Genome Expression Profiling Research Articles

Whole-Blood Gene Expression Profile After Hypoxic-Ischemic Encephalopathy

Induced hypothermia, the standard treatment for hypoxic-ischemic encephalopathy (HIE) in high-income countries (HICs), is less effective in the low-income populations in South Asia, who have the highest disease burden. To investigate the differences in blood genome expression profiles of neonates with HIE from an HIC vs neonates with HIE from South Asia. This case-control study analyzed data from (1) a prospective observational study involving neonates with moderate or severe HIE who underwent whole-body hypothermia between January 2017 and June 2019 and age-matched term healthy controls in Italy and (2) a randomized clinical trial involving neonates with moderate or severe HIE in India, Sri Lanka, and Bangladesh recruited between August 2015 and February 2019. Data were analyzed between October 2020 and August 2023. Whole-blood RNA that underwent next-generation sequencing. The primary outcomes were whole-blood genome expression profile at birth associated with adverse outcome (death or disability at 18 months) after HIE in the HIC and South Asia cohorts and changes in whole-genome expression profile during the first 72 hours after birth in neonates with HIE and healthy controls from the HIC cohort. Blood samples for RNA extraction were collected before whole-body hypothermia at 4 time points (6, 24, 48, and 72 hours after birth) for the HIC cohort. Only 1 blood sample was drawn within 6 hours after birth for the South Asia cohort. The HIC cohort was composed of 35 neonates (21 females [60.0%]) with a median (IQR) birth weight of 3.3 (3.0-3.6) kg and gestational age of 40.0 (39.0-40.6) weeks. The South Asia cohort consisted of 99 neonates (57 males [57.6%]) with a median (IQR) birth weight of 2.9 (2.7-3.3) kg and gestational age of 39.0 (38.0-40.0) weeks. Healthy controls included 14 neonates (9 females [64.3%]) with a median (IQR) birth weight of 3.4 (3.2-3.7) kg and gestational age of 39.2 (38.9-40.4) weeks. A total of 1793 significant genes in the HIC cohort and 99 significant genes in the South Asia cohort were associated with adverse outcome (false discovery rate <0.05). Only 11 of these genes were in common, and all had opposite direction in fold change. The most significant pathways associated with adverse outcome were downregulation of eukaryotic translation initiation factor 2 signaling in the HIC cohort (z score = -4.56; P < .001) and aldosterone signaling in epithelial cells in the South Asia cohort (z score = null; P < .001). The genome expression profile of neonates with HIE (n = 35) at birth, 24 hours, 48 hours, and 72 hours remained significantly different from that of age-matched healthy controls in the HIC cohort (n = 14). This case-control study found that disease mechanisms underlying HIE were primarily associated with acute hypoxia in the HIC cohort and nonacute hypoxia in the South Asia cohort. This finding might explain the lack of hypothermic neuroprotection.

Abstract B038: CD4Th1 cytokine interferon gamma regulates genome profiles and inhibits tumorigenesis of disseminated cancer cells in breast cancer

Abstract Detection and persistence of disseminated cancer cells (DCCs) in the bone marrow (BM) of breast cancer (BC) patients has been identified as a primary source for late recurrence and distant metastasis in multiple organs and the central nervous system. Selective targeting and eradication of DCCs in BM can be of a significant advantage to prevent future recurrence and enhance disease-free survival in BC patients. Unfortunately, no such targeted therapy presently exists. Instead, intense chemotherapy in the adjuvant or neoadjuvant setting are given with the ultimate goal to prevent DCC-driven metastasis in these patients. Clinical studies have confirmed that DCCs have not been effectively eradicated by conventional chemotherapies. DCCs express unique gene signatures that differ from circulating tumor cells (CTC) in BC, but only limited knowledge is available for the genome profiles of DCCs compared to primary and metastatic lesions in BC patients. Here we investigated the detailed gene expression profiles of DCCs compared to primary and metastatic lesions from a murine spontaneous metastasis model and BC patients. Using a two-step immunomagnetic enrichment assay, we were able to successfully isolate highly enriched EpCAM+ DCCs from both the BM aspirates of HER2+ early BC patients and BALB-HER2/neu transgenic (BALB-neuT) spontaneous metastasis mice. RNA sequencing revealed that DCCs from HER2+ BC patients and BALB-neuT mice displayed remarkably similar genomic expression profiles, but both had substantially different profiles when comparing to primary and metastatic lesions. We identified highly enriched signatures in DCCs associated with cancer stemness, epithelial to mesenchymal transition (EMT), cell cycle, cell adhesion, progesterone signaling and cholesterol biosynthesis. Notably, these DCCs showed loss of MHC class I, MHC class II, and CD1d expression leading to a defect in antigen presentation machinery and their subsequent escape from CD4 T, CD8 T, B and NKT-cell mediated clearance. Interestingly, we observed for the first time that anti-tumor CD4Th1 cells, through interferon gamma (IFN-γ) production, upregulated CD1d, MHC class I and II expressions in DCCs leading to high infiltration of CD4Th1, NKT and B cells into the BM to selectively target and eliminate DCC burden. IFN-γ remarkably downregulated stemness, EMT, self-renewing potential and their genome signatures and induced apoptosis and irreversible senescence in DCCs of HER2+ BC patients. Notably, these IFN-γ treated patient DCCs lost their ability to grow into tumors in an immunodeficient NSG mouse model. Collectively, these results provide a detailed genome profile of DCCs from HER2+ BC patients and a novel role for anti-tumor CD4Th1 response in inhibiting DCC-driven tumorigenesis and metastasis. Citation Format: Ganesan Ramamoorthi, Marie Catherine Lee, Krithika Kodumudi, Colin Snyder, Namrata Gautam, Saurabh K. Garg, Shari Pilon-Thomas, Brian Czerniecki. CD4Th1 cytokine interferon gamma regulates genome profiles and inhibits tumorigenesis of disseminated cancer cells in breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B038.

