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PubMed1997

Fiber-specific molecular features of tumors induced in rat peritoneum.

Molecular markers such as mutational spectra or mRNA expression patterns may give some indication of the mechanisms of carcinogenesis induced by fibers and other carcinogens. In our study, tumors were induced by application of crocidolite asbestos or benzo[a]pyrene (B[a]P) to rat peritoneum. DNA and RNA of these tumors were subjected to analysis of point mutations and to investigation of mRNA expression patterns. With both assays we found typical features depending on the type of carcinogen applied. The analysis of point mutations in the tumor suppressor gene p53 revealed mutations in the B[a]P-induced tumors. However, in the tumors induced by crocidolite asbestos that were of the same tumor type as those induced by B[a]P, mutations in p53 were not detectable. Every mutation detected on the DNA level causes an amino acid substitution within one of the functional domains of the tumor suppressor protein. Therefore, these mutations seem to be of biological relevance for tumor progression and indicate a difference in the carcinogenesis regarding the type of the carcinogenic substance. An additional specificity of crocidolite-induced tumors was detectable by analyzing the mRNA expression of the tumor suppressor gene WT1, which is known to be expressed in human mesothelial and mesothelioma cells. A relatively high amount of WT1 mRNA was measured by quantitative competitive reverse transcription-polymerase using RNA extracted from crocidolite-induced tumors. However, WT1 seems to be expressed on a rather low level in tumors induced by B[a]P.

Abdominal Neoplasms↗

PubMedDate not supplied

Gene expression in response to ionizing radiation: an overview of molecular features in hematopoietic cells.

We review the molecular mechanisms involved in response to ionizing radiation in various hematopoietic cell types. First, a general overview of the radiation induced cell signaling molecules in mammals is given. The importance of highly conserved kinases, such as ATM and ATR, as well as the p53 protein for maintaining the genome stability is highlighted. Next, particular attention is given to radiation-induced gene expression in the hematopoietic system. For some hemopoietic cell subpopulations, recent data are provided which might explain the differential radiosensitivity of these cells. Finally, radiation-induced cytokines are reviewed, as they affect the global response to radiation.

Animals↗

PubMed2026

Integrative multi-omics profiling of insomnia-related molecular features reveals microbiome, immune, and therapy-relevant heterogeneity in colorectal cancer.

Emerging evidence implicates insomnia as a potential risk factor in carcinogenesis, potentially involving systemic inflammation, circadian disruption, and microbiome alterations. However, the molecular associations linking insomnia-related features to colorectal cancer (CRC), particularly with respect to tumor biology, immune microenvironmental states, and therapy-relevant phenotypes, remain largely unexplored. Multi-omics integration of genomic, transcriptomic, and microbiome data from 3,026 CRC patients across seven independent cohorts, including a large, well-annotated Clinical Omics study of Colorectal Cancer in China (COCC) cohort, enabled insomnia-based molecular classification through unsupervised non-negative matrix factorization (NMF) clustering. The insomnia subtype (IS) was biologically characterized via pathway enrichment, immune deconvolution, microbial profiling, and single-cell transcriptomics. Furthermore, an insomnia score (ISscore) was developed and validated in multiple cohorts for risk stratification and assessment of treatment-response-related indicators in CRC. Unsupervised clustering revealed two distinct molecular subtypes (IS1/IS2), with IS2 demonstrating significantly poorer survival. IS2 exhibited marked activation of EMT/angiogenesis pathways versus cell cycle activation in IS1. The IS2 microenvironment showed increased immunosuppression-related infiltration and exhausted T cell signatures, together with intratumoral microbiome variation characterized by depletion of Ruminococcaceae UCG-002 and enrichment of Hungatella/Selenomonas. The ISscore system stratified survival risk and was associated with computational indicators of immunotherapy response. Single-cell analysis nominated PPIA-BSG as a potential cell-cell communication signal involving high-ISscore tumor cells, CXCL12+ endothelial cells, and CLEC9A+ dendritic cell subsets. This multi-omics characterization of insomnia-CRC interplay suggests that insomnia-related molecular features are associated with an immunologically distinct and microbiome-altered tumor ecosystem. The ISscore provides a reproducible framework for capturing insomnia-related molecular heterogeneity, supporting risk stratification and future evaluation of therapy-relevant phenotypes.IMPORTANCEChronic insomnia affects millions, but it is not typically considered a cancer risk factor. Our study, analyzing vast biological data from over 3,000 colorectal cancer patients, uncovers a potential link between a person's predisposition to insomnia and their risk of developing this disease. This suggests that the biological pathways related to sleep may play a role in cancer development. Understanding this connection opens up new avenues for identifying individuals at higher risk and developing novel prevention strategies for colorectal cancer.

