Comparative Expression Studies Research Articles

Comparative study of pro-inflammatory cytokine expression among two common freshwater Cichlids

Comparative study of pro-inflammatory cytokine expression among two common freshwater Cichlids

A haplotype-resolved genome assembly of Malus domestica ‘Red Fuji’

The ‘Red Fuji’ apple (Malus domestica), is one of the most important and popular economic crops worldwide in the fruit industry. Using PacBio HiFi long reads and Hi-C reads, we assembled a high-quality haplotype-resolved genome of ‘Red Fuji’, with sizes of 668.7 and 668.8 Mb, and N50 sizes of 34.1 and 31.4 Mb. About 97.2% of sequences were anchored in 34 chromosomes. We annotated both haploid genomes, identifying a total of 95,439 protein-coding genes in the two haplotype genomes, with 98% functional annotation. The haplotype-resolved genome of ‘Red Fuji’ apple stands as a precise benchmark for an array of analyses, such as comparative genomics, transcriptomics, and allelic expression studies. This comprehensive resource is paramount in unraveling variations in allelic expression, advancing quality improvements, and refining breeding efforts.

Exploring the Role of Debaryomyces hansenii as Biofertilizer in Iron-Deficient Environments to Enhance Plant Nutrition and Crop Production Sustainability.

The European "Green Deal" policies are shifting toward more sustainable and environmentally conscious agricultural practices, reducing the use of chemical fertilizer and pesticides. This implies exploring alternative strategies. One promising alternative to improve plant nutrition and reinforce plant defenses is the use of beneficial microorganisms in the rhizosphere, such as "Plant-growth-promoting rhizobacteria and fungi". Despite the great abundance of iron (Fe) in the Earth's crust, its poor solubility in calcareous soil makes Fe deficiency a major agricultural issue worldwide. Among plant promoting microorganisms, the yeast Debaryomyces hansenii has been very recently incorporated, for its ability to induce morphological and physiological key responses to Fe deficiency in plants, under hydroponic culture conditions. The present work takes it a step further and explores the potential of D. hansenii to improve plant nutrition and stimulate growth in cucumber plants grown in calcareous soil, where ferric chlorosis is common. Additionally, the study examines D. hansenii's ability to induce systemic resistance (ISR) through a comparative relative expression study by qRT-PCR of ethylene (ET) biosynthesis (ACO1), or ET signaling (EIN2 and EIN3), and salicylic acid (SA) biosynthesis (PAL)-related genes. The results mark a significant milestone since D. hansenii not only enhances nutrient uptake and stimulates plant growth and flower development but could also amplify induced systemic resistance (ISR). Although there is still much work ahead, these findings make D. hansenii a promising candidate to be used for sustainable and environmentally friendly integrated crop management.

Shedding a Light on Dark Genes: A Comparative Expression Study of PRR12 Orthologues during Zebrafish Development.

Haploinsufficiency of the PRR12 gene is implicated in a human neuro-ocular syndrome. Although identified as a nuclear protein highly expressed in the embryonic mouse brain, PRR12 molecular function remains elusive. This study explores the spatio-temporal expression of zebrafish PRR12 co-orthologs, prr12a and prr12b, as a first step to elucidate their function. In silico analysis reveals high evolutionary conservation in the DNA-interacting domains for both orthologs, with significant syntenic conservation observed for the prr12b locus. In situ hybridization and RT-qPCR analyses on zebrafish embryos and larvae reveal distinct expression patterns: prr12a is expressed early in zygotic development, mainly in the central nervous system, while prr12b expression initiates during gastrulation, localizing later to dopaminergic telencephalic and diencephalic cell clusters. Both transcripts are enriched in the ganglion cell and inner neural layers of the 72 hpf retina, with prr12b widely distributed in the ciliary marginal zone. In the adult brain, prr12a and prr12b are found in the cerebellum, amygdala and ventral telencephalon, which represent the main areas affected in autistic patients. Overall, this study suggests PRR12's potential involvement in eye and brain development, laying the groundwork for further investigations into PRR12-related neurobehavioral disorders.

