Ami Bhatt

All Publications

• Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nature biotechnology Moss, E. L., Maghini, D. G., Bhatt, A. S. 2020

  Abstract

  Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.

  View details for DOI 10.1038/s41587-020-0422-6

  View details for PubMedID 32042169

• A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation. Cell host & microbe Durrant, M. G., Li, M. M., Siranosian, B. A., Montgomery, S. B., Bhatt, A. S. 2019

  Abstract

  Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however, high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a bioinformatic toolbox that identifies integrative MGEs and their insertion sites by using short-read sequencing data. MGEfinder identifies the genomic site of each MGE insertion and infers the identity of the inserted sequence. We apply MGEfinder to 12,374 sequenced isolates of 9 prevalent bacterial pathogens, includingMycobacterium tuberculosis, Staphylococcus aureus, and Escherichia coli, and identify thousands of MGEs, including candidate insertion sequences, conjugative transposons, and prophage elements. The MGE repertoire and insertion rates vary across species, and integration sites often cluster near genes related to antibiotic resistance, virulence, and pathogenicity. MGE insertions likely contribute to antibiotic resistance in laboratory experiments and clinical isolates. Additionally, we identified thousands of mobility genes, a subset of which have unknown function opening avenues for exploration. Future application of MGEfinder to commensal bacteria will further illuminate bacterial adaptation and evolution.

  View details for DOI 10.1016/j.chom.2019.10.022

  View details for PubMedID 31862382

• Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. Cell Sberro, H., Fremin, B. J., Zlitni, S., Edfors, F., Greenfield, N., Snyder, M. P., Pavlopoulos, G. A., Kyrpides, N. C., Bhatt, A. S. 2019

  Abstract

  Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; 30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.

  View details for DOI 10.1016/j.cell.2019.07.016

  View details for PubMedID 31402174

• Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation. Trends in microbiology Brewster, R., Tamburini, F. B., Asiimwe, E., Oduaran, O., Hazelhurst, S., Bhatt, A. S. 2019

  Abstract

  Descriptive and translational investigations into the human gut microbiome (GM) are rapidly expanding; however, studies are largely restricted to industrialized populations in the USA and Europe. Little is known about microbial variability and its implications for health and disease in other parts of the world. Populations in Africa are particularly underrepresented. What limited research has been performed has focused on a few subject domains, including the impact of long-term lifestyle and dietary factors on GM ecology, its maturation during infancy, and the interrelationships between the microbiome, infectious disease, and undernutrition. Recently, international consortia have laid the groundwork for large-scale genomics and microbiome studies on the continent, with a particular interest in the epidemiologic transition to noncommunicable disease. Here, we survey the current landscape of GM scholarship in Africa and propose actionable recommendations to improve research capacity and output.

  View details for DOI 10.1016/j.tim.2019.05.006

  View details for PubMedID 31178123

• Precision identification of diverse bloodstream pathogens in the gut microbiome NATURE MEDICINE Tamburini, F. B., Andermann, T. M., Tkachenko, E., Senchyna, F., Banaei, N., Bhatt, A. S. 2018; 24 (12): 1809-+

  View details for DOI 10.1038/s41591-018-0202-8

  View details for Web of Science ID 000452392200008

• High-quality genome sequences of uncultured microbes by assembly of read clouds NATURE BIOTECHNOLOGY Bishara, A., Moss, E. L., Kolmogorov, M., Parada, A. E., Weng, Z., Sidow, A., Dekas, A. E., Batzoglou, S., Bhatt, A. S. 2018; 36 (11): 1067-+

  View details for DOI 10.1038/nbt.4266

  View details for Web of Science ID 000450374000020

• Digesting New Developments in Biosensors NEW ENGLAND JOURNAL OF MEDICINE Bhatt, A. S. 2018; 379 (7): 686?88

  View details for DOI 10.1056/NEJMcibr1806952

  View details for Web of Science ID 000441659100015

• Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages. Nature communications Siranosian, B. A., Tamburini, F. B., Sherlock, G., Bhatt, A. S. 2020; 11 (1): 280

  Abstract

  CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation.

  View details for DOI 10.1038/s41467-019-14103-3

  View details for PubMedID 31941900

• Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly. BMC bioinformatics Kang, J. B., Siranosian, B. A., Moss, E. L., Banaei, N., Andermann, T. M., Bhatt, A. S. 2019; 20 (Suppl 16): 585

  Abstract

  BACKGROUND: Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been restricted in part by current metagenomic sequencing technologies that are typically unable to reconstruct complete genomes for individual organisms present within a sequenced microbial community. We recently developed a metagenomic read cloud sequencing and assembly approach that generates improved draft genomes for individual organisms compared to conventional short-read sequencing and assembly methods. Herein, we applied metagenomic read cloud sequencing to four stool samples collected longitudinally from an HCT patient preceding treatment and over the course of heavy antibiotic exposure.RESULTS: Characterization of microbiome composition by taxonomic classification of reads reveals that that upon antibiotic exposure, the subject's gut microbiome experienced a marked decrease in diversity and became dominated by Escherichia coli. While diversity is restored at the final time point, this occurs without recovery of the original species and strain-level composition. Draft genomes for individual organisms within each sample were generated using both read cloud and conventional assembly. Read clouds were found to improve the completeness and contiguity of genome assemblies compared to conventional assembly. Moreover, read clouds enabled the placement of antibiotic resistance genes present in multiple copies both within a single draft genome and across multiple organisms. The occurrence of resistance genes associates with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various intestinal E. coli strains across time points as well as the bloodstream isolate showed that the subject's E. coli bloodstream infection likely originated from the intestine. The E. coli genome from the initial pre-transplant stool sample harbors 46 known antimicrobial resistance genes, while all other species from the pre-transplant sample each contain at most 5 genes, consistent with a model of heavy antibiotic exposure resulting in selective outgrowth of the highly antibiotic-resistant E. coli.CONCLUSION: This study demonstrates the application and utility of metagenomic read cloud sequencing and assembly to study the underlying strain-level genomic factors influencing gut microbiome dynamics under extreme selective pressures in the clinical context of HCT.

  View details for DOI 10.1186/s12859-019-3073-1

  View details for PubMedID 31787070

• Microbiome genome structure drives function. Nature microbiology Durrant, M. G., Bhatt, A. S. 2019; 4 (6): 912?13

  View details for DOI 10.1038/s41564-019-0473-y

  View details for PubMedID 31118502

• Making the microbiome personal NATURE MEDICINE Bhatt, A. S. 2019; 25 (5): 708

  View details for DOI 10.1038/s41591-019-0445-z

  View details for Web of Science ID 000468247800003

• Diversity of resistance mechanisms in carbapenem-resistant Enterobacteriaceae at a health care system in Northern California, from 2013 to 2016 DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE Senchyna, F., Gaur, R. L., Sandlund, J., Truong, C., Tremintin, G., Kutz, D., Gomez, C. A., Tamburini, F. B., Andermann, T., Bhatt, A., Tickler, I., Watz, N., Budvytiene, I., Shi, G., Tenover, F. C., Banaei, N. 2019; 93 (3): 250?57

  View details for DOI 10.1016/j.diagmicrobio.2018.10.004

  View details for Web of Science ID 000460196900013

• Whole blood RNA sequencing reveals a unique transcriptomic profile in patients with ARDS following hematopoietic stem cell transplantation RESPIRATORY RESEARCH Englert, J. A., Cho, M. H., Lamb, A. E., Shumyatcher, M., Barragan-Bradford, D., Basil, M. C., Higuera, A., Isabelle, C., Vera, M., Dieffenbach, P. B., Fredenburgh, L. E., Kang, J. B., Bhatt, A. S., Antin, J. H., Ho, V. T., Soiffer, R. J., Howrylak, J. A., Himes, B. E., Baron, R. M. 2019; 20

  View details for DOI 10.1186/s12931-019-0981-6

  View details for Web of Science ID 000458078000001

• Whole blood RNA sequencing reveals a unique transcriptomic profile in patients with ARDS following hematopoietic stem cell transplantation. Respiratory research Englert, J. A., Cho, M. H., Lamb, A. E., Shumyatcher, M., Barragan-Bradford, D., Basil, M. C., Higuera, A., Isabelle, C., Vera, M. P., Dieffenbach, P. B., Fredenburgh, L. E., Kang, J. B., Bhatt, A. S., Antin, J. H., Ho, V. T., Soiffer, R. J., Howrylak, J. A., Himes, B. E., Baron, R. M. 2019; 20 (1): 15

  Abstract

  BACKGROUND: The acute respiratory distress syndrome (ARDS) is characterized by the acute onset of hypoxemia and bilateral lung infiltrates in response to an inciting event, and is associated with high morbidity and mortality. Patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) are at increased risk for ARDS. We hypothesized that HSCT patients with ARDS would have a unique transcriptomic profile identifiable in peripheral blood compared to those that did not undergo HSCT.METHODS: We isolated RNA from banked peripheral blood samples from a biorepository of critically ill ICU patients. RNA-Seqwas performed on 11 patients with ARDS (5 that had undergone HSCT and 6 that had not) and 12 patients with sepsis without ARDS (5 that that had undergone HCST and 7 that had not).RESULTS: We identified 687 differentially expressed genes between ARDS and ARDS-HSCT (adjusted p-value <0.01), including IFI44L, OAS3, LY6E, and SPATS2L that had increased expression in ARDS vs. ARDS-HSCT; these genes were not differentially expressed in sepsis vs sepsis-HSCT. Gene ontology enrichment analysis revealed that many differentially expressed genes were related to response to type I interferon.CONCLUSIONS: Our findings reveal significant differences in whole blood transcriptomic profiles of patients with non-HSCT ARDS compared to ARDS-HSCT patients and point toward different immune responses underlying ARDS and ARDS-HSCT that contribute to lung injury.