colorectal cancer↗

PubMedDate not supplied

Clinicopathologic and molecular features of pancreatic adenocarcinoma associated with Peutz-Jeghers syndrome.

Pancreatic cancer is increasingly prevalent and almost uniformly fatal. Studies of the molecular genetics of sporadic and hereditary cases of pancreatic cancer as well as the molecular biology of pancreatic development may advance our understanding of the mechanism underlying pathogenesis of this malignancy. Based on a case of pancreatic adenocarcinoma in a patient with Peutz-Jeghers syndrome (PJS), the clinicopathologic features and molecular genetics of pancreatic tumors associated with this hereditary cancer syndrome are reviewed. Particular emphasis is placed on the developmental roles and biochemical functions of STK11/LKB1, the gene mainly responsible for PJS. Modeling pancreatic cancer in animal models such as the mouse and zebrafish will further our understanding of the pathogenesis of this important disease, and the studies derived from these model organisms can be potentially applied for developing novel preventive and therapeutic strategies.

AMP-Activated Protein Kinase Kinases↗

PubMed2000

Nosocomial bloodstream infections caused by Acinetobacter species in United States hospitals: clinical features, molecular epidemiology, and antimicrobial susceptibility.

We examined the clinical and epidemiological features of nosocomial bloodstream infections (BSIs) caused by Acinetobacter species and observed from 1 March 1995 through 28 February 1998 at 49 United States hospitals (SCOPE National Surveillance Program). Acinetobacter species were found in 24 hospitals (49%) and accounted for 1.5% of all nosocomial BSIs reported. One hundred twenty-nine isolates were identified either as A. baumannii (n=111) or other Acinetobacter species (n=18). Patients with A. baumannii BSI, compared with patients with nosocomial BSI caused by other gram-negative pathogens, were more frequently observed in the intensive care unit (69% vs. 47%, respectively; P<.001; odds ratio [OR] 2.4; 95% confidence interval [CI] 1.6-3.7) and were more frequently receiving mechanical ventilation (58% vs. 30%, respectively; P<.001; OR 3.2; 95% CI 2.1-4.8). Crude mortality in patients with A. baumannii BSI was 32%. Molecular relatedness of strains was studied by use of polymerase chain reaction-based fingerprinting. Clonal spread of a single strain occurred in 5 hospitals. Interhospital spread of epidemic A. baumannii strains was not observed. The most active antimicrobial agents against A. baumannii (90% minimum inhibitory concentration values) were imipenem (1 mg/L; 100% of isolates susceptible), amikacin (8 mg/L; 96%), tobramycin (4 mg/L; 92%), and doxycycline (4 mg/L; 91%). Thirty percent of isolates were resistant to > or =4 classes of antimicrobials and were considered to be multidrug resistant.

Acinetobacter↗

PubMed1991

Hepatitis E virus genome. Molecular features, expression of immunoreactive proteins and sequence divergence.

The strategy for molecular cloning of hepatitis E virus (HEV), the major etiologic agent of enterically-transmitted non-A, non-B hepatitis, is briefly described. The organization of the HEV genome is discussed and compared to those of two other vertebrate viruses that contain single-stranded, positive-sense, polyadenylated RNA genomes with three overlapping ORFs. Serologic cross-reactivity of expressed proteins and genetic divergence of HEV isolates are also described within the context of sequence variation, type-common epitopes, and type-specific epitopes.

Cloning, Molecular↗

PubMed1998

Molecular features of penicillin allergy.

