Increased Copy Number Research Articles

Abstract 5828: Functional role of long non-coding RNA YTHDF3-AS1 in breast cancer

Abstract Breast cancer (BrCa) is the most common form of cancer in women worldwide, impacting nearly 2.1 million women each year. Importantly, current treatment options for metastatic breast cancer fail to elicit an anti-tumor response, leading to a 5-year survival rate below 30%. While most classes of therapy focus on inhibiting or targeting specific proteins, long non-coding RNAs (lncRNAs) offer a unique, relatively untapped, source of potential therapeutic targets. Ongoing experiments are evaluating the regulatory role of the lncRNA YTHDF3-AS1 (ENSG00000270673), which has the potential to develop into a novel therapeutic intervention of BrCa. Through genome-wide analysis, we found that YTHDF3-AS1 expression correlates with essential developmental regulatory genes such as CA3, VPS28, EXOSC4, and TM2D2 and according to pathway analysis is likely linked with the Wnt pathway. Additionally, TCGA data reveals that over 5% of patients with BrCa have an increased copy number of YTHDF3-AS1. Although the role of YTHDF3-AS1 has yet to be explored, YTHDF3 expression was recently shown to be a critical driver of breast cancer metastasis. Of note, YTHDF3-AS1 is upstream of the protein-coding region, but within the promoter region of the YTHDF3 gene. Mechanistically, this allows the lncRNA YTHDF3-AS1 to potentially upregulate the expression of the protein-coding YTHDF3 gene, as two known functions of antisense lncRNAs describe the ability to 1) induce nearby gene expression through binding to the promoter region and 2) stabilize the RNA product of the nearby gene through binding to the 5’UTR. Interestingly, this manner of relationship between antisense (or "divergent") lncRNAs and their protein-coding partner was shown to be highly prevalent in pluripotent stem cells, with the downregulation of both the antisense and protein-coding transcripts following differentiation. Together, our preliminary analysis and previous literature suggest that the lncRNA YTHDF3-AS1 may contribute to the upregulation of YTHDF3, which is a known metastatic promoting protein. Our current study aims to determine the functional role of YTHDF3-AS1 in BrCa oncogenesis, with an emphasis on the mechanistic actions of this lncRNA for the development of future therapeutic approaches. Citation Format: Alakesh Bera, Surya Radhakrishnan, Eric Russ, Diya Biswas, Madhan Subramanian, Harvey B. Pollard, Hai Hu, Craig D. Shriver, Roopa Biswas, Meera Srivastava. Functional role of long non-coding RNA YTHDF3-AS1 in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5828.

Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome.

ABSTRACTPristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a 13C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a 13C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation.IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.

New Sights Into Long Non-Coding RNA LINC01133 in Cancer.

LINC01133 is a long intergenic non-coding RNA that regulates malignancy in several cancers, including those of the digestive, female reproductive, respiratory, and urinary system. LINC01133 is an extensively studied lncRNA that is highly conserved, and its relatively stable expression is essential for its robust biological function. Its expression is highly tissue-specific with a distinct subcellular localization. It functions as an oncogene or a tumor suppressor gene in different cancers via multiple mechanisms, such as those that involve competing with endogenous RNA and binding to RNA-binding proteins or DNA. Moreover, the secretion and transportation of LINC01133 by extracellular vesicles in the tumor micro-environment is regulated by other cells in the tumor micro-environment. To date, two mechanisms, an increase in copy number and regulation of transcription elements, have been found to regulate LINC01133 expression. Clinically, LINC01133 is an ideal marker for cancer prognosis and a potential therapeutic target in cancer treatment regimes. In this review, we aimed to summarize the aforementioned information as well as posit future directions for LINC01133 research.

