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1.
Front Cell Dev Biol ; 12: 1358583, 2024.
Article in English | MEDLINE | ID: mdl-38827528

ABSTRACT

Breast cancer metastases exhibit many different genetic alterations, including copy number amplifications (CNA). CNA are genetic alterations that are increasingly becoming relevant to breast oncology clinical practice. Here we identify CNA in metastatic breast tumor samples using publicly available datasets and characterize their expression and function using a metastatic mouse model of breast cancer. Our findings demonstrate that our organoid generation can be implemented to study clinically relevant features that reflect the genetic heterogeneity of individual tumors.

2.
Braz J Biol ; 84: e281671, 2024.
Article in English | MEDLINE | ID: mdl-38747863

ABSTRACT

Unmanned Aerial Vehicles (UAVs), often called drones, have gained progressive prevalence for their swift operational ability as well as their extensive applicability in diverse real-world situations. Of late, UAV usage in precision agriculture has attracted much interest from scientific community. This study will look at drone aid in precise farming. Big data has the ability to analyze enormous amounts of data. Due to this, it is one of the diverse crucial technologies of Information and Communication Technology (ICT) which had applied in precision agriculture for the abstraction of critical information as well as for assisting agricultural practitioners in the comprehension of the most feasible farming practices, and also for better decision-making. This work analyses communication protocols, as well as their application toward the challenge of commanding a drone fleet for protecting crops from infestations of parasites. For computer-vision tasks as well as data-intensive applications, the method of deep learning has shown much potential. Due to its vast potential, it can also be used in the field of agriculture. This research will employ several schemes to assess the efficacy of models includes Visual Geometry Group (VGG-16), the Convolutional Neural Network (CNN) as well as the Fully-Convolutional Network (FCN) in plant disease detection. The methods of Artificial Immune Systems (AIS) can be used in order to adapt deep neural networks to the immediate situation. Simulated outcomes demonstrate that the proposed method is providing superior performance over various other technologically-advanced methods.


Subject(s)
Agriculture , Animals , Unmanned Aerial Devices , Crops, Agricultural , Neural Networks, Computer , Plant Diseases/parasitology
3.
Cell Rep Med ; 5(5): 101511, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38614094

ABSTRACT

We present an integrated single-cell RNA sequencing atlas of the primary breast tumor microenvironment (TME) containing 236,363 cells from 119 biopsy samples across eight datasets. In this study, we leverage this resource for multiple analyses of immune and cancer epithelial cell heterogeneity. We define natural killer (NK) cell heterogeneity through six subsets in the breast TME. Because NK cell heterogeneity correlates with epithelial cell heterogeneity, we characterize epithelial cells at the level of single-gene expression, molecular subtype, and 10 categories reflecting intratumoral transcriptional heterogeneity. We develop InteractPrint, which considers how cancer epithelial cell heterogeneity influences cancer-immune interactions. We use T cell InteractPrint to predict response to immune checkpoint inhibition (ICI) in two breast cancer clinical trials testing neoadjuvant anti-PD-1 therapy. T cell InteractPrint was predictive of response in both trials versus PD-L1 (AUC = 0.82, 0.83 vs. 0.50, 0.72). This resource enables additional high-resolution investigations of the breast TME.


Subject(s)
Breast Neoplasms , Immune Checkpoint Inhibitors , Killer Cells, Natural , Single-Cell Analysis , Tumor Microenvironment , Humans , Breast Neoplasms/drug therapy , Breast Neoplasms/immunology , Breast Neoplasms/pathology , Breast Neoplasms/genetics , Female , Tumor Microenvironment/immunology , Single-Cell Analysis/methods , Immune Checkpoint Inhibitors/therapeutic use , Immune Checkpoint Inhibitors/pharmacology , Killer Cells, Natural/immunology , Epithelial Cells/immunology , Epithelial Cells/pathology , Epithelial Cells/metabolism , Epithelial Cells/drug effects , Programmed Cell Death 1 Receptor/antagonists & inhibitors , Programmed Cell Death 1 Receptor/genetics , Programmed Cell Death 1 Receptor/metabolism , Programmed Cell Death 1 Receptor/immunology , Gene Expression Regulation, Neoplastic , T-Lymphocytes/immunology , Genetic Heterogeneity
4.
Article in English | MEDLINE | ID: mdl-38305794

