Publications by authors named "Jyotirmoy Chatterjee"

75 Publications

Comprehensive Evaluation of PAXgene Fixation on Oral Cancer Tissues Using Routine Histology, Immunohistochemistry, and FTIR Microspectroscopy.

Biomolecules 2021 Jun 15;11(6). Epub 2021 Jun 15.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.

The choice of tissue fixation is critical for preserving the morphology and biochemical information of tissues. Fragile oral tissues with lower tensile strength are challenging to process for histological applications as they are prone to processing damage, such as tissue tear, wrinkling, and tissue fall-off from slides. This leads to loss of morphological information and unnecessary delay in experimentation. In this study, we have characterized the new PAXgene tissue fixation system on oral buccal mucosal tissue of cancerous and normal pathology for routine histological and immunohistochemical applications. We aimed to minimize the processing damage of tissues and improve the quality of histological experiments. We also examined the preservation of biomolecules by PAXgene fixation using FTIR microspectroscopy. Our results demonstrate that the PAXgene-fixed tissues showed significantly less tissue fall-off from slides. Hematoxylin and Eosin staining showed comparable morphology between formalin-fixed and PAXgene-fixed tissues. Good quality and slightly superior immunostaining for cancer-associated proteins p53 and CK5/6 were observed in PAXgene-fixed tissues without antigen retrieval than formalin-fixed tissues. Further, FTIR measurements revealed superior preservation of glycogen, fatty acids, and amide III protein secondary structures in PAXgene-fixed tissues. Overall, we present the first comprehensive evaluation of the PAXgene tissue fixation system in oral tissues. This study concludes that the PAXgene tissue fixation system can be applied to oral tissues to perform diagnostic molecular pathology experiments without compromising the quality of the morphology or biochemistry of biomolecules.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/biom11060889DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8232633PMC
June 2021

Arecanut-induced fibrosis display dual phases of reorganising glycans and amides in skin extracellular matrix.

Int J Biol Macromol 2021 Jun 20;185:251-263. Epub 2021 Jun 20.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal 721302, India.

The habit of chewing arecanut leads to fibrosis in the oral tissues, which can lead to cancer. Despite high mortality, fibrosis has limited clinical success owing to organ-specific variations, genetic predispositions, and slow progression. Fibrosis is a progressive condition that is unresponsive to medications in the severe phase. To understand underlying macromolecular changes we studied the extracellular matrix's (ECM) key molecular modifications in the early and late phase of arecanut-induced fibrosis in skin. To study the fibrosis, we topically applied arecanut extract on the mice skin. We observed that the matrix changes observe early and late phases based on ECM characteristics including the matrix proteins and the glycans. A spike in the levels of proteoglycans and β-sheet structures are noted in the early phase. A significant drop in the proteoglycans and strengthening of amide covalent interactions is observed in the late phase. Although, almost no physical changes are noticeable only in the early phase; the late phase observes thick collagen bundling and a 4-fold stiffening of the skin tissue. The study indicates that the temporal interplay of proteins and glycans determine the matrix's severity state while opening avenues to research directed towards the phase-specific clinical discovery.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijbiomac.2021.06.093DOI Listing
June 2021

Association of nasopharyngeal viruses and pathogenic bacteria in children and their parents with and without HIV.

Pneumonia (Nathan) 2021 May 5;13(1). Epub 2021 May 5.

School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.

Background: Bacteria and respiratory viruses co-occur in the nasopharynx, and their interactions may impact pathogenesis of invasive disease. Associations of viruses and bacteria in the nasopharynx may be affected by HIV.

Methods: We conducted a nested case-control study from a larger cohort study of banked nasopharyngeal swabs from families with and without HIV in West Bengal India, to look at the association of viruses and bacteria in the nasopharynx of parents and children when they are asymptomatic. Quantitative polymerase chain reaction for 4 bacteria and 21 respiratory viruses was run on 92 random nasopharyngeal swabs from children--49 from children living with HIV (CLH) and 43 from HIV uninfected children (HUC)-- and 77 swabs from their parents (44 parents of CLH and 33 parents of HUC).

Results: Bacteria was found in 67% of children, viruses in 45%, and both in 27% of child samples. Staphylococcus aureus (53%) was the most common bacteria, followed by Streptococcus pneumoniae (pneumococcus) (37%) in children and parents (53, 20%). Regardless of HIV status, viruses were detected in higher numbers (44%) in children than their parents (30%) (p = 0.049), particularly rhinovirus (p = 0.02). Human rhinovirus was the most frequently found virus in both CLH and HUC. Children with adenovirus were at six times increased risk of also having pneumococcus (Odds ratio OR 6, 95% CI 1.12-31.9) regardless of HIV status. In addition, the presence of rhinovirus in children was associated with increased pneumococcal density (Regression coeff 4.5, 1.14-7.9). In CLH the presence of rhinovirus increased the risk of pneumococcal colonization by nearly sixteen times (OR 15.6, 1.66-146.4), and, pneumococcus and S. aureus dual colonization by nearly nine times (OR 8.7).

Conclusions: Children more frequently carried viruses regardless of HIV status. In CLH the presence of rhinovirus, the most frequently detected virus, significantly increased co-colonization with pneumococcus and S. aureus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s41479-021-00088-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096464PMC
May 2021

Label-Free Method Development for Hydroxyproline PTM Mapping in Human Plasma Proteome.

Protein J 2021 Apr 11. Epub 2021 Apr 11.

Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.