  View details for PubMedID 30665420

• Evaluating Barriers and Opportunities in Delivering High-Quality Oncology Care in a Resource-Limited Setting Using a Comprehensive Needs Assessment Tool JOURNAL OF GLOBAL ONCOLOGY Nwachukwu, C. R., Mudasiru, O., Million, L., Sheth, S., Qamoos, H., Onah, J. O., Okemini, A., Rhodes, M., Barry, M., Banjo, A. A., Habeebu, M., Olasinde, T. A., Bhatt, A. S. 2018; 4

  View details for DOI 10.1200/JGO.18.00125

  View details for Web of Science ID 000462480700001

• Evaluating Barriers and Opportunities in Delivering High-Quality Oncology Care in a Resource-Limited Setting Using a Comprehensive Needs Assessment Tool. Journal of global oncology Nwachukwu, C. R., Mudasiru, O., Million, L., Sheth, S., Qamoos, H., Onah, J. O., Okemini, A., Rhodes, M., Barry, M., Banjo, A. A., Habeebu, M., Olasinde, T. A., Bhatt, A. S. 2018: 1?9

  Abstract

  PURPOSE: Despite recognition of both the growing cancer burden in low- and middle-income countries and the disproportionately high mortality rates in these settings, delivery of high-quality cancer care remains a challenge. The disparities in cancer care outcomes for many geographic regions result from barriers that are likely complex and understudied. This study describes the development and use of a streamlined needs assessment questionnaire (NAQ) to understand the barriers to providing quality cancer care, identifies areas for improvement, and formulates recommendations for implementation.METHODS: Using a comprehensive NAQ, in-depth interviews were conducted with 17 hospital staff involved in cancer care at two teaching hospitals in Nigeria. Data were analyzed using content analysis and organized into a framework with preset codes and emergent codes, where applicable.RESULTS: Data from the interviews were organized into six broad themes: staff, stuff, system, space, lack of palliative care, and provider bias, with key barriers within themes including: financial, infrastructural, lack of awareness, limited human capacity resources, lack of palliative care, and provider perspective on patient-related barriers to cancer care. Specific solutions based on ability to reasonably implement were subcategorized into short-, medium-, and long-term goals.CONCLUSION: This study provides a framework for a streamlined initial needs assessment and a unique discussion on the barriers to high-quality oncology care that are prevalent in resource-constrained settings. We report the feasibility of collecting and organizing data using a streamlined NAQ and provide a thorough and in-depth understanding of the challenges in this setting. Knowledge gained from the assessments will inform steps to improve oncology cancer in these settings.

  View details for PubMedID 30532992

• Institutionalizing healthcare hackathons to promote diversity in collaboration in medicine BMC MEDICAL EDUCATION Wang, J. K., Roy, S. K., Barry, M., Chang, R. T., Bhatt, A. S. 2018; 18

  View details for DOI 10.1186/s12909-018-1385-x

  View details for Web of Science ID 000450779900001

• Institutionalizing healthcare hackathons to promote diversity in collaboration in medicine. BMC medical education Wang, J. K., Roy, S. K., Barry, M., Chang, R. T., Bhatt, A. S. 2018; 18 (1): 269

  Abstract

  BACKGROUND: Medical students and healthcare professionals can benefit from exposure to cross-disciplinary teamwork and core concepts of medical innovation. Indeed, to address complex challenges in patient care, diversity in collaboration across medicine, engineering, business, and design is critical. However, a limited number of academic institutions have established cross-disciplinary opportunities for students and young professionals within these domains to work collaboratively towards diverse healthcare needs.METHODS: Drawing upon best practices from computer science and engineering, healthcare hackathons bring together interdisciplinary teams of students and professionals to collaborate, brainstorm, and build solutions to unmet clinical needs. Over the course of six months, a committee of 20 undergraduates, medical students, and physician advisors organized Stanford University's first healthcare hackathon (November 2016). Demographic data from initial applications were supplemented with responses from a post-hackathon survey gauging themes of diversity in collaboration, professional development, interest in medical innovation, and educational value. In designing and evaluating the event, the committee focused on measurable outcomes of diversity across participants (skillset, age, gender, academic degree), ideas (clinical needs), and innovations (projects).RESULTS: Demographic data (n=587 applicants, n=257 participants) reveal participants across diverse academic backgrounds, age groups, and domains of expertise were in attendance. From 50 clinical needs presented representing 19 academic fields, 40 teams ultimately formed and submitted projects spanning web (n=13) and mobile applications (n=13), artificial intelligence-based tools (n=6), and medical devices (n=3), among others. In post-hackathon survey responses (n=111), medical students and healthcare professionals alike noted a positive impact on their ability to work in multidisciplinary teams, learn from individuals of different backgrounds, and address complex healthcare challenges.CONCLUSIONS: Healthcare hackathons can encourage diversity across individuals, ideas, and projects to address clinical challenges. By providing an outline of Stanford's inaugural event, we hope more universities can adopt the healthcare hackathon model to promote diversity in collaboration in medicine.

  View details for PubMedID 30458759

• Persistence of endothelial thrombomodulin in a patient with infectious purpura fulminans treated with protein C concentrate BLOOD ADVANCES Bendapudi, P. K., Robbins, A., LeBoeuf, N., Pozdnyakova, O., Bhatt, A., Duke, F., Sells, R., McQuiston, J., Humrighouse, B., Rouaisnel, B., Colling, M., Stephenson, K. E., Saavedra, A., Losman, J. 2018; 2 (21): 2917?21

  View details for DOI 10.1182/bloodadvances.2018024430

  View details for Web of Science ID 000450684800011

• Persistence of endothelial thrombomodulin in a patient with infectious purpura fulminans treated with protein C concentrate. Blood advances Bendapudi, P. K., Robbins, A., LeBoeuf, N., Pozdnyakova, O., Bhatt, A., Duke, F., Sells, R., McQuiston, J., Humrighouse, B., Rouaisnel, B., Colling, M., Stephenson, K. E., Saavedra, A., Losman, J. 2018; 2 (21): 2917?21

  View details for PubMedID 30396911

• Antibiotic practice patterns in hematopoietic cell transplantation: A survey of blood and marrow transplant clinical trials network centers AMERICAN JOURNAL OF HEMATOLOGY Rashidi, A., Wangjam, T., Bhatt, A. S., Weisdorf, D. J., Holtan, S. G., BMT CTN Investigators 2018; 93 (11): E348?E350

  View details for PubMedID 30058189

  View details for PubMedCentralID PMC6196101

• Diversity of resistance mechanisms in carbapenem-resistant Enterobacteriaceae at a health care system in Northern California, from 2013 to 2016. Diagnostic microbiology and infectious disease Senchyna, F., Gaur, R. L., Sandlund, J., Truong, C., Tremintin, G., Kultz, D., Gomez, C. A., Tamburini, F. B., Andermann, T., Bhatt, A., Tickler, I., Watz, N., Budvytiene, I., Shi, G., Tenover, F. C., Banaei, N. 2018

  Abstract

  The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) blaOXA-48 like, 20.8% (5/24) blaKPC, 20.8% (5/24) blaNDM, 20.8% (5/24) blaSME, 8.3% (2/24) blaIMP, and 4.2% (1/24) blaVIM. Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing blaKPC were 100% susceptible to ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-relebactam; blaOXA-48 like-positive isolates were 100% susceptible to ceftazidime-avibactam; and metallo beta-lactamase-positive isolates were nearly all nonsusceptible to above antibiotics. Carbapenemase gene-negative CRE were 100% (38/38), 92.1% (35/38), 89.5% (34/38), and 31.6% (12/38) susceptible to ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, and ceftolozane-tazobactam, respectively. None of the CRE strains were identical by whole genome sequencing. At this health system, CRE were mediated by diverse mechanisms with predictable susceptibility to newer beta-lactamase inhibitors.

  View details for PubMedID 30482638

• Data mining of digitized health records in a resource-constrained setting reveals that timely immunophenotyping is associated with improved breast cancer outcomes. BMC cancer Lopez-Pineda, A., Rodriguez-Moran, M. F., Alvarez-Aguilar, C., Fuentes Valle, S. M., Acosta-Rosales, R., Bhatt, A. S., Sheth, S. N., Bustamante, C. D. 2018; 18 (1): 933

  Abstract

  BACKGROUND: Organizations that issue guidance on breast cancer recommend the use of immunohistochemistry (IHC) for providing appropriate and precise care. However, little focus has been directed to the identification of maximum allowable turnaround times for IHC, which is necessary given the diversity of hospital settings in the world. Much less effort has been committed to the development of digital tools that allow hospital administrators to monitor service utilization histories of their patients.METHODS: In this retrospective cohort study, we reviewed electronic and paper medical records of all suspected breast cancer patients treated at one secondary-care hospital of the Mexican Institute of Social Security (IMSS), located in western Mexico. We then followed three years of medical history of those patients with IHC testing.RESULTS: In 2014, there were 402 breast cancer patients, of which 30 (7.4% of total) were tested for some IHC biomarker (ER, PR, HER2). The subtyping allowed doctors to adjust (56.7%) or confirm (43.3%) the initial therapeutic regimen. The average turnaround time was 56days. Opportune IHC testing was found to be beneficial when it was available before or during the first rounds of chemotherapy.CONCLUSIONS: The use of data mining tools applied to health record data revealed that there is an association between timely immunohistochemistry and improved outcomes in breast cancer patients. Based on this finding, inclusion of turnaround time in clinical guidelines is recommended. As much of the health data in the country becomes digitized, our visualization tools allow a digital dashboard of the hospital service utilization histories.

