Publications

    Bradley Michael Wierbowski and Adrian Salic. 2021. “Molecular Mechanisms of Sonic Hedgehog Release and Delivery.” Harvard University Division of Medical Sciences.Abstract
    The Hedgehog signaling pathway numbers among the five highly conserved cell–cell signaling pathways that operate early in metazoan development. The pathway's activating ligand, the Sonic hedgehog (SHH) morphogen, is posttranslationally modified by palmitate and cholesterol, two lipids that tether SHH strongly to the membrane of producing cells. To effect many of its patterning roles, however, SHH must signal to faraway target cells, raising the question of how lipidated SHH is mobilized to act at a distance. In this dissertation, I investigate the biochemical basis for SHH movement between producing and responding cells by addressing two related questions: (1) how is lipidated SHH released, in a soluble form, from the membrane of producing cells and (2) how is SHH delivered to its receptor, Patched1 (PTCH1), on target cells?In Chapter 2, we address the first question by employing a quantitative cell-based assay to measure SHH release kinetics as a function of two known SHH release factors: the transporter-like membrane protein Dispatched1 (DISP1) and a secreted chaperone SCUBE2, which binds the lipidated termini of SHH. We determine that transfer of SHH from the producing cell membrane to exogenous SCUBE2 is rate-limited by DISP1 transporter activity, which we find is powered by the plasma membrane Na+ gradient.In Chapter 3, we address the second question by following the fate of the soluble SCUBE2–SHH complex. Using cell-based experiments and biochemical reconstitution, we discover that SHH transfer from SCUBE2 to PTCH1 is accomplished by the sequential activities of the SHH coreceptors CDON/BOC and GAS1, factors necessary for Hedgehog signaling in vivo but with yet-unclear molecular functions. We find that, first, CDON/BOC bind both SCUBE2 and SHH, to recruit SCUBE2–SHH to the cell surface. Next, GAS1, which we find binds SHH lipid moieties, accepts SHH from SCUBE2. Finally, GAS1 coordinates transfer of SHH lipids to PTCH1, activating the pathway.Collectively, these studies establish a biochemical framework for the movement of lipidated SHH from the producing cell membrane to the PTCH1 receptor, in which successive handoffs of the SHH lipid appendages along an extracellular chaperone cascade ultimately dictate its tissue distribution and cell-autonomous activity.
    George A Alba, Andriy O Samokhin, Rui-Sheng Wang, Ying-Yi Zhang, Bradley M Wertheim, Elena Arons, Edward A Greenfield, Martina H Lundberg Slingsby, Julia R Ceglowski, Kathleen J Haley, Frederick P Bowman, Yen-Rei Yu, John C Haney, George Eng, Richard N Mitchell, Anthony Sheets, Sara O Vargas, Sachiko Seo, Richard N Channick, Peter J Leary, Sudarshan Rajagopal, Joseph Loscalzo, Elisabeth M Battinelli, and Bradley A Maron. 2021. “NEDD9 Is a Novel and Modifiable Mediator of Platelet-Endothelial Adhesion in the Pulmonary Circulation.” Am J Respir Crit Care Med, 203, 12, Pp. 1533-1545.Abstract
    Rationale: Data on the molecular mechanisms that regulate platelet-pulmonary endothelial adhesion under conditions of hypoxia are lacking, but may have important therapeutic implications. Objectives: To identify a hypoxia-sensitive, modifiable mediator of platelet-pulmonary artery endothelial cell adhesion and thrombotic remodeling. Methods: Network medicine was used to profile protein-protein interactions in hypoxia-treated human pulmonary artery endothelial cells. Data from liquid chromatography-mass spectrometry and microscale thermophoresis informed the development of a novel antibody (Ab) to inhibit platelet-endothelial adhesion, which was tested in cells from patients with chronic thromboembolic pulmonary hypertension (CTEPH) and three animal models in vivo. Measurements and Main Results: The protein NEDD9 was identified in the hypoxia thrombosome network in silico. Compared with normoxia, hypoxia (0.2% O2) for 24 hours increased HIF-1α (hypoxia-inducible factor-1α)-dependent NEDD9 upregulation in vitro. Increased NEDD9 was localized to the plasma-membrane surface of cells from control donors and patients with CTEPH. In endarterectomy specimens, NEDD9 colocalized with the platelet surface adhesion molecule P-selectin. Our custom-made anti-NEDD9 Ab targeted the NEDD9-P-selectin interaction and inhibited the adhesion of activated platelets to pulmonary artery endothelial cells from control donors in vitro and from patients with CTEPH ex vivo. Compared with control mice, platelet-pulmonary endothelial aggregates and pulmonary hypertension induced by ADP were decreased in NEDD9-/- mice or wild-type mice treated with the anti-NEDD9 Ab, which also decreased chronic pulmonary thromboembolic remodeling in vivo. Conclusions: The NEDD9-P-selectin protein-protein interaction is a modifiable target with which to inhibit platelet-pulmonary endothelial adhesion and thromboembolic vascular remodeling, with potential therapeutic implications for patients with disorders of increased hypoxia signaling pathways, including CTEPH.