Genome Identification and Expression Profiling of the PIN-Formed Gene Family in Phoebe bournei under Abiotic Stresses.

PIN-formed (PIN) proteins-specific transcription factors that are widely distributed in plants-play a pivotal role in regulating polar auxin transport, thus influencing plant growth, development, and abiotic stress responses. Although the identification and functional validation of PIN genes have been extensively explored in various plant species, their understanding in woody plants-particularly the endangered species Phoebe bournei (Hemsl.) Yang-remains limited. P. bournei is an economically significant tree species that is endemic to southern China. For this study, we employed bioinformatics approaches to screen and identify 13 members of the PIN gene family in P. bournei. Through a phylogenetic analysis, we classified these genes into five sub-families: A, B, C, D, and E. Furthermore, we conducted a comprehensive analysis of the physicochemical properties, three-dimensional structures, conserved motifs, and gene structures of the PbPIN proteins. Our results demonstrate that all PbPIN genes consist of exons and introns, albeit with variations in their number and length, highlighting the conservation and evolutionary changes in PbPIN genes. The results of our collinearity analysis indicate that the expansion of the PbPIN gene family primarily occurred through segmental duplication. Additionally, by predicting cis-acting elements in their promoters, we inferred the potential involvement of PbPIN genes in plant hormone and abiotic stress responses. To investigate their expression patterns, we conducted a comprehensive expression profiling of PbPIN genes in different tissues. Notably, we observed differential expression levels of PbPINs across the various tissues. Moreover, we examined the expression profiles of five representative PbPIN genes under abiotic stress conditions, including heat, cold, salt, and drought stress. These experiments preliminarily verified their responsiveness and functional roles in mediating responses to abiotic stress. In summary, this study systematically analyzes the expression patterns of PIN genes and their response to abiotic stresses in P. bournei using whole-genome data. Our findings provide novel insights and valuable information for stress tolerance regulation in P. bournei. Moreover, the study offers significant contributions towards unraveling the functional characteristics of the PIN gene family.

Abstract A076: Spatial genomic expression profiling reveals metastatic gene markers in mucinous cystic carcinoma of the pancreas and regional lymph nodes

Abstract Pancreatic cancer is a highly lethal disease characterized by low detectability in its early stages, leading to limited treatment options in advanced stages. Mucinous cystic carcinoma (MCC) is a rare subtype of pancreatic cancer that produces mucin. In this study, we investigated the genetic characteristics of MCC and its metastatic potential. Using spatial genomic analysis, we observed the upregulation of several genes in MCC, including CPA1 and CPB1, which encode carboxypeptidases produced by the pancreas. These genes were highly expressed in both the pancreatic tumor and regional lymph nodes, suggesting their potential as gene markers for the metastatic potential of MCC. Moreover, we observed co-localization and upregulation of genes encoding chymotrypsin-like-elastase in both the pancreatic tissue and lymph nodes, indicating their potential involvement in metastasis. Furthermore, we observed significant elevation in the expression of pancreatic enzymes encoded by PRSS1, PRSSA, CLPS, and PLAG2GA in both the pancreatic tissue and lymph nodes. The presence of PRSS1 and PRSSA in the lymph node suggests the presence of cancer cells in the lymphatic system, which in turn promotes tumor growth, invasion, and metastasis. Additionally, elevated expression of CLPS in the lymph nodes may be associated with altered lipid metabolism and the breakdown of fat molecules in the tumor microenvironment. This upregulation was accompanied by increased levels of SPARC, an extracellular matrix protein, in both tissues, emphasizing the correlation between metastatic potential and tumorigenesis. Notably, commonly observed tumor markers for pancreatic cancer, such as SMAD4, did not exhibit upregulation in our MCC case, indicating alternative mechanisms of tumor development in this particular subtype. Additionally, we noted heightened expression of the CA 19-9 antigen, a valuable marker for monitoring the progression of pancreatic cancer. In conclusion, our findings reveal the upregulation of several gene markers in this rare subtype of pancreatic cancer and regional lymph nodes. Understanding the expression patterns of these markers can aid in identifying potential therapeutic targets and detecting metastatic potential at an early stage for MCC. Citation Format: Chirag S. Gopinath, Arshia Ghodrati, Lusine Demirkhanyan, Manu Gnanamony, Joseph A. Norton, Sonia T. Orcutt, Christopher S. Gondi. Spatial genomic expression profiling reveals metastatic gene markers in mucinous cystic carcinoma of the pancreas and regional lymph nodes [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A076.

