Comparative Gene Expression Analysis Research Articles

Identifying early response genes against apple Marssonina blotch via comparative gene expression analysis between resistant and susceptible cultivars

Apple Marssonina blotch, caused by the fungus Diplocarpon mali (D. mali), is a severe disease in the world. This disease causes early defoliation and reduces fruit quality and tree growth. Considering the importance of defense mechanisms that begin with early reactions, we tried to identify the genes showing early response against D. mali among flavonoid biosynthesis, antioxidants, transcription factors, and pathogenesis-related (PR) genes. We artificially inoculated D. mali suspensions on detached leaves of resistant and susceptible ‘Jiguan’ and ‘Mutsu’ apples as cultivars, respectively. Gene expression was examined at 0, 3, 6, 12, 24, 48, and 72 h post inoculation (hpi) and 7, 10, and 13 days post inoculation (dpi) and divided into early (0–12 hpi), middle (24–72 hpi), and late (7–13 dpi) stages. In ‘Jiguan’ inoculated leaves, up-regulated genes were mainly involved in the flavonoid pathway and antioxidant activity, which most likely have played an antifungal role against D. mali by maintaining free radicals and decreasing oxidative damage in plant cells. In particular, most flavonoid biosynthetic genes are significantly induced in the early stage, implying that they are early response genes. On the contrary, all PR genes were rapidly induced in inoculated ‘Mutsu’ leaves, especially when symptoms were clearly visible. These results provide insight into the genetic factors that contribute to suppressing or limiting D. mali infection at an early stage.

BOMA, a machine-learning framework for comparative gene expression analysis across brains and organoids

Our machine-learning framework, brain and organoid manifold alignment (BOMA), first performs a global alignment of developmental gene expression data between brains and organoids. It then applies manifold learning to locally refine the alignment, revealing conserved and specific developmental trajectories across brains and organoids. Using BOMA, we found that human cortical organoids better align with certain brain cortical regions than with other non-cortical regions, implying organoid-preserved developmental gene expression programs specific to brain regions. Additionally, our alignment of non-human primate and human brains reveals highly conserved gene expression around birth. Also, we integrated and analyzed developmental single-cell RNA sequencing (scRNA-seq) data of human brains and organoids, showing conserved and specific cell trajectories and clusters. Further identification of expressed genes of such clusters and enrichment analyses reveal brain- or organoid-specific developmental functions and pathways. Finally, we experimentally validated important specific expressed genes through the use of immunofluorescence. BOMA is open-source available as a web tool for community use.

Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa.

Rhodomyrtus tomentosa is an important fleshy-fruited tree and a well-known medicinal plant of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world. However, studies on the evolution and genomic breeding of R. tomentosa were hindered by the lack of a reference genome. Here, we presented a chromosome-level gap-free T2T genome assembly of R. tomentosa using PacBio and ONT long read sequencing. We assembled the genome with size of 470.35Mb and contig N50 of ~43.80Mb with 11 pseudochromosomes. A total of 33 382 genes and 239.31Mb of repetitive sequences were annotated in this genome. Phylogenetic analysis elucidated the independent evolution of R. tomentosa starting from 14.37MYA and shared a recent WGD event with other Myrtaceae species. We identified four major compounds of anthocyanins and their synthetic pathways in R. tomentosa. Comparative genomic and gene expression analysis suggested the coloring and high anthocyanin accumulation in R. tomentosa tends to be determined by the activation of anthocyanin synthesis pathway. The positive selection and up-regulation of MYB transcription factors were the implicit factors in this process. The copy number increase of downstream anthocyanin transport-related OMT and GST gene were also detected in R. tomentosa. Expression analysis and pathway identification enriched the importance of starch degradation, response to stimuli, effect of hormones, and cell wall metabolism during the fleshy fruit development in Myrtaceae. Our genome assembly provided a foundation for investigating the origins and differentiation of Myrtaceae species and accelerated the genetic improvement of R. tomentosa.

