Distinct Gene Expression Profiles Research Articles

Mutations in DARS2 result in global dysregulation of mRNA metabolism and splicing

Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL) is a rare neurological disorder caused by the mutations in the DARS2 gene, which encodes the mitochondrial aspartyl-tRNA synthetase. The objective of this study was to understand the impact of DARS2 mutations on cell processes through evaluation of LBSL patient stem cell derived cerebral organoids and neurons. We generated human cerebral organoids (hCOs) from induced pluripotent stem cells (iPSCs) of seven LBSL patients and three healthy controls using an unguided protocol. Single cells from 70-day-old hCOs were subjected to SMART-seq2 sequencing and bioinformatic analysis to acquire high-resolution gene and transcript expression datasets. Global gene expression analysis demonstrated dysregulation of a number of genes involved in mRNA metabolism and splicing processes within LBSL hCOs. Importantly, there were distinct and divergent gene expression profiles based on the nature of the DARS2 mutation. At the transcript level, pervasive differential transcript usage and differential spliced exon events that are involved in protein translation and metabolism were identified in LBSL hCOs. Single-cell analysis of DARS2 (exon 3) showed that some LBSL cells exclusively express transcripts lacking exon 3, indicating that not all LBSL cells can benefit from the “leaky” nature common to splice site mutations. At the gene- and transcript-level, we uncovered that dysregulated RNA splicing, protein translation and metabolism may underlie at least some of the pathophysiological mechanisms in LBSL. To confirm hCO findings, iPSC-derived neurons (iNs) were generated by overexpressing Neurogenin 2 using lentiviral vector to study neuronal growth, splicing of DARS2 exon 3 and DARS2 protein expression. Live cell imaging revealed neuronal growth defects of LBSL iNs, which was consistent with the finding of downregulated expression of genes related to neuronal differentiation in LBSL hCOs. DARS2 protein was downregulated in iNs compared to iPSCs, caused by increased exclusion of exon 3. The scope and complexity of our data imply that DARS2 is potentially involved in transcription regulation beyond its canonical role of aminoacylation. Nevertheless, our work highlights transcript-level dysregulation as a critical, and relatively unexplored, mechanism linking genetic data with neurodegenerative disorders.

Abstract P2174: Transcriptomic Profiling Of Immune Checkpoint Inhibitor Myocarditis Reveals Novel Therapeutic Targets

Introduction: Immune checkpoint inhibitor (ICI) therapy has revolutionized the treatment of advanced cancers. However, the increased use of ICI has also resulted in a higher incidence of ICI-related cardiovascular side effects, including myocarditis, which has a high mortality rate of nearly 50%. Understanding the mechanisms underlying ICI-related cardiotoxicity is essential for identifying new therapeutic targets and improving patient survival. Hypothesis: We hypothesized that ICI-myocarditis has a unique transcriptomic profile that could be used to identify new drug targets. Methods: To test our hypothesis, we isolated RNA from our ICI-myocarditis mouse hearts and performed RNA-seq using the Illumina NovaSeq 6000. We also reanalyzed a human IC-myocarditis dataset downloaded from the Gene Expression Omnibus database. Results: Our results demonstrated that in both our animal models and patients, the upregulated pathways in ICI myocarditis heart tissues were enriched for regulation of T cell activation, leukocyte adhesion, and multiple cytokine signaling pathways. Conversely, downregulated pathways included those involved in cellular respiration, oxidative phosphorylation, and cardiac conduction. The most significantly upregulated genes were involved in innate and adaptive immune responses, including the CD8-dependent gene program and response to interferon-gamma of macrophages. By querying the Drug Gene Interaction Database, we identified several novel biologically plausible therapeutic targets. Correspondingly, a number of FDA-approved drugs were revealed, including monoclonal or chimeric antibodies such as Tocilizumab and Alemtuzumab, recombinant proteins like Abatacept and Anakinra, as well as small molecules such as Ruxolitinib and Imiquimod. Conclusions: Our study is the first to use the entire transcriptomic profile of ICI myocarditis in both preclinical models and patients for drug discovery. Our results demonstrate that ICI myocarditis has a distinct gene expression profile compared to healthy and other cardiac diseases. By querying a drug-gene interaction database, we identified several novel drug targets and possible treatments for ICI-related cardiotoxicity.

Gene expression profiling of pancreatic ductal adenocarcinomas in response to neoadjuvant chemotherapy.

