In perpetual awe of how 'simple' microbial organisms can perturb complex, multicellular eukaryotic organisms, Ami Bhatt has chosen to dedicate her research program to inspecting, characterizing and dissecting the microbe-human interface. Nowhere is the interaction between hosts and microbes more potentially impactful than in immunocompromised hosts and global settings where infectious and environmental exposures result in drastic and sometimes fatal health consequences.
Ami's group identifies problems and questions that arise in the course of routine clinical care. Often in collaboration with excellent investigators at Stanford and beyond, the group applies modern genetic, molecular and computational techniques to seek answers to these questions, better understand host-microbe interactions and decipher how perturbation of these interactions may result in human disease phenotypes.
Director of Global Oncology, Center for Innovation in Global Health (2014 - Present)
Honors & Awards
Hall/Sewankambo Mid-Career Global Health Award, Consortiums of Universities for Global Health (2017)
Damon Runyon Clinical Investigator Award, Damon Runyon Foundation (2016)
McCormick and Gabilan Fellowship, Stanford University (2016)
Rosenkranz Prize for Healthcare Research in Developing Countries, Stanford University (2016)
World Cancer Young Leader Award, Union for International Cancer Control (2016)
NCI K08 Mentored Clinical Scientist CDA, National Cancer Institute (2014)
ASCO Young Investigator Award, ASCO (2013)
ASH Scholar Award, American Society of Hematology (2013)
Amy Strelzer Manasevit Scholar, National Marrow Donor Program (2013)
Barr Innovative Basic Science Research Award, Dana-Farber Cancer Institute (2013)
Career Development Award (Fellow), Leukemia and Lymphoma Society (2013)
AACR Clinical and Translational Fellowship, AACR (2012)
Alpha Omega Alpha, UCSF (2007)
Chancellor's Fellowship, UCSF (2004)
Richard Fineberg Award for Excellence in Teaching, UCSF (2002)
Boards, Advisory Committees, Professional Organizations
Editorial Board Member, Journal of Global Oncology, ASCO (2015 - Present)
Editorial Board Member, The Oncologist (2013 - Present)
Post-doctoral Fellowship, Broad Institute of Harvard and MIT (2014)
Hematology/Oncology Fellowship, Dana-Farber Cancer Institute, Harvard Medical School (2014)
Chief Residency, Brigham and Women's Hospital, Harvard Medical School (2011)
Residency, Brigham and Women's Hospital, Harvard Medical School (2009)
MD, University of California, San Francisco, Medicine (2007)
PhD, University of California, San Francisco, Biochemistry and Molecular Biology (2005)
Community and International Work
Global Oncology (Co-Founder, Co-President)
Improving cancer outcomes in impoverished settings
Patients with cancer in resource-limited settings
Opportunities for Student Involvement
Current Research and Scholarly Interests
Our lab seeks to exhaustively characterize the dynamics of the microbiota and environmental pathogens in immunocompromised and underserved populations, and to explore how changes in the microbiome are associated with diseases in these populations.
Specifically, our goals and objectives are:
a. To catalog, more completely, the components of the human microbiome in states of health and disease using high-thorughput and relatively unbiased methods such as shotgun DNA sequencing. .
b. To understand if shifts in the microbiome are associated with human disease phenotypes.
c. If alterations in the microbiome are associated with human disease phenotypes, identify and target microbial vulnerabilities with the hope of ameliorating these disease phenotypes.
Current projects include:
a. METAGENOTYPE to PHENOTYPE: Developing advanced molecular methods and computational pipelines to understand the taxonomic distribution and biological pathway representation in communities of microbes in patients undergoing treatment for hematologic malignancies.
b. GENETIC DETERMINANTS OF VIRULENCE: Using comparative microbial genomic, microbiological and genetic methods to determine the mechanisms of hypervirulence in specific known or candidate pathogens, such as Bacillus cereus and Bradyrhizobium enterica.
c. GENOMIC CHARACTERIZATION OF AN INFECTION-ASSOCIATED CANCER: Pathogenomic evaluation of host and parasite genetic characteristics in squamous cell cancer of the bladder in Northern and Western Africa (a collaboration with Prof. O. Hammam and the Bilharz Research Institute in Giza, Egypt).
d. GLOBALIZING ONCOLOGY: Improving cancer care, education and research in resource limited settings by encouraging technological, knowledge-sharing and research capacity building collaborations internationally (http://globalonc.org).
Globalizing oncology care, education and research, Stanford University & Global Oncology, Inc.
Improving cancer care, education and research in resource limited settings by encouraging technological, knowledge-sharing and research capacity building collaborations internationally (http://globalonc.org).
- Franklin Huang, Instructor, Medical Oncology, Dana-Farber Cancer Institute
For More Information:
Genomic characterization of an Infection-associated cancer, Stanford University and Bilharz Research Institute
Pathogenomic evaluation of host and parasite genetic characteristics in squamous cell cancer of the bladder in Northern and Western Africa (a collaboration with Prof. O. Hammam and the Bilharz Research Institute in Giza, Egypt).
- Olfat Hammam, Professor, Bilharz Research Institute
Metagenotype to phenotype, Stanford University
Developing advanced molecular methods and computational pipelines to understand the taxonomic distribution and biological pathway representation in communities of microbes in patients undergoing treatment for hematologic malignancies.
Genetic determinants of microbial virulence
Using comparative microbial genomic, microbiological and genetic methods to determine the mechanisms of hypervirulence in specific known or candidate pathogens, such as Bacillus cereus and Bradyrhizobium enterica.
