BRAF DNA Research Articles

CTNI-59. RARE AND NOVEL KIAA1549-BRAF FUSION BREAKPOINTS PREDICT POOR CLINICAL OUTCOME FOR PATIENTS WITH RECURRENT OR PROGRESSIVE PEDIATRIC LOW-GRADE GLIOMA: PHASE II PNOC001 TRIAL RESULTS

Abstract OBJECTIVES PNOC001 sought to estimate progression-free survival (PFS) associated with everolimus for progressive/recurrent pediatric low-grade glioma (pLGG) and to determine if activated PI3K/AKT/mTOR pathway as measured by positive phosphorylated-ribosomal protein S6 (p-RPS6) was associated with response. A secondary objective was to assess whether somatic drivers influence median PFS. METHODS Patients, 3-21 years of age, with recurrent/progressive pLGG received everolimus orally at 5 mg/m2 daily. Somatic drivers, when available, were associated with PFS and compared to four independent molecular pLGG cohorts with newly-diagnosed and progressive/recurrent patients. RESULTS From 2012 to 2019, 65 subjects enrolled [median age 9.6 years, 3.0-19.9; 46% female]; Median PFS for all-comers was 11.1 months (95%-CI 7.6-19.8, n = 64). PFS was not modulated by PI3K/AKT/mTOR pathway activation (median PFS 11.2 vs 9.4 months, P = 0.83, n = 62). BRAF alterations were identified in 67.8% (40/59) of patients. Rare/novel KIAA1549-BRAF fusion breakpoints were enriched in PNOC001 compared to newly-diagnosed pLGGs in independent cohorts (28.6% vs 2.6%, P = 1.4e-4, n = 214). In PNOC001, patients with rare/novel KIAA1549-BRAF fusion breakpoints had worse clinical outcomes than patients with common fusion breakpoints (median PFS 6.1 vs 16.7 months, P < 0.05, n = 20). Rare/novel KIAA1549-BRAF fusion breakpoints were also enriched in patients with progressive/recurrent disease in independent pLGG cohorts (17.6% vs 2.6%, P = 2e-3, n = 227). Integration of BRAF alterations and DNA methylation-based tumor subtypes further revealed that rare/novel KIAA1549-BRAF fusion breakpoints are more frequent in supratentorial midline (14.1%) compared to infratentorial (2.0%) pilocytic astrocytomas (P = 1e-4). KIAA1549-BRAF fusion breakpoints remained risk factors for progressive/recurrent disease in PNOC001 (P = 0.05) and independent pLGG cohorts (P < 0.05) after accounting for tumor location and DNA methylation subtypes. CONCLUSIONS Rare/novel KIAA1549-BRAF fusion breakpoints are more frequent in supratentorial midline pLGGs and define independent genomic risk factors for disease progression/recurrence. Our results indicate that future clinical trials must interrogate and define KIAA1549-BRAF fusion breakpoints for informative results and conclusions.

Dual detection system for cancer-associated point mutations assisted by a multiplexed LNA-based amperometric bioplatform coupled with rolling circle amplification

DNA point mutation in a BRAF proto-oncogene, V600E, is considered an important prognostic and predictive biomarker in various types of cancer, such as melanoma or colorectal cancer. We report here a novel electrochemical (EC) bioplatform for the analysis of BRAF V600E mutation coupled with rolling circle amplification (RCA) and locked nucleic acid (LNA) capture probes. A dual detection system was implemented, whereby two padlock probes complementary to either wild-type (wt) BRAF gene or DNA with V600E mutation (mut) led to amplification of wt or mut variant, respectively. Hybridization with specific LNA capture probes then increased the assay specificity, while EC detection provided rapid measurement times. The bioplatform was applied to analyze BRAF V600E mutation of cancer cells and tumor tissues from patients with melanoma or colorectal cancer. This is the first RCA-based EC bioplatform for BRAF analysis in a dual format without using PCR or sophisticated instrumentation.