A comparative study of morphological and Immunohistochemical expression of P40 and P63 immunomarkers in squamous cell carcinoma and adenocarcinoma lung

Background: Lung cancer is the leading cause of cancer related death worldwide and accounts for 28% of all cancer mortality and around 1.8 million new cases were diagnosed in 2012. The morphological distinction between pulmonary adenocarcinoma (ADC) and squamous cell carcinomas (SCC) is sometimes difficult, mainly in cases of poorly differentiated tumors or when degenerative changes, necrosis and crushing may obscure the cell characteristics. p63 is a homologue of the p53 tumour suppressor gene that is responsible for proliferation and differentiation of epithelial progenitor cells. p40 is consistently the predominant isoform expressed in squamous cell carcinoma; thus, it offers improved specificity for diagnosing squamous cell carcinoma. Material and Methods: This is a prospective and observational study conducted in the Department of Pathology, Tertiary care Teaching Hospital over a period of 1 year. Primary lung carcinoma cases included with unequivocal morphological diagnosis irrespective of age, gender and nature of biopsy material (endoscopic biopsy/ needle core biopsy / resected specimen). Cases diagnosed as Small cell carcinoma of lung, as metastatic lung cancers, poorly differentiated NSCLC-NOS and with inadequate material for IHC study were excluded from present study. Results: In the present study, a total of 150 patients were included out of which 112 (74.6%) were males and 38 (25.4%) were females. In our study, most of the patients were >61 years i.e., 63 out of 150 (42%), followed by 51-60 years, i.e., 40 out of 150 (26.7%). All 8 cases of well differentiated Adenocarcinoma were positive for P40 and 5 cases showed P63 expression. Out of 13 cases of moderately differentiated Adenocarcinoma, 3 cases were positive for P40 and 10 cases were positive for p63 marker. Out of 30 cases of well differentiated Squamous cell carcinoma 15 cases were P40 positive and 15 cases were P63 positive. All 53 cases of moderately differentiated Squamous cell carcinoma showed positive P40 and P63 expression.

BDNF specifically expressed in hippocampal neurons is involved in methylmercury neurotoxicity resistance.

Methylmercury (MeHg) causes selective neuronal damage to cerebrocortical neurons (CCNs) in the central nervous system, but not to hippocampal neurons (HiNs), which are highly vulnerable to neurodegenerative diseases. In our previous study using cultured rat neurons, we performed a comprehensive gene expression analysis and found that the brain-derived neurotrophic factor (BDNF), a neurotrophin (NT), was specifically expressed in HiNs. Therefore, to elucidate the causal factors of MeHg toxicity resistance in HiNs, we conducted a comparative study of the protein expression and function of several NTs, including BDNF, using CCNs showing vulnerability to MeHg toxicity and HiNs showing resistance. BDNF was specifically expressed in HiNs, whereas nerve growth factor was barely detectable in either neuron type. In addition, other NTs, NT3 and NT4/5, were expressed in small but nearly equal amounts in both neuron types. Furthermore, among the various pathways involved in MeHg neurotoxicity, the p44/42 MAPK pathway was specifically activated in HiNs, even without MeHg treatment. siRNAs were used to reduce NTs in both neuron types. Only a specific reduction in BDNF attenuated the resistance to MeHg toxicity and p44/42 MAPK activation in HiNs. In addition, the external addition of BDNF and NT4/5, which act on the same tyrosine receptor kinase (Trk), TrkB, suppressed MeHg neurotoxicity in both neuron types. These results suggest that BDNF, expressed specifically in HiNs, is involved in the resistance to MeHg neurotoxicity via TrkB. Additionally, the activation of the p44/42 MAPK pathway may contribute to the inhibitory effect of BDNF on MeHg neurotoxicity.

A comparative study of PRAME expression in sebaceous carcinoma and basal cell carcinoma.

A comparative study of PRAME expression in sebaceous carcinoma and basal cell carcinoma.

Specific Circular RNA Signature of Endothelial Cells: Potential Implications in Vascular Pathophysiology.

