Target-based drug discovery: Applications of fluorescence techniques in high throughput and fragment-based screening.

Target-based discovery of first-in-class therapeutics demands an in-depth understanding of the molecular mechanisms underlying human diseases. Precise measurements of cellular and biochemical activities are critical to gain mechanistic knowledge of biomolecules and their altered function in disease conditions. Such measurements enable the development of intervention strategies for preventing or treating diseases by modulation of desired molecular processes. Fluorescence-based techniques are routinely employed for accurate and robust measurements of in-vitro activity of molecular targets and for discovering novel chemical molecules that modulate the activity of molecular targets. In the current review, the authors focus on the applications of fluorescence-based high throughput screening (HTS) and fragment-based ligand discovery (FBLD) techniques such as fluorescence polarization (FP), Förster resonance energy transfer (FRET), fluorescence thermal shift assay (FTSA) and microscale thermophoresis (MST) for the discovery of chemical probe to exploring target's role in disease biology and ultimately, serve as a foundation for drug discovery. Some recent advancements in these techniques for compound library screening against important classes of drug targets, such as G-protein-coupled receptors (GPCRs) and GTPases, as well as phosphorylation- and acetylation-mediated protein-protein interactions, are discussed. Overall, this review presents a landscape of how these techniques paved the way for the discovery of small-molecule modulators and biologics against these targets for therapeutic benefits.

Unveiling the Significance of FGF8 Overexpression in Orchestrating the Progression of Ovarian Cancer.

The asymptomatic nature, high rate of disease recurrence, and resistance to platinum-based chemotherapy highlight the need to identify and characterize novel target molecules for ovarian cancer. Fibroblast growth factor 8 (FGF8) aids in the development and metastasis of ovarian cancer; however, its definite role is not clear. We employed ELISA and IHC to examine the expression of FGF8 in the saliva and tissue samples of epithelial ovarian cancer (EOC) patients and controls. Furthermore, various cell assays were conducted to determine how FGF8 silencing influences ovarian cancer cell survival, adhesion, migration, and invasion to learn more about the functions of FGF8. In saliva samples, from controls through low-grade to high-grade EOC, a stepped overexpression of FGF8 was observed. Similar expression trends were seen in tissue samples, both at protein and mRNA levels. FGF8 gene silencing in SKOV3 cells adversely affected various cell properties essential for cancer cell survival and metastasis. A substantial reduction was observed in the cell survival, cell adhesion to the extracellular matrix, migration, and adhesion properties of SKOV3 cells, suggesting that FGF8 plays a crucial role in the development of EOC. Conclusively, this study suggests a pro-metastatic function of FGF8 in EOC.

MicroLED light source for optical sectioning structured illumination microscopy.

Optical sectioning structured illumination microscopy (OS-SIM) provides optical sectioning capability in wide-field microscopy. The required illumination patterns have traditionally been generated using spatial light modulators (SLM), laser interference patterns, or digital micromirror devices (DMDs) which are too complex to implement in miniscope systems. MicroLEDs have emerged as an alternative light source for patterned illumination due to their extreme brightness capability and small emitter sizes. This paper presents a directly addressable striped microLED microdisplay with 100 rows on a flexible cable (70 cm long) for use as an OS-SIM light source in a benchtop setup. The overall design of the microdisplay is described in detail with luminance-current-voltage characterization. OS-SIM implementation with a benchtop setup shows the optical sectioning capability of the system by imaging within a 500 µm thick fixed brain slice from a transgenic mouse where oligodendrocytes are labeled with a green fluorescent protein (GFP). Results show improved contrast in reconstructed optically sectioned images of 86.92% (OS-SIM) compared with 44.31% (pseudo-widefield). MicroLED based OS-SIM therefore offers a new capability for deep tissue widefield imaging.

A Dense Conformal Electrode Array for High Spatial Resolution Stimulation of Electrosensory Systems.