Sulfur dots/Au@Ag nanorods array-based polarized ECL sensor for the detection of thyroid cancer biomarker

The combination of highly sensitive electrochemiluminescence (ECL) techniques with localized surface plasmon resonance (LSPR) effect can achieve the highly sensitive and specific detection in the analytical and biosensing applications. However, how to effectively improve the electromagnetic field intensity is an unresolved issue. Herein, we have developed an ECL biosensor based on sulfur dots and Au@Ag nanorod array architecture. Firstly, the high luminescent sulfur dots with ionic liquid capping (S dots (IL) have been prepared as the new ECL emitter. The ionic liquid greatly improved the conductivity of sulfur dots in the sensing process. Furthermore, Au@Ag nanorods array structure was constructed on the electrode surface by the evaporation induced self-assembly. On the one hand, the LSPR of Au@Ag nanorods was more significant than that of good nanomaterial due to the plasma hybridization and the competition between free electrons and oscillating electrons. On the other hand, nanorods array structure had strong electromagnetic field intensity as hot spots due to the surface plasmon coupling ECL effect (SPC-ECL) effect. Therefore, the Au @Ag nanorods array architecture not only greatly enhanced the ECL intensity of sulfur dots, but also changed the ECL signals into polarized emission. Finally, the constructed polarized ECL sensing system was used to detect the mutated BRAF DNA in the eluent of thyroid tumor tissue. The biosensor showed the linear range from 100 fM to 10 nM with a detection limit of 20 fM. The satisfactory results demonstrated that the developed sensing strategy had great potential in the clinical diagnosis of BRAF DNA mutation in thyroid cancer.

Abstract CT059: StrataPATHTM: a multicohort, non-randomized, open-label phase 2 trial to explore efficacy and safety of FDA-approved cancer therapies in novel biomarker-guided patient population

Abstract Purpose: The Strata Precision Indications for Approved Therapies (Strata PATH; NCT05097599) trial is a non-randomized open-label, prospective pan-tumor therapeutic trial designed to evaluate the efficacy and safety of multiple FDA-approved cancer therapies in new, biomarker-guided patient populations. Enrollment into a cohort of this basket trial is based on novel biomarkers including DNA, quantitative RNA expression and novel multivariate algorithms that account for both tumor and tumor microenvironment variables hypothesized to predict improved therapeutic response. The therapeutic classes evaluated in Strata PATH include targeted therapies, antibody-drug conjugates, immunotherapies, and angiogenesis inhibitors. Trial Design: Key eligibility criteria are pathologically confirmed solid tumor. Patients are assigned to treatment by tumor type and biomarker status (Table). All patients will be treated until disease progression, unacceptable toxicity, patient/physician decision to withdraw, or 3 years of treatment from the date of consent. Primary Outcome measure includes overall response rate (ORR) as assessed by the investigator according to RECIST version 1.1. Secondary outcome measures include ctDNA response, Duration of Response (DoR), Time to Treatment Discontinuation (TTD), Time to Next Treatment (TTNT), Overall Survival (OS), safety, and ctDNA Response Rate. Enrollment is ongoing with 35 participants per cohort for up to 20 cohorts (700 participants total). Summary: Strata PATH provides the next important step forward in precision medicine, guiding clinical trial and therapy selection by expanding biomarker testing to quantifiable RNA expression and multivariant algorithm based molecular testing. Table. Strata PATH Biomarker-guided cohorts for expanded treatment of already FDA-approved drugs outside approved tumor indications Biomarker Molecular Test Therapy ALK ROS1 DNA Lorlatinib BRAF DNA Binimetinib + Encorafenib BRCA, PALB2 DNA Talazoparib HER2 overexpression RNA fam-Trastuzumab deruxtecan-nxki Trop2 targeting algorithm Multivariate Algorithm Sacituzumab govitecan-hziy Immunotherapy Response Score (IRS) Multivariate Algorithm PD-1 inhibitor Angiogenesis Response Score (ARS) Multivariate Algorithm Axitinib Citation Format: Kat Kwiatkowski, Laura E. Lamb, Scott A. Tomlins, D. Brian Johnson, Daniel H. Hovelson, Nickolay Khazanov, Benjamin J. Bulen, Travis Reeder, Daniel R. Rhodes. StrataPATHTM: a multicohort, non-randomized, open-label phase 2 trial to explore efficacy and safety of FDA-approved cancer therapies in novel biomarker-guided patient population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT059.