Unraveling the mechanism of resistance in a glufosinate-resistant Palmer amaranth (Amaranthus palmeri) accession

AbstractGlufosinate resistance in Palmer amaranth (Amaranthus palmeri S. Watson) was recently detected in three accessions from Arkansas, USA. Amaranthus palmeri is the first and only broadleaf weed species resistant to this herbicide, and the resistance mechanism is still unclear. A previous study characterized the glufosinate resistance level in the accessions from Arkansas. A highly glufosinate-resistant accession was further used to investigate the mechanism conferring glufosinate resistance in A. palmeri. Experiments were designed to sequence the herbicide target enzyme cytosolic and chloroplastic glutamine synthetase isoforms (GS1 and GS2, respectively) and quantify copy number and expression. Absorption, translocation, and metabolism of glufosinate using the 14C-labeled herbicide were also evaluated in the resistant and susceptible accessions. The glufosinate-resistant accession had an increase in copy number and expression of GS2 compared with susceptible plants. All accessions showed only one GS1 copy and no differences in expression. No mutations were identified in GS1 or GS2. Absorption (54% to 60%) and metabolism (13% to 21%) were not different between the glufosinate-resistant and glufosinate-susceptible accessions. Most residues of glufosinate (94% to 98%) were present in the treated leaf. Glufosinate translocation to tissues above the treated leaf and in the roots was not different among accessions. However, glufosinate translocation to tissues below the treated leaf (not including roots) was greater in the resistant A. palmeri (2%) compared with the susceptible (less than 1%) accessions. The findings of this paper strongly indicate that gene amplification and increased expression of the chloroplastic glutamine synthetase enzyme are the mechanisms conferring glufosinate resistance in the A. palmeri accession investigated. Thus far, no additional resistance mechanism was observed, but further investigations are ongoing.

Convergent copy number increase of genes associated with freshwater colonization in fishes.

Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and cis-regulatory changes, little is known about the functional categories of genes in which CNV is important for adaptation to novel environments. It is also unclear whether the same genes repeatedly change the copy numbers for adapting to similar environments. Here, we investigate CNV associated with freshwater colonization in fishes, which was observed multiple times across different lineages. Using 48 ray-finned fishes across diverse orders, we identified 23 genes whose copy number increases were associated with freshwater colonization. These genes showed enrichment for peptide receptor activity, hexosyltransferase activity and unsaturated fatty acid metabolism. We further revealed that three of the genes showed copy number increases in freshwater populations compared to marine ancestral populations of the stickleback genus Gasterosteus. These results indicate that copy number increases of genes involved in fatty acid metabolism (FADS2), immune function (PSMB8a) and thyroid hormone metabolism (UGT2) may be important for freshwater colonization at both the inter-order macroevolutionary scale and at the intra-genus microevolutionary scale. Further analysis across diverse taxa will help to understand the role of CNV in the adaptation to novel environments. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.

Genetic and Epigenetic Mechanisms Deregulate the CRL2pVHL Complex in Hepatocellular Carcinoma.

Dysregulation of ubiquitin-proteasome pathway genes through copy number alteration, promoter hypomethylation, and miRNA deregulation is involved in cancer development and progression. Further characterizing alterations in these genes may uncover novel drug targets across a range of diseases in which druggable alterations are uncommon, including hepatocellular carcinoma (HCC). We analyzed 377 HCC and 59 adjacent non-malignant liver tissue samples, focusing on alterations to component genes of the widely studied CRL2pVHL E3 ubiquitin ligase complex. mRNA upregulation of the component genes was common, and was correlated with DNA hypomethylation and copy number increase, but many tumours displayed overexpression that was not explained by either mechanism. Interestingly, we found 66 miRNAs, including 39 previously unannotated miRNAs, that were downregulated in HCC and predicted to target one or more CRL2pVHL components. Several miRNAs, including hsa-miR-101-3p and hsa-miR-139-5p, were negatively correlated with multiple component genes, suggesting that miRNA deregulation may contribute to CRL2pVHL overexpression. Combining miRNA and mRNA expression, DNA copy number, and methylation status into one multidimensional survival analysis, we found a significant association between greater numbers of alterations and poorer overall survival for multiple component genes. While the intricacies of CRL2pVHL complex gene regulation require additional research, it is evident that multiple causes for the deregulation of these genes must be considered in HCC, including non-traditional mechanisms.

