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Article ; Online: A network pharmacology approach and experimental validation to investigate the anticancer mechanism of Qi-Qin-Hu-Chang formula against colitis-associated colorectal cancer through induction of apoptosis via JNK/p38 MAPK signaling pathway.

Wu, Yuguang / Fang, Yulai / Li, Yanan / Au, Ryan / Cheng, Cheng / Li, Weiyang / Xu, Feng / Cui, Yuan / Zhu, Lei / Shen, Hong

Journal of ethnopharmacology

2023 Volume 319, Issue Pt 3, Page(s) 117323

Abstract: Ethnopharmacological relevance: The Qi-Qin-Hu-Chang Formula (QQHCF) is ...

Abstract	Ethnopharmacological relevance: The Qi-Qin-Hu-Chang Formula (QQHCF) is a traditional Chinese medicine prescription that is clinically used at the Affiliated Hospital of Nanjing University of Chinese Medicine for the treatment of colitis-associated colorectal cancer (CAC). Aim of the study: To evaluate the potential therapeutic effects of QQHCF on a CAC mouse model and investigate its underlying mechanisms using network pharmacology and experimental validation. Materials and methods: The active components and potential targets of QQHCF were obtained from Traditional Chinese Medicine Systems Pharmacology (TCMSP) and herb-ingredient-targets gene network were constructed by Cytoscape 3.9.2. Target genes of CAC were obtained from GeneCards, Online Mendelian Inheritance in Man, and DrugBank database. The drug disease target protein-protein interaction (PPI) network was constructed and the core targets were visualized and identified using Cytoscape. The Metascape database was used for GO and KEGG enrichment analysis. UHPLC-MS/MS was used to further identify the active compounds in QQHCF. Subsequently, the therapeutic effects and potential mechanism of QQHCF against CAC were investigated in AOM/DSS-induced CAC mouse in vivo, and HT-29 and HCT116 cells in vitro. Finally, interactions between JNK, p38, and active ingredients were assessed by molecular docking. Results: A total of 176 active compounds, 273 potential therapeutic targets, and 2460 CAC-related target genes were obtained. The number of common targets between QQHCF and CAC were 165. KEGG pathway analysis indicated that the MAPK signaling pathway was closely associated with CAC, which may be the potential mechanism of QQHCF against CAC. Network pharmacology and UHPLC-MS/MS analyses showed that the active compounds of QQHCF included quercetin, kaempferol, luteolin, wogonin, oxymatrine, lupanine, and baicalin. Animal experiments demonstrated that QQHCF reduced tumor load, number, and size in AOM/DSS-treated mice, and induced apoptosis in colon tissue. In vitro experiments further showed that QQHCF induced apoptosis and inhibited cell viability, migration, and invasion in HCT116 and HT-29 cells. Notably, QQHCF activated the JNK/p38 MAPK signaling pathway both in vivo and in vitro. Molecular docking analysis revealed an ability for the main components of QQHCF and JNK/p38 to bind. Conclusion: The present study demonstrated that QQHCF could ameliorate AOM/DSS-induced CAC in mice by activating the JNK/p38 MAPK signaling pathway. These results have important implications for the development of effective treatment strategies for CAC.
MeSH term(s)	Humans ; Animals ; Mice ; Qi ; Colitis-Associated Neoplasms ; Network Pharmacology ; Molecular Docking Simulation ; Tandem Mass Spectrometry ; Signal Transduction ; Apoptosis ; Databases, Genetic ; p38 Mitogen-Activated Protein Kinases ; Drugs, Chinese Herbal/pharmacology ; Drugs, Chinese Herbal/therapeutic use
Chemical Substances	p38 Mitogen-Activated Protein Kinases (EC 2.7.11.24) ; Drugs, Chinese Herbal
Language	English
Publishing date	2023-10-16
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	134511-4
ISSN	1872-7573 ; 0378-8741
ISSN (online)	1872-7573
ISSN	0378-8741
DOI	10.1016/j.jep.2023.117323
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Article ; Online: NADPH oxidase and endoplasmic reticulum stress is associated with neuronal degeneration in orbitofrontal cortex of individuals with alcohol use disorder.

