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Results for “Comprehensive genomic profiling”

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PubMed2002

Molecular and physiological approaches to maize improvement for drought tolerance.

Average maize yields have increased steadily over the years in the USA and yet the variations in harvestable yield have also markedly increased. Much of the increase in yield variability can be attributed to (1) varying environmental stress conditions; (2) improved nitrogen inputs and better weed control; and (3) continuing sensitivity of different maize lines to the variation in input supply, especially rainfall. Drought stress alone can account for a significant percentage of average yield losses. Yet despite variable environments, new commercially available maize hybrids continue to be produced each year with ever-increasing harvestable yield. Since many factors contribute to high plant performance under water deficits, efforts are being made to elucidate the nature of water-stress tolerance in an attempt to improve maize hybrids further. Such factors include better partitioning of biomass to the developing ear resulting in faster spikelet growth and improved reproductive success. An emphasis on faster spikelet growth rate may result in a reduction in the number of spikelets formed on the ear that facilitates overall seed set by reducing water and carbon constraints per spikelet. To understand the molecular mechanisms for drought tolerance in improved maize lines better, a variety of genomic tools are being used. Newer molecular markers and comprehensive gene expression profiling methods provide opportunities to direct the continued breeding of genotypes that provide stable grain yield under widely varied environmental conditions.

Acclimatization↗

PubMed2002

An inner ear gene expression database.

Microarray technology has provided an unprecedented opportunity to study gene expression profiles at a whole-genome level. As a first step toward a comprehensive understanding of inner ear gene expression, mouse cochleas were examined at two developmental stages (P2 and P32) using GeneChip oligonucleotide arrays. A large number of genes and ESTs (> 10,000) were found to be expressed in the cochlea. Expression profiles derived from duplicate samples at the same developmental stages showed general agreement and indicated the reproducibility of the assay. The expression of many known hair-cell genes was detected in the whole-cochlea samples, demonstrating the relatively high sensitivity of the assay. Genes highly expressed only at P2 or P32 were also identified and their expression patterns correlate with their functions in the cochlea. A web-based database with external links was set up for public access, which should facilitate the discovery of genes important in the development and function of the inner ear and should aid the identification of additional deafness genes.

Animals↗

PubMed2023

Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.

Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.

RNA, Transfer↗

PubMed2000

Monitoring gene expression using DNA microarrays.

The concurrent development of high-density array technologies and the complete sequencing of a number of microbial genomes is providing the opportunity to comprehensively and efficiently survey the transcription profile of microorganisms under different conditions and well-defined genotypes. Microarray-based studies are uncovering broad patterns of genetic activity, providing new understanding of gene functions and, in some cases, generating unexpected insight into transcriptional processes and biological mechanisms. One topic that has come to the forefront is how best to effectively manage and interpret the large data sets being generated. Although progress has been made, this remains a challenging opportunity for functional genomics research.

Gene Expression Regulation, Bacterial↗

PubMed2003

Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications.

BACKGROUND: Both phenotypic and cytogenetic variability have been reported for clones of breast carcinoma cell lines but have not been comprehensively studied. Despite this, cell lines such as MCF-7 cells are extensively used as model systems. METHODS: In this work we documented, using CGH and RNA expression profiles, the genetic variability at the genomic and RNA expression levels of MCF-7 cells of different origins. Eight MCF-7 sublines collected from different sources were studied as well as 3 subclones isolated from one of the sublines by limit dilution. RESULTS: MCF-7 sublines showed important differences in copy number alteration (CNA) profiles. Overall numbers of events ranged from 28 to 41. Involved chromosomal regions varied greatly from a subline to another. A total of 62 chromosomal regions were affected by either gains or losses in the 11 sublines studied. We performed a phylogenetic analysis of CGH profiles using maximum parsimony in order to reconstruct the putative filiation of the 11 MCF-7 sublines. The phylogenetic tree obtained showed that the MCF-7 clade was characterized by a restricted set of 8 CNAs and that the most divergent subline occupied the position closest to the common ancestor. Expression profiles of 8 MCF-7 sublines were analyzed along with those of 19 unrelated breast cancer cell lines using home made cDNA arrays comprising 720 genes. Hierarchical clustering analysis of the expression data showed that 7/8 MCF-7 sublines were grouped forming a cluster while the remaining subline clustered with unrelated breast cancer cell lines. These data thus showed that MCF-7 sublines differed at both the genomic and phenotypic levels. CONCLUSIONS: The analysis of CGH profiles of the parent subline and its three subclones supported the heteroclonal nature of MCF-7 cells. This strongly suggested that the genetic plasticity of MCF-7 cells was related to their intrinsic capacity to generate clonal heterogeneity. We propose that MCF-7, and possibly the breast tumor it was derived from, evolved in a node like pattern, rather than according to a linear progression model. Due to their capacity to undergo rapid genetic changes MCF-7 cells could represent an interesting model for genetic evolution of breast tumors.

