Building flexible and robust analysis frameworks for molecular subtyping of cancers

Molecular subtyping is essential to infer tumor aggressiveness and predict prognosis. In practice, tumor profiling requires in-depth knowledge of bioinformatics tools involved in the processing and analysis of the generated data. Additionally, data incompatibility (e.g., microarray versus RNA sequencing data) and technical and uncharacterized biological variance between training and test data can pose challenges in classifying individual samples. In this article, we provide a roadmap for implementing bioinformatics frameworks for molecular profiling of human cancers in a clinical diagnostic setting. We describe a framework for integrating several methods for quality control, normalization, batch correction, classification and reporting, and develop a use case of the framework in breast cancer.

Surgical tumour resection deregulates Hallmarks of Cancer in resected tissue and the surrounding microenvironment

Surgery exposes tumor tissue to severe hypoxia and mechanical stress leading to rapid gene expression changes in the tumor and its microenvironment, which remain poorly characterized. We biopsied tumor and adjacent normal tissue from breast (BRC) (n=81) and head/neck squamous cancer (HNSC) patients (n=10) at the beginning (A), during (B) and end of surgery (C). Tumor/normal RNA from 46/81 breast cancer patients was subjected to mRNA-Seq using Illumina short-read technology, and from nine HNSC patients to whole transcriptome microarray with Illumina BeadArray. Pathways and genes involved in 7 of 10 known cancer hallmarks, namely, tumour promoting inflammation (TNF-A, NFK-B, IL-18 pathways), activation of invasion & migration [(various Extracellular Matrix (ECM) related pathways, cell migration)], sustained proliferative signaling (K-Ras Signaling), evasion of growth suppressors (P53 signaling, regulation of cell death), deregulating cellular energetics (response to lipid, secreted factors, adipogenesis), inducing angiogenesis (hypoxia signaling, myogenesis), and avoiding immune destruction (CTLA4 and PDL1) were significantly deregulated during surgical resection (time-points A vs B vs C). These findings were validated using NanoString assays in independent pre/intra/post-operative breast cancer samples from 48 patients. In a comparison of gene expression data from biopsy (analogous to time-point A) with surgical resection samples (analogous to time-point C) from The Cancer Genome Atlas (TCGA) study, the top deregulated genes were the same as identified in our analysis, in five of the seven studied cancer types. This study suggests that surgical extirpation deregulates the hallmarks of cancer in primary tumors and adjacent normal tissue across different cancers. Implications: Surgery deregulates hallmarks of cancer in human tissue.

Artificial intelligence and real-world data for drug and food safety - A regulatory science perspective

In 2013, the Global Coalition for Regulatory Science Research (GCRSR) was established with members from over ten countries (www.gcrsr.net). One of the main objectives of GCRSR is to facilitate communication among global regulators on the rise of new technologies with regulatory applications through the annual conference Global Summit on Regulatory Science (GSRS). The 11th annual GSRS conference (GSRS21) focused on "Regulatory Sciences for Food/Drug Safety with Real-World Data (RWD) and Artificial Intelligence (AI)." The conference discussed current advancements in both AI and RWD approaches with a specific emphasis on how they impact regulatory sciences and how regulatory agencies across the globe are pursuing the adaptation and oversight of these technologies. There were presentations from Brazil, Canada, India, Italy, Japan, Germany, Switzerland, Singapore, the United Kingdom, and the United States. These presentations highlighted how various agencies are moving forward with these technologies by either improving the agencies' operation and/or preparing regulatory mechanisms to approve the products containing these innovations. To increase the content and discussion, the GSRS21 hosted two debate sessions on the question of "Is Regulatory Science Ready for AI?" and a workshop to showcase the analytical data tools that global regulatory agencies have been using and/or plan to apply to regulatory science. Several key topics were highlighted and discussed during the conference, such as the capabilities of AI and RWD to assist regulatory science policies for drug and food safety, the readiness of AI and data science to provide solutions for regulatory science. Discussions highlighted the need for a constant effort to evaluate emerging technologies for fit-for-purpose regulatory applications. The annual GSRS conferences offer a unique platform to facilitate discussion and collaboration across regulatory agencies, modernizing regulatory approaches, and harmonizing efforts.