ABSTRACT

Opsarius siangi sp. nov., a previously undocumented species, has been identified from Siang River, Pasighat, Arunachal Pradesh, India. This newly described species is distinguished by a suite of unique morphological characteristics, notably including a complete lateral line, consisting of 65-77 scales, 32-39 pre-dorsal scales, 12-15 scales positioned between dorsal fin origin and lateral line, presence of two pairs of barbels, body depth ranging from 18.80% to 27.42% of standard length and a distinct pattern of 8-15 vertical bars adorning the body. A comprehensive genetic analysis was conducted by scrutinizing 78 Cytochrome oxidase I (COI) sequences extracted from Chedrinae fishes, with particular focus on Opsarius and Barilius genera. Phylogenetic analysis revealed that O. siangi sp. nov. occupies a distinctive clade, displaying close affinity with O. shacra. Intraspecific K2P genetic divergence, assessed at 0.02, falls well within established species delineation thresholds, while interspecific divergence in comparison to O. shacra was recorded at 0.112. Complementary species delimitation methodologies, including BIN and bPTP, further underscore taxonomic uniqueness of O. siangi sp. nov., within Chedrinae family. This description enriches our understanding of biodiversity within Siang River ecosystem and underscores the merit of employing multi-pronged approaches in taxonomic investigations.

5.
Indian J Community Med ; 48(2): 310-315, 2023.
Article in English | MEDLINE | ID: mdl-37323753

ABSTRACT

Background: Natural disasters cause much hardship and suffering, loss of property, and increased morbidity and mortality amongst those affected. Timely and effective response for relief and rescue services go a long way in mitigating these consequences. Material and Methods: This population-based cross-sectional, descriptive study conducted in the immediate aftermath of the catastrophic flood that occurred in Kerala, South India, in 2018, documents the experiences of the victims, the community's preparedness, and response to the disaster. Results: Flood waters reached levels of over four feet within the premises of 55% of the houses and nearly 97% had water flooding inside their homes. More than 93% of the households were evacuated to safer locations and relief camps. The elderly and those with chronic illnesses were the worst sufferers, unable to access medical aid. Many families (62%) received help from neighbors. Conclusion: However, the loss of lives was minimal, and could be attributed to the immediate response of the local community in rescue and relief work. This experience underscores the vital importance of the local community as first responders, and their preparedness for disasters.

6.
J Immunother Cancer ; 11(5)2023 05.
Article in English | MEDLINE | ID: mdl-37230537

ABSTRACT

BACKGROUND: Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) combined with endocrine therapy are a mainstay treatment for hormone receptor-positive breast cancer. While their principal mechanism is inhibition of cancer cell proliferation, preclinical and clinical evidence suggests that CDK4/6i can also promote antitumor T-cell responses. However, this pro-immunogenic property is yet to be successfully harnessed in the clinic, as combining CDK4/6i with immune checkpoint blockade (ICB) has not shown a definitive benefit in patients. METHOD: We performed an in-depth analysis of the changes in the tumor immune microenvironment and systemic immune modulation associated with CDK4/6i treatment in muring breast cancer models and in patients with breast cancer using high dimensional flow cytometry and RNA sequencing. Gain and loss of function in vivo experiments employing cell transfer and depletion antibody were performed to uncover immune cell populations critical for CDK4/6i-mediated stimulation of antitumor immunity. RESULTS: We found that loss of dendritic cells (DCs) within the tumor microenvironment resulting from CDK4/6 inhibition in bone marrow progenitors is a major factor limiting antitumor immunity after CDK4/6i and ICB. Consequently, restoration of DC compartment by adoptively transferring ex vivo differentiated DCs to mice treated with CDK4/6i and ICB therapy enabled robust tumor inhibition. Mechanistically, the addition of DCs promoted the induction of tumor-localized and systemic CD4 T-cell responses in mice receiving CDK4/6i-ICB-DC combination therapy, as characterized by enrichment of programmed cell death protein-1-negative T helper (Th)1 and Th2 cells with an activated phenotype. CD4 T-cell depletion abrogated the antitumor benefit of CDK4/6i-ICB-DC combination, with outgrowing tumors displaying an increased proportion of terminally exhausted CD8 T cells. CONCLUSIONS: Our findings suggest that CDK4/6i-mediated DC suppression limits CD4 T-cell responses essential for the sustained activity of CD8 T cells and tumor inhibition. Furthermore, they imply that restoring DC-CD4 T-cell crosstalk via DC transfer enables effective breast cancer immunity in response to CDK4/6i and ICB treatment.


