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Article ; Online: Implementation of pharmacogenomics testing for precision medicine.

Kanegusuku, Anastasia L Gant / Chan, Clarence W / O'Donnell, Peter H / Yeo, Kiang-Teck J

Critical reviews in clinical laboratory sciences

2023 Volume 61, Issue 2, Page(s) 89–106

Abstract: Great strides have been made in the past decade to lower barriers to clinical pharmacogenomics implementation. Nevertheless, PGx consultation prior to prescribing therapeutics is not yet mainstream. This review addresses the current climate surrounding ... ...

Abstract	Great strides have been made in the past decade to lower barriers to clinical pharmacogenomics implementation. Nevertheless, PGx consultation prior to prescribing therapeutics is not yet mainstream. This review addresses the current climate surrounding PGx implementation, focusing primarily on strategies for implementation at academic institutions, particularly at The University of Chicago, and provides an up-to-date guide of resources supporting the development of PGx programs. Remaining challenges and recent strategies for overcoming these challenges to implementation are discussed.
MeSH term(s)	Humans ; Precision Medicine ; Pharmacogenetics
Language	English
Publishing date	2023-09-30
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	280641-1
ISSN	1549-781X ; 1040-8363 ; 0590-8191
ISSN (online)	1549-781X
ISSN	1040-8363 ; 0590-8191
DOI	10.1080/10408363.2023.2255279
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Article ; Online: Is Adding IgM Antibody to Polymerase Chain Reaction Testing Useful for COVID-19 Travel Screening?

Yi, Xin / Chan, Clarence W / Yeo, Kiang-Teck J

American journal of clinical pathology

2021 Volume 155, Issue 3, Page(s) 321–323

MeSH term(s)	Antibodies, Viral/blood ; COVID-19/blood ; COVID-19/diagnosis ; COVID-19 Nucleic Acid Testing ; COVID-19 Serological Testing/methods ; Communicable Diseases, Imported/prevention & control ; Humans ; Immunoglobulin M/blood ; SARS-CoV-2 ; Travel Medicine/methods
Chemical Substances	Antibodies, Viral ; Immunoglobulin M
Language	English
Publishing date	2021-01-05
Publishing country	England
Document type	Editorial
ZDB-ID	2944-0
ISSN	1943-7722 ; 0002-9173
ISSN (online)	1943-7722
ISSN	0002-9173
DOI	10.1093/ajcp/aqaa270
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Article ; Online: Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding.

Chan, Clarence W / Mondragón, Alfonso

Nucleic acids research

2020 Volume 48, Issue 13, Page(s) 7569–7583

Abstract: Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the ... ...

Abstract	Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Bacillus subtilis ; Cobamides/chemistry ; RNA Folding ; Riboswitch ; Vitamin B 12/chemistry
Chemical Substances	Aptamers, Nucleotide ; Cobamides ; Riboswitch ; cobamamide (F0R1QK73KB) ; Vitamin B 12 (P6YC3EG204)
Language	English
Publishing date	2020-06-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa507
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Article: Addressing the risk and management of cardiometabolic complications in prostate cancer patients on androgen deprivation therapy and androgen receptor axis-targeted therapy: consensus statements from the Hong Kong Urological Association and the Hong Kong Society of Uro-Oncology.

Poon, Darren M C / Tan, Guang-Ming / Chan, Kuen / Chan, Marco T Y / Chan, Tim-Wai / Kan, Raymond W M / Lam, Martin H C / Leung, Clarence L H / Wong, Kenneth C W / Kam, Kevin K H / Ng, Chi-Fai / Chiu, Peter K F

Frontiers in oncology

2024 Volume 14, Page(s) 1345322

Abstract: Background: Androgen deprivation therapy (ADT) is the foundational treatment for metastatic prostate cancer (PCa). Androgen receptor (AR) axis-targeted therapies are a new standard of care for advanced PCa. Although these agents have significantly ... ...