Studies of electrosensory systems have led to insights into to a number of general issues in biology. However, investigations of these systems have been limited by the inability to precisely control spatial patterns of electrosensory input. In this paper, an electrode array and a system to selectively stimulate spatially restricted regions of an electroreceptor array is presented. The array has 96 channels consisting of chrome/gold electrodes patterned on a flexible parylene-C substrate and encapsulated with another parylene-C layer. The conformability of the electrode array allows for optimal current driving and surface interface conditions. Recordings of neural activity at the first central processing stage in weakly electric mormyrid fish support the potential of this system for high spatial resolution stimulation and mapping of electrosensory systems.

Breakdown of dipole Born approximation and the role of Rydberg's predissociation for the electron-induced ion-pair dissociation to oxygen in the presence of background gases.

We study the electron-induced ion-pair dissociation to gas-phase oxygen molecules using a state-of-the-art velocity-map ion-imaging technique. The analysis is entirely based on the conical time-gated wedge-shaped velocity slice images of O-/O2 nascent anionic fragments, and the resulting observations are in favor of Van Brunt et al.'s report [R. J. Van Brunt and L. J. Kieffer, J. Chem. Phys. 60, 3057 (1974)]. A new image reconstruction method, Jacobian over parallel slicing, is introduced to overcome the drawback of ion exaggeration in determining the kinetic energy distribution from the time-gated parallel slicing technique, which offers an alternative approach to the wedge slicing method. Most importantly, the role of the quintet-heavy Rydberg state has been drawn out to the complex ion-pair formalism. The extracted kinetic energy and angular distributions from the wedge slice images reveal a high momentum transfer during the ion-pair dissociation process, which could be the finest rationale to observe the breakdown of dipole Born approximation driven by multipole moment associated with the incident electron beam. Three distinct dissociative momentum bands have been precisely identified for O- dissociation. However, radiationless Rydberg's predissociation continuum (≥15%) has become an inherent character of electron-induced ion-pair dissociation, which could be dealt with using the beyond Born-Oppenheimer treatment. The incoherent sum of Σ and Π symmetric-associated ion-pair final states has been precisely identified by modeling the angular distribution of O-/O2 for each of the kinetic energy bands. A negligibly small amount of forward-backward asymmetry is observed in the angular distribution of O-/O2, which might be explained by the dissociative state-specific quantum coherence mechanism as reported [Krishnakumar et al., Nat. Phys. 14, 149 (2018); Kumar et al., arXiv:2206.15024 (2022)] by Prabhudesai et al.

Comprehensive molecular phenotyping of ARID1A-deficient gastric cancer reveals pervasive epigenomic reprogramming and therapeutic opportunities.

OBJECTIVE: Gastric cancer (GC) is a leading cause of cancer mortality, with ARID1A being the second most frequently mutated driver gene in GC. We sought to decipher ARID1A-specific GC regulatory networks and examine therapeutic vulnerabilities arising from ARID1A loss. DESIGN: Genomic profiling of GC patients including a Singapore cohort (>200 patients) was performed to derive mutational signatures of ARID1A inactivation across molecular subtypes. Single-cell transcriptomic profiles of ARID1A-mutated GCs were analysed to examine tumour microenvironmental changes arising from ARID1A loss. Genome-wide ARID1A binding and chromatin profiles (H3K27ac, H3K4me3, H3K4me1, ATAC-seq) were generated to identify gastric-specific epigenetic landscapes regulated by ARID1A. Distinct cancer hallmarks of ARID1A-mutated GCs were converged at the genomic, single-cell and epigenomic level, and targeted by pharmacological inhibition. RESULTS: We observed prevalent ARID1A inactivation across GC molecular subtypes, with distinct mutational signatures and linked to a NFKB-driven proinflammatory tumour microenvironment. ARID1A-depletion caused loss of H3K27ac activation signals at ARID1A-occupied distal enhancers, but unexpectedly gain of H3K27ac at ARID1A-occupied promoters in genes such as NFKB1 and NFKB2. Promoter activation in ARID1A-mutated GCs was associated with enhanced gene expression, increased BRD4 binding, and reduced HDAC1 and CTCF occupancy. Combined targeting of promoter activation and tumour inflammation via bromodomain and NFKB inhibitors confirmed therapeutic synergy specific to ARID1A-genomic status. CONCLUSION: Our results suggest a therapeutic strategy for ARID1A-mutated GCs targeting both tumour-intrinsic (BRD4-assocatiated promoter activation) and extrinsic (NFKB immunomodulation) cancer phenotypes.

