Robert F. Murphy, Ph.D. - US grants

Many biologically important molecules have been shown to enter cells by receptor-mediated endocytosis. Among these are molecules which stimulate cell growth in vitro, such as insulin and epidermal growth factor. Acidification of endocytic vesicles has been shown to play a crucial role in the entry into the cytoplasm of many toxins and viruses, and since many internal binding sites for growth factors have been demonstrated, it is possible that a similar process is involved in growth factor action. This possibility will be studied by a combination of flow cytometry and cell sorting. The pathways followed after receptor-mediated endocytosis of growth factors by cultured mouse fibroblasts will be investigated using fluorescent analogues which are sensitive to their environment. The kinetics of acidification of endocytic vesicles containing molecules endocytosed specifically or non-specifically will be determined by dual fluorescence flow cytometry with a mixture of fluorescein (pH sensitive) and rhodamine (pH insensitive) analogues. The frequency with which different molecules are contained in the same endocytic vesicle will be determined by fluorescence energy transfer. These experiments will help resolve current controversies regarding differential processing of endocytosed molecules. The ability of a variety of lysomotropic agents to affect growth stimulation by insulin and epidermal growth factor will be determined. An important goal will be to detemine which effects of these agents (neutralization, vacuolization, inhibition of vesicle fusion) cause inhibition of growth stimulation. The point of action of these agents in the cell cycle will be determined by simultaneous flow cytometric measurement of DNA, RNA and protein content. To directly examine the role o acidification in growth factor action, spontaneous and temperature-sensitive mutants which are unable to acidify endocytic vesicles containing specific probes will be isolated from serum-requiring cells by flow sorting. These cell lines will be tested fo their ability to be stimulated by a variety of growth factors. In addition to their usefulness for studies of growth factor action, those cell lines which have defects in lysosomal acidification should be particularly valuable as recipients for nucleic acids and proteins.

Receptor-mediated endocytosis plays an important role in allowing mammalian cells to sense and respond to their environment. During the last ten years, significant progress has been made in understanding this fundamental process, but a number of questions remain unanswered. The primary goal of the research described in this proposal is to make accurate, temporally-resolved measurements of the related processes of ligand/receptor acidification, exposure to hydrolytic (lysosomal) enzymes, and sorting of ligands and receptors, and to relate these measurements to the biological role of the ligand being studied. The kinetics of acidification and the temperature dependence of both internalization and acidification will be determined for transferrin, epidermal growth factor (EGF), histocompatibility antigen H-2K, and dextran; the kinetics and temperature dependence of entry of endocytosed fluid into compartments containing proteolytic enzymes will be measured using fluorogenic enzyme substrates. Differences in these properties between cell types, or the same cell type under different conditions (such as iron starvation), will also be determined. Flow cytometric analysis and density gradient centrifugation will be used to determine the kinetics with which the pathways of endocytosis of transferrin, EGF, H2K and dextran diverge, and to determine some of the biochemical characteristics of the compartments involved.

This is an open-label, multiple-dose, pharmacokinetic, safety and antiviral activity study of three dosing regimens of oral lobucavir in HIV-infected subjects who have plasma viral load of at least 10,000 HIV-RNA copies/ml within 14 days of randomization. Lobucavir is a guanine nucleoside analogue with a broad spectrum of antiviral activity in tissue culture models. Activity against DNA virus infections includes: Herpes simplex viruses and varicella zoster virus. The mechanism of action for lobucavir is inhibition of DNA polymerase by LBV-TP. Lobucavir-triphosphate acts by inhibiting viral DNA polymerase and by terminating nascent DNA chains. In animal models of HSV and CMV infection, lobucavir demonstrated significant protection. It is thought that lobucavir may have antiviral activity against HIV and this study will address that issue through testing of HIV-RNA levels. The endpoints of the study are pharmacokinetics, HIV viral load, CMV urine culture, CD4 counts, and safety.

The HIV-1 epidemic has had a major impact upon the urban centers of the United States now being the leading cause of death among men 25-44 years of age and the fourth leading cause of death in women in the same age group. The demographics of persons with AIDS in Chicago, reported to the CDC, reflect the increasing impact of the epidemic among women, the African-American and Hispanic/Latino communities. The Chicago AIDS Clinical Trials Unit plans to participate in AIDS Clinical Trials Group (ACTG) protocols that are hypothesis-based and pathogenesis-oriented and that are designed to evaluate therapy of the primary human immunodeficiency virus type-1 infection, the management and prevention of the infectious, oncologic and neurologic complications of the retrovirus infection and the immunologic treatment modalities. Specific aims include: 1. participation in phase I, II and III trials of anti-retroviral agents. 2. participation in immune based therapy trials. 3. participation in trials evaluating prophylaxis and treatment of opportunistic infections and in therapeutic protocols for malignant and neurologic complications of HIV-1 infection. 4. Maintenance of a preparative laboratory to support ACTG protocol mandated virologic and pharmacologic assays. 5. Continued maintenance of the capability to conduct core immunologic studies mandated by ACTG protocols. 6. Continued efforts to enroll women and members of underrepresented populations in ACTG protocols.

nelfinavir; saquinavir; nevirapine; HIV envelope protein gp41; synthetic peptide; HIV infections; AIDS therapy; antiAIDS agent; combination chemotherapy; antiviral agents; human therapy evaluation; human immunodeficiency virus 1; drug screening /evaluation; drug administration routes; pharmacokinetics; clinical research; human subject;

This study's primary objective is to assess the safety, tolerability, and antiviral activity of ABT-378/ritonavir in combination with two nucleoside reverse transcriptase inhibitors (at least one of which the patient has not received before) and nevirapine in protease inhibitor experienced HIV-infected patients. The secondary objective is to determine the steady-state pharmacokinetic profile of ABT-378/ritonavir and nevirapine in protease inhibitor experienced HIV-infected patients.

Protocol M97-720 is a Phase I/II, randomized, ABT-378 dose-blinded, multicenter study of ABT-378/ritonavir in combination with stavudine (d4T) and lamivudine (3TC) in otherwise healthy HIV-infected males and females. ABT-378 is a novel peptidomimetic HIV protease inhibitor with approximately 10-fold greater in vivo potency than ritonavir. The EC50 of ABT-378 in 50% human serum is approximately 0.1 micrometer. Against a panel of viral isolates demonstrating varying degrees of ritonavir resistance, ABT-378 demonstrated consistently superior activity compared with ritonavir. Co-administration of ABT-378 with ritonavir substantially improves the pharmacokinetic profile of the drug. The primary objective of this study is to assess the safety, tolerability, and antiviral activity of ABT-378/ritonavir when administered orally in antiretroviral naive HIV-infected patients. The study will also determine the steady-state pharmacokinetic profile and characterize HIV RNA decay profiles of ABT-378/ritonavir.