Building Biofoundry India: challenges and path forward

Biofoundry is a place where biomanufacturing meets automation. The highly modular structure of a biofoundry helps accelerate the design–build–test–learn workflow to deliver products fast and in a streamlined fashion. In this perspective, we describe our efforts to build Biofoundry India, where we see the facility add a substantial value in supporting research, innovation and entrepreneurship. We describe three key areas of our focus, harnessing the potential of non-expressing parts of the sequenced genomes, using deep learning in pathway reconstruction and synthesising enzymes and metabolites. Toward the end, we describe specific challenges in building such facility in India and the path to mitigate some of those working with the other biofoundries worldwide.

The mutational landscape of early- and typical-onset oral tongue squamous cell carcinoma

BACKGROUND

The incidence of oral tongue squamous cell carcinoma (OTSCC) is increasing among younger birth cohorts. The etiology of early-onset OTSCC (diagnosed before the age of 50 years) and cancer driver genes remain largely unknown.

METHODS

The Sequencing Consortium of Oral Tongue Cancer was established through the pooling of somatic mutation data of oral tongue cancer specimens (n = 227 [107 early-onset cases]) from 7 studies and The Cancer Genome Atlas. Somatic mutations at microsatellite loci and Catalog of Somatic Mutations in Cancer mutation signatures were identified. Cancer driver genes were identified with the MutSigCV and WITER algorithms. Mutation comparisons between early- and typical-onset OTSCC were evaluated via linear regression with adjustments for patient-related factors.

RESULTS

Two novel driver genes (ATXN1 and CDC42EP1) and 5 previously reported driver genes (TP53, CDKN2A, CASP8, NOTCH1, and FAT1) were identified. Six recurrent mutations were identified, with 4 occurring in TP53. Early-onset OTSCC had significantly fewer nonsilent mutations even after adjustments for tobacco use. No associations of microsatellite locus mutations and mutation signatures with the age of OTSCC onset were observed.

CONCLUSIONS

This international, multicenter consortium is the largest study to characterize the somatic mutational landscape of OTSCC and the first to suggest differences by age of onset. This study validates multiple previously identified OTSCC driver genes and proposes 2 novel cancer driver genes. In analyses by age, early-onset OTSCC had a significantly smaller somatic mutational burden that was not explained by differences in tobacco use.

LAY SUMMARY

This study identifies 7 specific areas in the human genetic code that could be responsible for promoting the development of tongue cancer. Tongue cancer in young patients (under the age of 50 years) has fewer overall changes to the genetic code in comparison with tongue cancer in older patients, but the authors do not think that this is due to differences in smoking rates between the 2 groups. The cause of increasing cases of tongue cancer in young patients remains unclear.

VASCULAR STENOSIS DETECTION USING TEMPORAL-SPECTRAL DIFFERENCES IN CORRELATED ACOUSTIC MEASUREMENTS

Central venous stenosis is often undiagnosed in patients with hemodialysis vascular access, partly due to imaging difficulties. Noninvasive, point-of-care detection could rely on detecting regions of turbulent blood flow caused by blood velocity changes. Here we present flexible microphone arrays for time-correlated measures of blood flow sounds and a new signal processing approach to calculate time correlation between spectral features. Continuous wavelet transform was used to produce an auditory spectral flux analytic signal, which was thresholded to identify systolic start and end phases. Microphone arrays were tested on pulsatile flow phantoms with blood flow rates of 850-1,200 mL/min and simulated stenosis from 10-85%. Measured results showed an inversion in the time onset of systolic spectral content for sites proximal and distal to stenosis for hemodynamically significant stenoses (+22 ms for stenosis<50% and -20 to -38 ms for stenosis>50%). Equivalent blood velocity increases were calculated as 142-155 cm/s in stenotic phantoms, which are within the physiologic range as measured by ultrasound.