Abstract A075: Spatial genomic expression profiling reveals differential marker expression patterns in mucinous cystic carcinoma of the pancreas with ductal involvement

Abstract Pancreatic cancer is a devastating disease with various subtypes, including the rare mucinous cystic carcinoma (MCC) of the pancreas. In this case report, we present a comprehensive spatial genomic expression analysis of MCC, focusing on the correlation between marker expression patterns and cystic versus ductal involvement. Using spatial genomics techniques, we assessed the expression of several markers in the cystic and ductal regions of MCC samples. Surprisingly, we found that the cystic region alone exhibited minimal expression of the MUC2 marker, while high expression of MUC2 was observed in the ductal region, irrespective of cystic involvement. Moreover, we identified a co-localization of high expression levels of REG4, FCGBP, TFF3, and S100A6 with MUC2 expression, suggesting a potential functional relationship in MCC pathogenesis. Notably, CLDN4 and SPINK4, markers previously associated with cystic carcinomas, exhibited predominant expression in the ductal region without cystic involvement. These findings suggest that MCC cases with ductal involvement may possess a more aggressive potential for developing into ductal adenocarcinoma. Interestingly, our analysis revealed that the expression of SPARC, a known tumor-related marker, did not show specific localization in either the ductal or cystic regions but exhibited coexpression with col1a1 and col1a2. This observation highlights potential interactions between SPARC and the extracellular matrix in MCC tumorigenesis. Contrary to previous studies focusing on cystic fluid aspirate, we did not observe significant genomic expression in the cystic fluid space. Additionally, we found that the expression of carcinoembryonic antigens CEACAM5/6, which are known serum markers for mucinous cystic neoplasm of the pancreas, were strongly expressed in the ductal region but not in the cystic regions. Surprisingly, we found that the expression levels of KRAS, a frequently mutated gene in pancreatic cancer, were insignificant in our MCC cases, suggesting alternative mechanisms driving tumorigenesis in this subtype. In conclusion, our findings indicate that mucinous cysts in MCC exhibit low mRNA expression levels, while the markers associated with cystic carcinoma demonstrate significant expression in the ductal region. These results suggest that MCC cases with ductal involvement may possess a greater potential for developing into the more aggressive ductal adenocarcinoma. Understanding the molecular characteristics of MCC can aid in identifying potential therapeutic targets and guiding personalized treatment strategies for this rare pancreatic cancer subtype. Citation Format: Arshia Ghodrati, Chirag S. Gopinath, Lusine Demirkhanyan, Manu Gnanamony, Joseph A. Norton, Sonia T. Orcutt, Christopher S. Gondi. Spatial genomic expression profiling reveals differential marker expression patterns in mucinous cystic carcinoma of the pancreas with ductal involvement [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A075.

Prognostic implication of a novel lactate score correlating with immunotherapeutic responses in pan-cancer.

A thorough assessment of lactate-related genes (LRGs) in different types of human cancers is currently lacking. To elucidate the molecular landscape of LRGs, we conducted a comprehensive analysis using genomic, mRNA, and microRNA expression profiles and developed a lactate score model using the least absolute shrinkage and selection operator (LASSO) algorithm. We found that our lactate score could be a prognostic marker instead of LDHA for several cancer patients who possess high-frequency variants in LRGs. The lactate score also demonstrated an association with CD8+ T cells infiltration in multiple cancer types. Furthermore, our findings indicate that the lactate score holds promise as a potential biomarker for immunotherapy in patients with bladder cancer (BLCA) and skin cutaneous melanoma (SKCM). Among the seventeen genes of the lactate score model, PDP1 showed the strongest positive correlation with lactate score and the potential as a standalone biomarker for prognosis. In general, our study has yielded crucial insights into the potential application of the lactate score as a predictive biomarker for both survival outcomes and the response to immunotherapy. By recognizing the prognostic significance of lactate metabolism, we open avenues for further investigations aimed at harnessing the therapeutic potential of lactate.