Subject(s)
CD4-Positive T-Lymphocytes , Immune Checkpoint Inhibitors , Mice , Animals , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use , Cell Line, Tumor , T-Lymphocytes, Helper-Inducer , Dendritic Cells
7.
bioRxiv ; 2023 Jan 31.
Article in English | MEDLINE | ID: mdl-36778256

ABSTRACT

Breast cancer metastases exhibit many different genetic alterations, including copy number amplifications. Using publicly available datasets, we identify copy number amplifications in metastatic breast tumor samples and using our organoid-based metastasis assays, and we validate FGFR1 is amplified in collectively migrating organoids. Because the heterogeneity of breast tumors is increasingly becoming relevant to clinical practice, we demonstrate our organoid method captures genetic heterogeneity of individual tumors.

8.
J Vis Exp ; (189)2022 11 11.
Article in English | MEDLINE | ID: mdl-36440890

ABSTRACT

Organoids are a reliable method for modeling organ tissue due to their self-organizing properties and retention of function and architecture after propagation from primary tissue or stem cells. This method of organoid generation forgoes single-cell differentiation through multiple passages and instead uses differential centrifugation to isolate mammary epithelial organoids from mechanically and enzymatically dissociated tissues. This protocol provides a streamlined technique for rapidly producing small and large epithelial organoids from both mouse and human mammary tissue in addition to techniques for organoid embedding in collagen and basement extracellular matrix. Furthermore, instructions for in-gel fixation and immunofluorescent staining are provided for the purpose of visualizing organoid morphology and density. These methodologies are suitable for myriad downstream analyses, such as co-culturing with immune cells and ex vivo metastasis modeling via collagen invasion assay. These analyses serve to better elucidate cell-cell behavior and create a more complete understanding of interactions within the tumor microenvironment.


Subject(s)
Neoplasms , Organoids , Humans , Mice , Animals , Diagnostic Imaging , Breast , Collagen , Tumor Microenvironment
9.
J Taibah Univ Med Sci ; 17(5): 818-825, 2022 Oct.
Article in English | MEDLINE | ID: mdl-36050955

ABSTRACT

Objectives: During orthodontic treatment, patients are often apprehensive about reduced food intake and loss of body weight. Body mass index (BMI) assessment is an inexpensive, easy method for screening and studying changes in weight categories. This research aimed to determine whether long-term changes in BMI, self-esteem, and food habits occur in patients during the first year of orthodontic treatment. Methods: BMI was calculated for 120 patients undergoing orthodontic treatment. Data were collected at baseline, and after the end of the first, second, third, sixth, and twelfth months. Rosenberg's self-esteem scale was used for scoring self-esteem. The Food Habit Assessment Scale was used to study changes in eating habits. Statistical analysis was performed with repeated measures ANOVA followed by Tukey HSD post-hoc test for BMI scores and Kruskal-Wallis test followed by Dunn's multiple comparison post-hoc tests for the Rosenberg scale and food habits questionnaire. Results: At the end of 12 months, 43.4% of patients had a decrease in BMI, 45.8% had a mild to moderate increase in BMI, and 10.8% of patients maintained their BMI levels. The changes were not statistically significant. Self-esteem changes were statistically significant for both genders. Changes in food habits were also significant. Conclusion: BMI decreased for the first 3 months and gradually recovered by the end of the first year of treatment. Self-esteem scores showed a significant improvement in both genders. Patients reverted to pre-treatment food habits by the end of the year.

10.
Cancer Immunol Res ; 10(7): 829-843, 2022 07 01.
Article in English | MEDLINE | ID: mdl-35561311

ABSTRACT

The MYC oncogene is frequently amplified in triple-negative breast cancer (TNBC). Here, we show that MYC suppression induces immune-related hallmark gene set expression and tumor-infiltrating T cells in MYC-hyperactivated TNBCs. Mechanistically, MYC repressed stimulator of interferon genes (STING) expression via direct binding to the STING1 enhancer region, resulting in downregulation of the T-cell chemokines CCL5, CXCL10, and CXCL11. In primary and metastatic TNBC cohorts, tumors with high MYC expression or activity exhibited low STING expression. Using a CRISPR-mediated enhancer perturbation approach, we demonstrated that MYC-driven immune evasion is mediated by STING repression. STING repression induced resistance to PD-L1 blockade in mouse models of TNBC. Finally, a small-molecule inhibitor of MYC combined with PD-L1 blockade elicited a durable response in immune-cold TNBC with high MYC expression, suggesting a strategy to restore PD-L1 inhibitor sensitivity in MYC-overexpressing TNBC.


