Bio

Clinical Focus


  • Gastroenterology

Academic Appointments


Honors & Awards


  • K08 Mentored Career Development Award, NIH-NIDDK (2013)
  • Postdoctoral Fellow (MD Trainee), California Institute for Regenerative Medicine (10/2010-08/2013)
  • GI Fellows Research Award, Inflammatory Bowel Disease Working Group (IBDWG) (2010)
  • Pilot/Feasibility Award, Stanford Digestive Disease Center (2010-2011)
  • Stanford Dean's Fellowship, Stanford University (2008-2010)

Professional Education


  • Fellowship:Stanford University School of Medicine (06/30/2010) CA
  • Residency:Stanford University School of Medicine (06/30/2007) CA
  • Medical Education:Univ of California San Francisco (06/30/2005) CA
  • Board Certification: Gastroenterology, American Board of Internal Medicine (2011)
  • Board Certification: Internal Medicine, American Board of Internal Medicine (2008)
  • MD/PhD, UCSF (2005)

Publications

Journal Articles


  • Quantitative assessment of single-cell RNA-sequencing methods. Nature methods Wu, A. R., Neff, N. F., Kalisky, T., Dalerba, P., Treutlein, B., Rothenberg, M. E., Mburu, F. M., Mantalas, G. L., Sim, S., Clarke, M. F., Quake, S. R. 2014; 11 (1): 41-46

    Abstract

    Interest in single-cell whole-transcriptome analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. We compared commercially available single-cell RNA amplification methods with both microliter and nanoliter volumes, using sequence from bulk total RNA and multiplexed quantitative PCR as benchmarks to systematically evaluate the sensitivity and accuracy of various single-cell RNA-seq approaches. We show that single-cell RNA-seq can be used to perform accurate quantitative transcriptome measurement in individual cells with a relatively small number of sequencing reads and that sequencing large numbers of single cells can recapitulate bulk transcriptome complexity.

    View details for DOI 10.1038/nmeth.2694

    View details for PubMedID 24141493

  • Gastrointestinal stromal tumor: an unusual cause of gastrointestinal bleeding. Digestive diseases and sciences Wong, R. J., Longacre, T. A., Poultsides, G., Park, W., Rothenberg, M. E. 2013; 58 (11): 3112-3116

    View details for DOI 10.1007/s10620-013-2678-x

    View details for PubMedID 23633157

  • 5-ASA Induced Recurrent Myopericarditis and Cardiac Tamponade in a Patient with Ulcerative Colitis DIGESTIVE DISEASES AND SCIENCES Sonu, I., Wong, R., Rothenberg, M. E. 2013; 58 (8): 2148-2150

    View details for DOI 10.1007/s10620-013-2566-4

    View details for Web of Science ID 000322650900007

    View details for PubMedID 23361575

  • Innate immune response to homologous rotavirus infection in the small intestinal villous epithelium at single-cell resolution PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Sen, A., Rothenberg, M. E., Mukherjee, G., Feng, N., Kalisky, T., Nair, N., Johnstone, I. M., Clarke, M. F., Greenberg, H. B. 2012; 109 (50): 20667-20672

    Abstract

    "Bulk" measurements of antiviral innate immune responses from pooled cells yield averaged signals and do not reveal underlying signaling heterogeneity in infected and bystander single cells. We examined such heterogeneity in the small intestine during rotavirus (RV) infection. Murine RV EW robustly activated type I IFNs and several antiviral genes (IFN-stimulated genes) in the intestine by bulk analysis, the source of induced IFNs primarily being hematopoietic cells. Flow cytometry and microfluidics-based single-cell multiplex RT-PCR allowed dissection of IFN responses in single RV-infected and bystander intestinal epithelial cells (IECs). EW replicates in IEC subsets differing in their basal type I IFN transcription and induces IRF3-dependent and IRF3-augmented transcription, but not NF-?B-dependent or type I IFN transcripts. Bystander cells did not display enhanced type I IFN transcription but had elevated levels of certain IFN-stimulated genes, presumably in response to exogenous IFNs secreted from immune cells. Comparison of IRF3 and NF-?B induction in STAT1(-/-) mice revealed that murine but not simian RRV mediated accumulation of IkB-? protein and decreased transcription of NF-?B-dependent genes. RRV replication was significantly rescued in IFN types I and II, as well as STAT1 (IFN types I, II, and III) deficient mice in contrast to EW, which was only modestly sensitive to IFNs I and II. Resolution of "averaged" innate immune responses in single IECs thus revealed unexpected heterogeneity in both the induction and subversion of early host antiviral immunity, which modulated host range.