Genomic identification and expression profiling of WRKY genes in alfalfa (Medicago sativa) elucidate their responsiveness to seed vigor

BackgroundSeed aging is a critical factor contributing to vigor loss, leading to delayed forage seed germination and seedling growth. Numerous studies have revealed the regulatory role of WRKY transcription factors in seed development, germination, and seed vigor. However, a comprehensive genome-wide analysis of WRKY genes in Zhongmu No.1 alfalfa has not yet been conducted.ResultsIn this study, a total of 91 MsWRKY genes were identified from the genome of alfalfa. Phylogenetic analysis revealed that these MsWRKY genes could be categorized into seven distinct subgroups. Furthermore, 88 MsWRKY genes were unevenly mapped on eight chromosomes in alfalfa. Gene duplication analysis revealed segmental duplication as the principal driving force for the expansion of this gene family during the course of evolution. Expression analysis of the 91 MsWRKY genes across various tissues and during seed germination exhibited differential expression patterns. Subsequent RT-qPCR analysis highlighted significant induction of nine selected MsWRKY genes in response to seed aging treatment, suggesting their potential roles in regulating seed vigor.ConclusionThis study investigated WRKY genes in alfalfa and identified nine candidate WRKY transcription factors involved in the regulation of seed vigor. While this finding provides valuable insights into understanding the molecular mechanisms underlying vigor loss and developing new strategies to enhance alfalfa seed germinability, further research is required to comprehensively elucidate the precise pathways through which the MsWRKY genes modulate seed vigor.

Whole Genome Expression Profiling of Semitendinosus Tendons from Children with Diplegic and Tetraplegic Cerebral Palsy.

Cerebral palsy (CP) is the most common movement disorder in children, with a prevalence ranging from 1.5 to 4 per 1000 live births. CP is caused by a non-progressive lesion of the developing brain, leading to progressive alterations of the musculoskeletal system, including spasticity, often leading to the development of fixed contractures, necessitating tendon lengthening surgery. Total RNA-sequencing analysis was performed on semitendinosus tendons from diplegic and tetraplegic CP patients subjected to tendon lengthening surgery compared to control patients undergoing anterior cruciate ligament reconstructive surgery. Tetraplegic CP patients showed increased expression of genes implicated in collagen synthesis and extracellular matrix (ECM) turnover, while only minor changes were observed in diplegic CP patients. In addition, tendons from tetraplegic CP patients showed an enrichment for upregulated genes involved in vesicle-mediated transport and downregulated genes involved in cytokine and apoptotic signaling. Overall, our results indicate increased ECM turnover with increased net synthesis of collagen in tetraplegic CP patients without activation of inflammatory and apoptotic pathways, similar to observations in athletes where ECM remodeling results in increased tendon stiffness and tensile strength. Nevertheless, the resulting increased tendon stiffness is an important issue in clinical practice, where surgery is often required to restore joint mobility.

Genome wide identification and expression profiling of PYL genes in barley

PYLs (pyrabactin resistance1/PYR1-like) sense ABA, an essential phytohormone that regulates plant growth and stress responses. PYLs act as the main controllers of ABA stress signaling in plants. In this study, a total of 10 HvPYLs were discovered in the barley genome using an in silico genome search technique. These HvPYLs were then grouped into 3 subfamilies based on a phylogenetic analysis that compared them to the genomes of Arabidopsis, Brachypodium, rice, and maize. These HvPYLs demonstrated conserved motif compositions and identical protein structures across clades. Additionally, this study includes detailed investigations of gene structure variations, chromosomal distributions, cis-regulatory elements, protein-protein interactions, expression profiles in different tissues, and stress responses. We identified various cis-elements in the HvPYL promoter regions related to plant development and stresses indicating their potential roles in development and stress management. Our analysis of the interaction network has identified that HvPYLs can interact with key components of the ABA signaling pathway, demonstrating the critical regulatory functions of HvPYL genes in managing stress and growth in barley. These findings provide a basis for future research aimed at exploring the functions of PYL genes, with the ultimate goal of enhancing stress tolerance in barley and other related species.

Comprehensive Genomic Analysis and Expression Profile of Hsp70 Gene Family Related to Abiotic and Biotic Stress in Cucumber

Heat shock protein 70 (Hsp70) is a class of HSPs involved in plant growth and development, stress response and regulation. The Hsp70 proteins exist widely in the plant world, but the detail information about Hsp70s is still unclear in cucumber. Based on the available cucumber genome, a total of 12 Hsp70 genes (CsHsp70-1 to CsHsp70-12) were identified in this study, and they were distributed among five out of seven chromosomes. The CsHsp70s were divided into four groups based on a phylogenetic analysis by using protein sequences from cucumber and other plants, and their conserved motifs were relatively conserved. Gene duplication analysis showed that segmental duplication is the main driving force of expansion in cucumber CsHsp70 genes. Promoter analysis of CsHsp70 genes showed that they contained many cis-acting elements involved in hormone and stress responses. Expression analysis by RNA-seq and qRT-PCR indicated that the expression of most CsHsp70 genes was associated with multiple biotic and abiotic stresses in cucumber. This study introduces the characteristics of cucumber CsHsp70 genes and the regulation of their expression levels in various abiotic and biotic stresses, which provided a basis for functional exploration and utilization of CsHsp70 genes in the future.