DESCRIPTION (adapted from applicant's abstract): The objectives of the NWACTU are to perform comprehensive analyses of virologic and immunologic events during HIV infection by systematic patient sampling and detailed laboratory studies in order to evaluate innovative therapies of HIV infection and its complications. The specific aims are relevant for many patients and reflect the aims of the AACTG. The aims include the study of novel HIV treatment strategies and agents; the treatment response of HIV in latent reservoirs; the impact of viral and host factors and treatment strategies on long-term and clinical and virologic outcomes; viral dynamic models for evaluating new therapies and guiding treatment strategies; treatment and prophylaxis discontinuation following HIV-treatment induced immune reconstitution; metabolic complications of HIV disease and antiretroviral therapy; the treatment of neuropathy and HIV-associated dementia; the mechanism of immune restoration; the validation of the immunologic determinants of clinical and virologic benefit medicated by therapy; enhancement of restoration of appropriate immune function by application of immune-based therapies; and long-term treatment strategies. The NWACTU is a collaborative effort of three Chicago institutions: Northwestern University Medical School, Rush-Presbyterian-St. Luke's Medical Center, and Cook County Hospital. The ACTU offers several components and capabilities and proposes to use them to make contributions to AIDS research. These components include: a consortium of experienced virologists, clinicians, immunologists, and molecular biologists with complementary areas of expertise; the ability to enroll and retain a large, diverse study population; a history of working together as evidenced by joint publications and investigator-initiated grants; the presence of a quality-controlled laboratory for processing, tracking, and storing specimens; participation in other NIH-directed AIDS research; an organizational plan for administrative, clinical and laboratory endeavors; and the provision of scientific and administrative leadership to the Adult AIDS Clinical Trials Group. These characteristics, and the basic science and clinical capabilities of the group, should allow the NWACTU to support a significant proportion of the specific aims and objectives of the AACTG.

[unreadable] DESCRIPTION (provided by applicant): [unreadable] Systematic knowledge of the subcellular locations of proteins and how these locations change in response to drugs, during the cell cycle, during development and during disease will be essential to current comprehensive proteomics efforts. The new field dealing with this subject, Location Proteomics, requires methods for fluorescently-tagging large numbers of proteins, rapidly collecting high-resolution fluorescence microscope images, and, critically, automatically analyzing the resulting distributions. The Murphy group has previously described automated systems that can recognize all major subcellular patterns in 2D and 3D images and can distinguish protein patterns better than visual examination. A critical component of these systems is sets of numerical features that describe each subcellular pattern without being overly sensitive to variations in cell size and shape. The first component of this proposal is research to develop and test solutions to new analysis problems. Within this goal, the first aim is the building of an optimal hierarchical grouping of proteins such that proteins whose patterns are statistically indistinguishable under all conditions are placed in the same group. The second is describing and classifying images based not only on their static patterns but on how those patterns change over time. The third is implementing fast methods for retrieving images from distributed databases based on similarity of protein location patterns. The second component is conversion of current "research-grade" software to "distribution-grade" so that it can be made available to researchers both as stand-alone applications and as part of an image database system. These include pattern classifiers and comparators for image sets. The project team includes leading experts in multimedia database retrieval and data mining and software engineering principles. The software to be developed will be useful not only for large-scale proteomics efforts but also for automated interpretation of traditional cell biology experiments. The hierarchical grouping of proteins by location, in combination with their sequences, will for the first time allow programs for predicting location to operate at the high resolution necessary for discovery of new targeting motifs. The comprehensive approach to location proteomics enabled by this project promises to identify protein differences associated with disease, which can be used as targets for therapies or as markers for early detection and classification of abnormalities. [unreadable] [unreadable]

[unreadable] DESCRIPTION (provided by applicant): The goal of this project is to build a software toolkit that will enable a biologist to create, from a collection of on-line articles, a database of protein subcellular localization information that can be queried, browsed, or used to support data-mining activities. We have developed a system, called SLIF, which can harvest fluorescence microscope images from online papers, analyze them using image-processing methods, and annotate them with information appearing in the accompanying textual description. We propose to improve and extend this system so as to produce a robust, comprehensive toolkit for extracting information about subcellular localization from the text and images found in online journals, as well as analyzing, verifying and querying the resulting body of information. [unreadable] [unreadable] [unreadable]

[unreadable] DESCRIPTION (provided by applicant): The goal of this project is to build a software toolkit that will enable a biologist to create, from a collection of on-line articles, a database of protein subcellular localization information that can be queried, browsed, or used to support data-mining activities. We have developed a system, called SLIF, which can harvest fluorescence microscope images from online papers, analyze them using image-processing methods, and annotate them with information appearing in the accompanying textual description. We propose to improve and extend this system so as to produce a robust, comprehensive toolkit for extracting information about subcellular localization from the text and images found in online journals, as well as analyzing, verifying and querying the resulting body of information. [unreadable] [unreadable] [unreadable]

[unreadable] DESCRIPTION (provided by applicant): The Northwestern University Clinical Trials Unit (NU-CTU) is an existing and very productive clinical unit within the AIDS Clinical Trails Group. The NU-CTU has been invited to participate in the current ACTG application for a Network which will focus on translational research/drug development, optimization of clinical management including co-morbidities, vaccine research and development, prevention of mother-to-child transmission and prevention of HIV infection. The NU-CTU consists of 5 individual clinical research sites (CRS) operating under the Northwestern University administrative umbrella. The 5 sites are: Northwestern University Clinical Research Site (NU-CRS), Rush University Clinical Research Site (R J-CRS), and the CORE Center Clinical Research Site (CC-CRS) all located in Chicago, an international site at Fann Hospital/Universite Cheikh Anta Diop in Dakar, Senegal (SN-CRS), and the Peabody Health Center, a member of the Black Clinical Research Consortium, located in Dallas (PC-CRS). The ACTG Leadership has invited the 3 existing ACTG sites, NU-CRS, RU-CRS, and CC-CRS to participate in this recompetitive network grant. The PC-CRS is not an existing site but it has received a special invitation to participate from the ACTG Leadership for the purpose of enhancing minority patient involvement and minority research investigator development. The SN-CRS was not formally invited as only existing ACTG international sites were eligible, however this site is an NIAID/CIPRA grant awardee and a Fogarty grantee and is fully capable of performing clinical trials to NIH standards. We include them now because they are as capable of performing clinical trials as the existing international sites, they would be the only site located in West Africa, the only site with patients predominantly infected with HIV-1 subtype A/G, and the only site with a significant minority of patients infected or co-infected with HIV-2.. We believe these unique features would greatly enhance the ACTG scientific agenda. The NU-CTU is a highly productive and efficient group with an already established track record in performing multicenter, translational research and therapeutic clinical trials, ranking #1 in patient accrual and #3 in scientific productivity for the last 5 year evaluation period. We expect a seamless transition to the new structure described in this application. [unreadable] [unreadable] [unreadable] ADMINISTRATIVE COMPONENT: [unreadable] [unreadable]

