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Article ; Online: Novel read through agent: ZKN-0013 demonstrates efficacy in APC

Graf, Martin R / Apte, Shruti / Terzo, Esteban / Padhye, Simran / Shi, Shuhao / Cox, Megan K / Clark, Roger B / Modur, Vijay / Badarinarayana, Vasudeo

Journal of molecular medicine (Berlin, Germany)

2023 Volume 101, Issue 4, Page(s) 375–385

Abstract: Familial adenomatous polyposis (FAP) is a precancerous, colorectal disease characterized by hundreds to thousands of adenomatous polyps caused by mutations in the tumor suppressor gene adenomatous polyposis coli (APC). Approximately 30% of these ... ...

Abstract	Familial adenomatous polyposis (FAP) is a precancerous, colorectal disease characterized by hundreds to thousands of adenomatous polyps caused by mutations in the tumor suppressor gene adenomatous polyposis coli (APC). Approximately 30% of these mutations are premature termination codons (PTC), resulting in the production of a truncated, dysfunctional APC protein. Consequently, the β-catenin degradation complex fails to form in the cytoplasm, leading to elevated nuclear levels of β-catenin and unregulated β-catenin/wnt-pathway signaling. We present in vitro and in vivo data demonstrating that the novel macrolide, ZKN-0013, promotes read through of premature stop codons, leading to functional restoration of full-length APC protein. Human colorectal carcinoma SW403 and SW1417 cells harboring PTC mutations in the APC gene showed reduced levels of nuclear β-catenin and c-myc upon treatment with ZKN-0013, indicating that the macrolide-mediated read through of premature stop codons produced bioactive APC protein and inhibited the β-catenin/wnt-pathway. In a mouse model of adenomatous polyposis coli, treatment of APC
MeSH term(s)	Humans ; Animals ; Mice ; Genes, APC ; beta Catenin/metabolism ; Codon, Nonsense ; Adenomatous Polyposis Coli/drug therapy ; Adenomatous Polyposis Coli/genetics ; Adenomatous Polyposis Coli/pathology ; Adenoma/genetics ; Macrolides ; Intestinal Polyps/genetics
Chemical Substances	beta Catenin ; Codon, Nonsense ; Macrolides
Language	English
Publishing date	2023-02-20
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1223802-8
ISSN	1432-1440 ; 0946-2716
ISSN (online)	1432-1440
ISSN	0946-2716
DOI	10.1007/s00109-023-02291-x
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Article ; Online: Pyruvate Oxidase as a Key Determinant of Pneumococcal Viability during Transcytosis across Brain Endothelium.

Anil, Anjali / Apte, Shruti / Joseph, Jincy / Parthasarathy, Akhila / Madhavan, Shilpa / Banerjee, Anirban

Journal of bacteriology

2021 Volume 203, Issue 24, Page(s) e0043921

Abstract: Streptococcus pneumoniae invades a myriad of host tissues following efficient breaching of cellular barriers. However, strategies adopted by pneumococcus for evasion of host intracellular defenses governing successful transcytosis across host cellular ... ...

Abstract	Streptococcus pneumoniae invades a myriad of host tissues following efficient breaching of cellular barriers. However, strategies adopted by pneumococcus for evasion of host intracellular defenses governing successful transcytosis across host cellular barriers remain elusive. In this study, using brain endothelium as a model host barrier, we observed that pneumococcus containing endocytic vacuoles (PCVs), formed following S. pneumoniae internalization into brain microvascular endothelial cells (BMECs), undergo early maturation and acidification, with a major subset acquiring lysosome-like characteristics. Exploration of measures that would preserve pneumococcal viability in the lethal acidic pH of these lysosome-like vacuoles revealed a critical role of the two-component system response regulator, CiaR, which was previously implicated in induction of acid tolerance response. Pyruvate oxidase (SpxB), a key sugar-metabolizing enzyme that catalyzes oxidative decarboxylation of pyruvate to acetyl phosphate, was found to contribute to acid stress tolerance, presumably via acetyl phosphate-mediated phosphorylation and activation of CiaR, independent of its cognate kinase CiaH. Hydrogen peroxide, the by-product of an SpxB-catalyzed reaction, was also found to improve pneumococcal intracellular survival by oxidative inactivation of lysosomal cysteine cathepsins, thus compromising the degradative capacity of the host lysosomes. As expected, a Δ
MeSH term(s)	Blood-Brain Barrier ; Cells, Cultured ; Endothelium, Vascular/metabolism ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Humans ; Microbial Viability ; Pyruvate Oxidase/genetics ; Pyruvate Oxidase/metabolism ; Streptococcus pneumoniae/enzymology ; Streptococcus pneumoniae/genetics ; Streptococcus pneumoniae/metabolism ; Transcytosis/physiology
Chemical Substances	Pyruvate Oxidase (EC 1.2.3.3)
Language	English
Publishing date	2021-10-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00439-21
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Article ; Online: Streptococcus pneumoniae

