Abstract 1515: Shannon entropy of mutational signatures predict sensitivity of signature detection in targeted sequencing

Mutational processes can cause driver mutations which are a proximal cause of tumorigenesis. COSMIC identifies signatures of biological and environmental events that drive mutational processes and can be identified by examining patterns of somatic mutations. We describe the complexity of the COSMIC mutational signatures and their impact. We introduce Shannon entropy as a metric to measure complexity of trinucleotide distributions, thus capturing a previously ignored dimension of mutational signatures that may predict their identification. Shannon entropy derives from the rich predictive mathematics of information theory. We calculated entropy for all the COSMIC mutation signatures and found that SBS3, homologous recombination repair deficiency (HRD) signature, had highest entropy of 6.326, while SBS2 signature, activation of AID/APOBEC cytidine deaminases, had the lowest entropy of 1.758.We discovered that high entropy signatures (such as HRD SBS3) require more somatic mutations to be reliably detected than do low entropy signatures, important when planning signature detection using targeted panels that have smaller genomic footprint. We demonstrate this correlation with two approaches i) by simulation using MutSigSim, a tool we developed for simulating mutational profiles given the number of mutations, and ii) by using real datasets. Simulation was performed for high, medium, and low entropy signatures. We used cosine similarity of 0.7 as the threshold for detection. For signatures with entropy <2, a signature can be detected 90% of the time with 10 or more mutations. Similarly, signatures with entropies between 2-3, 3-5 and >5 can be detected 90% of the time with 30, 40, and 100 mutations, respectively. Mutation signatures of 1500 samples from a pan solid tumor cohort sequenced with Oncomine Comprehensive Assay Plus or Oncomine TMB were used to confirm these conclusions. We saw that signatures with higher entropy were difficult to detect at cosine similarity threshold of 0.7 in samples with a smaller number of mutations. In a cohort of samples with MSI-high, we detected mismatch repair (MMR) signatures with low to medium entropy with high specificity and good sensitivity. Furthermore, in a cohort of Ovarian cancer samples, it was difficult to detect the high entropy HRD signature at 0.7 threshold when the number of somatic mutations was not high. We show that ability to detect mutation signatures using targeted panels is directly correlated to the complexity of signature and number of mutations. For research use only. Not for use in diagnostic procedures.

Citation Format: Ajithavalli Chellappan, Chintan Vora, Jagannath Patro, Shilpa Nair, Rushikesh S. Kanap, Fiona C. Hyland. Shannon entropy of mutational signatures predict sensitivity of signature detection in targeted sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1515.

Abstract 2079: Prediction of DDR and other mutation signatures using targeted panels for FFPE samples

Mutational processes can cause driver mutations and are considered the primary cause of tumorigenesis. Cosmic signatures classify environmental or intrinsic mutational processes. Identification of signatures including DNA Damage Response (DDR) signatures enables research into the origin of cancer mutagenesis and into treatment optimization. Typically, Mutation signatures are identified using Whole Genome Sequencing or Whole Exome Sequencing. We demonstrate signature prediction of mutation signatures with two amplification-based targeted panels, which have a high sequencing success rate for FFPE samples. ~2000 FFPE Samples from a pan-solid tumor cohort were sequenced with either of two AmpliSeq panels (OCAplus and OTMLA), sizes 1.4 Mb and 1.7 Mb, to optimize a method to identify mutation signatures. First, we identified somatic SNVs by filtering out likely population germline mutations, and used these to construct the single base change substitution (SBS) matrix. The COSMIC cancer signatures use properties of the whole genome: we normalized to extend signature detection to targeted panel data. We adjusted the mutation frequencies observed using the ratio of trinucleotide counts in the genome and the ratio in the panel. Next, we measured the cosine similarity between the normalized sample and the COSMIC signatures. We selected the signatures with a strong match (>0.7) to the normalized sample. We further impute the signatures using a reduced candidate set, to assess the signature fit in the sample and reduce false positives. These steps provide the optimized signatures. We detected optimized signatures in 33% of the samples. A single signature was detected in 9% of the samples, 2 signatures in 6%, and >2 signatures in 17% of the samples. ~3% of samples showed at least one MMR signatures (SBS6, SBS14, SBS15, SBS20, SBS21, SBS26 and SBS44). In all 10 OCAPlus samples with MMR signatures, we also detected mutation(s) in an MMR gene. APOBEC signatures, SBS2 and SBS13, were observed in 3% of samples sequenced with OCAPlus panel and TML panel. We found 3 samples showing HRR signature SBS3. We successfully identified the putative causal DDR mutation in a number of samples. For example, of 62 samples with NTHL1 mutations, 60 had NTHL1 related signature SBS30. A sample with MUTYH mutations was assigned the SBS36 signature. We sequenced matched Tumor/Normal pairs; in most cases, the tumor sample showed a stronger mutational signature, with their corresponding normal sample showing either no signature or a weaker matching signature. We assessed reproducibility of the mutational signature. Looking at duplicate and triplicate replicates, we found that replicates consistently displayed the same mutational signatures. We show identification of mutation signatures using targeted panels designed for FFPE samples.