    View details for DOI 10.1073/pnas.1212188109

    View details for Web of Science ID 000312605600104

    View details for PubMedID 23188796

  • Identification of a cKit(+) Colonic Crypt Base Secretory Cell That Supports Lgr5(+) Stem Cells in Mice GASTROENTEROLOGY Rothenberg, M. E., Nusse, Y., Kalisky, T., Lee, J. J., Dalerba, P., Scheeren, F., Lobo, N., Kulkarni, S., Sim, S., Qian, D., Beachy, P. A., Pasricha, P. J., Quake, S. R., Clarke, M. F. 2012; 142 (5): 1195-?

    Abstract

    Paneth cells contribute to the small intestinal niche of Lgr5(+) stem cells. Although the colon also contains Lgr5(+) stem cells, it does not contain Paneth cells. We investigated the existence of colonic Paneth-like cells that have a distinct transcriptional signature and support Lgr5(+) stem cells.We used multicolor fluorescence-activated cell sorting to isolate different subregions of colon crypts, based on known markers, from dissociated colonic epithelium of mice. We performed multiplexed single-cell gene expression analysis with quantitative reverse transcriptase polymerase chain reaction followed by hierarchical clustering analysis to characterize distinct cell types. We used immunostaining and fluorescence-activated cell sorting analyses with in vivo administration of a Notch inhibitor and in vitro organoid cultures to characterize different cell types.Multicolor fluorescence-activated cell sorting could isolate distinct regions of colonic crypts. Four major epithelial subtypes or transcriptional states were revealed by gene expression analysis of selected populations of single cells. One of these, the goblet cells, contained a distinct cKit/CD117(+) crypt base subpopulation that expressed Dll1, Dll4, and epidermal growth factor, similar to Paneth cells, which were also marked by cKit. In the colon, cKit(+) goblet cells were interdigitated with Lgr5(+) stem cells. In vivo, this colonic cKit(+) population was regulated by Notch signaling; administration of a ?-secretase inhibitor to mice increased the number of cKit(+) cells. When isolated from mouse colon, cKit(+) cells promoted formation of organoids from Lgr5(+) stem cells, which expressed Kitl/stem cell factor, the ligand for cKit. When organoids were depleted of cKit(+) cells using a toxin-conjugated antibody, organoid formation decreased.cKit marks small intestinal Paneth cells and a subset of colonic goblet cells that are regulated by Notch signaling and support Lgr5(+) stem cells.

    View details for DOI 10.1053/j.gastro.2012.02.006

    View details for Web of Science ID 000303113600038

    View details for PubMedID 22333952

  • Single-cell dissection of transcriptional heterogeneity in human colon tumors NATURE BIOTECHNOLOGY Dalerba, P., Kalisky, T., Sahoo, D., Rajendran, P. S., Rothenberg, M. E., Leyrat, A. A., Sim, S., Okamoto, J., Johnston, D. M., Qian, D., Zabala, M., Bueno, J., Neff, N. F., Wang, J., Shelton, A. A., Visser, B., Hisamori, S., Shimono, Y., Van De Wetering, M., Clevers, H., Clarke, M. F., Quake, S. R. 2011; 29 (12): 1120-U11

    Abstract

    Cancer is often viewed as a caricature of normal developmental processes, but the extent to which its cellular heterogeneity truly recapitulates multilineage differentiation processes of normal tissues remains unknown. Here we implement single-cell PCR gene-expression analysis to dissect the cellular composition of primary human normal colon and colon cancer epithelia. We show that human colon cancer tissues contain distinct cell populations whose transcriptional identities mirror those of the different cellular lineages of normal colon. By creating monoclonal tumor xenografts from injection of a single (n = 1) cell, we demonstrate that the transcriptional diversity of cancer tissues is largely explained by in vivo multilineage differentiation and not only by clonal genetic heterogeneity. Finally, we show that the different gene-expression programs linked to multilineage differentiation are strongly associated with patient survival. We develop two-gene classifier systems (KRT20 versus CA1, MS4A12, CD177, SLC26A3) that predict clinical outcomes with hazard ratios superior to those of pathological grade and comparable to those of microarray-derived multigene expression signatures.