Circular RNAs (circRNAs) are a recently characterized family of gene transcripts forming a covalently closed loop of single-stranded RNA. The extent of their potential for fine-tuning gene expression is still being discovered. Several studies have implicated certain circular RNAs in pathophysiological processes within vascular endothelial cells and cancer cells independently. However, to date, no comparative study of circular RNA expression in different types of endothelial cells has been performed and analysed through the lens of their central role in vascular physiology and pathology. In this work, we analysed publicly available and original RNA sequencing datasets from arterial, veinous, and lymphatic endothelial cells to identify common and distinct circRNA expression profiles. We identified 4713 distinct circRNAs in the compared endothelial cell types, 95% of which originated from exons. Interestingly, the results show that the expression profile of circular RNAs is much more specific to each cell type than linear RNAs, and therefore appears to be more suitable for distinguishing between them. As a result, we have discovered a specific circRNA signature for each given endothelial cell type. Furthermore, we identified a specific endothelial cell circRNA signature that is composed four circRNAs: circCARD6, circPLXNA2, circCASC15 and circEPHB4. These circular RNAs are produced by genes that are related to endothelial cell migration pathways and cancer progression. More detailed studies of their functions could lead to a better understanding of the mechanisms involved in physiological and pathological (lymph)angiogenesis and might open new ways to tackle tumour spread through the vascular system.

Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution.

Phylogenetic comparative methods are increasingly used to test hypotheses about the evolutionary processes that drive divergence in gene expression among species. However, it is unknown whether the distributional assumptions of phylogenetic models designed for quantitative phenotypic traits are realistic for expression data and importantly, the reliability of conclusions of phylogenetic comparative studies of gene expression may depend on whether the data is well described by the chosen model. To evaluate this, we first fit several phylogenetic models of trait evolution to 8 previously published comparative expression datasets, comprising a total of 54,774 genes with 145,927 unique gene-tissue combinations. Using a previously developed approach, we then assessed how well the best model of the set described the data in an absolute (not just relative) sense. First, we find that Ornstein-Uhlenbeck models, in which expression values are constrained around an optimum, were the preferred models for 66% of gene-tissue combinations. Second, we find that for 61% of gene-tissue combinations, the best-fit model of the set was found to perform well; the rest were found to be performing poorly by at least one of the test statistics we examined. Third, we find that when simple models do not perform well, this appears to be typically a consequence of failing to fully account for heterogeneity in the rate of the evolution. We advocate that assessment of model performance should become a routine component of phylogenetic comparative expression studies; doing so can improve the reliability of inferences and inspire the development of novel models.

A Comparative Study of CD56 and Smooth Muscle Actin Expression in Basal and Squamous Cell Carcinomas.

Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are the 2 most common types of nonmelanoma skin tumors. Clinical or histopathological diagnostic challenges are encountered on occasion. CD56 and smooth muscle actin (SMA) are highly expressed in BCCs. We aimed to investigate the frequency of these markers, along with B-cell lymphoma 2 (Bcl-2) and Ki67. This study was conducted to propose a method that could possibly be of diagnostic value. One hundred twenty-eight BCC and 39 SCC cases were included in this study. CD56, SMA, Bcl-2, and Ki67 immunohistochemical stains were applied. Ninety-nine (77.3%) BCC and 6 (15.4%) SCC cases showed CD56 immunoreactivity. SMA expression was detected in 78.1% of BCC and 5.1% of SCC cases. CD56, SMA, and Bcl-2 expressions were significantly higher in BCC cases. The Ki67 proliferation index was found significantly higher in SCC cases. When basosquamous carcinoma cases were compared with SCC cases, a significant correlation between tumors and expression of CD56, SMA, and Bcl-2 were obtained. CD56 and SMA, in addition to Bcl-2, favor BCC. Ki67 should also be included in the panel to demonstrate the proliferative activity.