Citation Format: Fiona Hyland, Ajithavalli Chellappan, Chintan Vora, Shilpa Nair, Jagannath Patro, Ritika Raj, Rushikesh Kanap. Prediction of DDR and other mutation signatures using targeted panels for FFPE samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2079.

Quality by Design Empowered Development and Optimisation of Time-Controlled Pulsatile Release Platform Formulation Employing Compression Coating Technology

The research was envisaged for development of time-controlled pulsatile release (PR) platform formulation to facilitate management of early morning chronological attacks. The development was started using prednisone as a model drug wherein core tablets were prepared using direct compression method and subsequently compression-coated with ethylcellulose (EC)-hydroxypropyl methylcellulose (HPMC) excipient blend. Initially, quality target product profile was established and risk assessment was performed using failure mode and effect analysis. In an endeavour to accomplish the objective, central composite design was employed as a design of experiment (DoE) tool. Optimised compression-coated tablet (CCT) exhibited 4-6 h lag time followed by burst release profile under variegated dissolution conditions viz. multi-media, change in apparatus/agitation and biorelevant media. Afterwards, five different drugs, i.e. methylprednisolone, diclofenac sodium, diltiazem hydrochloride, nifedipine and lornoxicam, were one-by-one incorporated into the optimised prednisone formula with replacement of former drug. Change in drug precipitated the issues like poor solubility and flow property which were respectively resolved through formulation of solid dispersion and preparation of active pharmaceutical ingredient (API) granules. Albeit, all drug CCTs exhibited desired release profile similar to prednisone CCTs. In nutshell, tour de force of research epitomised the objective of incorporating diverse drug molecules and penultimately obtaining robust release profile at varying dissolution conditions.

Myriad Molecules to Overcome Efflux Drug Transporters and Drug-Metabolizing Enzymes: A Journey from Synthetic to Natural

A vast range of prescribed drugs suffers from low and variable bioavailability mainly because of metabolism and permeation complications. This issue of bioavailability is a key problem that has been ongoing for many years. Various tactics have been introduced that have been quite beneficial for improving the bioavailability of poorly bioavailable drugs. Some of these tactics are targeted on cytochrome-P450 (CYP) enzymes and the permeability-glycoprotein (P-gp) efflux pump. Strategies include small-molecule inhibitors, novel drug-delivery systems, pharmaceutical synthetic excipients, and natural bioenhancers. This review discusses the role of synthetic excipients and natural bioenhancers in potentiating the activity of poorly bioavailable drugs, including their pharmacological background and their future applicability to health care. The molecules of synthetic origin such as Gelucire and those of natural origin such as quercetin and silibinin can provide noteworthy benefits to patients and the health care system by helping to reduce dosing and drug side effects.

Formulation Development, Process Optimization, and In Vitro Characterization of Spray-Dried Lansoprazole Enteric Microparticles

This research focuses on the development of enteric microparticles of lansoprazole in a single step by employing the spray drying technique and studies the effects of variegated formulation/process variables on entrapment efficiency and in vitro gastric resistance. Preliminary trials were undertaken to optimize the type of Eudragit and its various levels. Further trials included the incorporation of plasticizer triethyl citrate and combinations of other polymers with Eudragit S 100. Finally, various process parameters were varied to investigate their effects on microparticle properties. The results revealed Eudragit S 100 as the paramount polymer giving the highest gastric resistance in comparison to Eudragit L 100-55 and L 100 due to its higher pH threshold and its polymeric backbone. Incorporation of plasticizer not only influenced entrapment efficiency, but diminished gastric resistance severely. On the contrary, polymeric combinations reduced entrapment efficiency for both sodium alginate and glyceryl behenate, but significantly influenced gastric resistance for only sodium alginate and not for glyceryl behenate. The optimized process parameters were comprised of an inlet temperature of 150°C, atomizing air pressure of 2 kg/cm², feed solution concentration of 6% w/w, feed solution spray rate of 3 ml/min, and aspirator volume of 90%. The SEM analysis revealed smooth and spherical shape morphologies. The DSC and PXRD study divulged the amorphous nature of the drug. Regarding stability, the product was found to be stable under 3 months of accelerated and long-term stability conditions as per ICH Q1A(R2) guidelines. Thus, the technique offers a simple means to generate polymeric enteric microparticles that are ready to formulate and can be directly filled into hard gelatin capsules.

