Designing of inhibitors against CTX-M-15 type β-lactamase: potential drug candidate against β-lactamases-producing multi-drug-resistant bacteria

CTX-M-15 are the most prevalent types of β-lactamases that hydrolyze almost all antibiotics of β-lactam group lead to multiple-antibiotic resistance in bacteria. Three β-lactam inhibitors are available for use in combination with different antibiotics of cephalosporine group against the CTX-M-15-producing strains. Therefore, strategies to identify novel anti β-lactamase agents with specific mechanisms of action are the need of an hour. In this study, we screened three novel non-β-lactam inhibitors against CTX-M-15 by multi-step virtual screening approach. The potential for virtually screened drugs was estimated through in vitro cell assays. Hence, we proposed a study to understand the binding mode of CTX-M-15 with inhibitors using bioinformatics and experimental approach. We calculated the dissociation constants (K_d), association constant (K_a), stoichiometry (n) and binding energies (ΔG) of compounds with the respective targets. Molecular dynamic simulation carried out for 25 ns, revealed that these complexes were found stable throughout the simulation with relative RMSD in acceptable range. Moreover, microbiological and kinetic studies further confirmed high efficacies of these inhibitors by reducing the minimum inhibitory concentration (MIC) and catalysis of antibiotics by β-lactamases in the presence of inhibitors. Therefore, we conclude that these potential inhibitors may be used as a lead molecule for future drug candidates against β-lactamases-producing bacteria.

Abstract P1-14-01: Building an experience engine to make cancer treatment decisions using machine learning

Introduction: Experts at tertiary care centers provide solutions to complex cases not addressed by high quality evidence. They intuitively retrieve patterns from years of experience to make treatment decisions. Short of personal consultations, there is no way to access this vast “experience database.” Experience Engine (XE) is a machine learning solution to structure experiential knowledge relevant for decision making, derive a similarity metric for patients who have received similar treatments, and predict treatment decisions that experts are likely to recommend.

Methods: 277 patient histories relating to 743 breast cancer tumor board decisions at two tertiary care centers were abstracted as the training set for machine learning. 161 distinct histories relating to 496 decisions for a separate expert opinion service at one of the centers was the holdout test set. Data was structured into 690 features based on a novel ontology designed specifically for breast cancer decision making.

To uncover nonlinear similarities, (for example, treatments for younger patients with multiple comorbidities and elderly patients may be similar), treatment decisions were grouped by timing and modality into 13 groups, such as primary surgery, 1st line palliative chemotherapy, etc.

Similarity metric was derived using machine learning on the training set. The target for prediction was the specific treatment decision i.e. TAC or another adjuvant regimen. The primary endpoint was percent accuracy of agreement between XE's predicted decision and experts' actual decision in the holdout test set. Multiple similarity distance metrics including Bhattacharya, Eskin, Goodall, etc., and multiclass classification algorithms such as Extreme Gradient Boosted Trees, Support Vector Machines, etc., were systematically evaluated to arrive at the algorithms that best fit each treatment group.

Results: The winning XE algorithms were 71% to 89% accurate for the various treatment groups, in predicting the actual treatment decisions recommended by the experts. The most frequent treatments recommended across all groups were standard evidence based therapies, as are often recommended by experts. For instance, when XE recommended standard adjuvant therapies for Her2- patients, it was 88% to 97% accurate. When XE recommended nonstandard therapies for the same treatment group, it was 72% to 90% accurate, related to larger number of nonstandard therapies within each treatment group and smaller samples of patients who underwent each type of nonstandard therapy. XE learned to weigh features relating to comorbidities and toxicities when recommending nonstandard therapies.

Conclusion: Machine learning on a structured database of past treatment decisions made by experts, can yield a predicted treatment decision that an expert is likely to recommend for a new patient. By including complex decisions that consider toxicities and morbidities, a rich source of knowledge can be created. Despite the limited dataset, XE learned features that experts strongly consider when making decisions. XE has the potential to analyze variations in decision making at expert practices, assess when to recommend nonstandard therapies, and serve as a training tool for new oncologists to make expert grade treatment decisions.

Citation Format: Ramarajan N, Gupta S, Perry P, Srivastava G, Kumbla A, Miller J, Feldman N, Nair N, Badwe RA. Building an experience engine to make cancer treatment decisions using machine learning [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-14-01.