Post-translational modifications (PTMs) impart structural heterogeneities that can alter plasma proteins' functions in various pathophysiological processes. However, the identification and mapping of PTMs in untargeted plasma proteomics is still a challenge due to the presence of diverse components in blood. Here, we report a label-free method for identifying and mapping hydroxylated proteins using tandem mass spectrometry (MS/MS) in the human plasma sample. Our untargeted proteomics approach led us to identify 676 de novo sequenced peptides in human plasma that correspond to 201 proteins, out of which 11 plasma proteins were found to be hydroxylated. Among these hydroxylated proteins, Immunoglobulin A1 (IgA1) heavy chain was found to be modified at residue 285 (Pro to Hyp), which was further validated by MS/MS study. Molecular dynamics (MD) simulation analysis demonstrated that this proline hydroxylation in IgA1 caused both local and global structural changes. Overall, this study provides a comprehensive understanding of the protein profile containing Hyp PTMs in human plasma and shows the future perspective of identifying and discriminating Hyp PTM in the normal and the diseased proteomes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10930-021-09984-7DOI Listing
April 2021

Quantitative in situ imaging and grading of oral precancer with attenuation corrected-optical coherence tomography.

Oral Oncol 2021 Jun 16;117:105216. Epub 2021 Feb 16.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur, India.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.oraloncology.2021.105216DOI Listing
June 2021

Pathophysiological relationship between hypoxia associated oxidative stress, Epithelial-mesenchymal transition, stemness acquisition and alteration of Shh/ Gli-1 axis during oral sub-mucous fibrosis and oral squamous cell carcinoma.

Eur J Cell Biol 2021 Jan 23;100(1):151146. Epub 2020 Dec 23.

School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India.

Oral sub-mucous fibrosis (OSF) is a pathophysiological state of oral cavity or oropharynx having a high chance of conversion to oral squamous cell carcinoma (OSCC). It involves fibrotic transformation of sub-epithelial matrix along with epithelial abnormalities. The present work aims to unveil the mechanistic domain regarding OSF to OSCC conversion exploring the scenario of hypoxia associated oxidative stress, epithelial-mesenchymal transition (EMT), metastasis and stemness acquisition. The study involves histopathological analysis of the diseased condition along with the exploration of oxidative stress status, assessment of mitochondrial condition, immunohistochemical analysis of HIF-1α, E-cadherin, vimentin, ERK, ALDH-1, CD133, Shh, Gli-1 and survivin expressions in the oral epithelial region together with the quantitative approach towards collagen deposition in the sub-epithelial matrix. Oxidative stress was found to be associated with type-II EMT in case of OSF attributing the development of sub-epithelial fibrosis and type-III EMT in case of OSCC favoring malignancy associated metastasis. Moreover, the acquisition of stemness during OSCC can also be correlated with EMT. Alteration of Shh and Gli-1 expression pattern revealed the mechanistic association of hypoxia with the phenotypic plasticity and disease manifestation in case of OSF as well as OSCC. Shh/ Gli-1 signaling can also be correlated with survivin mediated cytoprotective phenomenon under oxidative stress. Overall, the study established the correlative network of hypoxia associated oxidative stress, EMT and manifestation of oral pre-cancerous and cancerous condition in a holistic approach that may throw rays of hope in the therapeutic domain of the concerned diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejcb.2020.151146DOI Listing
January 2021

Road Map to Understanding SARS-CoV-2 Clinico-Immunopathology and COVID-19 Disease Severity.

Pathogens 2020 Dec 23;10(1). Epub 2020 Dec 23.

Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India.

SARS-CoV-2, a novel coronavirus, was first identified in Wuhan, China in December 2019. The rapid spread of the virus worldwide prompted the World Health Organization (WHO) to declare COVID-19 a pandemic in March 2020. COVID-19 discontinuing's a global health crisis. Approximately 80% of the patients infected with SARS-CoV-2 display undetectable to mild inflammation confined in the upper respiratory tract. In remaining patients, the disease turns into a severe form affecting almost all major organs predominantly due to an imbalance of innate and adaptive arms of host immunity. The purpose of the present review is to narrate the virus's invasion through the system and the host's reaction. A thorough discussion on disease severity is also presented regarding the behavior of the host's immune system, which gives rise to the cytokine storm particularly in elderly patients and those with comorbidities. A multifaceted yet concise description of molecular aspects of disease progression and its repercussion on biochemical and immunological features in infected patients is tabulated. The summary of pathological, clinical, immunological, and molecular accounts discussed in this review is of theranostic importance to clinicians for early diagnosis of COVID-19 and its management.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/pathogens10010005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823523PMC
December 2020

Attenuation corrected-optical coherence tomography for quantitative assessment of skin wound healing and scar morphology.

J Biophotonics 2021 04 29;14(4):e202000357. Epub 2020 Dec 29.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India.

Imaging the structural modifications of underlying tissues is vital to monitor wound healing. Optical coherence tomography (OCT) images high-resolution sub-surface information, but suffers a loss of intensity with depth, limiting quantification. Hence correcting the attenuation loss is important. We performed swept source-OCT of full-thickness excision wounds for 300 days in mice skin. We used single-scatter attenuation models to determine and correct the attenuation loss in the images. The phantom studies established the correspondence of corrected-OCT intensity (reflectivity) with matrix density and hydration. We histologically validated the corrected-OCT and measured the wound healing rate. We noted two distinct phases of healing-rapid and steady-state. We also detected two compartments in normal scars using corrected OCT that otherwise were not visible in the OCT scans. The OCT reflectivity in the scar compartments corresponded to distinct cell populations, mechanical properties and composition. OCT reflectivity has potential applications in evaluating the therapeutic efficacy of healing and characterizing scars.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jbio.202000357DOI Listing
April 2021

Wound healing efficacy of Jamun honey in diabetic mice model through reepithelialization, collagen deposition and angiogenesis.

