Biology subjects

Chattopadhyay, A.

Publications and source records attributed to Chattopadhyay, A..

At least 19 recordsLinked to original sources

bioRxiv2026

MUC4-targeted CAR-T Cells Restrain Chemotherapy-resistant Colorectal Cancer

Colorectal cancer (CRC) is the leading cause of cancer mortality in young adults, with chemoresistance and metastatic progression severely limiting treatment options. MUC4, a membrane-bound mucin normally confined to the apical surface of epithelial cells, becomes aberrantly overexpressed across the tumor cell membrane in CRC and other cancer types, promoting cancer survival, immune evasion, and metastasis. Therefore, MUC4 is a promising candidate for the development of targeted therapies. We detected MUC4 cell surface expression in a panel of human CRC cell lines. We engineered MUC4-specific chimeric antigen receptor (CAR) T cells and evaluated their activity against methotrexate-resistant MUC4-expressing human CRC cell lines HT29-MTX and T84. MUC4 CAR-T cells efficiently eliminated HT29-MTX and T84 cells in vitro and delayed HT29-MTX subcutaneous tumor growth in vivo. Importantly, MUC4 CAR-T cell treatment significantly reduced tumor burden and improved survival in a highly aggressive and lethal CRC model, intraperitoneal HT29-MTX CRC metastatic dissemination in NSG mice. Mouse necropsies revealed no off-target in vivo toxicities associated with MUC4 CAR-T cell therapy. Altogether, our findings establish MUC4 as an important and clinically relevant CAR-T cell target and demonstrate therapeutic efficacy of MUC4 CAR-T cell therapy for invasive CRC, a setting where chemotherapy typically fails. MUC4-targeted CAR-T cell therapy has the potential to fill a critical treatment gap for patients with chemoresistant and invasive CRC and may extend to other MUC4-expressing solid tumors. Statement of PriorityColorectal cancer is increasingly diagnosed in younger individuals, a trend accompanied by a higher prevalence of aggressive and chemotherapy-resistant disease. Despite advances in systemic therapy, outcomes for patients with refractory or metastatic colorectal cancer remain poor, underscoring a critical unmet clinical need. CAR-T cell therapy offers a mechanism to selectively target tumor cells that evade conventional treatments and may thus be particularly valuable in mucinous, chemotherapy-resistant subsets. Developing effective CAR-T strategies for new targets in colorectal carcinoma, such as MUC4, is an urgent priority in this era of rising early-onset disease.

immunology↗

bioRxiv2026

Unique pore architecture underlies constitutive gating of human retinalTRPM1

Transient receptor potential melastatin 1 (TRPM1), a Ca{superscript 2}-permeable nonselective cation channel essential for retinal ON bipolar cell signaling and night vision, and implicated in congenital night blindness, has remained structurally and functionally poorly characterized. Here we report the first cryo-electron microscopy structure of human TRPM1 in conducting state. Although the channel assembles as a tetramer, it adopts an unexpected clockwise domain-swapped pore module with rotational geometry inverse to that observed in previously characterized 6-TM tetrameric channels. This inverted topology is accompanied by extensive remodeling of the S5-P-S6 module, dilation of the selectivity filter, expansion of the central cavity, and splaying of S6 to form a wide intracellular gate. Single-channel recordings reveal constitutive activity consistent with the conductive state captured. Together, these findings uncover a new 6-TM fold in tetrameric channel and provide a framework for understanding TRPM1 gating and disease-associated dysfunction.

biochemistry↗

bioRxiv2025

Liver transplant rejection features memory cell priming, spatially differentiated networks and novel drug targets.

Acute T-cell-mediated transplant rejection, the earliest contributor to immunological graft failure responds variably to T-cell suppression. Early rejection can co-exist with donor-specific antibodies which also shorten graft survival, without affecting graft histology visibly. Here, during early liver transplant rejection, blood leukocytes manifest primed T-cells with heat shock protein (HSP) signaling and transcriptional programs for memory cell expansion. Corresponding biopsies demonstrate upregulated immune synapse and proteasomal genes in T-cell-infiltrated portal and central regions of the liver lobule. With donor-specific antibodies, the intervening intralobular region demonstrates a germinal-center-like allograft response with upregulated CD40, chemokine, T-follicular and complement signaling, which intensifies along the direction of sinusoidal blood flow from portal to central regions. Proteasomal and HSP90 inhibitors suppress donor-specific alloresponses of T- and B-cells in blood samples from patients with early rejection. The molecular injury spectrum of early rejection is complex, spatially differentiated and reveals novel early immunosuppressive strategies to extend graft survival.