Comparative Analysis of Gene Expression in Selected Drought Resistant Vegetables

Comparative Analysis of Gene Expression in Selected Drought Resistant Vegetables

Dynamic Transcriptome Changes Driven by the Mutation of OsCOP1 Underlie Flavonoid Biosynthesis and Embryogenesis in the Developing Rice Seed

CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase, functions as a central repressor of light signaling and regulates various light-mediated developmental and metabolic processes in plants. However, detailed mechanisms underlying COP1-regulated flavonoid biosynthesis and embryogenesis in rice seeds remain largely unknown. Here, we performed transcriptome analysis of the rice cop1 (yellowish-pericarp embryo lethal [yel]) null mutant, characterized by flavonoid accumulation in pericarp and abnormal development of embryo, to identify and profile the expression genes involved in flavonoid biosynthesis and embryo development. Comparative transcriptome analysis of yel-hc and wild-type seeds revealed 979 differentially expressed genes (DEGs), of which 577 were upregulated and 402 were downregulated in yel-hc seeds. Functional annotation of DEGs revealed that DEGs were mainly enriched in ‘metabolism’, ‘transcription factors’, ‘secondary metabolites’, and ‘flavonoid biosynthesis’. The DEGs encoding AP2-EREBP, MYB, and bZIP transcription factors (TFs) were predominantly upregulated, whereas those encoding HB, bHLH, and ABI3VP1 TFs were downregulated in yel-hc seeds. Comparative gene expression analysis revealed that genes involved in the C-glycosyl flavone biosynthesis pathway, including OsP1, were activated, whereas anthocyanin biosynthesis genes showed no significant change in expression. In addition, transcript levels of embryo development-related genes, especially homeobox auxin regulation genes, as well as somatic embryogenesis-related genes, were significantly downregulated in yel-hc. Taken together, these results indicate that OsCOP1 plays a crucial role in regulation of flavonoid biosynthesis and embryo structure formation, and changes in the expression of light signal transduction-related genes could have a significant impact on flavonoid biosynthesis and embryogenesis in rice seed.

Unique Patterns of Heterogeneous Mismatch Repair Protein Expression in Colorectal Cancer Unveil Different Degrees of Tumor Mutational Burden and Distinct Tumor Microenvironment Features

Mismatch repair (MMR) protein expression in colorectal cancer (CRC) cells is usually homogeneously retained or lost. Rare lesions may show a heterogeneous pattern of MMR protein expression. We evaluated MMR protein expression (MLH1, MSH2, MSH6, and PMS2) in 200 CRCs, identifying 3 groups with proficient MMR protein expression (MMRp), deficient MMR protein expression (MMRd), and heterogeneous MMR protein expression (MMRh). MMRh tumors were microdissected on the basis of the expression of the heterogeneous marker. DNA was extracted and subjected to targeted sequencing. RNA was purified from bulk tumors of all MMRh cases and in a control series of 15 MMRp and 10 MMRd CRCs and analyzed using the PanCancer IO 360 Panel (NanoString Technologies). Twenty-nine of the 200 cases (14.5%) were MMRd. Nine cases (4.5%) showed a heterogeneous pattern of MMR expression, with 6 tumors harboring concomitant loss of one of the other MMR proteins, thus featuring areas with double loss at immunohistochemistry (IHC) testing (MMRh double-loss cases). Four of the 6 MMRh double-loss cases were suitable for a separate sequence variant analysis of IHC double-negative and IHC single-negative components of the tumor. In all lesions, both components exhibited a high tumor mutation burden (TMB). Nevertheless, a significant increase in TMB in the double-negative components was observed (mean TMB: negative, 70 mut/Mb vs positive, 59 mut/Mb) because of a higher number of subclonal variants compared with the other component. Comparative gene expression analyses among MMRd, MMRp, and MMRh CRCs highlighted differential gene expression patterns and an increased number of tumor-infiltrating lymphocytes in MMRh lesions, which is also characterized by a substantial population of exhausted CD8+ lymphocytes. We describe a unique subgroup of CRCs showing heterogeneous expression of MMR proteins in a background of concomitant loss of one of the other markers.

Identifying Biomarkers for Osteogenic Potency Assay Development.

There has been extensive exploration of how cells may serve as advanced therapy medicinal products to treat skeletal pathologies. Osteoblast progenitors responsible for production of extracellular matrix that is subsequently mineralized during bone formation have been characterised as a rare bone marrow subpopulation of cell culture plasticadherent cells. Conveniently, they proliferate to form single-cell derived colonies of fibroblastoid cells, termed colony forming unit fibroblasts that can subsequently differentiate to aggregates resembling small areas of cartilage or bone. However, donor heterogeneity and loss of osteogenic differentiation capacity during extended cell culture have made the discovery of reliable potency assay biomarkers difficult. Nonetheless, functional osteoblast models derived from telomerised human bone marrow stromal cells have allowed extensive comparative analysis of gene expression, microRNA, morphological phenotypes and secreted proteins. This chapter highlights numerous insights into the molecular mechanisms underpinning osteogenic differentiation of multipotent stromal cells and bone formation, discussing aspects involved in the choice of useful biomarkers for functional attributes that can be quantitively measured in osteogenic potency assays.

