Pan-tumor landscape of fibroblast growth factor receptor 1-4 genomic alterations.

BACKGROUND: Selective tyrosine kinase inhibitors targeting fibroblast growth factor receptor (FGFR) 1-4 genomic alterations are in development or have been approved for FGFR-altered cancers (e.g. bladder cancer and advanced intrahepatic cholangiocarcinoma). Understanding FGFR inhibitor-resistance mechanisms is increasingly relevant; we surveyed the pan-tumor landscape of FGFR1-4 genomic alterations [short variants (SVs), gene rearrangements (REs), and copy number alterations (CNAs)], including their association with tumor mutational burden (TMB) and the genomic comutational landscape. PATIENTS AND METHODS: Comprehensive genomic profiling of 355 813 solid tumor clinical cases was performed using the FoundationOne and FoundationOne CDx assays (Foundation Medicine, Inc.) to identify genomic alterations in >300 cancer-associated genes and TMB (determined on ≤1.1 megabases of sequenced DNA). RESULTS: FGFR1-4 SVs and REs occurred in 9603/355 813 (2.7%), and CNAs in 15 078/355 813 (4.2%) samples. Most common FGFR alterations for bladder cancer, intrahepatic cholangiocarcinoma, and glioma were FGFR3 SVs (1051/7739, 13.6%), FGFR2 REs (618/6641, 9.3%), and FGFR1 SVs (239/11 550, 2.1%), respectively. We found several, potentially clinically relevant, tumor-specific associations between FGFR1-4 genomic alterations and other genomic markers. FGFR3 SV-altered bladder cancers and FGFR1 SV-altered gliomas were significantly less likely to be TMB-high versus unaltered samples. FGFR3 SVs in bladder cancer significantly co-occurred with TERT and CDKN2A/B alterations; TP53 and RB1 alterations were mutually exclusive. In intrahepatic cholangiocarcinoma, FGFR2 REs significantly co-occurred with BAP1 alterations, whereas KRAS, TP53, IDH1, and ARID1A alterations were mutually exclusive. FGFR1 SVs in gliomas significantly co-occurred with H3-3A and PTPN11 alterations, but were mutually exclusive with TERT, EGFR, TP53, and CDKN2A/B alterations. CONCLUSIONS: Overall, our hypothesis-generating findings may help to stratify patients in clinical trials and guide optimal targeted therapy in those with FGFR alterations.

The clinical landscape of cell-free DNA alterations in 1671 patients with advanced biliary tract cancer.

BACKGROUND: Targeted therapies have transformed clinical management of advanced biliary tract cancer (BTC). Cell-free DNA (cfDNA) analysis is an attractive approach for cancer genomic profiling that overcomes many limitations of traditional tissue-based analysis. We examined cfDNA as a tool to inform clinical management of patients with advanced BTC and generate novel insights into BTC tumor biology. PATIENTS AND METHODS: We analyzed next-generation sequencing data of 2068 cfDNA samples from 1671 patients with advanced BTC generated with Guardant360. We carried out clinical annotation on a multi-institutional subset (n = 225) to assess intra-patient cfDNA-tumor concordance and the association of cfDNA variant allele fraction (VAF) with clinical outcomes. RESULTS: Genetic alterations were detected in cfDNA in 84% of patients, with targetable alterations detected in 44% of patients. Fibroblast growth factor receptor 2 (FGFR2) fusions, isocitrate dehydrogenase 1 (IDH1) mutations, and BRAF V600E were clonal in the majority of cases, affirming these targetable alterations as early driver events in BTC. Concordance between cfDNA and tissue for mutation detection was high for IDH1 mutations (87%) and BRAF V600E (100%), and low for FGFR2 fusions (18%). cfDNA analysis uncovered novel putative mechanisms of resistance to targeted therapies, including mutation of the cysteine residue (FGFR2 C492F) to which covalent FGFR inhibitors bind. High pre-treatment cfDNA VAF was associated with poor prognosis and shorter response to chemotherapy and targeted therapy. Finally, we report the frequency of promising targets in advanced BTC currently under investigation in other advanced solid tumors, including KRAS G12C (1.0%), KRAS G12D (5.1%), PIK3CA mutations (6.8%), and ERBB2 amplifications (4.9%). CONCLUSIONS: These findings from the largest and most comprehensive study to date of cfDNA from patients with advanced BTC highlight the utility of cfDNA analysis in current management of this disease. Characterization of oncogenic drivers and mechanisms of therapeutic resistance in this study will inform drug development efforts to reduce mortality for patients with BTC.