Pancreatic ductal adenocarcinoma (PDAC) has the lowest survival rate of all major cancers. Chemotherapy is the mainstay systemic therapy for PDAC, and chemoresistance is a major clinical problem leading to therapeutic failure. This study aimed to identify key differences in gene expression profile in tumors from chemoresponsive and chemoresistant patients. Archived formalin-fixed paraffin-embedded tumor tissue samples from patients treated with neoadjuvant chemotherapy were obtained during surgical resection. Specimens were macrodissected and gene expression analysis was performed. Multi- and univariate statistical analysis was performed to identify differential gene expression profile of tumors from good (0%-30% residual viable tumor [RVT]) and poor (>30% RVT) chemotherapy-responders. Initially, unsupervised multivariate modeling was performed by principal component analysis, which demonstrated a distinct gene expression profile between good- and poor-chemotherapy responders. There were 396 genes that were significantly (p < 0.05) downregulated (200 genes) or upregulated (196 genes) in tumors from good responders compared to poor responders. Further supervised multivariate analysis of significant genes by partial least square (PLS) demonstrated a highly distinct gene expression profile between good- and poor responders. A gene biomarker of panel (IL18, SPA17, CD58, PTTG1, MTBP, ABL1, SFRP1, CHRDL1, IGF1, and CFD) was selected based on PLS model, and univariate regression analysis of individual genes was performed. The identified biomarker panel demonstrated a very high ability to diagnose good-responding PDAC patients (AUROC: 0.977, sensitivity: 82.4%; specificity: 87.0%). A distinct tumor biological profile between PDAC patients who either respond or not respond to chemotherapy was identified.

Long non coding RNAs reveal important pathways in childhood asthma: a future perspective.

Asthma is a long-term inflammatory disease of the airways of the lungs refers changes that occur in conjunction with, or as a result of, chronic airway inflammation. Airway remodeling the subsequent of inflammation constitutes cellular and extracellular matrix changes in the wall airways, epithelial-to-mesenchymal-transition and airway smooth muscle cell proliferation. Diseases often begin in childhood and despite extensive research, causative pathogenic mechanisms still remain unclear. Transcriptome analysis of childhood asthma reveals distinct gene expression profiles of Long noncoding RNAs which have been reported to play a central regulatory role in various aspects of pathogenesis, clinical course and treatment of asthma. We briefly review current understanding of lnc-RNA dysregulation in children with asthma, focusing on their complex role in the inflammation, cell proliferation and remodeling of airway to guide future researches. We found that the lnc-RNAs increases activity of several oncogenes such c-Myc, Akt, and ERK and various signaling pathways such as MAPK (PI3K, Ras, JNK and p38), NF-κB and Wnt and crosstalk between these pathways by TGFβ, β-catenin, ERK and SKP2. Moreover, two different signal transduction pathways, Wnt and Notch1, can be activated by two lnc-RNAs through sponging the same miRNA for exacerbation cell proliferation.

Integrated Genomic and Transcriptomic Analysis Improves Disease Classification and Risk Stratification of MDS with Ring Sideroblasts.

Ring sideroblasts (RS) define the low-risk myelodysplastic neoplasm (MDS) subgroup with RS but may also reflect erythroid dysplasia in higher risk myeloid neoplasm. The benign behavior of MDS with RS (MDSRS+) is limited to SF3B1-mutated cases without additional high-risk genetic events, but one third of MDSRS+ carry no SF3B1 mutation, suggesting that different molecular mechanisms may underlie RS formation. We integrated genomic and transcriptomic analyses to evaluate whether transcriptome profiles may improve current risk stratification. We studied a prospective cohort of MDSRS+ patients irrespective of World Health Organization (WHO) class with regard to somatic mutations, copy-number alterations, and bone marrow CD34+ cell transcriptomes to assess whether transcriptome profiles add to prognostication and provide input on disease classification. SF3B1, SRSF2, or TP53 multihit mutations were found in 89% of MDSRS+ cases, and each mutation category was associated with distinct clinical outcome, gene expression, and alternative splicing profiles. Unsupervised clustering analysis identified three clusters with distinct hemopoietic stem and progenitor (HSPC) composition, which only partially overlapped with mutation groups. IPSS-M and the transcriptome-defined proportion of megakaryocyte/erythroid progenitors (MEP) independently predicted survival in multivariable analysis. These results provide essential input on the molecular basis of SF3B1-unmutated MDSRS+ and propose HSPC quantification as a prognostic marker in myeloid neoplasms with RS.