Comparative Analysis of Global Hepatic Gene Expression in Adolescents and Adults with Non-alcoholic Fatty Liver Disease.

To gain insights into the mechanisms underlying distinct nonalcoholic fatty liver disease (NAFLD) histological phenotypes between children and adults, we compared hepatic gene expression profiles associated with NAFLD phenotypes between the two age groups. Histological characteristics of intra-operative liver biopsies from adolescents and adults undergoing bariatric surgery were assessed by the same pathologist using the non-alcoholic steatohepatitis (NASH) Clinical Research Network scoring system. Hepatic gene expression was measured by microarray analysis. Transcriptomic signatures of histological phenotypes between the two groups were compared, with significance defined as p-value <0.05 and a fold change >1.5. In 67 adolescents and 76 adults, distribution of histological phenotypes was: not-NAFLD (controls) 51% vs 39%, NAFL 39% vs 37%, and NASH 10% vs 24%, respectively. There were 279 differentially expressed genes in adolescents and 213 in adults with NAFLD vs controls. In adolescents, transcriptomes for NAFL vs controls, and borderline vs definite NASH were undifferentiable, whereas in adults, NAFL and borderline NASH demonstrated a transcriptomic gradient between controls and definite NASH. When applied to adolescents, significant adult genes discriminated borderline and definite NASH from control and NAFL, but the majority of significant pediatric genes were not portable to adults. Genes associated with NASH in adolescents and adults showed some ontological consistency but notable differences. There is some similarity but major differences in the transcriptomic profiles associated with NAFLD between adolescents and adults with severe obesity. These data suggest different mechanisms contribute to the pathogenesis of NAFLD severity at different stages in life.

Вариабельность ответа костно-минерального обмена у женщин с хирургической менопаузой на менопаузальную гормональную терапию

Patients with surgical menopause rapidly develop signs of osteopenia and osteoporosis. Hormone replacement therapy (HRT) for menopause increases bone mineral density (BMD). However, the positive metabolic effects of HRT vary widely. The variability of response to HRT may depend on the sensitivity of these cells to steroid hormones, i.e., the level of steroid receptors in them. An indirect indicator of the sensitivity of osteoclasts to HRT components can be the level of transcription of estradiol and progesterone receptors in peripheral blood mononuclear cells (PBMCs). Objective. To determine the transcriptome of PBMCs in patients with surgical menopause against the background of HRT using a combination of 1 mg estradiol and 5 mg dydrogesterone in cyclic regimen and to study its effect on BMD. Patients and methods. A total of 16 women aged 40–55 years with a duration of surgical menopause ranging from 12 months to 6 years were examined. An inclusion criterion for this study was the absence of contraindications for HRT. The subject of the study was determination of BMD by dual-energy X-ray absorptiometry and expression levels of estradiol and progesterone receptor genes by polymerase chain reaction (PCR). Results. Comparative analysis of estrogen and progesterone gene expression in PBMCs revealed a difference in gene expression: a 2-fold decrease in membrane estradiol receptor (mER) expression (p = 0.0420), a 2-fold decrease in nuclear estradiol receptor (ERβ) expression (p = 0.0295), and a 3-fold decrease in nuclear progesterone receptor (PR-B) expression (p = 0.0480) in PBMCs of patients in the group with no HRT effect on BMD. Conclusion. Estradiol (mER and ERβ) and progesterone (PR-B) receptor mRNA levels in PBMCs of women with surgical menopause may serve as a prognostic marker of treatment efficacy. Key words: menopause, hormone replacement therapy, bone mineral density, peripheral blood mononuclear cells, dydrogesterone, estradiol

Dominant constraints on the evolution of rhythmic gene expression

Although the individual transcriptional regulators of the core circadian clock are distinct among different organisms, the autoregulatory feedback loops they form are conserved. This unified design principle explains how daily physiological activities oscillate across species. However, it is unknown whether analogous design principles govern the gene expression output of circadian clocks. In this study, we performed a comparative analysis of rhythmic gene expression in eight diverse species and identified four common distribution patterns of cycling gene expression across these species. We hypothesized that the maintenance of reduced energetic costs constrains the evolution of rhythmic gene expression. Our large-scale computational simulations support this hypothesis by showing that selection against high-energy expenditure completely regenerates all cycling gene patterns. Moreover, we find that the peaks of rhythmic expression have been subjected to this type of selective pressure. The results suggest that selective pressure from circadian regulation efficiently removes unnecessary gene products from the transcriptome, thereby significantly impacting its evolutionary path.