Qin, Liya / Vetreno, Ryan P / Crews, Fulton T

Addiction biology

2023 Volume 28, Issue 1, Page(s) e13262

Abstract: Many disorders of the central nervous system (CNS), including alcohol use disorder (AUD), are associated with induction of proinflammatory neuroimmune signalling and neurodegeneration. In previous studies, we found increased expression of Toll-like ... ...

Abstract	Many disorders of the central nervous system (CNS), including alcohol use disorder (AUD), are associated with induction of proinflammatory neuroimmune signalling and neurodegeneration. In previous studies, we found increased expression of Toll-like receptors (TLRs), activated NF-κB p65 (RELA), and other proinflammatory signalling molecules. Proinflammatory NADPH oxidases generate reactive oxygen species, which are linked to neurodegeneration. We tested the hypothesis that AUD increased RELA activation increases NADPH oxidase-oxidative stress and endoplasmic reticulum (ER) stress cell death cascades in association with neuronal cell death in the human orbitofrontal cortex (OFC). In the AUD OFC, we report mRNA induction of several NADPH oxidases, the dual oxidase DUOX2, and the oxidative stress lipid peroxidation marker 4-HNE and the DNA oxidation marker 8-OHdG that correlate with RELA, a marker of proinflammatory NF-κB activation. This was accompanied by increased expression of the ER stress-associated regulator protein glucose-regulated protein 78 (GRP78), transmembrane sensors activating transcription factor 6 (ATF6), protein kinase RNA-like endoplasmic reticulum kinase (PERK), and inositol-requiring kinase/endonuclease 1 (pIRE1), and the pro-apoptotic transcription factor C/EBP homologous protein (CHOP). Expression of NADPH oxidase-oxidative stress markers correlate with ER stress-associated molecules. Induction of oxidative stress and ER stress signalling pathways correlate with expression of cell death-associated caspases and neuronal cell loss. These data support the hypothesis that proinflammatory RELA-mediated induction of NADPH oxidase-oxidative stress and ER stress-associated signalling cascades is associated with neuronal cell death in the post-mortem human OFC of individuals with AUD.
MeSH term(s)	Humans ; NADPH Oxidases/metabolism ; Alcoholism ; NF-kappa B/metabolism ; Apoptosis ; Endoplasmic Reticulum Stress/physiology ; Prefrontal Cortex/metabolism
Chemical Substances	NADPH Oxidases (EC 1.6.3.-) ; NF-kappa B
Language	English
Publishing date	2023-03-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1324314-7
ISSN	1369-1600 ; 1355-6215
ISSN (online)	1369-1600
ISSN	1355-6215
DOI	10.1111/adb.13262
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Zs.A 4586: Show issues

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Article ; Online: HMGB1 neuroimmune signaling and REST-G9a gene repression contribute to ethanol-induced reversible suppression of the cholinergic neuron phenotype.

Crews, Fulton T / Fisher, Rachael P / Qin, Liya / Vetreno, Ryan P

Molecular psychiatry

2023 Volume 28, Issue 12, Page(s) 5159–5172

Abstract: Adolescent binge drinking increases Toll-like receptor 4 (TLR4), receptor for advanced glycation end products (RAGE), the endogenous TLR4/RAGE agonist high-mobility group box 1 (HMGB1), and proinflammatory neuroimmune signaling in the adult basal ... ...

