Biology subjects

Bose, M.

Publications and source records attributed to Bose, M..

32 records · Page 2Linked to original sources

bioRxiv2023

PRDM16 co-operates with LHX2 to shape the human brain

PRDM16 is a dynamic transcriptional regulator of various stem cell niches, including adipocytic, hematopoietic, cardiac progenitors, and neural stem cells. PRDM16 has been suggested to contribute to 1p36 deletion syndrome, one of the most prevalent subtelomeric microdeletion syndromes. We report a patient with a de novo nonsense mutation in the PRDM16 coding sequence, accompanied by lissencephaly and microcephaly features. Human stem cells were genetically modified to mimic this mutation, generating cortical organoids that exhibited altered cell cycle dynamics. RNA sequencing of cortical organoids at day 32 unveiled changes in cell adhesion and WNT-signaling pathways. ChIP-seq of PRDM16 identified binding sites in postmortem human fetal cortex, indicating the conservation of PRDM16 binding to developmental genes in mice and humans, potentially at enhancer sites. A shared motif between PRDM16 and LHX2 was identified and further examined through comparison with LHX2 ChIP-seq data from mice. These results suggested a collaborative partnership between PRDM16 and LHX2 in regulating a common set of genes and pathways in cortical radial glia cells, possibly via their synergistic involvement in cortical development.

developmental biology↗

bioRxiv2023

Overexpression of MUC1 influences the anti-proliferative effect of STAT3-inhibitor Napabucasin in epithelial cancers.

MUC1 is a transmembrane glycoprotein that is overexpressed and aberrantly glycosylated in epithelial cancers. The cytoplasmic tail of MUC1 (MUC1 CT) aids in tumorigenesis by upregulating the expression of multiple oncogenes. Signal transducer and activator of transcription 3 (STAT3) plays a crucial role in several cellular processes and is aberrantly activated in many cancers. In this study, we focus on recent evidence suggesting that STAT3 and MUC1 regulate each others expression in cancer cells in an auto-inductive loop and found that their interaction plays a prominent role in mediating epithelial-to-mesenchymal transition (EMT) and drug resistance. The STAT3 inhibitor Napabucasin was in clinical trials but was discontinued due to futility. We found that higher expression of MUC1 increased the sensitivity of cancer cells to Napabucasin. Therefore, high-MUC1 tumors may have a better outcome to Napabucasin therapy. We report how MUC1 regulates STAT3 activity and provide a new perspective on repurposing the STAT3-inhibitor Napabucasin to improve clinical outcome of epithelial cancer treatment.

cancer biology↗

bioRxiv2023

Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting

The CCR5 (R5) to CXCR4 (X4) coreceptor switch in natural HIV-1 infection is associated with faster progression to AIDS, but the underlying mechanisms remain unclear. The difficulty in capturing the earliest moment of coreceptor switch in vivo limits our understanding of this phenomenon. Here, by tracking the evolution of the transmitted/founder (T/F) HIV-1 in a prospective cohort of individuals at risk for HIV-1 infection identified very early in acute infection, we investigated this process with high resolution. The earliest X4 variants evolved from the R5 tropic T/F strains. Strong X4 usage can be conferred by a single mutation. The mutations responsible for coreceptor switch can confer escape to neutralization and drive X4 variants to replicate mainly in the central memory and naive CD4+ T cells. We propose a novel concept to explain the co-evolution of virus antigenicity and entry tropism termed "escape by shifting". This concept posits that for viruses with receptor or coreceptor flexibility, entry tropism alteration represents a mechanism of immune evasion in vivo.

microbiology↗

bioRxiv2022

Analysis of an Indian colorectal cancer faecal microbiome collection demonstrates universal colorectal cancer-associated patterns, but closest correlation with other Indian cohorts.