Genomic Identification and Expression Profiling of Lesion Simulating Disease Genes in Alfalfa (Medicago sativa) Elucidate Their Responsiveness to Seed Vigor.

Seed aging, a common physiological phenomenon during forage seed storage, is a crucial factor contributing to a loss of vigor, resulting in delayed seed germination and seedling growth, as well as limiting the production of hay. Extensive bodies of research are dedicated to the study of seed aging, with a particular focus on the role of the production and accumulation of reactive oxygen species (ROS) and the ensuing oxidative damage during storage as a primary cause of decreases in seed vigor. To preserve optimal seed vigor, ROS levels must be regulated. The excessive accumulation of ROS can trigger programmed cell death (PCD), which causes the seed to lose vigor permanently. LESION SIMULATING DISEASE (LSD) is one of the proteins that regulate PCD, encodes a small C2C2 zinc finger protein, and plays a molecular function as a transcriptional regulator and scaffold protein. However, genome-wide analysis of LSD genes has not been performed for alfalfa (Medicago sativa), as one of the most important crop species, and, presently, the molecular regulation mechanism of seed aging is not clear enough. Numerous studies have also been unable to explain the essence of seed aging for LSD gene regulating PCD and affecting seed vigor. In this study, we obtained six MsLSD genes in total from the alfalfa (cultivar Zhongmu No. 1) genome. Phylogenetic analysis demonstrated that the MsLSD genes could be classified into three subgroups. In addition, six MsLSD genes were unevenly mapped on three chromosomes in alfalfa. Gene duplication analysis demonstrated that segmental duplication was the key driving force for the expansion of this gene family during evolution. Expression analysis of six MsLSD genes in various tissues and germinating seeds presented their different expressions. RT-qPCR analysis revealed that the expression of three MsLSD genes, including MsLSD2, MsLSD5, and MsLSD6, was significantly induced by seed aging treatment, suggesting that they might play an important role in maintaining seed vigor. Although this finding will provide valuable insights into unveiling the molecular mechanism involved in losing vigor and new strategies to improve alfalfa seed germinability, additional research must comprehensively elucidate the precise pathways through which the MsLSD genes regulate seed vigor.

Primary Colorectal Tumor Displays Differential Genomic Expression Profiles Associated with Hepatic and Peritoneal Metastases.

Despite improvements in characterization of CRC heterogeneity, appropriate risk stratification tools are still lacking in clinical practice. This study aimed to elucidate the primary tumor transcriptomic signatures associated with distinct metastatic routes. Primary tumor specimens obtained from CRC patients with either isolated LM (CRC-Liver) or PM (CRC-Peritoneum) were analyzed by transcriptomic mRNA sequencing, gene set enrichment analyses (GSEA) and immunohistochemistry. We further assessed the clinico-pathological associations and prognostic value of our signature in the COAD-TCGA independent cohort. We identified a significantly different distribution of Consensus Molecular Subtypes between CRC-Liver and CRC-peritoneum groups. A transcriptomic signature based on 61 genes discriminated between liver and peritoneal metastatic routes. GSEA showed a higher expression of immune response and epithelial invasion pathways in CRC-Peritoneum samples and activation of proliferation and metabolic pathways in CRC-Liver samples. The biological relevance of RNA-Seq results was validated by the immunohistochemical expression of three significantly differentially expressed genes (ACE2, CLDN18 and DUSP4) in our signature. In silico analysis of the COAD-TCGA showed that the CRC-Peritoneum signature was associated with negative prognostic factors and poor overall and disease-free survivals. CRC primary tumors spreading to the liver and peritoneum display significantly different transcriptomic profiles. The implementation of this signature in clinical practice could contribute to identify new therapeutic targets for stage IV CRC and to define individualized follow-up programs in stage II-III CRC.

The Prognostic Value of ASPHD1 and ZBTB12 in Colorectal Cancer: A Machine Learning-Based Integrated Bioinformatics Approach.