Multimerin 1 aids in the progression of ovarian cancer possibly via modulation of DNA damage response and repair pathways.

Ovarian cancer is one of the leading causes of deaths among women. Despite advances in the treatment regimes, a high rate of diagnosis in the advanced stage makes it almost an incurable malignancy. Thus, more research efforts are required to identify potential molecular markers for early detection of the disease and therapeutic targets to augment the survival rate of ovarian cancer patients. Previously, in this context, we identified dysregulated expression of multimerin 1 (MMRN1) in ovarian cancer. To elucidate the relationship between MMRN1 expression and ovarian cancer progression, siRNA-based MMRN1 knockdown was employed and various cell assays were performed to study its effect on ovarian cancer cells. In addition, network of dysregulated proteins was identified by quantitative proteomics and associated pathways were explored by bioinformatics analysis. MMRN1 silencing showed a significant reduction in cell viability, adhesion, migration, and invasion and a high frequency of cell apoptosis. Label-free quantitative proteomics and in-depth statistical analysis identified 448 dysregulated proteins, majority of which were overexpressed in MMRN1 knockdown cells. The pathways overrepresented in ovarian cancer were DNA replication, mismatch repair, nucleotide excision repair, and cell cycle regulation. Conclusively, the findings of this study suggest that MMRN1 aids in the progression of ovarian cancer via modulation of DNA damage response and repair pathways.

Regulatory enhancer profiling of mesenchymal-type gastric cancer reveals subtype-specific epigenomic landscapes and targetable vulnerabilities.

OBJECTIVE: Gastric cancer (GC) comprises multiple molecular subtypes. Recent studies have highlighted mesenchymal-subtype GC (Mes-GC) as a clinically aggressive subtype with few treatment options. Combining multiple studies, we derived and applied a consensus Mes-GC classifier to define the Mes-GC enhancer landscape revealing disease vulnerabilities. DESIGN: Transcriptomic profiles of ~1000 primary GCs and cell lines were analysed to derive a consensus Mes-GC classifier. Clinical and genomic associations were performed across >1200 patients with GC. Genome-wide epigenomic profiles (H3K27ac, H3K4me1 and assay for transposase-accessible chromatin with sequencing (ATAC-seq)) of 49 primary GCs and GC cell lines were generated to identify Mes-GC-specific enhancer landscapes. Upstream regulators and downstream targets of Mes-GC enhancers were interrogated using chromatin immunoprecipitation followed by sequencing (ChIP-seq), RNA sequencing, CRISPR/Cas9 editing, functional assays and pharmacological inhibition. RESULTS: We identified and validated a 993-gene cancer-cell intrinsic Mes-GC classifier applicable to retrospective cohorts or prospective single samples. Multicohort analysis of Mes-GCs confirmed associations with poor patient survival, therapy resistance and few targetable genomic alterations. Analysis of enhancer profiles revealed a distinctive Mes-GC epigenomic landscape, with TEAD1 as a master regulator of Mes-GC enhancers and Mes-GCs exhibiting preferential sensitivity to TEAD1 pharmacological inhibition. Analysis of Mes-GC super-enhancers also highlighted NUAK1 kinase as a downstream target, with synergistic effects observed between NUAK1 inhibition and cisplatin treatment. CONCLUSION: Our results establish a consensus Mes-GC classifier applicable to multiple transcriptomic scenarios. Mes-GCs exhibit a distinct epigenomic landscape, and TEAD1 inhibition and combinatorial NUAK1 inhibition/cisplatin may represent potential targetable options.

Ultra-Thin Ceramic Substrates for Improved Heatsinking for microLEDs.