  View details for PubMedID 30261931

• Data mining of digitized health records in a resource-constrained setting reveals that timely immunophenotyping is associated with improved breast cancer outcomes BMC CANCER Lopez-Pineda, A., Rodriguez-Moran, M. F., Alvarez-Aguilar, C., Fuentes Valle, S. M., Acosta-Rosales, R., Bhatt, A. S., Sheth, S. N., Bustamante, C. D. 2018; 18

  View details for DOI 10.1186/s12885-018-4833-4

  View details for Web of Science ID 000445959100003

• A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection CELL HOST & MICROBE Jacobson, A., Lam, L., Rajendram, M., Tamburini, F., Honeycutt, J., Trung Pham, Van Treuren, W., Pruss, K., Stabler, S., Lugo, K., Bouley, D. M., Vilches-Moure, J. G., Smith, M., Sonnenburg, J. L., Bhatt, A. S., Huang, K., Monack, D. 2018; 24 (2): 296-+

  View details for DOI 10.1016/j.chom.2018.07.002

  View details for Web of Science ID 000441083900016

• A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection. Cell host & microbe Jacobson, A., Lam, L., Rajendram, M., Tamburini, F., Honeycutt, J., Pham, T., Van Treuren, W., Pruss, K., Stabler, S. R., Lugo, K., Bouley, D. M., Vilches-Moure, J. G., Smith, M., Sonnenburg, J. L., Bhatt, A. S., Huang, K. C., Monack, D. 2018

  Abstract

  The intestinal microbiota provides colonization resistance against pathogens, limiting pathogen expansion and transmission. These microbiota-mediated mechanisms were previously identified by observing loss of colonization resistance after antibiotic treatment or dietary changes, which severely disrupt microbiota communities. We identify a microbiota-mediated mechanism of colonization resistance against Salmonella enterica serovar Typhimurium (S. Typhimurium) by comparing high-complexity commensal communities with different levels of colonization resistance. Using inbred mouse strains with different infection dynamics and S. Typhimurium intestinal burdens, we demonstrate that Bacteroides species mediate colonization resistance against S. Typhimurium by producing the short-chain fatty acid propionate. Propionate directly inhibits pathogen growth invitro by disrupting intracellular pH homeostasis, and chemically increasing intestinal propionate levels protects mice from S.Typhimurium. In addition, administering susceptible mice Bacteroides, but not a propionate-production mutant, confers resistance to S. Typhimurium. This work provides mechanistic understanding into the role of individualized microbial communities in host-to-host variability of pathogen transmission.

  View details for PubMedID 30057174

• The Microbiome and Hematopoietic Cell Transplantation: Past, Present, and Future BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION Andermann, T. M., Peled, J. U., Ho, C., Reddy, P., Riches, M., Storb, R., Teshima, T., van den Brink, M. M., Alousi, A., Balderman, S., Chiusolo, P., Clark, W. B., Holler, E., Howard, A., Kean, L. S., Koh, A. Y., McCarthy, P. L., McCarty, J. M., Mohty, M., Nakamura, R., Rezvani, K., Segal, B. H., Shaw, B. E., Shpall, E. J., Sung, A. D., Weber, D., Whangbo, J., Wingard, J. R., Wood, W. A., Perales, M., Jenq, R. R., Bhatt, A. S., Blood Marrow Transplant Clinical 2018; 24 (7): 1322?40

  View details for DOI 10.1016/j.bbmt.2018.02.009

  View details for Web of Science ID 000440879800004

• Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota. Cell Tropini, C., Moss, E. L., Merrill, B. D., Ng, K. M., Higginbottom, S. K., Casavant, E. P., Gonzalez, C. G., Fremin, B., Bouley, D. M., Elias, J. E., Bhatt, A. S., Huang, K. C., Sonnenburg, J. L. 2018; 173 (7): 1742

  Abstract

  Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption, and widespread laxative use. Here, we assess the resilience of the gut ecosystem to osmotic perturbation at multiple length and timescales using mice as model hosts. Osmotic stress caused reproducible extinction of highly abundant taxa and expansion of less prevalent members in human and mouse microbiotas. Quantitative imaging revealed decimation of the mucus barrier during osmotic perturbation, followed by recovery. The immune system exhibited temporary changes in cytokine levels and a lasting IgG response against commensal bacteria. Increased osmolality prevented growth of commensal strains invitro, revealing one mechanism contributing to extinction. Environmental availability of microbiota members mitigated extinction events, demonstrating how species reintroduction can affect community resilience. Our findings (1) demonstrate that even mild osmotic diarrhea can cause lasting changes to the microbiota and host and (2) lay the foundation for interventions that increase system-wide resilience.

  View details for PubMedID 29906449

• Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota CELL Tropini, C., Moss, E., Merrill, B., Ng, K., Higginbottom, S., Casavant, E., Gonzalez, C., Fremin, B., Bouley, D., Elias, J., Bhatt, A., Huang, K., Sonnenburg, J. 2018; 173 (7): 1742-+

  View details for DOI 10.1016/j.cell.2018.05.008

  View details for Web of Science ID 000437004000021

• AGBT meeting report GENOME BIOLOGY Bhatt, A. S., Curtis, C. 2018; 19: 60

  Abstract

  The Annual Advances in Genome Biology and Technology (AGBT) General Meeting was held in Orlando, Florida, USA, on the 12-15 February 2018. Professors Ami S. Bhatt and Christina Curtis from Stanford University, USA, report advances and applications in the field that were discussed at the meeting.

  View details for PubMedID 29784033

• The Microbiome and Hematopoietic Cell Transplantation: Past, Present, and Future. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation Andermann, T. M., Peled, J. U., Ho, C., Reddy, P., Riches, M., Storb, R., Teshima, T., van den Brink, M. R., Alousi, A., Balderman, S., Chiusolo, P., Clark, W. B., Holler, E., Howard, A., Kean, L. S., Koh, A. Y., McCarthy, P. L., McCarty, J. M., Mohty, M., Nakamura, R., Rezvani, K., Segal, B. H., Shaw, B. E., Shpall, E. J., Sung, A. D., Weber, D., Whangbo, J., Wingard, J. R., Wood, W. A., Perales, M., Jenq, R. R., Bhatt, A. S., Blood and Marrow Transplant Clinical Trials Network 2018

  View details for PubMedID 29471034

• In Translation: With probiotics, resistance is not always futile Cell Host & Microbe Severyn, C. J., Bhatt, A. S. 2018; 24: 334-336

  View details for DOI 10.1016/j.chom.2018.08.014

• With Probiotics, Resistance Is Not Always Futile. Cell host & microbe Severyn, C. J., Bhatt, A. S. 2018; 24 (3): 334?36

  Abstract

  Probiotics and other bacteriotherapies are actively being explored and applied as symptom- and disease-modifying agents. In a recent issue of Cell, two papers contribute to our understanding of how live bacterial therapies variably affect individuals and the short- and longer-term impact of these therapies on colonization and host response.

  View details for PubMedID 30212646

• Read cloud sequencing elucidates microbiome dynamics in a hematopoietic cell transplant patient Kang, J., Siranosian, B., Moss, E., Andermann, T., Bhatt, A., Zheng, H., Callejas, Z., Griol, D., Wang, H., Hu, Schmidt, H., Baumbach, J., Dickerson, J., Zhang, L. IEEE. 2018: 234?41

  View details for Web of Science ID 000458654000043

• Household triclosan and triclocarban effects on the infant and maternal microbiome EMBO MOLECULAR MEDICINE Ribado, J. V., Ley, C., Haggerty, T. D., Tkachenko, E., Bhatt, A. S., Parsonnet, J. 2017; 9 (12): 1732?41

  View details for DOI 10.15252/emmm.201707882

  View details for Web of Science ID 000416867700009

• Allied Commensal Forces against Vancomycin-Resistant Enterococci CELL HOST & MICROBE Fremin, B. J., Bhatt, A. S. 2017; 21 (5): 559?60

  Abstract

  In this issue of Cell Host & Microbe, Caballero et al. (2017) define a precise, limited consortium of commensal bacteria that restores resistance to colonization by clinically vexing vancomycin-resistant Enterococcus species.

  View details for PubMedID 28494236

  View details for PubMedCentralID PMC5603308

• Quantitative Computed Tomography Assessment of Bronchiolitis Obliterans Syndrome after Lung Transplantation. Clinical transplantation Gazourian, L., Ash, S., Meserve, E. E., Diaz, A., Estepar, R. S., El-Chemaly, S. Y., Rosas, I. O., Divo, M., Fuhlbrigge, A. L., Camp, P. C., Ho, V. T., Bhatt, A. S., Goldberg, H. J., Sholl, L. M., Washko, G. R. 2017

  Abstract

  Bronchiolitis obliterans syndrome (BOS) is a clinical manifestation of chronic allograft rejection following lung transplantation. We examined the quantitative measurements of the proximal airway and vessels and pathologic correlations in subjects with BOS.Patients who received a lung transplant at the Brigham and Women's Hospital between December 1, 2002 and December 31, 2010 were included in this study. We characterized the quantitative CT measures of proximal airways and vessels and pathological changes.Ninety-four (46.1%) of the 204 subjects were included in the study. There was a significant increase in the airway vessel ratio in subjects who developed progressive BOS compared to controls and non-progressors. There was a significant increase in airway lumen area and decrease in vessel cross-sectional area in patients with BOS compared to controls. Patients with BOS had a significant increase in proximal airway fibrosis compared to controls.BOS is characterized by central airway dilation and vascular remodeling, the degree of which is correlated to decrements in lung function. Our data suggest that progressive BOS is a pathologic process that affects both the central and distal airways.

