Bio

Honors & Awards


  • Arthur Purdy Stout Stipend Award, Arthur Purdy Stout Society of Surgical Pathologists (2019)
  • American Society of Dermatopathology Mentorship Award, ASDP (2018)
  • Trainee Mentored Award in Precision Health, Department of Pathology, Stanford University School of Medicine (2018)
  • NIH Marshall Scholar, Marshall Aid Commemoration Commission, National Institutes of Health (2009-2013)

Professional Education


  • Fellowship, Stanford University School of Medicine, Dermatopathology (2021)
  • Residency, Stanford University School of Medicine, Anatomic Pathology (2020)
  • M.D., Johns Hopkins University School of Medicine, Medical Education (2017)
  • Ph.D., University College London, Genetics (2013)
  • B.A., Middlebury College, Molecular Biology and Biochemistry (2009)

Publications

All Publications


  • Biomarker discovery analysis: Alterations in p14, p16, p53, and BAP1 expression in nevi, cutaneous melanoma, and metastatic melanoma PIGMENT CELL & MELANOMA RESEARCH Sargen, M. R., Cloutier, J. M., Sarin, K. Y., Rieger, K. E., Chu, P., Swetter, S. M., Novoa, R. A. 2019; 32 (3): 474–78

    View details for DOI 10.1111/pcmr.12768

    View details for Web of Science ID 000465607700016

  • Necrotic Keratinocytes Are Common in Psoriasis and Have a Predilection to the Upper Epidermis: A Quantitative and Comparative Analysis. The American Journal of dermatopathology Cloutier, J. M., Hsi, A., Camacho, C., Lazova, R. 2019

    Abstract

    BACKGROUND: The most salient histopathological features of psoriasis are epidermal hyperplasia, hypogranulosis, parakeratosis, dilated capillaries in dermal papillae, and intraepidermal and intracorneal neutrophils. Several additional "nonclassic" features of psoriasis have recently been reported, including necrotic keratinocytes (NK). To determine the diagnostic utility of NK, we characterized NK in a large cohort of psoriasis cases compared with psoriasiform spongiotic dermatitis (PSD) and normal skin.METHODS: NK were quantified in 101 cases of psoriasis, 20 cases of PSD, and 20 cases of normal skin. The location of NK within the lower, middle, or upper thirds of the epidermis was recorded.RESULTS: NK were identified in 77/101 (76%) of psoriasis cases. By comparison, NK were seen in 8/20 (40%) cases of PSD and 4/20 (20%) cases of normal skin. The linear concentration of NK was significantly higher in psoriasis (0.36 NK/mm) compared with PSD (0.12 NK/mm) and normal skin (0.03 NK/mm) (P = 0.0009). NK were preferentially located in the upper (58%) and middle (31%) epidermis in psoriasis.CONCLUSIONS: NK are a common feature of psoriasis and have a predilection to the upper layers of epidermis. Superficial NK may provide additional diagnostic support for psoriasis in challenging or borderline cases.

    View details for PubMedID 31094719

  • Biomarker discovery analysis: Alterations in p14, p16, p53, and BAP1 expression in nevi, cutaneous melanoma, and metastatic melanoma. Pigment cell & melanoma research Sargen, M. R., Cloutier, J. M., Sarin, K. Y., Rieger, K. E., Chu, P., Swetter, S. M., Novoa, R. A. 2019

    Abstract

    Protein biomarkers for diagnosis and prognosis are currently lacking for melanoma, which predominantly relies on histologic features for diagnosis (cytologic and nuclear pleomorphism, growth pattern) and staging (Breslow depth, ulceration). In many cases, the histology of the primary tumor is an unreliable predictor of tumor behavior, and consequently sentinel lymph node biopsy along with imaging studies are often necessary to predict likelihood of mortality from disease. This article is protected by copyright. All rights reserved.

    View details for PubMedID 30672662

  • Diagnostic classification of soft tissue malignancies: A review and update from a surgical pathology perspective. Current problems in cancer Cloutier, J. M., Charville, G. W. 2019

    Abstract

    Soft tissue sarcomas encompass a broad spectrum of histologically, clinically, and molecularly diverse neoplasms that present unique diagnostic and therapeutic challenges. Accurate classification is essential both for appropriate risk stratification and for guiding clinical management. Once classified almost exclusively based on the morphologic appearance of the tumor by light microscopy, many soft tissue sarcomas are now known to manifest recurrent patterns of genetic alterations. In addition to enabling molecular confirmation of histologic diagnoses, discovery of these recurrent genetic alterations has helped to refine existing morphologic definitions of sarcoma subtypes and even prompted the discovery of new subtypes. As therapy for sarcoma has become increasingly tailored to a specific entity, the integration of molecular data has assumed added importance in diagnostic decision making. In this article, we summarize principles of the histologic evaluation of soft tissue sarcomas, discuss specific diagnostic features of several of the most common sarcoma subtypes, and describe our vision for a future of soft tissue sarcoma diagnosis that merges morphologic, genetic, and epigenetic features to arrive at diagnoses that are aligned with tumor-specific, biologically targeted treatment approaches.

