Peter Yang

Human and Simian Immunodeficiency Virus Capsid Proteins Are Major Viral Determinants of Early, Postentry Replication Blocks in Simian Cells

ABSTRACT The cells of most Old World monkey species exhibit early, postentry restrictions on infection by human immunodeficiency virus type 1 (HIV-1) but not by simian immunodeficiency virus of macaques (SIVmac). Conversely, SIVmac, but not HIV-1, infection is blocked in most New World monkey cells. By using chimeric HIV-1/SIVmac viruses capable of a single round of infection, we demonstrated that a major viral determinant of this restriction is the capsid (CA) protein. The efficiency of early events following HIV-1 and SIVmac entry is apparently determined by the interaction of the incoming viral CA and species-specific host factors.

Binding and Susceptibility to Postentry Restriction Factors in Monkey Cells Are Specified by Distinct Regions of the Human Immunodeficiency Virus Type 1 Capsid

ABSTRACT In cells of Old World and some New World monkeys, dominant factors restrict human immunodeficiency virus type 1 (HIV-1) infections after virus entry. The simian immunodeficiency virus SIVmac is less susceptible to these restrictions, a property that is determined largely by the viral capsid protein. For this study, we altered exposed amino acid residues on the surface of the HIV-1 capsid, changing them to the corresponding residues found on the SIVmac capsid. We identified two distinct pathways of escape from early, postentry restriction in monkey cells. One set of mutants that were altered near the base of the cyclophilin A-binding loop of the N-terminal capsid domain or in the interdomain linker exhibited a decreased ability to bind the restricting factor(s). Consistent with the location of this putative factor-binding site, cyclophilin A and the restricting factor(s) cooperated to achieve the postentry block. A second set of mutants that were altered in the ridge formed by helices 3 and 6 of the N-terminal capsid domain efficiently bound the restricting factor(s) but were resistant to the consequences of factor binding. These results imply that binding of the simian restricting factor(s) is not sufficient to mediate the postentry block to HIV-1 and that SIVmac capsids escape the block by decreases in both factor binding and susceptibility to the effects of the factor(s).

A Diacidic Motif in Human Immunodeficiency Virus Type 1 Nef Is a Novel Determinant of Binding to AP-2

ABSTRACT A key function of the Nef protein of immunodeficiency viruses is the downregulation of the T-cell and macrophage coreceptor, CD4, from the surfaces of infected cells. CD4 downregulation depends on a conserved (D/E)XXXL(L/I)-type dileucine motif in the C-terminal, flexible loop of Nef, which mediates binding to the clathrin adaptor complexes AP-1, AP-2, and AP-3. We now report the identification of a consensus (D/E)D motif within this loop as a second, conserved determinant of interaction of Nef with AP-2, though not with AP-1 and AP-3. Mutations in this diacidic motif abrogate both AP-2 binding and CD4 downregulation. We also show that a dileucine motif from tyrosinase, both in its native context and in the context of Nef, can bind to AP-2 independently of a diacidic motif. These results thus identify a novel type of AP-2 interaction determinant, support the notion that AP-2 is the key clathrin adaptor for the downregulation of CD4 by Nef, and reveal a previously unrecognized diversity among dileucine sorting signals.

Molecular subtype and response to dasatinib, an Src/Abl small molecule kinase inhibitor, in hepatocellular carcinoma cell lines in vitro

Hepatocellular carcinoma (HCC) is the fifth most common malignancy and is the third leading cause of cancer death worldwide. Recently, the multitargeted kinase inhibitor sorafenib was shown to be the first systemic agent to improve survival in advanced HCC. Unlike other malignancies such as breast cancer, in which molecular subtypes have been clearly defined (i.e., luminal, HER2 amplified, basal, etc.) and tied to effective molecular therapeutics (hormone blockade and trastuzumab, respectively), in HCC this translational link does not exist. Molecular profiling studies of human HCC have identified unique molecular subtypes of the disease. We hypothesized that a panel of human HCC cell lines would maintain molecular characteristics of the clinical disease and could then be used as a model for novel therapeutics. Twenty human HCC cell lines were collected and RNA was analyzed using the Agilent microarray platform. Profiles from the cell lines in vitro recapitulate previously described subgroups from clinical material. Next, we evaluated whether molecular subgroup would have predictive value for response to the Src/Abl inhibitor dasatinib. The results demonstrate that sensitivity to dasatinib was associated with a progenitor subtype. Dasatinib was effective at inducing cell cycle arrest and apoptosis in “progenitor‐like” cell lines but not in resistant lines. Conclusion: These findings suggest that cell line models maintain the molecular background of HCC and that subtype may be important for selecting patients for response to novel therapies. In addition, it highlights a potential role for Src family signaling in this progenitor subtype of HCC. (HEPATOLOGY 2013)

HemOnc.org: A Collaborative Online Knowledge Platform for Oncology Professionals

PURPOSE Cancer care involves extensive knowledge about numerous chemotherapy drugs and chemotherapy regimens. This information is constantly evolving, and there has been no freely available, comprehensive, centralized repository of chemotherapy information to date. METHODS We created an online, freely accessible, ad-free, collaborative wiki of chemotherapy information entitled HemOnc.org to address the unmet need for a central repository of this information. This Web site was developed with wiki development software and is hosted on a cloud platform. Chemotherapy drug and regimen information (including regimen variants), as well as other information of interest to hematology/oncology professionals, is housed on the site in a fully referenced and standardized format. Accredited users are allowed to freely contribute information to the site. RESULTS From its inception in November 2011, HemOnc.org has grown rapidly and most recently has detailed information on 383 drugs and 1,298 distinct chemotherapy regimens (not counting variants) in 92 disease subtypes. There are regularly more than 2,000 visitors per week from the United States and international locations. A user evaluation demonstrated that users find the site useful, usable, and recommendable. CONCLUSION HemOnc.org is now the largest free source of chemotherapy drug and regimen information and is widely used. Future enhancements, including more metadata about drugs and increasingly detailed efficacy and toxicity information, will continue to improve the value of the resource.