It is increasingly being recognised that changes in the gut microbiome have either a causative or associative relationship with colorectal cancer (CRC). However, most of this research has been carried out in a small number of developed countries with high CRC incidence. It is unknown if lower incidence countries such as India have similar microbial associations. Having previously established protocols to facilitate microbiome research in regions with developing research infrastructure, we have now collected and sequenced microbial samples from a larger cohort study of 46 Indian CRC patients and 43 healthy volunteers. When comparing to previous global collections, these samples resemble other Asian samples, with relatively high levels of Prevotella. Predicting cancer status between cohorts shows good concordance. When compared to a previous collection of Indian CRC patients, there was similar concordance, despite different sequencing technologies between cohorts. These results show that there does seem to be a global CRC microbiome, and that some inference between studies is reasonable. However, we also demonstrate that there is definite regional variation, with more similarities between location-matched comparisons. This emphasises the importance of developing protocols and advancing infrastructure to allow as many countries as possible to contribute to microbiome studies of their own populations. ImportanceColorectal cancer is increasing in many countries, thought to be partly due to the interaction between gut bacteria and changing diets. While it is known that populations in different parts of the world have very different gut microbiomes, the study of their role in colorectal cancer is almost exclusively based in the USA and Europe. We have previously shown that there is overlap between the colorectal cancer microbiome in multiple different countries, establishing robust protocols in the process. Here we expand that into a new Indian cohort. We show that while there are similarities between countries, by concentrating on one country, we can uncover important local patterns. This shows the value of sharing expertise and ensuring that work of this nature is possible wherever this disease occurs.

cancer biology↗

bioRxiv2022

In vitro Isolation of Treponema pallidum subsp. pallidum from Fresh and Frozen Needle Aspirates of Primary Experimental Syphilis Lesions

Isolation of Treponema pallidum subsp. pallidum strains still relies on rabbit intratesticular inoculation of clinical samples. Here, we report an alternative isolation approach based on the inoculation of fresh and frozen needle aspirates of primary experimental lesions into culture plates suitable for in vitro propagation of the syphilis agent. SUMMARYWe report on a rabbit-free in vitro isolation approach for syphilis strains that can be easily adapted to clinical specimens.

microbiology↗

bioRxiv2021

A comparative analysis of current phasing and imputation software

Whole-genome data has become significantly more accessible over the last two decades. This can largely be attributed to both reduced sequencing costs and imputation models which make it possible to obtain nearly whole-genome data from less expensive genotyping methods, such as microarray chips. Although there are many different approaches to imputation, the Hidden Markov Model remains the most widely used. In this study, we compared the latest versions of the most popular Hidden Markov Model based tools for phasing and imputation: Beagle 5.2, Eagle 2.4.1, Shapeit 4, Impute 5 and Minimac 4. We benchmarked them on three input datasets with three levels of chip density. We assessed each imputation software on the basis of accuracy, speed and memory usage, and showed how the choice of imputation accuracy metric can result in different interpretations. The highest average concordance rate was achieved by Beagle 5.2, followed by Impute 5 and Minimac 4, using a reference-based approach during phasing and the highest density chip. IQS and R2 metrics revealed that IMPUTE5 obtained better results for low frequency markers, while Beagle 5.2 remained more accurate for common markers (MAF>5%). Computational load as measured by run time was lower for Beagle 5.2 than Impute 5 and Minimac 4, while Minimac utilized the least memory of the imputation tools we compared. ShapeIT 4, used the least memory of the phasing tools examined, even with the highest density chip. Finally, we determined the combination of phasing software, imputation software, and reference panel, best suited for different situations and analysis needs and created an automated pipeline that provides a way for users to create customized chips designed to optimize their imputation results.