MicroLEDs provide unrivaled luminance and operating lifetime, which has led to significant activity using devices for display and non-display applications. The small size and high power density of microLEDs, however, causes increased adverse heating effects which can limit performance. A new generation of electrically insulating high thermal conductivity materials, such as alumina, has been proposed to mitigate these thermal effects when used as a substrate as an alternative to glass. This strategy then could be used as a method of passive heatsinking to improve the overall performance of the microLED. In this work, a newly available material, an 80 micron thick alumina ceramic substrate, is shown to yield a 30 % improvement on average in the maximum current drive over a glass substrate.

Comparative Evaluation of Shear Bond Strength of Tricalcium Silicate-based Materials to Composite Resin with Two Different Adhesive Systems: An In Vitro Study.

Background: Establishing a strong bond between the pulp capping agent and the restorative material is crucial to the success of the procedure. Without this bond, there is a risk of bacterial infiltration into the pulp, leading to treatment failure. In the past, calcium hydroxide was commonly used for such treatments, but it faced challenges, including poor adhesion to dentin, dissolution over time, and the development of multiple tunnel defects. Mineral trioxide aggregate (MTA), introduced to dentistry in 1993, offered an alternative but came with drawbacks like challenging handling and extended setting times. However, in recent times, several new calcium silicate-based materials have emerged to address MTA's limitations. Two notable examples are Biodentine and MTA Plus. Biodentine, for instance, exhibits excellent sealing ability, while MTA Plus distinguishes itself with a finer particle size compared to traditional MTA. These innovative materials offer promising solutions to enhance the efficacy of pulp capping procedures. Aim: Therefore, in this research, we conducted a comparative analysis of the shear bond strength (SBS) between composite resin and three materials-MTA, MTA Plus, and Biodentine. We examined the effects of applying two distinct adhesive systems in order to evaluate their influence on the bond strength. Materials and methods: A total of 60 acrylic blocks were evenly distributed into three groups, each containing 20 blocks-group I received Biodentine, group II was assigned MTA, and group III received MTA Plus. The respective test materials were compacted into the holes within the blocks. Following this, the samples were incubated for a period of 72 hours. Subsequently, the samples were divided into two subgroups, each consisting of 10 blocks-the self-etch and the total-etch subgroup. The SBS values were then carefully measured for analysis. Result: The SBS of the Biodentine group demonstrated a significantly higher value when compared to the other groups. It's worth noting that when the self-etch adhesive system was employed, the SBS of all the groups experienced a significant reduction. Conclusion: Biodentine cement proves to be an effective choice for pulp capping procedures, regardless of the specific adhesive system employed. Notably, the total-etch adhesive system consistently yields higher bond strength when compared to the self-etch adhesive system. How to cite this article: Kumar V, Showkat I, Manuja N, et al. Comparative Evaluation of Shear Bond Strength of Tricalcium Silicate-based Materials to Composite Resin with Two Different Adhesive Systems: An In Vitro Study. Int J Clin Pediatr Dent 2023;16(S-3):S272-S277.

Variation in CFHR3 determines susceptibility to meningococcal disease by controlling factor H concentrations.

Neisseria meningitidis protects itself from complement-mediated killing by binding complement factor H (FH). Previous studies associated susceptibility to meningococcal disease (MD) with variation in CFH, but the causal variants and underlying mechanism remained unknown. Here we attempted to define the association more accurately by sequencing the CFH-CFHR locus and imputing missing genotypes in previously obtained GWAS datasets of MD-affected individuals of European ancestry and matched controls. We identified a CFHR3 SNP that provides protection from MD (rs75703017, p value = 1.1 × 10-16) by decreasing the concentration of FH in the blood (p value = 1.4 × 10-11). We subsequently used dual-luciferase studies and CRISPR gene editing to establish that deletion of rs75703017 increased FH expression in hepatocyte by preventing promotor inhibition. Our data suggest that reduced concentrations of FH in the blood confer protection from MD; with reduced access to FH, N. meningitidis is less able to shield itself from complement-mediated killing.

Multicenter study on the genetics of glomerular diseases among southeast and south Asians: Deciphering Diversities - Renal Asian Genetics Network (DRAGoN).