Subject(s)
Membrane Proteins/genetics , Proto-Oncogene Proteins c-myc/metabolism , Triple Negative Breast Neoplasms , Animals , B7-H1 Antigen , Cell Line, Tumor , Epigenetic Repression , Humans , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use , Immune Evasion , Mice , Triple Negative Breast Neoplasms/drug therapy , Triple Negative Breast Neoplasms/genetics , Triple Negative Breast Neoplasms/pathology
11.
Chemosphere ; 293: 133475, 2022 Apr.
Article in English | MEDLINE | ID: mdl-34974045

ABSTRACT

The petroleum fuel demand with high price and its exhaustion imposes a pressure to find an alternative. The fossil fuel shortage has been deteriorating over the past few years, because of the rapid increase in population. Many attempts have been made to increase the quality of biofuel with additives. In this paper, two types of nanoparticles such as carbon nanotubes (CNT) and alumina (Al2O3) in chlorella microalgae biofuel were analyzed by experimental method. The added CNT and alumina act as a catalyst that induces complete combustion with retarded emissions. In addition to above, the noise and vibration qualities are also measured. A series of test conducted using single cylinders, four stroke, naturally aspirated compression ignition diesel engine was run by using pure diesel and also different fuel blends 'such as B10CNT50A50 Chlorella (Microalgae Biodiesel 10% + Diesel 90% + CNT 50 ppm), B20CNT50A50 (Microalgae Biodiesel 20% + Diesel 80% + CNT 50 ppm + Al2O3 50 ppm) and B30CNT50A50 (Microalgae Biodiesel 30% + Diesel 70% + CNT 50 ppm + Al2O3 50 ppm). At a constant load condition, all experimental tests were conducted at four different speeds such as 1500 rpm, 2000 rpm, 2500 rpm and 3000 rpm. The reference fuel of diesel B0 results was compared with blended fuel. From the results, it has been found that the nano additives of CNT and alumina reduced the greenhouse gas emissions of CO compared to plain diesel. Only considering the blended fuel, as the percentage of biofuel increases, the emission of nitric oxide and carbon dioxide is decreased with significant reduction in the amount of noise and vibration and also the combustion and performance qualities were also improved. The highest benefit in terms of all factors was achieved in the fuel blend of B30A50CNT50 amongst the other blends.


Subject(s)
Chlorella vulgaris , Microalgae , Nanotubes, Carbon , Acoustics , Biofuels , Carbon Monoxide/analysis , Environmental Pollution , Gasoline , Vehicle Emissions , Vibration
12.
Mol Biol Rep ; 49(1): 351-361, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34724129

ABSTRACT

BACKGROUND: The taxonomic status and geographical distribution of M. tengara are vague. No genetic diversity and phylogenetic study have been done till now to resolve its identity and distribution. In the present study, an integrated taxonomic approach has been applied to clarify the taxonomic status, identity, and distribution of bagrid catfish, Mystus tengara. METHODS AND RESULTS: Comparative morphometric evaluation of M. tengara identified in the present study from distant geographical locations revealed variations of the traits in response to body length and environment, without significant genetic distance. The observed morphometric traits of M. tengara were found to be overlapping with available morphometric traits of M. tengara, M. carcio and M. vittatus. Maximum likelihood and Bayesian phylogenetic analysis based on mitochondrial cytochrome c oxidase (COI) gene also could not resolve their identity, and five paraphyletic clades comprising of M. tengara, M. vittatus, and M. carcio from India, Nepal, and Bangladesh were observed. Morphological and genetic evidence along with comparative evaluation of M. tengara, from its type locality, we consider M. tengara identified in the present study to be true, with its distribution extending from North East India to West Bengal, North India, Central India, Northern peninsular India, and Bangladesh. CONCLUSION: The observation of paraphyletic subclades and evaluation of genetic distance between subclades reveals the presence of four cryptic species. Further confirmation on the identity of M. vittatus and M. carcio, by an integrated taxonomic approach based on fresh specimens collected from the type locality, is required.