Preparation and characterization of dipyridamole solid dispersions for stabilization of supersaturation: effect of precipitation inhibitors type and molecular weight

Dipyridamole (DPL) is a weakly basic BCS class II drug which precipitates upon entering into intestine leading to pH dependant and variable absorption. Thus, research envisaged focuses on developing formulations that maintain supersaturation following upon acid to neutral pH transition. In an endeavor to accomplish the objective, solid dispersion (SD) with hydroxypropylmethyl cellulose (HPMC) and polyvinylpyrrolidone (PVP) was prepared by a quench cooling method. The three molecular weight grades of HPMC (HPMC E5, HPMC E15 and HPMC E50) and two molecular weight grades of PVP (PVP K30 and PVP K90) were investigated to observe effect of increasing molecular weight on stabilizing DPL supersaturated solutions. Equilibrium solubility studies revealed increase in solubility with both HPMC and PVP with greater benefit from HPMC. In vitro supersaturated dissolution results demonstrated that HPMC formulations provided greater degree and extent of supersaturation as compared to PVP formulations. The formulation with HPMC E50 provided maximum stabilization to supersaturation upon acid to neutral pH transition. Moreover, the effect of increase in molecular weight was more pronounced in HPMC rather than PVP. Stronger interactions were observed for DPL with HPMC, while no interaction was observed with PVP which was evident from Fourier transform infra-red studies. Differential scanning calorimetry and powder X-ray diffraction studies revealed the amorphous state of DPL in SD.

Investigating effects of hydroxypropyl methylcellulose (HPMC) molecular weight grades on lag time of press-coated ethylcellulose tablets

The research undertaken exemplifies the effects of hydroxypropyl methylcellulose (HPMC) molecular weight (MW) grades of on lag time of press-coated ethylcellulose (EC) tablets. The formulation comprised an immediate release core (containing prednisone as a model drug) surrounded by compression coating with variegated EC-HPMC blends. Five selected HPMC grades (E5, E15, E50, K100LV and K4M) were explored at three different concentrations (10% w/w, 20% w/w and 30% w/w in outer coat) to understand their effects on lag time and drug release. In vitro drug release testing demonstrated that, with increase in concentration of E5 and E15, up to 30% w/w, the mean lag time decreased progressively; whereas with remaining grades, the mean lag time initially decreased up to 20% w/w level and thereafter increased for 30% w/w level. Importantly, with increase in HPMC concentration in the outer coat, the variability in lag time (%RSD; n = 6) was decreased for each of E5, E15 and E50, whereas increased for K100LV and K4M. In general, the variability in lag time was increased with increase in HPMC MW at studied concentration levels. Markedly, tablets with 30% w/w K4M in outer coat exhibited slight premature release (before the rupture of outer coat) along with high variability in lag time. Overall, the study concluded that low MW HPMCs (E5, E15 and E50) were found rather efficient than higher MW HPMCs for developing robust EC-based press-coated pulsatile release formulations where precise lag time followed by sharp burst release is desired.

A newfangled study using risk silhouette and uncertainty approximation for quantification of acyclovir in diverse formulation

Risk assessment and uncertainty approximation are two major and important parameters that need to be adopted for the development of pharmaceutical process to ensure reliable results. Additionally, there is a need to switch from the traditional method validation checklist to provide a high level of assurance of method reliability to measure quality attribute of a drug product. In the present work, evaluation of risk profile, combined standard uncertainty and expanded uncertainty in the analysis of acyclovir were studied. Uncertainty was calculated using cause-effect approach, and to make it more accurately applicable a method was validated in our laboratory as per the ICH guidelines. While assessing the results of validation, the calibration model was justified by the lack of fit and Levene׳s test. Risk profile represents the future applications of this method. In uncertainty the major contribution is due to sample concentration and mass. This work demonstrates the application of theoretical concepts of calibration model tests, relative bias, risk profile and uncertainty in routine methods used for analysis in pharmaceutical field.