Haptens, such as drugs and other low molecular weight chemicals, become immunogenic only upon binding to proteins. Among antibiotics, penicillins are most commonly used for the treatment of bacterial infections and constitute a typical example of allergy inducing drugs in humans. Previous work on their immunologic properties focused mainly on the examination of IgE-mediated hypersensitivity reactions; however, drug-specific T cell reactions are also involved in causing a serious allergic inflammatory response. This review will focus on the interaction between antibiotic molecules and penicillin-specific T lymphocytes in humans. Experimental data accumulated so far on the reactivity of T cells with penicillin G point to penicilloyl-modified, major histocompatibility complex-associated peptides as T cell epitopes. The recognition specificity of the respective T cell receptors appears to be directed at both the backbone and the specific side chain of penicillin. In contrast, the sequence of the carrier peptides appears to contribute little to the antigenic specificity, mainly as a holder for the haptenic determinant. Finally, recent results demonstrating the capacity of penicillins to modulate, in vitro, the Th0/Th2 phenotype of established T cell clones will be presented and discussed in relation to possible therapeutic applications.

Allergens↗

PubMed2025

Molecular features influencing clinical outcome of advanced HER2-positive gastric cancer receiving trastuzumab plus chemotherapy.

BACKGROUND: Less than half of the human epidermal growth factor receptor 2 (HER2)-positive gastric cancer (GC) patients respond to trastuzumab plus chemotherapy, and the outcomes are unsatisfactory. Understanding the underlying mechanisms remains crucial for identifying patients who are more likely to benefit from treatment. PATIENTS AND METHODS: We performed targeted DNA sequencing on paired pre-treatment and progressive tumour tissues from 22 HER2-positive advanced GC patients undergoing first-line treatment with trastuzumab and chemotherapy. Clinicopathological and genomic characteristics were assessed for the correlation with clinical outcomes. RESULTS: A performance status (PS) of 0-1 was associated with improved progression-free survival (PFS) and overall survival (OS) than a PS of 2. Poorly differentiated tumours exhibited shorter PFS than moderate or moderate-poor ones. Pre-treatment amplification of MYC or TOP2A gene was association with increased PFS, and suggested a potential benefit for OS. Patients with higher tumour mutation burden (TMB) experienced significantly worse PFS, while higher chromosome instability (CIN) appeared to be correlated with longer PFS. Compared to non-responders, responders had a higher CIN but similar TMB and intratumoural heterogeneity (ITH). PS and MYC amplification emerged as independent factors related to PFS according to multivariate survival analysis. Additionally, after treatment, TMB significantly increased in non-responders, while CIN significantly decreased in responders. CONCLUSIONS: Pre-treatment MYC amplification and PS were independently associated with clinical outcomes in HER2-positive advanced GC patients treated with first-line trastuzumab plus chemotherapy. Dynamic post-treatment changes in TMB and CIS provide valuable insights into the relationship between therapeutic response and distinct evolutionary trajectories.

Humans↗

PubMed2004

Gastrointestinal stromal tumors: overview of pathologic features, molecular biology, and therapy with imatinib mesylate.

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. These tumors develop at any site but are most commonly reported in the stomach. They originate from the neoplastic transformation of the intestinal pacemaker cell, the interstitial cell of Cajal. GISTs strongly express the receptor tyrosine kinase KIT and have mutations in the KIT gene, most frequently in exon 11 encoding the intracellular juxtamembranous region. Expression of KIT is seen in almost all GISTs, regardless of the site of origin, histologic appearance, or biologic behavior, and is therefore regarded as one of the key diagnostic markers. Distinction from smooth muscle tumors, such as leiomyosarcomas, and other mesenchymal tumors is very important because of prognostic differences and therapeutic strategies. Predicting the biologic behavior of GISTs is often difficult by conventional pathologic examination; tumor size and mitotic rate are the most important prognostic indicators. The prognostic significance of KIT mutations is controversial and thus far has not been clearly linked with biologic behavior. KIT mutations are associated with tumor development, and cytogenetic aberrations are associated with tumor progression. The pathogenesis of GISTs involves a gain-of-function mutation in the KIT proto-oncogene, leading to ligand-independent constitutive activation of the KIT receptor. KIT-wild-type GISTs have shown mutually exclusive platelet-derived growth factor receptor (PDGFR) mutation and activation. The use of imatinib mesylate (also known as Gleevec or STI-571) has greatly increased the therapeutic efficacy for this otherwise chemotherapy-resistant tumor. GISTs with very low levels of KIT expression may respond to imatinib mesylate therapy if the receptors are activated by specific mechanisms. KIT-activating mutations fall into two groups: the regulatory type and the enzymatic site type. The regulatory type of mutation is conserved at the imatinib binding site, whereas the enzymatic site mutation has a structurally changed drug-binding site, resulting in drug resistance. Resistance to the drug is the major cause of treatment failure in cancer therapy, emphasizing the need for researchers to understand KIT signaling pathways so as to identify new therapeutic targets. This review summarizes the pathologic features of GISTs, recent advances in understanding their molecular and biologic features, and therapy with imatinib mesylate.