    View details for DOI 10.1016/j.currproblcancer.2019.05.006

    View details for PubMedID 31200960

  • Metastatic breast Cancer simulating well-differentiated neuroendocrine neoplasms of visceral organs. Human pathology Cloutier, J., Thompson, E. D., Cimino-Mathews, A., Rooper, L. M., Matoso, A., Argani, P. 2018

    Abstract

    A series of metastatic breast carcinoma (MBC) mimicking visceral well-differentiated neuroendocrine neoplasms has not previously been reported. We identified five consultation cases originally submitted as neuroendocrine neoplasms in females but which were found to be MBC on subsequent review. All 5 neoplasms demonstrated nested architecture and relatively uniform nuclei. Four patients had a known history of breast cancer (remote in 3 and concurrent in 1), but the metastases (3 liver, 1 lung) labeled for chromogranin and/or synaptophysin, prompting misdiagnosis as neuroendocrine neoplasm. In a fifth case, a liver metastasis in a patient with a known pancreatic endocrine neoplasm was originally thought to be of pancreatic origin; an occult concurrent primary breast cancer (PBC) was subsequently identified as the source. On further immunohistochemistry (IHC, all metastases evaluated were diffusely, strongly positive for estrogen receptor (ER) (5/5 cases) and GATA3 (4/4 cases). Three patients had previously received ineffective treatment for neuroendocrine carcinoma. Based upon the consultation diagnosis, all four patients with follow-up received hormone therapy, which was effective in three. In a separate tissue microarray (TMA) cohort of paired PBCs and hematogenous MBCs, chromogranin and/or synaptophysin IHC labeling was typically negative, and increased from the PBC to the MBC in only 5% of cases. In conclusion, while neuroendocrine differentiation is uncommon in breast cancer and does not commonly increase in metastases, MBC with neuroendocrine differentiation should be considered in patients with visceral neuroendocrine neoplasms of unknown primary site. Diffuse IHC labeling for ER and GATA3 helps establish the correct diagnosis.

    View details for PubMedID 30031098

  • Metastatic Breast Cancer Simulating Well-Differentiated Neuroendocrine Neoplasms of Visceral Organs Cloutier, J., Thompson, E. D., Cimino-Mathews, A., Matoso, A., Argani, P. NATURE PUBLISHING GROUP. 2018: 55
  • Metastatic Breast Cancer Simulating Well-Differentiated Neuroendocrine Neoplasms of Visceral Organs Cloutier, J., Thompson, E. D., Cimino-Mathews, A., Matoso, A., Argani, P. NATURE PUBLISHING GROUP. 2018: 55
  • Interrogating the Functions of PRDM9 Domains in Meiosis. Genetics Thibault-Sennett, S., Yu, Q., Smagulova, F., Cloutier, J., Brick, K., Camerini-Otero, R. D., Petukhova, G. V. 2018

    Abstract

    Homologous recombination is required for proper segregation of homologous chromosomes during meiosis. It predominantly occurs at recombination hotspots that are defined by the DNA binding specificity of the PRDM9 protein. PRDM9 contains three conserved domains typically involved in regulation of transcription, yet, the role of PRDM9 in gene expression control is not clear. Here we analyze the germline transcriptome of Prdm9-/- male mice in comparison to Prdm9+/+ males and find no apparent differences in the mRNA and miRNA profiles. We further explore the role of PRDM9 in meiosis by analyzing the effect of the KRAB, SSXRD and post-SET zinc finger deletions in a cell culture expression system and the KRAB domain deletion in mice. We found that although the post-SET zinc finger and the KRAB domains are not essential for the methyltransferase activity of PRDM9 in cell culture, the KRAB domain mutant mice show only residual PRDM9 methyltransferase activity and undergo meiotic arrest. In aggregate, our data indicate that domains typically involved in regulation of gene expression do not serve that role in PRDM9, but are likely involved in setting the proper chromatin environment for initiation and completion of homologous recombination.