Association of DNA Promoter Methylation and BRAF Mutation in Thyroid Cancer.

The BRAF V600E mutation and DNA promoter methylation play important roles in the pathogenesis of thyroid cancer (TC). However, the association of these genetic and epigenetic alterations is not clear. In this study, using paired tumor and surrounding normal tissue from the same patients, on a genome-wide scale we tried to identify (a) any association between BRAF mutation and DNA promoter methylation, and (b) if the molecular findings may provide a basis for therapeutic intervention. We included 40 patients with TC (female = 28, male = 12) without distant metastasis. BRAF mutation was present in 18 cases. We identified groups of differentially methylated loci (DML) that are found in (a) both BRAF mutant and wild type, (b) only in BRAF mutant tumors, and (c) only in BRAF wild type. BRAF mutation-specific promoter loci were more frequently hypomethylated, whereas BRAF wild-type-specific loci were more frequently hypermethylated. Common DML were enriched in cancer-related pathways, including the mismatch repair pathway and Wnt-signaling pathway. Wild-type-specific DML were enriched in RAS signaling. Methylation status of checkpoint signaling genes, as well as the T-cell inflamed genes, indicated an opportunity for the potential use of PDL1 inhibitors in BRAF mutant TC. Our study shows an association between BRAF mutation and methylation in TC that may have biological significance.

EV-ADD, a database for EV-associated DNA in human liquid biopsy samples.

Extracellular vesicles (EVs) play a key role in cellular communication both in physiological conditions and in pathologies such as cancer. Emerging evidence has shown that EVs are active carriers of molecular cargo (e.g. protein and nucleic acids) and a powerful source of biomarkers and targets. While recent studies on EV‐associated DNA (EV‐DNA) in human biofluids have generated a large amount of data, there is currently no database that catalogues information on EV‐DNA. To fill this gap, we have manually curated a database of EV‐DNA data derived from human biofluids (liquid biopsy) and in‐vitro studies, called the Extracellular Vesicle‐Associated DNA Database (EV‐ADD). This database contains validated experimental details and data extracted from peer‐reviewed published literature. It can be easily queried to search for EV isolation methods and characterization, EV‐DNA isolation techniques, quality validation, DNA fragment size, volume of starting material, gene names and disease context. Currently, our database contains samples representing 23 diseases, with 13 different types of EV isolation techniques applied on eight different human biofluids (e.g. blood, saliva). In addition, EV‐ADD encompasses EV‐DNA data both representing the whole genome and specifically including oncogenes, such as KRAS, EGFR, BRAF, MYC, and mitochondrial DNA (mtDNA). An EV‐ADD data metric system was also integrated to assign a compliancy score to the MISEV guidelines based on experimental parameters reported in each study. While currently available databases document the presence of proteins, lipids, RNA and metabolites in EVs (e.g. Vesiclepedia, ExoCarta, ExoBCD, EVpedia, and EV‐TRACK), to the best of our knowledge, EV‐ADD is the first of its kind to compile all available EV‐DNA datasets derived from human biofluid samples. We believe that this database provides an important reference resource on EV‐DNA‐based liquid biopsy research, serving as a learning tool and to showcase the latest developments in the EV‐DNA field. EV‐ADD will be updated yearly as newly published EV‐DNA data becomes available and it is freely available at www.evdnadatabase.com.

Prognostic impact of FGFR2/3 alterations in patients with biliary tract cancers receiving systemic chemotherapy: the BITCOIN study