immunology↗

bioRxiv2025

Global transcriptome analysis identifies nicotinamide metabolism to play key roles in IFN-gamma and nitric oxide modulated responses

Interferon-gamma (IFN-{gamma}) is a key regulator of immune responses. A hallmark of the IFN-{gamma} response is inducible nitric oxide (NO) production, driven primarily by nitric oxide synthase 2 (NOS2). In this study, we investigated the influence of NO on the IFN-{gamma}-induced transcriptomic and metabolic changes in the RAW 264.7 macrophage cell line. IFN-{gamma} activation led to NO-dependent lactate production and lower cell survival. Bulk RNA sequencing analysis identified genes differentially expressed early by IFN-{gamma} that were either NO-independent or NO-dependent. Inhibition of NO modulated a minor subset of the transcriptome, notably affecting Klf6 (a tumor suppressor) and Zfp36 (a regulator of pro-inflammatory cytokines). Interestingly, both Klf6 and Zfp36 correlatively showed high expression in most cancers. The PPI network exhibited dense clustering with scale-free and small-world properties, identifying Stat1, Irf7, Irf1, Cxcl10, and Isg15 as top five hubs. The top IFN-{gamma} signalling genes exhibited deficient expression in the brain but were highly expressed in lung, spleen, and EBV-transformed lymphocytes. Gene-disease associations linked the IFN-{gamma}-regulated genes to immunodeficiencies, chronic inflammatory responses and malignancies. Interestingly, IFN-{gamma} upregulated genes were involved in nicotinamide metabolism, suggesting a transcriptional basis for modulation of metabolic pathways. This novel aspect was experimentally tested to show that IFN-{gamma} induced NAD amounts. Importantly, the inhibition of purine nucleoside phosphorylase (using Forodesine hydrochloride) which is involved in the endogenous pathway for NAD generation, lowered IFN-{gamma} induced nitrite and increased cell survival in vitro. Functionally, enriched nicotinamide metabolism by IFN-{gamma} may regulate inflammatory responses and the implications of our findings are discussed.

immunology↗

bioRxiv2024

Thermal Plasticity of Stage Specific Development Time in Drosophila melanogaster under Shifting Temperatures

We examined how thermal shifts influence development time and adult body size in Drosophila melanogaster. Individual flies were exposed to alternating temperatures of 25{degrees}C (optimal) and 17{degrees}C (cold), with shifts introduced at key developmental transitions: larval hatching and pupariation. We found while larval-stage temperature is the biggest determinant of thermal plasticity of development time and adult size, the egg-stage temperature also influences the pace of development and growth throughout pre-adult duration. The effect of low-to-high and high-to-low temperature shifts on development and growth may not be symmetric. When eggs are reared at 25{degrees}C and then shifted to 17{degrees}C, larval and pupal durations undergo reduction compared to constant 17{degrees}C, but it produces slightly larger adults. A higher egg-stage temperature thus seem to exert a carryover effect that accelerates subsequent development and growth when later stages experience colder temperatures. Surprisingly, flies whose egg stage is exposed to 17{degrees}C followed by a shift to 25{degrees}C also have reduced larval duration and larger size, relative to those developing at constant 25{degrees}C. We speculate this could be either because 17{degrees}C to 25{degrees}C represents a low-to-high temperature shift or a sub-optimal-to-optimal thermal shift that results in metabolic and/or hormonal changes accelerating differentiation and growth. While pupal duration is sensitive to current and to some extent prior thermal environments, it does not contribute substantially to thermal plasticity of size. Development time is longer in males than in females, and this difference seems to start from larval stage while the pupal duration plays a bigger role in creating this sex-specific difference. Overall, employing individual fly rearing, this study helped to unravel the effect of thermal shifts on growth and development in D. melanogaster with great precision.

evolutionary biology↗

bioRxiv2024

The Sodium/Glucose Cotransporter 2 Inhibitor Empagliflozin Inhibits Long QT 3 Late Sodium Currents in a Mutation Specific Manner