J Tradit Complement Med 2020 Nov 10;10(6):529-543. Epub 2019 Oct 10.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.

Diabetic patients are frequently afflicted with impaired wound healing where linear progression of molecular and cellular events compromised. Despite of meaningful progress in diabetic treatment, management of diabetic chronic wounds is still challenging. Jamun () honey may be a promising candidate for diabetic wound healing and need to explore in detail. So present study was designed to evaluate the efficacy of Jamun honey (JH) for diabetic wound healing in wound (primary fibroblasts) model and in of diabetic mice (Streptozotocin induced) model. The fibroblast cell model was studied for migratory behaviour and myofibrolasts infiltration under honey interventions scratch/migration assay, immuno-cytochemistry and western blot. We applied FDA approved Manuka honey (MH) as positive control and JH as test honey to evaluate wound re-epithelialization, sub-epithelial connective tissue modification and angiogenesis histo-pathological and immuno-histochemical analysis. JH (0.1% v/v) dilution has notably improved wound closure, migration with concomitant α-SMA expressions . Topical application of JH in diabetic mice model showed significant (*p ≤ 0.05) wound closure, reepithelialization, collagen deposition (I/III) and balanced the myofibroblasts formation. It also modulated vital angiogenic markers ( HIF-1α, VEGF, VEGF R-II) significantly (*p ≤ 0.05). All these observations depicted that JH promotes sequential stages of wound healing in diabetic mice model. The results of the present study established Jamun honey as good as Manuka honey considering wound closure, re-epithelialization, collagen deposition and pro-angiogenic potential.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jtcme.2019.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7588338PMC
November 2020

Epithelial Distribution of E-Cadherin, p63, and Mitotic Figures in ApoTome Images to Determine the Oncogenic Potentiality of Oral Submucous Fibrosis.

Microsc Microanal 2020 12;26(6):1198-1210

Centre for Biomaterials, Cellular and Molecular Theranostics, Vellore Institute of Technology, Room No. 402, ALM Building, Vellore632014, Tamil Nadu, India.

The exact process of the malignant conversion of oral submucous fibrosis (OSF) to oral cancer is not fully understood. This study aimed to detect and analyze E-cadherin expression, p63 expression, and number of mitotic figures, all correlated to cancer development, in ApoTome images of oral tissues to determine the oncogenic potentiality of OSF. ApoTome images of the study groups (6 normal, 16 OSF with dysplasia, and 10 OSF without dysplasia) were recorded. Cytoplasmic and membranous E-cadherin expression, breakages of the cell membrane, and p63 expression were detected in MATLAB 2016b. The number of mitotic figures detected by MATLAB was correlated with the number of chromosomes detected by ImageJ. A Mann–Whitney U test was done to determine a significant difference between the study groups for cytoplasmic and membranous E-cadherin distribution points. Statistical significant differences were found for cytoplasmic E-cadherin distribution between normal and OSF (with dysplasia) (p = 0.0278). There was an increase in mitotic figures, p63 expression, and cytoplasmic E-cadherin expression and a decrease in membranous E-cadherin expression from normal to diseased condition. Hence, automated detection and quantification of E-cadherin, p63, and mitotic figures in ApoTome images of oral biopsies can help in determining the oncogenic potentiality of OSF.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1017/S1431927620024538DOI Listing
December 2020

Structural mechanics modeling reveals stress-adaptive features of cutaneous scars.

Biomech Model Mechanobiol 2021 Feb 12;20(1):371-377. Epub 2020 Sep 12.

School of Medical Science and Technology, IIT Kharagpur, Kharagpur, India.

The scar is a predominant outcome of adult mammalian wound healing despite being associated with partial function loss. Here in this paper, we have described the structure of a full-thickness normal scar as a "di-fork" with dual biomechanical compartments using in vivo and ex vivo experiments. We used structural mechanics simulations to model the deformation fields computationally and stress distribution in the scar in response to external forces. Despite its loss of tissue components, we have found that the scar has stress-adaptive features that cushion the underlying tissues from external mechanical impacts. Thus, this new finding can motivate research to understand the biomechanical advantages of a scar in maintaining the primary function of the skin, i.e., mechanical barrier despite permanent loss of some tissues and specialized functions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10237-020-01384-7DOI Listing
February 2021

Dual cross-linked honey coupled 3D antimicrobial alginate hydrogels for cutaneous wound healing.

Mater Sci Eng C Mater Biol Appl 2020 Nov 20;116:111218. Epub 2020 Jun 20.

Instability and Soft Patterning Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India. Electronic address:

We report potentiation of healing efficacy of alginate by value addition at its structural level. Dual crosslinked (ionically and covalently) sodium alginate hydrogel coupled with honey (HSAG) brings about an intermediate stiffness in the fabric, confers consistent swelling property and limits erratic degradation of the polymer which ultimately provides conducive milieu to cellular growth and proliferation. In this work honey concentrations in HSAGs are varied from 2% to 10%. FTIR, XRD and nanoindentation studies on the HSAGs exhibited physicochemical integrity. In vitro degradation study provided the crucial finding on 4% HSAG having controlled degradation rate up to 12 days with a weight loss of 87.36 ± 1.14%. This particular substrate also has an ordered crystalline surface morphology with decent cellular viability (HaCaT and 3T3) and antimicrobial potential against Methicillin Resistant Staphylococcus aureus (MRSA) and Escherichia coli. The in vivo wound contraction kinetics on murine models (4% HSAG treated wound contraction: 94.56 ± 0.1%) has been monitored by both invasive (histopathology) and noninvasive (Swept Source Optical Coherence Tomography) imaging and upon corroborating them it evidenced that 4% HSAG treated wound closure achieved epithelial thickness resembling to that of unwounded skin. Thus, the work highlights structurally modified alginate hydrogel embedded with honey as a potential antimicrobial healing agent.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.msec.2020.111218DOI Listing
November 2020

Multifractal Alterations in Oral Sub-Epithelial Connective Tissue During Progression of Pre-Cancer and Cancer.