41854 A Comparative Study of PRAME Expression in Sebaceous Carcinoma and Basal Cell Carcinoma

41854 A Comparative Study of PRAME Expression in Sebaceous Carcinoma and Basal Cell Carcinoma

Comparative Study of Immunohistochemical Expression of ER and PR as Prognostic Markers and Correlation with Clinicopathological Parameters in Human Endometrial Adenocarcinoma

In human steroid sensitive tissue, progesterone receptors (PRs) and estrogen receptors (ERs) have been demonstrated at the mRNA and/or protein levels by using molecular biology and immunohistochemistry techniques. Estrogen and progesterone receptors are present both in endometrial hyperplasia and in neoplastic endometrium. The aim of the present work was to compare the expression of ER and PR as prognostic biomarkers in human endometrial adenocarcinoma versus benign tumors and normal endometrial tissues as well as their correlation with different pathological and histological parameters. Immunohistochemical technique was used to examine the expression of ER and PR in normal, benign as well as in endometrial adenocarcinoma. Present results showed higher expression of ER and PR in endometrial adenocarcinoma comparing to normal and benign endometrial tissues.

High-level recombinant protein production with Corynebacterium glutamicum using acetate as carbon source.

In recent years, biotechnological conversion of the alternative carbon source acetate has attracted much attention. So far, acetate has been mainly used for microbial production of bioproducts with bulk applications. In this study, we aimed to investigate the potential of acetate as carbon source for heterologous protein production using the acetate-utilizing platform organism Corynebacterium glutamicum. For this purpose, expression of model protein eYFP with the promoter systems T7lac and tac was characterized during growth of C. glutamicum on acetate as sole carbon source. The results indicated a 3.3-fold higher fluorescence level for acetate-based eYFP production with T7 expression strain MB001(DE3) pMKEx2-eyfp compared to MB001 pEKEx2-eyfp. Interestingly, comparative eyfp expression studies on acetate or glucose revealed an up to 83% higher biomass-specific production for T7 RNAP-dependent eYFP production using acetate as carbon source. Furthermore, high-level protein accumulation on acetate was demonstrated for the first time in a high cell density cultivation process with pH-coupled online feeding control, resulting in a final protein titer of 2.7g/L and product yield of 4g per 100 g cell dry weight. This study presents a first proof of concept for efficient microbial upgrading of potentially low-cost acetate into high-value bioproducts, such as recombinant proteins.

Comparative Study of PD-L1 Expression in Different Sites of Non-small Cell Lung Cancer

背景与目的程序性死亡配体1（programmed cell death ligand 1, PD-L1）作为非小细胞肺癌（non-small cell lung cancer, NSCLC）免疫治疗患者分层标志物已进入临床病理常规检测。然而PD-L1表达在肺内和肺外不同转移部位的空间异质性是困扰临床检测的难题。本研究旨在探讨NSCLC不同部位组织样本的PD-L1表达评分的差异，从而有助于晚期肺癌患者的PD-L1检测策略的制定。方法回顾性收集PD-L1（22c3抗体，Dako）临床病理连续检测的131例肺外转移性NSCLC以及同期非配对肺内肿瘤972例进行对照分析，对比肺外与肺内肿瘤组织样本检测的PD-L1肿瘤阳性比例评分（tumor proportion score, TPS）差异。结果肺外转移性NSCLC的PD-L1阳性表达率（TPS≥1%）为61.83%，TPS评分显著高于同期肺内肿瘤（P=0.03）。不同部位组织样本的PD-L1表达评分具有显著差异（P=0.007）。肝脏和肾上腺转移瘤的PD-L1阳性率高，分别为85.71%和77.78%，其TPS评分均显著高于肺内肿瘤（P < 0.05）。淋巴结、骨、脑、软组织和胸膜转移瘤的PD-L1表达率为40.00%-66.67%，TPS评分与肺内肿瘤无显著差异。组织学和样本类型分析显示，腺癌类型和手术切除的肺外样本PD-L1表达评分显著高于同类型肺内肿瘤。临床病理参数分析显示，PD-L1阳性表达和高表达均与患者男性、吸烟史以及表皮生长因子受体（epidermal growth factor receptor, EGFR）野生型显著相关。结论肺外转移性NSCLC样本的PD-L1表达评分高于肺内肿瘤，且不同部位组织样本的PD-L1表达阳性率存在差异。肺外转移性肿瘤与肺内肿瘤的PD-L1检测差异可能与不同转移部位、组织学和样本类型相关。

Comparative study of cyp1a expression in Oreochromis aureus from different regions of Lake Manzala, Egypt

Comparative study of cyp1a expression in Oreochromis aureus from different regions of Lake Manzala, Egypt

"Neural stem cells puzzle" missing piece: telomerase reverse transcriptase expression patterns during nervous system ontogenesis in rats.