  View details for DOI 10.1111/ctr.12943

  View details for PubMedID 28244139

• Technological solutions for global hematology and oncology BLOOD ADVANCES Bhatt, A. S. 2017; 1 (6): 396

  View details for PubMedID 29296953

• Antibiotic-mediated modification of the intestinal microbiome in allogeneic hematopoietic stem cell transplantation BONE MARROW TRANSPLANTATION Whangbo, J., Ritz, J., Bhatt, A. 2017; 52 (2): 183-190

  Abstract

  Allogeneic hematopoietic stem cell transplantation (HSCT) is curative for many patients with severe benign and malignant hematologic disorders. The success of allogeneic HSCT is limited by the development of transplant-related complications such as acute graft-versus-host disease (GvHD). Early pre-clinical studies suggested that intestinal microflora contribute to the pathogenesis of acute GvHD, and that growth suppression or eradication of intestinal bacteria prevented the development of acute GvHD even in MHC-mismatched transplants. These observations led to the practice of gut decontamination (GD) with oral non-absorbable antibiotics in patients undergoing allogeneic HSCT as a method of acute GvHD prophylaxis. Microbiome studies in the modern sequencing era are beginning to challenge the benefit of this practice. In this review, we provide a historical perspective on the practice of GD and highlight findings from the limited number of clinical trials evaluating the use of GD for acute GvHD prevention in allogeneic HSCT patients. In addition, we examine the role of the gut microbiota in allogeneic HSCT in the context of recent studies linking the microflora to regulation of intestinal immune homeostasis. We discuss the implications of these findings for future strategies to reduce acute GvHD risk by selective manipulation of the microbiota.Bone Marrow Transplantation advance online publication, 15 August 2016; doi:10.1038/bmt.2016.206.

  View details for DOI 10.1038/bmt.2016.206

  View details for Web of Science ID 000394134300003

• Microbes prevent HSPCs from "NOD"-ing off. Blood Bhatt, A. S. 2017; 129 (2): 139-140

  View details for DOI 10.1182/blood-2016-11-750562

  View details for PubMedID 28082290

• Household triclosan and triclocarban effects on the infant and maternal microbiome. EMBO molecular medicine Ribado, J. V., Ley, C., Haggerty, T. D., Tkachenko, E., Bhatt, A. S., Parsonnet, J. 2017; 9 (12): 1732?41

  Abstract

  In 2016, the US Food and Drug Administration banned the use of specific microbicides in some household and personal wash products due to concerns that these chemicals might induce antibiotic resistance or disrupt human microbial communities. Triclosan and triclocarban (referred to as TCs) are the most common antimicrobials in household and personal care products, but the extent to which TC exposure perturbs microbial communities in humans, particularly during infant development, was unknown. We conducted a randomized intervention of TC-containing household and personal care products during the first year following birth to characterize whether TC exposure from wash products perturbs microbial communities in mothers and their infants. Longitudinal survey of the gut microbiota using 16S ribosomal RNA amplicon sequencing showed that TC exposure from wash products did not induce global reconstruction or loss of microbial diversity of either infant or maternal gut microbiotas. Broadly antibiotic-resistant species from the phylum Proteobacteria, however, were enriched in stool samples from mothers in TC households after the introduction of triclosan-containing toothpaste. When compared by urinary triclosan level, agnostic to treatment arm, infants with higher triclosan levels also showed an enrichment of Proteobacteria species. Despite the minimal effects of TC exposure from wash products on the gut microbial community of infants and adults, detected taxonomic differences highlight the need for consumer safety testing of antimicrobial self-care products on the human microbiome and on antibiotic resistance.

  View details for PubMedID 29030459

• Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients. PloS one Moss, E. L., Falconer, S. B., Tkachenko, E., Wang, M., Systrom, H., Mahabamunuge, J., Relman, D. A., Hohmann, E. L., Bhatt, A. S. 2017; 12 (8): e0182585

  Abstract

  Immunocompromised individuals are at high risk of developing Clostridium difficile-associated disease (CDAD). Fecal microbiota transplantation (FMT) is a highly effective therapy for refractory or recurrent CDAD and, despite safety concerns, has recently been offered to immunocompromised patients. We investigated the genomics of bacterial composition following FMT in immunocompromised patients over a 1-year period. Metagenomic, strain and gene-level bacterial dynamics were characterized in two CDAD-affected hematopoietic stem cell (HCT) recipients following FMT. We found alterations in gene content, including loss of virulence and antibiotic resistance genes. These alterations were accompanied by long-term bacterial divergence at the species and strain levels. Our findings suggest limited durability of the specific bacterial consortium introduced with FMT and indicate that alterations of the functional potential of the microbiome are more complex than can be inferred by taxonomic information alone. Our observation that FMT alone cannot induce long-term donor-like alterations of the microbiota of HCT recipients suggests that FMT cannot indefinitely supersede environmental and/or host factors in shaping bacterial composition.

  View details for PubMedID 28827811

• The Burden of Cancer in Asian Americans: A Report of National Mortality Trends by Asian Ethnicity CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Thompson, C. A., Gomez, S. L., Hastings, K. G., Kapphahn, K., Yu, P., Shariff-Marco, S., Bhatt, A. S., Wakelee, H. A., Patel, M. I., Cullen, M. R., Palaniappan, L. P. 2016; 25 (10): 1371-1382

  Abstract

  Asian Americans (AA) are the fastest growing U.S. population, and when properly distinguished by their ethnic origins, exhibit substantial heterogeneity in socioeconomic status, health behaviors, and health outcomes. Cancer is the second leading cause of death in the United States, yet trends and current patterns in the mortality burden of cancer among AA ethnic groups have not been documented.We report age-adjusted rates, standardized mortality ratios, and modeled trends in cancer-related mortality in the following AA ethnicities: Asian Indians, Chinese, Filipinos, Japanese, Koreans, and Vietnamese, from 2003 to 2011, with non-Hispanic whites (NHW) as the reference population.For most cancer sites, AAs had lower cancer mortality than NHWs; however, mortality patterns were heterogeneous across AA ethnicities. Stomach and liver cancer mortality was very high, particularly among Chinese, Koreans, and Vietnamese, for whom these two cancer types combined accounted for 15% to 25% of cancer deaths, but less than 5% of cancer deaths in NHWs. In AA women, lung cancer was a leading cause of death, but (unlike males and NHW females) rates did not decline over the study period.Ethnicity-specific analyses are critical to understanding the national burden of cancer among the heterogeneous AA population.Our findings highlight the need for disaggregated reporting of cancer statistics in AAs and warrant consideration of tailored screening programs for liver and gastric cancers. Cancer Epidemiol Biomarkers Prev; 25(10); 1371-82. ©2016 AACR.

  View details for DOI 10.1158/1055-9965.EPI-16-0167

  View details for PubMedID 27694108

• Infection Rates among Acute Leukemia Patients Receiving Alternative Donor Hematopoietic Cell Transplantation. Biology of blood and marrow transplantation Ballen, K., Woo Ahn, K., Chen, M., Abdel-Azim, H., Ahmed, I., Aljurf, M., Antin, J., Bhatt, A. S., Boeckh, M., Chen, G., Dandoy, C., George, B., Laughlin, M. J., Lazarus, H. M., MacMillan, M. L., Margolis, D. A., Marks, D. I., Norkin, M., Rosenthal, J., Saad, A., Savani, B., Schouten, H. C., Storek, J., Szabolcs, P., Ustun, C., Verneris, M. R., Waller, E. K., Weisdorf, D. J., Williams, K. M., Wingard, J. R., Wirk, B., Wolfs, T., Young, J. H., Auletta, J., Komanduri, K. V., Lindemans, C., Riches, M. L. 2016; 22 (9): 1636-1645

  Abstract

  Alternative graft sources (umbilical cord blood [UCB], matched unrelated donors [MUD], or mismatched unrelated donors [MMUD]) enable patients without a matched sibling donor to receive potentially curative hematopoietic cell transplantation (HCT). Retrospective studies demonstrate comparable outcomes among different graft sources. However, the risk and types of infections have not been compared among graft sources. Such information may influence the choice of a particular graft source. We compared the incidence of bacterial, viral, and fungal infections in 1781 adults with acute leukemia who received alternative donor HCT (UCB, n=?568; MUD, n?=?930; MMUD, n?=?283) between 2008 and 2011. The incidences of bacterial infection at 1 year were 72%, 59%, and 65% (P?