Subject(s)
Catfishes/anatomy & histology , Catfishes/classification , Electron Transport Complex IV/genetics , Animals , Bangladesh , Bayes Theorem , Catfishes/genetics , Fish Proteins/genetics , India , Likelihood Functions , Mitochondrial Proteins/genetics , Nepal , Phylogeny , Phylogeography
13.
Indian J Occup Environ Med ; 25(2): 114-118, 2021.
Article in English | MEDLINE | ID: mdl-34421249

ABSTRACT

BACKGROUND: Domestic squalor refers to households that are extremely cluttered, in a filthy condition, and where the accumulation of items such as personal possessions, rubbish, excrement and decomposing food creates an environment that jeopardizes the health and wellbeing of the occupant(s). In India, an estimated 258 million are migrants. They are more likely to live in squalor due to inferior socio-economic status and no permanent residence. This poses a threat to the health of the migrants and the neighbors. OBJECTIVE: To assess the squalor and morbidity pattern among the migrants of Migrant colonies in Thiruvalla using Rapid survey technique. METHODOLOGY: The state of squalor in migrant colonies was assessed by Lot Quality Assurance Sampling Methodology using the Environment Cleanliness and Clutter Scale (ECCS). The sample size for each lot/colony was '14' dwellings according to LQAS table. The details were collected from 14 inhabitants of different dwellings of the same colony. The inhabitants were selected randomly and were excluded if he belonged to the same dwelling. Fifteen colonies were randomly selected to achieve the sample size of 210 (15*14). The study was done in Tiruvalla municipality. RESULTS AND CONCLUSION: Only two colonies (n = 15) were squalor free. Majority of the dwellings (n = 210) were having an ECCS score between 13 and 15. Common ailments affecting migrants include Common cold, Skin disorders, and dental caries and gastritis. Squalor was found in most of the migrant colonies as they are living in inhuman conditions.

14.
Cells ; 10(6)2021 05 21.
Article in English | MEDLINE | ID: mdl-34063789

ABSTRACT

Mast cells are unique tissue-resident immune cells of the myeloid lineage that have long been implicated in the pathogenesis of allergic and autoimmune disorders. More recently, mast cells have been recognized as key orchestrators of anti-tumor immunity, modulators of the cancer stroma, and have also been implicated in cancer cell intrinsic properties. As such, mast cells are an underrecognized but very promising target for cancer immunotherapy. In this review, we discuss the role of mast cells in shaping cancer and its microenvironment, the interaction between mast cells and cancer therapies, and strategies to target mast cells to improve cancer outcomes. Specifically, we address (1) decreasing cell numbers through c-KIT inhibition, (2) modulating mast cell activation and phenotype (through mast cell stabilizers, FcεR1 signaling pathway activators/inhibitors, antibodies targeting inhibitory receptors and ligands, toll like receptor agonists), and (3) altering secreted mast cell mediators and their downstream effects. Finally, we discuss the importance of translational research using patient samples to advance the field of mast cell targeting to optimally improve patient outcomes. As we aim to expand the successes of existing cancer immunotherapies, focused clinical and translational studies targeting mast cells in different cancer contexts are now warranted.


Subject(s)
Immunotherapy/methods , Mast Cells , Neoplasms/therapy , Tumor Microenvironment/immunology , Animals , Humans , Mast Cells/cytology , Mast Cells/immunology , Toll-Like Receptors/immunology
15.
Genome Med ; 13(1): 70, 2021 04 26.
Article in English | MEDLINE | ID: mdl-33902690