genomics↗

bioRxiv2021

EZTraits: a Programmable Tool to Evaluate Multi-site Deterministic Traits

The vast majority of human traits, including many disease phenotypes, are affected by alleles at numerous genomic loci. With a continually increasing set of variants with published clinical disease or biomarker associations, an easy-to-use tool for non-programmers to rapidly screen VCF files for risk alleles is needed. We have developed EZTraits as a tool to quickly evaluate genotype data (e.g., from microarrays) against a set of rules defined by the user. These rules can be defined directly in the scripting language Lua, for genotype calls using variant ID (RS number) or chromosomal position. Alternatively, EZTraits can parse simple and intuitive text including concepts like any or all. Thus, EZTraits is designed to support rapid genetic analysis and hypothesis-testing by researchers, regardless of programming experience or technical background. The software is implemented in C++ and compiles and runs on Linux and MacOS. The source code is available under the MIT license from https://github.com/selfdecode/rd-eztraits Contact: manfred@selfdecode.com

bioinformatics↗

bioRxiv2021

Target-Dependent Coordinated Biogenesis Ensure Cascaded Expression of miRNAs in Activated Macrophage

MicroRNAs (miRNAs) repress protein expression by binding to the 3 UTR of the target mRNAs. By exploring the effect of target mRNA on biogenesis of cognate miRNAs, we have noted miRNA with higher number of binding sites (primary miRNA) coordinates the biogenesis and activity of another miRNA (secondary miRNA) having binding sites on the 3 UTR of a common target mRNA. From the quantitative data obtained from macrophage cells, we detected miR-146a-5p as a "primary" miRNA that coordinates biogenesis of "secondary" miR-125b, miR-21 or miR-142-3p to target new sets of mRNAs to balance the immune response in activated macrophage cells. Interestingly, target dependent coordinated biogenesis of miRNAs, happening on the rough endoplasmic reticulum attached membrane, ensures a cumulative mode of action of primary and secondary miRNAs on the secondary target mRNAs where a cascaded effect of primary miRNA on its secondary targets has been detected. Extensive computational analysis for the presence of coordinated biogenesis pairs of miRNAs in mammalian cells has also allowed us to construct a coordinate biogenesis repository to determine context specific coordinated biogenesis relationships exists for specific pairs of miRNAs in mammalian cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/448041v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@318871org.highwire.dtl.DTLVardef@1f4d3a3org.highwire.dtl.DTLVardef@72adceorg.highwire.dtl.DTLVardef@f0d79e_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LImiRNA with higher number of binding sites (primary miRNA) can coordinates the biogenesis and activity of another miRNA (secondary miRNA) C_LIO_LITarget dependent coordinated biogenesis of miRNAs ensures a cumulative mode of action of primary and secondary miRNAs on the secondary target mRNAs on rER attached polysomes C_LIO_LImiR-146a-5p acts as a "primary" miRNA to coordinate biogenesis of "secondary" miR-125b, miR-21 or miR-142-3p in activated macrophage cells C_LIO_LICoordinate biogenesis balance the immune response in activated macrophage cells by ensuring propagation of primary miRNAs effect to diverse target mRNAs through secondary miRNAs. C_LI

molecular biology↗

bioRxiv2021

Liquid-to-solid phase transition of oskar RNP granules is essential for their function in the Drosophila germline

Asymmetric localization of oskar RNP granules to the oocyte posterior is crucial for abdominal patterning and germline formation of the Drosophila embryo. We show that oskar RNP granules in the oocyte are condensates with solid-like physical properties. Using purified oskar RNA and scaffold proteins Bruno and Hrp48, we confirm in vitro that oskar granules undergo a liquid-to-solid phase transition. Whereas the liquid phase allows RNA incorporation, the solid phase precludes incorporation of additional RNA while allowing RNA-dependent partitioning of specific proteins. Genetic modification of scaffold granule proteins, or tethering the intrinsically disordered region of human Fused in Sarcoma to oskar mRNA, allowed modulation of granule material properties in vivo. The resulting liquid-like properties impaired oskar localization and translation with severe consequences on embryonic development. Our study reflects how physiological phase transitions shape RNA-protein condensates to regulate localization and expression of a maternal RNA that instructs germline formation.

cell biology↗

bioRxiv2020

Repression of MUC1 promotes expansion and suppressive function of myeloid-derived suppressor cells in pancreatic ductal adenocarcinoma and breast cancer murine models.