Preclinical Head and Neck Squamous Cell Carcinoma Models for Combined Targeted Therapy Approaches.

Simple SummaryHead and neck squamous cell carcinoma are characterized by a high degree of inter- and intratumoral heterogeneity. Well-characterized preclinical models represent the heterogeneity of this disease and enable the development of innovative therapeutic concepts. The present work dealt with the establishment of patient-individual tumor models to explore new treatment approaches for HNSCC patients and to identify suitable biomarkers for predicting treatment response. In this study, tumor specimens from advanced cancers of the oral cavity, hypopharynx, and larynx were used to establish individual tumor models. These novel cell lines were used to apply different combinations of strategies, preclinically, and to overcome intrinsic resistance mechanisms.This study aimed to refine combined targeted approaches on well-characterized, low-passage tumor models. Upon in vivo xenografting in immunodeficient mice, three cell lines from locally advanced or metastatic HNSCC were established. Following quality control and basic characterization, drug response was examined after therapy with 5-FU, Cisplatin, and cyclin-dependent kinase inhibitors (abemaciclib, THZ1). Our cell lines showed different in vitro growth kinetics, morphology, invasive potential, and radiosensitivity. All cell lines were sensitive to 5-FU, Cisplatin, and THZ1. One cell line (HNSCC48 P0 M1) was sensitive to abemaciclib. Here, Cyto-FISH revealed a partial CDKN2a deletion, which resulted from a R58* mutation. Moreover, this cell line demonstrated chromosome 12 polysomy, accompanied by an increase in CDK4-specific copy numbers. In HNSCC16 P1 M1, we likewise identified polysomy-associated CDK4-gains. Although not sensitive to abemaciclib per se, the cell line showed a G1-arrest, an increased number of acidic organelles, and a swollen structure. Notably, intrinsic resistance was conquered by Cisplatin because of cMYC and IDO-1 downregulation. Additionally, this Cisplatin-CDKI combination induced HLA-ABC and PD-L1 upregulation, which may enhance immunogenicity. Performing functional and molecular analysis on patient-individual HNSCC-models, we identified CDK4-gains as a biomarker for abemaciclib response prediction and describe an approach to conquer intrinsic CDKI resistance.

Copiotrophic Bacterial Traits Increase With Burn Severity One Year After a Wildfire

Wildfire and burn severity influence soil microbial communities during post-fire recovery. If post-fire differences in microbial communities affect soil carbon (C) pool dynamics, altered microbial communities could influence the transition of forests from C sources to C sinks during ecosystem recovery. For example, fire may change the abundance of copiotrophic and oligotrophic bacteria, influencing the kinetic rates of soil C pools due to differences in C-acquisition strategies and nutrient requirements. We assessed differences in soil bacterial communities and soil C pool kinetics 1 year after a wildfire in a mixed-conifer forest in northern California, United States. We determined whether differences in bacterial communities and soil C pools were related to copiotrophic versus oligotrophic life history strategies. Specifically, we assessed bacterial community oligotrophy versus copiotrophy based on phyla relative abundances and predicted 16S gene copy numbers. We then determined whether these life-histories were correlated with C pool kinetic rates. We further determined whether C degradation metabolic pathways predicted using PICRUSt2 were related to C pool kinetics. We found that copiotrophic bacteria exhibited greater abundance in burned areas than unburned areas, evidenced by increases in 16S rRNA gene copy number and by taxonomic classifications. Furthermore, the abundance of predicted metabolic pathways associated with fast-cycling C compounds increased with severity, including carbohydrate, alcohol, and amine degradation pathways, suggesting increased copiotrophic metabolic strategies. In contrast, the abundance of metabolic pathways of slow-cycling aromatic C compounds did not change, indicating oligotrophic metabolic strategies did not increase. The kinetic rate of the active C pool was positively related to the copiotrophic metabolic pathway of alcohol degradation, and negatively related to oligotrophic pathways like aromatic compound degradation. The links between C pool kinetics and phylum-level life-strategy classifications were ambiguous. Overall, our results suggest that metabolic life-strategies are related to soil C pool kinetics and could have short- and long-term impacts on soil C persistence during post-fire recovery. In the short-term, increased copiotrophy could increase soil C effluxviarapid cycling of labile C pools. However, over the longer-term lower prevalence of oligotrophic strategies could allow aromatic compounds associated with pyrogenic C to accumulate, increasing stable soil C stocks.