Profiling Immunological Phenotypes in Individuals During the First Year After Traumatic Spinal Cord Injury: A Longitudinal Analysis.

Abstract Individuals with SCI are severely affected by immune system changes, resulting in increased risk of infections and persistent systemic inflammation. While recent data support that immunological changes after SCI differ in the acute and chronic phases of living with SCI, only limited immunological phenotyping in humans is available. To characterize dynamic molecular and cellular immune phenotypes over the first year, we assess RNA (bulk-RNA sequencing), protein, and flow cytometry (FACS) profiles of blood samples from 12 individuals with SCI at 0-3 days and at 3, 6, and 12 months post injury (MPI) compared to 23 uninjured individuals (controls). We identified 967 differentially expressed (DE) genes in individuals with SCI (FDR <0.001) compared to controls. Within the first 6 MPI we detected a reduced expression of NK cell genes, consistent with reduced frequencies of CD56bright, CD56dim NK cells present at 12 MPI. Over 6MPI, we observed increased and prolonged expression of genes associated with inflammation (e.g. HMGB1, Toll-like receptor signaling) and expanded frequencies of monocytes acutely. Canonical T-cell related DE genes (e.g. FOXP3, TCF7, CD4) were upregulated during the first 6 MPI and increased frequencies of activated T cells at 3-12 MPI. Neurological injury severity was reflected in distinct whole blood gene expression profiles at any time after SCI, verifying a persistent 'neurogenic' imprint. Overall, 2876 DE genes emerge when comparing motor complete to motor incomplete SCI (ANOVA, FDR <0.05), including those related to neutrophils, inflammation, and infection. In summary, we identify a dynamic immunological phenotype in humans, including molecular and cellular changes which may provide potential targets to reduce inflammation, improve immunity, or serve as candidate biomarkers of injury severity.

Characterizing the Pathogenicity and Immunogenicity of Simian Retrovirus Subtype 8 (SRV-8) Using SRV-8-Infected Cynomolgus Monkeys.

Simian retrovirus subtype 8 (SRV-8) infections have been reported in cynomolgus monkeys (Macaca fascicularis) in China and America, but its pathogenicity and immunogenicity are rarely reported. In this work, the SRV-8-infected monkeys were identified from the monkeys with anemia, weight loss, and diarrhea. To clarify the impact of SRV-8 infection on cynomolgus monkeys, infected monkeys were divided into five groups according to disease progression. Hematoxylin (HE) staining and viral loads analysis showed that SRV-8 mainly persisted in the intestine and spleen, causing tissue damage. Additionally, the dynamic variations of blood routine indexes, innate and adaptive immunity, and the transcriptomic changes in peripheral blood cells were analyzed during SRV-8 infection. Compared to uninfected animals, red blood cells, hemoglobin, and white blood cells were reduced in SRV-8-infected monkeys. The percentage of immune cell populations was changed after SRV-8 infection. Furthermore, the number of hematopoietic stem cells decreased significantly during the early stages of SRV-8 infection, and returned to normal levels after antibody-mediated viral clearance. Finally, global transcriptomic analysis in PBMCs from SRV-8-infected monkeys revealed distinct gene expression profiles across different disease stages. In summary, SRV-8 infection can cause severe pathogenicity and immune disturbance in cynomolgus monkeys, and it might be responsible for fatal virus-associated immunosuppressive syndrome.

Dissecting neuron-specific functions of circadian genes using modified cell-specific CRISPR approaches

Circadian behavioral rhythms in Drosophila melanogaster are regulated by about 75 pairs of brain neurons. They all express the core clock genes but have distinct functions and gene expression profiles. To understand the importance of these distinct molecular programs, neuron-specific gene manipulations are essential. Although RNAi based methods are standard to manipulate gene expression in a cell-specific manner, they are often ineffective, especially in assays involving smaller numbers of neurons or weaker Gal4 drivers. We and others recently exploited a neuron-specific CRISPR-based method to mutagenize genes within circadian neurons. Here, we further explore this approach to mutagenize three well-studied clock genes: the transcription factor gene vrille, the photoreceptor gene Cryptochrome (cry), and the neuropeptide gene Pdf (pigment dispersing factor). The CRISPR-based strategy not only reproduced their known phenotypes but also assigned cry function for different light-mediated phenotypes to discrete, different subsets of clock neurons. We further tested two recently published methods for temporal regulation in adult neurons, inducible Cas9 and the auxin-inducible gene expression system. The results were not identical, but both approaches successfully showed that the adult-specific knockout of the neuropeptide Pdf reproduces the canonical loss-of-function mutant phenotypes. In summary, a CRISPR-based strategy is a highly effective, reliable, and general method to temporally manipulate gene function in specific adult neurons.