AimFGFR2 rearrangements have been identified as a novel therapeutic target of biliary tract cancer (BTC). However, reliable prevalence estimates of this molecular alteration and its prognostic role have not been fully elucidated. MethodsA retrospective mono-institutional series of 286 patients affected by locally advanced or metastatic BTC (183 intrahepatic cholangiocarcinomas, 67 extrahepatic cholangiocarcinomas, 36 gallbladder carcinomas) was profiled by means of targeted DNA/RNA next-generation sequencing, immunohistochemistry and fluorescence in situ hybridisation for FGFR2/3, ERBB2, NTRK alterations, IDH1/2 and BRAF mutations and DNA mismatch repair complex proteins alterations/microsatellite instability. ResultsFGFR2 rearrangements, amplifications and point mutations were detected in 15 (5.2%), 1 and 3 cases, respectively. FGFR3 alterations were observed in 5 (1.7%) cases. IDH1/2 were mutated in 35/223 cases (15.7%). A total of 9/258 (3.5%) and 6/260 (2.3%) BTCs had ERBB2 and BRAF gene alterations, respectively. Two cases (2/242; 0.8%) had NTRK1 amplifications but no rearrangement was found. A deficit of mismatch repair protein expression was identified in 9/237 cases (3.8%). At multivariate analysis, age, ECOG performance status, number of metastatic sites, tumour stage, FGFR2/3 alterations and IDH1/2 mutations were prognostic factors of overall survival. ConclusionsThese data provide a strong proof – challenged with a robust and detailed multivariate model – that FGFR2/3 aberrations (including FGFR2 rearrangements) and IDH1/2 mutations can be prognostic for better survival in patients with BTC . The recognition and the measurement of their prognostic impact could be of primary importance for the correct interpretation of currently available data and in the design of new therapeutic trials.

Mononuclear and polymeric zinc(II) β-diketonate complexes with aromatic N-donor ligands: Structural, spectral, thermal, theoretical and docking studies

Four new compounds, {[Zn(μ-DPP)(DBM)2].2MeOH}n (1), {[Zn(μ-Pyrazine)(DBM)2]}n (2), [Zn(PHEN)(DBM)2] (3) and [Zn(2,2′-BPY)(DBM)(CH3COO)] (4) (DPP: 1,3-di(4-pyridyl)propane, HDBM: dibenzoylmethanato, PHEN: 1,10-phenanthrolin, 2,2′-BPY: 2,2′-bipyridine), were prepared and identified by elemental analysis, FT-IR and 1H NMR spectroscopy and single-crystal X-ray diffraction. In addition, the thermal stability of the compounds was evaluated by thermogravimetric analysis (TGA and DTA). The complexes 1 and 2 form 1D coordination polymers whereas 3 and 4 adopt a mononuclear structure. In these structures, the zinc atoms have octahedral (1–3) and square-pyramidal (4) geometries. The charge distribution pattern of the complexes 3 and 4 and their ligands was studied by NBO analysis and their ability to interact with ten biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) is investigated by docking calculations.

Coordination of an amino alcoholic Schiff base ligand toward the zinc(II) ion: spectral, structural, theoretical, and docking studies

A new zinc(II) complex of 2-(((2-((2-hydroxyethyl)amino)ethyl)imino)methyl)phenol (L), [Zn(Lz)Br2] (1), is prepared and identified by elemental analysis, FTIR and 1H NMR spectroscopy, and single crystal X-ray diffraction. The X-ray structure analysis of 1 reveals a tetrahedrally coordinated zinc(II) complex containing the NO-donor amino alcoholic Schiff base ligand and two bromo ligands. After complexation, the ligand (L) converts to its zwitterionc form (Lz) of phenol → phenolate; amine → ammonium. In this structure, hydrogen bonds between amine and alcohol units form different types of hydrogen bond motifs, including R21(7), R22(7), R22(10), R44(24), R44(30), R66(38), and R66(44). In addition to the hydrogen bonds in this crystal network, there are π—π stacking interactions between the phenyl ring and the imine group. The ability of the ligand and its isostructural complexes [Zn(Lz)Br2] (1), [Zn(Lz)Cl2] (2), and [Zn(Lz)I2] (3) to interact with ten selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II, and B-DNA) is investigated by docking studies. The results show that in some cases, the studied compound can interact with proteins and DNA better than doxorubicin. The charge distribution pattern of the ligand and complex 1 is studied by the NBO analysis.

Evaluation of biological activities of cobalt(II) and copper(II) complexes synthesized from methylcarboxylate and amino alcohol ligand mixtures: spectroscopic, structural and docking studies

Two cobalt(II) and copper(II) complexes, [Co2(PDCA)(µ-PDCA)(H2O)5]·2H2O (1); H2PDCA: pyridine-2,6-dicarboxylic acid and [Cu(DEA)(PDCA)] (2); DEA: diethanolamine, were prepared from a mixed ligand amine/PDCA methyl ester mixture and identified by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction. X-ray structure analysis of 1 revealed a binuclear octahedrally coordinated cobalt(II) complex formed by bridging a PDCA2− between metal centers. In the mononuclear complex 2, the copper atom has an octahedral geometry with CuN2O4 environment formed by one DEA and one PDCA2– ligands in mer form. The ability of the H2PDCA and DEA ligands along with complexes 1 and 2 to interact with ten selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) were investigated by docking studies. The results showed that the studied compounds can bind to DNA and proteins.