ABSTRACT

BACKGROUND: Inflammatory breast cancer (IBC) has a highly invasive and metastatic phenotype. However, little is known about its genetic drivers. To address this, we report the largest cohort of whole-genome sequencing (WGS) of IBC cases. METHODS: We performed WGS of 20 IBC samples and paired normal blood DNA to identify genomic alterations. For comparison, we used 23 matched non-IBC samples from the Cancer Genome Atlas Program (TCGA). We also validated our findings using WGS data from the International Cancer Genome Consortium (ICGC) and the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We examined a wide selection of genomic features to search for differences between IBC and conventional breast cancer. These include (i) somatic and germline single-nucleotide variants (SNVs), in both coding and non-coding regions; (ii) the mutational signature and the clonal architecture derived from these SNVs; (iii) copy number and structural variants (CNVs and SVs); and (iv) non-human sequence in the tumors (i.e., exogenous sequences of bacterial origin). RESULTS: Overall, IBC has similar genomic characteristics to non-IBC, including specific alterations, overall mutational load and signature, and tumor heterogeneity. In particular, we observed similar mutation frequencies between IBC and non-IBC, for each gene and most cancer-related pathways. Moreover, we found no exogenous sequences of infectious agents specific to IBC samples. Even though we could not find any strongly statistically distinguishing genomic features between the two groups, we did find some suggestive differences in IBC: (i) The MAST2 gene was more frequently mutated (20% IBC vs. 0% non-IBC). (ii) The TGF ß pathway was more frequently disrupted by germline SNVs (50% vs. 13%). (iii) Different copy number profiles were observed in several genomic regions harboring cancer genes. (iv) Complex SVs were more frequent. (v) The clonal architecture was simpler, suggesting more homogenous tumor-evolutionary lineages. CONCLUSIONS: Whole-genome sequencing of IBC manifests a similar genomic architecture to non-IBC. We found no unique genomic alterations shared in just IBCs; however, subtle genomic differences were observed including germline alterations in TGFß pathway genes and somatic mutations in the MAST2 kinase that could represent potential therapeutic targets.


Subject(s)
Genome, Human , Inflammatory Breast Neoplasms/genetics , Mutation/genetics , Whole Genome Sequencing , Clone Cells , DNA Copy Number Variations/genetics , Evolution, Molecular , Humans , Inflammatory Breast Neoplasms/microbiology , Inflammatory Breast Neoplasms/pathology , Molecular Sequence Annotation , Phenotype , Signal Transduction/genetics
16.
J Immunother Cancer ; 9(3)2021 03.
Article in English | MEDLINE | ID: mdl-33653801

ABSTRACT

Immune checkpoint inhibitors (ICIs) have improved overall survival for cancer patients, however, optimal duration of ICI therapy has yet to be defined. Given ICIs were first used to treat patients with metastatic melanoma, a condition that at the time was incurable, little attention was initially paid to how much therapy would be needed for a durable response. As the early immunotherapy trials have matured past 10 years, a significant per cent of patients have demonstrated durable responses; it is now time to determine whether patients have been overtreated, and if durable remissions can still be achieved with less therapy, limiting the physical and financial toxicity associated with years of treatment. Well-designed trials are needed to identify optimal duration of therapy, and to define biomarkers to predict who would benefit from shorter courses of immunotherapy. Here, we outline key questions related to health, financial and societal toxicities of over treating with ICI and present four unique clinical trials aimed at exposing criteria for early cessation of ICI. Taken together, there is a serious liability to overtreating patients with ICI and future work is warranted to determine when it is safe to stop ICI.


Subject(s)
Immune Checkpoint Inhibitors/administration & dosage , Neoplasms/drug therapy , Clinical Trials as Topic , Drug Administration Schedule , Evidence-Based Medicine , Humans , Immune Checkpoint Inhibitors/adverse effects , Neoplasms/immunology , Neoplasms/mortality , Neoplasms/pathology , Patient Safety , Risk Assessment , Risk Factors , Time Factors , Treatment Outcome
17.
Nat Commun ; 11(1): 1839, 2020 04 15.
Article in English | MEDLINE | ID: mdl-32296058

ABSTRACT

Complex tumor microenvironmental (TME) features influence the outcome of cancer immunotherapy (IO). Here we perform immunogenomic analyses on 67 intratumor sub-regions of a PD-1 inhibitor-resistant melanoma tumor and 2 additional metastases arising over 8 years, to characterize TME interactions. We identify spatially distinct evolution of copy number alterations influencing local immune composition. Sub-regions with chromosome 7 gain display a relative lack of leukocyte infiltrate but evidence of neutrophil activation, recapitulated in The Cancer Genome Atlas (TCGA) samples, and associated with lack of response to IO across three clinical cohorts. Whether neutrophil activation represents cause or consequence of local tumor necrosis requires further study. Analyses of T-cell clonotypes reveal the presence of recurrent priming events manifesting in a dominant T-cell clonotype over many years. Our findings highlight the links between marked levels of genomic and immune heterogeneity within the physical space of a tumor, with implications for biomarker evaluation and immunotherapy response.