Surve, Manalee V / Apte, Shruti / Bhutda, Smita / Kamath, Kshama G / Kim, Kwang S / Banerjee, Anirban

Current research in microbial sciences

2020 Volume 1, Page(s) 62–68

Abstract: Adoption of an endocytosis route promoting safe intracellular trafficking is a pre-requisite for development of invasive diseases by Streptococcus pneumoniae (SPN). We aim to explore the contribution of various endocytic routes in internalization and ... ...

Abstract	Adoption of an endocytosis route promoting safe intracellular trafficking is a pre-requisite for development of invasive diseases by Streptococcus pneumoniae (SPN). We aim to explore the contribution of various endocytic routes in internalization and survival of SPN in blood brain barrier (BBB), a key event in development of pneumococcal meningitis. Pneumococcal entry and survival in brain endothelial cells were evaluated following treatment with combinations of inhibitors to block multiple endocytosis pathways leaving a single entry port open. Entry of SPN into brain endothelium through a novel dynamin independent pathway dictates a separate downstream trafficking itinerary. This allows SPN to evade lysosomal degradation, potentially promoting safe transit across BBB, leading to development of meningitis.
Language	English
Publishing date	2020-08-16
Publishing country	Netherlands
Document type	Journal Article
ISSN	2666-5174
ISSN (online)	2666-5174
DOI	10.1016/j.crmicr.2020.08.001
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Article ; Online: A Novel Class of Ribosome Modulating Agents Exploits Cancer Ribosome Heterogeneity to Selectively Target the CMS2 Subtype of Colorectal Cancer.

Terzo, Esteban / Apte, Shruti A / Padhye, Simran / Rashed, Saleh / Austin, Wesley / Caponegro, Michael / Reddy, Anupama / Shi, Shuhao / Wang, Christy / Clark, Roger B / Sidransky, David / Modur, Vijay / Badarinarayana, Vasudeo

Cancer research communications

2023 Volume 3, Issue 6, Page(s) 969–979

Abstract: Ribosomes in cancer cells accumulate numerous patient-specific structural and functional modifications that facilitate tumor progression by modifying protein translation. We have taken a unique synthetic chemistry approach to generate novel macrolides, ... ...

Abstract	Ribosomes in cancer cells accumulate numerous patient-specific structural and functional modifications that facilitate tumor progression by modifying protein translation. We have taken a unique synthetic chemistry approach to generate novel macrolides, Ribosome modulating agents (RMA), that are proposed to act distal to catalytic sites and exploit cancer ribosome heterogeneity. The RMA ZKN-157 shows two levels of selectivity: (i) selective translation inhibition of a subset of proteins enriched for components of the ribosome and protein translation machinery that are upregulated by MYC; and (ii) selective inhibition of proliferation of a subset of colorectal cancer cell lines. Mechanistically, the selective ribosome targeting in sensitive cells triggered cell-cycle arrest and apoptosis. Consequently, in colorectal cancer, sensitivity to ZKN-157 in cell lines and patient-derived organoids was restricted to the consensus molecular subtype 2 (CMS2) subtype that is distinguished by high MYC and WNT pathway activity. ZKN-157 showed efficacy as single agent and, the potency and efficacy of ZKN-157 synergized with clinically approved DNA-intercalating agents which have previously been shown to inhibit ribogenesis as well. ZKN-157 thus represents a new class of ribosome modulators that display cancer selectivity through specific ribosome inhibition in the CMS2 subtype of colorectal cancer potentially targeting MYC-driven addiction to high protein translation. Significance: This study demonstrates that ribosome heterogeneity in cancer can be exploited to develop selective ribogenesis inhibitors. The colorectal cancer CMS2 subtype, with a high unmet need for therapeutics, shows vulnerability to our novel selective ribosome modulator. The mechanism suggests that other cancer subtypes with high MYC activation could also be targeted.
MeSH term(s)	Humans ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; Protein Biosynthesis ; Ribosomes/genetics ; Ribosomes/metabolism ; Cell Cycle Checkpoints
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Journal Article
ISSN	2767-9764
ISSN (online)	2767-9764
DOI	10.1158/2767-9764.CRC-22-0469
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Article ; Online: An innate pathogen sensing strategy involving ubiquitination of bacterial surface proteins.