[unreadable] DESCRIPTION (provided by applicant): The primary goal of this proposal is to collect high-resolution information on the distribution of proteins within mammalian cells and to link it to nucleotide and protein sequences. It builds on extensive prior work on development of protein tagging methods by the co-PIs and on development of software systems for automated analysis of subcellular patterns in fluorescence microscope images by the PI. 25,000 independent cell lines expressing GFP protein fusions will be created in NIH 3T3 cells using high-throughput CD-tagging (protein-trapping) methods. As the cell lines are created, high-resolution fluorescence microscope images will be collected using fluorescence microscopy and the gene and protein tagged in each cell line will be determined by high-throughput molecular analysis methods. The images will be subjected to automated, computerized image analysis to group proteins with statistically indistinguishable patterns. The determined location for each protein will be compared to whatever information is available from protein databases, journal articles and location predictors. Each assigned location will be accompanied by a confidence estimate derived from combining these sources. In addition, the images for each protein group will be used to build generative models that can synthesize new protein distributions statistically equivalent to the original images. The ability to synthesize distributions will provide an important structural framework for systems biology modeling of cell behavior in normal and disease states. [unreadable] [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): Northwestern University proposes to establish a Northwestern University Fogarty AIDS International Training and Research Program (NU AITRP) to strengthen HIV/AIDS and TB therapeutics through training and research for clinicians, scientists, and allied healthcare providers from Nigeria. The NU AITRP will build upon the historic linkages between the faculty at NU and the faculty at University College Hospital (UCH)AJniversity of Ibadan in Ibadan and Jos University Teaching Hospital (JUTH) in Jos, Nigeria. The goal of the NU AITRP is to create and sustain an AIDS research infrastructure in partnership with UCH and JUTH that facilitates collaboration, provides access to a full range of research resources, and promotes training and education. The expertise and infrastructure for HIV and TB research training at the Center for HIV and TB Research (SEREFO), University of Bamako, Bamako, Mali will be leveraged to train the Nigerians, and serve as a platform for expanded collaboration. The objective of the NU AITRP is to continue to support the efforts of productive, creative and innovative scientists to perform detailed, intensive and interrelated research studies through a collaborative research training program. The impetus and rationale for the center is to continue to provide scientific leadership and administrative mechanisms and infrastructure to enable a greater level and quality of interdisciplinary and inter-institutional scientific collaboration and translational research conducted by diverse, exceptionally qualified, and committed scientists spanning a broad range of clinical and basic science disciplines. The justification for this integrated approach is based on the supposition that progress in AIDS research is made by groups of basic scientists and clinician-investigators working together across disciplines and institutions to translate discovery into new approaches for the treatment and prevention of disease. The proposed NU AITRP will encompass short-term programs, long term programs and the development of long-term research support and development partnership.

[unreadable] DESCRIPTION (provided by applicant): Northwestern University proposes to establish a campus-wide Office of Global Health Programs, whose mission is to transform international health education at Northwestern by creating a truly interdisciplinary campus-wide program that will prepare our students and faculty to meet the 21st century challenges of global health, such as the global burden of disease, immigrant health, brain drain of medical personnel from resource-poor settings to resource-rich settings, and health disparities in access to health care. Our program builds on the successful Global Health programs developed at Northwestern over the past few years, including: (1) a Global Health Minor with over 250 enrolled students; (2) new curricular offerings in Global Health 10 courses now offered; (3) public health programs abroad designed for Northwestern students in collaboration with partner institutions in Mexico, China, South Africa, Uganda, and France; (4) global health programs for first year medical students; and (5) directed group research in Global Health. We propose to significantly expand this initiative and to develop a truly integrated university-wide program. The office of Global Health Programs will implement initiatives designed to expand faculty interest and expertise in global health, develop new global health courses, expand international study and research, strengthen international partnerships, and develop the institutional infrastructure required to facilitate global health study and research and create truly interdisciplinary collaborations across schools and disciplines. Some of the specific mechanisms proposed include: (1) curriculum development grants; (2) integration of Global Health into the core medical curriculum; (3) a Global Health concentration in the Medical School; (4) a MPH five-year option for Minors in Global Health; (5) Global Health Team Projects for student research abroad; (6) faculty globalization grants; (7) new research sites in Bolivia and Rwanda; (8) planning grants for interdisciplinary faculty research; (10) Bringing the world to Northwestern, a major initiative to sponsor visits by global health scholars, and to conduct research on healthcare delivery innovations abroad; and (11) creation of an Interactive Public Website to disseminate and publish scholarly and programmatic materials developed through the program, facilitate communication with project participants on campus and abroad, and contribute to Global Health knowledge and curriculum development at other institutions. Public Health Relevance: Increasing awareness of the complexity and immediacy of global health problems has not resulted in needed reorganization of educational and research programs at many of our institutions of higher learning. As a result, students and healthcare professionals often go abroad with inadequate preparation and are unable to make a real contribution to the long-term solution of global health problems. Our program is designed to provide students and faculty a deep understanding of the complex interaction between domestic and global forces, the cultural and political realities that impact health policies in different societies, and the international environment that spreads the impact of these problems throughout the world. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): Broad interdisciplinary training programs which address critical needs in low and middle income countries (LMIC) can significantly increase the translation of research findings into realized health benefits. Northwestern University proposes to establish comprehensive training programs in biomedical engineering that includes identification of critical health care needs, product design, delivery, clinical evaluation, scalablity and product launch. The theme of our program involves the development of effective, affordable, and easy to use innovative biomedical devices that can advance diagnostics, therapeutic interventions and disease monitoring. Our proposal builds on Northwestern's successful original Framework Programs for Global Health (Frameworks-1) which supported the development of a multidisciplinary global health curricula and creation of the Center for Global Health in the Feinberg School of Medicine, the Center for Innovation in Global Health Technologies in the McCormick School of Engineering and the Global Health Initiative at the Kellogg School of Management. Frameworks-1 specifically lead to the close collaboration of clinical and basic research involving medical, engineering and business schools as well as the establishment of the Northwestern Global Health Foundation, an independent not-for-profit which supports post-university commercial development of new healthcare products. Our LMIC partners include the University of Cape Town in South Africa, the University of Ibadan and Lagos University in Nigeria, the University of Bamako in Mali, and the University of Nairobi in Kenya. These LMIC institutions have many existing relationships with Northwestern including active faculty and student exchange programs, the President's Emergency Plan for AIDS Relief (PEPFAR), the Medical Education Partnership Initiative (MEPI), and the AIDS International Training and Research Program (AITRP), among others. The overall goal of this proposal is to provide the tools to develop critically needed healthcare technologies in LMICs. The specific aims of the proposal are: 1) establish new and enhance existing training programs in biomedical engineering in Africa; 2) train biomedical engineers and medical doctors how to evaluate newly developed testing and treatment products; and 3) train post graduates from business schools to scale up development and launch new products in LMICs. The healthcare technologies to be developed and employed will include any innovation that improves health outcomes and is cost-effective including novel point-of-care medical diagnostic devices, therapeutic interventions, information systems, and telemedicine diagnostics facilitated through mobile phones. Our bottom-up approach and emphasis on South-South research training and assessment makes this proposal unique and ground-breaking. The overall result of these efforts is to develop trans-institutional, cross disciplinary and innovative training programs in biomedical engineering starting with needs assessment and product design, continuing to validation, intellectual property protection, production and finally to marketing and distribution in the LMICs.