Subject(s)
Genomics/methods , Melanoma/metabolism , Biomarkers, Tumor/genetics , DNA Copy Number Variations/genetics , Humans , Melanoma/genetics , Mutation/genetics , Neutrophil Activation/genetics , Neutrophil Activation/physiology , Tumor Microenvironment/genetics , Tumor Microenvironment/physiology
18.
Expert Rev Anticancer Ther ; 20(3): 151-158, 2020 03.
Article in English | MEDLINE | ID: mdl-32067545

ABSTRACT

Introduction: In March 2019, atezolizumab became the first immune checkpoint inhibitor to receive a breast cancer-specific approval. Based on a significant improvement in progression-free survival as well as a 10-month improvement in overall survival (on interim analysis) seen in the IMpassion 130 trial, the combination of atezolizumab and nab-paclitaxel was approved for patients with unresectable locally advanced or metastatic triple-negative breast cancer (TNBC).Areas covered: This article reviews current data and ongoing research on atezolizumab for the treatment of breast cancer. Results of atezolizumab monotherapy trials in the context of other early immune checkpoint blockade trials in breast cancer are discussed as well as data from combination clinical trials with chemotherapy in both early-stage and metastatic breast cancer. We focus on the safety and efficacy analyses from the phase III IMpassion trial that led to FDA and EMA approval of atezolizumab and nab-paclitaxel in patients whose tumor tested positive for PD-L1 by the Ventana SP142 companion diagnostic immunohistochemical assay.Expert opinion: The FDA and EMA approvals of atezolizumab mark an important advance for treatment of metastatic TNBC. However, ongoing investigations need to define better biomarkers of response, determine resistance mechanisms, and identify strategies to increase response rates.


Subject(s)
Antibodies, Monoclonal, Humanized/administration & dosage , Immune Checkpoint Inhibitors/administration & dosage , Triple Negative Breast Neoplasms/drug therapy , Animals , Antibodies, Monoclonal, Humanized/adverse effects , Antibodies, Monoclonal, Humanized/pharmacology , Antineoplastic Combined Chemotherapy Protocols/administration & dosage , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Female , Humans , Immune Checkpoint Inhibitors/adverse effects , Immune Checkpoint Inhibitors/pharmacology , Neoplasm Staging , Progression-Free Survival , Survival Rate , Triple Negative Breast Neoplasms/pathology
19.
Nature ; 577(7791): 549-555, 2020 01.
Article in English | MEDLINE | ID: mdl-31942075

ABSTRACT

Treatment with immune checkpoint blockade (ICB) has revolutionized cancer therapy. Until now, predictive biomarkers1-10 and strategies to augment clinical response have largely focused on the T cell compartment. However, other immune subsets may also contribute to anti-tumour immunity11-15, although these have been less well-studied in ICB treatment16. A previously conducted neoadjuvant ICB trial in patients with melanoma showed via targeted expression profiling17 that B cell signatures were enriched in the tumours of patients who respond to treatment versus non-responding patients. To build on this, here we performed bulk RNA sequencing and found that B cell markers were the most differentially expressed genes in the tumours of responders versus non-responders. Our findings were corroborated using a computational method (MCP-counter18) to estimate the immune and stromal composition in this and two other ICB-treated cohorts (patients with melanoma and renal cell carcinoma). Histological evaluation highlighted the localization of B cells within tertiary lymphoid structures. We assessed the potential functional contributions of B cells via bulk and single-cell RNA sequencing, which demonstrate clonal expansion and unique functional states of B cells in responders. Mass cytometry showed that switched memory B cells were enriched in the tumours of responders. Together, these data provide insights into the potential role of B cells and tertiary lymphoid structures in the response to ICB treatment, with implications for the development of biomarkers and therapeutic targets.