Sequence-Specific Detection of ORF1a, BRAF, and ompW DNA Sequences with Loop Mediated Isothermal Amplification on Lateral Flow Immunoassay Strips Enabled by Molecular Beacons.

Loop-mediated isothermal amplification (LAMP) holds great potential for point-of-care (POC) diagnostics due to its speed and sensitivity. However, differentiation between spurious amplification and amplification of the target sequence is a challenge. Herein, we develop the use of molecular beacon (MB) probes for the sequence-specific detection of LAMP on commercially available lateral flow immunoassay (LFIA) strips. The detection of three unique DNA sequences, including ORF1a from SARS-CoV-2, is demonstrated. In addition, the method is capable of detecting clinically relevant single-nucleotide polymorphisms (BRAF V600E). For all sequences tested, the LFIA method offers similar sensitivity to fluorescence detection using a qPCR instrument. We also demonstrate the coupling of the method with solid-phase microextraction to enable isolation and detection of the target sequences from human plasma, pond water, and artificial saliva. Lastly, a 3D printed device is designed and implemented to prevent contamination caused by opening the reaction containers after LAMP.

An ultrasensitive biosensor for dual-specific DNA based on deposition of polyaniline on a self-assembled multi-functional DNA hexahedral-nanostructure

Kras and Braf are major oncogenes. The mutation of Kras codon 12 or Braf V600E can lead to ovarian carcinoma. The detection of oncogene-related DNAs and their mutations offers solution for early diagnosis of ovarian cancer. Herein, a size-tunable multi-functional DNA hexahedral-nanostructure (DHN) has been rationally designed and modified on the electrode to response to Kras and Braf DNA. The size of DHN is controlled via polyadenines (polyA). The complete self-assembly of DHN depends on the presence of both target DNAs and two assistant probes. Meanwhile, a HRP-mimicking DNAzyme forms in DHN, which catalyzes the polymerization of aniline. The produced polyaniline is utilized as the output signal through differential pulse voltammetry (DPV). The biosensor shows the linear range from 100 fM to 1 μM, with the detection limit of 48.7 fM for Kras gene; and the linear range from 100 fM to 100 nM, with the detection limit of 44.1 fM for Braf gene, respectively. Since the current response depends on both gene sequences, the high specificity of the biosensor endows it to operate in an “OR”-type logic gate to discriminate the mutation of both genes. When Kras codon 12 or Braf V600E mutation happens, the response decreases significantly due to the incomplete formation of DNAzyme in DHN. The practicability of the biosensor has been verified through challenging human serum samples. Thus, it has great potential for clinical diagnosis of ovarian cancer through simultaneous detection of Kras and Braf genes and their mutations.

Investigation of the binding ability of a new thiosemicarbazone-based ligand and its Zn(II) complex toward proteins and DNA: spectral, structural, theoretical, and docking studies

A new thiosemicarbazone derivative ligand N-(4-chlorophenyl)-2-(pyridin-2-ylmethylene)hydra­zine-1-carbothioamide (HL) and its zinc(II) complex [ZnL2]·CH2Cl2 (1) are prepared and cha­racterized by elemental analysis, FTIR and 1H NMR spectroscopy, and single crystal X-ray diffraction (for 1). The X-ray analysis reveals that the zinc atom is octahedrally coordinated by two NpyNimineSthiolate-donor ligands with the mer form. The HL ligand is deprotonated during the complexation process through the thiol group. In the crystal network of 1, the N—H⋯S hydrogen bonds form R22(8) hydrogen bond motifs. In addition, the crystal network is more stabilized by π—π stacking and C—H⋯π interactions. The ability of complex 1 to interact with ten selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II, and B-DNA) is investigated by docking studies. The results show that in many cases, complex 1 can interact with proteins better than doxorubicin.