Molecular dynamics simulation and free energy landscape methods in probing L215H, L217R and L225M βI-tubulin mutations causing paclitaxel resistance in cancer cells

Drug resistance poses a threatening challenge for mankind, as the development of resistance to already well-established drugs causes serious therapeutic problems. Resistance to paclitaxel (Ptxl), a complex diterpenoid working as microtubule stabilizer, is one such issue in cancer treatment. Microtubule stabilizer drugs, stabilises microtubules upon binding to β-tubulin subunit of tubulin heterodimer thus causing mitotic arrest leading to death of cancer cell. Leucine point mutations viz. L215H, L217R, and L225M were reported for Ptxl resistance in various cancers. In the current study, molecular mechanism of these resistance causing mutations was explored using molecular docking, molecular dynamics (MD) simulation, binding energy estimation (MMPBSA), free energy decomposition, principle component analysis (PCA) and free energy landscape (FEL) methods. A total of five systems including unbound βI-tubulin (Apo), docked wild+Ptxl, L215H+Ptxl, L217R+Ptxl and L225M+Ptxl were prepared, and 50 ns MD simulation was performed for each system. Binding energy estimation indicated that leucine mutation reduces the binding affinity of Ptxl in mutant types (MTs) as compared to wild type (WT). Further, in contrast to WT Ptxl interactions with the M-loop (PHE270-VAL286), S6-S7 loop and H9-H10 were significantly altered in MTs. Results showed that in MTs, Ptxl had weak interaction with M-loop residues, while having strong affinity with S6-S7 loop and H6-H7 loop. Moreover, PCA and FEL analysis revealed that M-loop flexible region (THR274-LEU284) was strongly bound with Ptxl in WT preventing its flexible movement and the causing factor for microtubule stabilization. In MTs due to poor interaction with Ptxl, M-loop flexible region retains its flexibility, therefore unable to stabilize microtubule. This study will give an insight into the importance of M-loop flexible region interaction with Ptxl for microtubule stabilization. In addition, it clearly provides the molecular basis of Ptxl resistance mechanism in leucine MTs. This work will help in developing novel microtubule stabilizers molecules active against MTs.

Identification of pathologically insignificant prostate cancer is not accurate in unscreened men

Background:

Identification of men harbouring insignificant prostate cancer (PC) is important in selecting patients for active surveillance. Tools have been developed in PSA-screened populations to identify such men based on clinical and biopsy parameters.

Methods:

Prospectively collected case series of 848 patients was treated with radical prostatectomy between July 2007 and October 2011 at an English tertiary care centre. Tumour volume was assessed by pathological examination. For each tool, receiver operator characteristics were calculated for predicting insignificant disease by three different criteria and the area under each curve compared. Comparison of accuracy in screened and unscreened populations was performed.

Results:

Of 848 patients, 415 had Gleason 3+3 disease on biopsy. Of these, 32.0% had extra-prostatic extension and 50.2% were upgraded. One had positive lymph nodes. Two hundred and six (24% of cohort) were D'Amico low risk. Of these, 143 had more than two biopsy cores involved. None of the tools evaluated has adequate discriminative power in predicting insignificant tumour burden. Accuracy is low in PSA-screened and -unscreened populations.

Conclusions:

In our unscreened population, tools designed to identify insignificant PC are inaccurate. Detection of a wider size range of prostate tumours in the unscreened may contribute to relative inaccuracy.

Abstract P2-10-07: Ep-ICD overexpression associates with poor prognosis in invasive ductal carcinoma

Background: Despite improvements in treatment strategies recurrence rates are still high among breast cancer patients. This may be attributed to heterogeneous nature of breast cancers representing varied morphologic and biological features, behavior, and response to therapy. Even among breast tumors of similar histologic type and grade, prognosis varies. Currently, breast cancer prognosis assessment methods have limited accuracy, are expensive, and in 20-30% of cases lead to over-treatment with adverse effects. None of the currently known prognostic factors has the ability to predict accurately which breast cancer patients are at high risk of recurrence. Thus, there is an increasing need for identification and validation of prognostic markers for assessment of risk for disease recurrence in breast cancer patients.

Epithelial cell adhesion molecule (EpCAM) is a glycosylated, 30- to 40-kDa type I membrane protein, expressed in several human epithelial tissues and overexpressed in cancers, as well as in progenitors, normal and cancer stem cells, and is implicated in epithelial mesenchymal transition (EMT). Regulated intra-membrane proteolysis (RIP) of EpCAM by tumor-necrosis-factor alpha converting enzyme (TACE) results in shedding of its extracellular domain (EpEx) and release of intracellular domain, Ep-ICD, into the cytoplasm. Ep-ICD can signal into the cell nucleus by engagement of components of the Wnt pathway proteins including four and one half LIM domains protein 2 (FHL2), β-catenin and Lef, leading to activation of its oncogenic activity.