DESCRIPTION (provided by applicant): AIDS malignancies are a serious problem in sub-Saharan Africa because of the widespread HIV epidemic and a high burden of oncogenic viral co-infections. Antiretroviral treatment programs put into place by PEPFAR, the Global Fund and others, have resulted in a remarkable decrease in HIV-related morbidity and mortality, however, the rate of malignancies and other non-communicable diseases is rising while at the same time, the population is aging. Most medical and research institutions in Africa are ill prepared to deal with these emerging health challenges. The University of Jos and Jos University Teaching Hospital (JUTH) HIV Care and Treatment Program, established in 2002, currently provides care, treatment and support to over 20,000 HIV- infected adults and children. This university-based center is one of the largest providers of HIV care in Africa. In an effort to improve the management of AIDS-associated malignancies in West Africa and the continent, University of Jos/JUTH in conjunction with Northwestern University, proposes to build a multidisciplinary research-training program, which will build upon collaborations and enhance capacity in Nigeria by developing research teams focused on innovative collaborative endeavors in AIDS-defining malignancies (cervical cancer, Kaposi sarcoma, and non-Hodgkin lymphoma). Our primary hypothesis is that building capacity in cancer epidemiology, clinical trials, translational, and laboratory research on AIDS-defining malignancies will lead to a significant reduction in incidence and related morbidity and mortality. We will build on existing in-country training capacity provided by the United States President's Emergency Program for AIDS Relief (PEPFAR), Northwestern University AIDS International Training and Research Program (Northwestern-AITRP), and Medical Education Partnership Initiative Nigeria (MEPIN) to achieve our objectives in this important health priority area. The specific aims of this proposal are: 1) advance training of HIV clinician-investigators capable of performing translational research on the pathogenesis, epidemiology, and prevention of AIDS-defining malignancies; 2) initiate training of oncology clinician-investigators capable of performing clinical trial research on novel interventions for the treatment and prevention of AIDS-defining malignancies; 3) develop training of pathology and virology scientists to perform research on oncogenic mechanisms and pathogenesis; 4) create a multidisciplinary research team capable of performing advanced in-country research on AIDS-defining malignancies in Jos, Nigeria. We will accomplish our training goals through strong mentorship and a combination of long-term master's and PhD degree granting programs, medium-term research project-driven training experiences, short-term in-country workshops, and innovative distance learning approaches. At the end of this project, we aspire to make the University of Jos a center of excellence in the research and care of AIDS malignancies in Nigeria and West Africa.

DESCRIPTION (provided by applicant): The Chicago Clinical Trials Unit (CCTU) is a consortium of five Clinical Research Sites (CRSs) which will address three priority clinical research areas of the NIAID: 1) adult HIV therapeutic strategies including HIV cure, noninfectious comorbidities, and infectious co-morbidities of hepatitis and tuberculosis; 2) vaccines to prevent HIV; and 3) integrated HIV prevention strategies. The CCTU consists of five highly experienced and scientifically productive CRSs that are uniquely positioned to develop, implement and adapt the clinical research priorities of the NIAID clinical research priority areas. The CCTU has a proven track record and will continue its productivity through active engagement with a diverse host of at risk and HIV-impacted communities, participation in high impact, ground-breaking clinical research studies, efficient management of resources and critical performance oversight of the clinical activities, laboratories, and pharmacies. The CCTU includes CRSs and personnel that have long term and productive involvement with three of the research networks; the fourth-antibacterial resistance-being a new network in this consortium. The CRSs and their network affiliations include: Northwestern University (adult HIV therapeutic strategies); University of Illinois Chicago (vaccines to prevent HIV, integrated HIV prevention). Rush University (adult HIV therapeutic strategies), University of Chicago (integrated HIV prevention strategies) and Trinity Health & Wellness Center (adult HIV therapeutic strategies). Four of the CRSs are located in Chicago, an ethnically and racially diverse urban area of 9.5 million persons that is the third largest metropolitan region in the United States and one of the major urban HIV epicenters. The aims of this proposal are: development, implementation and adaptation of the clinical research program of the 1) Adult HIV Therapeutics Strategy, Network, 2) the Vaccines to Prevent HIV Network, 3) the Integrated HIV Prevention Strategies Network, and 4) Bidirectional, engagement of the relevant and at risk HIV-infected/impacted communities with the CCTU clinical researchers. The CCTU is well positioned to reach diverse populations and contribute significantly to the NIAID research agenda.

DESCRIPTION (provided by applicant): The practice of biomedical research has undergone dramatic changes in recent years, largely driven by new biotechnology for high-throughput data generation. These technologies include high-throughput methods for imaging, genetic sequencing, proteomics, structure determination, and numerous other tasks that now make it possible to finely characterize numerous aspects of living systems from the molecular to the organismal levels. These advances in biotechnology and the vast amounts of data they are producing have revolutionized biomedical research. They have also, however, created a pressing need for scientists capable of working in a field that is increasingly data-driven and dependent on advanced computational methods. In particular, modern biomedical research depends on a new breed of computationally and mathematically sophisticated researchers who can understand new biotechnologies, develop innovative mathematical models and computer algorithms needed to make sense of their data, and apply this knowledge to drive biological and medical advances. To do so, these researchers require a strong command of computational science, the biomedical applications on which they work, and the biological and physical sciences that inform them. The Carnegie Mellon University/University of Pittsburgh Ph.D. Program in Computational Biology (CPCB) was created to meet this need for training experts in computational biology. The program aims to prepare the future leaders of computational biology: research scientists with deep knowledge of computational theory, biological and physical sciences, and a growing body of specialized interdisciplinary knowledge at the intersection of these areas. To accomplish this, the program leverages the shared strengths of its two hosts institutions, collectively world leaders in computer science, engineering, and medical research with long track records of innovation in computational biology research and educational. The training program includes an innovative curriculum covering fundamentals of computational biology, broadly defined, and a large body of advanced elective coursework spanning four broad domains of computational biology research: bioimage informatics, cellular and systems modeling, computational genomics, and computational structural biology. Program students perform thesis research in any of numerous laboratories at the cutting edge of computational biology research. These primary components of coursework and thesis research are supplemented by numerous mechanisms to facilitate student success, promote professional development, encourage responsible conduct of research, and aid in recruiting and retaining underrepresented groups. The proposed program seeks to renew training support for a select subset of students in the broader CPCB graduate program. It will provide the most promising students with two years of research support, providing them added resources and flexibility to pursue the most innovative research directions and to aid in their development into future leaders of computational biology and biomedical research as a whole.