  View details for DOI 10.1016/j.bbmt.2016.06.012

  View details for PubMedID 27343716

• Antibiotics in Hematopoietic Cell Transplantation: Adversaries or Allies? BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION Andermann, T. M., Bhatt, A. S. 2016; 22 (6): 972-974

  View details for DOI 10.1016/j.bbmt.2016.04.002

  View details for PubMedID 27095689

• Mapping global cancer research and control in areas of low and middle income: The need for shared data on a single, interactive platform Chisti, A., Sharara, N., Gupta, M., Rosenberg, I., Abudu, R., Morgan, C., Duncan, K., Silkensen, S., Craycroft, J., Silva, J., Andre, B., Trimble, E., Bhatt, A., Huang, F. W. AMER SOC CLINICAL ONCOLOGY. 2016

  View details for DOI 10.1200/JCO.2016.34.15_suppl.e18048

  View details for Web of Science ID 000404711503193

• Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice SCIENCE TRANSLATIONAL MEDICINE Shono, Y., Docampo, M. D., Peled, J. U., Perobelli, S. M., Velardi, E., Tsai, J. J., Slingerland, A. E., Smith, O. M., Young, L. F., Gupta, J., Lieberman, S. R., Jay, H. V., Ahr, K. F., Rodriguez, K. A., Xu, K., Calarfiore, M., Poeck, H., Caballero, S., Devlin, S. M., Rapaport, F., Dudakov, J. A., Hanash, A. M., Gyurkocza, B., Murphy, G. F., Gomes, C., Liu, C., Moss, E. L., Falconer, S. B., Bhatt, A. S., Taur, Y., Pamer, E. G., van den Brink, M. R., Jenq, R. R. 2016; 8 (339)

  Abstract

  Intestinal bacteria may modulate the risk of infection and graft-versus-host disease (GVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients often develop neutropenic fever, which is treated with antibiotics that may target anaerobic bacteria in the gut. We retrospectively examined 857 allo-HSCT recipients and found that treatment of neutropenic fever with imipenem-cilastatin and piperacillin-tazobactam antibiotics was associated with increased GVHD-related mortality at 5 years (21.5% for imipenem-cilastatin-treated patients versus 13.1% for untreated patients, P = 0.025; 19.8% for piperacillin-tazobactam-treated patients versus 11.9% for untreated patients, P = 0.007). However, two other antibiotics also used to treat neutropenic fever, aztreonam and cefepime, were not associated with GVHD-related mortality (P = 0.78 and P = 0.98, respectively). Analysis of stool specimens from allo-HSCT recipients showed that piperacillin-tazobactam administration was associated with perturbation of gut microbial composition. Studies in mice demonstrated aggravated GVHD mortality with imipenem-cilastatin or piperacillin-tazobactam compared to aztreonam (P < 0.01 and P < 0.05, respectively). We found pathological evidence for increased GVHD in the colon of imipenem-cilastatin-treated mice (P < 0.05), but no difference in the concentration of short-chain fatty acids or numbers of regulatory T cells. Notably, imipenem-cilastatin treatment of mice with GVHD led to loss of the protective mucus lining of the colon (P < 0.01) and the compromising of intestinal barrier function (P < 0.05). Sequencing of mouse stool specimens showed an increase in Akkermansia muciniphila (P < 0.001), a commensal bacterium with mucus-degrading capabilities, raising the possibility that mucus degradation may contribute to murine GVHD. We demonstrate an underappreciated risk for the treatment of allo-HSCT recipients with antibiotics that may exacerbate GVHD in the colon.

  View details for DOI 10.1126/scitranslmed.aaf2311

  View details for PubMedID 27194729

• Fecal Microbiota Transplant Is a Potentially Safe and Effective Treatment for Clostridium Difficile Infection in Hematopoietic Stem Cell Recipients Falconer, S., Moss, E., Andermann, T., Systrom, H., Mahabamunuge, J., Hohmann, E., Bhatt, A. S. ELSEVIER SCIENCE INC. 2016: S53?S54

  View details for DOI 10.1016/j.bbmt.2015.11.340

  View details for Web of Science ID 000370910300050

• Microbiota Manipulation With Prebiotics and Probiotics in Patients Undergoing Stem Cell Transplantation CURRENT HEMATOLOGIC MALIGNANCY REPORTS Andermann, T. M., Rezvani, A., Bhatt, A. S. 2016; 11 (1): 19-28

  Abstract

  Hematopoietic stem cell transplantation (HSCT) is a potentially life-saving therapy that often comes at the cost of complications such as graft-versus-host disease and post-transplant infections. With improved technology to understand the ecosystem of microorganisms (viruses, bacteria, fungi, and microeukaryotes) that make up the gut microbiota, there is increasing evidence of the microbiota's contribution to the development of post-transplant complications. Antibiotics have traditionally been the mainstay of microbiota-altering therapies available to physicians. Recently, interest is increasing in the use of prebiotics and probiotics to support the development and sustainability of a healthier microbiota. In this review, we will describe the evidence for the use of prebiotics and probiotics in combating microbiota dysbiosis and explore the ways in which they may be used in future research to potentially improve clinical outcomes and decrease rates of graft-versus-host disease (GVHD) and post-transplant infection.

  View details for DOI 10.1007/s11899-016-0302-9

  View details for Web of Science ID 000372595100004

• Microbiota Manipulation With Prebiotics and Probiotics in Patients Undergoing Stem Cell Transplantation. Current hematologic malignancy reports Andermann, T. M., Rezvani, A., Bhatt, A. S. 2016

  Abstract

  Hematopoietic stem cell transplantation (HSCT) is a potentially life-saving therapy that often comes at the cost of complications such as graft-versus-host disease and post-transplant infections. With improved technology to understand the ecosystem of microorganisms (viruses, bacteria, fungi, and microeukaryotes) that make up the gut microbiota, there is increasing evidence of the microbiota's contribution to the development of post-transplant complications. Antibiotics have traditionally been the mainstay of microbiota-altering therapies available to physicians. Recently, interest is increasing in the use of prebiotics and probiotics to support the development and sustainability of a healthier microbiota. In this review, we will describe the evidence for the use of prebiotics and probiotics in combating microbiota dysbiosis and explore the ways in which they may be used in future research to potentially improve clinical outcomes and decrease rates of graft-versus-host disease (GVHD) and post-transplant infection.

  View details for PubMedID 26780719

• Complete hematologic response of early T-cell progenitor acute lymphoblastic leukemia to the ?-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case. Cold Spring Harbor molecular case studies Knoechel, B., Bhatt, A., Pan, L., Pedamallu, C. S., Severson, E., Gutierrez, A., Dorfman, D. M., Kuo, F. C., Kluk, M., Kung, A. L., Zweidler-McKay, P., Meyerson, M., Blacklow, S. C., DeAngelo, D. J., Aster, J. C. 2015; 1 (1)

  Abstract

  Notch pathway antagonists such as ?-secretase inhibitors (GSIs) are being tested in diverse cancers, but exceptional responses have yet to be reported. We describe the case of a patient with relapsed/refractory early T-cell progenitor acute lymphoblastic leukemia (ETP-ALL) who achieved a complete hematologic response following treatment with the GSI BMS-906024. Whole-exome sequencing of leukemic blasts revealed heterozygous gain-of-function driver mutations in NOTCH1, CSF3R, and PTPN11, and a homozygous/hemizygous loss-of-function mutation in DNMT3A. The three gain-of-function mutations were absent from remission marrow cells, but the DNMT3A mutation persisted in heterozygous form in remission marrow, consistent with an origin for the patient's ETP-ALL from clonal hematopoiesis. Ex vivo culture of ETP-ALL blasts confirmed high levels of activated NOTCH1 that were repressed by GSI treatment, and RNA-seq documented that GSIs downregulated multiple known Notch target genes. Surprisingly, one potential target gene that was unaffected by GSIs was MYC, a key Notch target in GSI-sensitive T-ALL of cortical T-cell type. H3K27ac super-enhancer landscapes near MYC showed a pattern previously reported in acute myeloid leukemia (AML) that is sensitive to BRD4 inhibitors, and in line with this ETP-ALL blasts downregulated MYC in response to the BRD4 inhibitor JQ1. To our knowledge, this is the first example of complete response of a Notch-mutated ETP-ALL to a Notch antagonist and is also the first description of chromatin landscapes associated with ETP-ALL. Our experience suggests that additional attempts to target Notch in Notch-mutated ETP-ALL are merited.

  View details for DOI 10.1101/mcs.a000539

  View details for PubMedID 27148573

• Launching an Interactive Cancer Projects Map: A Collaborative Approach to Global Cancer Research and Program Development. Journal of global oncology Trimble, E. L., Chisti, A. A., Craycroft, J. A., Duncan, K., Gupta, M., Gutierrez, D., Rosenberg, I., Sharara, N., Sivaram, S., Topazian, H. M., Wang, J. J., Williams, M. J., Huang, F. W., Bhatt, A. S. 2015; 1 (1): 7?10

  View details for PubMedID 28804766

• Epidemiologic Investigation of a Cluster of Neuroinvasive Bacillus cereus Infections in 5 Patients With Acute Myelogenous Leukemia. Open forum infectious diseases Rhee, C., Klompas, M., Tamburini, F. B., Fremin, B. J., Chea, N., Epstein, L., Halpin, A. L., Guh, A., Gallen, R., Coulliette, A., Gee, J., Hsieh, C., Desjardins, C. A., Pedamullu, C. S., DeAngelo, D. J., Manzo, V. E., Folkerth, R. D., Milner, D. A., Pecora, N., Osborne, M., Chalifoux-Judge, D., Bhatt, A. S., Yokoe, D. S. 2015; 2 (3): ofv096-?