Interobserver Agreement Among Pathologists in the Differentiation of Sessile Serrated From Hyperplastic Polyps

Colorectal cancer (CRC) is the third most common cancer in the United States, with approximately 135,430 new cases and 50,260 deaths every year. 1 Jemal A. et al. J Natl Cancer Inst. 2017; 109: djx030 Crossref Scopus (777) Google Scholar ,2 Siegel R.L. et al. CA Cancer J Clin. 2017; 67: 177-193 Crossref PubMed Scopus (2659) Google Scholar It has been widely recognized now that approximately 20%–30% of CRCs arise from serrated polyps through a serrated/methylated pathway that includes BRAF mutation and DNA methylation that is distinct from the traditional adenoma-carcinoma sequence. 3 Noffsinger A.E. Serrated polyps and colorectal cancer: new pathway to malignancy. Annu Rev Pathol. 2009; 4: 343-364 Crossref PubMed Scopus (178) Google Scholar , 4 Ogino S. et al. CpG island methylator phenotype, microsatellite instability, BRAF mutation and clinical outcome in colon cancer. Gut. 2009; 58: 90-96 Crossref PubMed Scopus (613) Google Scholar , 5 Kambara T. et al. BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum. Gut. 2004; 53: 1137-1144 Crossref PubMed Scopus (594) Google Scholar Sessile serrated polyps are flat/sessile and have similar color to the surrounding mucosa, making it difficult to differentiate between the normal colonic mucosa and the polyp itself. Serrated lesions are classified pathologically per the World Health Organization (WHO) criteria 6 Bosman F.T. et al. WHO classification of tumours of the digestive system. World Health Organization, 2010 Google Scholar into (1) hyperplastic polyp (HP), (2) sessile serrated adenoma (SSA)/sessile serrated polyp (SSP) with or without cytologic dysplasia, and (3) traditional serrated adenoma (TSA). Differentiating sessile serrated adenomas from hyperplastic polyps is difficult but clinically important because it guides surveillance intervals.

Associations between molecular characteristics of colorectal serrated polyps and subsequent advanced colorectal neoplasia.

BRAF mutation and DNA hypermethylation have linked sessile serrated adenomas/polyps (SSA/Ps) to serrated colorectal cancer (CRC) in cross-sectional studies, but they have not been evaluated in a longitudinal study. We aimed to evaluate the associations between molecular markers of serrated polyps and subsequent advanced colorectal neoplasia. Study subjects included Kaiser Permanente Washington members aged 20-75years who received an index colonoscopy between 1/1/1998 and 12/31/2007 and had hyperplastic polyps (HPs) or SSA/Ps according to study pathology review. Polyps from index colonoscopies were removed and assayed for BRAF mutation, CpG island methylator phenotype (CIMP), and MLH1 methylation. Pathology reports and biopsies from the subsequent lower gastrointestinal endoscopy through 1/1/2013 were reviewed for advanced colorectal neoplasia. We identified additional incident CRC cases through linkage to the Seattle-Puget Sound Surveillance Epidemiology and End Results registry. We used generalized estimating equations to calculate adjusted odds ratios (OR) and 95% confidence intervals (CI) for subsequent advanced colorectal neoplasia, comparing index serrated polyps with different molecular markers. We included 553 individuals with index serrated polyps (420 HPs and 133 SSA/Ps) and 795 subsequent endoscopies. The prevalence of BRAF-mutant, CIMP-high, and MLH1-methylated serrated polyps were 51%, 4%, and 2%, respectively. BRAF and CIMP were not associated with subsequent advanced colorectal neoplasia. MLH1-methylated SSP/As were significantly more likely to have subsequent advanced neoplasia (OR = 4.66, 95% CI 1.06-20.51). Our results suggest that BRAF-mutant and CIMP-high serrated polyps are not associated with subsequent advanced colorectal neoplasia. Among SSA/Ps, MLH1 methylation may be an important marker to identify high-risk CRC precursors.