- Chanu Rhee, Associate Physician, Massachusetts General Hospital
- Advanced Seminar on Prokaryotic Molecular Biology
BIO 346, CSB 346, GENE 346 (Aut, Win)
- Gut Microbiota in Health and Disease
BIOE 221G, GENE 208, MI 221 (Spr)
Independent Studies (11)
- Directed Reading in Genetics
GENE 299 (Aut, Win, Spr)
- Directed Reading in Medicine
MED 299 (Aut, Win, Spr, Sum)
- Early Clinical Experience in Medicine
MED 280 (Aut, Win, Spr, Sum)
- Graduate Research
GENE 399 (Win, Spr, Sum)
- Graduate Research
MED 399 (Aut, Win, Spr, Sum)
- Medical Scholars Research
GENE 370 (Aut, Win, Spr)
- Medical Scholars Research
MED 370 (Aut, Win, Spr, Sum)
- Out-of-Department Advanced Research Laboratory in Experimental Biology
BIO 199X (Aut, Win, Spr)
- Supervised Study
GENE 260 (Aut, Win, Spr)
- Undergraduate Research
GENE 199 (Aut, Win, Spr)
- Undergraduate Research
MED 199 (Aut, Win, Spr, Sum)
- Directed Reading in Genetics
- Prior Year Courses
Graduate and Fellowship Programs
Biomedical Informatics (Phd Program)
Hematology (Fellowship Program)
Oncology (Fellowship Program)
The human microbiome in hematopoiesis and hematologic disorders.
2015; 126 (3): 311-318
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
View details for PubMedCentralID PMC4504946
Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome
NEW ENGLAND JOURNAL OF MEDICINE
2013; 369 (6): 517-528
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
- NK-Cell and B-Cell Deficiency with a Thymic Mass NEW ENGLAND JOURNAL OF MEDICINE 2011; 364 (6): 586-588
Coordinate expression and functional profiling identify an extracellular proteolytic signaling pathway
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2007; 104 (14): 5771-5776
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
Quantitative Computed Tomography Assessment of Bronchiolitis Obliterans Syndrome after Lung Transplantation.
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
- Antibiotic-mediated modification of the intestinal microbiome in allogeneic hematopoietic stem cell transplantation BONE MARROW TRANSPLANTATION 2017; 52 (2): 183-190
The Burden of Cancer in Asian Americans: A Report of National Mortality Trends by Asian Ethnicity
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
2016; 25 (10): 1371-1382
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 Web of Science ID 000385642800002
View details for PubMedID 27694108
View details for PubMedCentralID PMC5218595
Infection Rates among Acute Leukemia Patients Receiving Alternative Donor Hematopoietic Cell Transplantation.
Biology of blood and marrow transplantation
2016; 22 (9): 1636-1645
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 < .0001) for UCB, MUD, and MMUD, respectively. Incidences of viral infection at 1 year were 68%, 45%, and 53% (P < .0001) for UCB, MUD, and MMUD, respectively. In multivariable analysis, bacterial, fungal, and viral infections were more common after either UCB or MMUD than after MUD (P < .0001). Bacterial and viral but not fungal infections were more common after UCB than MMUD (P = .0009 and <.0001, respectively). The presence of viral infection was not associated with an increased mortality. Overall survival (OS) was comparable among UCB and MMUD patients with Karnofsky performance status (KPS) ≥ 90% but was inferior for UCB for patients with KPS < 90%. Bacterial and fungal infections were associated with poorer OS. Future strategies focusing on infection prevention and treatment are indicated to improve HCT outcomes.
View details for DOI 10.1016/j.bbmt.2016.06.012
View details for PubMedID 27343716
View details for PubMedCentralID PMC5008458
Antibiotic-mediated modification of the intestinal microbiome in allogeneic hematopoietic stem cell transplantation.
Bone marrow transplantation
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 PubMedID 27526283
Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice
SCIENCE TRANSLATIONAL MEDICINE
2016; 8 (339)
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 Web of Science ID 000376468300004
View details for PubMedID 27194729
View details for PubMedCentralID PMC4991773
Microbiota Manipulation With Prebiotics and Probiotics in Patients Undergoing Stem Cell Transplantation
CURRENT HEMATOLOGIC MALIGNANCY REPORTS
2016; 11 (1): 19-28
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
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
2015; 1 (1)
Notch pathway antagonists such as γ-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
View details for PubMedCentralID PMC4850884
Epidemiologic Investigation of a Cluster of Neuroinvasive Bacillus cereus Infections in 5 Patients With Acute Myelogenous Leukemia.
Open forum infectious diseases
2015; 2 (3): ofv096-?
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
View details for PubMedCentralID PMC4531223
DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors
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 < 0.001). In particular, there was a higher frequency of E2F3 amplification in metastases (30% vs 7%, p = 0.046). Paired primary and metastatic tissue was available for 11 patients and 3 of these had amplifications of potential clinical relevance in metastases that were not in the primary tumor including ERBB2, CDK4, CCND1, E2F3, and AKT1. The transcriptional activity of these amplifications was supported by RNA expression data.The discordance in alterations between primary and metastatic tissue may be of clinical relevance in the era of genomically directed precision cancer medicine.
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
2014; 111 (51): E5564-E5573
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
In Search of a Candidate Pathogen for Giant Cell Arteritis: Sequencing-Based Characterization of the Giant Cell Arteritis Microbiome
ARTHRITIS & RHEUMATOLOGY
2014; 66 (7): 1939-1944
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 2014; 507 (7492): 315-322
MT-SP1 proteolysis and regulation of cell-microenvironment interactions
FRONTIERS IN BIOSCIENCE-LANDMARK
2008; 13: 528-539
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
Hepatocyte growth factor is a preferred in vitro substrate for human hepsin, a membrane-anchored serine protease implicated in prostate and ovarian cancers
2005; 390: 125-136
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
2005; 24 (34): 5333-5343
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
2005; 62 (1): 1-13
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
2003; 384 (2): 257-266
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