Tgfb3 transcription, while the Meis2 neuron isoform promotes neuronal differentiation. These observations indicate that transcription regulators are differentially spliced between cell types in the developing neocortex. [The sex has not been reported to affect cortical neurogenesis in mice, and embryos of both sexes were studied without distinguishing one or the other.]Significance Statement How alternative splicing regulates cell-type-specific gene expression in the developing neocortex remains understudied. Here, analyses of sorted cell types and single-cell long-reads uncover cell-type-specific splicing that is enriched in transcription regulators. Rbfox proteins, including the pan-neuronal marker NeuN/Rbfox3, preferentially switch splice forms of transcription regulators and are required for radial neuronal migration. We further show that the progenitor and neuron isoforms of a transcription regulator Meis2 function differently. Overall, this study suggests a cross-talk between alternative splicing and transcription for neuronal gene regulation.

'Re-Wilding' an Animal Model With Microbiota Shifts Immunity and Stress Gene Expression During Infection.

The frequency of emerging disease is growing with ongoing human activity facilitating new host-pathogen interactions. Novel infection outcomes can also be shaped by the host microbiota. Caenorhabditis elegans nematodes experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, have been shown to suffer higher mortality than those infected by the pathogen alone. Understanding the host responses to such microbiota-pathogen ecological interactions is key to pinpointing the mechanism underlying severe infection outcomes. We conducted transcriptomic analyses of C. elegans colonised by its native microbiota, S. aureus and both in combination. Correlations between altered collagen gene expression and heightened mortality in co-colonised hosts suggest the microbiota modified host resistance to infection. Furthermore, microbiota colonised hosts showed increased expression of immunity genes and variable expression of stress response genes during infection. Changes in host immunity and stress response could encompass both causes and effects of severe infection outcomes. 'Re-wilding' this model nematode host with its native microbiota indicated that typically commensal microbes can mediate molecular changes in the host that are costly when challenged by a novel emerging pathogen.

PATH-36. DO GENE EXPRESSION PROFILES BETTER PREDICT OLIGODENDROGLIOMA SURVIVAL?

Abstract The WHO 2021 classification of oligodendroglioma grade 2 (G2) and grade 3 (G3), is separated by histopathology alone and does not universally reflect survival outcome. DNA methylation-based profiling also fails to separate oligodendroglioma grades. Our aim was to define transcriptome-based molecular subgroups that predict survival of oligodendroglioma (IDH-mutant and 1p/19q-codeleted) patients. Clinical and whole-transcriptome data for oligodendroglioma were obtained from TCGA (n=132), CGGA (n=53), and the Exsegen Genomics Research Biobank (n=16) (CTRI/2021/09/036861); while that of control brain samples (n=9) were obtained from CPTAC. Overall survival (OS) was significantly different in TCGA samples between WHO CNS G2 and G3 oligodendrogliomas (log-rank test, p=0.0001); but, not in CGGA (p=0.1833) or Exsegen (p>0.06) samples. Genes with highly variable expression (Median Absolute Deviation, i.e. MAD>1; 1645 genes) across TCGA oligodendroglioma and CPTAC control brain samples were used to exclude 9 oligodendroglioma samples with Pearson’s correlation>0.75 with control brain samples. Consensus clustering (K-means and spectral) of remaining 124 TCGA oligodendroglioma samples identified three significantly different (SigClust, p<0.05) transcriptomic classes using 1347 highly variable genes (MAD>1) in these samples. Principal component analysis (PCA) on expression of 1347 genes in TCGA samples revealed partial overlap of G2 and G3 tumours; but transcriptomic classes with distinct OS could be identified at both extremes of survival. Gene expression signatures for each transcriptomic class were developed using core TCGA samples from each class. For further validation, gene signatures were used to predict the transcriptomic classes of CGGA and Exsegen samples based on highest cosine similarity between sample gene expression and gene signature of each transcriptomic class. OS was significantly different between the transcriptomic classes in TCGA samples and predicted ones in CGGA samples. Transcriptome profiling separated oligodendrogliomas into distinct classes which can predict survival and potentially augment grading and refine prognostication and treatment options.

DeSide: A unified deep learning approach for cellular deconvolution of tumor microenvironment

Cellular deconvolution via bulk RNA sequencing (RNA-seq) presents a cost-effective and efficient alternative to experimental methods such as flow cytometry and single-cell RNA-seq (scRNA-seq) for analyzing the complex cellular composition of tumor microenvironments. Despite challenges due to heterogeneity within and among tumors, our innovative deep learning-based approach, DeSide, shows exceptional accuracy in estimating the proportions of 16 distinct cell types and subtypes within solid tumors. DeSide integrates biological pathways and assesses noncancerous cell types first, effectively sidestepping the issue of highly variable gene expression profiles (GEPs) associated with cancer cells. By leveraging scRNA-seq data from six cancer types and 185 cancer cell lines across 22 cancer types as references, our method introduces distinctive sampling and filtering techniques to generate a high-quality training set that closely replicates real tumor GEPs, based on The Cancer Genome Atlas (TCGA) bulk RNA-seq data. With this model and high-quality training set, DeSide outperforms existing methods in estimating tumor purity and the proportions of noncancerous cells within solid tumors. Our model precisely predicts cellular compositions across 19 cancer types from TCGA and proves its effectiveness with multiple additional external datasets. Crucially, DeSide enables the identification and analysis of combinatorial cell type pairs, facilitating the stratification of cancer patients into prognostically significant groups. This approach not only provides deeper insights into the dynamics of tumor biology but also highlights potential therapeutic targets by underscoring the importance of specific cell type or subtype interactions.

Genomic, epigenomic and transcriptomic inter- and intra-tumor heterogeneity in desmoid tumors.

Desmoid tumors are bland fibroblastic tumors that do not metastasize but have a high rate of local recurrence. Previously published studies proposed two different transcriptomic signatures to predict relapse. Molecular heterogeneity has been well established in high-grade sarcomas but little is known about molecular variability within locally aggressive tumors such as desmoids. We performed transcriptomic profiling of 31 specimens from 20 primary desmoid tumors to identify genes predictive of relapse. We also performed multi-omic analysis including DNA methylation, copy number alterations, point mutations and gene expression on 24 specimens from different regions of primary and recurrent desmoid tumors from 3 patients (7-9 specimens per patient). We observed highly variable expression of transcriptomic prognostic signatures, both in patients who did or did not progress. Signatures associated with favorable and unfavorable outcome were detected in different regions within the same tumor. Further multi-omic studies showed remarkable intra- and inter-tumor heterogeneity of genomic, epigenomic and transcriptomic patterns. The transcriptomic profiles showed the highest degree of variability within tumors and between primary and recurrent tumors from the same patient. This study shows an unexpected degree of intra- and inter-tumor heterogeneity in desmoid tumors. Our analysis indicates that molecular analysis of a single tumor biopsy may underestimate the magnitude of molecular alterations in desmoid tumors. Our study also shows that recurrent desmoid tumors acquire multiple new molecular alterations. Thus, molecular heterogeneity is an important consideration in drug development and validation of prognostic and predictive biomarkers for desmoid tumors.