Abstract	Background: Androgen deprivation therapy (ADT) is the foundational treatment for metastatic prostate cancer (PCa). Androgen receptor (AR) axis-targeted therapies are a new standard of care for advanced PCa. Although these agents have significantly improved patient survival, the suppression of testosterone is associated with an increased risk of cardiometabolic syndrome. This highlights the urgency of multidisciplinary efforts to address the cardiometabolic risk of anticancer treatment in men with PCa. Methods: Two professional organizations invited five urologists, five clinical oncologists, and two cardiologists to form a consensus panel. They reviewed the relevant literature obtained by searching PubMed for the publication period from April 2013 to April 2023, to address three discussion areas: (i) baseline assessment and screening for risk factors in PCa patients before the initiation of ADT and AR axis-targeted therapies; (ii) follow-up and management of cardiometabolic complications; and (iii) selection of ADT agents among high-risk patients. The panel convened four meetings to discuss and draft consensus statements using a modified Delphi method. Each drafted statement was anonymously voted on by every panelist. Results: The panel reached a consensus on 18 statements based on recent evidence and expert insights. Conclusion: These consensus statements serve as a practical recommendation for clinicians in Hong Kong, and possibly the Asia-Pacific region, in the management of cardiometabolic toxicities of ADT or AR axis-targeted therapies in men with PCa.
Language	English
Publishing date	2024-01-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2024.1345322
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Article ; Online: Use of a Vanadate Oxidation Conjugated Bilirubin Assay to Reduce Test Cancellations Resulting from Hemolyzed Specimens in Pediatric Patients.

Kaumeyer, Benjamin A / Tjota, Melissa Y / Parker, Kyle / Chan, Clarence W / Gant Kanegusuku, Anastasia / Baldwin, Angel D / Yeo, Kiang-Teck J

American journal of clinical pathology

2022

Abstract: Objectives: We sought to replace the highly hemolysis-susceptible diazo conjugated bilirubin (Bc) assay with the more robust vanadate oxidation method and determine its impact on test cancellation in the pediatric population.: Methods: Analytical ... ...

Abstract	Objectives: We sought to replace the highly hemolysis-susceptible diazo conjugated bilirubin (Bc) assay with the more robust vanadate oxidation method and determine its impact on test cancellation in the pediatric population. Methods: Analytical validation of the Randox vanadate assay and comparison with the Roche diazo method were performed. The frequency of pediatric sample cancellation because of hemolysis was compared between the diazo and vanadate methods by retrospective analysis of clinical test data. Results: The vanadate assay demonstrated no clinically significant interference from hemolysis up to a hemolysis index of 1,300 (approximately 13 g/L hemoglobin). There was a strong correlation with the diazo method (r2 = 0.97) but with a positive slope bias of 1.27. Implementing the vanadate method resulted in a significantly lower proportion of pediatric samples cancelled because of hemolysis compared with the diazo method (0.6% of 688 patients vs 30.6% of 10,464 patients, respectively; P < .001), with a 0.6% (n = 513) vs 43.2% (n = 6,464) reduction in test cancellations (P < .001) for children younger than 6 months of age. Conclusions: The vanadate method showed robust performance against hemolysis. Its implementation resulted in a significant decrease in pediatric tests cancelled because of hemolysis.
Language	English
Publishing date	2022-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2944-0
ISSN	1943-7722 ; 0002-9173
ISSN (online)	1943-7722
ISSN	0002-9173
DOI	10.1093/ajcp/aqac139
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Article ; Online: Implementation of a Sample Pooling Strategy for the Direct Detection of SARS-CoV-2 by Real-Time Polymerase Chain Reaction During the COVID-19 Pandemic.

Chan, Clarence W / Kwon, Seunghyug / Matushek, Scott M / Ciaglia, Carol / Bethel, Cindy / Beavis, Kathleen G

American journal of clinical pathology

2021 Volume 156, Issue 1, Page(s) 15–23

Abstract: Objectives: To report our institutional experience in devising and implementing a pooling protocol and process for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) testing over a 3- ... ...

Abstract	Objectives: To report our institutional experience in devising and implementing a pooling protocol and process for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) testing over a 3-month period in the fall of 2020. Methods: The widespread testing implemented in the United States for detecting SARS-CoV-2 infection in response to the coronavirus disease 2019 pandemic has led to a significant shortage of testing supplies and therefore has become a major impediment to the public health response. To date, several institutions have implemented sample pooling, but publications documenting these experiences are sparse. Nasal and nasopharyngeal samples collected from low-positivity (<5%) areas were tested in pools of five on the Roche cobas 6800 analyzer system. Routine SARS-CoV-2 RT-PCR turnaround times between sample collection to result reporting were monitored and compared before and after sample pooling implementation. Results: A total of 4,131 sample pools were tested over a 3-month period (during which 39,770 RT-PCR results were reported from the Roche system), allowing our laboratory to save 13,824 tests, equivalent to a conservation rate of 35%. A 48-hour or less turnaround time was generally maintained throughout the pooling period. Conclusions: Sample pooling offers a viable means to mitigate shortfalls of PCR testing supplies in the ongoing pandemic without significantly compromising overall turnaround times.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/genetics ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Humans ; RNA, Viral/genetics ; Real-Time Polymerase Chain Reaction/methods ; Reverse Transcriptase Polymerase Chain Reaction/methods ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; Specimen Handling/methods
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-05-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2944-0
ISSN	1943-7722 ; 0002-9173
ISSN (online)	1943-7722
ISSN	0002-9173
DOI	10.1093/ajcp/aqab035
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Article ; Online: Crystal Structure of Human Rpp20/Rpp25 Reveals Quaternary Level Adaptation of the Alba Scaffold as Structural Basis for Single-stranded RNA Binding.