Science advances

2023 Volume 9, Issue 12, Page(s) eade1851

Abstract: Sensing of pathogens by ubiquitination is a critical arm of cellular immunity. However, universal ubiquitination targets on microbes remain unidentified. Here, using in vitro, ex vivo, and in vivo studies, we identify the first protein-based ... ...

Abstract	Sensing of pathogens by ubiquitination is a critical arm of cellular immunity. However, universal ubiquitination targets on microbes remain unidentified. Here, using in vitro, ex vivo, and in vivo studies, we identify the first protein-based ubiquitination substrates on phylogenetically diverse bacteria by unveiling a strategy that uses recognition of degron-like motifs. Such motifs form a new class of intra-cytosolic pathogen-associated molecular patterns (PAMPs). Their incorporation enabled recognition of nonubiquitin targets by host ubiquitin ligases. We find that SCF
MeSH term(s)	Humans ; F-Box-WD Repeat-Containing Protein 7/genetics ; F-Box-WD Repeat-Containing Protein 7/metabolism ; F-Box Proteins/genetics ; F-Box Proteins/metabolism ; Cell Cycle Proteins/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Membrane Proteins/metabolism ; Phosphorylation ; Ubiquitination ; Bacteria/metabolism
Chemical Substances	F-Box-WD Repeat-Containing Protein 7 ; F-Box Proteins ; Cell Cycle Proteins ; Bacterial Proteins ; Membrane Proteins
Language	English
Publishing date	2023-03-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.ade1851
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Article ; Online: Fusobacterium nucleatum

Desai, Sanket / Dharavath, Bhasker / Manavalan, Sujith / Rane, Aishwarya / Redhu, Archana Kumari / Sunder, Roma / Butle, Ashwin / Mishra, Rohit / Joshi, Asim / Togar, Trupti / Apte, Shruti / Bala, Pratyusha / Chandrani, Pratik / Chopra, Supriya / Bashyam, Murali Dharan / Banerjee, Anirban / Prabhash, Kumar / Nair, Sudhir / Dutt, Amit

NAR cancer

2022 Volume 4, Issue 1, Page(s) zcac006

Abstract: Persistent pathogen infection is a known cause of malignancy, although with sparse systematic evaluation across tumor types. We present a comprehensive landscape of 1060 infectious pathogens across 239 whole exomes and 1168 transcriptomes of breast, lung, ...

Abstract	Persistent pathogen infection is a known cause of malignancy, although with sparse systematic evaluation across tumor types. We present a comprehensive landscape of 1060 infectious pathogens across 239 whole exomes and 1168 transcriptomes of breast, lung, gallbladder, cervical, colorectal, and head and neck tumors. We identify known cancer-associated pathogens consistent with the literature. In addition, we identify a significant prevalence of
Language	English
Publishing date	2022-03-04
Publishing country	England
Document type	Journal Article
ISSN	2632-8674
ISSN (online)	2632-8674
DOI	10.1093/narcan/zcac006
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Article ; Online: A low dietary ratio of omega-6 to omega-3 Fatty acids may delay progression of prostate cancer.

Apte, Shruti A / Cavazos, David A / Whelan, Kaitlin A / Degraffenried, Linda A

Nutrition and cancer

2013 Volume 65, Issue 4, Page(s) 556–562

Abstract: Prostate cancer (PCa) is the second leading cause of cancer-related deaths in men. Studies show that consumption of polyunsaturated fatty acids (PUFA) modulates the development and progression of prostate cancer. High amounts of omega-6 fatty acids have ... ...