Detection of High-Risk Human Papillomavirus in Oral Cavity Squamous Cell Carcinoma Using Multiple Analytes and Their Role in Patient Survival

PURPOSE

Accurate detection of human papillomavirus (HPV) in oral cavity squamous cell carcinoma (OSCC) is essential to understanding the role of HPV in disease prognosis and management of patients. We used different analytes and methods to understand the true prevalence of HPV in a cohort of patients with OSCC with different molecular backgrounds, and we correlated HPV data with patient survival.

METHODS

We integrated data from multiple analytes (HPV DNA, HPV RNA, and p16), assays (immunohistochemistry, polymerase chain reaction [PCR], quantitative PCR [qPCR], and digital PCR), and molecular changes (somatic mutations and DNA methylation) from 153 patients with OSCC to correlate p16 expression, HPV DNA, and HPV RNA with HPV incidence and patient survival.

RESULTS

High prevalence (33% to 58%) of HPV16/18 DNA did not correlate with the presence of transcriptionally active viral genomes (15%) in tumors. Eighteen percent of the tumors were p16 positive and only 6% were both HPV DNA and HPV RNA positive. Most tumors with relatively high copy number HPV DNA and/or HPV RNA, but not with HPV DNA alone (irrespective of copy number), were wild-type for TP53 and CASP8 genes. In our study, p16 protein, HPV DNA, and HPV RNA, either alone or in combination, did not correlate with patient survival. Nine HPV-associated genes stratified the virus-positive from the virus-negative tumor group with high confidence ( P < .008) when HPV DNA copy number and/or HPV RNA were considered to define HPV positivity, and not HPV DNA alone, irrespective of copy number ( P < .2).

CONCLUSION

In OSCC, the presence of both HPV RNA and p16 is rare. HPV DNA alone is not an accurate measure of HPV positivity and therefore may not be informative. HPV DNA, HPV RNA, and p16 do not correlate with patients' outcome.

Functional genomics screen with pooled shRNA library and gene expression profiling with extracts of Azadirachta indica identify potential pathways for therapeutic targets in head and neck squamous cell carcinoma

Tumor suppression by the extracts of Azadirachta indica (neem) works via anti-proliferation, cell cycle arrest, and apoptosis, demonstrated previously using cancer cell lines and live animal models. However, very little is known about the molecular targets and pathways that neem extracts and their associated compounds act through. Here, we address this using a genome-wide functional pooled shRNA screen on head and neck squamous cell carcinoma cell lines treated with crude neem leaf extracts, known for their anti-tumorigenic activity. We analyzed differences in global clonal sizes of the shRNA-infected cells cultured under no treatment and treatment with neem leaf extract conditions, assayed using next-generation sequencing. We found 225 genes affected the cancer cell growth in the shRNA-infected cells treated with neem extract. Pathway enrichment analyses of whole-genome gene expression data from cells temporally treated with neem extract revealed important roles played by the TGF-β pathway and HSF-1-related gene network. Our results indicate that neem extract affects various important molecular signaling pathways in head and neck cancer cells, some of which may be therapeutic targets for this devastating tumor.

CAFE MOCHA: An Integrated Platform for Discovering Clinically Relevant Molecular Changes in Cancer-An Example of Distant Metastasis- and Recurrence-Linked Classifiers in Head and Neck Squamous Cell Carcinoma

PURPOSE

With large amounts of multidimensional molecular data on cancers generated and deposited into public repositories such as The Cancer Genome Atlas and International Cancer Genome Consortium, a cancer type agnostic and integrative platform will help to identify signatures with clinical relevance. We devised such a platform and showcase it by identifying a molecular signature for patients with metastatic and recurrent (MR) head and neck squamous cell carcinoma (HNSCC).