DESCRIPTION (provided by applicant): Active Viral Hepatitis Diagnostics to Support Prevention/Treatment of HCC Hepatocellular carcinoma (HCC) is very common in sub-Saharan Africa due to highly prevalent chronic hepatitis B (HBV) and hepatitis C (HCV) viral infection. Currently, patients in sub-Saharan Africa typically present in late stage disease, having a life expectancy of just three months. Earlier diagnosis could reduce HCC mortality in two ways: 1) patients with HBV or HCV would be staged earlier and tumors, if present, would be smaller and therefore easier to treat with alcohol ablation, the current standard of care in the region; and 2) patients identified earlier with chronic HBV or HCV could be treated with direct acting antiviral agents (DAAs) leading to reduced morbidity including less HCC. The goal of this application is to develop low cost point-of-care diagnostic tests to detect and monitor the treatment of active HBV and/or HCV infections. The first test to be developed will be an HCV core antigen qualitative test to identify patients with an active HCV infection. This assay will be ported on th LYNX immunoassay platform developed in collaboration with the Northwestern Global Health Foundation (NGHF). The test conditions developed for the LYNX p24 Antigen Rapid Lateral Flow Assay for Rapid Diagnosis of HIV Infection in Infants will be adapted to address a highly analogous problem: the detection of the HCV core antigen viral marker from plasma. The second test will be a multiplexed HBV/HCV viral load assay to determine when to initiate therapy and to monitor the viral response to DAA treatment. This assay will be ported onto the Savanna integrated nucleic acid extraction, amplification & detection system that is currently being developed in collaboration with the Quidel Corporation and NGHF. The test conditions developed for the Savanna RealTime HIV-1 Assay(R) will be used for the HBV/HCV viral load assay. Both the LYNX and the Savanna platforms have been designed for use in limited resource settings. They are inexpensive, easy to operate and robust. All reagents are provided with the test kits and no refrigeration is required. The analytical and clinical performance of these assays will be demonstrated in both laboratory and clinical validation studies at the Jos University Teaching Hospital in Jos, Nigeria. The tests will be transferred to their respective manufacturers, and regulatory approval for will be sought. The impact of earlier detection and improved monitoring of viral hepatitis will prompt earlier treatment resulting in prevention of carcinogenesis and/or earlier stage diagnosis with improved outcomes in patients in low and middle income countries.

? DESCRIPTION (provided by applicant): This research is aimed at developing and testing methods that will enable automated, information--?rich studies of the subcellular organization of proteins and other biomolecules. We propose to develop the computational foundation for deciphering the spatiotemporal morphological pathways of different subcellular structures during important subcellular processes automatically from microscopy images. We will leverage our progress in the previous project period, in which we established the Cell Organizer system for building image-?derived models of cell organization, to build new modeling capabilities for cisternal and reticular structures, for capturing the relationships between different cellular components, and for learning how aspects of cell organization change during processes such as the cell cycle. Given the importance of the endoplasmic reticulum in numerous cellular processes (as well as diseases including hematological disorders, cranio--? lenticulo--?sutural dysplasia, chylomicro retention disease, etc.), we expect the modeling approaches we propose to provide important mechanistic clues as to the normal (non-- athological) morphological pathways of these structures and how they may be perturbed in disease. To provide valuable images to drive the development of modeling capabilities, and to simultaneously identify candidate lead compounds for treatment of diseases with ER defects, we will conduct extensive compound screening studies on cells expressing normal and mutant alleles of atlastin (which plays a critical role in ER structure). The computational methods we develop will be integrated into our open source CellOrganizer system (http://CellOrganizer.org). In addition to the applications mentioned above, we anticipate the computational frameworks we develop will be valuable for a wide range of imaging assays including drug screens, RNAi screens, cytology, and pathology.

DESCRIPTION (provided by applicant): AIDS malignancies are a serious problem in sub-Saharan Africa because of the widespread HIV epidemic and a high burden of oncogenic viral co-infections. Antiretroviral treatment programs put into place by PEPFAR, the Global Fund and others, have resulted in a remarkable decrease in HIV-related morbidity and mortality, however, the rate of malignancies and other non-communicable diseases is rising while at the same time, the population is aging. Most medical and research institutions in Africa are ill prepared to deal with these emerging health challenges. The University of Jos and Jos University Teaching Hospital (JUTH) HIV Care and Treatment Program, established in 2002, currently provides care, treatment and support to over 20,000 HIV- infected adults and children. This university-based center is one of the largest providers of HIV care in Africa. In an effort to improve the management of AIDS-associated malignancies in West Africa and the continent, University of Jos/JUTH in conjunction with Northwestern University, proposes to build a multidisciplinary research-training program, which will build upon collaborations and enhance capacity in Nigeria by developing research teams focused on innovative collaborative endeavors in AIDS-defining malignancies (cervical cancer, Kaposi sarcoma, and non-Hodgkin lymphoma). Our primary hypothesis is that building capacity in cancer epidemiology, clinical trials, translational, and laboratory research on AIDS-defining malignancies will lead to a significant reduction in incidence and related morbidity and mortality. We will build on existing in-country training capacity provided by the United States President's Emergency Program for AIDS Relief (PEPFAR), Northwestern University AIDS International Training and Research Program (Northwestern-AITRP), and Medical Education Partnership Initiative Nigeria (MEPIN) to achieve our objectives in this important health priority area. The specific aims of this proposal are: 1) advance training of HIV clinician-investigators capable of performing translational research on the pathogenesis, epidemiology, and prevention of AIDS-defining malignancies; 2) initiate training of oncology clinician-investigators capable of performing clinical trial research on novel interventions for the treatment and prevention of AIDS-defining malignancies; 3) develop training of pathology and virology scientists to perform research on oncogenic mechanisms and pathogenesis; 4) create a multidisciplinary research team capable of performing advanced in-country research on AIDS-defining malignancies in Jos, Nigeria. We will accomplish our training goals through strong mentorship and a combination of long-term master's and PhD degree granting programs, medium-term research project-driven training experiences, short-term in-country workshops, and innovative distance learning approaches. At the end of this project, we aspire to make the University of Jos a center of excellence in the research and care of AIDS malignancies in Nigeria and West Africa.

? DESCRIPTION (provided by applicant): In Mali and many parts of Africa, the incidence of mycobacterial infection is very high and driven in large part by the overlapping HIV epidemic. Mycobacterium tuberculosis (MTB) and Mycobacterium africanum (MAF), both closely related members of the M.tuberculosis complex (MTBC), as well as non-tuberculous mycobacterium (NTM) cause human mycobacterial infections and disease in West Africa. MTBC has been widely studied; however, little is known about differences in pathogenesis, genetics, epidemiology, diagnosis, and management between MTB, MAF, and NTM among HIV-infected individuals. The University of Sciences, Techniques, and Technologies of Bamako, Mali (USTTB; University of Bamako) in collaboration with the Point- G and Gabriel Touré Teaching Hospitals in Bamako, are well equipped to build a translational research-training program in HIV-associated mycobacterial infection. The research team at USTTB has received substantial and continuous support from the NIH starting with its intramural malaria research program in the late 1980s. In 2005, this program was expanded to include HIV and tuberculosis research, which included development of a BSL-3 high containment laboratory capable of testing for mycobacterial drug resistance and testing for Ebola virus. NIAID has continuously supported the HIV and tuberculosis programs since its formation. In 2014, NIAID committed an additional 4 years of development support for the University Clinical Research Center (UCRC) in order to enhance clinical research opportunities. In our proposed program, we will continue developing HIV and mycobacterial research capacity at USTTB with established collaborators at Northwestern University, Johns Hopkins University and NIAID by leveraging ongoing research training efforts at these institutions to address each of the following aims: 1) produce and enhance the careers of Malian researchers capable of performing advanced research on the molecular biology, genetics, immunology, clinical investigation and microbiology of HIV-associated mycobacterial infection; 2) enhance and strengthen the graduate training programs at USTTB which focus on HIV infection and its mycobacterial co-morbidities through faculty enrichment and support of clinical and laboratory scientists; and 3) develop new intensive USTTB Diploma programs in retrovirology, HIV co-morbidities and mycobacteriology which will serve as core training programs for existing faculty and staff locally and from other low- and middle-income institutions throughout the region. Through this program, we will achieve the overall goal of training the next generation of investigators focused on HIV-associated mycobacterial infection who will be able to conduct HIV-related research on the evolving epidemic in Mali. We aspire to take USSTB investigators to the next level of research capacity and to make USSTB a center of excellence in the research and care of HIV and associated mycobacterial infections in West Africa.