Abstract	Prostate cancer (PCa) is the second leading cause of cancer-related deaths in men. Studies show that consumption of polyunsaturated fatty acids (PUFA) modulates the development and progression of prostate cancer. High amounts of omega-6 fatty acids have been linked with increased prostate cancer risk, whereas omega-3 fatty acids have been shown to inhibit PCa growth. However, because omega-3 and omega-6 are both essential fatty acids and part of a complete diet, it is more relevant to determine the ideal ratio of the two that would allow patients to benefit from the therapeutic properties of omega-3 fatty acids. LNCaP prostate cancer cells were treated with dietary-based ratios of omega-6 to omega-3 fatty acids under hormone-deprivation conditions, and effects on various cellular processes were determined. A low omega-6 to omega-3 PUFA ratio can delay the progression of cells toward castration-resistance by suppressing pathways involved in prostate cancer progression, such as the Akt/mTOR/NFκB axis. It also suppresses the expression of cyclin D1, and activation of caspase-3 and annexin V staining shows induction of proapoptotic events. Taken together, our data demonstrates that maintaining a low omega-6 to omega-3 fatty acids ratio can enhance efficacy of hormone ablation therapy.
MeSH term(s)	Apoptosis/drug effects ; Caspase 3/metabolism ; Cell Line, Tumor/drug effects ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; Cyclin D1/metabolism ; Fatty Acids, Omega-3/pharmacology ; Fatty Acids, Omega-6/pharmacology ; Humans ; Male ; NF-kappa B/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Prostatic Neoplasms/diet therapy ; Prostatic Neoplasms/metabolism ; Prostatic Neoplasms/pathology ; Prostatic Neoplasms, Castration-Resistant/metabolism ; Prostatic Neoplasms, Castration-Resistant/prevention & control ; Signal Transduction/drug effects ; TOR Serine-Threonine Kinases/metabolism
Chemical Substances	Fatty Acids, Omega-3 ; Fatty Acids, Omega-6 ; NF-kappa B ; Cyclin D1 (136601-57-5) ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; Caspase 3 (EC 3.4.22.-)
Language	English
Publishing date	2013
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	424433-3
ISSN	1532-7914 ; 0163-5581
ISSN (online)	1532-7914
ISSN	0163-5581
DOI	10.1080/01635581.2013.775316
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Article: A Low Dietary Ratio of Omega-6 to Omega-3 Fatty Acids May Delay Progression of Prostate Cancer

Apte, Shruti A / Cavazos, David A / Whelan, Kaitlin A / deGraffenried, Linda A

Nutrition and cancer. 2013 May 1, v. 65, no. 4

2013

Abstract	Prostate cancer (PCa) is the second leading cause of cancer-related deaths in men. Studies show that consumption of polyunsaturated fatty acids (PUFA) modulates the development and progression of prostate cancer. High amounts of omega-6 fatty acids have been linked with increased prostate cancer risk, whereas omega-3 fatty acids have been shown to inhibit PCa growth. However, because omega-3 and omega-6 are both essential fatty acids and part of a complete diet, it is more relevant to determine the ideal ratio of the two that would allow patients to benefit from the therapeutic properties of omega-3 fatty acids. LNCaP prostate cancer cells were treated with dietary-based ratios of omega-6 to omega-3 fatty acids under hormone-deprivation conditions, and effects on various cellular processes were determined. A low omega-6 to omega-3 PUFA ratio can delay the progression of cells toward castration-resistance by suppressing pathways involved in prostate cancer progression, such as the Akt/mTOR/NFκB axis. It also suppresses the expression of cyclin D1, and activation of caspase-3 and annexin V staining shows induction of proapoptotic events. Taken together, our data demonstrates that maintaining a low omega-6 to omega-3 fatty acids ratio can enhance efficacy of hormone ablation therapy.
Keywords	caspase-3 ; diet ; essential fatty acids ; medicinal properties ; men ; omega-3 fatty acids ; omega-6 fatty acids ; patients ; polyunsaturated fatty acids ; prostatic neoplasms ; risk ; therapeutics
Language	English
Dates of publication	2013-0501
Size	p. 556-562.
Publishing place	Taylor & Francis Group
Document type	Article
ZDB-ID	2025822-7
ISSN	1532-7914 ; 0163-5581
ISSN (online)	1532-7914
ISSN	0163-5581
DOI	10.1080/01635581.2013.775316
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Article: Design, Synthesis, and Pharmacological Evaluation of Second Generation EZH2 Inhibitors with Long Residence Time.

Khanna, Avinash / Côté, Alexandre / Arora, Shilpi / Moine, Ludivine / Gehling, Victor S / Brenneman, Jehrod / Cantone, Nico / Stuckey, Jacob I / Apte, Shruti / Ramakrishnan, Ashwin / Bruderek, Kamil / Bradley, William D / Audia, James E / Cummings, Richard T / Sims, Robert J / Trojer, Patrick / Levell, Julian R

ACS medicinal chemistry letters

2020 Volume 11, Issue 6, Page(s) 1205–1212

Abstract: Histone methyltransferase EZH2, which is the catalytic subunit of the PRC2 complex, catalyzes the methylation of histone H3K27-a transcriptionally repressive post-translational modification (PTM). EZH2 is commonly mutated in hematologic malignancies and ... ...