METHODS

We devised a statistical framework accompanied by a graphical user interface-driven application, Clinical Association of Functionally Established MOlecular CHAnges ( CAFE MOCHA; https://github.com/binaypanda/CAFEMOCHA), to discover molecular signatures linked to a specific clinical attribute in a cancer type. The platform integrates mutations and indels, gene expression, DNA methylation, and copy number variations to discover a classifier first and then to predict an incoming tumor for the same by pulling defined class variables into a single framework that incorporates a coordinate geometry-based algorithm called complete specificity margin-based clustering, which ensures maximum specificity. CAFE MOCHA classifies an incoming tumor sample using either its matched normal or a built-in database of normal tissues. The application is packed and deployed using the install4j multiplatform installer. We tested CAFE MOCHA in HNSCC tumors (n = 513) followed by validation in tumors from an independent cohort (n = 18) for discovering a signature linked to distant MR.

RESULTS

CAFE MOCHA identified an integrated signature, MR44, associated with distant MR HNSCC, with 80% sensitivity and 100% specificity in the discovery stage and 100% sensitivity and 100% specificity in the validation stage.

CONCLUSION

CAFE MOCHA is a cancer type and clinical attribute agnostic statistical framework to discover integrated molecular signatures.

Stenosis Characterization and Identification for Dialysis Vascular Access

Vascular access dysfunction is the leading cause of hospitalization for hemodialysis patients and accounts for the most medical costs in this patient population. Vascular access flow is commonly hindered by blood vessel narrowing (stenosis). Current screening methods involving imaging to detect stenosis are too costly for routine use at the point of care. Noninvasive, real-time screening of patients at risk of vascular access dysfunction could potentially identify high-risk patients and reduce the likelihood of emergency surgical interventions. Bruits (sounds produced by turbulent blood flow near stenoses) can be interpreted by skilled clinical staff using conventional stethoscopes. To improve the sensitivity of detection, digital analysis of blood flow sounds (phonoangiograms or PAGs) is a promising approach for classifying vascular access stenosis using non-invasive auditory recordings. Here, we demonstrate auditory and spectral features of PAGs which estimate both the location and degree of stenosis (DOS). Auditory recordings from nine stenosis phantoms with variable DOS and hemodynamic flow rate were obtained using a digital recording stethoscope and analyzed to extract classification features. Autoregressive modeling and discrete wavelet transforms were used for multiresolution signal decomposition to produce 14 distinct features, most of which were linearly correlated with DOS. Our initial results suggest that the widely-used auditory spectral centroid is a simple way to calculate features which can estimate both the location and severity of vascular access stenosis.

SKIN-COUPLED PVDF MICROPHONES FOR NONINVASIVE VASCULAR BLOOD SOUND MONITORING

Vascular access is the "Achilles Heel" of hemodialysis, as maintaining high flow characteristics (access patency) is critical to achieving efficient dialysis treatment. Thus, monitoring of vascular access is essential for maintaining long-term dialysis success. Blood sounds change in the presence of stenosis and can be analyzed digitally as phonoangiograms (PAGs) to determine changes in hemodynamic flow. We propose a multi-channel PAG recording sensor suitable for rapid, non-invasive vascular access monitoring. Here we present the initial design and characterization of sensors appropriate for recording PAGs from the skin surface. An optimized sensor size and backing material was selected to improve sensitivity and to provide a neutral frequency response. The sensor performance was finally compared with a conventional stethoscope on a controlled blood flow stenosis benchtop phantom.

A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma

Selection of the right reference gene(s) is crucial in the analysis and interpretation of gene expression data. The aim of the present study was to discover and validate a minimal set of internal control genes in head and neck tumor studies. We analyzed data from multiple sources (in house whole-genome gene expression microarrays, previously published quantitative real-time PCR (qPCR) data and RNA-seq data from TCGA) to come up with a list of 18 genes (discovery set) that had the lowest variance, a high level of expression across tumors, and their matched normal samples. The genes in the discovery set were ranked using four different algorithms (BestKeeper, geNorm, NormFinder, and comparative delta Ct) and a web-based comparative tool, RefFinder, for their stability and variance in expression across tissues. Finally, we validated their expression using qPCR in an additional set of tumor:matched normal samples that resulted in five genes (RPL30, RPL27, PSMC5, MTCH1, and OAZ1), out of which RPL30 and RPL27 were most stable and were abundantly expressed across the tissues. Our data suggest that RPL30 or RPL27 in combination with either PSMC5 or MTCH1 or OAZ1 can be used as a minimal set of control genes in head and neck tumor gene expression studies.