Breast Neoplasms↗

PubMed2002

Genome-wide profiling of gene expression in 29 normal human tissues with a cDNA microarray.

We have performed a comprehensive analysis of the expression profiles in 25 adult and 4 fetal human tissues by means of a cDNA microarray consisting of 23,040 human genes. This study revealed a number of genes that were expressed specifically in each of those tissues. Among the 29 tissues examined, 4,080 genes were highly expressed (at least a five-fold expression ratio) in one or only a few tissues and 1,163 of those were expressed exclusively (more than a ten-fold higher expression ratio) in a particular tissue. Expression of some of the genes in the latter category was confirmed by northern analysis. A hierarchical clustering analysis of gene-expression profiles in nerve tissues (adult brain, fetal brain, and spinal cord), lymphoid tissues (bone marrow, thymus, spleen, and lymph node), muscle tissues (heart and skeletal muscle), or adipose tissues (mesenteric adipose and mammary gland) identified a set of genes that were commonly expressed among related tissues. These data should provide useful information for medical research, especially for efforts to identify tissue-specific molecules as potential targets of novel drugs to treat human diseases.

Adult↗

PubMed2025

Diffusely metastatic glioblastoma with FGFR3::TACC3 fusion: cell-free DNA fragmentation analyses and molecular characterization of matched primary and metastatic tumor sites.

Extracranial metastasis of IDH-wildtype glioblastoma is very rare and poorly understood at the molecular level. We report a case of FGFR3::TACC3 fusion IDH-wildtype glioblastoma in a 61-year-old male, whose preoperative blood sample showed highly aberrant cfDNA fragmentation patterns, which could be suggestive of early systemic dissemination, undetected by standard-of-care imaging of his body. Eleven months post-resection and adjuvant therapy, he developed widespread extracranial metastases. Comprehensive molecular profiling of matched primary and metastatic tumors revealed broadly conserved genomic, transcriptomic, and copy number landscapes, with the metastasis harboring an additional ERCC6 deletion and enriched expression of receptor tyrosine kinase signaling genes. These findings provide rare insight into the genetic continuity and evolution underlying IDH-wildtype glioblastoma metastasis.

Humans↗

PubMed2002

Transcriptional regulation of solventogenesis in Clostridium acetobutylicum.

Solvent synthesis in Clostridium acetobutylicum is induced in concert with sporulation to counteract the dangerous effects of produced butyric and acetic acids and to provide the cell with sufficient time to complete endospore formation. Cardinal transcription units for butanol and acetone production are the sol and adc operons encoding butyraldehyde/butanol dehydrogenase and coenzyme A transferase as well as acetoacetate decarboxylase. Induction is achieved by a decreased level of DNA supercoiling and the transcription factor Spo0A, possibly in cooperation with other regulatory proteins. A number of other operons is also turned on during this metabolic switch, whose physiological relevance, however, is only partly understood. The recent completion of C. acetobutylicum genome sequencing will pave the way for transcriptional profiling and thus allow comprehension of the coherent regulatory networks of solventogenesis and sporulation.

Acetone↗

PubMed2002

Cancer genomics.

The draft human genome sequence and the dissemination of high throughput technology provides opportunities for systematic analysis of cancer cells. Genome-wide mutation screens, high resolution analysis of chromosomal abberations and expression profiling all give comprehensive views of genetic alterations in cancer cells. From these analyses will come a complete list of the genetic changes that drive malignant transformation and of the therapeutic targets that may be exploited for clinical benefit.

Cell Transformation, Neoplastic↗

PubMed2026

Epigenetic profiling of circulating cell-free DNA for early detection and minimal residual disease assessment in lung cancer: a focus on DNA methylation.

