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Article: The role of Smarcad1 in retroviral repression in mouse embryonic stem cells.

Bren, Igor / Tal, Ayellet / Strauss, Carmit / Schlesinger, Sharon

2024 Volume 15, Issue 1, Page(s) 4

Abstract: Background: Moloney murine leukemia virus (MLV) replication is suppressed in mouse embryonic stem cells (ESCs) by the Trim28-SETDB1 complex. The chromatin remodeler Smarcad1 interacts with Trim28 and was suggested to allow the deposition of the histone ... ...

Abstract	Background: Moloney murine leukemia virus (MLV) replication is suppressed in mouse embryonic stem cells (ESCs) by the Trim28-SETDB1 complex. The chromatin remodeler Smarcad1 interacts with Trim28 and was suggested to allow the deposition of the histone variant H3.3. However, the role of Trim28, H3.3, and Smarcad1 in MLV repression in ESCs still needs to be fully understood. Results: In this study, we used MLV to explore the role of Smarcad1 in retroviral silencing in ESCs. We show that Smarcad1 is immediately recruited to the MLV provirus. Based on the repression dynamics of a GFP-reporter MLV, our findings suggest that Smarcad1 plays a critical role in the establishment and maintenance of MLV repression, as well as other Trim28-targeted genomic loci. Furthermore, Smarcad1 is important for stabilizing and strengthening Trim28 binding to the provirus over time, and its presence around the provirus is needed for proper deposition of H3.3 on the provirus. Surprisingly, the combined depletion of Smarcad1 and Trim28 results in enhanced MLV derepression, suggesting that these two proteins may also function independently to maintain repressive chromatin states. Conclusions: Overall, the results of this study provide evidence for the crucial role of Smarcad1 in the silencing of retroviral elements in embryonic stem cells. Further research is needed to fully understand how Smarcad1 and Trim28 cooperate and their implications for gene expression and genomic stability.
Language	English
Publishing date	2024-03-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2536054-1
ISSN	1759-8753
ISSN	1759-8753
DOI	10.1186/s13100-024-00314-z
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Article ; Online: Bioinspired and biomolecular catalysts for energy conversion and storage.

Salamatian, Alison A / Bren, Kara L

FEBS letters

2022

Abstract: Metalloenzymes are remarkable for facilitating challenging redox transformations with high efficiency and selectivity. In the area of alternative energy, scientists aim to capture these properties in bioinspired and engineered biomolecular catalysts for ... ...

Abstract	Metalloenzymes are remarkable for facilitating challenging redox transformations with high efficiency and selectivity. In the area of alternative energy, scientists aim to capture these properties in bioinspired and engineered biomolecular catalysts for the efficient and fast production of fuels from low-energy feedstocks such as water and carbon dioxide. In this short review, efforts to mimic biological catalysts for proton reduction and carbon dioxide reduction are highlighted. Two important recurring themes are the importance of the microenvironment of the catalyst active site and the key role of proton delivery to the active site in achieving desired reactivity. Perspectives on ongoing and future challenges are also provided.
Language	English
Publishing date	2022-11-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14533
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Article: Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening.

Jukič, Marko / Kralj, Sebastjan / Kolarič, Anja / Bren, Urban

Pharmaceuticals (Basel, Switzerland)

2023 Volume 16, Issue 8

Abstract: Peptides, or short chains of amino-acid residues, are becoming increasingly important as active ingredients of drugs and as crucial probes and/or tools in medical, biotechnological, and pharmaceutical research. Situated at the interface between small ... ...

Abstract	Peptides, or short chains of amino-acid residues, are becoming increasingly important as active ingredients of drugs and as crucial probes and/or tools in medical, biotechnological, and pharmaceutical research. Situated at the interface between small molecules and larger macromolecular systems, they pose a difficult challenge for computational methods. We report an in silico peptide library generation and prioritization workflow using CmDock for identifying tetrapeptide ligands that bind to Fc regions of antibodies that is analogous to known in vitro recombinant peptide libraries' display and expression systems. The results of our in silico study are in accordance with existing scientific literature on in vitro peptides that bind to antibody Fc regions. In addition, we postulate an evolving in silico library design workflow that will help circumvent the combinatorial problem of in vitro comprehensive peptide libraries by focusing on peptide subunits that exhibit favorable interaction profiles in initial in silico peptide generation and testing.
Language	English
Publishing date	2023-08-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph16081170
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Article ; Online: A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover.