Synthesis, antitubercular evaluation and 3D-QSAR study of N-phenyl-3-(4-fluorophenyl)-4-substituted pyrazole derivatives.

As a part of our ongoing research to develop novel antitubercular agents, a series of N-phenyl-3-(4-fluorophenyl)-4-substituted pyrazoles have been synthesized and tested for antimycobacterial activity in vitro against Mycobacterium tuberculosis H37Rv strain using the BACTEC 460 radiometric system. A 3D-QSAR study based on CoMFA and CoMSIA was performed on these pyrazole derivatives to correlate their chemical structures with the observed activity against M. tuberculosis. The CoMFA model provided a significant correlation of steric and electrostatic fields with the biological activity while the CoMSIA model could additionally shed light on the role of hydrogen bonding and hydrophobic features. The important features identified in the 3D-QSAR models have been used to propose new molecules whose activities are predicted higher than the existing systems. This study provides valuable directions to our ongoing endeavor of rationally designing more potent antitubercular agents.

Diagnostic fine-needle aspiration in postoperative wound infections is more accurate at predicting causative organisms than wound swabs.

INTRODUCTION: Postoperative wound infections are common. Antibiotics are often prescribed empirically, usually in the absence of any microbiological sensitivity data. This study demonstrates the role of fine-needle aspiration microbiology (FNAM) in determining the causative organisms in these wounds compared to wound swabs taken from the same patients. PATIENTS AND METHODS: A total of 20 patients with clinical signs of soft tissue infection were tested using wound swabs and fine-needle aspiration. RESULTS: Six of the wound swabs yielded a single organism but 16 out 20 of the FNAM group yielded a single organism (P = 0.002). CONCLUSIONS: The FNAM approach allows antibiotic sensitivities to be obtained enabling specific antimicrobial therapy to be implemented early. FNAM also has a higher yield of cultures than wound swabs. Cellulitic areas can be sampled even when use of wound swabs is not possible.

A portal to validated websites on cosmetic surgery: the design of an archetype.

There has recently been an increase in the usage of the Internet as a source of patient information. It is very difficult for laypersons to establish the accuracy and validity of these medical websites. Although many website assessment tools exist, most of these are not practical.A combination of consumer- and clinician-based website assessment tools was applied to 200 websites on cosmetic surgery. The top-scoring websites were used as links from a portal website that was designed using Microsoft Macromedia Suite.Seventy-one (35.5%) websites were excluded. One hundred fifteen websites (89%) failed to reach an acceptable standard.The provision of new websites has proceeded without quality controls. Patients need to be better educated on the limitations of the Internet. This paper suggests an archetypal model, which makes efficient use of existing resources, validates them, and is easily transferable to different health settings.

Aqueous phase hexylchloroformate derivatization and solid phase microextraction: determination of benzoylecgonine in urine by gas chromatography-quadrupole ion trap mass spectrometry.