An illustration of human sperm morphology and their functional ability among different group of subfertile males

Condensed sperm chromatin is a prerequisite for natural fertilization. Some reports suggested the prevalence of chromatin condensation defects in teratozoospermia cases with head anomalies; conversely, earlier studies exemplified its occurrence in morphologically normal spermatozoa too. The aim of this study was to compare the condensation defects in correlation with head anomalies among different groups of subfertile males and its impact on the rate of fertilization in assisted reproduction procedures. Ultrastructure analysis of spermatozoa through scanning electron microscopy and atomic force microscopy could facilitate an in-depth evaluation of sperm morphology. Nuclear condensation defects (%) in spermatozoa were analyzed in 666 subjects, and its effect on the rate of fertilization was analyzed in 116 IVF and 90 intracytoplasmic sperm injection cases. There was no correlation of condensation defects with head anomalies (%). Student's t-test showed no significant changes in mean values of condensation defects in abnormal semen samples in comparison with the normal group. Condensation defects were observed in normal spermatozoa too, which was negatively associated with the rate of fertilization in IVF (p < 0.01), but intracytoplasmic sperm injection outcome remained unaffected. Ultrastructure study revealed sperm morphological features in height, amplitude, and three-dimensional views in atomic force microscopy images presenting surface topography, roughness property of head, and compact arrangement of mitochondria over axoneme with height profile at nanoscale. In pathological forms, surface roughness and nuclear thickness were marked higher than the normal spermatozoa. Thus, percentage of normal spermatozoa with condensation defects could be a predictive factor for the rate of fertilization in IVF. From diverse shapes of nucleus in AFM imaging, it could be predicted that defective nuclear shaping might be impeding the activity of some proteins/ biological motors, those regulate the proper Golgi spreading over peri-nuclear theca.

Comparative analyses of putative toxin gene homologs from an Old World viper, Daboia russelii

Availability of snake genome sequences has opened up exciting areas of research on comparative genomics and gene diversity. One of the challenges in studying snake genomes is the acquisition of biological material from live animals, especially from the venomous ones, making the process cumbersome and time-consuming. Here, we report comparative sequence analyses of putative toxin gene homologs from Russell’s viper (Daboia russelii) using whole-genome sequencing data obtained from shed skin. When compared with the major venom proteins in Russell’s viper studied previously, we found 45–100% sequence similarity between the venom proteins and their putative homologs in the skin. Additionally, comparative analyses of 20 putative toxin gene family homologs provided evidence of unique sequence motifs in nerve growth factor (NGF), platelet derived growth factor (PDGF), Kunitz/Bovine pancreatic trypsin inhibitor (Kunitz BPTI), cysteine-rich secretory proteins, antigen 5, andpathogenesis-related1 proteins (CAP) and cysteine-rich secretory protein (CRISP). In those derived proteins, we identified V11 and T35 in the NGF domain; F23 and A29 in the PDGF domain; N69, K2 and A5 in the CAP domain; and Q17 in the CRISP domain to be responsible for differences in the largest pockets across the protein domain structures in crotalines, viperines and elapids from the in silico structure-based analysis. Similarly, residues F10, Y11 and E20 appear to play an important role in the protein structures across the kunitz protein domain of viperids and elapids. Our study highlights the usefulness of shed skin in obtaining good quality high-molecular weight DNA for comparative genomic studies, and provides evidence towards the unique features and evolution of putative venom gene homologs in vipers.

Molecular findings from 537 individuals with inherited retinal disease

BACKGROUND

Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide.

METHODS

We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC).

RESULTS

Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals.

CONCLUSIONS

Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.