Glass, David S / Bren, Anat / Vaisbourd, Elizabeth / Mayo, Avi / Alon, Uri

Cell

2024 Volume 187, Issue 4, Page(s) 931–944.e12

Abstract: Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant ... ...

Abstract	Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.
MeSH term(s)	Cell Differentiation ; Escherichia coli/cytology ; Escherichia coli/genetics ; Integrases/metabolism ; Synthetic Biology/methods ; Genetic Fitness ; Drug Resistance, Bacterial
Chemical Substances	Integrases (EC 2.7.7.-)
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2024.01.024
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Article: Novel Small-Molecule Inhibitors of the SARS-CoV-2 Spike Protein Binding to Neuropilin 1.

Kolarič, Anja / Jukič, Marko / Bren, Urban

Pharmaceuticals (Basel, Switzerland)

2022 Volume 15, Issue 2

Abstract: Furin cleavage of the SARS-CoV-2 spike protein results in a polybasic terminal sequence termed the C-end rule (CendR), which is responsible for the binding to neuropilin 1 (NRP1), enhancing viral infectivity and entry into the cell. Here we report the ... ...

Abstract	Furin cleavage of the SARS-CoV-2 spike protein results in a polybasic terminal sequence termed the C-end rule (CendR), which is responsible for the binding to neuropilin 1 (NRP1), enhancing viral infectivity and entry into the cell. Here we report the identification of 20 small-molecule inhibitors that emerged from a virtual screening of nearly 950,000 drug-like compounds that bind with high probability to the CendR-binding pocket of NRP1. In a spike NRP1 binding assay, two of these compounds displayed a stronger inhibition of spike protein binding to NRP1 than the known NRP1 antagonist
Language	English
Publishing date	2022-01-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph15020165
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Article ; Online: Neuropilin (NRPs) Related Pathological Conditions and Their Modulators.

Broz, Matic / Kolarič, Anja / Jukič, Marko / Bren, Urban

International journal of molecular sciences

2022 Volume 23, Issue 15

Abstract: Neuropilin 1 (NRP1) represents one of the two homologous neuropilins (NRP, splice variants of neuropilin 2 are the other) found in all vertebrates. It forms a transmembrane glycoprotein distributed in many human body tissues as a (co)receptor for a ... ...

Abstract	Neuropilin 1 (NRP1) represents one of the two homologous neuropilins (NRP, splice variants of neuropilin 2 are the other) found in all vertebrates. It forms a transmembrane glycoprotein distributed in many human body tissues as a (co)receptor for a variety of different ligands. In addition to its physiological role, it is also associated with various pathological conditions. Recently, NRP1 has been discovered as a coreceptor for the SARS-CoV-2 viral entry, along with ACE2, and has thus become one of the COVID-19 research foci. However, in addition to COVID-19, the current review also summarises its other pathological roles and its involvement in clinical diseases like cancer and neuropathic pain. We also discuss the diversity of native NRP ligands and perform a joint analysis. Last but not least, we review the therapeutic roles of NRP1 and introduce a series of NRP1 modulators, which are typical peptidomimetics or other small molecule antagonists, to provide the medicinal chemistry community with a state-of-the-art overview of neuropilin modulator design and NRP1 druggability assessment.
MeSH term(s)	Animals ; COVID-19 ; Humans ; Neoplasms ; Neuropilin-1/chemistry ; Neuropilin-1/genetics ; Neuropilin-2/genetics ; SARS-CoV-2
Chemical Substances	Neuropilin-2 ; Neuropilin-1 (144713-63-3)
Language	English
Publishing date	2022-07-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23158402
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Article ; Online: Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing.

