Circulating tumor DNA in neoadjuvant-treated breast cancer reflects response and survival.

BACKGROUND: Pathologic complete response (pCR) to neoadjuvant chemotherapy (NAC) is strongly associated with favorable outcome. We examined the utility of serial circulating tumor DNA (ctDNA) testing for predicting pCR and risk of metastatic recurrence. PATIENTS AND METHODS: Cell-free DNA (cfDNA) was isolated from 291 plasma samples of 84 high-risk early breast cancer patients treated in the neoadjuvant I-SPY 2 TRIAL with standard NAC alone or combined with MK-2206 (AKT inhibitor) treatment. Blood was collected at pretreatment (T0), 3 weeks after initiation of paclitaxel (T1), between paclitaxel and anthracycline regimens (T2), or prior to surgery (T3). A personalized ctDNA test was designed to detect up to 16 patient-specific mutations (from whole-exome sequencing of pretreatment tumor) in cfDNA by ultra-deep sequencing. The median follow-up time for survival analysis was 4.8 years. RESULTS: At T0, 61 of 84 (73%) patients were ctDNA positive, which decreased over time (T1: 35%; T2: 14%; and T3: 9%). Patients who remained ctDNA positive at T1 were significantly more likely to have residual disease after NAC (83% non-pCR) compared with those who cleared ctDNA (52% non-pCR; odds ratio 4.33, P = 0.012). After NAC, all patients who achieved pCR were ctDNA negative (n = 17, 100%). For those who did not achieve pCR (n = 43), ctDNA-positive patients (14%) had a significantly increased risk of metastatic recurrence [hazard ratio (HR) 10.4; 95% confidence interval (CI) 2.3-46.6]; interestingly, patients who did not achieve pCR but were ctDNA negative (86%) had excellent outcome, similar to those who achieved pCR (HR 1.4; 95% CI 0.15-13.5). CONCLUSIONS: Lack of ctDNA clearance was a significant predictor of poor response and metastatic recurrence, while clearance was associated with improved survival even in patients who did not achieve pCR. Personalized monitoring of ctDNA during NAC of high-risk early breast cancer may aid in real-time assessment of treatment response and help fine-tune pCR as a surrogate endpoint of survival.

Detection of ubiquitous and heterogeneous mutations in cell-free DNA from patients with early-stage non-small-cell lung cancer.

BACKGROUND: The aim of this pilot study was to assess whether both ubiquitous and heterogeneous somatic mutations could be detected in cell-free DNA (cfDNA) from patients with early-stage non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS: Three stage I and one stage II primary NSCLC tumors were subjected to multiregion whole-exome sequencing (WES) and validated with AmpliSeq. A subset of ubiquitous and heterogeneous single-nucleotide variants (SNVs) were chosen. Multiplexed PCR using custom-designed primers, coupled with next-generation sequencing (mPCR-NGS), was used to detect these SNVs in both tumor DNA and cfDNA isolated from plasma obtained before surgical resection of the tumors. The limit of detection for each assay was determined using cfDNA from 48 presumed-normal healthy volunteers. RESULTS: Tumor DNA and plasma-derived cfDNA was successfully amplified and sequenced for 37/50 (74%) SNVs using the mPCR-NGS method. Twenty-five (68%) were ubiquitous and 12 (32%) were heterogeneous SNVs. Variant detection by mPCR-NGS and WES-AmpliSeq in tumor tissue was well correlated (R(2) = 0.8722, P < 0.0001). Sixteen (43%) out of 37 SNVs were detected in cfDNA. Twelve of these were ubiquitous SNVs with a variant allele frequency (VAF) range of 0.15-23.25%, and four of these were heterogeneous SNVs with a VAF range of 0.28-1.71%. There was a statistically significant linear relationship between the VAFs for tumor and cfDNA (R(2) = 0.5144; P = 0.0018). For all four patients, at least two variants were detected in plasma. The estimated number of copies of variant DNA present in each sample ranged from 5 to 524. The average number of variant copies required for detection (VCRD) was 3.16 (range: 0.2-7.6 copies). CONCLUSIONS: The mPCR-NGS method revealed intratumor heterogeneity in early-stage NSCLC tumors, and was able to detect both ubiquitous and heterogeneous SNVs in cfDNA. Further validation of mPCR-NGS in cfDNA is required to define its potential use in clinical practice.