DESCRIPTION (provided by applicant): AIDS malignancies are a serious problem in sub-Saharan Africa because of the widespread HIV epidemic and a high burden of oncogenic viral co-infections. Antiretroviral treatment programs put into place by PEPFAR, the Global Fund and others, have resulted in a remarkable decrease in HIV-related morbidity and mortality, however, the rate of malignancies and other non-communicable diseases is rising while at the same time, the population is aging. Most medical and research institutions in Africa are ill prepared to deal with these emerging health challenges. The University of Jos and Jos University Teaching Hospital (JUTH) HIV Care and Treatment Program, established in 2002, currently provides care, treatment and support to over 20,000 HIV- infected adults and children. This university-based center is one of the largest providers of HIV care in Africa. In an effort to improve the management of AIDS-associated malignancies in West Africa and the continent, University of Jos/JUTH in conjunction with Northwestern University, proposes to build a multidisciplinary research-training program, which will build upon collaborations and enhance capacity in Nigeria by developing research teams focused on innovative collaborative endeavors in AIDS-defining malignancies (cervical cancer, Kaposi sarcoma, and non-Hodgkin lymphoma). Our primary hypothesis is that building capacity in cancer epidemiology, clinical trials, translational, and laboratory research on AIDS-defining malignancies will lead to a significant reduction in incidence and related morbidity and mortality. We will build on existing in-country training capacity provided by the United States President's Emergency Program for AIDS Relief (PEPFAR), Northwestern University AIDS International Training and Research Program (Northwestern-AITRP), and Medical Education Partnership Initiative Nigeria (MEPIN) to achieve our objectives in this important health priority area. The specific aims of this proposal are: 1) advance training of HIV clinician-investigators capable of performing translational research on the pathogenesis, epidemiology, and prevention of AIDS-defining malignancies; 2) initiate training of oncology clinician-investigators capable of performing clinical trial research on novel interventions for the treatment and prevention of AIDS-defining malignancies; 3) develop training of pathology and virology scientists to perform research on oncogenic mechanisms and pathogenesis; 4) create a multidisciplinary research team capable of performing advanced in-country research on AIDS-defining malignancies in Jos, Nigeria. We will accomplish our training goals through strong mentorship and a combination of long-term master's and PhD degree granting programs, medium-term research project-driven training experiences, short-term in-country workshops, and innovative distance learning approaches. At the end of this project, we aspire to make the University of Jos a center of excellence in the research and care of AIDS malignancies in Nigeria and West Africa.

VI. TR&D4 - Abstract The overall goal of this project is to develop tools for making maximal use of the information in biological images to enable the construction of predictive, multiscale models of structure and dynamics at the subcellular and cellular level. The tools will be especially useful for studies of how cell organization is created and maintained and how that organization differs from cell type to cell type and during disease. While existing software primarily provides descriptions of images, the focus of this project is on construction of generative models of cell organization. Generative models are learned from a collection of images and are capable of producing new images that are statistically equivalent to the images used for training. These models have distinct advantages over discriminative or descriptive approaches. They attempt to make use of all information in images, rather than to just extract selected descriptors or features. Further, while features are not useful for comparing and communicating results between different laboratories due to their dependence upon the specifics of image acquisition, generative models capture the underlying reality that gave rise to images and can therefore be compared across different microscopes and laboratories. They are also combinable and reusable, in that models can be linked together to make predictions about new relationships, and models for organelle shape and distribution learned for one cell type can be provisionally extended to new cell types. Work during the prior funding led to the development of extensive generative model capabilities that were incorporated into the open source CellOrganizer system. We propose to build upon this work to build new capabilities for constructing models that consider the extensive interrelationships between organelles and structures in cells, and for modeling the dynamics of proteins and organelles. In conjunction with TR&D3, we will also develop new methods for using images to constrain estimation of the affinities between components of a biological system. Lastly, we will develop new approaches for constructing models from both electron and fluorescence microscope images. The proposed work makes use of best available methods in machine learning and computer vision, including advanced inference methods and convolutional neural nets (so called ?deep learning? methods). The work builds on the extensive progress that has been made under what was Aim 1 of TR&D3 in the prior funding period, which resulted in eleven publications that acknowledged P41 support.

Project Summary Epigenomic Biomarkers of HIV-Associated Cancers in Nigeria is a proposal from U.S. and Nigerian scientists to establish a consortium for research on two high priority HIV-associated cancers in Nigeria: hepatocellular carcinoma (HCC) and cervical cancer. The consortium will also support the enhancement of research capacity in Nigeria, a low strata middle-income sub-Saharan country with the second highest burden of HIV infection in the world. The theme of this proposal is to conduct molecular epidemiologic research to understand the epigenetic determinants of these deadly cancers. The premise for our proposal is that cancer epigenetics and infections are inextricably linked, yet significantly understudied in countries like Nigeria which have a high burden of HIV, HCC and cervical cancer. HIV and its adverse effects on the immune system promote transmission and reactivation of oncogenic viral co-infections such as hepatitis B and C, and human papilloma virus (HPV), greatly increasing the oncogenic potential in HIV-infected individuals. HIV-infected patients may also experience immune activation from HIV replication and increased exposure to traditional risk factors. All of these factors affect epigenetic biomarkers such as DNA methylation, which is considered a hallmark of cancer, and aberrations of DNA methylation in both blood and tissue have linked to increased risk of various cancers. The consortium will be led by investigators from Northwestern University and Mayo Medical School in the U.S., with partners University of Lagos and University of Jos in Nigeria. The consortium proposes to perform two Research Projects which will identify DNA methylation signatures specific to HIV-associated HCC (Project 1) and cervical cancer (Project 2). Study of epigenomic biomarkers will improve our understanding of the role of HIV co-infection and offers the main advantage of earlier diagnosis of premalignant and early stage cancers which may in turn lead to effective strategies for prevention, diagnosis and treatment. The aims of our consortium are: 1) identify epigenetic determinants of HIV-associated HCC and cervical caner in Nigeria; 2) examine whether epigenetic biomarkers are associated with clinical features of HIV-associated HCC and cervical cancer and whether such biomarkers predict development of for these two cancers; 3) provide training and mentoring opportunities for Nigerian investigators in conducting molecular epidemiology studies with a focus on epigenetic biomarkers; and 4) establish two shared core facilities for i) biomedical informatics and statistics, and ii) pathology and genomics. This cooperative agreement will provide an exceptional opportunity to leverage our existing expertise and expand that effort at two of the leading medical universities in Nigeria, the most populous country in Africa with an exceptionally high burden HIV and oncogenic viruses such as HPV and hepatitis B and C. Our results will provide useful and novel information for HIV-associated cancer prevention and treatment most relevant to low- and middle-income countries.