Expression heterogeneity of ABC-transporter family genes and chemosensitivity genes in gastric tumor, carcinomatosis and lymph node metastases

Introduction. Metastatic tumors (particularly gastric cancer) have been found to be characterized by heterogeneity between the primary tumor and metastases. This type of heterogeneity comes to the fore when treating primary-metastatic forms of tumor and is an important reason for the low effectiveness of their treatment. In this regard, comparative analysis of ABC-transporter gene expression and chemosensitivity genes will allow to characterize to a certain extent the resistance and sensitivity of primary tumor, carcinomatosis and metastases to therapy and provide the basis for personalized treatment approach.Aim. To evaluate expression heterogeneity of ABC-transporter genes and chemosensitivity genes in gastric tumor, carcinomatosis and lymph node metastases.Materials and methods. Overall 41 patients with disseminated gastric cancer stage IV with carcinomatosis of peritoneum were included in the investigation. All patients underwent surgery according to Roux palliative gastrectomy. After surgery patients underwent chemotherapy depending on indications. RNA was isolated using RNeasy Plus mini kit (Qiagen, Germany). The expression level of ABC transporter genes (ABCB1, ABCC1, ABCC2, ABCC5, ABCG1, ABCG2) and chemosensitivity genes (BRCA1, RRM1, ERCC1, TOP1, TOP2α, TUBβ3, TYMS, GSTP1) was assessed by reverse transcription polymerase chain reaction (RT-PCR) in primary tumor, carcinomatosis and lymph node metastases.Results. The expression levels of the genes under study were shown to vary widely. For ABC transporter genes, ABCG1 (3.1 ± 1.1; max 32.0), ABCG2 (7.9 ± 2.3; max 54.1), ABCG2 (9.6 ± 3.8; max 101.0) were the most expressed genes in gastric tumor tissue, carcinomatosis and lymph node metastasis, respectively. Hyperexpression among chemosensitivity genes at all three sites was characteristic only of TOP2α (17.2 ± 6.0; max. 161.9; 10.8 ± 4.1; max. 105.1; 35.3 ± 0.8; max. 439.6, respectively). We found that TOP2α and BRCA1 gene expression levels were higher in lymph node metastasis compared with gastric tumor tissue and carcinomatosis (at p = 0.005 and p = 0.001). Whereas ABCC1 gene expression was statistically significantly higher in carcinomatosis (p = 0.03).Conclusion. Thus, a high level of expression heterogeneity is observed in gastric cancer, which affects the expression patterns of various genes in different localizations. The expression profile can be used to determine the level of heterogeneity and approach to personalized therapy tactics.

Resistance to chicken amyloid arthropathy is associated with a dysfunctional mutation in serum amyloid A.

Chicken amyloid arthropathy is a debilitating disease with a major impact on animal welfare. Since the disease is triggered by bacterial infection, preventative treatment also contributes to the widespread overuse of antibiotics. Bacterial infection initiates an acute phase response including increased serum amyloid A (SAA) production by the liver. SAA accumulates at sites of infection and in particular in large joints of affected birds. Interestingly, white egg-laying chickens (WL) are resistant to the disease whilst brown egg-laying chickens (BL) are most affected. Disease susceptibility has an immunological basis but the possible contribution of underlying genetic risk factors is not understood. Using a whole genome sequencing approach, we discovered a novel variant in the SAA gene in WL, which is predicted to result in an arginine to serine substitution at position 90 (SAA.R90S). Surprisingly, when overexpressed in chicken hepatocellular carcinoma cells, SAA.R90S was expressed at a higher rate and secreted to a greater degree than the wild-type SAA protein. Moreover, RNASeq analysis showed that the R90S mutant exerted a differential effect on the expression of core transcription factors linked to cell fate determination and cell differentiation. Comparative analysis of gene expression in murine CD4 T-cells stimulated with IL-6/SAA, suggests that SAA.R90S might block an induced cell fate change toward pro-inflammatory T helper 17 cells, which are required for immunological protection against pathogenic bacteria during an acute phase response. Our results provide first mechanistic insights into the genetic resistance of WL to amyloid arthropathy and could be applied to commercial layer breeding programs to improve animal welfare and reduce the negative effects of the overuse of antibiotics.