Detection of 793/B serotype of infectious bronchitis virus in tissue sample by indirect immunoperoxidase assay.

The indirect immunoperoxidase (IIP) assay was compared with the reverse transcription-polymerase chain reaction (RT-PCR) for detection of 793/B serotype of infectious bronchitis virus in tissues samples collected from experimentally infected chickens. This technique was optimized in specific pathogen-free (SPF)-embryonated chicken eggs and broiler chickens inoculated with the Iranian IR/773/2001 strain of 793/B serotype The trachea, lung, kidney, and cecal tonsil tissue samples from experimentally infected chicken embryos and chickens were collected in order to prepare tissue sections in IIP assay and to detect in RT-PCR. The sensitivity and specificity values of IIP assay were, respectively, 83 and 84 %, and the positive and negative prediction values were 71 and 91 % when compared with RT-PCR.

Association between the interleukin 6 genotype at position -174 and atopic dermatitis.

BACKGROUND: Atopic dermatitis (AD) is a chronic skin disorder of unknown origin that usually manifests for the first time in early infancy. Different types of genetic predisposition and environmental factors seem to be associated with the disease. METHODS: This study was performed to evaluate the frequency of alleles, genotypes, and haplotypes of interleukin (IL) 6 single-nucleotide polymorphisms (SNPs) at positions -174 and nt565 in 89 Iranian children with AD and 139 healthy controls. RESULTS: The G allele was significantly more frequent at position -174 in IL6 in atopic patients than in the healthy controls (P < .001; OR, 2.82). Genotype GG was found at the same position in 71% of the patients; this frequency was significantly higher than the frequency of 30% recorded in the controls (P < .001; OR, 5.60). The GG haplotype of IL6 (-174, nt565) was significantly more frequent in the atopic patients than in the healthy controls (P < .001; OR, 2.99). CONCLUSIONS: A significant increase in the frequency of the G allele and GG genotype at position -174 of IL6 was found in patients with AD, thus suggesting that production of this cytokine is greater in atopic patients.

Lidocaine Cyclodextrin complex Ophthalmic Drop, a New Topical Anesthetic Choice.

BACKGROUND: Topical anesthesia is a safe and cost-effective method considered as the first-choice in many procedures. Due to the physiological characteristics of eye, most of the local anesthetics cannot efficiently penetrate through the conjunctiva deep to tenon. The aim of this pilot study was to find a new form of lidocaine to give a sufficient level of anesthesia. METHODS: Lidocaine Cyclodextrin complex ophthalmic drop was produced and its pharmacological properties were studied [tested] in standard temperature and pressure. 30 patients (18 males, 12 females) with the mean age of 30.68±8.02 years enrolled in this clinical trial. All the patients were fully informed and signed the ethics committee consent forms. The patients were given tetracaine drop as the anesthetic: 3 drops separated 2 minute apart 10 min before the intervention. If we achieved a sufficient level of anesthesia, the procedure was done after. If the patient could not tolerate the procedure, the method was changed to lidocaine drop (administered after wash-out period like the first drop).The last option was conventional injection method if the patient could not tolerate the procedure with the second method either.We used this type of anesthesia for conventional procedures such as forced duction test, symblepharon, pterygium, and disport injection into extra-ocular muscles. All the procedures were done by one surgeon in a university hospital. We used a 0 to 10 visual analogue scale for pain and two 0 to 4 patient and physician satisfaction scales designed for this study. RESULTS: The mean pain score was 7.53±0.90 in group 1 and 3.03±1.83 in group 2 (P=0.00). Patient and surgeon satisfaction in group 1 were 1.33±0.48 and 1.40±0.56 respectively; while 3.23±1.00 and 3.56±0.77 for group 2 (P=0.00). Tetracaine drop could not induce sufficient anesthesia for none of the patients. Cyclodextrin based lidocaine drop was successful except For two patients for whom we changed the anesthesia to Sub-conjunctival injection method. CONCLUSION: Our newly manufactured cyclodextrin based lidocaine eye drop could successfully induce sufficient anesthesia for 28 of 30 patients. Further studies with larger sample sizes are now being designed to find more clinical evidence about this method.