    Markus Nilsson, Greta Eklund, Filip Szczepankiewicz, Mikael Skorpil, Karin Bryskhe, Carl-Fredrik Westin, Claes Lindh, Lennart Blomqvist, and Fredrik Jäderling. 2021. “Mapping Prostatic Microscopic Anisotropy Using Linear and Spherical B-Tensor Encoding: A Preliminary Study.” Magn Reson Med, 86, 4, Pp. 2025-33.Abstract
    PURPOSE: Tensor-valued diffusion encoding provides more specific information than conventional diffusion-weighted imaging (DWI), but has mainly been applied in neuroimaging studies. This study aimed to assess its potential for the imaging of prostate cancer (PCa). METHODS: Seventeen patients with histologically proven PCa were enrolled. DWI of the prostate was performed with linear and spherical tensor encoding using a maximal b-value of 1.5 ms/µm2 and a voxel size of 3 × 3 × 4 mm3 . The gamma-distribution model was used to estimate the mean diffusivity (MD), the isotropic kurtosis (MKI ), and the anisotropic kurtosis (MKA ). Regions of interest were placed in MR-defined cancerous tissues, as well as in apparently healthy tissues in the peripheral and transitional zones (PZs and TZs). RESULTS: DWI with linear and spherical encoding yielded different image contrasts at high b-values, which enabled the estimation of MKA and MKI . Compared with healthy tissue (PZs and TZs combined) the cancers displayed a significantly lower MD (P < .05), higher MKI (P < 10-5 ), and lower MKA (P < .05). Compared with the TZ, tissue in the PZ showed lower MD (P < 10-3 ) and higher MKA (P < 10-3 ). No significant differences were found between cancers of different Gleason scores, possibly because of the limited sample size. CONCLUSION: Tensor-valued diffusion encoding enabled mapping of MKA and MKI in the prostate. The elevated MKI in PCa compared with normal tissues suggests an elevated heterogeneity in the cancers. Increased in-plane resolution could improve tumor delineation in future studies.
    Somenath Bakshi, Emanuele Leoncini, Charles Baker, Silvia J Cañas-Duarte, Burak Okumus, and Johan Paulsson. 2021. “Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence.” Nat Microbiol, 6, 6, Pp. 783-791.Abstract
    As bacteria transition from exponential to stationary phase, they change substantially in size, morphology, growth and expression profiles. These responses also vary between individual cells, but it has proved difficult to track cell lineages along the growth curve to determine the progression of events or correlations between how individual cells enter and exit dormancy. Here, we developed a platform for tracking more than 105 parallel cell lineages in dense and changing cultures, independently validating that the imaged cells closely track batch populations. Initial applications show that for both Escherichia coli and Bacillus subtilis, growth changes from an 'adder' mode in exponential phase to mixed 'adder-timers' entering stationary phase, and then a near-perfect 'sizer' upon exit-creating broadly distributed cell sizes in stationary phase but rapidly returning to narrowly distributed sizes upon exit. Furthermore, cells that undergo more divisions when entering stationary phase suffer reduced survival after long periods of dormancy but are the only cells observed that persist following antibiotic treatment.