For almost three decades, neural stem cells remain still up-to-date and enigmatic topic. The main problem for their studying is the non-existence of an exclusive neural stem cell marker and the heterogeneity of them across the nervous system. As one of the novel markers of neural stem/progenitor cells may serve telomerase reverse transcriptase (TERT), a catalytic subunit of the telomerase enzyme, responsible for retaining the cell immortality. Thus, the aim of our study was to reveal if TERT, as an enzyme for ensuring the immortality of proliferating cells, could be used as a potential marker of neural stem/progenitor cells during the ontogenesis of the rat central nervous system. In this study, we used various markers related to neural stem or progenitor cells character and examined their co-localization with TERT expression. Our experiments were performed on the tissue of the brain and spinal cord during several stages of postnatal development and the neural tube during the 14th embryonal day. Cytoplasmatic TERT expression was found in alar plate progenitors and ventral horn neuroblasts of E14 rats. In the postnatal stages of spinal cord ontogenesis, a cytoplasmatic expression in neurons and nuclear expression in astrocytes was defined. In the brain, nuclear TERT expression was found in neural progenitor cells of neurogenic areas. This study provides the first comparative study of TERT expression across the central nervous system ontogenesis. The nuclear presence of TERT may be used as a potential marker of neural stem/progenitor cells, however, further studies are required to confirm these assumptions.

Immunohistochemical Expression of Alpha (Α) A Crystallin in Senile Degenerative and Non-Cataract Lenses

Aim: Comparative immunohistochemical study of expression of α A Crystallin in non-cataract lenses and age-related cataract lenses in humans. Methodology: This was an observational cross sectional study. There are two groups in this study. Group A comprised of 121 senile degenerative cataract lenses from diagnosed patients. Group B included of 10 non-cataract lenses from patients who underwent surgeries for enucleation due to trauma and retinoblastoma. Lenses were fixed in 10% Buffered Neutral Formalin and processed to make paraffin blocks. Immunohistochemistry (IHC) staining was performed on sections using primary antibody for α A crystallin. Data was analyzed through SPSS software version 24. Results: Immunohistochemical staining of group A showed 80.2% Strong Positive expression while 19.8% showed Intermediate Positive expression of α A Crystallin. 100% Strong Positive expression of α A Crystallin was seen in group B. Comparison of expression of α A Crystallin in two groups showed significant decrease (p&lt;0.001) in expression. Conclusion: Decreased expression of α A Crystallin in IHC stained senile cataract lens indicates the role of structural alterations of lens fibers in pathogenesis of senile cataract. If mechanism involved in causing these alterations can be identified and targeted so that progression of senile cataract may be delayed. Keywords: Immunohistochemistry, α A crystallin expression, senile cataract, Human eye Lens, Lens Fiber.

A Comparative Immunohistochemical Study of Expression of Syndecan-1 (CD138) and Podoplanin in Keratocystic Odontogenic Tumor, Orthokeratinized Odontogenic Cyst and Dentigerous Cyst