IEEE J Biomed Health Inform 2021 01 5;25(1):152-162. Epub 2021 Jan 5.

Bright-field microscopy (BFM) encrypts the optical transillumination profile of the transmitted light attenuated by the complex micro-structural tissue convolutions, manifested by the dense and compact regions of the specimen under examination. The connotations of idiosyncratic tissue interaction dynamics with the onset of pre-cancerous activity are encoded in the BFM acquired oral mucosa histopathological images (OMHI). In the present study, our analysis is focused on the sub-epithelium region of the oral mucosa, which has high clinical significance but sparsely explored in the literature from the textural domain. Histopathology being the gold-standard technique till date, we have used the light microscopic histopathology images for tissue characterization. The tissue-index transmission patches (TITP) from the sub-epithelium region are cropped under the guidance of oral onco-pathologists. After that, the TITPs are characterized for its multi-scale spatial-deformation dynamics, while keeping the intrinsic anisotropic geometry, and local contour connectivity within tolerable limits. With recent studies exhibiting multifractal's potency in diverse biological system analysis, here, we exploit the 2D multifractal detrended fluctuation analysis (2D-MFDFA) on TITPs for exploring a discriminative set of multifractal signatures for healthy, oral potentially malignant disorders and oral cancer tissue sample. The predictive model's competency is validated on an experimentally collected corpus of TITP samples and substantiated via confirmatory data statistics and analysis, showing its inter-class segregation efficacy. Moreover, the 2D-MFDFA analysis evinces the complex multifractal patterns in TITPs, which is due to the presence of composite long-range correlations in the oral mucosa tissue fabric.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/JBHI.2020.2997875DOI Listing
January 2021

Impact of intercellular connectivity on epithelial mesenchymal transition plasticity.

Biochim Biophys Acta Mol Cell Res 2020 10 23;1867(10):118784. Epub 2020 Jun 23.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India.

Epithelial mesenchymal transition (EMT) in development, tissue repair and carcinogenesis involves cellular plasticity with varying degrees of epithelial and mesenchymal properties. Several recent studies have focused on EMT phenotypic dynamism; however, information on cellular interaction in the context of EMT is inadequate. In our previous study, we investigated EMT phenotypic plasticity and anticipated it as a population driven interactive process. Present study has characterized cellular connectivity as a representative of interactivity during EMT in epithelial normal and cancer cell. It has also explored dynamism of connectivity and phenotype employing Markov model. Further, plasticity was substantiated with cell surface microvilli and molecular marker. The study unveiled interplay between phenotype and connectivity too. Findings have revealed that intercellular connectivity fueled EMT plasticity and its dynamism was more prominent in cancer population. However, normal cells are more vibrant in transition and phenotypic plasticity. We have proposed connectivity plasticity as a hallmark of EMT and needs to be studied in depth. Present study also paves the way in translating in vitro EMT findings in histopathological practices.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbamcr.2020.118784DOI Listing
October 2020

Manipulating magnetoelectric energy landscape in multiferroics.

Nat Commun 2020 Jun 5;11(1):2836. Epub 2020 Jun 5.

Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA.

Magnetoelectric coupling at room temperature in multiferroic materials, such as BiFeO, is one of the leading candidates to develop low-power spintronics and emerging memory technologies. Although extensive research activity has been devoted recently to exploring the physical properties, especially focusing on ferroelectricity and antiferromagnetism in chemically modified BiFeO, a concrete understanding of the magnetoelectric coupling is yet to be fulfilled. We have discovered that La substitutions at the Bi-site lead to a progressive increase in the degeneracy of the potential energy landscape of the BiFeO system exemplified by a rotation of the polar axis away from the 〈111〉 towards the 〈112〉 discretion. This is accompanied by corresponding rotation of the antiferromagnetic axis as well, thus maintaining the right-handed vectorial relationship between ferroelectric polarization, antiferromagnetic vector and the Dzyaloshinskii-Moriya vector. As a consequence, La-BiFeO films exhibit a magnetoelectric coupling that is distinctly different from the undoped BiFeO films.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-16727-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275047PMC
June 2020

ROS and oncogenesis with special reference to EMT and stemness.

Eur J Cell Biol 2020 Apr 19;99(2-3):151073. Epub 2020 Mar 19.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.

Elevation of the level of intracellular reactive oxygen species (ROS) has immense implication in the biological system. On the one hand, ROS promote the signaling cascades for the maintenance of normal physiological functions, the phenomenon referred to as redox biology, and on the other hand increased ROS can cause damages to the cellular macromolecules as well as genetic material, the process known as oxidative stress. Oxidative stress acts as an etiological factor for wide varieties of pathologies, cancer being one of them. ROS is regarded as a "double-edged sword" with respect to oncogenesis. It can suppress as well as promote the malignant progression depending on the type of signaling pathway it uses. Moreover, the attribution of ROS in promoting phenotypic plasticity as well as acquisition of stemness during neoplasia has become a wide area of research. The current review discussed all the aspects of ROS in the perspective of tumor biology with special reference to epithelial-mesenchymal transition (EMT) and cancer stem cells.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejcb.2020.151073DOI Listing
April 2020

Impact of pneumococcal conjugate vaccine on the carriage density of and in children living with HIV: a nested case-control study.