Chan, Clarence W / Kiesel, Benjamin R / Mondragón, Alfonso

Journal of molecular biology

2018 Volume 430, Issue 10, Page(s) 1403–1416

Abstract: Ribonuclease P (RNase P) catalyzes the removal of 5' leaders of tRNA precursors and its central catalytic RNA subunit is highly conserved across all domains of life. In eukaryotes, RNase P and RNase MRP, a closely related ribonucleoprotein enzyme, share ... ...

Abstract	Ribonuclease P (RNase P) catalyzes the removal of 5' leaders of tRNA precursors and its central catalytic RNA subunit is highly conserved across all domains of life. In eukaryotes, RNase P and RNase MRP, a closely related ribonucleoprotein enzyme, share several of the same protein subunits, contain a similar catalytic RNA core, and exhibit structural features that do not exist in their bacterial or archaeal counterparts. A unique feature of eukaryotic RNase P/MRP is the presence of two relatively long and unpaired internal loops within the P3 region of their RNA subunit bound by a heterodimeric protein complex, Rpp20/Rpp25. Here we present a crystal structure of the human Rpp20/Rpp25 heterodimer and we propose, using comparative structural analyses, that the evolutionary divergence of the single-stranded and helical nucleic acid binding specificities of eukaryotic Rpp20/Rpp25 and their related archaeal Alba chromatin protein dimers, respectively, originate primarily from quaternary level differences observed in their heterodimerization interface. Our work provides structural insights into how the archaeal Alba protein scaffold was adapted evolutionarily for incorporation into several functionally-independent eukaryotic ribonucleoprotein complexes.
MeSH term(s)	Archaeal Proteins/chemistry ; Archaeal Proteins/metabolism ; Autoantigens/chemistry ; Autoantigens/metabolism ; Crystallography, X-Ray ; Evolution, Molecular ; Fungal Proteins/chemistry ; Fungal Proteins/metabolism ; Humans ; Models, Molecular ; Multienzyme Complexes/chemistry ; Multienzyme Complexes/metabolism ; Protein Domains ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Secondary ; RNA/metabolism ; Ribonuclease P/chemistry ; Ribonuclease P/metabolism
Chemical Substances	Archaeal Proteins ; Autoantigens ; Fungal Proteins ; Multienzyme Complexes ; POP7 protein, human ; RPP25 protein, human ; RNA (63231-63-0) ; Ribonuclease P (EC 3.1.26.5)
Language	English
Publishing date	2018-04-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2018.03.029
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Article ; Online: Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs.

Chan, Clarence W / Badong, Deanna / Rajan, Rakhi / Mondragón, Alfonso

RNA (New York, N.Y.)

2019 Volume 26, Issue 3, Page(s) 278–289

Abstract: Ubiquitous across all domains of life, tRNAs constitute an essential component of cellular physiology, carry out an indispensable role in protein synthesis, and have been historically the subject of a wide range of biochemical and biophysical studies as ... ...

Abstract	Ubiquitous across all domains of life, tRNAs constitute an essential component of cellular physiology, carry out an indispensable role in protein synthesis, and have been historically the subject of a wide range of biochemical and biophysical studies as prototypical folded RNA molecules. Although conformational flexibility is a well-established characteristic of tRNA structure, it is typically regarded as an adaptive property exhibited in response to an inducing event, such as the binding of a tRNA synthetase or the accommodation of an aminoacyl-tRNA into the ribosome. In this study, we present crystallographic data of a tRNA molecule to expand on this paradigm by showing that structural flexibility and plasticity are intrinsic properties of tRNAs, apparent even in the absence of other factors. Based on two closely related conformations observed within the same crystal, we posit that unbound tRNAs by themselves are flexible and dynamic molecules. Furthermore, we demonstrate that the formation of the T-loop conformation by the tRNA TΨC stem-loop, a well-characterized and classic RNA structural motif, is possible even in the absence of important interactions observed in fully folded tRNAs.
MeSH term(s)	Anticodon/chemistry ; Anticodon/genetics ; Crystallography ; Escherichia coli/chemistry ; Escherichia coli/ultrastructure ; Nucleic Acid Conformation ; Nucleotide Motifs/genetics ; RNA, Transfer/chemistry ; RNA, Transfer/ultrastructure ; RNA, Transfer, Amino Acyl/chemistry ; RNA, Transfer, Amino Acyl/ultrastructure ; Ribosomes/genetics ; Ribosomes/ultrastructure
Chemical Substances	Anticodon ; RNA, Transfer, Amino Acyl ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2019-12-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.073478.119
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Article ; Online: Refractory vaccine-induced immune thrombotic thrombocytopenia (VITT) managed with delayed therapeutic plasma exchange (TPE).