Abstract	Adolescent binge drinking increases Toll-like receptor 4 (TLR4), receptor for advanced glycation end products (RAGE), the endogenous TLR4/RAGE agonist high-mobility group box 1 (HMGB1), and proinflammatory neuroimmune signaling in the adult basal forebrain in association with persistent reductions of basal forebrain cholinergic neurons (BFCNs). In vivo preclinical adolescent intermittent ethanol (AIE) studies find anti-inflammatory interventions post-AIE reverse HMGB1-TLR4/RAGE neuroimmune signaling and loss of BFCNs in adulthood, suggesting proinflammatory signaling causes epigenetic repression of the cholinergic neuron phenotype. Reversible loss of BFCN phenotype in vivo is linked to increased repressive histone 3 lysine 9 dimethylation (H3K9me2) occupancy at cholinergic gene promoters, and HMGB1-TLR4/RAGE proinflammatory signaling is linked to epigenetic repression of the cholinergic phenotype. Using an ex vivo basal forebrain slice culture (FSC) model, we report EtOH recapitulates the in vivo AIE-induced loss of ChAT+IR BFCNs, somal shrinkage of the remaining ChAT+ neurons, and reduction of BFCN phenotype genes. Targeted inhibition of EtOH-induced proinflammatory HMGB1 blocked ChAT+IR loss while disulfide HMBG1-TLR4 and fully reduced HMGB1-RAGE signaling decreased ChAT+IR BFCNs. EtOH increased expression of the transcriptional repressor RE1-silencing transcription factor (REST) and the H3K9 methyltransferase G9a that was accompanied by increased repressive H3K9me2 and REST occupancy at promoter regions of the BFCN phenotype genes Chat and Trka as well as the lineage transcription factor Lhx8. REST expression was similarly increased in the post-mortem human basal forebrain of individuals with alcohol use disorder, which is negatively correlated with ChAT expression. Administration of REST siRNA and the G9a inhibitor UNC0642 blocked and reversed the EtOH-induced loss of ChAT+IR BFCNs, directly linking REST-G9a transcriptional repression to suppression of the cholinergic neuron phenotype. These data suggest that EtOH induces a novel neuroplastic process involving neuroimmune signaling and transcriptional epigenetic gene repression resulting in the reversible suppression of the cholinergic neuron phenotype.
MeSH term(s)	HMGB1 Protein/metabolism ; HMGB1 Protein/genetics ; Animals ; Ethanol/pharmacology ; Cholinergic Neurons/metabolism ; Cholinergic Neurons/drug effects ; Signal Transduction/drug effects ; Histone-Lysine N-Methyltransferase/metabolism ; Histone-Lysine N-Methyltransferase/genetics ; Phenotype ; Male ; Repressor Proteins/metabolism ; Repressor Proteins/genetics ; Basal Forebrain/metabolism ; Basal Forebrain/drug effects ; Mice ; Toll-Like Receptor 4/metabolism ; Toll-Like Receptor 4/genetics ; Neuroimmunomodulation/drug effects ; Neuroimmunomodulation/physiology ; Binge Drinking/metabolism ; Binge Drinking/genetics ; Humans
Chemical Substances	HMGB1 Protein ; Ethanol (3K9958V90M) ; RE1-silencing transcription factor ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; Repressor Proteins ; Toll-Like Receptor 4
Language	English
Publishing date	2023-07-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1330655-8
ISSN	1476-5578 ; 1359-4184
ISSN (online)	1476-5578
ISSN	1359-4184
DOI	10.1038/s41380-023-02160-6
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Zs.A 4812: Show issues

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Article ; Online: Correction to "Lung SPLUNC1 Peptide Derivatives in the Lipid Membrane Headgroup Kill Gram-Negative Planktonic and Biofilm Bacteria".

Jakkampudi, Tanvi / Lin, Qiao / Mitra, Saheli / Vijai, Aishwarya / Qin, Weiheng / Kang, Ann / Chen, Jespar / Ryan, Emma / Wang, Runxuan / Gong, Yuqi / Heinrich, Frank / Song, Junming / Di, Yuan-Pu Peter / Tristram-Nagle, Stephanie

Biomacromolecules

2024

Language	English
Publishing date	2024-04-19
Publishing country	United States
Document type	Published Erratum
ISSN	1526-4602
ISSN (online)	1526-4602
DOI	10.1021/acs.biomac.4c00501
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Article ; Online: Utility of CT colonography and/or PET-CT preoperatively in obstructing left-sided colorectal cancers - a systematic review.