Histological assessment and gene expression analysis of intra-oral soft tissue graft donor sites.

To determine the structural and gene expression features of different intra-oral soft tissue donor sites (i.e., anterior palate, posterior palate, maxillary tuberosity and retromolar pad). Standardized mucosal tissue punch biopsies were collected from at least one donor site per subject. Histological processing was performed to determine tissue morphometry and quantify collagen composition. Site-specific gene distribution was mapped using targeted gene expression analysis and validated using real time polymerase chain reaction (qPCR). A total of 50 samples from 37 subjects were harvested. Epithelial thickness did not differ between sites. However, lamina propria was thicker in the maxillary tuberosity (2.55 ± 0.92 mm) and retromolar pad (1.98 ± 0.71 mm) than in the lateral palate. Type I collagen was the predominant structural protein in the lamina propria (75.06%-80.21%). Genes involving collagen maturation and extracellular matrix regulation were highly expressed in the maxillary tuberosity and retromolar pad, while lipogenesis-associated genes were markedly expressed in the lateral palate. The retromolar pad showed the most distinct gene expression profile, and the anterior and posterior palate displayed similar transcription profiles. Tissue samples harvested from the anterior and posterior palate differed morphologically from those from the maxillary tuberosity and retromolar pad. Each intra-oral site showed a unique gene expression profile, which might impact their biological behaviour and outcomes of soft tissue augmentation procedures.

Individual variation in preference behavior in sailfin fish refines the neurotranscriptomic pathway for mate preference.

Social interactions can drive distinct gene expression profiles which may vary by social context. Here we use female sailfin molly fish (Poecilia latipinna) to identify genomic profiles associated with preference behavior in distinct social contexts: male interactions (mate choice) versus female interactions (shoaling partner preference). We measured the behavior of 15 females interacting in a non-contact environment with either two males or two females for 30 min followed by whole-brain transcriptomic profiling by RNA sequencing. We profiled females that exhibited high levels of social affiliation and great variation in preference behavior to identify an order of magnitude more differentially expressed genes associated with behavioral variation than by differences in social context. Using a linear model (limma), we took advantage of the individual variation in preference behavior to identify unique gene sets that exhibited distinct correlational patterns of expression with preference behavior in each social context. By combining limma and weighted gene co-expression network analyses (WGCNA) approaches we identified a refined set of 401 genes robustly associated with mate preference that is independent of shoaling partner preference or general social affiliation. While our refined gene set confirmed neural plasticity pathways involvement in moderating female preference behavior, we also identified a significant proportion of discovered that our preference-associated genes were enriched for 'immune system' gene ontology categories. We hypothesize that the association between mate preference and transcriptomic immune function is driven by the less well-known role of these genes in neural plasticity which is likely involved in higher-order learning and processing during mate choice decisions.

Transcriptional analysis reveals distinct gene expression profiles of three bowenoid papulosis patients.

Bowenoid papulosis (BP) is a benign and possibly carcinogenic disease associated with human papillomavirus (HPV) infection, which has been increasingly recognised and paid attention to in recent years, but the potential mechanisms still remain unclear. In our study, three patients who were diagnosed with BP were enrolled into our research. Skin biopsies were taken and were separated into two parts, one part was for HE staining and the others were for RNA-sequencing (RNA-seq). All the three patents were human papillomavirus (HPV) positive and HE staining revealed typical skin histopathological changes in BP, including dyskeratosis, hyperplasia and hypertrophy of the granular and spinous layers, atypical keratinocytes. RNA-seq analysis demonstrated that a total of 486 differentially expressed genes (DEGs) were detected between the skin tissues from BP and the controls, among which, 320 genes were significantly upregulated and 166 genes were dramatically downregulated. GO enrichment revealed that antigen binding, cell cycle, immune response and keratinisation to be the most notably altered pathways, whereas KEGG analysis indicated that cell cycle cytokine-cytokine receptor interaction, ECM receptor interaction and p53 signalling pathway to be the most significantly changed signalling pathways in BP. Furthermore, metabolism-associated enrichment analysis showed that cholesterol metabolism, metabolism of xenobiotics by cytochrome p450 and pyrimidine metabolism to be the most dramatically dysregulated metabolic pathways in BP as compared to normal controls. Our study revealed that inflammation, metabolism and cell proliferation signalling pathways might be the most important pathways for BP disease, targeted inhibiting of these signals might be a potential method for BP treatment.