BackgroundSodium/glucose cotransporter 2 inhibitors (SGLT2is) such as empagliflozin have demonstrated substantial cardioprotective effects in patients with or without diabetes. The SGLT2is have been shown to selectively inhibit the late component of cardiac sodium current (late INa). Induction of late INa is also the primary mechanism involved in the pathophysiology of congenital long QT syndrome type 3 (LQT3) gain-of-function mutations in the SCN5A gene that encodes the major cardiac sodium channel isoform Nav1.5. Therefore, we investigated the effect of empagliflozin on late INa in thirteen known LQT3 mutations located in distinct regions of the channel structure. MethodsThe whole-cell patch-clamp technique was used to investigate the effect of empagliflozin (10 {micro}M) on late INa in recombinantly expressed Nav1.5 channels containing different LQT3 mutations. Molecular modeling of human Nav1.5 and simulations in a mathematical model of human ventricular myocytes were used to extrapolate our experimental results to excitation contraction coupling. ResultsEmpagliflozin selectively inhibited late INa in LQT3 mutations residing in the inactivation gate region of Nav1.5, with no effect on either peak current or channel kinetics. In contrast, empagliflozin caused inhibition of both peak and late INa in mutations in the S4 voltage-sensing regions as well as changes in activation and inactivation kinetics and a slowing of recovery from inactivation. Empagliflozin had no effect on late/peak INa or channel kinetics in channels containing LQT3 mutations located in the putative empagliflozin binding region. Simulation of our experimental findings in a mathematical model of human ventricular myocytes predicts that empagliflozin may have a desirable therapeutic effect in LQT3 mutations located in the inactivation gate region. ConclusionsOur results show that empagliflozin selectively inhibits late INa, without affecting gating kinetics, in LQT3 mutations residing in the inactivation gate region. Patients with mutations in voltage-sensing regions are less suitable candidates as empagliflozin may prevent action potential firing. The SGLT2is may therefore be a promising novel precision medicine approach for patients with certain LQT3 mutations.

pharmacology and toxicology↗

bioRxiv2023

Long-term cold adaptation leads to increased thermal plasticity of male body size and thermal canalization of fecundity in populations of Drosophila melanogaster: an experimental evolution study

From laboratory populations of Drosophila melanogaster maintained at 25{degrees}C for many decades, new populations were derived and maintained at 17{degrees}C for over 60 generations. Fitness traits such as body size and fecundity of the cold and warm selected populations were quantified at both 17{degrees}C and 25{degrees}C. Flies from both selection regimes had similar body weight when grown at 25{degrees}C, but 17{degrees}C selected males had greater dry weight and less relative water content than 25{degrees}C selected males, when grown at 17{degrees}C. Cold selected males thus evolved greater thermal plasticity of body weight and density compared to controls. Fecundity data showed, 25{degrees}C selected females laid less eggs at 17{degrees}C compared to 25{degrees}C treatment, but 17{degrees}C selected females did not show significant difference in fecundity between 25{degrees}C and 17{degrees}C. Cold evolved flies thus showed thermal canalization of fecundity, possibly buffering the repressing effect of cold. Whether or not (i) greater body mass and density of cold evolved males, and (b) unrepressed fecundity of cold evolved females, both observed when reared at cold, are causally related, remain to be investigated. The study thus shows thermal selection can lead to evolution of greater thermal plasticity in a trait, while result in thermal canalization of another.

evolutionary biology↗

bioRxiv2023

Interferon-γ lowers tumour growth by increasing glycolysis and lactate production in a nitric oxide-dependent manner: implications for cancer immunotherapy

Interferon-gamma (IFN-{gamma}), the sole member of the type-II interferon family, is well known to protect the host from infectious diseases as well as mount anti-tumour responses. The amounts of IFN-{gamma} in the tumour microenvironment determine the host responses against tumours; however, several tumours employ evasive strategies by responding to low IFN-{gamma} signalling. In this study, the response of various tumour cell lines to IFN-{gamma} was studied in vitro. IFN-{gamma}-activation increases glycolytic flux and reduces mitochondrial function in a nitric oxide (NO)- and reactive oxygen species (ROS)-dependent manner in the H6 hepatoma tumour cell line. The higher glycolysis further fuelled NO and ROS production, indicating a reciprocal regulation. These processes are accompanied by Hypoxia inducing factor (HIF)-1 stabilization and HIF-1-dependent augmentation of the glycolytic flux. The IFN-{gamma} enhancement of lactate production also occurred in other NO-producing cell lines: RAW 264.7 monocyte/macrophage and Renca renal adenocarcinoma. However, two other tumour cell lines, CT26 colon carcinoma and B16F10 melanoma, did not produce NO and lactate upon IFN-{gamma}-activation. HIF-1 stabilization upon IFN-{gamma}-activation led to lower cell growth of B16F10 but not CT26 cells. Importantly, the IFN-{gamma}-activation of both CT26 and B16F10 cells demonstrated significant cellular growth reduction upon metabolic rewiring by exogenous administration of potassium lactate. Clinical studies have shown the crucial roles of IFN-{gamma} for successful cancer immunotherapies involving checkpoint inhibitors and chimeric antigen receptor T cells. The positive implications of this study on the metabolic modulation of IFN-{gamma} activation on heterogeneous tumour cells are discussed.