Impact of salivary and pancreatic amylase gene copy numbers on diabetes, obesity, and functional profiles of microbiome in Northern Japanese population

Amylase genes reside in a structurally complex locus, and their copy numbers vary greatly, and several studies have reported their association with obesity. The mechanism of this effect was partially explained by changes in the oral and gut microbiome compositions; however, a detailed mechanism has been unclarified. In this study, we showed their association with diabetes in addition to obesity, and further discovered a plausible mechanism of this association based on the function of commensal bacteria. First, we confirmed that the amylase copy number in the population tends to be larger than that reported in other studies and that there is a positive association between obesity and diabetes (p = 1.89E–2 and 8.63E–3). Second, we identified that relative abundance of some genus level microbiome, Capnocytophaga, Dialister, and previously reported bacteria, were significantly associated with amylase copy numbers. Finally, through functional gene-set analysis using shotgun sequencing, we observed that the abundance of genes in the Acarbose pathway in the gut microbiome was significantly decreased with an increase in the amylase copy number (p-value = 5.80E–4). Our findings can partly explain the mechanism underlying obesity and diabetes in populations with high amylase copy numbers.

Genotype by environment interactions for chronic wasting disease in farmed US white-tailed deer.

Despite implementation of enhanced management practices, chronic wasting disease in US white-tailed deer (Odocoileus virginianus) continues to expand geographically. Herein, we perform the largest genome-wide association analysis to date for chronic wasting disease (n = 412 chronic wasting disease-positive; n = 758 chronic wasting disease-nondetect) using a custom Affymetrix Axiom single-nucleotide polymorphism array (n = 121,010 single-nucleotide polymorphisms), and confirm that differential susceptibility to chronic wasting disease is a highly heritable () polygenic trait in farmed US white-tailed deer, but with greater trait complexity than previously appreciated. We also confirm PRNP codon 96 (G96S) as having the largest-effects on risk (P ≤ 3.19E-08; phenotypic variance explained ≥ 0.025) across 3 US regions (Northeast, Midwest, South). However, 20 chronic wasting disease-positive white-tailed deer possessing codon 96SS genotypes were also observed, including one that was lymph node and obex positive. Beyond PRNP, we also detected 23 significant single-nucleotide polymorphisms (P-value ≤ 5E-05) implicating ≥24 positional candidate genes; many of which have been directly implicated in Parkinson’s, Alzheimer’s and prion diseases. Genotype-by-environment interaction genome-wide association analysis revealed a single-nucleotide polymorphism in the lysosomal enzyme gene ARSB as having the most significant regional heterogeneity of effects on chronic wasting disease (P ≤ 3.20E-06); with increasing copy number of the minor allele increasing susceptibility to chronic wasting disease in the Northeast and Midwest; but with opposite effects in the South. In addition to ARSB, 38 significant genotype-by-environment single-nucleotide polymorphisms (P-value ≤ 5E-05) were also detected, thereby implicating ≥ 36 positional candidate genes; the majority of which have also been associated with aspects of Parkinson’s, Alzheimer’s, and prion diseases.