Investigating critical effects of variegated lubricants, glidants and hydrophilic additives on lag time of press coated ethylcellulose tablets

The research envisaged focuses on vital impacts of variegated lubricants, glidants and hydrophilic additives on lag time of press coated ethylcellulose (EC) tablets using prednisone as a model drug. Several lubricants and glidants such as magnesium stearate, colloidal SiO2, sodium stearyl fumarate, talc, stearic acid, polyethylene glycol (6000) and glyceryl behenate were investigated to understand their effects on lag time by changing their concentrations in outer coat. Further, the effects of hydrophilic additives on lag time were examined for hydroxypropylmethylcellulose (E5), hydroxypropylcellulose (EF and SSL), povidone (K30), copovidone, polyethylene glycol (4000), lactose and mannitol. In vitro drug release testing revealed that each selected lubricant/glidant, if present even at concentration of 0.25% w/w, significantly reduced the lag time of press coated tablets. Specifically, colloidal SiO2 and/or magnesium stearate were detrimental while other lubricants/glidants were relatively less injurious. Among hydrophilic additives, freely water soluble fillers had utmost influence in lag time, whereas, comparatively less impact was observed with polymeric binders. Concisely, glidant and lubricant should be chosen to have minimal impact on lag time and further judicious selection of hydrophilic additives should be exercised for modulating lag time of pulsatile release formulations.

Recent patents and advances on anti - tuberculosis drug delivery and formulations

Tuberculosis has remained, unambiguously, a significant health care problem since long times, particularly in developing countries. The endeavoring battle against multi drug resistant TB, multiple dosing, their prominent side effects and bioavailability hiccups related to fixed dose combinations has undeniably become a Herculean task indicating rigorous research requirement in anti TB drug therapy. In view of the fact that patenting a drug molecule, a drug delivery system or a formulation has been very fruitful for the growth and sustainment of pharmaceutical industry, a meticulous review of recent developments, providing a balanced view on merits/demerits, will facilitate researchers to update themselves, thereby focusing their research in more relevant areas to furnish desired quality traits. This article reviews the present scenario in terms of drug delivery approaches for TB chemotherapy. The review encompasses and summarizes recent patents and advances on variegated facets of dosage forms, together with from conventional solid oral to novel controlled release oral formulations and additionally alternative weapons for anti TB drug delivery. A critical review of multidisciplinary approaches to boost anti TB therapy may facilitate the scientists to resolve existing technological gaps.

Dissolution criticality in developing solid oral formulations: from inception to perception

Currently, dissolution testing has become a vital tool for accessing product performance, especially in the hierarchy of solid oral dosage forms. With advances in complicated, expensive, and sophisticated analytical instruments, characterization of formulations has become easier, but simple dissolution assembly is gradually gaining momentum from industrial environs as well as regulatory agencies. As such, simple dissolution testing involves many complexities which must be properly understood to reach correct conclusions. The appropriate selection of multiple parameters (e.g., apparatus, medium, agitation, etc.) involved in dissolution testing and understanding their impact on analysis require thorough subject knowledge. In the words of regulatory provisions, in vitro dissolution testing can become a surrogate for expensive and tedious bioequivalence studies in special cases (i.e., when a biowaiver is recommended). As a consequence, reduced human testing as well as lower product development cost ultimately benefit patients and society. Therefore, the dissolution science has recently become one of the keys for success for formulation scientists, especially generic manufacturers. While designing dissolution methodologies, generic manufacturers need to follow the respective regulatory guidelines at the product development stage; concomitant data are required for the approval process. This comprehensive review is an earnest attempt to acquaint readers with the history, contemporary practices, and relevant issues regarding dissolution which may become a guiding tool for overcoming challenges and opening better prospects in product development.

Genome-environment interactions that modulate aging: powerful targets for drug discovery

Aging is the major biomedical challenge of this century. The percentage of elderly people, and consequently the incidence of age-related diseases such as heart disease, cancer, and neurodegenerative diseases, is projected to increase considerably in the coming decades. Findings from model organisms have revealed that aging is a surprisingly plastic process that can be manipulated by both genetic and environmental factors. Here we review a broad range of findings in model organisms, from environmental to genetic manipulations of aging, with a focus on those with underlying gene-environment interactions with potential for drug discovery and development. One well-studied dietary manipulation of aging is caloric restriction, which consists of restricting the food intake of organisms without triggering malnutrition and has been shown to retard aging in model organisms. Caloric restriction is already being used as a paradigm for developing compounds that mimic its life-extension effects and might therefore have therapeutic value. The potential for further advances in this field is immense; hundreds of genes in several pathways have recently emerged as regulators of aging and caloric restriction in model organisms. Some of these genes, such as IGF1R and FOXO3, have also been associated with human longevity in genetic association studies. The parallel emergence of network approaches offers prospects to develop multitarget drugs and combinatorial therapies. Understanding how the environment modulates aging-related genes may lead to human applications and disease therapies through diet, lifestyle, or pharmacological interventions. Unlocking the capacity to manipulate human aging would result in unprecedented health benefits.