    View details for DOI 10.1038/nbt.2038

    View details for Web of Science ID 000298038700023

    View details for PubMedID 22081019

  • The Myc Connection: ES Cells and Cancer CELL Rothenberg, M. E., Clarke, M. F., Diehn, M. 2010; 143 (2): 184-186

    Abstract

    Gene profiling experiments have revealed similarities between cancer and embryonic stem (ES) cells. Kim et al. (2010) dissect the gene expression signature of ES cells into three functional modules and find that the Myc module, including genes targeted by Myc-interacting proteins, accounts for most of the similarity between ES and cancer cells.

    View details for DOI 10.1016/j.cell.2010.09.046

    View details for Web of Science ID 000283052200007

    View details for PubMedID 20946977

  • Evidence for an Evolutionarily-Conserved Mechanism Regulating Stem and Progenitor Cell Numbers in the Regenerative Response to Ulcerative Colitis Gastroenterology Rothenberg ME, Dalerba PD, Nusse Y, Lee J, Lobo N, Kalisky T, Leyrat A, Quake SR, Beachy P, Diehn M, Clarke MF 2010; 138 (5): S111
  • Successful Use of Octreotide to Treat Menetrier's Disease: A Rare Cause of Abdominal Pain, Weight Loss, Edema, and Hypoalbuminemia DIGESTIVE DISEASES AND SCIENCES Rothenberg, M., Pai, R., Stuart, K. 2009; 54 (7): 1403-1407

    View details for DOI 10.1007/s10620-009-0754-z

    View details for Web of Science ID 000266654900003

    View details for PubMedID 19255847

  • Adenovirus-Induced Acute Liver Failure DIGESTIVE DISEASES AND SCIENCES Rothenberg, M., Cheung, R., Ahmed, A. 2009; 54 (2): 218-221

    View details for DOI 10.1007/s10620-008-0628-9

    View details for Web of Science ID 000262968200006

    View details for PubMedID 19034647

  • Cancer Stem Cells (Chapter 53) Essentials of Stem Cell Biology 2nd ed. (ed. Robert Lanza) Michael Evan Rothenberg, Michael F Clarke 2009
  • Antibiotics in the management of hepatic encephalopathy: an evidence-based review. Reviews in gastroenterological disorders Rothenberg, M. E., Keeffe, E. B. 2005; 5: 26-35

    Abstract

    Hepatic encephalopathy (HE) is an increasingly prevalent and debilitating condition that occurs in functional hepatic insufficiency. It is marked by fluctuating neuropsychiatric and cognitive impairment, which can be severe and life threatening. Hepatic encephalopathy is a diagnosis of exclusion; thus, it is challenging to diagnose definitively and to investigate in clinical trials. High response rates in the placebo arms of well-conducted studies demonstrate that the most effective treatment for HE is the correction of known precipitating triggers. However, pharmacological therapies may also be helpful. Although the precise pathogenesis remains unknown, bacterially derived neurotoxins from enteric flora likely play an important role. Based on this hypothesis and on accumulating clinical experience documented in randomized trials, oral antibiotics have emerged as an important treatment adjunct. This article addresses the qualities of an ideal antibiotic and reviews the literature on 4 antibiotics used to treat HE: neomycin, metronidazole, vancomycin, and rifaximin, with the most promising of these drugs appearing to be rifaximin. Unfortunately, most studies of the treatment of HE are difficult to interpret due to small sample sizes, methodological flaws, vulnerability to bias, and the intrinsic challenges of studying HE. Many studies have erroneously concluded that treatments are equivalent simply because no significant difference between treatment arms was detected. Consequently, the literature generally lacks definitive data from large, randomized, placebo-controlled trials. Nevertheless, the data suggest that minimally absorbed antibiotics are emerging as a safe and effective approach for the treatment of HE.