Gene expression comparison between primary aggressive luminal breast cancer and paired axillary and sentinel lymph node metastasis.

e13060 Background: More aggressive and therapy-resistant hormone receptor (HR)-positive breast cancer (hereafter luminal breast cancer, LBC) remains a great challenge. Few studies examine the genomics of axillary lymph node (ALN) metastasis in LBC. The aim of this study was to characterize and compare the mRNA expression patterns of primary breast cancers and paired ALN metastases. Methods: Aggressive pT1-2N2-3M0 LBC patients aged over 18 years who were treated at Shandong Provincial Hospital Affiliated to Shandong First Medical University and had available matched primary and metastatic tumor samples for gene expression analyses were retrospectively recruited. Bulk mRNA expression levels were determined by RNA sequencing (Illumina NovaSeq 6000 system) and calculated using featureCounts. Differential gene expression analysis was performed using DESeq2. All analyses were carried out with differentially expressed genes (DEGs) with an FDR &lt;0.05. Changes of intrinsic subtypes from primary to metastatic disease were assessed. Results: Ten LBC patients with paired tumor samples were included. Compared with the primary tumor, ALN metastatic tumor had 1509 statistically significant DEGs, including 743 upregulated genes and 766 downregulated genes. Notably, there was an upregulation of genes related to immune response-activating signal transduction, T cell receptor signaling pathway, B cell receptor signaling pathway, and cytokine-cytokine receptor interaction in the ALN metastasis. The downregulation of genes were mainly enriched in the PI3K-Akt signaling pathway, ECM-receptor interaction, Wnt signaling pathway, and TGF-beta signaling pathway. Intrinsic subtype distribution in primary tumors was different from those in ALN metastatic tumors, such as Luminal A (30% vs. 50%), Luminal B (10% vs. 20%), HER2-enriched (20% vs. 10%), Basal-like (10% vs. 10%), and Normal-like (30% vs. 10%). These results suggest that LBC is a highly heterogeneous disease. Conclusions: In aggressive pT1-2N2-3M0 LBC, ALN metastases have a distinct gene expression profile and show upregulation of immune-related genes ( CR2, BLK, PAX5, CD19, FCRL1, TNFRSF13B). Genes associated with signaling pathways are involved in the development of breast cancer ( FST, TNN, LAMC3, SFRP2, FGF18), and are downregulated when compared to autologous primary cancer. These pathways are potential targeted pathways in the treatment of breast cancer. LBC cells metastatic to lymph nodes undergo a change to metastasize and survive in the new microenvironment, which may provide insights into the metastatic process. Besides, a switch towards more aggressive intrinsic subtype from primary to advanced disease is also observed.

Characterisation of cell lines derived from prostate cancer patients with localised disease.

Prostate cancer is a broad-spectrum disease, spanning from indolent to a highly aggressive lethal malignancy. Prostate cancer cell lines are essential tools to understanding the basic features of this malignancy, as well as in identifying novel therapeutic strategies. However, most cell lines routinely used in prostate cancer research are derived from metastatic disease and may not fully elucidate the molecular events underlying the early stages of cancer development and progression. Thus, there is a need for new cell lines derived from localised disease to better span the disease spectrum. Prostatic tissue from the primary site, and adjacent non-cancerous tissue was obtained from four patients with localised disease undergoing radical prostatectomy. Epithelial cell outgrowths were immortalised with human papillomavirus type 16 (HPV16) E6 and E7 to establish monoclonal cell lines. Chromosomal ploidy was imaged and STR profiles were determined. Cell morphology, colony formation and cell proliferation characteristics were assessed. Androgen receptor (AR) expression and AR-responsiveness to androgen treatment were analysed by immunofluorescence and RT-qPCR, respectively. RNA-seq analysis was performed to identify prostate lineage markers and expression of prostate cancer tumorigenesis-related genes. Two benign cell lines derived from non-cancer cells (AQ0420 and AQ0396) and two tumour tissue derived cancer cell lines (AQ0411 and AQ0415) were immortalised from four patients with localised prostatic adenocarcinoma. The cell lines presented an epithelial morphology and a slow to moderate proliferative rate. None of the cell lines formed anchorage independent colonies or displayed AR-responsiveness. Comparative RNA-seq expression analysis confirmed the prostatic lineage of the four cell lines, with a distinct gene expression profile from that of the metastatic prostate cancer cell lines, PC-3 and LNCaP. Comprehensive characterization of these cell lines may provide new in vitro tools that could bridge the current knowledge gap between benign, early-stage and metastatic disease.