Introduction: Colorectal cancer (CRC) is a common cancer associated with poor outcomes, underscoring a need for the identification of novel prognostic and therapeutic targets to improve outcomes. This study aimed to identify genetic variants and differentially expressed genes (DEGs) using genome-wide DNA and RNA sequencing followed by validation in a large cohort of patients with CRC. Methods: Whole genome and gene expression profiling were used to identify DEGs and genetic alterations in 146 patients with CRC. Gene Ontology, Reactom, GSEA, and Human Disease Ontology were employed to study the biological process and pathways involved in CRC. Survival analysis on dysregulated genes in patients with CRC was conducted using Cox regression and Kaplan-Meier analysis. The STRING database was used to construct a protein-protein interaction (PPI) network. Moreover, candidate genes were subjected to ML-based analysis and the Receiver operating characteristic (ROC) curve. Subsequently, the expression of the identified genes was evaluated by Real-time PCR (RT-PCR) in another cohort of 64 patients with CRC. Gene variants affecting the regulation of candidate gene expressions were further validated followed by Whole Exome Sequencing (WES) in 15 patients with CRC. Results: A total of 3576 DEGs in the early stages of CRC and 2985 DEGs in the advanced stages of CRC were identified. ASPHD1 and ZBTB12 genes were identified as potential prognostic markers. Moreover, the combination of ASPHD and ZBTB12 genes was sensitive, and the two were considered specific markers, with an area under the curve (AUC) of 0.934, 1.00, and 0.986, respectively. The expression levels of these two genes were higher in patients with CRC. Moreover, our data identified two novel genetic variants-the rs925939730 variant in ASPHD1 and the rs1428982750 variant in ZBTB1-as being potentially involved in the regulation of gene expression. Conclusions: Our findings provide a proof of concept for the prognostic values of two novel genes-ASPHD1 and ZBTB12-and their associated variants (rs925939730 and rs1428982750) in CRC, supporting further functional analyses to evaluate the value of emerging biomarkers in colorectal cancer.

Transcriptome Analysis Reveals Changes in Whole Gene Expression, Biological Process, and Molecular Functions Induced by Nickel in Jack Pine (Pinus banksiana).

Understanding the genetic response of plants to nickel stress is a necessary step to improving the utility of plants in environmental remediation and restoration. The main objective of this study was to generate whole genome expression profiles of P. banksiana exposed to nickel ion toxicity compared to reference genotypes. Pinus banksiana seedlings were screened in a growth chamber setting using a high concentration of 1600 mg of nickel per 1 kg of soil. RNA was extracted and sequenced using the Illumina platform, followed by de novo transcriptome assembly. Overall, 25,552 transcripts were assigned gene ontology. The biological processes in water-treated samples were analyzed, and 55% of transcripts were distributed among five categories: DNA metabolic process (19.3%), response to stress (13.3%), response to chemical stimuli (8.7%), signal transduction (7.7%) and response to biotic stimulus (6.0%). For molecular function, the highest percentages of genes were involved in nucleotide binding (27.6%), nuclease activity (27.3%) and kinase activity (10.3%). Sixty-two percent of genes were associated with cellular compartments. Of these genes, 21.7% were found in the plasma membrane, 16.1% in the cytosol, 12.4% with the chloroplast and 11.9% in the extracellular region. Nickel ions induced changes in gene expression, resulting in the emergence of differentially regulated categories. Overall, there were significant changes in gene expression with a total 4128 genes upregulated and 3754 downregulated genes detected in nickel-treated genotypes compared to water-treated control plants. For biological processes, the highest percentage of upregulated genes in plants exposed to nickel were associated with the response to stress (15%), the response to chemicals (11,1%), carbohydrate metabolic processes (7.4%) and catabolic processes (7.4%). The largest proportions of downregulated genes were associated with the biosynthetic process (21%), carbohydrate metabolic process (14.3%), response to biotic stimulus (10.7%) and response to stress (10.7%). For molecular function, genes encoding for enzyme regulatory and hydrolase activities represented the highest proportion (61%) of upregulated gene. The majority of downregulated genes were involved in the biosynthetic processes. Overall, 58% of upregulated genes were located in the extracellular region and the nucleus, while 42% of downregulated genes were localized to the plasma membrane and 33% to the extracellular region. This study represents the first report of a transcriptome from a conifer species treated with nickel.

Genomic landscape and expression profile of consensus molecular subtype four of colorectal cancer.

Compared to other subtypes, the CMS4 subtype is associated with lacking of effective treatments and poorer survival rates. A total of 24 patients with CRC were included in this study. DNA and RNA sequencing were performed to acquire somatic mutations and gene expression, respectively. MATH was used to quantify intratumoral heterogeneity. PPI and survival analyses were performed to identify hub DEGs. Reactome and KEGG analyses were performed to analyze the pathways of mutated or DEGs. Single-sample gene set enrichment analysis and Xcell were used to categorize the infiltration of immune cells. The CMS4 patients had a poorer PFS than CMS2/3. CTNNB1 and CCNE1 were common mutated genes in the CMS4 subtype, which were enriched in Wnt and cell cycle signaling pathways, respectively. The MATH score of CMS4 subtype was lower. SLC17A6 was a hub DEG. M2 macrophages were more infiltrated in the tumor microenvironment of CMS4 subtype. The CMS4 subtype tended to have an immunosuppressive microenvironment. This study suggested new perspectives for exploring therapeutic strategies for the CMS4 subtype CRC.

Molecular subtypes from comprehensive clustering from multi-omics dataset to predict the therapeutic efficacy of immunotherapeutic agent-based treatments in advanced hepatocellular carcinoma.