Hum Vaccin Immunother 2020 08 29;16(8):1918-1922. Epub 2020 Jan 29.

School of Medical Science & Technology, Indian Institute of Technology Kharagpur , Kharagpur, India.

Nasopharyngeal colonization density of (pneumococcus) is associated with disease severity and transmission. Little is known about the density of pneumococcal carriage in children with HIV (CLH). Pneumococcal vaccines may impact the density of pneumococcus and competing microbes within the nasopharynx. We examined the impact of one dose of PCV13 on carriage density of pneumococcus and , in CLH, HIV-uninfected children (HUC), and their unvaccinated parents. We conducted a pilot-nested case-control study, within a larger prospective cohort study, on the impact of PCV13, in families in West Bengal India. Quantitative real-time PCR was run on 147 nasopharyngeal swabs from 27 CLH and 23 HUC, and their parents, before and after PCV13 immunization. CLH had higher median pneumococcal carriage density, compared to HUC: 6.28 × 10 copies/mL vs. 2.11 × 10 copies/mL ( = .005). Following one dose of PCV13, pneumococcal densities dropped in both groups, with an increase in carriage to 80% from 48% in CLH, and to 60% in HUC from 25%. While limited in sample size, this pilot study shows that CLH carried higher densities of pneumococcus. PCV13 was associated with a decrease in pneumococcal density and a temporal increase in carriage regardless of HIV status.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/21645515.2019.1706411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7482878PMC
August 2020

Evaluating the role of hsa-miR-200c in reversing the epithelial to mesenchymal transition in prostate cancer.

Gene 2020 Mar 21;730:144264. Epub 2019 Nov 21.

Department of Biochemistry, University of Calcutta, Kolkata 700019, West Bengal, India. Electronic address:

Deregulated epithelial-to-mesenchymal transition constitutes one of the major aspects of cancer progression. In this study, to identify key molecular principles of EMT pathway in prostate carcinogenesis, an elaborate gene expression profiling was conducted by qRT-PCR and Western blot analyses. A preponderance of mesenchymal trait was observed in the pathological samples of prostate cancer. To simulate an appropriate in vitro model, PC3 cell line was subjected to hypoxic stress, which resulted in elevated expression of vimentin along with EMT-mediating transcription factors Zeb1 and Slug. To conciliate this mesenchymal behavior of PC3 cells, hsa-miR-200c was deliberately overexpressed which led to a marked reduction of cell motility and expression of vimentin, N-cadherin, Zeb1 and Slug with concurrent increase in level of β-catenin. hsa-miR-200c was demonstrated to appease hypoxia-aggravated changes in cellular morphology by coordinated repression of vimentin, Zeb1 and Slug. Mode of action for hsa-miR-200c was mediated through transcriptional repression of Zeb1 and Slug interacting with E-box sequences in the vimentin promoter as documented by promoter assay. This ability of hsa-miR-200c to reclaim epithelial traits leads to the anticipation that molecular reprogramming of Zeb1-Slug/vimentin axis may relieve aggressiveness of prostate cancer.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gene.2019.144264DOI Listing
March 2020

Elucidation of Differential Nano-Textural Attributes for Normal Oral Mucosa and Pre-Cancer.

Microsc Microanal 2019 10;25(5):1224-1233

School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, West Bengal, India.

Computational analysis on altered micro-nano-textural attributes of the oral mucosa may provide precise diagnostic information about oral potentially malignant disorders (OPMDs) instead of an existing handful of qualitative reports. This study evaluated micro-nano-textural features of oral epithelium from scanning electron microscopic (SEM) images and the sub-epithelial connective tissue from light microscopic (LM) and atomic force microscopic (AFM) images for normal and OPMD (namely oral sub-mucous fibrosis, i.e., OSF). Objective textural descriptors, namely discrete wavelet transform, gray-level co-occurrence matrix (GLCM), and local binary pattern (LBP), were extracted and fed to standard classifiers. Best classification accuracy of 87.28 and 93.21%; sensitivity of 93 and 96%; specificity of 80 and 91% were achieved, respectively, for SEM and AFM. In the study groups, SEM analysis showed a significant (p < 0.01) variation for all the considered textural descriptors, while for AFM, a remarkable alteration (p < 0.01) was only found in GLCM and LBP. Interestingly, sub-epithelial collagen nanoscale and microscale textural information from AFM and LM images, respectively, were complementary, namely microlevel contrast was more in normal (0.251) than OSF (0.193), while nanolevel contrast was more in OSF (0.283) than normal (0.204). This work, thus, illustrated differential micro-nano-textural attributes for oral epithelium and sub-epithelium to distinguish OPMD precisely and may be contributory in early cancer diagnostics.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1017/S1431927619014867DOI Listing
October 2019

Segmentation and analysis of surface characteristics of oral tissues obtained by scanning electron microscopy to differentiate normal and oral precancerous condition.

Tissue Cell 2019 Aug 16;59:82-87. Epub 2019 Jul 16.