Spectral, structural, biological and molecular docking studies of a new mixed-valence V(IV)/V(V) ofloxacin complex

In this study, a biologically active mixed-valence V(IV)/V(V) complex [VO(Hofloz)2(H2O)][V4O12]0.5.6H2O (1) (Hofloz = zwitterionic isomer of ofloxacin) was synthesized by the reaction of VOSO4 with ofloxacin (Hofloz) in presence of KOH with 1:1:1 ratio. The complex was characterized through the usage of elemental analysis, FT-IR, molar conductivity and single-crystal X-ray diffraction and thermogravimetric analysis (TGA). The results of single crystal X-ray structure determination revealed an ionic structure consisting of [VO(Hofloz)2(H2O)]2+ and [V4O12]4− units with 1:0.5 stoichiometry. The V+4 ion in the cationic unit has octahedral geometry while each V+5 ion of the eight-member cyclic tetravanadate anion is tetrahedrally coordinated. In regards to the crystal structure of 1, the bidentate ofloxacin ligand is coordinated to the V+4 ion in its zwitterionic form (+HN–···–COO-) through the oxygen atoms of the pyridone and carboxylato groups. The thermodynamic stability of two isomeric forms of Hoflo and 1 along with their charge distribution patterns was studied by DFT and NBO analysis. Also, the ability of the ligand to interact with ten selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) was investigated by docking calculations. These studies revealed that this ligand can bind to the proteins and DNA molecule and could be consider as biologically active compound. Finally, the antibacterial activities of the free Hoflo ligand and its vanadium complex have been evaluated against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) strains through the utilization of broth microdilution and well diffusion methods. The complex showed antibacterial effect similar to the free Hoflo ligand on the selected bacterial strains and these compounds were more active against Gram-negative bacteria.

Pancreatic Neoplasms With Acinar Differentiation: A Review of Pathologic and Molecular Features.

Pancreatic acinar lesions encompass a broad spectrum of malignant tumors and benign reactive processes affecting both adults and children, with clinical, pathologic, and molecular features that are distinct from more common ductal neoplasms. Accurate morphologic diagnosis and molecular assessment of these uncommon neoplasms is critical for effective patient care. To review the clinical, pathologic, and molecular features of pancreatic neoplasms with acinar differentiation, the most common of which is acinar cell carcinoma but which also includes mixed carcinomas with acinar components, cystic acinar lesions, and pancreatoblastoma. We assessed the current primary literature, as well as recently updated diagnostic manuals. Pancreatic acinar neoplasms are a morphologically and molecularly heterogeneous group of diseases that are characterized by acinar differentiation of at least a subset of the neoplastic cells, defined either morphologically (granular cytoplasm, single prominent nucleoli) or immunohistochemically. Squamoid nests are a key morphologic feature of pancreatoblastoma. Alterations in WNT signaling and chromosomal 11p loss are common molecular features of both acinar cell carcinoma and pancreatoblastoma. Targetable molecular alterations in acinar carcinoma include BRAF rearrangements and DNA repair defects, including mismatch repair deficiency and BRCA pathway defects. For practicing pathologists, morphologic recognition of such acinar neoplasms is critical, and in the future, molecular diagnostics to identify lesions susceptible to targeted therapy will likely form an important component of patient care.

Macrocyclic copper(II) complexes containing diazacyclam-based ligand: spectral, structural and docking studies

The macrocyclic copper complex, [Cu(ACE)(NO3)2] (ACE = 1,3,6,10,12,15-hexaazatricyclo[13.3.1.16,10]eicosane), was synthesized by template condensation from a mixture of N1-(2-aminoethyl)-1,3-diaminopropane, formaldehyde and copper(II) nitrate. Replacement of the nitrate with thiocyanato and azido ligands gives [Cu(ACE)NSC]NSC (2) and the 1D-coordination polymer, [Cu(ACE)(μ-N3)]n[N3]n (3), respectively. Complex 1, [Cu(ACE)(NO3)]NO3, is an intermediate product in which one of the nitrate ions is separated from its parent molecule. The formation of 1 allowed us to conclude that the mechanism of ion exchange in the parent molecule is similar to SN1. These complexes have been characterized by FT-IR spectroscopy and X-ray crystallography. In the crystal structures of 1 and 2, the copper(II) ion has a distorted square pyramidal geometry in which the N4-donor ACE ligand lies on the equatorial plane and other ligand occupies the axial position. The copper(II) ion in 3 has an octahedral geometry, coordinating to one ACE ligand in the equatorial plane and two N-donor bridging azido groups in the axial positions. In all structures, owing to the Jahn-Teller effect, the coordinated bond length of the axial position is longer than the equatorial ones. The ability of the ACE ligand and its complexes 1 and 2, along with their analogues, to interact with 10 selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) was investigated by docking calculations and compared with that of doxorubicin.