4112 Background: In advanced hepatocellular carcinoma (HCC), combined treatment using anti-PD-L1 and anti-VEGF antibodies is a major therapeutic strategy in addition to using anti-PD-1 and anti-CTLA4 target agents. To identify clinically relevant molecular biomarkers for immunotherapeutic agents-based treatment in advanced HCC by comprehensive molecular profiling using genomics alterations and transcriptomic data. Methods: Multi-omics data from clinical tumor samples of patients treated with atezolizumab + bevacizumab (94 patients), nivolumab (40 patients), and ipilimumab + nivolumab (32 patients) were obtained from tumor biopsies or surgical resections in a single institution. The targeted panel sequencing was conducted via the Oncomine comprehensive assay (ThermoFisher, USA). QuantSeq mRNA sequencing (Lexogen, USA) was used to generate datasets for the genomic alterations and gene expression profiles. Results: A total of 166 target sequences for genomic alterations and 136 transcriptomic sequences were performed in patients with advanced HCC treated with immunotherapeutic agent-based treatment options. High tumor mutation burden was significantly associated with favorable therapeutic efficacy (disease control rate, P=0.036) and progression-free survival (P=0.037) in patients who had atezolizumab with bevacizumab treatment. The genomic alteration of CTNNB1 mutation correlated with the favorable therapeutic efficacy of nivolumab monotherapy (PFS, P=0.022), contrary to TP53 mutation (PFS, P=0.063) which demonstrated unfavorable outcomes. CD274(PD-L1) mRNA expression was significantly associated with a high drug response following nivolumab monotherapy (objective response rate, P=0.047) and oncologic outcomes (PFS, P=0.021). Interestingly, PLA2G4A, known as a downstream molecule of the VEGF signaling pathway, was highly correlated with unfavorable therapeutic efficacy of the combined atezolizumab with bevacizumab treatment (disease control rate, P=0.002) and related oncologic outcomes (PFS, P=0.003). We also identified the clinically relevant molecular subtypes from unbiased clustering using the ontologic pathway collection. We also used gene expression profiles to predict the therapeutic response and oncologic outcomes from immunotherapeutic agent-based treatment options. Conclusions: We identified clinically relevant molecular biomarkers from comprehensive clustering of a multi-omics dataset to predict the therapeutic efficacy and oncologic outcomes. Further prospective studies with clinical validation are warranted to confirm clinical implications.

Genomic landscape and gene expression profiles of feline oral squamous cell carcinoma.

Feline oral squamous cell carcinoma (FOSCC) is a cancer of the squamous cell lining in the oral cavity and represents up to 80% of all oral cancers in cats, with a poor prognosis. We have used whole exome sequencing (WES) and RNA sequencing of the tumor to discover somatic mutations and gene expression changes that may be associated with FOSCC occurrence. FOSCC offers a potential comparative model to study human head and neck squamous cell carcinoma (HNSCC) due to its similar spontaneous formation, and morphological and histological features. In this first study using WES to identify somatic mutations in feline cancer, we have identified tumor-associated gene mutations in six cats with FOSCC and found some overlap with identified recurrently mutated genes observed in HNSCC. Four samples each had mutations in TP53, a common mutation in all cancers, but each was unique. Mutations in other cellular growth control genes were also found such as KAT2B and ARID1A. Enrichment analysis of FOSCC gene expression profiles suggests a molecular similarity to human OSCC as well, including alterations in epithelial to mesenchymal transition and IL6/JAK/STAT pathways. In this preliminary study, we present exome and transcriptome results that further our understanding of FOSCC.

Analysis of the mechanism of propagated sensation along meridians based on gene expression profiles.

Propagated sensation along meridians (PSM) is an important basis for the formation of the meridian theory, but its mechanism is still unclear. The study explored the mechanism of PSM from the perspective of gene expression. PSM induced by moxibustion was determined and classified according to the Modern Study of Meridians of Chinese Medicine. Seven subjects with obvious PSM (obvious PSM group) and five subjects with unobvious PSM (unobvious PSM group) were selected from 33 healthy volunteers according to the scores in their infrared radiant track along meridians (IRRTM) and the degree of subjective transduction. Agilent Human 4×44K Gene Expression Microarrays V2 were used to detect the whole genome expression profile of subjects in the two groups. KEGG and GO were applied to analyze differentially expressed genes. Compared with the unobvious PSM group, 120 genes were differentially expressed in the obvious PSM group, including 76 up-regulated and 44 down-regulated genes. The differentially expressed genes were enriched in dopaminergic synapse, 5-hydroxychrominable synapse, glutamatergic synapse, calcium release channel, gap junction, and adherens junction pathways. The study provides a comprehensive set of gene expression data of subjects with obvious PSM, which indicates that the molecular basis of PSM may be closely related to neurotransmitters, calcium ions and cell junction pathways. This study combines the holistic concept of traditional Chinese medicine with modern molecular biology technology to explore the molecular mechanism of PSM from the perspective of genomics, which may shed new insights into the molecular mechanism of PSM.