Multinational studies have reported monogenic etiologies in 25%-30% of children with steroid-resistant nephrotic syndrome. Such large studies are lacking in Asia. We established Deciphering Diversities: Renal Asian Genetics Network (DRAGoN) and aimed to describe the genetic and clinical spectrums in Asians. We prospectively studied a cohort of 183 probands with suspected genetic glomerulopathies from South and Southeast Asia, of whom 17% had positive family history. Using multi-gene panel sequencing, we detected pathogenic variants in 26 (14%) probands, of whom one-third had COL4A4 or COL4A5 variants (n = 9, 5%). Of those with COL4A5 defects, only 25% had features suggestive of Alport syndrome. Besides traditional predictors for genetic disease (positive family history and extrarenal malformations), we identified novel predictors, namely older age (6.2 vs. 2.4 years; p = 0.001), hematuria (OR 5.6; 95% CI 2.1-14.8; p < 0.001), and proteinuria in the absence of nephrotic syndrome (OR 4.6; 95% CI 1.8-11.8; p = 0.001) at first manifestation. Among patients who first presented with proteinuria without nephrotic syndrome, the genetic diagnostic rates were >60% when a second risk factor (positive family history or extrarenal manifestation) co-existed. The genetic spectrum of glomerulopathies appears different in Asia. Collagen IV genes may be included in sequencing panels even when suggestive clinical features are absent.

Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer.

Gastric cancer heterogeneity represents a barrier to disease management. We generated a comprehensive single-cell atlas of gastric cancer (>200,000 cells) comprising 48 samples from 31 patients across clinical stages and histologic subtypes. We identified 34 distinct cell-lineage states including novel rare cell populations. Many lineage states exhibited distinct cancer-associated expression profiles, individually contributing to a combined tumor-wide molecular collage. We observed increased plasma cell proportions in diffuse-type tumors associated with epithelial-resident KLF2 and stage-wise accrual of cancer-associated fibroblast subpopulations marked by high INHBA and FAP coexpression. Single-cell comparisons between patient-derived organoids (PDO) and primary tumors highlighted inter- and intralineage similarities and differences, demarcating molecular boundaries of PDOs as experimental models. We complemented these findings by spatial transcriptomics, orthogonal validation in independent bulk RNA-sequencing cohorts, and functional demonstration using in vitro and in vivo models. Our results provide a high-resolution molecular resource of intra- and interpatient lineage states across distinct gastric cancer subtypes. SIGNIFICANCE: We profiled gastric malignancies at single-cell resolution and identified increased plasma cell proportions as a novel feature of diffuse-type tumors. We also uncovered distinct cancer-associated fibroblast subtypes with INHBA-FAP-high cell populations as predictors of poor clinical prognosis. Our findings highlight potential origins of deregulated cell states in the gastric tumor ecosystem. This article is highlighted in the In This Issue feature, p. 587.

Epigenetic promoter alterations in GI tumour immune-editing and resistance to immune checkpoint inhibition.

OBJECTIVES: Epigenomic alterations in cancer interact with the immune microenvironment to dictate tumour evolution and therapeutic response. We aimed to study the regulation of the tumour immune microenvironment through epigenetic alternate promoter use in gastric cancer and to expand our findings to other gastrointestinal tumours. DESIGN: Alternate promoter burden (APB) was quantified using a novel bioinformatic algorithm (proActiv) to infer promoter activity from short-read RNA sequencing and samples categorised into APBhigh, APBint and APBlow. Single-cell RNA sequencing was performed to analyse the intratumour immune microenvironment. A humanised mouse cancer in vivo model was used to explore dynamic temporal interactions between tumour kinetics, alternate promoter usage and the human immune system. Multiple cohorts of gastrointestinal tumours treated with immunotherapy were assessed for correlation between APB and treatment outcomes. RESULTS: APBhigh gastric cancer tumours expressed decreased levels of T-cell cytolytic activity and exhibited signatures of immune depletion. Single-cell RNAsequencing analysis confirmed distinct immunological populations and lower T-cell proportions in APBhigh tumours. Functional in vivo studies using 'humanised mice' harbouring an active human immune system revealed distinct temporal relationships between APB and tumour growth, with APBhigh tumours having almost no human T-cell infiltration. Analysis of immunotherapy-treated patients with GI cancer confirmed resistance of APBhigh tumours to immune checkpoint inhibition. APBhigh gastric cancer exhibited significantly poorer progression-free survival compared with APBlow (median 55 days vs 121 days, HR 0.40, 95% CI 0.18 to 0.93, p=0.032). CONCLUSION: These findings demonstrate an association between alternate promoter use and the tumour microenvironment, leading to immune evasion and immunotherapy resistance.