    View details for DOI 10.1534/genetics.118.300565

    View details for PubMedID 29674518

  • Mammalian meiotic silencing exhibits sexually dimorphic features CHROMOSOMA Cloutier, J. M., Mahadevaiah, S. K., Elinati, E., Toth, A., Turner, J. 2016; 125 (2): 215-226

    Abstract

    During mammalian meiotic prophase I, surveillance mechanisms exist to ensure that germ cells with defective synapsis or recombination are eliminated, thereby preventing the generation of aneuploid gametes and embryos. Meiosis in females is more error-prone than in males, and this is in part because the prophase I surveillance mechanisms are less efficient in females. A mechanistic understanding of this sexual dimorphism is currently lacking. In both sexes, asynapsed chromosomes are transcriptionally inactivated by ATR-dependent phosphorylation of histone H2AFX. This process, termed meiotic silencing, has been proposed to perform an important prophase I surveillance role. While the transcriptional effects of meiotic silencing at individual genes are well described in the male germ line, analogous studies in the female germ line have not been performed. Here we apply single- and multigene RNA fluorescence in situ hybridization (RNA FISH) to oocytes from chromosomally abnormal mouse models to uncover potential sex differences in the silencing response. Notably, we find that meiotic silencing in females is less efficient than in males. Within individual oocytes, genes located on the same asynapsed chromosome are silenced to differing extents, thereby generating mosaicism in gene expression profiles across oocyte populations. Analysis of sex-reversed XY female mice reveals that the sexual dimorphism in silencing is determined by gonadal sex rather than sex chromosome constitution. We propose that sex differences in meiotic silencing impact on the sexually dimorphic prophase I response to asynapsis.

    View details for DOI 10.1007/s00412-015-0568-z

    View details for Web of Science ID 000374304000005

    View details for PubMedID 26712235

    View details for PubMedCentralID PMC4830877

  • Histone H2AFX Links Meiotic Chromosome Asynapsis to Prophase I Oocyte Loss in Mammals PLOS GENETICS Cloutier, J. M., Mahadevaiah, S. K., Elinati, E., Nussenzweig, A., Toth, A., Turner, J. M. 2015; 11 (10)

    Abstract

    Chromosome abnormalities are common in the human population, causing germ cell loss at meiotic prophase I and infertility. The mechanisms driving this loss are unknown, but persistent meiotic DNA damage and asynapsis may be triggers. Here we investigate the contribution of these lesions to oocyte elimination in mice with chromosome abnormalities, e.g. Turner syndrome (XO) and translocations. We show that asynapsed chromosomes trigger oocyte elimination at diplonema, which is linked to the presence of phosphorylated H2AFX (γH2AFX). We find that DNA double-strand break (DSB) foci disappear on asynapsed chromosomes during pachynema, excluding persistent DNA damage as a likely cause, and demonstrating the existence in mammalian oocytes of a repair pathway for asynapsis-associated DNA DSBs. Importantly, deletion or point mutation of H2afx restores oocyte numbers in XO females to wild type (XX) levels. Unexpectedly, we find that asynapsed supernumerary chromosomes do not elicit prophase I loss, despite being enriched for γH2AFX and other checkpoint proteins. These results suggest that oocyte loss cannot be explained simply by asynapsis checkpoint models, but is related to the gene content of asynapsed chromosomes. A similar mechanistic basis for oocyte loss may operate in humans with chromosome abnormalities.

    View details for DOI 10.1371/journal.pgen.1005462

    View details for Web of Science ID 000364401600005

    View details for PubMedID 26509888

    View details for PubMedCentralID PMC4624946

  • Antagonistic roles of ubiquitin ligase HEI10 and SUMO ligase RNF212 regulate meiotic recombination. Nature genetics Qiao, H., Prasada Rao, H. B., Yang, Y., Fong, J. H., Cloutier, J. M., Deacon, D. C., Nagel, K. E., Swartz, R. K., Strong, E., Holloway, J. K., Cohen, P. E., Schimenti, J., Ward, J., Hunter, N. 2014; 46 (2): 194-199

    Abstract

    Crossover recombination facilitates the accurate segregation of homologous chromosomes during meiosis. In mammals, poorly characterized regulatory processes ensure that every pair of chromosomes obtains at least one crossover, even though most recombination sites yield non-crossovers. Designation of crossovers involves selective localization of the SUMO ligase RNF212 to a minority of recombination sites, where it stabilizes pertinent factors such as MutSγ (ref. 4). Here we show that the ubiquitin ligase HEI10 (also called CCNB1IP1) is essential for this crossover/non-crossover differentiation process. In HEI10-deficient mice, RNF212 localizes to most recombination sites, and dissociation of both RNF212 and MutSγ from chromosomes is blocked. Consequently, recombination is impeded, and crossing over fails. In wild-type mice, HEI10 accumulates at designated crossover sites, suggesting that it also has a late role in implementing crossing over. As with RNF212, dosage sensitivity for HEI10 indicates that it is a limiting factor for crossing over. We suggest that SUMO and ubiquitin have antagonistic roles during meiotic recombination that are balanced to effect differential stabilization of recombination factors at crossover and non-crossover sites.