Lung Cancer (LC) continues to be the biggest cause of cancer-related deaths around the world, mostly because of delayed diagnosis. Even if tissue biopsies and circulating tumor DNA (ctDNA) tests have revolutionized clinical management of LC patients, their effectiveness is restricted in settings with lower tumor burden, molecular heterogeneity, and bias in sampling approaches. In this scenario, the epigenetic profiling of cell-free DNA (cfDNA) stands out as a promising, less invasive approach, accurately detect cancer traces. Evidence from stage I-II disease and CT-detected pulmonary nodules supports the diagnostic potential of cfDNA methylation, although further validation in prospective screening cohorts remains necessary. Beyond genomic alterations, cfDNA epigenetic changes, including DNA methylation, chromatin organization, nucleosome positioning, and fragmentation patterns, reflect multi-dimensional complexity of tumor biology. These properties convey both the functional status and the origin of the circulating DNA fragments, accelerating for tumor integrating genomic analysis. Within this group, DNA methylation is the biologically robust and clinically well-established epigenetic marker, as alterations in methylation linked to cancer often occur in the early stages of tumorigenesis and are commonly found across different cancer cell types. Here, we explored the biological and clinical relevance of the epigenetic landscape of cfDNA in LC patients, particularly focusing on DNA methylation-based biomarkers and their evolving applications towards early diagnosis and post-surgical monitoring of minimal residual disease (MRD). We aimed to comprehensively overview analytical approaches for cfDNA methylation analysis, including targeted and genome-wide profiling strategies, and discuss their integration with machine learning (ML) and multi-omics frameworks in order to improve diagnostic performance and clinical applicability in LC management.

DNA methylation↗

PubMed2003

Comparing gene expression profiles in human liver, gastric, and pancreatic tissues using full-length-enriched cDNA libraries.

In the post-genome-sequencing era, full-length cDNA-sequence resources are extremely useful for functional analyses of genes. In addition, comprehensive gene profiling of human tissues at the mRNA level is also useful in understanding the molecular mechanisms of tissue-specific functions and disease pathogenesis. In this study, to obtain a wide variety of full-length cDNA clones derived from digestive tissues, numerous expressed sequence tags were generated from libraries enriched with full-length cDNAs. In total, 13575 sequences were obtained from three cDNA libraries, which were constructed from tissues and cell lines of human liver, stomach, and pancreas. The integration of overlapping clones categorized the sequences into 5936 clusters (1666, 2746, and 2222 clusters in the liver, stomach, and pancreas, respectively). Of these, 1138 clones were scored as full-length cDNAs. Surprisingly, the redundant clones from all three tissues were assembled to show that only 101 genes (1.7% of the assembled 5936 genes) were shared. These results suggest that functional differences between tissues are probably related to their divergent gene expression profiles, and form a basis for understanding the molecular mechanisms underlying tissue-specific pathogenesis that are expressed in different organs. In addition, the full-length cDNAs obtained in this study should prove useful for future functional analyses of the genes expressed in digestive tissues.

Journal Article↗

PubMed2026

SpacerScope: binary-vectorized, genome-wide off-target profiling for RNA-guided nucleases without prior candidate-site bias.

The precision of CRISPR/Cas systems is fundamental to their application in plant and animal biotechnology. However, comprehensive sequence-based off-target candidate discovery remains a computational bottleneck, particularly in large and complex genomes. Here we developed SpacerScope, an off-target candidate discovery framework that enables unbiased, genome-wide discovery by leveraging binary vectorization, bitwise filtering, and right-end-anchored alignment. Benchmarking against human CIRCLE-seq data demonstrated that SpacerScope recovered 100% of validated off-target sites (6142/6142), matching the sensitivity of exhaustive algorithms. Crucially, SpacerScope achieved this maximum candidate recovery while substantially reducing computational overhead. In large-genome evaluations, SpacerScope maintained low peak memory usage of 2.20 GiB and achieved substantial runtime improvements over indel-aware comparator tools, including more than 50-fold speedup relative to Cas-OFFinder 3 (544 s versus 29 185 s). Furthermore, comparative analyses in polyploid species, such as the octoploid strawberry, revealed that SpacerScope identified larger sequence-compatible candidate burdens than standard web-based design platforms. Our results establish SpacerScope as a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes. The source code and program was publicly available at https://github.com/charlesqu666/SpacerScope. Short Abstract CRISPR/Cas sequence-based off-target candidate discovery remains computationally challenging in large, repetitive, and polyploid genomes. Existing tools either miss indel-containing candidate sites or incur prohibitive runtime and memory costs. We developed SpacerScope, a binary-vectorized framework that enables unbiased, genome-wide off-target candidate discovery without pre-selected candidate sites. By integrating bitwise filtering with right-end-anchored alignment, SpacerScope recovered 100% of validated off-target sites in human CIRCLE-seq data while using only 2.20 GiB of memory and achieving more than 10-fold speedup over indel-aware alternatives. Evaluation in plant genomes, including rice and octoploid strawberry, further demonstrated SpacerScope's capacity to identify larger sequence-compatible candidate burdens overlooked by standard tools. SpacerScope thus provides a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes, supporting downstream prioritization.