Bren, Anat / Glass, David S / Kohanim, Yael Korem / Mayo, Avi / Alon, Uri

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 51, Page(s) e2312651120

Abstract: Antibiotic effectiveness depends on a variety of factors. While many mechanistic details of antibiotic action are known, the connection between death rate and bacterial physiology is poorly understood. A common observation is that death rate in ... ...

Abstract	Antibiotic effectiveness depends on a variety of factors. While many mechanistic details of antibiotic action are known, the connection between death rate and bacterial physiology is poorly understood. A common observation is that death rate in antibiotics rises linearly with growth rate; however, it remains unclear how other factors, such as environmental conditions and whole-cell physiological properties, affect bactericidal activity. To address this, we developed a high-throughput assay to precisely measure antibiotic-mediated death. We found that death rate is linear in growth rate, but the slope depends on environmental conditions. Growth under stress lowers death rate compared to nonstressed environments with similar growth rate. To understand stress's role, we developed a mathematical model of bacterial death based on resource allocation that includes a stress-response sector; we identify this sector using RNA-seq. Our model accurately predicts the minimal inhibitory concentration (MIC) with zero free parameters across a wide range of growth conditions. The model also quantitatively predicts death and MIC when sectors are experimentally modulated using cyclic adenosine monophosphate (cAMP), including protection from death at very low cAMP levels. The present study shows that different conditions with equal growth rate can have different death rates and establishes a quantitative relation between growth, death, and MIC that suggests approaches to improve antibiotic efficacy.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Bacterial Physiological Phenomena ; Bacteria ; Microbial Sensitivity Tests ; Models, Theoretical
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-12-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2312651120
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Article ; Online: Differential effect of histone H3.3 depletion on retroviral repression in embryonic stem cells.

Tal, Ayellet / Aguilera, Jose David / Bren, Igor / Strauss, Carmit / Schlesinger, Sharon

Clinical epigenetics

2023 Volume 15, Issue 1, Page(s) 83

Abstract: Background: Integration of retroviruses into the host genome can impair the genomic and epigenomic integrity of the cell. As a defense mechanism, epigenetic modifications on the proviral DNA repress retroviral sequences in mouse embryonic stem cells ( ... ...

Abstract	Background: Integration of retroviruses into the host genome can impair the genomic and epigenomic integrity of the cell. As a defense mechanism, epigenetic modifications on the proviral DNA repress retroviral sequences in mouse embryonic stem cells (ESC). Here, we focus on the histone 3 variant H3.3, which is abundant in active transcription zones, as well as centromeres and heterochromatinized repeat elements, e.g., endogenous retroviruses (ERV). Results: To understand the involvement of H3.3 in the epigenetic silencing of retroviral sequences in ESC, we depleted the H3.3 genes in ESC and transduced the cells with GFP-labeled MLV pseudovirus. This led to altered retroviral repression and reduced Trim28 recruitment, which consequently led to a loss of heterochromatinization in proviral sequences. Interestingly, we show that H3.3 depletion has a differential effect depending on which of the two genes coding for H3.3, H3f3a or H3f3b, are knocked out. Depletion of H3f3a resulted in a transient upregulation of incoming retroviral expression and ERVs, while the depletion of H3f3b did not have the same effect and repression was maintained. However, the depletion of both genes resulted in a stable activation of the retroviral promoter. These findings suggest that H3.3 is important for regulating retroviral gene expression in mouse ESC and provide evidence for a distinct function of the two H3.3 genes in this regulation. Furthermore, we show that Trim28 is needed for depositing H3.3 in retroviral sequences, suggesting a functional interaction between Trim28 recruitment and H3.3 loading. Conclusions: Identifying the molecular mechanisms by which H3.3 and Trim28 interact and regulate retroviral gene expression could provide a deeper understanding of the fundamental processes involved in retroviral silencing and the general regulation of gene expression, thus providing new answers to a central question of stem cell biology.
MeSH term(s)	Animals ; Mice ; Histones/genetics ; Histones/metabolism ; Nuclear Proteins/genetics ; Repressor Proteins/genetics ; DNA Methylation ; Gene Silencing ; Embryonic Stem Cells/metabolism ; Endogenous Retroviruses/genetics ; Endogenous Retroviruses/metabolism ; Proviruses/genetics
Chemical Substances	Histones ; Nuclear Proteins ; Repressor Proteins
Language	English
Publishing date	2023-05-11
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553921-8
ISSN	1868-7083 ; 1868-7075
ISSN (online)	1868-7083
ISSN	1868-7075
DOI	10.1186/s13148-023-01499-5
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Article ; Online: Kidney Biopsy Findings and Clinical Outcomes of US Veterans with Inflammatory Bowel Disease.