Myeloid-derived suppressor cells (MDSCs) are immature myeloid cells that are responsible for immunosuppression in tumor microenvironment. Here we report the impact of mucin 1 (MUC1), a transmembrane glycoprotein, on proliferation and functional activity of MDSCs. To determine the role of MUC1 in MDSC phenotype, we analyzed MDSCs derived from wild type (WT) and MUC1-knockout (MUC1KO) mice bearing pancreatic ductal adenocarcinoma KCKO and breast cancer C57MG xenografts. We observed enhanced tumor growth in MUC1KO mice compared to WT mice in both pancreatic KCKO and breast C57MG cancer models due to increased MDSC population and enrichment of Tregs in tumor microenvironment. Our current study shows that knockdown of MUC1 in MDSCs promotes proliferation and immature suppressive phenotype indicated by increased level of iNOS, ARG1 activity and TGF-{beta} secretion under cancer conditions. Increased activity of MDSCs leads to repression of IL-2 and IFN-{gamma} production by T-cells. We were able to find that MDSCs from MUC1KO mice have higher levels of c-Myc and activated pSTAT3 as compared to MUC1 WT mice, that are signaling pathways leading to increased survival, proliferation and prevention of maturation. In summary, MUC1 regulates signaling pathways that maintain immunosuppressive properties of MDSCs. Thus, immunotherapy must target only tumor associated MUC1 on epithelial cells and not MUC1 on hematopoietic cells to avoid expansion and suppressive functions of MDSC.

cancer biology↗

bioRxiv2020

Tumor -Associated MUC1 Regulates TGF-β Signaling and Function in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal human cancers. Transforming Growth Factor Beta (TGF-{beta}) is a cytokine that switches from a tumor-suppressor to a tumor promoter throughout tumor development, by a yet unknown mechanism. Tumor associated MUC1 (tMUC1) is aberrantly glycosylated and overexpressed in >80% of PDAs and is associated with poor prognosis. The cytoplasmic tail of MUC1 (MUC1-CT) interacts with other oncogenic proteins promoting tumor progression and metastasis. We hypothesize that tMUC1 levels regulate TGF-{beta} functions in PDA in vitro and in vivo. We report that high-tMUC1 expression positively correlates to TGF-{beta}RII and negatively to TGF-{beta}RI receptors. In response to TGF-{beta}1, high tMUC1 expressing PDA cells undergo c-Src phosphorylation, and activation of the Erk/MAPK pathway; while low tMUC1 expressing cells activate the Smad2/3 pathway, enhancing cell death. Correspondingly, mice bearing tMUC1-high tumors responded to TGF-{beta}1 neutralizing antibody in vivo showing significantly retarded tumor growth. Analysis of clinical data from TCGA revealed significant alterations in gene-gene correlations in the TGF-{beta} pathway in tMUC1 high versus tMUC1 low samples. This study deepens our understanding of tMUC1-regulated TGF-{beta}s paradoxical function in PDA and establishes tMUC1 as a potential biomarker to predict response to TGF-{beta}-targeted therapies.

cancer biology↗

bioRxiv2020

Modulation of macrophage defense responses by Mycobacterial persistence protein MprA (Rv0981) in human THP-1 cells: effect of single amino acid variation on host-pathogen interactions

M. tuberculosis is one of the most successful human pathogens causing tuberculosis that leads to highest daily morbidity worldwide. The evasion of the host immune responses is an important strategy that M. tuberculosis adopts. MprA (Rv0981), the response regulator of two component system is known for DNA binding activity in the pathogen and its role in persistent infection in the host. MprA is recognized as a late stage antigen during infection. A variant form of the protein MprA with G70S polymorphism (MprA*) is observed in one of our local and in several global clinical isolates of M. tuberculosis. Here we report the nuclear localization of MprA and MprA* in differentiated macrophages. MprA and MprA* increase the expression of TGF-{beta} and IL-10, the immune suppressive cytokines in THP-1 derived macrophage cells. Concurrently the phago-lysosome fusion is significantly reduced as shown by infection with M.bovis BCG. We show that single nucleotide variation in clinical isolates lead to quantitative variations resulting in host immune suppression and support the survival and persistence of the pathogen.

microbiology↗

bioRxiv2020

Correlation of drug resistance with Single Nucleotide Variations through genome analysis and experimental validation in a multi-drug resistant clinical isolate of M.tuberculosis.