immunology↗

bioRxiv2022

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. An. stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, have been reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a TNF-like gene, which is the homolog of the eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of wengen (wgn) and grindelwald (grnd) genes in IndInt, which are known to be the receptors for eiger in Drosophila. We have identified all the genes in IndInt required for eiger-mediated signaling by analogy to TNF-TNFR system, suggesting the presence of a functionally active eiger signaling pathway present in IndInt. Comparative genomics of high-quality genome assemblies of the three type-forms with that of IndInt, reveals structurally disruptive mutations in eiger gene in all three strains of the type-form, alluding to compromised innate immunity in the type-form as the cause of high vectorial capacity in these strains. This is the first report of the presence of an intact evolutionarily-conserved TNF-TNFR signaling system in malaria vectors, with a potential role in Plasmodium resistance.

genomics↗

bioRxiv2022

Wireless closed-loop smart bandage for chronic wound management and accelerated tissue regeneration

Chronic non-healing wounds represent a major source of morbidity for patients and a significant economic burden. Current wound care treatments are generally passive and are unable to adapt to changes in the wound environment in real time. By integrating multimodal sensors and adding stimulators in a bandage, real-time physiological monitoring is possible and provides an opportunity for active intervention into the complex wound environment. Here, we develop a battery-free flexible bioelectronic system consisting of wirelessly powered, closed-loop sensing and stimulation circuits with tissue-interfacing tough conducting hydrogel electrodes for robust signal transduction, on-demand adhesion, and detachment. Using multiple pre-clinical models, we demonstrate the capability of our wound care system to continuously monitor skin impedance and temperature, to trigger directional electrical stimulation. The accelerated wound closure was confirmed to be due to the activation of pro-regenerative genes linked to accelerated wound closure, increased neovascularization, and enhanced dermal recovery.

bioengineering↗

bioRxiv2021

Of Biofilms and Beehives: An Analogy-Based Instructional Tool to Introduce Biofilms to High-School and Undergraduate Students

The concept of biofilms and biofilm-based research is largely absent or minimally described in high school and undergraduate life science curriculum. While it is well-established that microbes, such as bacteria and fungi most often exist in multicellular biofilm communities, descriptions in standard biology textbooks continue to focus on the single-celled form of microbial life. We have developed an analogy-based instructional tool to introduce and explain biofilms to high school and undergraduate students. The module employs an analogy with beehives, given that biofilms and beehives are both superorganism states, to explain key biofilm features such as development and structure, chemical communication, division of labor and emergent properties. We delivered this analogy based learning tool to a cohort of 49 high school and undergraduate students, and based on participant feedback and learnings, present a formal evaluation of the instructional tool. Further, we outline prerequisites and learning approaches that can enable the delivery of this module in classroom and virtual learning settings, including suggestions for pre-lesson reading, student-centred interactive activities, and specific learning objectives. Taken together, this instructional analogy holds potential to serve as an educational tool to introduce biofilms in high school and undergraduate curricula in a relatable and comprehensible manner.

scientific communication and education↗

bioRxiv2021

Light Potentials of Photosynthetic Energy Storage in the Field: What limits the ability to use or dissipate rapidly increased light energy?

The responses of plant photosynthesis to rapid fluctuations in environmental conditions are thought to be critical for efficient capture of light energy. Such responses are not well represented under laboratory conditions, but have also been difficult to probe in complex field environments. We demonstrate an open science approach to this problem that combines multifaceted measurements of photosynthesis and environmental conditions, and an unsupervised statistical clustering approach. In a selected set of data on mint (Mentha sp.), we show that the "light potential" for increasing linear electron flow (LEF) and nonphotochemical quenching (NPQ) upon rapid light increases are strongly suppressed in leaves previously exposed to low ambient PAR or low leaf temperatures, factors that can act both independently and cooperatively. Further analyses allowed us to test specific mechanisms. With decreasing leaf temperature or PAR, limitations to photosynthesis during high light fluctuations shifted from rapidly-induced NPQ to photosynthetic control (PCON) of electron flow at the cytochrome b6f complex. At low temperatures, high light induced lumen acidification, but did not induce NPQ, leading to accumulation of reduced electron transfer intermediates, a situation likely to induce photodamage, and represents a potential target for improving the efficiency and robustness of photosynthesis. Finally, we discuss the implications of the approach for open science efforts to understand and improve crop productivity.