The Prostate Stromal Transcriptome in Aggressive and Lethal Prostate Cancer.

Prostate cancer has a heterogeneous prognosis. Most previous studies have focused on the identification of prognostic biomarkers in the prostate cancer tumor. However, it is increasingly recognized that the tumor microenvironment contributes to prostate cancer aggressiveness and progression. We therefore examined whole transcriptome expression of the prostate stroma and associations with aggressive and lethal prostate cancer. We performed RNA sequencing (Illumina TruSeq Exome Capture) of 272 tumor-adjacent and 120 benign-adjacent macrodissected prostate stromal samples from 293 men with prostate cancer from the Health Professionals Follow-up Study and Physicians' Health Study. We performed differential expression analysis comparing gene expression and pathways by Gleason score and lethal outcome. We also tested a previously developed stromal gene signature of Gleason score in these datasets. Comparing high- with low-Gleason score cancers, 26 genes (P < 0.001) and 12 pathways (FDR < 0.20) were significantly differentially expressed in tumor-adjacent stroma, including pathways related to stroma composition remodeling and DNA repair, with 73 genes and 65 pathways significant in benign-adjacent stroma. Comparing lethal with nonlethal prostate cancer, 11 genes were differentially expressed in tumor-adjacent and 15 genes in benign-adjacent stroma, and pathways involved in inflammatory response were differentially enriched in both tumor and benign-adjacent stroma. In addition, our previously identified Gleason stromal gene signature was validated to be associated with Gleason score in these data. Implications: Our study uncovers stroma-specific genes and pathways that are differentially enriched with high Gleason score and lethal prostate cancer, demonstrating that the molecular investigation of the tumor microenvironment can provide additional information about prostate cancer prognosis.

Comparative transcriptomics of growth metabolism and virulence reveal distinct morphogenic profiles of yeast-like cells and hyphae of the fungus Metarhizium rileyi

Metarhizium rileyiis an entomopathogenic fungus with a narrow host range which distinguishes it from other Metarhiziumspecies with broad host ranges. This species is also unique because the initial yeast-like growth on solid media is only observed in liquid culture in other Metharizium species. A lack of knowledge about the metabolism and genetic signatures of M. rileyiduring this yeast-like phase on solid and in liquid media is a bottleneck for its large-scale production as a commercial biocontrol agent.In this study wefound that M. rileyiyeast-like cells produced on solid medium infected and killed the important insect pest Spodoptera frugiperda with comparable efficiency as yeast-like cells grown in liquid medium. Secondly, we used comparative transcriptomic analysis to investigate theactive genes and genomic signatures of the M. rileyi yeast-like morphotypes produced on solid and in liquid media. Yeast-like cells grown in liquid medium had upregulated genes relating specifically to signal transduction andparticular membrane transporters. Thirdly, we compared the transcriptomic profiles of yeast-like phases of M. rileyi with those of M. anisopliae. The yeast-like phase of M. rileyi grown on solid medium upregulated unique genes not found in otherMetarhiziumspecies including specific membrane proteins and several virulence factors. Orthologous genes associated with heat shock protein, iron permease, membrane proteins and key virulence traits (e.g. collagen-like protein Mcl1) were upregulated in both species. Comparative transcriptome analyses of gene expression showed more differences than similarities between M. anisopliae and M. rileyi yeast-like cells.