Objective. Evaluate the prognostic significance of Ep-ICD overexpression in invasive ductal carcinoma (IDC).

Methodology: Formalin fixed paraffin embedded (FFPE) tissue sections obtained from IDCs (n = 180) and normal breast tissues (n = 45) were used for immunostaining for Ep-ICD using specific monoclonal antibody. A semi-quantitative visual scoring of the immunostaining results for Ep-ICD based on percentage of tumor cells stained and intensity of scoring was used to compare the expression in breast cancers and normal tissues. Statistical analysis was carried out to determine the association of Ep-ICD expression with clinical outcome.

Results: Among the 180 IDCs analyzed, nuclear Ep-ICD was observed in 75 tissues (41.7%) while cytoplasmic positivity was observed in 145 tissues (80.6%). In comparison, nuclear Ep-ICD localization was observed only in 11 normal tissues (23.9%) and cytoplasmic positivity was observed in 39 normal tissues (86.7%). The nuclear / cytoplasmic Ep-ICD expression has been correlated with at least 5 years follow-up data of 180 breast cancer patients after primary treatment. Kaplan Meier survival analysis showed significantly reduced 5 year disease free survival in IDC patients showing nuclear positivity (p < 0.001) or cytoplasmic positivity (p = 0.048). In Cox multivariate regression analysis, nuclear Ep-ICD overexpression emerged as an independent indicator of poor prognosis in IDCs (p = 0.008, H.R. = 81.18).

Conclusion: Among invasive ductal carcinomas of the breast, nuclear Ep-ICD overexpression predicts reduced 5-year disease free survival.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-10-07.

Long-term outcome with lenalidomide and dexamethasone therapy for newly diagnosed multiple myeloma

The combination of lenalidomide and dexamethasone (Len-Dex) is a commonly used initial therapy for newly diagnosed multiple myeloma (MM). Although the initial response rates and toxicity are well known, long-term outcome is not well described. We studied 286 consecutive patients with newly diagnosed MM initially treated with Len-Dex. The median (range) age at diagnosis was 63 (28-92) years, 166 (58%) patients ≤ 65 years and 175 (61%) male. The median estimated duration on Len-Dex was 5.3 months with overall response (≥ partial response) of 72%, including 26% with very good partial response or better. The median overall survival (OS) from the diagnosis was not reached (NR) and the estimated 5-year survival was 71%. The median time to first disease progression, irrespective of transplant status, was 30.2 months. Overall, 143 (50%) patients underwent stem cell transplant. The median OS was NR for patients ≤ 70 years and 5.8 years for the older patients (P=0.01). The 5-year OS estimate for patients in International Staging System stage 1, 2 and 3 were 82, 65, and 44% respectively. There were 21 new second malignancies after MM diagnosis (6.6%). The median survival exceeding 7 years reflects the efficacy of novel agents. The risk of second malignancies doesn't appear to be excessive in this population.

Accommodation: its relation to refractive errors, amblyopia and biometric parameters

AIM

To study accommodation in relation to different refractive errors, amblyopia and to measure the anatomical changes in the accommodating eye

MATERIALS AND METHODS

We studied the amplitude of accommodation (AA) in 150 patients in the age group 11 ± 30 years which included emmetropes, myopes, hypermetropes and hypermetropic amblyopes using the Royal Air Force (RAF) rule. The anterior chamber depth (ACD), axial length (AxL) and lens thickness (LT) changes during accommodation were measured using an A-scan. Myopes and hypermetropes were further divided based on the amount of refractive error : less than 2D, 2 -4D and greater than 4D.

RESULTS

Corrected low myopes had the highest accommodation amplitude (p less than 0.05) followed by emmetropes. Corrected hypermetropes were found to have the lowest amplitude of accommodation (p less than 0.05). The amblyopic eye had a significantly low AA compared to the non-amblyopic eye (p less than 0.05). ACD decreased (p less than 0.05) and LT increased (p less than 0.05) during accommodation. The AxL increase was maximum in myopes (p less than 0.05) followed by hypermetropes but the change was not significant in hypermetropes (p greater than 0.05).

CONCLUSION

The amblyopic eye has low amplitudes of accommodation proving the benefit of near adds in amblyopic patients. Prolonged near work might induce myopia in susceptible eyes by increasing the axial length.