Background: Odontogenic lesions can bring about diagnostic challenges due to overlapping histology among pathologists. Thus, there are few tumor markers that provide accurate diagnosis. Syndecan-1 (CD-138) and podoplanin (PDPN) are proteoglycans that have been described as substantial diagnostic and prognostic markers in various odontogenic lesions. Aim: This study aims to evaluate and compare the immunohistochemical expression of syndecan-1 (CD-138) and podoplanin in keratocystic odontogenic tumor, orthokeratinized odontogenic cyst (OOC), and dentigerous cyst (DC). Materials and Methods: The formalin-fixed paraffin-embedded tissue blocks of KCOT, OOC, and DCs were retrieved form the archives of department. Three sections each of 3 μm thickness were made using a rotary microtome and they were stained with syndecan-1 (CD-138) and podoplanin (PDPN) using immunohistochemical methods and standard hematoxylin and eosin stain. Results: Immunohistochemical expression of syndecan-1in KCOT was found to be weakly to moderately positive in 6 cases with 2 cases exhibiting positive expression. In OOC, 3 cases displayed negative expression-1 whereas 7 cases were weakly to moderately positive. Immunohistochemical expression of podoplanin in KCOT was observed to be weakly to moderately positive in 4 cases with 5 cases exhibiting strongly positive expression. In OOC, 3 cases displayed negative immunohistochemical expression for podoplanin and 4 cases were strongly positive. Immunoreactivity for podoplanin in DC was negative in 3 cases whereas 5 cases were weakly to moderately positive. Conclusion: The absence of significant correlation between expression of syndecan-1 and podoplanin reinforces the exact role of these proteins in the differentiation of odontogenic lesions which need to be elucidated further.

Comparative study of laminin332-γ2 chain expression in oral lichen planus and squamous cell carcinoma by immunohistochemistry.

Classification of oral lichen planus (OLP) as a condition with malignant potential is still controversial. One of the major properties of malignancy is invasion. Ln332-γ2 chain plays a critical role in invasive activity of cancer cells. This study aims to compare Ln332-γ2 chain expression in OLP, oral epithelial dysplasia (OED) and oral squamous cell carcinoma (OSCC). Ln332-γ2 expression was evaluated in 16 epithelial hyperplasia with no dysplasia (group A), 16 OLP (group B), 18 OED (group C) and 18 OSCC (group D) by immunohistochemistry. Except in A group, Ln332-γ2 expression was detected in other groups. There was a significant difference in Ln332-γ2 expression among B, C and D groups as well as between B and D, C and D groups (P<0.001). However, there was no significant difference between B and C groups (P=0.999). According to the findings of this study, the likelihood of similarity of OLP with premalignant dysplastic lesion can be suggested. This is not corroborating OLP definitive transformation to an OSCC. But it might be advisable that OLPs with >10% Ln332- γ2 expression may have a higher risk of cellular invasion occurrence and malignant transformation.

A systematic analysis of ATPase Cation transporting 13A2 (ATP13A2) transcriptional expression and prognostic value in human brain cancer

P-type transport ATPase’s are active transporters that dispense the majority of the cellular functions. ATP13A2 have a role in neurodegeneration which is commonly associated with lysosomal dysfunction. Lysosome plays a significant role in the metabolism, secretion, signaling, plasma membrane repair, and autophagy which have fundamental implications in different carcinomas. ATP13A2 is placed in the lysosome and the late endosome and the drastic dysfunction in the lysosome is caused from its mutation. However, this systematic study was done to evaluate ATP13A2 as the possible prognostic marker for the glioblastoma multiform (GBM) is the utmost frequent primary cancer of the central nervous system. Within this cumulative study, we have inspected the pattern of expression of ATP13A2 and their corresponding outcome in GBM patients using different available databases. We examined a comparative study of ATP13A2 expression between the normal tissues and their cancers using the UALCAN, Oncomine, GEPIA2, and GENT2 databases. Both analyses showed significantly high ATP13A2 mRNA and protein expression in GBM than those of normal tissues. We investigate clinicopathological expression and methylation characteristics of GBM using UALCAN database, which analysis showed clinicopathological expression of ATP13A2 was down regulated and methylation was over-expressed in GBM compared to normal tissues. We also investigate mutations and the alterations of copy number of ATP13A2 using a database called cBioPortal, which showing about 5 (0.2%) alteration and 0.6% mutation frequency and co-expression profile through the Oncomine. We used the Enricher tool to predict the signaling pathways in GBM through gene ontology and pathway analysis of co-expressed genes. The PrognoScan analysis revealed that the increased ATP13A2 expression correlates with worse patient survival. Finally, our derived data apprises that, ATP13A2 may serve as a potential biomarker of GBM/brain cancer patients.