McGarry, Jennifer / Ng, Zi Qin / Ryan, Fintan / Theophilus, Mary

ANZ journal of surgery

2023 Volume 93, Issue 6, Page(s) 1487–1494

Abstract: Purpose: 15-20% of patients present with near obstructing left-sided colorectal cancer. CT colonography (CTC) or PET-CT has been used to detect synchronous lesions, which may alter preoperative planning of colonic resection. We aim to synthesize the ... ...

Abstract	Purpose: 15-20% of patients present with near obstructing left-sided colorectal cancer. CT colonography (CTC) or PET-CT has been used to detect synchronous lesions, which may alter preoperative planning of colonic resection. We aim to synthesize the usefulness of CT colonography and/or PET-CT in detecting synchronous proximal colon carcinomas in patients who have undergone an incomplete colonoscopy due to a stenosing or obstructing distal colorectal cancer. Methodology: A systematic review was performed by searching the databases up to December 2021. Data collected included demographics of the study population, rate of detection of synchronous carcinomas and impact on management of detection of synchronous carcinomas. Results: A total of 22 studies were included: 17 studies focused on CTC, 3 on PET-CT, and 2 integrated PET-CT with CTC; 2855 patients were included; 53% of patients were male, and 47% were female. All studies reported detection of synchronous proximal colorectal carcinomas using CTC, PET-CT or CTC, and PET-CT combined. CTC detected synchronous carcinomas in 0.2-12.2% of patients. PET-CT was useful in detecting synchronous carcinomas in 4.05-23% of patients. Integrated PET-CT and CTC detected synchronous carcinomas in 2-15% of patients. The surgical plan was changed in 2.4-14.3% of patients after the use of CTC. One PET-CT study reported a change in management in 13.5%. No complication was reported by the use of CTC. Conclusion: CTC is an effective and useful adjunct to colonoscopy in assessing the proximal colon when colonoscopy fails to do so. However, more evidence is needed with the use of PET-CT for this patient population.
MeSH term(s)	Humans ; Male ; Female ; Colonography, Computed Tomographic ; Positron Emission Tomography Computed Tomography ; Colorectal Neoplasms/complications ; Colorectal Neoplasms/diagnostic imaging ; Colorectal Neoplasms/surgery ; Colonoscopy ; Carcinoma
Language	English
Publishing date	2023-04-06
Publishing country	Australia
Document type	Systematic Review ; Journal Article ; Review
ZDB-ID	2050749-5
ISSN	1445-2197 ; 1445-1433 ; 0004-8682
ISSN (online)	1445-2197
ISSN	1445-1433 ; 0004-8682
DOI	10.1111/ans.18450
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Zs.A 180: Show issues

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Article ; Online: A suicidal mechanism for the exquisite temperature sensitivity of TRPV1.

Mugo, Andrew / Chou, Ryan / Chin, Felix / Liu, Beiying / Jiang, Qiu-Xing / Qin, Feng

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

2023 Volume 120, Issue 36, Page(s) e2300305120

Abstract: The vanilloid receptor TRPV1 is an exquisite nociceptive sensor of noxious heat, but its temperature-sensing mechanism is yet to define. Thermodynamics dictate that this channel must undergo an unusually energetic allosteric transition. Thus, it is of ... ...