Spatiotemporal profiles of gene activity in stamen delineate nucleo-cytoplasmic interaction in a male-sterile somatic cybrid citrus.

Cytoplasmic male sterility (CMS) has long been used to produce seedless fruits in perennial woody crops like citrus. A male-sterile somatic cybrid citrus (G1 + HBP) was generated by protoplast fusion between a CMS callus parent 'Guoqing No. 1' Satsuma mandarin (Citrus unshiu, G1) and a fertile mesophyll parent Hirado Buntan pummelo (Citrus grandis, HBP). To uncover the male-sterile mechanism of G1 + HBP, we compared the transcriptome profiles of stamen organ and cell types at five stages between G1 + HBP and HBP, including the initial stamen primordia, enlarged stamen primordia, pollen mother cells, tetrads, and microspores captured by laser microdissection. The stamen organ and cell types showed distinct gene expression profiles. A majority of genes involved in stamen development were differentially expressed, especially CgAP3.2, which was downregulated in enlarged stamen primordia and upregulated in tetrads of G1 + HBP compared with HBP. Jasmonic acid- and auxin-related biological processes were enriched among the differentially expressed genes of stamen primordia, and the content of jasmonic acid biosynthesis metabolites was higher in flower buds and anthers of G1 + HBP. In contrast, the content of auxin biosynthesis metabolites was lower in G1 + HBP. The mitochondrial tricarboxylic acid cycle and oxidative phosphorylation processes were enriched among the differentially expressed genes in stamen primordia, meiocytes, and microspores, indicating the dysfunction of mitochondria in stamen organ and cell types of G1 + HBP. Taken together, the results indicate that malfunction of mitochondria-nuclear interaction might cause disorder in stamen development, and thus lead to male sterility in the citrus cybrid.

OC-113 GENETIC AND BIOLOGIC RISK FACTORS ASSOCIATED WITH HERNIA FORMATION: A SYSTEMATIC REVIEW

Abstract Aim The aim of this systematic review is to identify genetic and biologic markers associated with abdominal hernia formation. Methods A systematic review, using PRIMSA-guidelines, searched PubMed, MEDLINE, Embase, Scopus, and COCHRANE databases on 25AUG2022. All articles with qualitative or quantitative data regarding biologic factors of hernia formation were included. Review articles, editorials, and non-English articles were excluded. Data from articles were collected for analysis. The Newcastle-Ottawa Scale was used to assess risk of bias. Results Of 5,946 initial studies, 77 were included: 17 incisional/ventral, 42 inguinal, 4 hiatal, 1 parastomal, and 13 multiple hernias. Five inguinal hernia studies identified 92 susceptible loci in regions of 66 genes involved largely in antigen processing/presentation and immune-response pathways after enrichment analysis. Three studies identified significant DNA sequence variants (DSV) of three additional genes. Among various biomarkers, eleven studies found increased MMP-2, with seven noting MMP-2 significantly higher in direct versus indirect. In incisional hernias, one study demonstrated 167 genes in skin and 7 genes in fascia with distinct gene-expression profiles associated with the activation of inflammatory response plasma proteins, regulation of immune response, and cell-adhesion. A separate genetic study identified 3 independent loci. Biomarkers were discussed in 15 studies, with inconclusive results. In both incisional/ventral and inguinal hernias, type I/type III collagen ratios were decreased. Data synthesis could not be completed for hiatal and parastomal hernias. Conclusion While there is reasonable consensus regarding the role of biologic risk factors in inguinal hernias, further research investigating genetic predisposition to incisional hernias is encouraged.