  Abstract

  Background. ?Five neuroinvasive Bacillus cereus infections (4 fatal) occurred in hospitalized patients with acute myelogenous leukemia (AML) during a 9-month period, prompting an investigation by infection control and public health officials. Methods. ?Medical records of case-patients were reviewed and a matched case-control study was performed. Infection control practices were observed. Multiple environmental, food, and medication samples common to AML patients were cultured. Multilocus sequence typing was performed for case and environmental B cereus isolates. Results. ?All 5 case-patients received chemotherapy and had early-onset neutropenic fevers that resolved with empiric antibiotics. Fever recurred at a median of 17 days (range, 9-20) with headaches and abrupt neurological deterioration. Case-patients had B cereus identified in central nervous system (CNS) samples by (1) polymerase chain reaction or culture or (2) bacilli seen on CNS pathology stains with high-grade B cereus bacteremia. Two case-patients also had colonic ulcers with abundant bacilli on autopsy. No infection control breaches were observed. On case-control analysis, bananas were the only significant exposure shared by all 5 case-patients (odds ratio, 9.3; P = .04). Five environmental or food isolates tested positive for B cereus, including a homogenized banana peel isolate and the shelf of a kitchen cart where bananas were stored. Multilocus sequence typing confirmed that all case and environmental strains were genetically distinct. Multilocus sequence typing-based phylogenetic analysis revealed that the organisms clustered in 2 separate clades. Conclusions. ?The investigation of this neuroinvasive B cereus cluster did not identify a single point source but was suggestive of a possible dietary exposure. Our experience underscores the potential virulence of B cereus in immunocompromised hosts.

  View details for DOI 10.1093/ofid/ofv096

  View details for PubMedID 26269794

• The human microbiome in hematopoiesis and hematologic disorders. Blood Manzo, V. E., Bhatt, A. S. 2015; 126 (3): 311-318

  Abstract

  Humans are now understood to be in complex symbiosis with a diverse ecosystem of microbial organisms, including bacteria, viruses, and fungi. Efforts to characterize the role of these microorganisms, commonly referred as the microbiota, in human health have sought to answer the fundamental questions of what organisms are present, how are they functioning to interact with human cells, and by what mechanism are these interactions occurring. In this review, we describe recent efforts to describe the microbiota in healthy and diseased individuals, summarize the role of various molecular technologies (ranging from 16S ribosomal RNA to shotgun metagenomic sequencing) in enumerating the community structure of the microbiota, and explore known interactions between the microbiota and humans, with a focus on the microbiota's role in hematopoiesis and hematologic diseases.

  View details for DOI 10.1182/blood-2015-04-574392

  View details for PubMedID 26012569

• DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors BMC CANCER Bambury, R. M., Bhatt, A. S., Riester, M., Pedamallu, C. S., Duke, F., Bellmunt, J., Stack, E. C., Werner, L., Park, R., Iyer, G., Loda, M., Kantoff, P. W., Michor, F., Meyerson, M., Rosenberg, J. E. 2015; 15

  Abstract

  To date, there have been no reports characterizing the genome-wide somatic DNA chromosomal copy-number alteration landscape in metastatic urothelial carcinoma. We sought to characterize the DNA copy-number profile in a cohort of metastatic samples and compare them to a cohort of primary urothelial carcinoma samples in order to identify changes that are associated with progression from primary to metastatic disease.Using molecular inversion probe array analysis we compared genome-wide chromosomal copy-number alterations between 30 metastatic and 29 primary UC samples. Whole transcriptome RNA-Seq analysis was also performed in primary and matched metastatic samples which was available for 9 patients.Based on a focused analysis of 32 genes in which alterations may be clinically actionable, there were significantly more amplifications/deletions in metastases (8.6% vs 4.5%, p?

  View details for DOI 10.1186/s12885-015-1192-2

  View details for Web of Science ID 000352603600001

  View details for PubMedID 25886454

• Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Perry, J. A., Kiezun, A., Tonzi, P., Van Allen, E. M., Carter, S. L., Baca, S. C., Cowley, G. S., Bhatt, A. S., Rheinbay, E., Pedamallu, C. S., Helman, E., Taylor-Weiner, A., McKenna, A., DeLuca, D. S., Lawrence, M. S., Ambrogio, L., Sougnez, C., Sivachenko, A., Walensky, L. D., Wagle, N., Mora, J., de Torres, C., Lavarino, C., Aguiar, S. d., Yunes, J. A., Brandalise, S. R., Mercado-Celis, G. E., Melendez-Zajgla, J., Cardenas-Cardos, R., Velasco-Hidalgo, L., Roberts, C. W., Garraway, L. A., Rodriguez-Galindo, C., Gabriel, S. B., Lander, E. S., Golub, T. R., Orkin, S. H., Getz, G., Janeway, K. A. 2014; 111 (51): E5564-E5573

  Abstract

  Osteosarcoma is the most common primary bone tumor, yet there have been no substantial advances in treatment or survival in three decades. We examined 59 tumor/normal pairs by whole-exome, whole-genome, and RNA-sequencing. Only the TP53 gene was mutated at significant frequency across all samples. The mean nonsilent somatic mutation rate was 1.2 mutations per megabase, and there was a median of 230 somatic rearrangements per tumor. Complex chains of rearrangements and localized hypermutation were detected in almost all cases. Given the intertumor heterogeneity, the extent of genomic instability, and the difficulty in acquiring a large sample size in a rare tumor, we used several methods to identify genomic events contributing to osteosarcoma survival. Pathway analysis, a heuristic analytic algorithm, a comparative oncology approach, and an shRNA screen converged on the phosphatidylinositol 3-kinase/mammalian target of rapamycin (PI3K/mTOR) pathway as a central vulnerability for therapeutic exploitation in osteosarcoma. Osteosarcoma cell lines are responsive to pharmacologic and genetic inhibition of the PI3K/mTOR pathway both in vitro and in vivo.

  View details for DOI 10.1073/pnas.1419260111

  View details for Web of Science ID 000346767200013

  View details for PubMedID 25512523

• Bacillus Cereus: A Leukemia-Specific, Neuroinvasive Pathogen? Rhee, C., Manzo, V., Shea, T., Desjardins, C., van der Auwera, G., Young, S., Riley, A., DeAngelo, D. J., Baden, L. R., Gee, J., Meyerson, M., Klompas, M., Yokoe, D., Weiser, L., Pedamallu, C., Bhatt, A. S. AMER SOC HEMATOLOGY. 2014

  View details for Web of Science ID 000349242707200

• In Search of a Candidate Pathogen for Giant Cell Arteritis: Sequencing-Based Characterization of the Giant Cell Arteritis Microbiome ARTHRITIS & RHEUMATOLOGY Bhatt, A. S., Manzo, V. E., Pedamallu, C. S., Duke, F., Cai, D., Bienfang, D. C., Padera, R. F., Meyerson, M., Docken, W. P. 2014; 66 (7): 1939-1944

  Abstract

  To characterize the microbiome of the temporal artery in patients with giant cell arteritis (GCA), and to apply an unbiased and comprehensive shotgun sequencing-based approach to determine whether there is an enrichment of candidate pathogens in the affected tissue.Temporal artery biopsy specimens were collected from patients at a single institution over a period of 4 years, and unbiased DNA sequencing was performed on 17 formalin-fixed, paraffin-embedded specimens. Twelve of the 17 patients fulfilled the clinical and histopathologic criteria for GCA, and the other 5 patients served as controls. Using PathSeq software, human DNA sequences were computationally subtracted, and the remaining non-human DNA sequences were taxonomically classified using a comprehensive microbial sequence database. The relative abundance of microbes was inferred based on read counts assigned to each organism. Comparison of the microbial diversity between GCA cases and controls was carried out using hierarchical clustering and linear discriminant analysis of effect size.Propionibacterium acnes and Escherichia coli were the most abundant microorganisms in 16 of the 17 samples, and Moraxella catarrhalis was the most abundant organism in 1 control sample. Pathogens previously described to be correlated with GCA were not differentially abundant in cases compared to controls. There was not a significant burden of likely pathogenic viruses.DNA sequencing of temporal artery biopsy specimens from GCA cases, in comparison with non-GCA controls, showed no evidence of previously identified candidate GCA pathogens. A single pathogen was not clearly and consistently associated with GCA in this case series.