    View details for DOI 10.1038/ng.2858

    View details for PubMedID 24390283

    View details for PubMedCentralID PMC4356240

  • ATR acts stage specifically to regulate multiple aspects of mammalian meiotic silencing GENES & DEVELOPMENT Royo, H., Prosser, H., Ruzankina, Y., Mahadevaiah, S. K., Cloutier, J. M., Baumann, M., Fukuda, T., Hoog, C., Toth, A., De Rooij, D. G., Bradley, A., Brown, E. J., Turner, J. M. 2013; 27 (13): 1484-1494

    Abstract

    In mammals, homologs that fail to synapse during meiosis are transcriptionally inactivated. This process, meiotic silencing, drives inactivation of the heterologous XY bivalent in male germ cells (meiotic sex chromosome inactivation [MSCI]) and is thought to act as a meiotic surveillance mechanism. The checkpoint protein ATM and Rad3-related (ATR) localizes to unsynapsed chromosomes, but its role in the initiation and maintenance of meiotic silencing is unknown. Here we show that ATR has multiple roles in silencing. ATR first regulates HORMA (Hop1, Rev7, and Mad2) domain protein HORMAD1/2 phosphorylation and localization of breast cancer I (BRCA1) and ATR cofactors ATR-interacting peptide (ATRIP)/topoisomerase 2-binding protein 1 (TOPBP1) at unsynapsed axes. Later, it acts as an adaptor, transducing signaling at unsynapsed axes into surrounding chromatin in a manner that requires interdependence with mediator of DNA damage checkpoint 1 (MDC1) and H2AFX. Finally, ATR catalyzes histone H2AFX phosphorylation, the epigenetic event leading to gene inactivation. Using a novel genetic strategy in which MSCI is used to silence a chosen gene in pachytene, we show that ATR depletion does not disrupt the maintenance of silencing and that silencing comprises two phases: The first is dynamic and reversible, and the second is stable and irreversible. Our work identifies a role for ATR in the epigenetic regulation of gene expression and presents a new technique for ablating gene function in the germline.

    View details for DOI 10.1101/gad.219477.113

    View details for Web of Science ID 000321303600006

    View details for PubMedID 23824539

    View details for PubMedCentralID PMC3713429

  • Meiotic DNA double-strand breaks and chromosome asynapsis in mice are monitored by distinct HORMAD2-independent and -dependent mechanisms GENES & DEVELOPMENT Wojtasz, L., Cloutier, J. M., Baumann, M., Daniel, K., Varga, J., Fu, J., Anastassiadis, K., Stewart, A. F., Remenyi, A., Turner, J. M., Toth, A. 2012; 26 (9): 958-973

    Abstract

    Meiotic crossover formation involves the repair of programmed DNA double-strand breaks (DSBs) and synaptonemal complex (SC) formation. Completion of these processes must precede the meiotic divisions in order to avoid chromosome abnormalities in gametes. Enduring key questions in meiosis have been how meiotic progression and crossover formation are coordinated, whether inappropriate asynapsis is monitored, and whether asynapsis elicits prophase arrest via mechanisms that are distinct from the surveillance of unrepaired DNA DSBs. We disrupted the meiosis-specific mouse HORMAD2 (Hop1, Rev7, and Mad2 domain 2) protein, which preferentially associates with unsynapsed chromosome axes. We show that HORMAD2 is required for the accumulation of the checkpoint kinase ATR along unsynapsed axes, but not at DNA DSBs or on DNA DSB-associated chromatin loops. Consistent with the hypothesis that ATR activity on chromatin plays important roles in the quality control of meiotic prophase, HORMAD2 is required for the elimination of the asynaptic Spo11(-/-), but not the asynaptic and DSB repair-defective Dmc1(-/-) oocytes. Our observations strongly suggest that HORMAD2-dependent recruitment of ATR to unsynapsed chromosome axes constitutes a mechanism for the surveillance of asynapsis. Thus, we provide convincing evidence for the existence of a distinct asynapsis surveillance mechanism that safeguards the ploidy of the mammalian germline.

    View details for DOI 10.1101/gad.187559.112

    View details for Web of Science ID 000303538900009

    View details for PubMedID 22549958

    View details for PubMedCentralID PMC3347793

  • Meiotic sex chromosome inactivation CURRENT BIOLOGY Cloutier, J. M., Turner, J. M. 2010; 20 (22): R962-R963

    View details for Web of Science ID 000284923700007

    View details for PubMedID 21093783