Installation and Optimization of 68Ga Synthesis Module for Clinical Use: An Institutional Experience.

INTRODUCTION: With advent of gallium-labeling somatostatin analogs and its evaluation under positron emission tomography-computed tomography, there has been a tremendous surge in its application. Gallium 68 can be made available either from onsite cyclotron production or in the form of ready-to-use 68Ge/68Ga generators. Wherein setting up and running of cyclotron amounts to huge investment and dedicated team, the 68Ge/68Ga generator has proved to be a better option and viable project. Moreover, due to long half-life of 68Ge, i.e. 271 days, it enables the usage of generator for several months. The preparation of gallium-labeled peptides is much simpler in comparison to 18F radiochemistry, but the radiation exposure has always been an area of concern owing to high-energy annihilation photon of 511 keV. MATERIALS AND METHODS: In this study, we share our experience of self-installation of 68Ge/68Ga generator during lockdown and the various steps involved in installation of fully automated peptide-labeling system in customized mini hot cell module, synthesis steps, and quality control steps of gallium-based radiopharmaceutical. RESULTS: The installation was successfully completed with online assistance during the pandemic situation. The average elution yield met company specification (>80%), and 68Ga-labeled peptides were prepared with high radiochemical purity (>95%). The overall exposure in single batch of production and quality control never exceeded 3 µSv as shielding was well-taken care of with customized mini hot cell. CONCLUSION: With the described experience and validation process, one can easily think of making an installation at his/her center and cater to the needs of society with a new radiopharmaceutical.

Importance of Understanding and Analyzing Daily Quality Assurance Test of Positron Emission Tomography/Computed Tomography Equipment in Minimizing the Downtime of Equipment in Remote Places.

This article briefly describes the event of a defective detector block in a daily quality assurance scan/blank scan and insists on implementing guidelines to scan or not to scan in such a scenario. The nuclear medicine physicist should have a clear understanding of the blank scan graph, which shall help rectify the right cause of problem and give confidence to the physician in reporting the acquired study. A routine blank scan in positron emission tomography signifies various parameters of the crystal (coincidence count rate, single count rate, dead time, and coincidence time along with energy response) and in some respect is analogous to the daily uniformity flood image for gamma cameras, providing an overall assessment of detector response. We encountered a bad detector block in our routine quality assurance scan/blank scan and analyzed the root cause behind such an error which was finally restored to normalcy by replacing the defected part with a new one and an error-free blank scan was established. The analysis was carried out by performing various possible checks and discussing the issue with service engineer to help identify the defects much before service engineer actually arrived in our department. This allowed us to take the correct decision and enabled us to get the scanner repaired faster. Hence, a good understanding of the daily quality control test and proper analysis of the same may result in swift decision-making and faster repair of equipment leading to minimal disruption in the clinical workflow as well as avoidance of suboptimal scanning leading to the wrong diagnosis.

Target identification for small-molecule discovery in the FOXO3a tumor-suppressor pathway using a biodiverse peptide library.