CRISPR-Cas Systems↗

PubMed2002

Complementary whole-genome technologies reveal the cellular response to proteasome inhibition by PS-341.

Although the biochemical targets of most drugs are known, the biological consequences of their actions are typically less well understood. In this study, we have used two whole-genome technologies in Saccharomyces cerevisiae to determine the cellular impact of the proteasome inhibitor PS-341. By combining population genomics, the screening of a comprehensive panel of bar-coded mutant strains, and transcript profiling, we have identified the genes and pathways most affected by proteasome inhibition. Many of these function in regulated protein degradation or a subset of mitotic activities. In addition, we identified Rpn4p as the transcription factor most responsible for the cell's ability to compensate for proteasome inhibition. Used together, these complementary technologies provide a general and powerful means to elucidate the cellular ramifications of drug treatment.

Boronic Acids↗

PubMed2001

On the birth of breast cancer.

Breast carcinoma is one of the most common neoplasms in women and is a leading cause of cancer related deaths worldwide. In recent years improved diagnostic tools have made it possible to detect breast cancers at early, even pre-invasive stages leading to a significant decrease in breast cancer mortality rates over the past decades. The increased number of patients diagnosed with pre-invasive breast tumors opened up new avenues in research and new dilemmas in clinical practice, since our understanding of the pathophysiology of such lesions is just beginning to emerge. Part of the delay and difficulty with analyzing pre-invasive tumors including ductal carcinoma in situ has been due to the lack of appropriate techniques suitable for studies of small, frequently microscopic size tumors. Recently developed technologies such as DNA microarrays and SAGE (serial analysis of gene expression) have made it possible to obtain comprehensive gene expression profiles of breast carcinomas of all stages. The application of these genomics approaches in combination with the complete sequence of the human genome and extensive molecular epidemiological studies is likely to further our understanding of the molecular basis of mammary tumorigenesis and will identify targets for risk prediction, cancer prevention and treatment.

Animals↗

PubMed2026

Age- and sex-adjusted genomic differences between Korean and Beat AML cohorts.

Genomic profiling plays a central role in risk stratification and therapeutic decision-making in acute myeloid leukemia (AML), yet the clinical implications of population-specific genomic architectures remain incompletely defined. We conducted a prospective, multicenter study of 603 adults with newly diagnosed AML in Korea, integrating targeted sequencing of 83 recurrently mutated genes with comprehensive clinical annotation across treatment intensities, including allogeneic hematopoietic stem cell transplantation (allo-HSCT). For contextual comparison, genomic profiles were evaluated against the Beat AML cohort. The overall genomic landscape was broadly conserved, supporting shared core disease biology across populations. However, RUNX1::RUNX1T1, CEBPA, GATA2, KIT, and DDX41 mutations were more frequent in the Korean cohort, whereas FLT3 and NPM1 mutations were less common. These differences translated into a distinct distribution of European LeukemiaNet (ELN) 2022 risk categories, with implications for therapeutic stratification. Notably, most DDX41 alterations were germline (3.2%), highlighting the need for systematic germline evaluation with implications for genetic counseling and donor selection. Although unadjusted overall survival appeared longer in the Korean cohort, this difference was not significant after adjustment for key clinical variables. These findings indicate that population-specific genomic distributions reshape the clinical application of risk stratification and support population-aware precision medicine strategies in AML.