A novel isoform of the 8p22 tumor suppressor gene DLC1 suppresses tumor growth and is frequently silenced in multiple common tumors

The critical 8p22 tumor suppressor deleted in liver cancer 1 (DLC1) is frequently inactivated by aberrant CpG methylation and/or genetic deletion and implicated in tumorigeneses of multiple tumor types. Here, we report the identification and characterization of its new isoform, DLC1 isoform 4 (DLC1-i4). This novel isoform encodes an 1125-aa (amino acid) protein with distinct N-terminus as compared with other known DLC1 isoforms. Similar to other isoforms, DLC1-i4 is expressed ubiquitously in normal tissues and immortalized normal epithelial cells, suggesting a role as a major DLC1 transcript. However, differential expression of the four DLC1 isoforms is found in tumor cell lines: Isoform 1 (longest) and 3 (short thus probably nonfunctional) share a promoter and are silenced in almost all cancer and immortalized cell lines, whereas isoform 2 and 4 utilize different promoters and are frequently downregulated. DLC1-i4 is significantly downregulated in multiple carcinoma cell lines, including 2/4 nasopharyngeal, 8/16 (50%) esophageal, 4/16 (25%) gastric, 6/9 (67%) breast, 3/4 colorectal, 4/4 cervical and 2/8(25%) lung carcinoma cell lines. The functional DLC1-i4 promoter is within a CpG island and is activated by wild-type p53. CpG methylation of the DLC1-i4 promoter is associated with its silencing in tumor cells and was detected in 38-100% of multiple primary tumors. Treatment with 5-aza-2'-deoxycytidine or genetic double knockout of DNMT1 and DNMT3B led to demethylation of the promoter and reactivation of its expression, indicating a predominantly epigenetic mechanism of silencing. Ectopic expression of DLC1-i4 in silenced tumor cells strongly inhibited their growth and colony formation. Thus, we identified a new isoform of DLC1 with tumor suppressive function. The differential expression of various DLC1 isoforms suggests interplay in modulating the complex activities of DLC1 during carcinogenesis.

Use of a MET-specific photoprobe to identify bladder tumors in an orthotopic xenograft model of bladder cancer

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Background: Met over-expression has been found in bladder cancer (CaB). Stage and grade increases in urothelial carcinoma have been found to correlate with increases in Met expression. To assess whether molecular optical imaging could enhance the detection of bladder tumors, we used a Met-specific soluble photoprobe in an orthotopic xenograft model of bladder transitional cell carcinoma (TCC).

Methods: An orthotopic xenograft murine model of CaB was developed with T24-Luciferase-positive bladder cancer cells. Presence of tumor was confirmed by luciferase optical imaging (Xenogen IVIS) of mice, 4 weeks after TCC cell implantation. Mice were euthanized and their bladders removed and bivalved. Bladders were incubated for 30 minutes with unbound fluorophore (Cy5**, Peak emission at 675 nM) and subsequently for another 30 minutes with Cy5** bound to a Met-specific peptide. Fluorescence imaging (Maestro) was performed before and after each incubation period. Following imaging, presence of tumor was confirmed histologically.

Results: Cy5**-Met- peptide bound in sufficient density to tumor tissue in bladders for visualization by optical imaging. The tumor to normal bladder imaging ratio ranged from 2:1 to 8:1. Bladder regions with high uptake of Cy5**-Met-peptide corresponded to tumor areas confirmed by histological analysis.

Conclusions: Cy5**-Met-peptide successfully targets Met in an orthotopic xenograft model of bladder cancer. Our results suggest that this agent maybe useful for the enhanced visualization of bladder cancer tumors during cystoscopy.

No significant financial relationships to disclose.

Effect of the orally available MET inhibitor PF-2341066 on tumor burden and metastasis in an orthotopic xenograft model of bladder cancer

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Background: Met over-expression has been found in bladder cancer (CaB). However, to date, the effects of Met inhibition in CaB have not been reported. We used a small, orally available, highly specific Met-inhibitor currently on phase 2 clinical trials, to assess its effects in an orthotopic xenograft model of bladder transitional cell carcinoma (TCC).

Methods: An orthotopic xenograft murine model of TCC of the bladder was developed with T24-Luciferase positive bladder cancer cells. NIH 3T3 cells producing human hepatocyte growth factor (hHGF) were implanted subcutaneously in mice to provide a source of hHGF. Animals were treated with the selective Met inhibitor (PF-2341066) intra-peritoneally after positive detection of bladder tumor primary and/or metatastatic disease. Fluorescence imaging (Xenogen IVIS) of mice was performed weekly. Mice were euthanized 4 weeks after the start of treatment and their tissues studied histologically.