A derivatization/solid phase microextraction (SPME) method for the determination of benzoylecgonine in urine was developed. The derivatization is conducted directly in 1 mL of urine while sonicating for 3 min with 12 microL of hexyl chloroformate and 70 microL of a mixture containing acetonitrile:water:hexanol:2-dimethylaminopyridine (5:2:2:1 v/v), yielding benzoylecgonine hexyl ester (BHE) as the product. After the 3 min period, an aliquot of 250 microL is transferred to a vial for SPME. After the desired extraction time the 100 microns polydimethylsiloxane SPME fiber was transferred to the GC-MS for separation and analysis with a quadrupole ion trap mass spectrometer. The hexyl chloroformate derivatization and SPME procedures were optimized for compatibility and sensitivity. The method was found linear for 0.10 to 20.0 micrograms/mL (r2 = 0.999) of benzoylecgonine in urine using benzoylecgonine-d3 as an internal standard (1.5 micrograms/mL). Intra-day precisions were 8.8 and 6.8% RSD for 0.30 microgram/mL and 17 micrograms/mL benzoylecgonine standards in urine (n = 6), respectively. Inter-day precision (n = 3) were < or = 3.3% RSD, indicating good reproducibility. A detection limit of 0.03 microgram/mL (S/N = 3) was achieved, thus making the SPME method a simplified alternative to SPE for GC-MS confirmation after EMIT tests for benzoylecgonine which have a cutoff of 0.30 microgram/mL. Quantitative results by SPME and SPE of two clinical urine specimens known positive for cocaine by EMIT were in excellent agreement. Benzoylecgonine was detected by the derivatization/SPME method in 22 out of 22 other urine specimens known positive for cocaine.

Determination of cannabinoids in water and human saliva by solid-phase microextraction and quadrupole ion trap gas chromatography/mass spectrometry.

Solid-phase microextraction (SPME) is applied to the determination of cannabidiol, delta 8-tetrahydrocannabinol (delta 8-THC), delta 9-tetrahydrocannabinol (delta 9-THC), and cannabinol in pure water and human saliva. The inherent extraction behavior of the cannabinoids in pure water is evaluated along with optimization of the method in human saliva. The commercially available poly(dimethylsiloxane) (PDMS) SPME fibers were found to be the best class for the cannabinoid analysis. Partition coefficients were found to be extremely large for all of the cannabinoids (log K > 4.0). Equilibrium times for the 7- and 30-micron PDMS fibers were 50 and 240 min, respectively. A shorter extraction time of 10 min with the 30-micron PDMS fiber may be used for multiple extractions from the same vial, thus conserving the sample necessary for analysis and speeding up the total analysis time. Recoveries for the cannabinoids in saliva, relative to pure water, were dramatically improved by a method developed in our laboratory involving addition of glacial acetic acid to the sample vial prior to performing SPME. Using this method, recoveries relative to SPME in pure water ranged from 21 to 47% depending on the cannabinoid. The linear range for spiked saliva samples was established at 5-500 ng/mL (r2 > 0.994) with precisions between 11 and 20% RSD. The ultimate level of detection by SPME for the cannabinoids in saliva was 1.0 ng/mL, with signal-to-noise values of > or = 12. A saliva sample collected 30 min after marijuana smoking was subject to SPME and traditional liquid-liquid extraction analysis. Internal standard quantitation results for delta 9-THC by both methods yielded comparable results, indicating that the SPME method of analysis is highly accurate and precise. The level of delta 9-THC by SPME was found to be 9.54 ng/mL for the saliva sample.

Management of severe hemorrhagic cystitis in pregnancy. A report of two cases.

Acute hemorrhagic cystitis (AHC) is gross hematuria and symptoms of cystitis. Usually a self-limiting entity, it is found mainly in children and cancer patients receiving chemotherapy or radiation. In a small number of patients, AHC can be severe and require aggressive management. We present two cases of severe acute hemorrhagic cystitis in pregnant women that led to hemorrhage, resistance to antibiotic therapy and premature labor. Continuous bladder irrigation with normal saline was attempted with success in stopping the hematuria and arresting the premature labor. Severe hemorrhagic cystitis in pregnancy may require aggressive management when associated with a significant blood loss and preterm labor.

Extramammary Paget's disease of the scrotum: need for early biopsy.

We have described a patient with Paget's disease of the scrotum, with a two-year history of erythematous and indurated skin lesion. Biopsy established the diagnosis of Paget's disease. The patient's symptoms were relieved after wide excision of the affected scrotal skin.