Rapid evolution and mechanism elucidation for efficient cellobiose-utilizing Saccharomyces cerevisiae through Synthetic Chromosome Rearrangement and Modification by LoxPsym-mediated Evolution

Lack of cellobiose utilization capability for many microorganisms results in carbon source waste in lignocellulosic biorefinery. In this study, genes for cellobiose transport and hydrolysis were introduced to Saccharomyces cerevisiae synV, a semi-synthetic yeast with an inducible SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxPsym-mediated Evolution) system incorporated into its chromosome V, endowing cellobiose utilization capability to this strain. Thereafter, two evolved strains with 98.1% and 79.2% improvement, respectively, in cellobiose utilization rate were obtained through induced SCRaMbLE. Further studies suggested that the enhanced cellobiose utilization capability directly correlated with copy number increases of introduced genes and some chromosome structural variations. In particular, it was experimentally demonstrated for the first time that deletion of redox stress related gene MXR1 and ATP conversion related gene ADK2 contributed to enhanced cellobiose conversion. Thereafter, the effectiveness of MXR1 and ADK2 deletions was demonstrated in artificial hydrolysate and rice straw hydrolysate, respectively.

Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager’s activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

Basophil depletion alters host immunity, intestinal permeability and mammalian host-to-mosquito transmission in malaria.

Abstract Malaria-induced bacteremia has been shown to result from intestinal mast cell (MC) activation (Chau et al. 2013, Potts et al. 2016, Céspedes et al. 2020). The appearance of MCs in the ileum and increased permeability to enteric bacteria are preceded by an early Th2-biased host immune response to infection, characterized by the appearance of IL-4, IL-10, mast cell protease (Mcpt)1 and Mcpt4, and an increase in circulating basophils and eosinophils. Given the functional similarities of basophils and MCs in the context of allergic inflammation and the capacity of basophils to produce IL-4 in large amounts, we sought to define the role of basophils in the development of increased intestinal permeability and in MC influx and the development of bacteremia in the context of malaria. Upon infection with non-lethal Plasmodium yoelii yoelii 17XNL, mice that lack basophils exhibited increased intestinal permeability and increased ileal MC numbers, without any increase in bacterial 16S ribosomal DNA copy numbers in the blood, relative to non-depleted mice. Analysis of cytokines, chemokines and MC-associated factors in the ileum revealed significantly increased TNFα and IL-13 at day 6 post infection (PI) in basophil-depleted mice compared to non-depleted mice. Moreover, network analysis revealed profound differences between depleted and non-depleted mice over time following infection in both systemic and local immune responses to parasites and translocated bacteria. Finally, basophil depletion was associated with significantly increased gametocytemia and parasite transmission to mosquitoes, suggesting that basophils play a previously undescribed role in controlling gametocytemia and in turn, mammalian host-to-mosquito transmission. This work was supported by NIH NIAID RO1 AI131609 to Shirley Luckhart.

Increased tryptase expression in HαT is associated with upregulation of epithelia-derived MRGPRX2 agonists and MRGPRX2+ MCs in the GI mucosa

Abstract Hereditary α-tryptasemia (HαT) is a genetic trait characterized by elevated serum tryptase and increased copy number of the TPSAB1 gene. It is associated with flushing, itching, GI symptoms and anaphylaxis. HαT gut epithelia undergo increased rates of pyroptosis, and HαT gut mast cells (MCs) are increased in number with highly expressed FCER1 and CD203C. Gut MCs express Mas-related G protein–coupled receptor-X2 (MRGPRX2). Studies have clearly shown that this receptor contributes to host defense, mediates pseudo-allergy, and is involved in a number of atopic skin conditions. Herein, we sought to evaluate the impact of MRGPRX2 in individuals with HαT and GI symptoms. We observed increased numbers of MRGPRX2+ mast cells in HαT versus non-HαT gastrointestinal (GI) biopsies (colon->duodenum->stomach->Ileum). mRNA expression of tryptase and MRGPRX2 in intestine of HαT increased ~6-fold and 3-fold respectively over non-HαT biopsies. Epithelial derived agonists of MGPRX2 including human beta defensin (HBD) 2 and adrenomedullin (PAMP12) mRNA expression were also found to be upregulated ~2-fold and ~3-folds in HαT over non-HαT biopsies. MC protease carboxydeptidase-3 was also increased. Taken together, this data suggests that in addition to upregulation of MRGPRX2 in MCs, increased tryptase expression in HαT leads to upregulation of MRGPRX2 agonists and modifiers in gut epithelial cells, nociceptors and MCs, and results in GI symptoms. This work was supported by National Institutes of Health grants R01-AI124182, R01-AI143185 and R01-AI149487 to Hydar Ali.