Centre for Biomaterials, Cellular and Molecular Theranostics, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India. Electronic address:

Abnormal epithelial stratification is a sign of oral dysplasia and hence evaluation of surface characteristics of oral epithelial region can help in detection of cancerous progression. Surface characteristics can be better visualised by Scanning Electron Microscopy (SEM) in comparison to light microscopy. In our study we have developed automated image processing algorithms i.e. Gaussian with median filtering and Gradient filtering, using MATLAB 2016b, to segment the surface characteristics i.e. the ridges and pits in the SEM images of oral tissue of normal (13 samples) and Oral Submucous Fibrosis (OSF) (36 samples) subjects. After segmentation, quantitative measurement of the parameters like area, thickness and textural features like entropy, contrast and range filter of ridges as well as area of pit and the ratio of area of ridge vs. area of pit was done. Statistical significant differences were obtained in between normal and OSF study groups for thickness (p=0.0107), entropy (p<0.00001) and contrast of ridge (p<0.00001) for Gaussian with median filtering and for all the parameters except thickness of the ridge(p=1.386), for Gradient filtering. Thus, computer aided image processing by Gradient filter followed by quantitative measurement of the surface characteristics provided precise differentiation between normal and precancerous oral condition.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tice.2019.07.004DOI Listing
August 2019

Computer-assisted delineation of hematoma from CT volume using autoencoder and Chan Vese model.

Int J Comput Assist Radiol Surg 2019 Feb 30;14(2):259-269. Epub 2018 Oct 30.

Electrical Engineering, Indian Institute of Technology, Kharagpur, India.

Purpose: To reduce the inter- and intra- rater variability as well as time and effort, a method for computer-assisted delineation of hematoma is proposed. Delineation of hematoma is done for further automated analysis such as the volume of hematoma, anatomical location of hematoma, etc. for proper surgical planning.

Methods: Fuzzy-based intensifier was used as a pre-processing technique for enhancing the computed tomography (CT) volume. Autoencoder was trained to detect the CT slices with hematoma for initialization. Then active contour Chan-Vese model was used for automated delineation of hematoma from CT volume.

Results: The proposed algorithm was tested on 48 hemorrhagic patients. Two radiologists have independently segmented the hematoma manually from CT volume. The intersection of two volumes was used as ground-truth for comparison with the segmentation performed by the proposed method. The accuracy was determined by using similarity matrices. The result of sensitivity, positive predictive value, Jaccard index and Dice similarity index were calculated as 0.71 ± 0.12, 0.73 ± 0.18, 0.55 ± 0.14, and 0.70 ± 0.12 respectively.

Conclusions: A new approach for delineation of hematoma is proposed. The algorithm works well with the whole volume. Similarity indices of the proposed method are comparable with the existing state of art.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11548-018-1873-9DOI Listing
February 2019

Novel multifunctional RKKY coupling layer for ultrathin perpendicular synthetic antiferromagnet.

Sci Rep 2018 Aug 6;8(1):11724. Epub 2018 Aug 6.

Univ. Grenoble Alpes, CEA, CNRS, Grenoble-INP, INAC-SPINTEC, Grenoble, France.

A novel multi-functional antiferromagnetic coupling layer (MF-AFC) combining Ru and W is revealed to realize an extremely thin (3.8 nm), back-end-of-line compatible as well as magnetically and electrically stable perpendicular synthetic antiferromagnetic layer (pSAF), essential for spintronic memory and logic device applications. In addition to achieving antiferromagnetic RKKY coupling, this MF-AFC also acts as a Boron sink and texture-breaking layer. A detailed optimization of the thickness of the various involved layers has been carried out to obtain extremely thin-pSAF reference layer with stable magnetic properties, which enables the realization of sub-20 nm STT-MRAM cells. Two important advantages are provided by this ultrathin reference layer: the easing of the reference layer etching and the minimization of the dipolar field acting on the storage layer magnetization.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-29913-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6079069PMC
August 2018

Endorsing cellular competitiveness in aberrant epithelium of oral submucous fibrosis progression: neighbourhood analysis of immunohistochemical attributes.

Histochem Cell Biol 2018 Jul 23;150(1):61-75. Epub 2018 Apr 23.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721 302, India.

Epithelial abnormality during the transformation of oral submucous fibrosis (OSF) into oral squamous cell carcinoma has been well studied and documented. However, the differential contribution of atrophy and hyperplasia for malignant potentiality of OSF is yet to be resolved. Existing diagnostic conjectures lack precise diagnostic attributes which may be effectively resolved by substantiation of specific molecular pathology signatures. Present study elucidates existence of cellular competitiveness in OSF conditions using computer-assisted neighbourhood analysis in quantitative immunohistochemistry (IHC) framework. The concept of field cancerization was contributory in finding correspondence among neighbouring cells of epithelial layers with reference to differential expression of cardinal cancer-related genes [c-Myc (oncogene), p53 (tumour suppressor), and HIF-1α (hypoxia regulator)] which are known to be important sensors in recognizing cellular competitive interface. Our analyses indicate that different states of OSF condition may be associated with different forms of competitiveness within epithelial neighbouring cells which might be responsible to shape the present and future of the pre-malignant condition. Analytical findings indicated association of atrophic epithelium with stress-driven competitive environment having low c-Myc, high-p53, and stable HIF-1α (the looser cells) which undergo apoptosis. Whereas, the cells with high c-Myc (winner cells) give rise to hyperplastic epithelium via possible mutation in p53. The epithelial dysplasia plausibly occurs due to clonal expansion of c-Myc and p53 positive supercompetitor cells. Present study proposes quantitative IHC along with neighbourhood analysis which might help us to dig deeper on to the interaction among epithelial cell population to provide a better understanding of field cancerization and malignant transformation of pre-malignancy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00418-018-1671-zDOI Listing
July 2018

Immunohistochemical evaluation of prime molecules in cervical lesions towards assessment of malignant potentiality.