An Improved Genome Assembly of Azadirachta indica A. Juss

Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of a neem plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using additional short reads from Illumina and long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error-corrected long reads using Platanus, an assembler designed to perform well for heterozygous genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of valid transcriptome alignments; 13.4-fold less misassembly and 1.85-fold increase in the percentage repeat, over the earlier assembly (v1.0). The current assembly also maps better to the genes known to be involved in the terpenoid biosynthesis pathway. Together, the data represent an improved assembly of the A. indica genome.

Integrated analysis of oral tongue squamous cell carcinoma identifies key variants and pathways linked to risk habits, HPV, clinical parameters and tumor recurrence

Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (<50yrs) is on the rise; many of whom lack the typical associated risk factors of alcohol and/or tobacco exposure. We present data on single nucleotide variations (SNVs), indels, regions with loss of heterozygosity (LOH), and copy number variations (CNVs) from fifty-paired oral tongue primary tumors and link the significant somatic variants with clinical parameters, epidemiological factors including human papilloma virus (HPV) infection and tumor recurrence. Apart from the frequent somatic variants harbored in TP53, CASP8, RASA1, NOTCH and CDKN2A genes, significant amplifications and/or deletions were detected in chromosomes 6-9, and 11 in the tumors. Variants in CASP8 and CDKN2A were mutually exclusive. CDKN2A, PIK3CA, RASA1 and DMD variants were exclusively linked to smoking, chewing, HPV infection and tumor stage. We also performed a whole-genome gene expression study that identified matrix metalloproteases to be highly expressed in tumors and linked pathways involving arachidonic acid and NF-k-B to habits and distant metastasis, respectively. Functional knockdown studies in cell lines demonstrated the role of CASP8 in a HPV-negative OTSCC cell line. Finally, we identified a 38-gene minimal signature that predicts tumor recurrence using an ensemble machine-learning method. Taken together, this study links molecular signatures to various clinical and epidemiological factors in a homogeneous tumor population with a relatively high HPV prevalence.

Gene and miRNA expression changes in squamous cell carcinoma of larynx and hypopharynx

Laryngo-pharyngeal squamous cell carcinomas are one of the most common head and neck cancers. Despite the presence of a large body of information, molecular biomarkers are not currently used in the diagnosis, treatment and management of patients for this group of cancer. Here, we have profiled expression of genes and microRNAs of larynx and hypopharynx tumors using high-throughput sequencing experiments. We found that matrix metalloproteinases along with SCEL, CRNN, KRT4, SPINK5, and TGM3 among others have significantly altered expression in these tumors. Alongside gene expression, the microRNAs hsa-miR-139, hsa-miR-203 and the hsa-miR-424/503 cluster have aberrant expression in these cancers. Using target genes for these microRNAs, we found the involvement of pathways linked to cell cycle, p53 signaling, and viral carcinogenesis significant (P-values 10(-13), 10(-9) and 10(-7) respectively). Finally, using an ensemble machine-learning tool, we discovered a unique 8-gene signature for this group of cancers that differentiates the group from the other tumor subsites of head and neck region. We investigated the role of promoter methylation in one of these genes, WIF1, and found no correlation between DNA methylation and down-regulation of WIF1. We validated our findings of gene expression, 8-gene signature and promoter methylation using q-PCR, data from TCGA and q-MSP respectively. Data presented in this manuscript has been submitted to the NCBI Geo database with the accession number GSE67994.

Abstract A08: Cancer stem cell-like cells in drug resistance of head and neck squamous cell carcinoma