MOTS‐c protein expression increases following aerobic exercise training and remains elevated during detraining

Mitochondrial open reading frame of the 12S rRNA‐c (MOTS‐c) is a mitochondrial‐derived peptide that is released into the circulation following intense physical activity and, purportedly, has systemic impacts on energy metabolism and insulin sensitivity. Exogenous administration of MOTS‐c in rodent models enhances physical activity / endurance and reduces fat mass in aged mice through the regulation of, in part, the glycolysis / pentose phosphate pathway and amino acid metabolism. Considering that mitochondrial volume and mitochondrial DNA copy number increase following chronic aerobic exercise training, we hypothesized that MOTS‐c expression also would be elevated in exercise‐trained skeletal muscle. MOTS‐c protein expression from phenotypically mixed plantaris muscles of adult female Sprague Dawley rats were compared from six conditions: sedentary (SED; n=11), voluntary exercise training for four (EX4; n=9), six (EX6; n=6), or eight weeks (EX8; n=8), and detraining after four (DETR4) or six (DETR6) weeks, which followed four or six weeks of exercise training, respectively. Total running distances were ~551±61, 371±94, 560±71, 321±44, and 519±27 km for EX4, EX6, EX8, DETR4 and DETR6, respectively. DETR4 rat running distance was significantly lower than EX4, EX8, and DETR6 rats (p<0.01). Total muscle protein homogenate was isolated from mid‐belly muscle chunks and separated using 15% SDS‐PAGE gels (10 μg/sample). Following transfer, membranes were incubated with a custom rabbit anti‐rat MOTS‐c polyclonal antibody, developed, scanned, stripped and re‐probed for GAPDH as a loading control. MOTS‐c protein was significantly elevated from SED (set at 100%) to 188±61, 158±37, 212±27, 168±29, 223±36% in EX4, EX6, EX8, DETR4 and DETR6, respectively (p<0.05). Furthermore, preliminary findings indicate that MOTS‐c is present exclusively within the cytoplasm of skeletal muscle and not compartmentalized within the nuclei or mitochondria. Given that long‐term aerobic exercise augments mitochondrial volume within skeletal muscle, our data suggest that the observed increase in MOTS‐c protein in the present study parallels this mitochondrial adaptation to aerobic physical activity. Taken together, these findings indicate that a more aerobically‐trained individual would have an enhanced MOTS‐c presence within skeletal muscle and, therefore, a greater potential to regulate energy and insulin sensitivity when MOTS‐c is released systemically; additionally, the potential benefits of MOTS‐c are sustained during a period of physical inactivity (e.g., detraining) following exercise training.

Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals.

The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (Dicentrarchus labrax). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (Hermetia illucens, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families Bacillaceae, Enterococcaceae, and Lachnospiraceae and the Actinobacteria family Actinomycetaceae, which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in Paenibacillus and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (Tenebrio molitor, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from Paenibacillus species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.

Effects of Tolerance-Induced Preconditioning on Mitochondrial Biogenesis in Undifferentiated and Differentiated Neuronal Cells.