Computerized Approach to Creating a Systematic Ontology of Hematology/Oncology Regimens

Purpose The systemic treatment of cancer is primarily through the administration of complex chemotherapy protocols. To date, this knowledge has not been systematized, because of the lack of a consistent nomenclature and the variation in which regimens are documented. For example, recording of treatment events in electronic health record notes is often through shorthand and acronyms, limiting secondary use. A standardized hierarchic ontology of cancer treatments, mapped to standard nomenclatures, would be valuable to a variety of end users. Methods We leveraged the knowledge contained in a large wiki of hematology/oncology drugs and treatment regimens, HemOnc.org. Through algorithmic parsing, we created a hierarchic ontology of treatment concepts in the World Wide Web Consortium Web Ontology Language. We also mapped drug names to RxNorm codes and created optional filters to restrict the ontology by disease and/or drug class. Results As of December 2017, the main ontology includes 30,526 axioms (eg, doxorubicin is an anthracycline), 1,196 classes (eg, regimens used in the neoadjuvant treatment of human epidermal growth factor receptor 2-positive breast cancer, nitrogen mustards), and 1,728 individual entities. More than 13,000 of the axioms are annotations including RxNorm codes, drug synonyms, literature references, and direct links to published articles. Conclusion This approach represents, to our knowledge, the largest effort to date to systematically categorize and relate hematology/oncology drugs and regimens. The ontology can be used to reason individual components from regimens mentioned in electronic health records (eg, R-CHOP maps to rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) and also to probabilistically reconstruct regimens from individual drug components. These capabilities may be particularly valuable in the implementation of rapid-learning health systems on the basis of real-world evidence. The derived Web Ontology Language ontology is freely available for noncommercial use through the Creative Commons 4.0 Attribution-NonCommercial-ShareAlike license.

Overcoming the Straw Man Effect in Oncology: Visualization and Ranking of Chemotherapy Regimens Using an Information Theoretic Approach

Purpose Despite the plethora of randomized controlled trial (RCT) data, most cancer treatment recommendations are formulated by experts. Alternatively, network meta-analysis (NMA) is one method of analyzing multiple indirect treatment comparisons. However, NMA does not account for mixed end points or temporality. Previously, we described a prototype information theoretical approach for the construction of ranked chemotherapy treatment regimen networks. Here, we propose modifications to overcome an apparent straw man effect, where the most studied regimens were the most negatively valued. Methods RCTs from two scenarios—upfront treatment of chronic myelogenous leukemia and relapsed/refractory multiple myeloma—were assembled into ranked networks using an automated algorithm based on effect sizes, statistical significance, surrogacy of end points, and time since RCT publication. Vertex and edge color, transparency, and size were used to visually analyze the network. This analysis led to the additional incorporation of value propagation. Results A total of 18 regimens with 42 connections (chronic myelogenous leukemia) and 28 regimens with 25 connections (relapsed/refractory multiple myeloma) were analyzed. An initial negative correlation between vertex value and size was ameliorated after value propagation, although not eliminated. Updated rankings were in close agreement with published guidelines and NMAs. Conclusion Straw man effects can distort the comparative efficacy of newer regimens at the expense of older regimens, which are often cheaper or less toxic. Using an automated method, we ameliorated this effect and produced rankings consistent with common practice and published guidelines in two distinct cancer settings. These findings are likely to be generalizable and suggest a new means of ranking efficacy in cancer trials.

Usability evaluation of HemOnc.org, a collaborative online hematology/oncology reference.

244 Background: With an ever-growing body of medical knowledge, open access to accurate information is critical to quality care. HemOnc.org is a free online collaborative wiki created by health care professionals to record, access, and share information about chemotherapy treatment regimens and drugs. As of June 2013, the site contains referenced information for 931 regimens and 316 drugs. The site receives >7,000 visits/mo and has had >425,000 total page views from around the world (29% from outside the United States). We conducted a survey to evaluate the usability of the site. METHODS The survey was open May 1 to May 31, 2013. Participants were invited by site announcements, social media, and emails to hematology/oncology fellowship programs. Usability was assessed by 100-point scales (higher = better). Other data were collected via multiple choice questions with optional free text entry. RESULTS There were 139 respondents; demographics are shown in the Table. They felt that the site was useful (median 90, interquartile range (IQR) 76-99.5), usable (median 85, IQR 69-98), and recommendable to colleagues (median 87, IQR 72-99). Although 100% of users reported using other references (e.g. textbooks), 70.5% reported accuracy issues with these references (Table). CONCLUSIONS HemOnc.org provides a new way to access and share curated knowledge. No resource is 100% accurate, but the open and transparent nature of the site allows users to actively correct errors and inconsistencies. Feedback has been positive, suggesting that an unmet need for information is being satisfied. Our goal is to improve collaboration, foster greater knowledge sharing among the oncology community, and improve quality of care through open dissemination of accurate information to a widespread audience. [Table: see text].