plant biology↗

bioRxiv2021

Spatiotemporal evaporating droplet dynamics on fomites enhances long term bacterial pathogenesis

Naturally drying bacterial droplets on inanimate surfaces representing fomites are the most consequential mode for transmitting infection through oro-fecal route. We provide a multiscale holistic approach to understand flow dynamics induced bacterial pattern formation on fomites leading to pathogenesis. The most virulent gut pathogen, Salmonella Typhimurium (STM), typically found in contaminated food and water, is used as model system in the current study. Evaporation-induced flow in sessile droplets facilitates the transport of STM, forming spatio-temporally varying bacterial deposition patterns based on droplet mediums nutrient scale. Mechanical and low moisture stress in the drying process, reduced bacterial viability but interestingly induced hyper-proliferation of STM in macrophages, augmenting virulence in fomites. In vivo studies of fomites in mice confirm that STM maintains virulence. This work demonstrates that stressed bacterial deposit morphologies formed over small timescale (minutes) on organic and inorganic surfaces, plays significant role in enhancing fomites pathogenesis over hours and days.

microbiology↗

bioRxiv2020

COVID-19: Variant screening, an important step towards precision epidemiology

Precision epidemiology using genomic technologies allows for a more targeted approach to COVID-19 control and treatment at individual and population level, and is the urgent need of the day. It enables identification of patients who may be at higher risk than others to COVID-19-related mortality, due to their genetic architecture, or who might respond better to a COVID-19 treatment. The COVID-19 virus, similar to SARS-CoV, uses the ACE2 receptor for cell entry and employs the cellular serine protease TMPRSS2 for viral S protein priming. This study aspires to present a multi-omics view of how variations in the ACE2 and TMPRSS2 genes affect COVID-19 infection and disease progression in affected individuals. It reports, for both genes, several variant and gene expression analysis findings, through (i) comparison analysis over single nucleotide polymorphisms (SNPs), that may account for the difference of COVID-19 manifestations among global sub-populations; (ii) calculating prevalence of structural variations (copy number variations (CNVs) / insertions), amongst populations; and (iii) studying expression patterns stratified by gender and age, over all human tissues. This work is a good first step to be followed by additional studies and functional assays towards informed treatment decisions and improved control of the infection rate.

genomics↗

bioRxiv2020

NAT8L mRNA oxidation is linked to neurodegeneration in multiple sclerosis

RNA oxidation has been implicated in neurodegeneration, but the underlying mechanism for such effects is unclear. Recently, we demonstrated extensive RNA oxidation within the neurons in multiple sclerosis (MS) brain. In this report we identified selectively oxidized mRNAs in neuronal cells that pertained to neuropathological pathways. N-acetyl aspartate transferase 8 like (NAT8L) mRNA is one such transcript, whose translated product enzymatically synthesizes N-acetyl aspartic acid (NAA), a neuronal metabolite important for myelin synthesis. We reasoned that impediment of translation of an oxidized NAT8L mRNA will result in reduction in its cognate protein, thus lowering NAA level. This assertion is directly supported by our studies on a model cellular system, an MS animal model and postmortem human MS brain. Reduced NAA level in the brain hampers myelin integrity making neuronal axons more susceptible to damage, which contributes in MS neurodegeneration. Overall, this work provides a framework for mechanistic understanding of the link between RNA oxidation and neurodegenerative diseases.

molecular biology↗

bioRxiv2019

Identification and Utilization of Copy Number Information for Correcting Hi-C Contact Map of Cancer Cell Line