Comparative global gene expression analysis of biofilm forms of Salmonella Typhimurium ATCC 14028 and its seqA mutant

In this study, comparative transcriptomic analyzes (mRNA and miRNA) were performed on the biofilm forms of S. Typhimurium ATCC 14028 wild-type strain and its seqA gene mutant in order to determine the regulation characteristics of the seqA gene in detail. The results of global gene expression analyses showed an increase in the expression level of 54 genes and a decrease in the expression level of 155 genes (p < 0.05) in the seqA mutant compared to the wild-type strain. 10 of the 48 miRNAs identified on behalf of sequence analysis are new miRNA records for Salmonella. Transcripts of 14 miRNAs differed between wild-type strain and seqA mutant (p < 0.05), of which eight were up-regulated and six were down-regulated. Bioinformatic analyzes showed that differentially expressed genes in the wild-type strain and its seqA gene mutant play a role in different metabolic processes as well as biofilm formation, pathogenicity and virulence. When the transcriptomic data were interpreted together with the findings obtained from phenotypic tests such as motility, attachment to host cells and biofilm morphotyping, it was determined that the seqA gene has a critical function especially for the adhesion and colonization stages of biofilm formation, as well as for biofilm stability. Transcriptomic data pointing out that the seqA gene is also a general positive regulator of T3SS effector proteins active in cell invasion in S. Typhimurium wild-type biofilm, proves that this gene is involved in Salmonella host cell invasion.

532 Unexpected expression of hemoglobin α as an endogenous antioxidant in epidermal keratinocytes

As epidermal keratinocytes differentiate toward the external environment, they express protective genes against foreign insults such as ultraviolet (UV) irradiation, a major cause of oxidative stress in the skin. Oxidative stress is an imbalance between reactive oxygen species and antioxidants, leading to various pathophysiological conditions including skin cancers. To identify novel epidermal genes with UV-protective function expressed in the upper epidermis, we performed a comparative microarray analysis of gene expression between the whole and upper epidermis separated from healthy human skins.

Single-Cell Profiling of Acute Myeloid Leukemia Identified ARMH1, a Novel Protein Associated with Proliferation, Migration, and Drug Resistance

Despite advancements in treatments, half of pediatric acute myeloid leukemia (AML) patients relapse (Chen, J. & Glasser, C.L., 2020), making it pertinent to identify novel biomarkers that can be used for better stratification of patients post end of induction (EOI) therapy as well as to develop targeted therapies that could lead to higher clinical remission (CR) rates. Single-cell RNA sequencing (scRNAseq) analysis has revolutionized cancer research by identifying novel cell types, genes, and pathways. Our group used scRNAseq analysis of pediatric AML bone marrow (BM) samples collected at diagnosis (Dx) and EOI to identify the upregulation of multiple genes including a novel gene, Armadillo like helical domain containing 1 (ARMH1)/C1orf228, in cancerous blast cells (Thomas, B.E. et al., 2020). ARMH1 has not been previously associated with AML. Also, ARMH1 expression was observed to be significantly higher at Dx in samples from patients with relapse compared to samples from patients with CR (P<2.2e-16). Independent validation for ARMH1 blast-association using single cell and bulk transcriptome profiling revealed that ARMH1 expression was significantly higher in scRNAseq data of AML Dx blast cells compared to EOI non-blast cells (fold change, FC=1.8, P<2.2e-31) as well as in bulk RNAseq data of Dx samples with high blast% (>90%) compared to EOI samples (FC=1.8, P=.003) (Ulukaya, G. et al., 2021). Further analysis on other leukemias like T cell-acute lymphocytic leukemia (T-ALL) and mixed phenotypic acute leukemia (MPAL) also revealed higher expression of ARMH1 in the blast cells as compared to non-blast cells. Survival analysis on bulk RNAseq data using the survival genie platform (Dwivedi, B. et al., 2022) revealed that higher expression of ARMH1 was significantly associated with poor overall survival (OS) in both AML (P=.003) (Ulukaya, G. et al., 2021) and T-ALL (P=.014) datasets. Comparative gene expression analysis using the the Pediatric Single Cell Cancer Atlas - PedSCAtlas - tool (Mumme, H.L. et al., 2021), revealed negligible expression of ARMH1 in normal lymphoid, myeloid, and erythroid cell lineages, further confirming the leukemic blasts-specific over-expression of ARMH1. ARMH1 encodes a cytosolic protein of yet unknown function. The malignant blast specificity of ARMH1 suggested a role in leukemic cells' survival/maintenance. To ascertain its functional involvement in cancer cells, ARMH1 was silenced using siRNAs in both normal and AML cell lines. Through in vitro assays, we demonstrate that ARMH1 silencing significantly reduced leukemic cells' capacity to proliferate (P=.0041) and migrate (P=.0001). We also observed slightly increased sensitivity to chemotherapy drug, Cytarabine in the ARMH1 silenced cancer cells compared to control cancer cells in which the gene is fully functional. However, suppression of ARMH1 expression had no effect on cell growth in the normal HEK293t cell line (P=0.913). On the other hand, overexpression of ARMH1 via transient transfection of ARMH1 gene into the AML cell line, made the cells more resistant to Cytarabine and significantly increased both migration (P=.041) and cell proliferation (P=.032). In conclusion, we demonstrate for the first time that ARMH1, a still poorly understood protein, contributes to the increased proliferation and migration of malignant AML cells. With specific overexpression in blast cells of several pediatric leukemias and the newly discovered roles in proliferation, migration, and chemotherapy resistance, ARMH1 may be a good candidate for targeted treatment of pediatric leukemias.