Journal Article↗

PubMed1997

In search of differentially expressed genes and proteins.

A great challenge for modern cell biology is the successful examination of the co-expression of thousands of genes under physiological or pathological conditions and how the expression patterns define the different states of a single cell, tissue or a microorganism. Gene expression can be analyzed today on a large scale by advanced technical approaches for differential screening of proteins and mRNAs. The identification of differentially expressed mRNAs has been successfully applied to understand gene function and the underlying molecular mechanism(-s) of differentiation, development and disease state. Analysis of gene expression by the systematic mapping of thousands of proteins present in a cell or tissue can be achieved by the use of two-dimensional (2D) gel electrophoresis, quantitative computer image analysis, and protein identification techniques. In this article, we comment on some of these techniques and try to stress their advantages and drawbacks. We show how data from RNA/DNA mapping, sequence information from genome projects and protein pattern profiling can be linked with each other and annotated. These comprehensive approaches permit the study of differential gene and protein expressions in cells or tissues.

Animals↗

PubMed2025

scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell Data.

Measuring single-cell genomic profiles at different timepoints enables our understanding of cell development. This understanding is more comprehensive when we perform an integrative analysis of multiple measurements (or modalities) across various developmental stages. However, obtaining such measurements from the same set of single cells is resource-intensive, restricting our ability to study them jointly. We introduce scMultiNODE, an unsupervised integration model that combines gene expression and chromatin accessibility measurements in developing single cells, while preserving cell type variations and cellular dynamics. First, scMultiNODE uses a scalable, Quantized Gromov-Wasserstein optimal transport to align a large number of cells across different measurements. Next, it utilizes neural ordinary differential equations to explicitly model cell development with a regularization term to learn a dynamic latent space. Experiments on six real-world developmental single-cell datasets demonstrate that scMultiNODE can integrate temporally profiled multi-modal single-cell measurements more effectively than existing methods that focus on cell type variations and often overlook cellular dynamics. We also demonstrate that scMultiNODE's joint latent space facilitates several insightful downstream analyses of single-cell development, including the investigation of complex cell trajectories and the enabling of cross-modal label transfer. The data and code are publicly available at https://github.com/rsinghlab/scMultiNODE.

autoencoders↗

PubMed2026

Serotypic and Genomic Diversity of Vibrio anguillarum in Rainbow Trout Farms in Turkey: Implications for Vibriosis Control and Vaccine Candidate Selection.

Outbreaks of vibriosis caused by Vibrio anguillarum are a persistent constraint on rainbow trout (Oncorhynchus mykiss) aquaculture. However, information on the population structure of field strains in Turkey has been lacking. Here, we report the first systematic serotypic, proteomic, and genomic characterization of 23 V. anguillarum isolates collected over 10 years from rainbow trout farms located in six major aquaculture regions of Turkey. Serological analyses based on microagglutination, supported by ELISA characterization of hyperimmune sera, identified a clear predominance of serotype O1, whereas isolate V12 exhibited a non-agglutinating, atypical O-antigen profile. Protein profiling (SDS-PAGE) and immunoblotting showed largely conserved whole-cell protein patterns among the isolates, but distinct immunogenic bands at 14, 18, and 40 kDa were detected in isolates V18 and V21. Long-read whole-genome sequencing revealed that most Turkish isolates grouped within the global O1 clade, while V12, V25, and V28 isolates occupied more distant branches. Comparative genomics demonstrated a conserved core virulence gene set (RTX toxins, siderophore and iron-uptake systems, motility and adhesion factors, Type VI secretion system), with strain-dependent variation in accessory loci such as anguibactin and T6SS-I. Experimental infections of rainbow trout demonstrated significant differences in virulence among isolates (p < 0.05), with the V18 isolate showing high, the V15 intermediate, and the V12 low-mortality rates. By elucidating the relationship among the serotype, immunogenic protein profiles, virulence gene repertoires, and in vivo pathogenicity, this study provides a comprehensive overview of the antigenic and genomic diversity of Vibrio anguillarum isolates from Turkey. Notably, the identification of V18 and V21 as promising candidate strains for further vaccine evaluation, characterized by high virulence and unique immunogenic features, provides a scientific foundation for the development of serotype-specific vaccination strategies to mitigate vibriosis-associated losses in aquaculture.

Animals↗