Abstract	The vanilloid receptor TRPV1 is an exquisite nociceptive sensor of noxious heat, but its temperature-sensing mechanism is yet to define. Thermodynamics dictate that this channel must undergo an unusually energetic allosteric transition. Thus, it is of fundamental importance to measure directly the energetics of this transition in order to properly decipher its temperature-sensing mechanism. Previously, using submillisecond temperature jumps and patch-clamp recording, we estimated that the heat activation for TRPV1 opening incurs an enthalpy change on the order of 100 kcal/mol. Although this energy is on a scale unparalleled by other known biological receptors, the generally imperfect allosteric coupling in proteins implies that the actual amount of heat uptake driving the TRPV1 transition could be much larger. In this paper, we apply differential scanning calorimetry to directly monitor the heat flow in TRPV1 that accompanies its temperature-induced conformational transition. Our measurements show that heat invokes robust, complex thermal transitions in TRPV1 that include both channel opening and a partial protein unfolding transition and that these two processes are inherently coupled. Our findings support that irreversible protein unfolding, which is generally thought to be destructive to physiological function, is essential to TRPV1 thermal transduction and, possibly, to other strongly temperature-dependent processes in biology.
MeSH term(s)	Biological Transport ; Hot Temperature ; Temperature ; Thermodynamics ; TRPV Cation Channels
Chemical Substances	TRPV Cation Channels
Language	English
Publishing date	2023-08-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2300305120
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Article ; Online: Alkyl sulfinates as cross-coupling partners for programmable and stereospecific installation of C(sp

Zhou, Min / Tsien, Jet / Dykstra, Ryan / Hughes, Jonathan M E / Peters, Byron K / Merchant, Rohan R / Gutierrez, Osvaldo / Qin, Tian

Nature chemistry

2023 Volume 15, Issue 4, Page(s) 550–559

Abstract: In recent years, a variety of cycloalkyl groups with quaternary carbons, in particular cyclopropyl and cyclobutyl trifluoromethyl groups, have emerged as promising bioisosteres in drug-like molecules. The modular installation of such bioisosteres remains ...

Abstract	In recent years, a variety of cycloalkyl groups with quaternary carbons, in particular cyclopropyl and cyclobutyl trifluoromethyl groups, have emerged as promising bioisosteres in drug-like molecules. The modular installation of such bioisosteres remains challenging to synthetic chemists. Alkyl sulfinate reagents have been developed as radical precursors to prepare functionalized heterocycles with the desired alkyl bioisosteres. However, the innate (radical) reactivity of this transformation poses reactivity and regioselectivity challenges for the functionalization of any aromatic or heteroaromatic scaffold. Here we showcase the ability of alkyl sulfinates to engage in sulfurane-mediated C(sp
Language	English
Publishing date	2023-03-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2464596-5
ISSN	1755-4349 ; 1755-4330
ISSN (online)	1755-4349
ISSN	1755-4330
DOI	10.1038/s41557-023-01150-z
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Article ; Online: Manganese(II) EOB-Pyclen Diacetate for Liver-Specific MRI.

Hall, Ryan C / Qin, Jingcan / Laney, Victoria / Ayat, Nadia / Lu, Zheng-Rong

ACS applied bio materials

2022 Volume 5, Issue 2, Page(s) 451–458

Abstract: MRI is increasingly utilized for the diagnosis of liver disease and focal liver lesions. Although liver-targeted gadolinium-based contrast agents (GBCAs) have high efficacy, there continue to be safety concerns regarding release of toxic Gd(III) ions. ... ...

Abstract	MRI is increasingly utilized for the diagnosis of liver disease and focal liver lesions. Although liver-targeted gadolinium-based contrast agents (GBCAs) have high efficacy, there continue to be safety concerns regarding release of toxic Gd(III) ions. Herein, Mn(EOB-PC2A) is synthesized as a nongadolinium alternative for liver-specific MRI. Mn(EOB-PC2A) has an
MeSH term(s)	Azabicyclo Compounds ; Contrast Media ; Gadolinium DTPA ; Humans ; Ions ; Liver/diagnostic imaging ; Magnetic Resonance Imaging ; Manganese
Chemical Substances	Azabicyclo Compounds ; Contrast Media ; Ions ; pyclen ; Manganese (42Z2K6ZL8P) ; Gadolinium DTPA (K2I13DR72L)
Language	English
Publishing date	2022-02-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2576-6422
ISSN (online)	2576-6422
DOI	10.1021/acsabm.1c01259
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Article ; Online: Electrode Treatments for Redox Flow Batteries

Harsh Agarwal / Esha Roy / Nirala Singh / Peter A.A. Klusener / Ryan M. Stephens / Qin Tracy Zhou

Advanced Science, Vol 11, Iss 1, Pp n/a-n/a (2024)

Translating Our Understanding from Vanadium to Aqueous‐Organic

2024

Abstract: Abstract Redox flow batteries (RFBs) are a promising technology for long‐duration energy storage; but they suffer from inefficiencies in part due to the overvoltages at the electrode surface. In this work, more than 70 electrode treatments are reviewed ... ...