Comprehensive Genome Analysis of Cellulose and Xylan-Active CAZymes from the Genus Paenibacillus: Special Emphasis on the Novel Xylanolytic Paenibacillus sp. LS1.

Xylan is the most abundant hemicellulose in hardwood and graminaceous plants. It is a heteropolysaccharide comprising different moieties appended to the xylose units. Complete degradation of xylan requires an arsenal of xylanolytic enzymes that can remove the substitutions and mediate internal hydrolysis of the xylan backbone. Here, we describe the xylan degradation potential and underlying enzyme machinery of the strain, Paenibacillus sp. LS1. The strain LS1 was able to utilize both beechwood and corncob xylan as the sole source of carbon, with the former being the preferred substrate. Genome analysis revealed an extensive xylan-active CAZyme repertoire capable of mediating efficient degradation of the complex polymer. In addition to this, a putative xylooligosaccharide ABC transporter and homologues of the enzymes involved in the xylose isomerase pathway were identified. Further, we have validated the expression of selected xylan-active CAZymes, transporters, and metabolic enzymes during growth of the LS1 on xylan substrates using qRT-PCR. The genome comparison and genomic index (average nucleotide identity [ANI] and digital DNA-DNA hybridization) values revealed that strain LS1 is a novel species of the genus Paenibacillus. Lastly, comparative genome analysis of 238 genomes revealed the prevalence of xylan-active CAZymes over cellulose across the Paenibacillus genus. Taken together, our results indicate that Paenibacillus sp. LS1 is an efficient degrader of xylan polymers, with potential implications in the production of biofuels and other beneficial by-products from lignocellulosic biomass. IMPORTANCE Xylan is the most abundant hemicellulose in the lignocellulosic (plant) biomass that requires cooperative deconstruction by an arsenal of different xylanolytic enzymes to produce xylose and xylooligosaccharides. Microbial (particularly, bacterial) candidates that encode such enzymes are an asset to the biorefineries to mediate efficient and eco-friendly deconstruction of xylan to generate products of value. Although xylan degradation by a few Paenibacillus spp. is reported, a complete genus-wide understanding of the said trait is unavailable till date. Through comparative genome analysis, we showed the prevalence of xylan-active CAZymes across Paenibacillus spp., therefore making them an attractive option towards efficient xylan degradation. Additionally, we deciphered the xylan degradation potential of the strain Paenibacillus sp. LS1 through genome analysis, expression profiling, and biochemical studies. The ability of Paenibacillus sp. LS1 to degrade different xylan types obtained from different plant species, emphasizes its potential implication in lignocellulosic biorefineries.

Identification of molecular candidates which regulate calcium-dependent CD8+ T-cell cytotoxicity

Cytotoxic CD8+ T lymphocytes (CTL) eliminate infected cells or transformed tumor cells by releasing perforin-containing cytotoxic granules at the immunological synapse. The secretion of such granules depends on Ca2+-influx through store operated Ca2+ channels, formed by STIM (stromal interaction molecule)-activated Orai proteins. Whereas molecular mechanisms of the secretion machinery are well understood, much less is known about the molecular machinery that regulates the efficiency of Ca2+-dependent target cell killing. CTL killing efficiency is of high interest considering the number of studies on CD8+ T lymphocytes modified for clinical use. Here, we isolated total RNA from primary human cells: natural killer (NK) cells, non-stimulated CD8+ T-cells, and from Staphylococcus aureus enterotoxin A (SEA) stimulated CD8+ T-cells (SEA-CTL) and conducted whole genome expression profiling by microarray experiments. Based on differential expression analysis of the transcriptome data and analysis of master regulator genes, we identified 31 candidates which potentially regulate Ca2+-homeostasis in CTL. To investigate a putative function of these candidates in CTL cytotoxicity, we transfected either SEA-stimulated CTL (SEA-CTL) or antigen specific CD8+ T-cell clones (CTL-MART-1) with siRNAs specific against the identified candidates and analyzed the killing capacity using a real-time killing assay. In addition, we complemented the analysis by studying the effect of inhibitory substances acting on the candidate proteins if available. Finally, to unmask their involvement in Ca2+ dependent cytotoxicity, candidates were also analyzed under Ca2+-limiting conditions. Overall, we identified four hits, CCR5 (C-C chemokine receptor type five), KCNN4 (potassium calcium-activated channel subfamily N), RCAN3 (regulator of calcineurin) and BCL (B-cell lymphoma) 2 which clearly affect the efficiency of Ca2+ dependent cytotoxicity in CTL-MART-1 cells, CCR5, BCL2, and KCNN4 in a positive manner, and RCAN3 in a negative way.