Placental transcriptome analysis of hypertensive pregnancies identifies distinct gene expression profiles of preeclampsia superimposed on chronic hypertension

BackgroundThe pathogenesis of preeclampsia superimposed on chronic hypertension (SI) is poorly understood relative to preeclampsia (PreE) occurring in pregnant people without chronic hypertension. Placental transcriptomes in pregnancies complicated by PreE and SI have not been previously compared.MethodsWe identified pregnant people in the University of Michigan Biorepository for Understanding Maternal and Pediatric Health with hypertensive disorders affecting singleton, euploid gestations (N = 36) along with non-hypertensive control subjects (N = 12). Subjects were grouped as: (1) normotensive (N = 12), (2) chronic hypertensive (N = 13), (3) preterm PreE with severe features (N = 5), (4) term PreE with severe features (N = 11), (5) preterm SI (N = 3), or (6) term SI (N = 4). Bulk RNA sequencing of paraffin-embedded placental tissue was performed. The primary analysis assessed differential gene expression relative to normotensive and chronic hypertensive placentas, where Wald adjusted P values < 0.05 were considered significant. Unsupervised clustering analyses and correlation analyses were performed between conditions of interest, and a gene ontology was constructed.ResultsComparing samples from pregnant people with hypertensive diseases to non-hypertensive controls, there were 2290 differentially expressed genes. The log2-fold changes in genes differentially expressed in chronic hypertension correlated better with term (R = 0.59) and preterm (R = 0.63) PreE with severe features than with term (R = 0.21) and preterm (R = 0.22) SI. A relatively poor correlation was observed between preterm SI and preterm PreE with severe features (0.20) as well as term SI and term PreE with severe features (0.31). The majority of significant genes were downregulated in term and preterm SI versus normotensive controls (92.1%, N = 128). Conversely, most term and preterm PreE with severe features genes were upregulated compared to the normotensive group (91.8%, N = 97). Many of the upregulated genes in PreE with the lowest adjusted P values are known markers of abnormal placentation (e.g., PAAPA, KISS1, CLIC3), while the downregulated genes with the greatest adjusted P values in SI have fewer known pregnancy-specific functions.ConclusionsWe identified unique placental transcriptional profiles in clinically relevant subgroups of individuals with hypertension in pregnancy. Preeclampsia superimposed on chronic hypertension was molecularly distinct from preeclampsia in individuals without chronic hypertension, and chronic hypertension without preeclampsia, suggesting that preeclampsia superimposed on hypertension may represent a distinct entity.

Investigating the roles of fetal-specific genes in hematopoiesis

Abstract Hematopoiesis, the process which generates blood cells, changes significantly during mammalian development. Fetal hematopoiesis primarily takes place in the fetal liver (FL), where hematopoietic stem cells (FL HSCs) are characterized by high self-renewal capacity and a distinctive program of multilineage differentiation. After birth, the main location of hematopoiesis is the bone marrow (BM), where stem cells (BM HSCs) are less proliferative and have a more restricted differentiation capacity. How exactly fetal hematopoiesis transitions to adult hematopoiesis and which cell-intrinsic properties or environmental factors aid this process have yet to be defined. This project aims to elucidate the cell-intrinsic mechanisms behind this transition. Studies show that FL and BM HSCs have distinct gene expression profiles, which may account for some of their phenotypic differences. Genes, such as LIN28B, which encodes an RNA binding protein, are highly expressed in the fetus, yet are absent in postnatal life. The re-expression of such fetal specific genes can confer fetal-like self-renewal and proliferation. Previous work in the Muljo lab demonstrated that LIN28B re-expression partially reprograms BM HSCs to undergo fetal-like lymphopoiesis, which is characterized by increased development of innate-like lymphocytes. I aim to fully reprogram adult BM HSCs to phenotypically resemble FL HSCs in their ability to generate cell types that develop early in life. FL HSCs, though clinically promising, are not readily available for therapeutic use. Reprogramming adult BM HSCs may be a suitable alternative that could improve current HSC transplantation procedures. This work is supported by the Intramural Research Program of NIAID, NIH. Intramural Research Program NIAID NIH

Abstract 351: Developing A Human Bone Marrow Organoid Culture System To Study The Diabetic Immune System