    T.A. Grotzer, E. Gonzalez, and E. Schibuk. 2021. “Cause and Effect: Mechanism and Prediction.” In Crosscutting Concepts: Strengthening Science and Engineering Learning, edited by J. Nordine and O. Lee, Pp. 89-113. NSTA.
    Michael Rosenberg, Roy Blum, Barry Kesner, Eric Aeby, Jean-Michel Garant, Attila Szanto, and Jeannie T. Lee. 2021. “Motif-driven interactions between RNA and PRC2 are rheostats that regulate transcription elongation.” Nature Structural & Molecular Biology, 28, 1, Pp. 103–117. Publisher's VersionAbstract
    Although polycomb repressive complex 2 (PRC2) is now recognized as an RNA-binding complex, the full range of binding motifs and why PRC2–RNA complexes often associate with active genes have not been elucidated. Here, we identify high-affinity RNA motifs whose mutations weaken PRC2 binding and attenuate its repressive function in mouse embryonic stem cells. Interactions occur at promoter-proximal regions and frequently coincide with pausing of RNA polymerase II (POL-II). Surprisingly, while PRC2-associated nascent transcripts are highly expressed, ablating PRC2 further upregulates expression via loss of pausing and enhanced transcription elongation. Thus, PRC2-nascent RNA complexes operate as rheostats to fine-tune transcription by regulating transitions between pausing and elongation, explaining why PRC2–RNA complexes frequently occur within active genes. Nascent RNA also targets PRC2 in cis and downregulates neighboring genes. We propose a unifying model in which RNA specifically recruits PRC2 to repress genes through POL-II pausing and, more classically, trimethylation of histone H3 at Lys27.
    Kaixuan Huang, Sham M. Kakade, Jason D. Lee, and Qi Lei. 2021. A Short Note on the Relationship of Information Gain and Eluder Dimension. ArXiv Report. arXiv VersionAbstract
    Eluder dimension and information gain are two widely used methods of complexity measures in bandit and reinforcement learning. Eluder dimension was originally proposed as a general complexity measure of function classes, but the common examples of where it is known to be small are function spaces (vector spaces). In these cases, the primary tool to upper bound the eluder dimension is the elliptic potential lemma. Interestingly, the elliptic potential lemma also features prominently in the analysis of linear bandits/reinforcement learning and their nonparametric generalization, the information gain. We show that this is not a coincidence -- eluder dimension and information gain are equivalent in a precise sense for reproducing kernel Hilbert spaces.
    Xiyang Liu, Weihao Kong, Sham Kakade, and Sewoong Oh. 2021. “Robust and Differentially Private Mean Estimation.” In NeurIPS. arXiv VersionAbstract
    Differential privacy has emerged as a standard requirement in a variety of applications ranging from the U.S. Census to data collected in commercial devices, initiating an extensive line of research in accurately and privately releasing statistics of a database. An increasing number of such databases consist of data from multiple sources, not all of which can be trusted. This leaves existing private analyses vulnerable to attacks by an adversary who injects corrupted data. Despite the significance of designing algorithms that guarantee privacy and robustness (to a fraction of data being corrupted) simultaneously, even the simplest questions remain open. For the canonical problem of estimating the mean from i.i.d. samples, we introduce the first efficient algorithm that achieves both privacy and robustness for a wide range of distributions. This achieves optimal accuracy matching the known lower bounds for robustness, but the sample complexity has a factor of d1/2 gap from known lower bounds. We further show that this gap is due to the computational efficiency; we introduce the first family of algorithms that close this gap but takes exponential time. The innovation is in exploiting resilience (a key property in robust estimation) to adaptively bound the sensitivity and improve privacy.