  View details for DOI 10.1002/art.38631

  View details for Web of Science ID 000339092800029

  View details for PubMedID 24644069

  View details for PubMedCentralID PMC4113339

• Comprehensive molecular characterization of urothelial bladder carcinoma NATURE Weinstein, J. N., Akbani, R., Broom, B. M., Wang, W., Verhaak, R. G., McConkey, D., Lerner, S., Morgan, M., Creighton, C. J., Smith, C., Kwiatkowski, D. J., Cherniack, A. D., Kim, J., Pedamallu, C. S., Noble, M. S., Al-Ahmadie, H. A., Reuter, V. E., Rosenberg, J. E., Bajorin, D. F., Bochner, B. H., Solit, D. B., Koppie, T., Robinson, B., Gordenin, D. A., Fargo, D., Klimczak, L. J., Roberts, S. A., Au, J., Laird, P. W., Hinoue, T., Schultz, N., Ramirez, R., Hansel, D., Hoadley, K. A., Kim, W. Y., Damrauer, J. S., Baylin, S. B., Mungall, A. J., Robertson, A. G., Chu, A., Kwiatkowski, D. J., Sougnez, C., Cibulskis, K., Lichtenstein, L., Sivachenko, A., Stewart, C., Lawrence, M. S., Getz, G., Lander, E., Gabriel, S. B., Creighton, C. J., Donehower, L., Cherniack, A. D., Kim, J., Carter, S. L., Saksena, G., Schumacher, S. E., Sougnez, C., Freeman, S. S., Jung, J., Pedamallu, C. S., Bhatt, A. S., Pugh, T., Getz, G., Beroukhim, R., Gabriel, S. B., Meyerson, M., Mungall, A. J., Robertson, A. G., Chu, A., Ally, A., Balasundaram, M., Butterfield, Y. S., Dhalla, N., Hirst, C., Holt, R. A., Jones, S. J., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Wong, T., Wye, N., Bowlby, R., Chuah, E., Guin, R., Jones, S. J., Marra, M. A., Hinoue, T., Shen, H., Bootwalla, M. S., Triche, T., Lai, P. H., Van den Berg, D. J., Weisenberger, D. J., Laird, P. W., Hansel, D., Hoadley, K. A., Balu, S., Bodenheimer, T., Damrauer, J. S., Hoyle, A. P., Jefferys, S. R., Meng, S., Mose, L. E., Simons, J. V., Soloway, M. G., Wu, J., Kim, W. Y., Parker, J. S., Hayes, D. N., Roach, J., Buda, E., Jones, C. D., Mieczkowski, P. A., Tan, D., Veluvolu, U., Waring, S., Auman, J. T., Perou, C. M., Wilkerson, M. D., Santoso, N., Parfenov, M., Ren, X., Pantazi, A., Hadjipanayis, A., Seidman, J., Kucherlapati, R., Lee, S., Yang, L., Park, P. J., Baylin, S. B., Xu, A. W., Protopopov, A., Zhang, J., Bristow, C., Mahadeshwar, H. S., Seth, S., Song, X., Tang, J., Zeng, D., Chin, L., Guo, C., Weinstein, J. N., Akbani, R., Broom, B. M., McConkey, D., Casasent, T. D., Liu, W., Ju, Z., Motter, T., Peng, B., Ryan, M., Wang, W., Verhaak, R. G., Su, X., Yang, J., Lorenzi, P. L., Yao, H., Zhang, N., Zhang, J., Mills, G. B., Kim, J., Noble, M. S., Cho, J., DiCara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Lin, P., Liu, Y., Stojanov, P., Voet, D., Zhang, H., Zou, L., Chin, L., Getz, G., Bernard, B., Kreisberg, D., Reynolds, S., Rovira, H., Shmulevich, I., Ramirez, R., Schultz, N., Gao, J., Jacobsen, A., Aksoy, B. A., Antipin, Y., Ciriello, G., Dresdner, G., Gross, B., Lee, W., Reva, B., Shen, R., Sinha, R., Sumer, S. O., Weinhold, N., Ladanyi, M., Sander, C., Benz, C., Carlin, D., Haussler, D., Ng, S., Paull, E. O., Stuart, J., Zhu, J., Liu, Y., Zhang, W., Taylor, B. S., Lichtenberg, T. M., Zmuda, E., Barr, T., Black, A. D., George, M., Hanf, B., Helsel, C., McAllister, C., Ramirez, N. C., Tabler, T. R., Weaver, S., Wise, L., Bowen, J., Gastier-Foster, J. M., Weinstein, J. N., Lerner, S., Jian, W., Tello, S., Ittman, M., Castro, P., McClenden, W. D., Morgan, M., Gibbs, R., Liu, Y., Saller, C., Tarvin, K., DiPiero, J. M., Owens, J., Bollag, R., Li, Q., Weinberger, P., Czerwinski, C., Huelsenbeck-Dill, L., Iacocca, M., Petrelli, N., Rabeno, B., Swanson, P., Shelton, T., Curley, E., Gardner, J., Mallery, D., Penny, R., Nguyen Van Bang, N. V., Phan Thi Hanh, P. T., Kohl, B., Xuan Van Le, X. V., Bui Duc Phu, B. D., Thorp, R., Nguyen Viet Tien, N. V., Le Quang Vinh, L. Q., Sandusky, G., Burks, E., Christ, K., Gee, J., Holway, A., Moinzadeh, A., Sorcini, A., Sullivan, T., Al-Ahmadie, H. A., Bajorin, D. F., Bochner, B. H., Garcia-Grossman, I. R., Regazzi, A. M., Solit, D. B., Rosenberg, J. E., Reuter, V. E., Koppie, T., Boice, L., Rathmell, W. K., Thorne, L., Bastacky, S., Davies, B., Dhir, R., Gingrich, J., Hrebinko, R., Maranchie, J., Nelson, J., Parwani, A., Bshara, W., Gaudioso, C., Morrison, C., Alexopoulou, V., Bartlett, J., Engel, J., Kodeeswaran, S., Antic, T., O'Donnell, P. H., Smith, N. D., Steinberg, G. D., Egea, S., Gomez-Fernandez, C., Herbert, L., Jorda, M., Soloway, M., Beaver, A., Carter, S., Kapur, P., Lewis, C., Lotan, Y., Robinson, B., Hansel, D., Guo, C., Bondaruk, J., Czerniak, B., Akbani, R., Broom, B. M., Liu, Y., Zhang, W., Weinstein, J. N., Lerner, S., Morgan, M., Kim, J., Cherniack, A. D., Freeman, S. S., Pedamallu, C. S., Noble, M. S., Kwiatkowski, D. J., Al-Ahmadie, H. A., Bajorin, D. F., Bochner, B. H., Solit, D. B., Rosenberg, J. E., Reuter, V. E., Koppie, T., Robinson, B., Skinner, E., Ramirez, R., Schultz, N., Hansel, D., Kim, W. Y., Guo, C., Bondaruk, J., Aldape, K., Czerniak, B., Jensen, M. A., Kahn, A. B., Pihl, T. D., Pot, D. A., Srinivasan, D., Wan, Y., Ferguson, M. L., Zenklusen, J. C., Davidsen, T., Demchok, J. A., Shaw, K. R., Sheth, M., Tarnuzzer, R., Wang, Z., Yang, L., Hutter, C., Ozenberger, B. A., Sofia, H. J., Eley, G. 2014; 507 (7492): 315-322

  View details for DOI 10.1038/nature12965

  View details for Web of Science ID 000333029000025

• Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome NEW ENGLAND JOURNAL OF MEDICINE Bhatt, A. S., Freeman, S. S., Herrera, A. F., Pedamallu, C. S., Gevers, D., Duke, F., Jung, J., Michaud, M., Walker, B. J., Young, S., Earl, A. M., Kostic, A. D., Ojesina, A. I., Hasserjian, R., Ballen, K. K., Chen, Y., Hobbs, G., Antin, J. H., Soiffer, R. J., Baden, L. R., Garrett, W. S., Hornick, J. L., Marty, F. M., Meyerson, M. 2013; 369 (6): 517-528

  Abstract

  Immunosuppression is associated with a variety of idiopathic clinical syndromes that may have infectious causes. It has been hypothesized that the cord colitis syndrome, a complication of umbilical-cord hematopoietic stem-cell transplantation, is infectious in origin.We performed shotgun DNA sequencing on four archived, paraffin-embedded endoscopic colon-biopsy specimens obtained from two patients with cord colitis. Computational subtraction of human and known microbial sequences and assembly of residual sequences into a bacterial draft genome were performed. We used polymerase-chain-reaction (PCR) assays and fluorescence in situ hybridization to determine whether the corresponding bacterium was present in additional patients and controls.DNA sequencing of the biopsy specimens revealed more than 2.5 million sequencing reads that did not match known organisms. These sequences were computationally assembled into a 7.65-Mb draft genome showing a high degree of homology with genomes of bacteria in the bradyrhizobium genus. The corresponding newly discovered bacterium was provisionally named Bradyrhizobium enterica. PCR identified B. enterica nucleotide sequences in biopsy specimens from all three additional patients with cord colitis whose samples were tested, whereas B. enterica sequences were absent in samples obtained from healthy controls and patients with colon cancer or graft-versus-host disease.We assembled a novel bacterial draft genome from the direct sequencing of tissue specimens from patients with cord colitis. Association of these sequences with cord colitis suggests that B. enterica may be an opportunistic human pathogen. (Funded by the National Cancer Institute and others.)

  View details for DOI 10.1056/NEJMoa1211115

  View details for Web of Science ID 000322842000008

  View details for PubMedID 23924002

  View details for PubMedCentralID PMC3889161

• NK-Cell and B-Cell Deficiency with a Thymic Mass NEW ENGLAND JOURNAL OF MEDICINE Ng, S., Fanta, C., Okam, M., Bhatt, A. S. 2011; 364 (6): 586-588

  View details for Web of Science ID 000287139900041

  View details for PubMedID 21306273

• MT-SP1 proteolysis and regulation of cell-microenvironment interactions FRONTIERS IN BIOSCIENCE-LANDMARK Darragh, M. R., Bhatt, A. S., Craik, C. S. 2008; 13: 528-539

  Abstract

  MT-SP1 is a type II transmembrane serine protease implicated in a range of human cancers including those of the breast, cervix, ovaries, prostate, colon and gastrointestinal tract. Mouse models have shown it to be critical for proper epidermal development and postnatal survival. However, the role of this enzyme in normal and malignant biology has not yet been fully elucidated. Several groups have identified putative substrates of MT-SP1 in an effort to understand the possible biological processes in which this protease may be involved. Methods for substrate identification include comparing known protein cleavage sequences with MT-SP1 specificity data, in vitro cleavage assays, examining genetic microarrays for enzyme/substrate coexpression, immunohistochemistry for colocalization, and a variety of phenotypic observations using cell culture and mouse models. Given the inherent limitations of each individual method, substrate plausibility is best substantiated using a combination of experimental approaches. Here we review MT-SP1 substrates identified to date and the possible physiological implications of substrate cleavage in cell-microenvironment interactions. This data indicates that MT-SP1 is capable of playing roles in growth factor activation, receptor activation and inactivation, protease activation, and ectodomain shedding. We also present for the first time vascular endothelial growth factor receptor 2 (VEGFR-2) as a putative substrate for MT-SP1.