Analysis of F9 point mutations and their correlation to severity of haemophilia B disease.

Haemophilia B is an X-linked recessive disorder caused by deficiency of functional coagulation factor IX, which results almost exclusively from mutations in the F9 gene. We sought to determine features, which could distinguish between mutations that cause severe disease symptoms from those that cause non-severe disease symptoms. Towards this objective, we have performed a statistical analysis of reported point mutations in F9. These include: potential local changes in mRNA free energy, codon usage, charge and type of mutated amino acid, location of the mutation with regard to protein secondary structure and functional domain and amino acids' evolutionary conservation scores. Wilcoxon signed-rank tests showed highly significant differences between severe and non-severe disease causing mutations in their effect on free energy of small mRNA fragments and evolutionarily conserved amino acids. Our results suggest that information at the mRNA level as well as conservation of the amino acid correlate well with disease severity. This study demonstrates that computational tools may be used to characterize the severity of haemophilia B associated with point mutations and suggests their utility in predicting the outcome of sequence changes in recombinant proteins.

Long-term results of venous revascularization for Paget-Schroetter syndrome in athletes.

The indications for surgical management of primary subclavian vein thrombosis are not agreed upon. This report describes our experience in the treatment of exertional thrombosis causing Paget-Schroetter syndrome in 10 athletes between 18 and 45 years of age. In seven patients urokinase was injected and this resulted in complete revascularization in three cases (42.9%). The remaining three patients were treated by anticoagulation using heparin with adjuvant Coumadin after resolution of thrombosis. Duplex ultrasonography and dynamic phlebography were performed to assess the results of drug treatment. Decompression of the thoracic outlet was performed secondarily using various techniques, including first-rib resection in 10 cases, scalenectomy in 9, and resection of a clavicular callus in 1 case. In six patients, persistent debilitating venous stasis required revascularization by axillojugular bypass in three cases, thrombectomy in two, and axillojugular anastomosis in one case. All patients were reexamined. Mean follow-up was 45 months. Symptomatic relief and vein patency was achieved in all cases. All patients were able to resume sports activity. In agreement with previous studies, our findings confirm the efficacy of immediate anticoagulation, thrombolysis, and complete decompression of the thoracic outlet. Should this approach fail to reestablish patency, axillosubclavian vein revascularization can provide good mid-term results.

Baker's cyst simulating deep vein thrombosis.

Phlebography is frequently requested to confirm or exclude deep venous thrombosis in patients presenting with a painful, swollen calf or leg. We have noted a small proportion of those with negative phlebograms to have compression or lateral deviation of the popliteal vein. These patients were submitted to contrast arthrography. Eighty per cent of this selected group were found to have dissecting or ruptured Baker's cysts; almost a third of these were dissections upwards into the thigh. A positive diagnosis in these patients is important as management differs from deep vein thrombosis. The optimum diagnostic strategy in patients with a swollen, painful leg is firstly to perform ultrasound of the femoral vein and popliteal fossa to exclude obvious thrombus or ruptured Baker's cyst. If this examination is negative, or a Baker's cyst is shown with no evidence of rupture, phlebography should be performed to exclude calf vein thrombosis. If this examination is negative, but a Baker's cyst is present, or deviation or compression of the popliteal vein is detected, contrast arthrography is suggested to look for rupture of the cyst.