    Alekh Agarwal, Sham M. Kakade, Jason D. Lee, and Gaurav Mahajan. 2021. “On the Theory of Policy Gradient Methods: Optimality, Approximation, and Distribution Shift.” Journal of Machine Learning Research, 22 . arXiv VersionAbstract
    Policy gradient methods are among the most effective methods in challenging reinforcement learning problems with large state and/or action spaces. However, little is known about even their most basic theoretical convergence properties, including: if and how fast they converge to a globally optimal solution or how they cope with approximation error due to using a restricted class of parametric policies. This work provides provable characterizations of the computational, approximation, and sample size properties of policy gradient methods in the context of discounted Markov Decision Processes (MDPs). We focus on both: "tabular" policy parameterizations, where the optimal policy is contained in the class and where we show global convergence to the optimal policy; and parametric policy classes (considering both log-linear and neural policy classes), which may not contain the optimal policy and where we provide agnostic learning results. One central contribution of this work is in providing approximation guarantees that are average case -- which avoid explicit worst-case dependencies on the size of state space -- by making a formal connection to supervised learning under distribution shift. This characterization shows an important interplay between estimation error, approximation error, and exploration (as characterized through a precisely defined condition number).
    Marco Bianco, Antonio Balena, Marco Pisanello, Filippo Pisano, Leonardo Sileo, Barbara Spagnolo, Cinzia Montinaro, Bernardo L Sabatini, Massimo De Vittorio, and Ferruccio Pisanello. 2021. “Comparative study of autofluorescence in flat and tapered optical fibers towards application in depth-resolved fluorescence lifetime photometry in brain tissue.” Biomed Opt Express, 12, 2, Pp. 993-1010.Abstract
    As the scientific community seeks efficient optical neural interfaces with sub-cortical structures of the mouse brain, a wide set of technologies and methods is being developed to monitor cellular events through fluorescence signals generated by genetically encoded molecules. Among these technologies, tapered optical fibers (TFs) take advantage of the modal properties of narrowing waveguides to enable both depth-resolved and wide-volume light collection from scattering tissue, with minimized invasiveness with respect to standard flat fiber stubs (FFs). However, light guided in patch cords as well as in FFs and TFs can result in autofluorescence (AF) signal, which can act as a source of time-variable noise and limit their application to probe fluorescence lifetime in vivo. In this work, we compare the AF signal of FFs and TFs, highlighting the influence of the cladding composition on AF generation. We show that the autofluorescence signal generated in TFs has a peculiar coupling pattern with guided modes, and that far-field detection can be exploited to separate functional fluorescence from AF. On these bases, we provide evidence that TFs can be employed to implement depth-resolved fluorescence lifetime photometry, potentially enabling the extraction of a new set of information from deep brain regions, as time-correlating single photon counting starts to be applied in freely-moving animals to monitor the intracellular biochemical state of neurons.