    View details for PubMedID 17713457

  • Cell biology - The hippo hypothesis NATURE Rothenberg, M. E., Jan, Y. N. 2003; 425 (6957): 469-470

    View details for DOI 10.1038/425469a

    View details for Web of Science ID 000185648100031

    View details for PubMedID 14523431

  • Drosophila pod-1 crosslinks both actin and microtubules and controls the targeting of axons NEURON Rothenberg, M. E., Rogers, S. L., Vale, R. D., Jan, L. Y., Jan, Y. N. 2003; 39 (5): 779-791

    Abstract

    Actin and microtubules (MTs) are tightly coordinated during neuronal growth cone navigation and are dynamically regulated in response to guidance cues; however, little is known about the underlying molecular mechanisms. Here, we characterize Drosophila pod-1 (dpod1) and show that purified Dpod1 can crosslink both actin and MTs. In cultured S2 cells, Dpod1 colocalizes with lamellar actin and MTs, and overexpression remodels the cytoskeleton to promote dynamic neurite-like actin-dependent projections. Consistent with these observations, Dpod1 localizes to the tips of growing axons, regions where actin and MTs interact, and is especially abundant at navigational choice points. In either the absence or overabundance of Dpod1, growth cone targeting but not outgrowth is disrupted. Taken together, these results reveal novel activities for pod-1 and show that proper levels of Dpod1, an actin/MT crosslinker, must be maintained in the growth cone for correct axon guidance.

    View details for Web of Science ID 000185079300008

    View details for PubMedID 12948445

  • salvador - The persistence of proliferation CANCER CELL Rothenberg, M. E., Jan, Y. N. 2002; 2 (3): 171-173

    Abstract

    Despite years of extensive studies on genes that regulate proliferation and cell death, two processes that must be tightly coordinated throughout development to regulate cell number, remarkably few genes have been shown to affect both processes. Using an elegant genetic screen in the fly eye, have identified a gene, salvador, which is especially significant, because it not only regulates and coordinates both exit from the cell cycle and apoptosis, but also has a human homolog that may play a key role in tumorigenesis.

    View details for Web of Science ID 000178353000004

    View details for PubMedID 12242148

  • casanova plays an early and essential role in endoderm formation in zebrafish DEVELOPMENTAL BIOLOGY Alexander, J., Rothenberg, M., Henry, G. L., Stainier, D. Y. 1999; 215 (2): 343-357

    Abstract

    The cellular and molecular mechanisms that regulate endoderm development in vertebrates have only recently begun to be explored. Here we show that the zebrafish locus casanova plays an early and essential role in this process. casanova mutants lack a gut tube and do not express any molecular markers of endoderm differentiation. The early endodermal expression of genes such as axial, gata5, and fkd2 does not initiate in casanova mutants, indicating that the endoderm is defective from the onset of gastrulation. Mosaic analysis demonstrates that casanova functions cell autonomously within the endodermal progenitors. We also report the isolation of a zebrafish homologue of Mixer, a gene important for early endoderm formation in Xenopus. casanova does not encode zebrafish Mixer, and mixer expression is normal in casanova mutants, indicating that casanova acts downstream of, or parallel to, mixer to promote endoderm formation. We further find that the forerunner cells, a specialized group of noninvoluting dorsal mesendodermal cells, do not form in casanova mutants. Studies of casanova mutants do not support an important role for the forerunner cells in either dorsal axis or tail development, as has been previously proposed. In addition, although different populations of mesodermal precursors are generated normally in casanova mutants, morphogenetic defects in the heart, vasculature, blood, and kidney are apparent, suggesting a possible role for the endoderm in morphogenesis of these organs.