Objectives: There is limited understanding on how diabetes negatively impacts wound healing after ischemic tissue damage. Murine models for limb ischemia and myocardial infarction have demonstrated that recruitment of bone marrow hematopoietic stem cell (HSC)-derived immune cells at all stages of ischemic tissue remodeling and healing. By leveraging our lab’s three-dimensional (3D) bone marrow organoid culture system used to study human HSC, we aim to study the effect of diabetes on immune cell development. Methods: Surgically discarded bone marrow tissue samples from patients undergoing lower extremity amputation for non-healing ulcer or tissue loss was used to develop our bone marrow 3D organoid culture system. Human HSCs are identified using fluorescence-tagged antibodies against cell surface markers. Hematopoietic potential of bone marrow-derived HSCs was tested using colony forming unit assay. In vitro immune cell differentiation into monocyte and macrophage was performed. Bulk RNA libraries were sequenced on the NextSeq 500 system (Illumina) and analysis done on DeBrowser. Results: Our novel human bone marrow co-culture system provides a method for bone marrow cell expansion from primary human bone marrow tissue explants. De novo sprouting cells can be observed growing from bone marrow tissue explants harvested from non-diabetic and diabetic donors. Using fluorescence-activated cell sorting analysis, we identified a trend towards reduced HSC numbers in diabetic when compared to non-diabetic donors. HSC derived from both diabetic and non-diabetic bone marrow tissue explants were able to undergo hematopoiesis and immune cell differentiation. Bulk RNA sequencing demonstrates distinct gene expression profiles of the cells expanded from non-diabetic and diabetic bone marrow cells. Conclusions: Our 3D bone marrow organoid culture system will allow for future comparative studies between the non-diabetic and diabetic immune system. The preliminary data suggest that there are gene expression profile differences between bone marrow progenitor cells from diabetic and non-diabetic donors. These gene expression differences may attribute to alterations in the HSC number and immune cell development observed in diabetes.

Distinct gene expression profiles underlie morphological and etiological differences in pediatric cataracts.

Pediatric cataract is a major cause of preventable childhood blindness worldwide. Although genetic mutations or infections have been described in patients, the mechanistic basis of human cataract development remains poorly understood. Therefore, gene expression of structural, developmental, profibrotic, and transcription factors in phenotypically and etiologically distinct forms of pediatric cataracts were evaluated. This cross-sectional study included 89 pediatric cataract subjects subtyped into 1) prenatal infectious (cytomegalovirus, rubella, and combined cytomegalovirus with rubella infection), 2) prenatal non-infectious, 3) posterior capsular anomalies, 4) postnatal, 5) traumatic, and 6) secondary, and compared to clear, non-cataractous material of eyes with the subluxated lenses. Expression of lens structure-related genes (Aqp-0, HspA4/Hsp70, CrygC), transcription factors (Tdrd7, FoxE3, Maf, Pitx 3) and profibrotic genes (Tgfβ, Bmp7, αSmA, vimentin) in surgically extracted cataract lens material were studied and correlated clinically. In cataract material, the lens-related gene expression profiles were uniquely associated with phenotype/etiology of different cataracts. Postnatal cataracts showed a significantly altered FoxE3 expression. Low levels of Tdrd7 expression correlated with posterior subcapsular opacity, whereas CrygC correlated significantly with anterior capsular ruptures. The expression of Aqp0 and Maf was elevated in infectious cataracts, particularly in CMV infections, compared to other cataract subtypes. Tgfβ showed significantly low expression in various cataract subtypes, whereas vimentin had elevated gene expression in infectious and prenatal cataracts. A significant association between lens gene expression patterns in phenotypically and etiologically distinct subtypes of pediatric cataracts suggests regulatory mechanisms in cataractogenesis. The data reveal that cataract formation and presentation is a consequence of altered expression of a complex network of genes.

A Novel Two-Gene Expression-Based Prognostic Score in Malignant Pleural Mesothelioma.

Malignant pleural mesothelioma (MPM) is a rare cancer type with an increasing incidence worldwide. We aimed to develop a rational gene expression-based prognostic score in MPM using publicly available datasets. We developed and validated a two-gene prognostic score (2-PS) using three independent publicly available gene expression datasets. The 2-PS was built using the Robust Likelihood-Based Survival Modeling with Microarray Data method. We narrowed down the model building to the analysis of 179 genes, which have been shown previously to be of importance to MPM development. Our statistical approach showed that a model including two genes (GOLT1B and MAD2L1) was the best predictor for overall survival (OS) (p < 0.0001). The binary score based on the median of the continuous score stratified the patients into low and high score groups and also showed statistical significance in uni- and multivariate models. The 2-PS was validated using two independent transcriptomic datasets. Furthermore, gene set enrichment analysis using training and validation datasets showed that high score patients had distinct gene expression profiles. Our 2-PS also showed a correlation with the estimated infiltration by some immune cell fractions such as CD8+ T cells and M1/2 macrophages. Finally, 2-PS correlated with sensitivity or resistance to some commonly used chemotherapeutic drugs. This is the first study to demonstrate good performance of only two-gene expression-based prognostic scores in MPM. Our initial approach for features selection allowed for an increased likelihood for the predictive value of the developed score, which we were also able to demonstrate.