This study attempts to evaluate the correlation between cancer stem cell (CSC) like-cells and drug resistance in Head and Neck Squamous Cell Carcinoma. Single and triple resistant sub-lines of CAL-27 and HEp-2 cells developed in the lab were used to correlate increased prevalence of stem cell-like cells with drug resistance.The drug resistant sublines were initially evaluated for their resistance by MTT assay, apoptosis assay and expression of drug resistance genes. They were subsequently evaluated for expression of stemness specific genes (CD44, CD133, ALDHA1, ABCG2, BMi1, SOX-2, NOTCH, NANOG, and OCT-4) using Quantitative real-time PCR (QRT-PCR). Increased self-renewal, migration and tumorigenic property of these cells were assessed using spheroid formation, clonogenic survival, wound healing and tumorigenicity assays. Transcriptome sequencing is currently going on to profile the drug resistant cancer stem cell properties. Stemness specific genes were also validated using in normal, primary and recurrent patient samples using QRT-PCR. Assessment of the four drug resistant head and neck cancer sub-lines (CAL-27CisR, HEp-2CisR, CAL-27 TPFR and HEp-2 TPFR) by MTT assay revealed an increase in the IC50 values (RI &gt;3) in a three independent experiments (* p&lt;0.05). Apoptosis assay also showed an increased resistance to apoptosis while expression profiling indicated a significant up regulation of all the resistant genes (MDR1, MRP2, Survivin, ERCC1 and CTR1). Quantitative expression profiling of resistant cells showed an up-regulation of genes characterizing stem-cell like properties. Cell cycle analysis showed a decreased percentage of cells in the G1/G0 and an increased presence in G2/M in cisplatin resistant cells and the TPFR cell lines in a three independent experiments (* p&lt;0.05). Functional assays indicated an increased spheroid formation, colony formation and increased migration properties in TPFR resistant cell lines as compared to the parental counterparts. Similar studies are ongoing in the cisplatin resistant cell lines to evaluate their functional properties. Validation in patient sample also showed an increase in stemness gene expression in recurrent patients. This study indicates that the resistant sub-lines of HNSCC cells showed an enrichment of cancer stem cell-like cells. Further studies in this direction are warranted towards delineating the molecular and cellular basis of this association

Citation Format: Safeena Kulsum, Sindhu VG, Ramanan Somasundara Pandian, Debashish Das, Binay Panda, Wesley Hicks, Mukund Seshadri, Moni Abraham Kuriakose, Amritha Suresh. Cancer stem cell-like cells in drug resistance of head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr A08.

Role of the N6-methyladenosine RNA mark in gene regulation and its implications on development and disease

Epigenetics is a field that encompasses chemical modifications of DNA and histone proteins, both of which alter gene expression without changing the underlying nucleotide sequence. DNA methylation and modifications of histone tails have been studied in detail and are now known to be global gene regulatory mechanisms. An analogous post-transcriptional modification is chemical modification of specific nucleotides in RNA. Study of RNA modifications is a nascent field as yet, and the significance of these marks in controlling cell growth and differentiation is just beginning to be appreciated. The addition of a methyl group to adenosine (N-methyl-6-adenosine) or m6A is the most abundant modification in mammalian mRNAs. Though identified four decades ago, interest in this particular modification was set off by the discovery that the obesity gene FTO was an RNA demethylase. Since then, many studies have investigated m6A modification in different species. In this review, we summarize the current literature and hypotheses about the presence and function of this ubiquitous RNA modification in mammals, viruses, yeast and plants in terms of the consensus sequence and the methyltransferase/demethylation machinery identified thus far. We discuss its potential role in regulating molecular and physiological processes in each of these organisms, especially its role in RNA splicing, RNA degradation and development. We also enlist the methodologies developed so far, both locus-specific and transcriptome-wide, to study this modification. Lastly, we discuss whether m6A alterations have consequences on modulating disease aetiology, and speculate about its potential role in cancer.

The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal

Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essential amino acids in cereals and C4 photosynthesis being one of the most sought-after phenotypes in protein-rich legume crops, the genome of one of the grain amaranths is likely to play a critical role in crop research. We have sequenced the genome and transcriptome of Amaranthus hypochondriacus, a diploid (2n = 32) belonging to the order Caryophyllales with an estimated genome size of 466 Mb. Of the 411 linkage single-nucleotide polymorphisms (SNPs) reported for grain amaranths, 355 SNPs (86%) are represented in the scaffolds and 74% of the 8.6 billion bases of the sequenced transcriptome map to the genomic scaffolds. The genome of A. hypochondriacus, codes for at least 24,829 proteins, shares the paleohexaploidy event with species under the superorders Rosids and Asterids, harbours 1 SNP in 1,000 bases, and contains 13.76% of repeat elements. Annotation of all the genes in the lysine biosynthetic pathway using comparative genomics and expression analysis offers insights into the high-lysine phenotype. As the first grain species under Caryophyllales and the first C4 dicot genome reported, the work presented here will be beneficial in improving crops and in expanding our understanding of angiosperm evolution.