Abstract	Abstract Redox flow batteries (RFBs) are a promising technology for long‐duration energy storage; but they suffer from inefficiencies in part due to the overvoltages at the electrode surface. In this work, more than 70 electrode treatments are reviewed that are previously shown to reduce the overvoltages and improve performance for vanadium RFBs (VRFBs), the most commercialized RFB technology. However, identifying treatments that improve performance the most and whether they are industrially implementable is challenging. This study attempts to address this challenge by comparing treatments under similar operating conditions and accounting for the treatment process complexity. The different treatments are compared at laboratory and industrial scale based on criteria for VRFB performance, treatment stability, economic feasibility, and ease of industrial implementation. Thermal, plasma, electrochemical oxidation, CO2 treatments, as well as Bi, Ag, and Cu catalysts loaded on electrodes are identified as the most promising for adoption in large scale VRFBs. The similarity in electrode treatments for aqueous‐organic RFBs (AORFBs) and VRFBs is also identified. The need of standardization in RFBs testing along with fundamental studies to understand charge transfer reactions in redox active species used in RFBs moving forward is emphasized.
Keywords	aqueous‐organic redox flow batteries ; carbon felts ; electrocatalysts ; electrode treatments ; flow batteries ; quinones ; Science ; Q
Subject code	660
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
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Article ; Online: Automatic peak detection algorithm based on continuous wavelet transform for complex chromatograms from multi-detector micro-scale gas chromatographs.

Zhao, Xiangyu / Aridi, Ryan / Hume, Jacob / Subbiah, Swetha / Wu, Xingqi / Chung, Hyunwon / Qin, Yutao / Gianchandani, Yogesh B

Journal of chromatography. A

2023 Volume 1714, Page(s) 464582

Abstract: Peak detection for chromatograms, including the detection of peak retention times, peak start locations, and peak end locations, is an important processing step for extracting peak information that is used for chemical recognition. Compared to benchtop ... ...

Abstract	Peak detection for chromatograms, including the detection of peak retention times, peak start locations, and peak end locations, is an important processing step for extracting peak information that is used for chemical recognition. Compared to benchtop gas chromatographs, the chromatograms generated by microscale gas chromatographs (µGCs) often contain higher noise levels, peak overlap, peak asymmetry, and both positive and negative chromatographic peaks, increasing the challenges for peak detection. This paper reports an automatic peak detection algorithm based on continuous wavelet transform (CWT) for chromatograms generated by multi-detector µGCs. The relationship between chemical retention time and peak width is leveraged to differentiate chromatographic peaks from noise and baseline drift. Special features in the CWT coefficients are leveraged to detect peak overlap and asymmetry. For certain detectors that may generate positive and negative chromatographic peaks, the peaks cannot be independently detected reliably, but the peak information can be well extracted using peak information generated by other in-line single-polarity detectors. The implemented algorithm provided a true positive rate of 97.2 % and false discovery rate of 7.8 % for chromatograms generated by a µGC with three integrated detectors, two capacitive and one photoionization. The chromatograms included complex scenarios with positive and negative chromatographic peaks, up to five consecutive overlapping peaks, peak asymmetry factor up to 24, and signal-to-noise ratios spanning 9-2800.
MeSH term(s)	Wavelet Analysis ; Algorithms ; Chromatography, Gas/methods
Language	English
Publishing date	2023-12-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1171488-8
ISSN	1873-3778 ; 0021-9673
ISSN (online)	1873-3778
ISSN	0021-9673
DOI	10.1016/j.chroma.2023.464582
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