Abstract	Histone methyltransferase EZH2, which is the catalytic subunit of the PRC2 complex, catalyzes the methylation of histone H3K27-a transcriptionally repressive post-translational modification (PTM). EZH2 is commonly mutated in hematologic malignancies and frequently overexpressed in solid tumors, where its expression level often correlates with poor prognosis. First generation EZH2 inhibitors are beginning to show clinical benefit, and we believe that a second generation EZH2 inhibitor could further build upon this foundation to fully realize the therapeutic potential of EZH2 inhibition. During our medicinal chemistry campaign, we identified 4-thiomethyl pyridone as a key modification that led to significantly increased potency and prolonged residence time. Leveraging this finding, we optimized a series of EZH2 inhibitors, with enhanced antitumor activity and improved physiochemical properties, which have the potential to expand the clinical use of EZH2 inhibition.
Language	English
Publishing date	2020-03-26
Publishing country	United States
Document type	Journal Article
ISSN	1948-5875
ISSN	1948-5875
DOI	10.1021/acsmedchemlett.0c00045
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Article ; Online: Docosahexaenoic acid selectively induces human prostate cancer cell sensitivity to oxidative stress through modulation of NF-κB.

Cavazos, David A / Price, Ramona S / Apte, Shruti S / deGraffenried, Linda A

The Prostate

2011 Volume 71, Issue 13, Page(s) 1420–1428

Abstract: Background: Oxidative burden is strongly implicated in the pathogenesis of age-related diseases, including prostate cancer tumor formation. As omega-3 fatty acids possess known antioxidant properties, we investigated the effects of docosahexaenoic acid ( ...

Abstract	Background: Oxidative burden is strongly implicated in the pathogenesis of age-related diseases, including prostate cancer tumor formation. As omega-3 fatty acids possess known antioxidant properties, we investigated the effects of docosahexaenoic acid (DHA-22:6n-3), one component of fish oil, in modulating the effects of oxidative DNA damage in LNCaP and PacMetUT1 human prostate adenocarcinoma cells and in a normal human prostate cell line, PrEC. Methods: Cell survival was determined by an inhibition of colony formation assay. DNA double-strand breaks, NF-κB subcellular localization and relative survivin expression levels were determined by immunofluorescence and survivin expression levels confirmed by immunoblot assay. Measurement of NF-κB transcriptional activity was investigated by dual luciferase assay. Results: LNCaP and PacMetUT1 cells pretreated with DHA and pulsed with 32 µM H(2) O(2) exhibit decreased survival compared to PrEC. γ-H2AX foci, indicating DNA double-strand breaks, were associated with translocation of NF-κB into the nucleus, whereas exposure to DHA prior to H(2) O(2) treatment prevented NF-κB translocation. Further, DHA attenuated H(2) O(2) -induced NF-κB transcriptional activity and diminished expression of the downstream target, survivin. Conclusions: NF-κB is heavily implicated in promoting prosurvival signaling and may be critical for resistance to the chronic oxidative stress observed in the pathogenesis of prostate cancer. Our studies indicate that exposure of cells to physiologically achievable levels of DHA prior to treatment with H(2) O(2) results in decreased cancer cell survival which is associated with nuclear exclusion of NF-κB. We therefore propose that DHA selectively sensitizes prostate cancer cells to growth arrest through attenuation of the NF-κB survival pathway.
MeSH term(s)	Apoptosis ; Cell Line, Tumor ; Cell Nucleus/metabolism ; Docosahexaenoic Acids/pharmacology ; Humans ; Hydrogen Peroxide/pharmacology ; Inhibitor of Apoptosis Proteins/antagonists & inhibitors ; Male ; NF-kappa B/antagonists & inhibitors ; Oxidative Stress ; Prostatic Neoplasms/drug therapy ; Prostatic Neoplasms/metabolism ; Prostatic Neoplasms/pathology
Chemical Substances	BIRC5 protein, human ; Inhibitor of Apoptosis Proteins ; NF-kappa B ; Docosahexaenoic Acids (25167-62-8) ; Hydrogen Peroxide (BBX060AN9V)
Language	English
Publishing date	2011-09-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	604707-5
ISSN	1097-0045 ; 0270-4137
ISSN (online)	1097-0045
ISSN	0270-4137
DOI	10.1002/pros.21359
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