J Cancer Res Ther 2018 Jan-Mar;14(2):377-381

Department of Medical Science and Technology, Indian Institute of Technology, Kharagpur, India.

Objective: A comparative immunohistochemical evaluation of p63, CD105, and E-cadherin expression pattern in histopathologically confirmed normal cervical epithelium (NCM), dysplastic cervical epithelium (DYS) and squamous cell carcinoma (SCC) of uterine cervix towards assessing malignant potentiality of the precancerous condition.

Materials And Methods: The biopsies from cervical mucosa (normal, dysplasia, and cancer) were studied by routine hematoxylin and eosin (H and E) and by immunohistochemistry for p63, E-cadherin, and CD105 expression. The expressions of these molecules were assessed in a semiquantitative way by (i) counting p63 cell population and distribution, (ii) intensity scoring of E-cadherin along the expression path, and (iii) measuring CD105 expression density.

Result: p63 cells were highest in carcinomas followed by dysplasia and normal. An abrupt increase in CD105 expression was observed through change of normal to dysplasia and cancer. A decrease in membranous E-cadherin expression was noticed in the transformation from normal to precancer and cancers.

Conclusion: The malignant potential of the dysplastic conditions is likely to be correlated with upregulation in p63 and CD105 expression and a simultaneous downregulation of membranous E-cadherin.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4103/0973-1482.158029DOI Listing
August 2018

Spectropathology-corroborated multimodal quantitative imaging biomarkers for neuroretinal degeneration in diabetic retinopathy.

Clin Ophthalmol 2017 22;11:2073-2089. Epub 2017 Nov 22.

Multimodal Imaging and Computing for Theranostics Laboratory, School of Medical Science and Technology, Indian Institute of Technology-Kharagpur, Kharagpur, West Bengal, India.

Introduction: Image-based early detection for diabetic retinopathy (DR) needs value addition due to lack of well-defined disease-specific quantitative imaging biomarkers (QIBs) for neuroretinal degeneration and spectropathological information at the systemic level. Retinal neurodegeneration is an early event in the pathogenesis of DR. Therefore, development of an integrated assessment method for detecting neuroretinal degeneration using spectropathology and QIBs is necessary for the early diagnosis of DR.

Methods: The present work explored the efficacy of intensity and textural features extracted from optical coherence tomography (OCT) images after selecting a specific subset of features for the precise classification of retinal layers using variants of support vector machine (SVM). Fourier transform infrared (FTIR) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy were also performed to confirm the spectropathological attributes of serum for further value addition to the OCT, fundoscopy, and fluorescein angiography (FA) findings. The serum metabolomic findings were also incorporated for characterizing retinal layer thickness alterations and vascular asymmetries.

Results: Results suggested that OCT features could differentiate the retinal lesions indicating retinal neurodegeneration with high sensitivity and specificity. OCT, fundoscopy, and FA provided geometrical as well as optical features. NMR revealed elevated levels of ribitol, glycerophosphocholine, and uridine diphosphate -acetyl glucosamine, while the FTIR of serum samples confirmed the higher expressions of lipids and β-sheet-containing proteins responsible for neoangiogenesis, vascular fragility, vascular asymmetry, and subsequent neuroretinal degeneration in DR.

Conclusion: Our data indicated that disease-specific spectropathological alterations could be the major phenomena behind the vascular attenuations observed through fundoscopy and FA, as well as the variations in the intensity and textural features observed in OCT images. Finally, we propose a model that uses spectropathology corroborated with specific QIBs for detecting neuroretinal degeneration in early diagnosis of DR.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2147/OPTH.S140110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703157PMC
November 2017

Identification of α-enolase as a prognostic and diagnostic precancer biomarker in oral submucous fibrosis.

J Clin Pathol 2018 Mar 18;71(3):228-238. Epub 2017 Aug 18.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India.

Aims: Diagnostic ambiguities regarding the malignant potentiality of oral submucous fibrosis (OSF), an oral precancerous condition having dysplastic and non-dysplastic isoforms are the major failure for early intervention of oral squamous cell carcinoma (OSCC) patients. Our goal is to identify proteomic signatures from biopsies that can be used as precancer diagnostic marker for patient suffering from OSF.

Methods: The high throughput techniques adopting de novo peptide sequencing (1D SDS-PAGE coupled nanoLC MALDI tandem mass spectrometry (MS/MS)-based peptide mass fingerprint), immunohistochemistry (IHC), Western blot (WB) and real-time PCR (RT-PCR) analysis are considered for such biomarker identification and multilevel validations.

Results: Alpha-enolase is identified as an overexpressed protein in biopsies of oral submucous fibrosis with dysplasia (OSFWD) compared with oral submucous fibrosis without dysplasia (OSFWT) and normal oral mucosa (NOM). Total proteome analysis of an overexpressed protein band around 47 kDa of OSFWD identifies 334 peptides corresponding to 61 human proteins. Among them α-enolase is identified as a prime protein with highest number of peptides (44 out of 334 peptides) and sequence coverage (66.4%). Furthermore, RT-PCR, WB and IHC analysis also show mRNA and tissue level upregulation of α-enolase in OSFWD validating α-enolase as precancer marker.