Abstract We propose to establish a Consortium to study ?Epigenomic Biomarkers of HIV-Associated Cancers in Nigeria.? Our research focus and core services development plan has been prioritized by our Nigerian partners at University of Jos (UniJos), Plateau State, Nigeria located in the center of the country and University of Lagos (UniLag), Lagos State in the densely populated southwest. Our focus on the epigenetics of HIV- associated hepatocellular carcinoma (HCC) and cervical cancer is justified by our extensive collaborative research history in viral diseases including HIV, human papilloma virus, hepatitis B and C viruses. Northwestern University and Mayo Medical School will serve as the high-income American partner institutions which is justified by the long history of research and research training collaboration with the Nigerian institutions coupled with its expertise in global health and ample complementary resources. A major component of our proposal is to enhance the careers of Nigerian scientists including junior investigators and expand the overall scientific capacity at the Nigerian consortium institutions. The Career Enhancement Core (CEC) will support research-related activities that will facilitate and enhance the professional development of Nigerian investigators. The aims of the CEC are to: 1. develop mentored research activities for junior investigators at UniJos and UniLag that will enhance their future research leadership capabilities, 2. establish a program which will support mentored research pilot studies to be led by junior investigators at UniJos and UniLag focused on epigenetic biomarkers of HIV-associated cancers, including by not limited to the ones being studied in Projects 1 and 2 of this proposal, and 3. enhance research core competencies, technical skills, and leadership and management capabilities of UniJos and UniLag investigators to assure successful independent research funding of junior investigators to sustain future research. All mentored research activities will be developed jointly with American and Nigerian mentors. These activities will be focused on activities surrounding the conduct of Projects 1 (HCC) and 2 (cervical). Pilot projects supported under the CEC will be related to the existing Projects 1 and 2 or may involve different cancers or biomarkers. Pilot projects will have specific requirements and procedures for applicant eligibility, application process, selection of projects, evaluation, protection of human subjects, regulatory requirements, and ethics committee approval. CEC training activities will include both didactic and experiential training in specific scientific and technical skills not available in the home institutions (such as DNA methylation laboratory techniques), formal didactic and experiential training in core research competencies including biostatistics and research analytics, research methodologies, ethics, team science, project leadership/management skills, manuscript writing, grant writing, and scientific presentation.

Summary Administrative Core (Admin Core) The Center for Innovation in Point-of-Care Technologies for HIV/AIDS at Northwestern University (C- THAN) will be a vital partner in the NIBIB Point-of-Care Technologies Research Network (POCTRN). It has the goal of developing a pipeline of point-of-care technologies critical for improved management of HIV/AIDS infected individuals in low-and-middle-income countries (LMICs) and facilitating technology commercialization. The Administrative Core will establish the administrative structure, governance policies, communication plan, budget management, decision making and conflict resolution processes for the four cores of the center. The Admin Core will be overseen by the C-THAN Network Steering Committee which consists of the NIH Project Scientist(s) and the MPIs with equal voting rights. The Network Steering Committee will act as the main governing board that will review the progress of research activities, develop collaborative protocols, identify technological impediments to the progress, select strategies to surmount them and identify opportunities for sharing techniques and tools developed within each individual project. The Scientific Sub-Committee (SSC) of the Network Steering Committee will actively oversee the Technology Development/Refinement (Technology Dev), Clinical Translation and Validation (Clinical Trans Valid), the Technology Training and Dissemination (Technology Train Dis) Cores and projects. We will establish the External Advisory Board consisting of the NIH Program Officer, external scientific and regulatory experts in biomedical engineering and medicine from the U.S. and Africa and coordinate administrative efforts between the Network Steering Committee, the Scientific Sub-Committee, the Technology Dev, the Clinical Trans Valid, and the Technology Train Dis Cores. The output of the coordinated activities of our center will be a pipeline of products of high clinical impact with strong commercial potential.

Summary Overall The Center for Innovation in Point-of-Care Technologies for HIV/AIDS at Northwestern University (C- THAN) will develop a pipeline of needs-based point-of-care technologies critical for improved management of HIV/AIDS infected individuals in low-and-middle-income countries (LMICs). C-THAN will harness our existing expertise and our research and clinical network which has a 17-year history of dynamic and productive collaboration on addressing infectious diseases in sub-Saharan Africa. Northwestern University is joined by the Universities of Lagos, Ibadan and Jos (Nigeria), Cape Town and Stellenbosch (South Africa), University of Sciences, Techniques and Technologies Bamako (Mali) and Muhimbili University of Health and Allied Sciences (Tanzania). The United Nations' Program on HIV and AIDS (UNAIDS) has set the ambitious 90-90-90 goals to achieve detection of 90% of HIV cases, treatment for 90% of those cases, and viral suppression for 90% of those treated, by 2020. This will not be achieved in LMICs without improvement of the current diagnostic pathway with POC diagnostic tests that are affordable, rapid, easy to use, and require little maintenance. C-THAN will serve as a platform for the support of research projects to develop POC technologies that address this unmet need across multiple levels of technology readiness which are amenable to the conditions of the developing world. Projects supported will range from needs assessment to commercialization, with a view to ensuring translation into clinical impact. Our overall goal is to support the development of POC technologies to promote high priority topics of NIH HIV/AIDS research, including: Reducing HIV incidence by improving screening, detection and treatment monitoring related to HIV, HIV drug resistance, and antiretroviral drug levels; Diagnosing HIV-associated comorbidities which include tuberculosis (TB), non-tuberculosis mycobacteria (NTM), hepatitis B (HBV), and hepatitis C (HCV); Reducing health disparities by developing testing technology that can function in underserved community settings; and Training of the workforce able to translate POC technologies from Reseach & Development to implementation. The C-THAN structure will incorporate clinical and user needs in project development while providing expertise and resources to address early barriers to commercialization and implementation. Its Core components will operate in an integrated manner to deliver a scope of work entailing: 1) assessment of unmet clinical needs in POC testing for HIV/AIDS and its comorbidities; 2) collaboration with relevant scientists, physicians, researchers and engineers; 3) development of essential technical, clinical, industrial and regulatory partnerships; 4) clinical testing of prototype POC devices in the field; and 5) creation of training opportunities for technology developers, evaluators, and other stakeholders. C-THAN will have major impact on the prevention and clinical management of HIV/AIDS in LMICs and globally, and will lay a knowledge foundation to sustain POC technology development beyond its lifespan. 1