Left pulmonary artery agenesis with pulmonary hypoplasia in an elderly patient: a rare case report

Proximal interruption of the unilateral pulmonary artery is a rare congenital anomaly, which is often associated with other cardiovascular abnormalities. It is usually diagnosed in children but rarely discovered in adulthood as an isolated phenomenon, occurring more frequently on the right side and is often associated with a contralateral aortic arch. We are presenting a rare case of a sixty year old male who was diagnosed with left lung hypoplasia due to proximal interruption of left pulmonary artery with left sided aortic arch without any associated cardiovascular anomalies. DOI: http://dx.doi.org/10.3329/bjms.v12i4.13689 Bangladesh Journal of Medical Science Vol. 12 No. 04 October ’13 Page 462-466

Augmenting transcriptome assembly by combining de novo and genome-guided tools

Researchers interested in studying and constructing transcriptomes, especially for non-model species, face the conundrum of choosing from a number of available de novo and genome-guided assemblers. None of the popular assembly tools in use today achieve requisite sensitivity, specificity or recovery of full-length transcripts on their own. Here, we present a comprehensive comparative study of the performance of various assemblers. Additionally, we present an approach to combinatorially augment transciptome assembly by using both de novo and genome-guided tools. In our study, we obtained the best recovery and most full-length transcripts with Trinity and TopHat1-Cufflinks, respectively. The sensitivity of the assembly and isoform recovery was superior, without compromising much on the specificity, when transcripts from Trinity were augmented with those from TopHat1-Cufflinks.

A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica

Background

The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach.

Results

The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs.

Conclusions

This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides.

Primary atony of the lower uterine segment as a distinct cause of early postpartum haemorrhage: a case series and management recommendations

Primary atony of the lower uterine segment appears to be a distinct cause of postpartum haemorrhage. We report a case series of women with postpartum haemorrhage where ultrasound and clinical findings revealed a well contracted fundus and upper uterine segment and a ballooned out lower uterine segment, a condition we have called primary atony of the lower uterine segment. We hope that this case series will lead to increased recognition of this condition, stimulate others to report their experience and lead to additional studies to better characterise this entity, and develop more effective therapies.

Enhanced poly-?-hydroxybutyrate accumulation in a unicellular cyanobacterium, Synechocystis sp. PCC 6803

AIM

To stimulate poly-beta-hydroxybutyrate (PHB) accumulation in Synechocystis sp. PCC 6803 by manipulating culture conditions.

METHODS AND RESULTS

Stationary phase cultures of Synechocystis sp. PCC 6803 were subjected to N- and P-deficiency, chemoheterotrophy and limitations of gas-exchange. Enhanced PHB accumulation was observed under all the above conditions. However, interaction of P-deficiency with gas-exchange limitation (GEL) in the presence of exogenous carbon boosted PHB accumulation maximally.

CONCLUSIONS

Combined effects of P-deficiency and GEL boosted PHB accumulation up to 38% (w/w) of dry cell weight (dcw) in Synechocystis sp. PCC 6803 in the presence of fructose and acetate. This value is about eightfold higher as compared with the accumulation under photoautotrophic growth condition.

SIGNIFICANCE AND IMPORTANCE OF THE STUDY

These results showed a good potential of Synechocystis sp. PCC 6803 in accumulating poly-beta-hydroxybutyrate, an appropriate raw material for biodegradable and biocompatible plastic. Poly-beta-hydroxybutyrate could be an important material for plastic and pharmaceutical industries.