Coordination of a triazine ligand with CuII and AgI investigated by spectral, structural, theoretical and docking studies.

Two complexes of 5-phenyl-3-(pyridin-2-yl)-1,2,4-triazine (PPTA), namely (ethanol-κO)bis(nitrato-κO)[5-phenyl-3-(pyridin-2-yl-κN)-1,2,4-triazine-κN2]copper(II), [Cu(NO3)2(C14H10N4)(C2H6O)] or [Cu(NO3)2(PPTA)(EtOH)] (1), and bis[μ-5-phenyl-3-(pyridin-2-yl)-1,2,4-triazine]-κ3N1:N2,N3;κ3N2,N3:N1-bis[(nitrato-κO)silver(I)], [Ag2(NO3)2(C14H10N4)2] or [Ag2(NO3)2(μ-PPTA)2] (2), were prepared and characterized by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction. The X-ray structure analysis of 1 revealed a copper complex with square-pyramdial geometry containing two O-donor nitrate ligands along with an N,N'-donor PPTA ligand and one O-donor ethanol ligand. In the binuclear structure of 2, formed by the bridging of two PPTA ligands, each Ag atom has an AgN3O environment and square-planar geometry. In addition to the four dative interactions, each Ag atom interacts with two O atoms of two nitrate ligands on adjacent complexes to complete a pseudo-octahedral geometry. Density functional theory (DFT) calculations revealed that the geometry around the Cu and Ag atoms in 1opt and 2opt (opt is optimized) for an isolated molecule is the same as the experimental results. In 1, O-H...O hydrogen bonds form R12(4) motifs. In the crystal network of the complexes, in addition to the hydrogen bonds, there are π-π stacking interactions between the aromatic rings (phenyl, pyridine and triazine) of the ligands on adjacent complexes. The ability of the ligand and complexes 1 and 2 to interact with ten selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) was investigated by docking studies. The results show that the studied compounds can interact with proteins better than doxorubicin (except for TrxR and Top II).

Reaction of 2-[(2-aminoethyl)amino]ethanol with pyridine-2-carbaldehyde and complexation of the products with CuII and CdII along with docking studies.

The reaction between 2-[2-(aminoethyl)amino]ethanol and pyridine-2-carbaldehyde in a 1:2 molar ratio affords a mixture containing 2-({2-[(pyridin-2-ylmethylidene)amino]ethyl}amino)ethanol (PMAE) and 2-[2-(pyridin-2-yl)oxazolidin-3-yl]-N-(pyridin-2-ylmethylidene)ethanamine (POPME). Treatment of this mixture with copper(II) chloride or cadmium(II) chloride gave trichlorido[(2-hydroxyethyl)({2-[(pyridin-2-ylmethylidene)amino]ethyl})azanium]copper(II) monohydrate, [Cu(C10H16N3O)Cl3]·H2O or [Cu(HPMAE)Cl3]·H2O, 1, and dichlorido{2-[2-(pyridin-2-yl)oxazolidin-3-yl]-N-(pyridin-2-ylmethylidene)ethanamine}cadmium(II), [CdCl2(C16H18N4O)] or [CdCl2(POPME)], 2, which were characterized by elemental analysis, FT-IR, Raman and 1H NMR spectroscopy and single-crystal X-ray diffraction. PMAE is potentially a tetradentate N3O-donor ligand but coordinates to copper here as an N2 donor. In the structure of 1, the geometry around the Cu atom is distorted square pyramidal. In 2, the Cd atom has a distorted octahedral geometry. In addition to the hydrogen bonds, there are π-π stacking interactions between the pyridine rings in the crystal packing of 1 and 2. The ability of PMAE, POPME and 1 to interact with ten selected biomolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) was investigated by docking studies and compared with doxorubicin.