    View details for Web of Science ID 000083726600017

    View details for PubMedID 10545242

  • Partner of numb colocalizes with numb during mitosis and directs numb asymmetric localization in Drosophila neural and muscle progenitors CELL Lu, B. W., Rothenberg, M., Jan, L. Y., Jan, Y. N. 1998; 95 (2): 225-235

    Abstract

    During mitosis of multiple types of precursor cells in Drosophila, Numb is asymmetrically distributed between the two daughter cells and confers distinct daughter cell fates. Here we report the identification of a novel gene product, Partner of Numb (PON), based on its physical interaction with Numb. PON is asymmetrically localized during mitosis and colocalizes with Numb. Loss of pon function disrupts Numb localization in muscle progenitors and delays Numb crescent formation in neural precursors. Moreover, ectopically expressed PON responds to the apical-basal polarity of epithelial cells and is sufficient to localize Numb basally. We propose that PON is one component of a multimolecular machinery that localizes Numb by responding to polarity cues conserved in neural precursors and epithelial cells.

    View details for Web of Science ID 000076538300010

    View details for PubMedID 9790529

  • Mot(3) a Zn finger transcription factor that modulates gene expression and attenuates mating pheromone signaling in Saccharomyces cerevisiae GENETICS Grishin, A. V., Rothenberg, M., Downs, M. A., Blumer, K. 1998; 149 (2): 879-892

    Abstract

    In the yeast Saccharomyces cerevisiae, mating pheromone response is initiated by activation of a G protein- and mitogen-activated protein (MAP) kinase-dependent signaling pathway and attenuated by several mechanisms that promote adaptation or desensitization. To identify genes whose products negatively regulate pheromone signaling, we screened for mutations that suppress the hyperadaptive phenotype of wild-type cells overexpressing signaling-defective G protein beta subunits. This identified recessive mutations in MOT3, which encodes a nuclear protein with two Cys2-His2 Zn fingers. MOT3 was found to be a dosage-dependent inhibitor of pheromone response and pheromone-induced gene expression and to require an intact signaling pathway to exert its effects. Several results suggested that Mot3 attenuates expression of pheromone-responsive genes by mechanisms distinct from those used by the negative transcriptional regulators Cdc36, Cdc39, and Mot2. First, a Mot3-lexA fusion functions as a transcriptional activator. Second, Mot3 is a dose-dependent activator of several genes unrelated to pheromone response, including CYC1, SUC2, and LEU2. Third, insertion of consensus Mot3 binding sites (C/A/T)AGG(T/C)A activates a promoter in a MOT3-dependent manner. These findings, and the fact that consensus binding sites are found in the 5' flanking regions of many yeast genes, suggest that Mot3 is a globally acting transcriptional regulator. We hypothesize that Mot3 regulates expression of factors that attenuate signaling by the pheromone response pathway.

    View details for Web of Science ID 000074028400035

    View details for PubMedID 9611199

  • Numb-associated kinase interacts with the phosphotyrosine binding domain of numb and antagonizes the function of numb in vivo MOLECULAR AND CELLULAR BIOLOGY Chien, C. T., Wang, S. W., Rothenberg, M., Jan, L. Y., Jan, Y. N. 1998; 18 (1): 598-607

    Abstract

    During asymmetric cell division, the membrane-associated Numb protein localizes to a crescent in the mitotic progenitor and is segregated predominantly to one of the two daughter cells. We have identified a putative serine/threonine kinase, Numb-associated kinase (Nak), which interacts physically with the phosphotyrosine binding (PTB) domain of Numb. The PTB domains of Shc and insulin receptor substrate bind to an NPXY motif which is not present in the region of Nak that interacts with Numb PTB domain. We found that the Numb PTB domain but not the Shc PTB domain interacts with Nak through a peptide of 11 amino acids, implicating a novel and specific protein-protein interaction. Overexpression of Nak in the sensory organs causes both daughters of a normally asymmetric cell division to adopt the same cell fate, a transformation similar to the loss of numb function phenotype and opposite the cell fate transformation caused by overexpression of Numb. The frequency of cell fate transformation is sensitive to the numb gene dosage, as expected from the physical interaction between Nak and Numb. These findings indicate that Nak may play a role in cell fate determination during asymmetric cell divisions.

    View details for Web of Science ID 000071195700060

    View details for PubMedID 9418906

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