Subject(s)
B-Lymphocytes/immunology , Carcinoma, Renal Cell/drug therapy , Carcinoma, Renal Cell/immunology , Immunotherapy , Melanoma/drug therapy , Melanoma/immunology , Tertiary Lymphoid Structures/immunology , B-Lymphocytes/cytology , B-Lymphocytes/metabolism , Biomarkers, Tumor/analysis , Carcinoma, Renal Cell/pathology , Carcinoma, Renal Cell/surgery , Cell Cycle Checkpoints/drug effects , Cell Cycle Checkpoints/immunology , Clone Cells/cytology , Clone Cells/immunology , Clone Cells/metabolism , Dendritic Cells, Follicular/cytology , Dendritic Cells, Follicular/immunology , Gene Expression Regulation, Neoplastic , Humans , Immunologic Memory/immunology , Mass Spectrometry , Melanoma/pathology , Melanoma/surgery , Neoplasm Metastasis/genetics , Phenotype , Prognosis , RNA-Seq , Receptors, Immunologic/immunology , Single-Cell Analysis , T-Lymphocytes/cytology , T-Lymphocytes/immunology , Transcriptome
20.
J Ethnopharmacol ; 250: 112435, 2020 Mar 25.
Article in English | MEDLINE | ID: mdl-31785384

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: Albizia procera L. (Leguminosae) commonly known as Konda vagai in Tamil, is used for the treatment of stomach and intestinal disorders. A decoction of the bark is prescribed for rheumatism and haemorrhage. Traditionally, literature claims Albizia procera as a drug to have antirheumatic properties and hence used by Tribal for the management of chronic rheumatism. Consequently, the present study has been undertaken to illustrate the beneficial outcome of Albizia procera in adjuvant induced arthritic rat model with respect to its antioxidant and anti-inflammatory activities. AIM OF THE STUDY: The present study is aimed to investigate the oxidative stress and the expression of inflammatory markers in arthritic rats treated with ethanolic bark extract of Albizia procera. MATERIALS AND METHODS: Ethanolic bark extract was characterized by HPTLC analysis. Acute oral toxicity study was performed according to the OECD test guideline 423 - Acute toxic class method. The anti-inflammatory effect of ETBE (100, 200 mg/kg/day/p.o.) was evaluated in complete Freund's adjuvant induced arthritic rats using diclofenac as positive control (0.3 mg/kg/day/p. o.). Plasma levels of interleukins TNF- α, IFN-α, IL-2, IL-6, myeloperoxidase and Cathepsin D levels were measured to assess the inflammatory effect of ETBE extract of Albizia procera. Further, the effect of ETBE on superoxide dismutase (SOD), glutathione peroxidase (GPX), reduced glutathione (GSH) and lipid peroxidation (LPO) were assessed in plasma. RESULTS: HPTLC analysis showed the presence of 0.57% w/w of biochanin-A in ETBE. ETBE did not show any toxic signs up to 2000 mg/kg body weight. It exhibited the significant anti-inflammatory and antioxidant potential and did not show mortality up to 2000 mg/kg body weight. ETBE treatment significantly reduced the levels of TNF- α, IFN-α, IL-2, IL-6 and myeloperoxidase, and increased cathepsin D levels compared to vehicle treated animals. SOD, GSH and GPX levels were significantly restored to normal levels while LPO was significantly reduced at 200 mg/kg b. wt. Treated animals. Histopathological studies showed complete cartilage regeneration and near normal joint in ETBE treated arthritic rats. CONCLUSION: ETBE demonstrated potent anti-inflammatory activity by modulating the expression of inflammatory cytokines and restoring the antioxidant enzyme levels.


Subject(s)
Albizzia , Anti-Inflammatory Agents/therapeutic use , Antioxidants/therapeutic use , Arthritis, Experimental/drug therapy , Plant Extracts/therapeutic use , Animals , Anti-Inflammatory Agents/pharmacology , Anti-Inflammatory Agents/toxicity , Antioxidants/pharmacology , Antioxidants/toxicity , Arthritis, Experimental/blood , Arthritis, Experimental/genetics , Arthritis, Experimental/pathology , Biphenyl Compounds/chemistry , Cytokines/blood , Cytokines/genetics , Ethanol/chemistry , Female , Glutathione/blood , Glutathione Peroxidase/blood , Joints/drug effects , Joints/pathology , Lipid Peroxidation/drug effects , Nitric Oxide/chemistry , Oxidative Stress/drug effects , Picrates/chemistry , Plant Bark/chemistry , Plant Extracts/chemistry , Plant Extracts/pharmacology , Plant Extracts/toxicity , Rats, Sprague-Dawley , Solvents/chemistry , Superoxide Dismutase/blood
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