MotivationHi-C and its variant techniques have been developed to capture the spatial organization of chromatin. Normalization of Hi-C contact maps is essential for accurate modeling and interpretation of genome-wide chromatin conformation. Most Hi-C correction methods are originally developed for normal cell lines and mainly target systematic biases. In contrast, cancer genomes carry multi-level copy number variations (CNVs). Copy number influences interaction frequency between genomic loci. Therefore, CNV-driven bias needs to be corrected for generating euploid-equivalent chromatin contact maps.\n\nResultsWe developed HiCNAtra framework that extracts read depth (RD) signal from Hi-C or 3C-seq reads to generate the high-resolution CNV profile and use this information to correct the contact map. We proposed the \"entire restriction fragment\" counting for better estimation of the RD signal and generation of CNV profiles. HiCNAtra integrates CNV information along with other systematic biases for explicitly correcting the interaction matrix using Poisson regression model. We demonstrated that RD estimation of HiCNAtra recapitulates the whole-genome sequencing (WGS)-derived coverage signal of the same cell line. Benchmarking against OneD method (only explicit method to target CNV bias) showed that HiCNAtra fared better in eliminating the impact of CNV on the contact maps.\n\nAvailability and implementationHiCNAtra is an open source software implemented in MATLAB and is available at https://github.com/AISKhalil/HiCNAtra.

bioinformatics↗

bioRxiv2019

Aneuploidy Spectrum Analysis as a Primer for Copy Number Profiling of Cancer Cells

MotivationHyperploidy and segmental aneuploidy are hallmarks of cancer cells due to chromosome segregation errors and genomic instability. In such situations, accurate aneuploidy profiling of cancer data is critical for calibration of copy number (CN)-detection tools. Additionally, cancer cell populations suffer from different levels of clonal heterogeneity and aneuploidy alterations over time. The degree of heterogeneity adversely affects the segregation of the depth of coverage (DOC) signal into integral CN states. This, in turn, strongly influences the reliability of this data for ploidy profiling and copy number variation (CNV) analysis.\n\nResultsWe developed AStra framework for aneuploidy profiling of cancer data and assessing their suitability for copy number analysis without any prior knowledge of the input sequencing data. AStra estimates the best-fit aneuploidy profile as the spectrum with most genomic segments around integral CN states. We employ this spectrum to extract the CN-associated features such as the homogeneity score (HS), whole-genome ploidy level, and CN correction factor. The HS measures the percentage of genomic regions around CN states. It is used as a reliability assessment of sequencing data for downstream aneuploidy profiling and CNV analysis. We evaluated the accuracy of AStra using 31 low-coverage datasets from 20 cancer cell lines. AStra successfully identified the aneuploidy spectrum of complex cell lines with HS greater than 75%. Benchmarking against nQuire tool showed that AStra is superior in detecting the ploidy level using both low- and high-coverage data. Furthermore, AStra accurately estimated the ploidy of 26/27 strains of MCF7 (hyperploid) cell line which exhibit varied levels of aneuploidy spectrum and heterogeneity. Remarkably, we found that HS is strongly correlated with the doubling time of these strains.\n\nAvailability and implementationAStra is an open source software implemented in Python and is available at https://github.com/AISKhalil/AStra

bioinformatics↗

bioRxiv2019

Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes

MotivationDetection of copy number alterations (CNA) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level structural aberrations of chromosomes that pose challenges to discover CNAs of different length scales with distinct biological origin and function. Although several tools are available to identify CNAs using read depth (RD) of coverage, they fail to distinguish between large-scale and focal alterations due to inaccurate modeling of the RD signal of cancer genomes. These tools are also affected by RD signal variations, pronounced in low-coverage data, which significantly inflate false detection of change points and inaccurate CNA calling.\n\nResultsWe have developed CNAtra to hierarchically discover and classify large-scale and focal copy number gain/loss from whole-genome sequencing (WGS) data. CNAtra provides an analytical and visualization framework for CNV profiling using single sequencing sample. CNAtra first utilizes multimodal distribution to estimate the copy number (CN) reference from the complex RD profile of the cancer genome. We utilized Savitzy-Golay filter and Modified Varri segmentation to capture the change points. We then developed a CN state-driven merging algorithm to identify the large segments with distinct copy number. Next, focal alterations were identified in each large segment using coverage-based thresholding to mitigate the adverse effects of signal variations. We tested CNAtra calls using experimentally verified segmental aneuploidies and focal alterations which confirmed CNAtras ability to detect and distinguish the two alteration phenomena. We used realistic simulated data for benchmarking the performance of CNAtra against other detection tools where we artificially spiked-in CNAs in the original cancer profiles. We found that CNAtra is superior in terms of precision, recall, and f-measure. CNAtra shows the highest sensitivity of 93% and 97% for detecting focal and large-scale alterations respectively. Visual inspection of CNAs showed that CNAtra is the most robust detection tool for low-coverage cancer data.\n\nAvailability and implementationCNAtra is an open source software implemented in MATLAB, and is available at https://github.com/AISKhalil/CNAtra

bioinformatics↗