Conclusions: This study for the first time identifies and validates α-enolase as a novel biomarker for early diagnosis of malignant potentiality of OSF. Hence, the identified protein marker, α-enolase can help in early therapeutic intervention of OSF patients leading to the reduction of patient's pain, treatment cost and enhancement of patient's quality of life.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/jclinpath-2017-204430DOI Listing
March 2018

Honey Extracted Polyphenolics Reduce Experimental Hypoxia in Human Keratinocytes Culture.

J Agric Food Chem 2017 May 20;65(17):3460-3473. Epub 2017 Apr 20.

School of Medical Science and Technology, Indian Institute of Technology Kharagpur , Kharagpur 721302, West Bengal, India.

Hypoxic assault affects fundamental cellular processes and generates oxidative stress on healthy cells/molecules. Honey extracted polyphenolics (HEP) as a natural antioxidant reduced hypoxic cytotoxicity in this study. Different honey samples were physicochemically characterized to identify preferred (jamun) honey [pH 3.55 ± 0.04, conductivity (μs/cm) = 6.66 ± 0.14, water content % (w/w) = 14.70 ± 0.35, total solid content % (w/w) = 85.30 ± 0.35, phenol content (mg GAE/100 g) = 403.55 ± 0.35, flavonoid content (mg QE/100 g) = 276.76 ± 4.10, radical scavenging activity (% 500 μL) = 147.75 ± 3.13, catalase activity (absorbance at 620 nm) = 0.226 ± 0.01]. HEP was tested in different doses on hypoxic and normoxic cells (HaCaT) using viability and antioxidant assays. Cardinal molecular expressions such as cadherin-catenin-cytoskeleton complex (namely, E-cadherin, β-catenin, and F-actin), hypoxia marker (Hif 1 α), proliferation marker (Ki67), and epithelial master regulator (p63) were studied by immuno-cytochemisty (ICC) and qRT-PCR. The 0.063 mg/mL HEP demonstrated better vitality and functionality of HaCaT cells as per viability assay (*, P < 0.01) even under hypoxia. ICC and qRT-PCR observations indicated restoration of cellular survival and homeostasis under 0.063 mg/mL HEP after hypoxic assault. Furthermore, major spectral changes for nucleic acid and membrane phospholipid reorganizations by Fourier transform infrared spectroscopy illustrated a positive impact of 0.063 mg/mL HEP on hypoxic cells considering proliferation and cellular integrity. It was concluded that a specific dose of jamun HEP reduces hypoxic cytotoxicity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jafc.7b00366DOI Listing
May 2017

Transfer learning based classification of optical coherence tomography images with diabetic macular edema and dry age-related macular degeneration.

Biomed Opt Express 2017 Feb 4;8(2):579-592. Epub 2017 Jan 4.

School of Medical Science and Technology, IIT Kharagpur, Kharagpur, India.

We present an algorithm for identifying retinal pathologies given retinal optical coherence tomography (OCT) images. Our approach fine-tunes a pre-trained convolutional neural network (CNN), GoogLeNet, to improve its prediction capability (compared to random initialization training) and identifies salient responses during prediction to understand learned filter characteristics. We considered a data set containing subjects with diabetic macular edema, or dry age-related macular degeneration, or no pathology. The fine-tuned CNN could effectively identify pathologies in comparison to classical learning. Our algorithm aims to demonstrate that models trained on non-medical images can be fine-tuned for classifying OCT images with limited training data.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1364/BOE.8.000579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330546PMC
February 2017

Multimodal characterization of radiologically detectable lung lesions.

Annu Int Conf IEEE Eng Med Biol Soc 2016 Aug;2016:1422-1425

Diagnosing radiologically detectable lung lesions on the basis of cyto/histopathological staining often suffers from ambiguity, leading to faulty detection of lung diseases, especially cancer. Present study attempted to perform a multimodal characterzation of clinical samples from patients with radiologically detected lung lesions, in order to classify diseases with higher precision. The study included analysing nuclear morphometric and intensity based differences between benign and malignant lung lesions in a quantitative way. Simultaneous analysis of serum samples taken from similar sets of patients was performed by Fourier transform infra red (FTIR) spectroscopy which provided differential global biochemical insights of normal and diseased states. Both nuclear and serum biochemical features were helpful in accomplishing high classification accuracy in distinguishing benign and different malignant cases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/EMBC.2016.7590975DOI Listing
August 2016

Risk prediction for oral potentially malignant disorders using fuzzy analysis of cytomorphological and autofluorescence alterations in habitual smokers.

Future Oncol 2017 Mar 18;13(6):499-511. Epub 2016 Nov 18.

Centre for Healthcare Science & Technology, Indian Institute of Engineering Science and Technology Shibpur, Howrah-711103, India.

Aim: This study aims to develop a novel noninvasive method for early cancer trend diagnosis in habitual smokers by corroborating cytomorphological and autofluorescence alterations.

Materials & Methods: A total of 120 subjects were included and categorized into nonsmoker, smoker and clinically diagnosed oral potentially malignant disorder (OPMD) patients. Oral exfoliative epithelial cells were studied through differential interference contrast and fluorescence microscopy. Fuzzy trend analysis was performed using measured parameters for determining the risk factors among smokers.

Results: The risk assessment in this study showed a positive correlation of smoking duration with early cancer risk factors with a correlation co-efficient of 0.86.

Conclusion: Alterations in cellular morphology and autofluorescence intensities showed positive correlation with OPMD. The present study will benefit to investigate early prediction of OPMD among susceptible individuals.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2217/fon-2016-0382DOI Listing
March 2017
-->