Mitochondrial biogenesis occurs in response to chronic stresses as an adaptation to the increased energy demands and often renders cells more refractive to subsequent injuries which is referred to as preconditioning. This phenomenon is observed in several non-neuronal cell types, but it is not yet fully established in neurons, although it is fundamentally important for neuroprotection and could be exploited for therapeutic purposes. This study was designed to examine whether the preconditioning treatment with hypoxia or nitric oxide could trigger biogenesis in undifferentiated and differentiated neuronal cells (rat PC12 and human NT2 cells) as well as in primary mouse cortical neurons. The results showed that both preconditioning paradigms induced mitochondrial biogenesis in undifferentiated cell lines, as indicated by an increase of mitochondrial mass (measured by flow cytometry of NAO fluorescence) and increased expression of genes required for mitochondrial biogenesis (Nrf1, Nrf2, Tfam, Nfκb1) and function (Cox3, Hk1). All these changes translated into an increase in the organelle copy number from an average of 20-40 to 40-60 mitochondria per cell. The preconditioning treatments also rendered the cells significantly less sensitive to the subsequent oxidative stress challenge brought about by oxygen/glucose deprivation, consistent with their improved cellular energy status. Mitochondrial biogenesis was abolished when preconditioning treatments were performed in the presence of antioxidants (vitamin E or CoQ10), indicating clearly that ROS-signaling pathway(s) played a critical role in the induction of this phenomenon in undifferentiated cells. However, mitochondrial biogenesis could not be re-initiated by preconditioning treatments in any of the post-mitotic neuronal cells tested, i.e., neither rat PC12 cells differentiated with NGF, human NT2 cells differentiated with retinoic acid nor mouse primary cortical neurons. Instead, differentiated neurons had a much higher organelle copy number per cell than their undifferentiated counterparts (100-130 mitochondria per neuron vs. 20-40 in proliferating cells), and this feature was not altered by preconditioning. Our study demonstrates that mitochondrial biogenesis occurred during the differentiation process resulting in more beneficial energy status and improved tolerance to oxidative stress in neurons, putting in doubt whether additional enhancement of this phenomenon could be achieved and successfully exploited as a way for better neuroprotection.

Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection.

The spread of genes encoding antibiotic resistance is often mediated by horizontal gene transfer (HGT). Many of these genes are associated with transposons, a type of mobile genetic element that can translocate between the chromosome and plasmids. It is widely accepted that the translocation of antibiotic resistance genes onto plasmids potentiates their spread by HGT. However, it is unclear how this process is modulated by environmental factors, especially antibiotic treatment. To address this issue, we asked whether antibiotic exposure would select for the transposition of resistance genes from chromosomes onto plasmids and, if so, whether antibiotic concentration could tune the distribution of resistance genes between chromosomes and plasmids. We addressed these questions by analysing the transposition dynamics of synthetic and natural transposons that encode resistance to different antibiotics. We found that stronger antibiotic selection leads to a higher fraction of cells carrying the resistance on plasmids because the increased copy number of resistance genes on multicopy plasmids leads to higher expression of those genes and thus higher cell survival when facing antibiotic selection. Once they have transposed to plasmids, antibiotic resistance genes are primed for rapid spread by HGT. Our results provide quantitative evidence for a mechanism by which antibiotic selection accelerates the spread of antibiotic resistance in microbial communities.

Increased Expression of SETDB1 Predicts Poor Prognosis in Multiple Myeloma

Several genes on chromosome 1q21 region predict a high risk of multiple myeloma (MM); however, the underlying molecular pathology remains elusive. Overexpression, amplification, or activation of SET Domain Bifurcated 1 (SETDB1), which is located on 1q21, is closely associated with poor prognosis of many human solid malignancies. In our study, upregulation of SETDB1 might indicate an unfavorable prognosis of MM using bioinformatics analysis from GEO databases and MMRF-CoMMpass. Here, increased SETDB1 expression was observed in the plasma cells from newly diagnosed multiple myeloma patients compared to those from the normal controls. Meanwhile, SETDB1 overexpression was the result of increased copy numbers of SETDB1 gene. In MM patients, the Kaplan-Meier analysis was employed to demonstrate that increased SETDB1 expression was associated with shorter overall survival (OS) and event-free survival (EFS). Besides, we conducted multifactorial cox regression analysis to state that SETDB1 expression was an independent biomarker for OS and EFS. MM patients with higher SETDB1 expression showed higher levels of beta-2 microglobulin (β2M), lactate dehydrogenase (LDH), and bone marrow biopsy plasma cells (BMPC) and lower levels of haemoglobin (HGB). Functional enrichment analysis suggested that SETDB1 could promote cell cycle progression in myeloma. Finally, we observed that SETDB1 was distinctly correlated with tumor immunity in MM. SETDB1 expression in myeloma cells was positively correlated with CD56dim natural killer cells but negatively correlated with infiltrating levels of type17 T helper cells, effector memory CD8 T cells, activated dendritic cells, and natural killer T cells from whole bone marrow (WBM) biopsies. Taken together, these results indicated that SETDB1 could be used as a novel biomarker for predicting the prognosis of MM patients.