Study on effectiveness of transfusion program in thalassemia major patients receiving multiple blood transfusions at a transfusion centre in Western India

Background:

Children suffering from beta-thalassemia major require repeated blood transfusions which may be associated with dangers like iron overload and contraction of infections such as HIV, HCV, and HBsAg which ultimately curtail their life span. On the other hand, inadequate transfusions lead to severe anemia and general fatigue and debility.

Materials and Methods:

Data were obtained from 142 beta-thalassemia major patients aged 3 years or more receiving regular blood transfusions at a transfusion centre in Western India from 1 April 2009 to 30 June 2009. The clinical data and laboratory results were subsequently analyzed.

Results:

Of the 142 patients, 76 (53.5%) were undertransfused (mean Hb <10 gm%). 96 (67%) of the patients were taking some form of chelation therapy but out of them only 2 (2%) were adequately chelated (S. ferritin <1000 ng/ml). 5 (3.5%) of the patients were known diabetics on insulin therapy. 103 (72%) of the patients were retarded in terms of growth. The prevalence of transfusion-transmitted infections (TTIs) such as HCV, HIV, and HBsAg was respectively 45%, 2%, and 2%, with the prevalence of HCV being significantly more than the general population. The HCV prevalence showed positive correlation with the age of the patients and with the total no of blood transfusions received. As many as 15% (6 out of 40) children who were born on or after 2002 were HCV positive despite the blood they received being subjected to screening for HCV.

Conclusions:

The study suggests the need to step up the transfusions to achieve hemoglobin goal of 10 gm% (as per the moderate transfusion regimen) and also to institute urgent and effective chelation measures with the aim of keeping serum ferritin levels below 1000 ng/ml to avoid the systemic effects of iron overload. In addition, strict monitoring of the children for endocrinopathy and other systemic effects of iron overload should be done. Rigid implementation of quality control measures for the ELISA kits used to detect HCV in donor blood needs to be done urgently. Alternately, more sensitive and specific measures (like NAT testing) should be employed for detection of HCV. In the absence of a definitive cure accessible and available to all patients, strict implementation of the above suggested measures will go a long way in improving the quality (and quantity) of life in patients of beta-thalassemia major.

Phase II trial of bevacizumab plus pemetrexed and carboplatin in previously untreated advanced nonsquamous non-small cell lung cancer

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Background: A randomized phase III trial has demonstrated the efficacy and safety of high dose bevacizumab (15 mg/kg) with carboplatin and paclitaxel in previously untreated advanced nonsquamous NSCLC (Sandler et al, NEJM 2006). Pemetrexed has also shown significant activity in advanced NSCLC. Clinical investigation of combination bevacizumab (BEV), pemetrexed (PEM) and carboplatin (CARBO) is therefore of interest in this population. Methods: Phase II, open label study in stage IIIB/IV NSCLC: eligible patients have non- squamous histology and no prior chemotherapy, brain metastasis, gross hemoptysis, tumor proximity to major vessels, uncontrolled hypertension or anticoagulation. All patients receive PEM (500 mg/m2), CARBO (AUC 6) and BEV (15 mg/kg) every 21 days. Patients are pretreated with vitamin B12 1,000 mcg every 9 weeks and folic acid 1 mg daily. Responses are assessed every 2 cycles. Patients with CR, PR or SD receive maximum of 6 cycles followed by BEV (15 mg/kg) maintenance. Our primary objective is to determine time to progression and secondary objectives include response rate, overall survival, and safety of the combination. Results: 14 patients (9 female/ 5 male; median age 62 years; range 34–77; 2 stage IIIB/12 stage IV, all ECOG PS 0 or 1) have been entered. Median number of cycles received is 5.5 (range 2 - 15). 12 patients are evaluable for response. 9 patients continued to have disease control at a median duration of 20.2 weeks (range 5–52) with 6 PRs and 3 SDs (response rate 60%; disease control rate 75%). 5 patients proceeded to BEV maintenance with 2 still ongoing. Overall survival data is immature to date. Toxicity data is available for all patients. Grade 3/4 toxicities have included neutropenia (4), nausea/vomiting (2), BEV related allergic reaction (1) and epistaxis (1). Conclusions: Combination BEV, PEM and CARBO is safe, well tolerated and shows promising activity to date. The regimen is not associated with alopecia, neuropathy or arthralgias/myalgias, and is conveniently administered. Enrollment continues and updated results will be presented.

No significant financial relationships to disclose.