Major, Ajay / Carll, Timothy / Chan, Clarence W / Christenson, Chancey / Aldarweesh, Fatima / Wool, Geoffrey D / Cohen, Kenneth S

Journal of clinical apheresis

2021 Volume 37, Issue 1, Page(s) 117–121

Abstract: Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a newly described hematologic disorder, which presents as acute thrombocytopenia and thrombosis after administration of the ChAdOx1 nCov-19 (AstraZeneca) and Ad26.COV2.S (Johnson & Johnson) ... ...

Abstract	Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a newly described hematologic disorder, which presents as acute thrombocytopenia and thrombosis after administration of the ChAdOx1 nCov-19 (AstraZeneca) and Ad26.COV2.S (Johnson & Johnson) adenovirus-based vaccines against COVID-19. Due to positive assays for antibodies against platelet factor 4 (PF4), VITT is managed similarly to autoimmune heparin-induced thrombocytopenia (HIT) with intravenous immunoglobulin (IVIG) and non-heparin anticoagulation. We describe a case of VITT in a 50-year-old man with antecedent alcoholic cirrhosis who presented with platelets of 7 × 10
MeSH term(s)	Ad26COVS1/adverse effects ; Humans ; Male ; Middle Aged ; Plasma Exchange/methods ; Platelet Count ; Platelet Factor 4/immunology ; Purpura, Thrombocytopenic, Idiopathic/etiology ; Purpura, Thrombocytopenic, Idiopathic/therapy ; Vaccination/adverse effects
Chemical Substances	Ad26COVS1 ; PF4 protein, human ; Platelet Factor 4 (37270-94-3)
Language	English
Publishing date	2021-10-21
Publishing country	United States
Document type	Case Reports
ZDB-ID	604912-6
ISSN	1098-1101 ; 0733-2459
ISSN (online)	1098-1101
ISSN	0733-2459
DOI	10.1002/jca.21945
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Article: Crystal Structure of Human Rpp20/Rpp25 Reveals Quaternary Level Adaptation of the Alba Scaffold as Structural Basis for Single-stranded RNA Binding

Chan, Clarence W / Kiesel, Benjamin R / Mondragón, Alfonso

Journal of molecular biology. 2018 May 11, v. 430, no. 10

2018

Abstract: Ribonuclease P (RNase P) catalyzes the removal of 5′ leaders of tRNA precursors and its central catalytic RNA subunit is highly conserved across all domains of life. In eukaryotes, RNase P and RNase MRP, a closely related ribonucleoprotein enzyme, share ... ...

Abstract	Ribonuclease P (RNase P) catalyzes the removal of 5′ leaders of tRNA precursors and its central catalytic RNA subunit is highly conserved across all domains of life. In eukaryotes, RNase P and RNase MRP, a closely related ribonucleoprotein enzyme, share several of the same protein subunits, contain a similar catalytic RNA core, and exhibit structural features that do not exist in their bacterial or archaeal counterparts. A unique feature of eukaryotic RNase P/MRP is the presence of two relatively long and unpaired internal loops within the P3 region of their RNA subunit bound by a heterodimeric protein complex, Rpp20/Rpp25. Here we present a crystal structure of the human Rpp20/Rpp25 heterodimer and we propose, using comparative structural analyses, that the evolutionary divergence of the single-stranded and helical nucleic acid binding specificities of eukaryotic Rpp20/Rpp25 and their related archaeal Alba chromatin protein dimers, respectively, originate primarily from quaternary level differences observed in their heterodimerization interface. Our work provides structural insights into how the archaeal Alba protein scaffold was adapted evolutionarily for incorporation into several functionally-independent eukaryotic ribonucleoprotein complexes.
Keywords	Archaea ; chromatin ; crystal structure ; dimerization ; divergent evolution ; eukaryotic cells ; humans ; molecular biology ; ribonucleases ; ribonucleoproteins ; ribozymes ; scaffolding proteins
Language	English
Dates of publication	2018-0511
Size	p. 1403-1416.
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2018.03.029
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