Antineoplastic Agents↗

PubMed2002

Clinical and molecular features of adPEO due to mutations in the Twinkle gene.

We have analyzed Twinkle, the causative gene for autosomal dominant progressive external ophthalmoplegia (adPEO) on chromosome 10, in 11 Australian autosomal dominant progressive external ophthalmoplegia families of Caucasian origin, and investigated whether there are distinct molecular and clinical features associated with mutations in this gene. We found two new mutations in Twinkle, in 3 of the 11 pedigrees examined. One resides in the linker region of this gene while the other is in the primase domain. Both regions are highly conserved between species. Multiple deletions in the mtDNA from muscle are not always prominent and there are significant variations in the clinical presentation within and between families with mutations in the Twinkle gene. Therefore, genotype/phenotype predictions are difficult. No mutations were found in adenine nucleotide translocator 1 (ANT1), another known adPEO causative gene, in four of the seven remaining families investigated. Thus, Twinkle appears to be the most common gene associated with adPEO in Australian families.

Amino Acid Sequence↗

PubMed1992

Clinical, hematological, and molecular features in Sicilians with sickle cell disease.

We report the clinical, hematological, and molecular findings observed in 32 Sicilian patients with sickle cell disease. None of our patients received regular blood transfusions and careful infectious disease prophylaxis was carried out for all. Haplotyping of beta S chromosomes was performed in all patients; all were homozygous for haplotype #19 (Benin). Gene mapping excluded the presence of an alpha-thalassemia in 13 of our patients; none of the relatives showed any evidence of the presence of alpha-thalassemia. Hb F levels were 11.8 +/- 5.9% with G gamma representing 39.6 +/- 3.6% of total gamma chain. Hb F levels were higher in females than in males (12.5 +/- 5.9% versus 9.7 +/- 6.5%) but the difference was not statistically significant. All patients, regardless of age and sex, were anemic with normal mean corpuscular hemoglobin concentration, high mean corpuscular volume and mean corpuscular hemoglobin, and mild reticulocytosis. Analysis of clinical manifestations suggests that our patients have a disease of moderate severity.

Adolescent↗

PubMed1980

Molecular features of immunoreactive myelin basic protein in cerebrospinal fluid of persons with multiple slcerosis.

The molecular weight of the myelin basic protein (BP)-like material appearing in cerebrospinal fluid (CSF) of 2 persons with active-phase multiple sclerosis (MS) and 3 with recent cerebral infarctions was determined by gel filtration chromatography under acidic conditions. Column fractions were examined by radioimmunoassay for BP peptide 43-88 antigen as well as for binding activity to BP. Material cross-reactive with BP peptide 43-88 eluted over a wide spectrum of molecular weights. Greater representation of lower molecular weight species occurred in MS. Fractionated CSF from 2 patients with MS and 2 with cerebral infarction contained binding activity, presumably antibody, to BP which was greater than that in unfractionated CSF. Binding to BP was also examined in unfractionated CSF from 70 persons, including 16 with MS and 36 with other neurological diseases. Although CSF from MS patients showed higher binding, the presence of BP binding activity was not specific for MS. Our findings suggest that the antigen cross-reacting with BP and its fragments in CSF appears in a spectrum of molecular weight species, with lower forms predominating in MS. The detection of binding activity to BP as well as its enhancement by treatment at low pH suggest that the BP-like antigen in CSF may exist in free as well as in complexed forms.

Adolescent↗

PubMed2026

Early-Onset Colorectal Cancer: Clinical and Molecular Features with Emerging Insights from Comprehensive Genomic Profiling.