PROJECT SUMMARY The Northwestern/Nigeria Research Training Program in HIV and Malignancies (NN-HAM) addresses a high priority NIH research area and significant problem in sub-Saharan Africa because of the widespread HIV epidemic made worse by the high burden of oncogenic viral co-infections. Antiretroviral therapy programs put into place by PEPFAR, the Global Fund and others, have resulted in a remarkable decrease in HIV-related morbidity and mortality; however, the rate of certain malignancies are rising while the population is aging. Most African medical and research institutions are ill-prepared to confront these emerging challenges. Since 2014, Northwestern University and University of Jos in Nigeria successfully collaborated in a research training program for HIV and malignancies (Northwestern and Jos University Research Training Program in HIV and Malignancies, D43 TW009575). Program highlights include: 2 master's degree-level Clinical Investigation scientists and 2 PhDs in Health Services & Outcomes Research trained; senior faculty enrichment; and 6 mentored trainee pilot awards. We further formed a network with Northwestern, University of Lagos, and University of Jos to successfully compete for an NCI-funded U54 (Epigenomic Biomarkers of HIV-Associated Cancers in Nigeria, 1U54CA221205). This renewal Fogarty HIV Research Training Program for LMICs proposal will further enhance Nigerian scientists' capacity for large population-based HIV-malignancy research by training scientists focused on cancer molecular epidemiology. Our primary hypothesis is that building capacity in molecular cancer epidemiology, biostatistics, and bioinformatics on HIV-associated malignancies will significantly enhance our understanding of cancer epidemiology and promote mechanistic biomarker-based research that will inform preventive and therapeutic strategies, ultimately leading to a reduction in cancer incidence and mortality. This renewal application's specific aims are to: 1. train cancer molecular epidemiologists capable of: i) designing and conducting population-based molecular epidemiology studies, ii) developing protocols for biospecimen collection, processing, and storage, and iii) developing biomarkers that can be used for prevention and improved treatment of HIV-associated malignancies; 2. train several master's degree-level biostatisticians and scientists in medical informatics and bioinformatics who can manage and handle data from clinical, laboratory, and population settings, and perform comprehensive biostatistical and bioinformatic analyses generated from large population studies; and 3. create a multidisciplinary research team capable of performing advanced in-country molecular epidemiology research, including high throughput ?omic? research, on HIV-associated malignancies at our network sites, University of Jos and University of Lagos. We will achieve our goals through strong mentorship and research training including: 1 PhD degree and 4 master's degrees (long-term), 3 medium-term research-project-driven training programs, several short-term in-country workshops, and innovative distance learning.

The ?C-THAN POCTRN COVID-19 Proposal? is a supplement to the existing Center for Innovation in Point-of- Care Technologies for HIV/AIDS at Northwestern (C-THAN) which aims to support development of technologies which can help address the urgent healthcare needs created by the COVID-19 pandemic. The extent and urgency of the situation requires an aggressive and innovative approach to accelerate the delivery of solutions to address immediate and future needs. Our approach augments the strong technical and clinical expertise within our own and the existing four POCTRN centers and their Coordinating Center. The specific aims are: 1) develop a SARS-CoV-2 ten-minute molecular diagnostic test based on the Minute Molecular Platform; and 2) scale up C-THAN?s established international network for COVID-19 technological development and testing of relevant products and assays in sub-Saharan Africa and other low- and middle- income countries (LMICs). For aim 1, C-THAN proposes the development of a ten-minute SARS-CoV-2 test for the Minute Molecular DASH (Diagnosis Analyzer for Selective Hybridization), a sample-to-answer platform for point-of-care use in medical clinics, emergency departments and urgent care centers. The DASH platform exploits novel fast PCR and microfluidic fabrication technologies developed at the Center for Innovation in Global Health Technologies (CIGHT) at Northwestern University. DASH technology can be adapted for high throughput uses such as airports, hospitals, nursing homes, emergency departments and drive-through testing sites. For aim 2, we will scale up C-THAN resources to expand addressing the impact of the pandemic. The C-THAN network consists of four biomedical engineering (BME) technology development sites plus three clinical validation/needs assessment sites. The BME sites include University of Cape Town and Stellenbosch University in South Africa, and University of Lagos and University of Ibadan in Nigeria. The seven clinical validation/needs assessment sites include ones located with the engineering sites plus at University of Jos in Nigeria, University of Bamako in Mali and Muhimbili University in Tanzania. The relationship of these sites with Northwestern University go back up to 22 years. We will utilize Northwestern?s Institute for Global Health Catalyzer Award Program which has been funding promising research projects addressing critical global health needs for over 10 years. Two weeks ago, the Institute redirected all proposals to address only COVID-19 activities. Basic scientists, biomedical engineers, infectious diseases specialists, virologist, pharmacologists and public health faculty are encouraged to apply for Catalyzer awards which are in the range of $25,000 for a one-year project. With this POCTRN supplement, we will ?plus-up? these awards to a maximum of $100,000 each to increase the scope and pace of the development. Applications are being accepted on a rolling basis, and funding decisions are made within 7 days. These two approaches will rapidly accelerate the development of promising COVID-19 technologies both in the US and globally.

The overarching goal of this five year research training program, ?Building the Next Generation of Researchers in HIV/TB Diagnostics in Mali? (B-NextGen), is to strengthen the scientific capacity at the Université des Sciences, Téchniques et des Téchnologies de Bamako (USTTB; University of Bamako) to conduct HIV research on the evolving HIV epidemic in Mali. B-NextGen will address four NIH high priority HIV research topics, including: 1) Reducing HIV incidence by improving screening and detection, treatment monitoring assays, and HIV drug resistance assays; 2) Diagnosing HIV-associated TB and non- tuberculous mycobacteria (NTM); 3) Reducing health disparities by developing testing technology that can function in underserved community settings; and 4) Training the LMIC workforce to conduct high priority HIV/AIDS research. Mali is a low-income country in Sub-Saharan West Africa where the incidence of mycobacterial infections, primarily tuberculosis (TB), remains high driven in a large part by the persistence of the HIV epidemic with TB being the main cause of dealth in HIV-infected adults and children. The World Health Organization (WHO) guidelines for managing HIV recommend rapid initiation of antiretroviral therapy (ART) and enhanced screening and diagnosis of TB, yet detection rates for HIV and TB, particularly in children, remain low in Mali as the current diagnostic and treatment monitoring tools are not adapted to the low- and middle-income (LMIC) environment. Northwestern University, Johns Hopkins University, and Stellenbosch University, have been successfully collaborating with USTTB for over a decade on several major projects focused on HIV and mycobacterial diseases including the predecessor to this renewal proposal ?HIV and Mycobacterial Disease in Mali? (R Murphy, S Diallo, MPIs), which has been highly productive providing three ?sandwich? PhD and ten MS degrees; > 200 short-term university diplomas; 25 peer-reviewed publications; and four major NIH grant awards. We will train the same number of researchers in this renewal proposal while we leverage this success to focus on outcome indicators of high public health importance. Our aims are: 1) Create a Department of Biomedical Engineering at the Mali National School of Engineering and establish a Master of Science in Biomedical Engineering focused on the development of devices and assays critical for the diagnosis and/or monitoring of HIV and mycobacterial diseases; 2) Develop an interdisciplinary core of research scientists from virology, applied molecular biology, immunology and microbiology to enhance the capacity to diagnose, treat, and monitor HIV and mycobacterial diseases; 3) Train clinical researchers and basic scientists in research methodology, validation and implementation applied principles, and career development activities essential for developing independent faculty; and 4) Develop the next generation of academic leaders in diagnostics, virology and mycobacteriology. Through this program, we will achieve the overall goal of training the next generation of investigators and leaders in diagnostics of HIV and mycobacterial diseases for adults and children in Mali.