  View details for DOI 10.2741/2698

  View details for Web of Science ID 000255775700042

  View details for PubMedID 17981566

• Coordinate expression and functional profiling identify an extracellular proteolytic signaling pathway PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bhatt, A. S., Welm, A., Farady, C. J., Vasquez, M., Wilson, K., Craik, C. S. 2007; 104 (14): 5771-5776

  Abstract

  A multidisciplinary method combining transcriptional data, specificity profiling, and biological characterization of an enzyme may be used to predict novel substrates. By integrating protease substrate profiling with microarray gene coexpression data from nearly 2,000 human normal and cancerous tissue samples, three fundamental components of a protease-activated signaling pathway were identified. We find that MT-SP1 mediates extracellular signaling by regulating the local activation of the prometastatic growth factor MSP-1. We demonstrate MT-SP1 expression in peritoneal macrophages, and biochemical methods confirm the ability of MT-SP1 to cleave and activate pro-MSP-1 in vitro and in a cellular context. MT-SP1 induced the ability of MSP-1 to inhibit nitric oxide production in bone marrow macrophages. Addition of HAI-1 or an MT-SP1-specific antibody inhibitor blocked the proteolytic activation of MSP-1 at the cell surface of peritoneal macrophages. Taken together, our work indicates that MT-SP1 is sufficient for MSP-1 activation and that MT-SP1, MSP-1, and the previously shown MSP-1 tyrosine kinase receptor RON are required for peritoneal macrophage activation. This work shows that this triad of growth factor, growth factor activator protease, and growth factor receptor is a protease-activated signaling pathway. Individually, MT-SP1 and RON overexpression have been implicated in cancer progression and metastasis. Transcriptional coexpression of these genes suggests that this signaling pathway may be involved in several human cancers.

  View details for DOI 10.1073/pnas.0606514104

  View details for Web of Science ID 000245657600015

  View details for PubMedID 17389401

  View details for PubMedCentralID PMC1838401

• Hepatocyte growth factor is a preferred in vitro substrate for human hepsin, a membrane-anchored serine protease implicated in prostate and ovarian cancers BIOCHEMICAL JOURNAL Herter, S., Piper, D. E., Aaron, W., Gabriele, T., Cutler, G., Cao, P., Bhattt, A. S., Choe, Y., CRAIK, C. S., Walker, N., Meininger, D., Hoey, T., Austin, R. J. 2005; 390: 125-136

  Abstract

  Hepsin is a membrane-anchored, trypsin-like serine protease with prominent expression in the human liver and tumours of the prostate and ovaries. To better understand the biological functions of hepsin, we identified macromolecular substrates employing a tetrapeptide PS-SCL (positional scanning-synthetic combinatorial library) screen that rapidly determines the P1-P4 substrate specificity. Hepsin exhibited strong preference at the P1 position for arginine over lysine, and favoured threonine, leucine or asparagine at the P2, glutamine or lysine at the P3, and proline or lysine at the P4 position. The relative activity of hepsin toward individual AMC (7-amino-4-methylcoumarin)-tetrapeptides was generally consistent with the overall peptide profiling results derived from the PC-SCL screen. The most active tetrapeptide substrate Ac (acetyl)-KQLR-AMC matched with the activation cleavage site of the hepatocyte growth factor precursor sc-HGF (single-chain HGF), KQLR downward arrowVVNG (where downward arrow denotes the cleavage site), as identified by a database analysis of trypsin-like precursors. X-ray crystallographic studies with KQLR chloromethylketone showed that the KQLR peptide fits well into the substrate-binding cleft of hepsin. This hepsin-processed HGF induced c-Met receptor tyrosine phosphorylation in SKOV-3 ovarian cancer cells, indicating that the hepsin-cleaved HGF is biologically active. Activation cleavage site mutants of sc-HGF with predicted non-preferred sequences, DPGR downward arrowVVNG or KQLQ downward arrowVVNG, were not processed, illustrating that the P4-P1 residues can be important determinants for substrate specificity. In addition to finding macromolecular hepsin substrates, the extracellular inhibitors of the HGF activator, HAI-1 and HAI-2, were potent inhibitors of hepsin activity (IC50 4+/-0.2 nM and 12+/-0.5 nM respectively). Together, our findings suggest that the HGF precursor is a potential in vivo substrate for hepsin in tumours, where hepsin expression is dysregulated and may influence tumorigenesis through inappropriate activation and/or regulation of HGF receptor (c-Met) functions.

  View details for DOI 10.1042/BJ20041955

  View details for Web of Science ID 000231492800014

  View details for PubMedID 15839837

• Adhesion signaling by a novel mitotic substrate of src kinases ONCOGENE Bhatt, A. S., Erdjument-Bromage, H., Tempst, P., CRAIK, C. S., Moasser, M. M. 2005; 24 (34): 5333-5343

  Abstract

  Src kinases are activated and relocalize to the cytoplasm during mitosis, but their mitotic function has remained elusive. We describe here a novel mitotic substrate of src kinases. Trask (transmembrane and associated with src kinases) is a 140 kDa type I transmembrane glycoprotein unrelated to currently known protein families. Src kinases phosphorylate Trask in vitro and mediate its mitotic hyperphosphorylation in vivo. Trask associates with both yes and src, is localized to the cell membrane during interphase, and undergoes cytoplasmic relocalization during mitosis. Overexpression of Trask leads to cell rounding and a loss of adhesion phenotype. Consistent with a function in cell adhesion, Trask interacts with a number of adhesion and matrix proteins including cadherins, syndecans, and the membrane-type serine protease 1 (MT-SP1), and is proteolytically cleaved by MT-SP1. Trask is unique among cell adhesion molecules in that it is under cell cycle regulation and thus links src kinases with the mitotic regulation of cell adhesion. This suggests a potential pathway by which hyperactive src kinases in tumors can deregulate adhesion signaling and mediate the metastatic phenotype.

  View details for DOI 10.1038/sj.onc.1208582

  View details for Web of Science ID 000231158500007

  View details for PubMedID 16007225

• Substrates of the prostate-specific serine protease prostase/KLK4 defined by positional-scanning peptide libraries PROSTATE Matsumura, M., Bhatt, A. S., Andress, D., Clegg, N., Takayama, T. K., CRAIK, C. S., Nelson, P. S. 2005; 62 (1): 1-13

  Abstract

  Prostase/KLK4 is a member of the human kallikrein (KLK) gene family that is expressed in prostate epithelial cells under the regulation of androgenic hormones. In this study, we sought to characterize the substrate specificity of KLK4 in order to gain insight into potential physiological roles of the enzyme.A chimeric form of KLK4 was constructed in which the pro-region of KLK4 was replaced with the signal and propeptide sequence of trypsinogen (proT-KLK4) to create an activation site susceptible to enterokinase cleavage. proT-KLK4 was expressed in Drosophila S2 cells, purified, and activated with enterokinase to generate mature KLK4. The extended substrate specificity of KLK4 was defined by screening tetrapeptide positional scanning synthetic combinatorial libraries (PS-SCL).The preferred P1-P4 positions as determined by PS-SCL were: P1-Arg; P2-Gln/Leu/Val; P3-Gln/Ser/Val; P4-Ile/Val. The trypsin-like specificity of KLK4 was further confirmed using synthetic chromogenic peptides. Based upon the optimal cleavage site residues, a database search for potential KLK4 substrates identified several proteins with potential roles mediating normal prostate physiology or neoplastic growth including KLK3/PSA, parathyroid hormone-related peptide (PTHrP), and members of the bone morphogenetic protein (BMP) family. Recombinant KLK4 was able to activate pro-PSA/KLK3 and degrade members of the insulin-like growth factor (IGF) binding protein (IGFBP) family.These results identify potential KLK4 substrates that may serve to define the role of this protease in normal prostate physiology, and facilitate studies of the consequences of KLK4 expression in pathological conditions.

  View details for DOI 10.1002/pros.20101

  View details for Web of Science ID 000225704700001

  View details for PubMedID 15389820

• Quantitation of membrane type serine protease 1 (MT-SP1) in transformed and normal cells BIOLOGICAL CHEMISTRY Bhatt, A. S., Takeuchi, T., Ylstra, B., Ginzinger, D., Albertson, D., Shuman, M. A., CRAIK, C. S. 2003; 384 (2): 257-266

  Abstract

  Membrane type serine protease 1 (MT-SP1) is a representative member of a large family of related enzymes known as type II transmembrane serine proteases or membrane type serine proteases. MT-SP1 has been implicated in the selective proteolysis of key extracellular substrates but its physiological role is still not fully understood. MT-SP1 expression at the protein and RNA level has been previously examined by nonquantitative methods such as in situ hybridization, Northern blotting and immunohistochemistry. To establish an introductory understanding of the quantitative mRNA expression of MT-SP1 and to correlate these levels with urokinase-type plasminogen activator receptor (uPAR), a key component of extracellular proteolysis, quantitative RT-PCR was carried out. RNA expression was analyzed in 34 human cancer cell lines, 26 human tissues and 18 primary human breast cancer tissue samples. MT-SP1 mRNA is highly expressed in many breast, ovarian, prostate and colon cancer cell lines and normal human tissues of endodermal origin. At the transcript level, MT-SP1 shows a highly statistically significant correlation (Pearson's product moment correlation r = 0.784, p < 0.001) with uPAR in human breast cancer tissue. The exact role of MT-SP1 in concert with proteins such as uPAR and other members of the plasminogen activator cascade has yet to be ascertained. However, the significant correlation between MT-SP1 and uPAR transcript levels in this initial study suggests further work to establish the role of MT-SP1 as a possible prognostic, diagnostic or therapeutic target for breast cancer.

  View details for Web of Science ID 000181175000010

  View details for PubMedID 12675519