Early‑onset colorectal cancer (EOCRC), defined as colorectal cancer (CRC) diagnosed before 50 years of age, is increasing globally. Colorectal cancer is currently the third most commonly diagnosed cancer and the second leading cause of cancer-related death worldwide, with GLOBOCAN 2024 estimating approximately 2.04 million new cases and 917,895 deaths in 2024. Recent studies indicate a sustained rise in EOCRC incidence across multiple regions and birth cohorts, with the greatest increases observed among younger adults. Although hereditary cancer syndromes account for 20-25% of EOCRC cases, most occur in the absence of known genetic predispositions or established risk factors. Emerging evidence implicates the gut microbiome as a potential contributor to EOCRC, with distinct microbial signatures differentiating it from late‑onset colorectal cancer (LOCRC) diagnosed after 50 years of age. This review synthesizes current evidence on clinical, molecular, and diagnostic features distinguishing EOCRC from LOCRC, including differences in anatomical distribution, histopathology, genomic and epigenetic alterations, microbiome composition, and immune landscape, and discusses their implications for personalised screening and therapeutic strategies. We performed a retrospective secondary analysis of comprehensive genomic and immune profiling data from 1737 patients with colorectal cancer tested between June 2021 and June 2023. The analysis showed that tumours arising in patients with EOCRC had lower tumour mutational burden than tumours diagnosed as LOCRC, whereas other immune-related biomarkers, including tumour immunogenicity score, did not remain significantly different after correction for multiple testing. Despite these emerging biological differences, current screening strategies remain largely dependent on an age threshold of 50 years, and EOCRC is not addressed by age‑specific treatment approaches. We therefore review the translational potential of emerging biomarkers, including microbial signatures and liquid biopsy approaches, and propose a framework for integrating molecular profiling into clinical practice. Finally, we highlight the unmet need for coordinated efforts to improve screening in younger populations, address fertility preservation considerations, and ensure adequate psychosocial support for patients with EOCRC.

Early-onset colorectal cancer↗

PubMed2005

Clinical, morphologic, and molecular features defining so-called telangiectatic focal nodular hyperplasias of the liver.

BACKGROUND & AIMS: Telangiectatic focal nodular hyperplasia (TFNH) of the liver is generally believed to belong to the focal nodular hyperplasia (FNH) family. The aim of this study was to use molecular markers, in addition to morphologic features, to better characterize TFNH. METHODS: Thirteen patients with TFNH were compared with 28 patients with FNH and 17 patients with hepatocellular adenoma. Full clinical and morphologic data were analyzed. Molecular markers included determination of clonality by examining the active X chromosome, genome-wide allelotyping, a search for hepatocyte nuclear factor 1alpha (HNF1alpha) mutations, and determination of ANGPT1/ANGPT2 transcript levels. RESULTS: No clinical differences were evident between patients with TFNH and adenoma; in particular, bleeding was observed in 77% and 53% of the cases, respectively. Patients with TFNH were more likely to experience nodule recurrence and the presence of multiple nodules than those with either FNH or adenoma. All TFNH and adenoma samples that were available for analysis were monoclonal, in contrast to 40% of the FNH samples. Chromosome losses confirmed monoclonality and were significantly less frequent in TFNH and FNH (22% and 26%) than in adenoma (53%). HNF1alpha mutations were found exclusively in half of the adenomas. ANGPT2 was overexpressed in TFNH and down-regulated in adenoma (P < .01) and FNH (P < .0005). CONCLUSIONS: TFNHs are monoclonal lesions frequently subject to bleeding that are similar to adenomas not carrying HNF1alpha mutations and require a similar type of treatment. However, morphologic and molecular data support the hypothesis that TFNH is a separate entity.

Adenoma, Liver Cell↗

PubMed1993

Porcine respiratory coronavirus: molecular features and virus-host interactions.

Since 1984, a previously unrecognized respiratory coronavirus, causing a mostly unapparent infection, has rapidly and massively spread within the swine population in Europe, and few years later, a virus with similar characteristics has been identified in the USA. The agent, designated PRCV, appears to be derived from the porcine enteric coronavirus TGEV. The aim of the present article is to review comprehensively the state of the knowledge about this new virus and its infection. The review includes the following topics: epizootiology, molecular characterization and antigenic features of PRCV, pathogenesis and clinical aspects, immunity and laboratory diagnosis. The authors' views concerning the impact of the emergence of PRCV on both coronavirus research and swine production are presented in the conclusion.