BackgroundGenome sequencing and genetic polymorphism analysis of clinical isolates of M.tuberculosis is carried out to gain further insight into molecular pathogenesis and host-pathogen interaction. Therefore the functional evaluation of the effect of single nucleotide variation (SNV) is essential. At the same time, the identification of invariant sequences unique to M.tuberculosis contributes to infection detection by sensitive methods. In the present study, genome analysis is accompanied by evaluation of the functional implication of the SNVs in a MDR clinical isolate VPCI591. ResultBy sequencing and comparative analysis of VPCI591 genome with 1553 global clinical isolates of M.tuberculosis, we identified 143 unique strain specific SNVs. A novel intergenic variation in VPCI591 in the putative promoter/regulatory region mapping between embC (Rv3793) and embA (Rv3794) genes was found to enhance the expression of embAB, which correlates with the high resistance of the VPCI591 to ethambutol. Similarly, the unique combination of three genic SNVs in RNA polymerase {beta} gene (rpoB) in VPCI591 was evaluated for its effect on rifampicin resistance through molecular docking analysis. The comparative genomics also showed that along with variations, there are genes that remain invariant. 173 such genes were identified in our analysis. ConclusionWe have demonstrated that SNVs are not always benign and can also have functional effect. We show that variations bring about quantitative changes in transcription. Our results show the collective effect of SNVs on the structure of protein, impacting the interaction between the target protein and the drug molecule, with rpoB as an example.

microbiology↗

bioRxiv2019

Overcoming Immunological Resistance Enhances the Efficacy of a Novel anti-tMUC1 CAR T Cell Treatment Against Pancreatic Ductal Adenocarcinoma

Chimeric antigen receptor engineered T cells (CAR T cells) have shown remarkable success in treating hematologic cancers. However, this efficacy has yet to translate to treatment in solid tumors. Pancreatic ductal adenocarcinoma (PDA) is a fatal malignancy with poor prognosis. Treatment options are limited and commonly associated with severe side effects. We have developed and characterized a second generation CAR engineered T cell using the light and heavy chain sequence derived from a novel monoclonal antibody, TAB004, that specifically binds the tumor associated antigen, tMUC1. tMUC1 is overexpressed in varying levels on ~85% of all human PDA. We present data showing that the TAB004 derived CAR T cells (tMUC1-CAR T cells) specifically bind to tMUC1 on PDA cells and is cytotoxic against the majority of the PDA cell lines. The tMUC1-CAR T cells do not bind or kill normal epithelial cells. We further demonstrate that the tMUC1-CAR T cells control the growth of orthotopic pancreatic tumors in vivo. PDAs are generally cold tumors with resistance to many standard treatment modalities, thus, it was not surprising that some of the PDA cell lines were refractory to CAR T cell treatment. qPCR analysis of several genes known to be associated with immune resistance revealed overexpression of indoleamine 2, 3-dioxygenases-1 (IDO1), Cyclooxygenase 1 and 2 (COX1 and COX2), Adenosine deaminases acting on RNA (ADAR1) and galectin-9 (Gal-9). We treated resistant PDA cells with a combination of CAR T cells and biological inhibitors of IDO1, COX1/2, ADAR1, and Gal-9. Results showed a significant enhancement of CAR T cell cytotoxicity against PDA cells when inhibiting IDO1, COX1/2, and Gal-9 but not ADAR1 or COX2. Overcoming CAR T cell resistance in PDA is a significant advancement in the field and may lead to future combination therapies that are less toxic but more efficient against this deadly disease.

cancer biology↗