Genetic screening technologies to identify and validate macromolecular interactions (MMIs) essential for complex pathways remain an important unmet need for systems biology and therapeutics development. Here, we use a library of peptides from diverse prokaryal genomes to screen MMIs promoting the nuclear relocalization of Forkhead Box O3 (FOXO3a), a tumor suppressor more frequently inactivated by post-translational modification than mutation. A hit peptide engages the 14-3-3 family of signal regulators through a phosphorylation-dependent interaction, modulates FOXO3a-mediated transcription, and suppresses cancer cell growth. In a crystal structure, the hit peptide occupies the phosphopeptide-binding groove of 14-3-3ε in a conformation distinct from its natural peptide substrates. A biophysical screen identifies drug-like small molecules that displace the hit peptide from 14-3-3ε, providing starting points for structure-guided development. Our findings exemplify "protein interference," an approach using evolutionarily diverse, natural peptides to rapidly identify, validate, and develop chemical probes against MMIs essential for complex cellular phenotypes.

Assessment of Effective Dose Received in Various Computed Tomography Protocols and Factors Affecting It.

PURPOSE OF STUDY: The purpose of the study was to evaluate the effect of patient characteristics and equipment-related factors on the computed tomography (CT) dose received by patients from positron emission tomography-CT (PET-CT) using system-generated dose-length product (DLP) values and also to check the effective dose (ED) received from various CT protocols at our institute. MATERIALS AND METHODS: This retrospective study included 78 adult patients who underwent F-18 fluorodeoxyglucose whole-body PET-CT and were divided into three groups based on the area of primary cancerous lesion. In Group A, we had 44 patients who underwent PET-CT (head-and-neck protocol), in Group B, we had 24 patients who underwent PET-CT (whole body with brain protocol), and in Group C, we had 10 patients who underwent PET-CT (pelvis protocol). All of the patients under the study are of South Asian ethnicity. A majority of patients 53.85% were males and remaining 46.15% were females. The product of conversion factor (k-coefficient), as described in "American Association of Physicists in Medicine Report No. 96" and DLP value generated by the scanner, was used to calculate the ED. Moreover, we also performed regression analysis to check relation between body weight, height, scan range, tube current, Volume computed tomography dose index (CTDIvol), DLP, and ED. RESULTS: The regression analysis shows that scan range, patient height, weight, tube current, and DLP were significantly correlated with ED (P < 0.05 for all). Moreover, the DLP and conversion factor method estimated the ED from various groups. Patients under Group A (head-and-neck protocol), Group B (whole body with brain protocol), Group C (pelvis protocol) received an average ED of 22.45 mSv, 22.40 mSv, and 21.24 mSv, respectively. CONCLUSION: ED from CT component of PET-CT can be assessed as the product of scanner-generated DLP and conversion factor for selected range. Moreover, body weight, scan range, and tube current had an independent significant effect on ED received from CT.

Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer.

BACKGROUND: Deregulated gene expression is a hallmark of cancer; however, most studies to date have analyzed short-read RNA sequencing data with inherent limitations. Here, we combine PacBio long-read isoform sequencing (Iso-Seq) and Illumina paired-end short-read RNA sequencing to comprehensively survey the transcriptome of gastric cancer (GC), a leading cause of global cancer mortality. RESULTS: We performed full-length transcriptome analysis across 10 GC cell lines covering four major GC molecular subtypes (chromosomal unstable, Epstein-Barr positive, genome stable and microsatellite unstable). We identify 60,239 non-redundant full-length transcripts, of which > 66% are novel compared to current transcriptome databases. Novel isoforms are more likely to be cell line and subtype specific, expressed at lower levels with larger number of exons, with longer isoform/coding sequence lengths. Most novel isoforms utilize an alternate first exon, and compared to other alternative splicing categories, are expressed at higher levels and exhibit higher variability. Collectively, we observe alternate promoter usage in 25% of detected genes, with the majority (84.2%) of known/novel promoter pairs exhibiting potential changes in their coding sequences. Mapping these alternate promoters to TCGA GC samples, we identify several cancer-associated isoforms, including novel variants of oncogenes. Tumor-specific transcript isoforms tend to alter protein coding sequences to a larger extent than other isoforms. Analysis of outcome data suggests that novel isoforms may impart additional prognostic information. CONCLUSIONS: Our results provide a rich resource of full-length transcriptome data for deeper studies of GC and other gastrointestinal malignancies.