Amino Acid Sequence↗

PubMed1991

Molecular features of hypothalamic plaques in Alzheimer's disease.

The pathology of Alzheimer's disease (AD) involves subcortical as well as cortical structures. The authors have used immunohistochemical methods to study the molecular composition of AD plaques in the hypothalamus. In contrast to previous studies using histochemical methods, the authors observed large numbers of diffuse plaques in the AD hypothalamus labeled with an antiserum to the beta-amyloid, or A4 peptide, of the beta-amyloid precursor proteins (beta APPs), whereas A4-immunoreactive plaques were uncommon in the hypothalamus of patients without AD. Unlike plaques in the cortex and hippocampus of AD patients, hypothalamic plaques did not contain epitopes corresponding to other regions of the beta APPs, nor did they contain tau-, neurofilament-, or microtubule-associated protein-reactive epitopes, and did not disrupt the neuropil or produce astrogliosis. These findings demonstrate that there are substantial molecular and cellular differences in the pathologic features of AD in the hypothalamus compared with those observed in hippocampal and cortical structures, which may provide insight into the pathogenetic mechanisms of AD.

Aged↗

PubMed1998

Molecular features of a new human lymphoma cell line carrying both BCL2 and BCL6 gene rearrangements.

Chromosomal translocations and/or their molecular equivalents involving the BCL6 gene on 3q27 band have been suggested to be involved in the development of non-Hodgkin's lymphoma of B-cell type (B-NHL). The rearrangement of BCL6 sometimes coexists with other translocations specific to B-NHL. Here, we report a novel B-cell lymphoma cell line, YM, established from a patient with diffuse large cell lymphoma. The YM cells expressed B-cell-associated antigens in addition to mu delta/kappa monoclonal immunoglobulin. Southern blot analysis of DNA from YM cells demonstrated rearrangement of the BCL2 gene within the 5' flanking region (5'-BCL2). Polymerase chain reaction (PCR) using primer pairs for the BCL2 exons 1 and 2, and for the constant region of the immunoglobulin kappa light chain gene (IGkappa) revealed PCR products encompassing the 5'-BCL2/IGkappa fusion, indicating that the YM cells had a t(2;18)(p11;q21) translocation. The BCL6 gene was rearranged at a point within the first intron, and cloning of the rearranged BCL6 revealed unidentified sequences juxtaposed to the 5' side of the gene. The isolated clones were mapped to 16p11.2 by high resolution fluorescence in situ chromosomal hybridization. Thus, the YM cells carried a 3q27 translocation involving 16p11.2 as a partner. Chromosome painting of metaphase spreads confirmed that the YM cells had both t(2;18) and t(3;16). Northern blot analysis using a fragment immediately adjacent to the breakpoint on 16p11.2 revealed transcriptional activity within this locus. The YM cells expressed abundant transcripts with aberrant sizes from BCL2 and BCL6, indicating deregulated overexpression of the two genes resulting from the t(2;18) and t(3;16). The YM cell line will therefore be useful to study whether BCL2 and BCL6 genes collaborate in the pathogenesis of B-NHL.

Base Sequence↗

PubMed2025

Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability.

The disproportionate expansion of telencephalic structures during human evolution involved tradeoffs that imposed greater connectivity and metabolic demands on midbrain dopaminergic neurons. Despite the central role of dopaminergic neurons in human-enriched disorders, molecular specializations associated with human-specific features and vulnerabilities of the dopaminergic system remain unexplored. Here, we establish a phylogeny-in-a-dish approach to examine gene regulatory evolution by differentiating pools of human, chimpanzee, orangutan, and macaque pluripotent stem cells into ventral midbrain organoids capable of forming long-range projections, spontaneous activity, and dopamine release. We identify human-specific gene expression changes related to axonal transport of mitochondria and reactive oxygen species buffering and candidate cis- and trans-regulatory mechanisms underlying gene expression divergence. Our findings are consistent with a model of evolved neuroprotection in response to tradeoffs related to brain expansion and could contribute to the discovery of therapeutic targets and strategies for treating disorders involving the dopaminergic system.

Brain evolution↗