Abstract P2-05-02: Low molecular weight cyclin E facilitate replication stress tolerance in breast cancer development

Abstract Low Molecular Weight Cyclin E (LMW-E) are the tumor specific, oncogenic forms of cyclin E that are post translationally generated by neutrophil elastase (NE) mediated cleavage of the 50 KDa full-length cyclin E1 (FL-cycE, encoded by CCNE1 gene). While FL-cycE localizes mainly to the cell nucleus, LMW-E lack the N-terminus nuclear localization signal and are detected in both the nucleus and cytoplasm. Compared to FL-cycE, LMW-E exhibit longer half-life and higher affinity to their kinase partner CDK2 and are resistant to natural CDK inhibitors such as p21 and p27. It is currently assumed that LMW-E drive the tumorigenic process by promoting G1/S cell cycle transition and accelerating mitotic exit. Here we report that LMW-E overexpression also promotes genomic instability by deregulating DNA replication in a CDC6 dependent manner. To this end, we developed an immunohistochemistry (IHC) assay with a cyclin E antibody that can identify LMW-E expressing tumors and examined the association of genetic instability of each tumor with LMW-E status in 2 different cohorts of breast cancer patients. Cohort 1 is a retrospective cohort of 725 patients with stage I-II breast cancer treated at MD Anderson (Houston, TX) between 1985 and 1999. Cohort 2 is a prospective cohort of 85 patients with stage I-II breast cancer who enrolled in our study at MD Anderson between January 2000 and June 2010. Our results show that positive LMW-E status in stage 1 or 2 breast cancer patients correlates with increasing copy number variations, as identified by Molecular Inversion Probe (MIP) in cohort 1 and somatic mutations, as identified by Whole Exome Sequencing (WES) in cohort 2. Second, using immortalized human mammary epithelial cells (hMECs) engineered to express doxycycline inducible LMW-E or FL-cycE in CCNE1 knock-out background, we found that FL-cycE over-expression leads to DNA damage, cell cycle arrest and cell death. LMW-E overexpression, on the other hand, facilitates cell proliferation with damaged DNA, resulting in multi-nuclei and micro-nuclei formation in daughter cells. Third, overexpression of FL-cycE reduces chromatin bound MCM complex, while LMW-E overexpression promotes the chromatin loading of pre-replication complex including MCMs. Lastly, we show that LMW-E but not FL-cycE is the major form of cyclin E that binds to the chromatin. Specifically, in both LMW-Einducible hMECs and LMW-Ehighbreast tumor cell lines, CDC6 is required for the nuclear translocation and chromatin loading of LMW-E. Our findings have revealed the unique oncogenic function of LMW-E in deregulating replication licensing, promoting replication stress tolerance and genomic instability that fuels tumor development. These findings also provide potential novel therapeutic strategies for treating LMW-Ehigh breast tumors, who do not respond to the current standard of care therapies. Citation Format: Mi Li, Kwang Huei Low, Tuyen Bui, Kelly K Hunt, Khandan Keyomarsi. Low molecular weight cyclin E facilitate replication stress tolerance in breast cancer development [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-05-02.