Results: PF-2341066 was found to reduce tumor burden to below detectable levels in both primary and metastatic sites in all mice treated. No noticeable side effects were detected in treated mice secondary to drug administration.

Conclusions: This study is the first to test a small orally available Met-selective inhibitor in an orthotopic, HGF-driven model of human CaB. Our results demonstrate that Met-inhibition by PF-2341066 reduces TCC tumor burden supporting its potential use in patients with bladder cancer.

No significant financial relationships to disclose.

Absence of Epstein-Barr virus in oesophageal squamous cell carcinoma

Aim-To identify the possible role of Epstein-Barr virus (EBV), in Chinese patients, in the pathogenesis of oesophageal squamous cell carcinoma.Methods-Formalin fixed, paraffin wax embedded tissues from 74 cases of oesophageal squamous cell carcinoma (28 with well differentiated, 27 with moderately differentiated and 18 with poorly differentiated carcinomas) were analysed for EBV using in situ hybridisation for EBV encoded small RNAs.Results-EBV was detected in only a few lymphocytes adjacent to the tumour epithelia in 14 (19%) cases of oesophageal carcinoma. The adjacent, non-pathological oesophageal tissue was EBV negative.Conclusions-EBV does not play a major role in the aetiology of oesophageal squamous cell carcinoma.

Accumulation of p53 protein in inverted transitional cell papilloma of the urinary bladder

Aims-To study the possible accumulation of p53 protein in inverted papilloma of the urinary bladder.Methods-Formalin fixed, paraffin wax embedded sections from 14 cases of inverted papilloma of the urinary bladder were studied retrospectively. Accumulation of p53 was detected by immunohistochemistry using a mouse monoclonal antibody directed against p53. p53 protein reactivity was scored as follows: 0 = 10%; 1 = 10% to <30%; 2 = 30% to <50%; and 3 = >50% of cells p53 positive.Results-The 14 sections were scored as follows: 3 in four cases; 2 in four cases; 1 in one case; and 0 in five cases. Overall, nine (64%) of the 14 cases were positive for p53 protein.Conclusions-The accumulation of p53 protein in inverted papilloma of the urinary bladder suggests that p53 may have has an important role in the neoplastic process of this tumour. However, the benign nature of inverted papillomas suggests that p53 protein accumulation is not related to tumour invasiveness and metastasis. p53 reactivity cannot be used as a marker of malignancy for urothelial neoplasia. Further studies are required to determine the role of p53 protein in the oncogenesis of urothelial neoplasms.

Frequent epigenetic inactivation of Rb1 in addition to p15 and p16 in mantle cell and follicular lymphoma

Dysregulation of cell cycle control is an important mechanism in carcinogenesis. Gene promoter hypermethylation is an alternative mechanism of gene inactivation. We analyzed the methylation status of the tumor suppressor components of the INK4/Rb pathway in mantle cell lymphoma and follicular lymphoma by methylation-specific polymerase chain reaction for p15, p16, p18, and Rb1 in 23 mantle cell lymphoma and 30 follicular lymphoma cases and lymphoma cell lines. The methylation-specific polymerase chain reaction results showed that in mantle cell lymphoma, frequent p16 (82%) but infrequent p15 (8.7%) or Rb1 (17.4%) hypermethylation occurred, with p16 and Rb1 hypermethylation being mutually exclusive (P=.01). In follicular lymphoma, frequent hypermethylation of p15 (36.7%), p16 (56.7%), and Rb1 (43.3%) occurred, with p15 and Rb1 hypermethylation being mutually exclusive (P=.05). Concurrent methylation of p15 and p16 occurred in 26.7% of patients with follicular lymphoma and 8.7% of patients with mantle cell lymphoma. Compared with mantle cell lymphoma, there was more frequent p15 (P=.025) hypermethylation but comparable Rb1 (P=.07) and p16 (P=.07) hypermethylation in follicular lymphoma. In a patient with follicular lymphoma with sequential biopsies, Rb1 was unmethylated and expressed at diagnosis but became methylated and down-regulated at relapse. Moreover, methylation analysis of these 4 genes in an additional 8 patients with grade I follicular lymphoma showed that Rb, but not the other genes, was preferentially methylated in grade II (P=.03). In summary, most patients with mantle cell lymphoma and follicular lymphoma had epigenetic aberrations targeting the INK4/Rb pathway. There is more frequent p16 hypermethylation in mantle cell lymphoma and p15 or Rb1 hypermethylation in follicular lymphoma. The role of Rb methylation in disease or histologic transformation in follicular lymphoma warrants further study.