Comparative whole transcriptome analysis of gene expression in three canine soft tissue sarcoma types.

Soft tissue sarcomas are pleiotropic tumors of mesenchymal cell origin. These tumors are rare in humans but common in veterinary practice, where they comprise up to 15% of canine skin and subcutaneous cancers. Because they present similar morphologies, primary sites, and growth characteristics, they are treated similarly, generally by surgical resection followed by radiation therapy. Previous studies have examined a variety of genetic changes as potential drivers of tumorigenesis and progression in soft tissue sarcomas as well as their use as markers for soft tissue sarcoma subtypes. However, few studies employing next generation sequencing approaches have been published. Here, we have examined gene expression patterns in canine soft tissue sarcomas using RNA-seq analysis of samples obtained from archived formalin-fixed and paraffin-embedded tumors. We provide a computational framework for using resulting data to categorize tumors, perform cross species comparisons and identify genetic changes associated with tumorigenesis. Functional overrepresentation analysis of differentially expressed genes further implicate both common and tumor-type specific transcription factors as potential mediators of tumorigenesis and aggression. Implications for tumor-type specific therapies are discussed. Our results illustrate the potential utility of this approach for the discovery of new therapeutic approaches to the management of canine soft tissue sarcomas and support the view that both common and tumor-type specific mechanisms drive the development of these tumors.

Comparative analysis of differential gene expression in two species of crucian carps in response to Cyprinid herpesvirus 2 (CyHV-2) infection

We assessed the expressions of MHCI, LYZC, keratin8, MPO, DUSP1, IκBα, Rab21, and Rac2 between two species of carps (Erqisi river crucian carp and allogynogenetic crucian carp) after Cyprinid herpesvirus 2 (CyHV-2) infection. The relative expressions of MHCI, LYZC, and keratin8 in the virus-challenged groups were significantly higher than control groups. Moreover, the expression of IκBα in the virus-challenged groups was significantly lower than in the control groups. Compared with the virus-challenged ERO group, the expression of IκBα in the virus-challenged ZHO group decreased. The expression of Rab21 in the virus-challenged groups gradually increased and was significantly higher than in the control groups, and then its expression began to decrease after 24 h. At 72 h, the expression of IκBα in both virus-challenged groups was significantly lower than in the control groups. In addition, the expression of Rab21 in the virus-challenged ZHO group was significantly higher than the virus-challenged ERO group at all time points except for 72 h. Before 24 h, the expression of Rac2 remained unchanged in these four groups, and its expression in the virus-challenged ZHO group was significantly higher than in the other three groups. Nevertheless, its expression began to decrease after 24 h but was still slightly higher than the control group at 72 h. MPO showed a similar expression pattern as Rac2. The expression of DUSP1 in the four groups was the same at 0 h. However, its expression in the virus-challenged ZHO group was significantly higher than in the other three groups at other time points.

Comparative analysis of ICE1 and ICE2 gene expression in Arum Korolkovii (Araceae family) under low temperature stress

The identification of mechanisms of plant resistance and adaptation to adverse environmental factors opens broad prospects for the development of breeding biotechnology. The subject of the present study was Arum Korolkovii, a rare endemic species in Central Asia, included in the Red Book of Kazakhstan. In the present work a comparative analysis of expression of ICE1 and ICE2 genes involved in abiotic stress response in the studied plant under cold and frost conditions was carried out. Low temperature stress was induced by placing the plants in cold rooms and reducing the temperature to 0...+2°C for seven days (cold stress), followed by temperature reduction to -4...-6°C for five days (freezing). The relative level of gene expression was analysed by classical polymerase chain reaction. Under stress induction, increased expression of both studied genes, with different levels of expression already at the stage of acclimatization, was shown. The genes studied can be resistance markers for finding donors in gene collections