Ravipati, Prasanth / Reule, Scott / Bren, Alyssa / Bu, Lihong / Vaughn, Byron P / Nachman, Patrick H

Glomerular diseases

2023 Volume 3, Issue 1, Page(s) 233–240

Abstract: Introduction: Patients with inflammatory bowel disease (IBD; ulcerative colitis [UC] and Crohn's disease [CD]) may have unique patterns of kidney injury related to their underlying or coexisting disease or to medications. We present the kidney biopsy ... ...

Abstract	Introduction: Patients with inflammatory bowel disease (IBD; ulcerative colitis [UC] and Crohn's disease [CD]) may have unique patterns of kidney injury related to their underlying or coexisting disease or to medications. We present the kidney biopsy findings and clinical outcomes of veterans with UC or CD from the US Department of Veteran's Affairs (VA) health system. Methods: Histopathologic and clinical data were extracted by retrospective review of the VA electronic health record of patients with IBD and a kidney biopsy between 2000 and 2018. Incident end-stage kidney disease (ESKD) was defined as requirement of kidney replacement therapy. Statistical analyses were performed using SAS. Results: A total of 140 patients (UC: 91 and CD: 49) underwent kidney biopsy. The three most common diagnoses were IgA nephropathy (17.1%), diabetic nephropathy (14.3%), and acute interstitial nephritis (9.3%). Significant interstitial fibrosis, tubular atrophy, and arteriosclerosis were present in 45% of biopsies. Twenty-six percent of patients with UC and 20% of those with CD progressed to ESKD, with a mean time from kidney biopsy of 3.1 and 1.9 years, respectively. Forty-five percent of patients with UC and 34% of those with CD died, with a mean time from kidney biopsy of 4.3 and 4.6 years, respectively. Conclusion: Among US veterans with IBD who underwent a kidney biopsy, IgA nephropathy, diabetic nephropathy, and interstitial nephritis were among the most common findings. Additionally, features of advanced kidney disease with rapid clinical progression to ESKD or death were observed. These findings suggest a delay and possibly a low rate of diagnosis.
Language	English
Publishing date	2023-09-30
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-3633
ISSN (online)	2673-3633
DOI	10.1159/000534062
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Article: Identification of Triazolopyrimidinyl Scaffold SARS-CoV-2 Papain-Like Protease (PL

Kralj, Sebastjan / Jukič, Marko / Bahun, Miha / Kranjc, Luka / Kolarič, Anja / Hodošček, Milan / Ulrih, Nataša Poklar / Bren, Urban

Pharmaceutics

2024 Volume 16, Issue 2

Abstract: The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its companion disease, COVID-19, has reminded us of the importance of basic coronaviral research. In this study, a comprehensive approach using molecular docking, in ... ...

Abstract	The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its companion disease, COVID-19, has reminded us of the importance of basic coronaviral research. In this study, a comprehensive approach using molecular docking, in vitro assays, and molecular dynamics simulations was applied to identify potential inhibitors for SARS-CoV-2 papain-like protease (PL
Language	English
Publishing date	2024-01-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527217-2
ISSN	1999-4923
ISSN	1999-4923
DOI	10.3390/pharmaceutics16020169
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