    Travis C. Evans, Joseph DeGutis, David Rothlein, Audreyana Jagger-Rickels, Ayumu Yamashita, Catherine B. Fortier, Jennifer R. Fonda, William Milberg, Regina McGlinchey, and Michael Esterman. 2021. “Punishment and reward normalize error-related cognitive control in PTSD by modulating salience network activation and connectivity.” Cortex: A Journal Devoted to the Study of the Nervous System and Behavior, 145, Pp. 295-314.Abstract
    Posttraumatic Stress Disorder (PTSD) symptomatology disrupts inhibitory control during sustained attention. However, PTSD-related inhibitory control deficits are partially ameliorated when punishments and rewards are administered based on task performance, which suggests motivational processes contribute to these deficits. Additionally, PTSD may also impair error-related cognitive control following inhibitory control failures as measured by post-error slowing (PES). However, it remains unclear if motivational processes also contribute to impaired error-related cognitive control in PTSD. Using an incentivized sustained attention paradigm in two independent samples of post-9/11 veterans, we characterized PTSD-related differences in PES during both non-motivated conditions (no task-based incentives) and motivated conditions (task-based rewards and punishments). In Study 1 (n = 139), PTSD symptom severity was modestly associated with smaller PES in the non-motivated condition, whereas no PTSD-related association was observed in the motivated condition. In Study 2 (n = 35), we replicated and extended these results by using fMRI to characterize modulation of the triple network system comprised of the Salience Network (SN), Frontoparietal Control Network (FPCN), and Default Mode Network (DMN). In the non-motivated condition, PTSD symptom severity was associated with non-specific SN and FPCN hyperactivation during both failed and successful inhibitory control. In the motivated condition, PTSD symptom severity was associated with greater focal activation of both the SN and Superior Parietal Lobule cluster (an FPCN node) during punished inhibitory control failures and weaker SN-FPCN connectivity during rewarded inhibitory control successes. Together, these results suggest that dysregulated motivational processes in PTSD may contribute to impaired error-related cognitive control. (PsycInfo Database Record (c) 2021 APA, all rights reserved)
    Jasmeet P Hayes, Meghan Pierce, Kate Valerio, Mark Miller, Bertrand R Huber, Catherine Fortier, Jennifer Fonda, William Milberg, and Regina McGlinchey. 2021. “The association between blast exposure and transdiagnostic health symptoms on systemic inflammation.” medRxiv.Abstract
    Chronic elevation of systemic inflammation is observed in a wide range of disorders including PTSD, depression, and traumatic brain injury, all of which are relatively common in United States Veterans. Although previous work has demonstrated a link between inflammation and various diagnoses separately, few studies have examined transdiagnostic symptoms and inflammation within the same model. The objective of this study was to examine relationships between psychiatric and health variables and systemic inflammation, and to determine whether mild traumatic brain injury (mTBI) and/or exposure to blast munitions moderate these relationships. Confirmatory factor analysis in a large sample (N = 357) of post-9/11 Veterans demonstrated good fit to a four-factor model reflecting traumatic stress, affective, somatic, and metabolic latent variables. Hierarchical regression models revealed that each of the latent variables were associated with higher levels of systemic inflammation. However, the strongest relationship with inflammation emerged among those who had both war-zone blast exposures and metabolic dysregulation, even after adjusting for mental health latent variables. Exploratory analyses showed that blast exposure was associated with metabolic dysregulation in a dose-response manner, with self-reported closer blast proximity associated with the greatest metabolic dysregulation. Together, these results provide greater understanding of the types of symptoms most strongly associated with inflammation, and underscore the importance of maintaining a healthy lifestyle to reduce the impact of obesity and other metabolic symptoms on future chronic disease in younger to middle-aged Veterans.
    J. A. Sumner, A. X. Maihofer, V. Michopoulos, A. O. Rothbaum, L. M. Almli, O. A. Andreassen, A. E. Ashley-Koch, D. G. Baker, J. C. Beckham, B. Bradley, G. Breen, J. R. I. Coleman, A. M. Dale, M. F. Dennis, N. C. Feeny, C. E. Franz, M. E. Garrett, C. F. Gillespie, G. Guffanti, M. A. Hauser, S. M. J. Hemmings, T. Jovanovic, N. A. Kimbrel, W. S. Kremen, B. R. Lawford, M.W. Logue, A. Lori, M. J. Lyons, J. Maples-Keller, M. R. Mavissakalian, R.E. McGlinchey, D. Mehta, R. Mellor, W. Milberg, M. W. Miller, C. P. Morris, M. S. Panizzon, K. J. Ressler, V. B. Risbrough, B. O. Rothbaum, P. Roy-Byrne, S. Seedat, A. K. Smith, J. S. Stevens, L. L. van den Heuvel, J. Voisey, R. M. Young, L. A. Zoellner, C. M. Nievergelt, and E.J. Wolf. 2021. “Examining Individual and Synergistic Contributions of PTSD and Genetics to Blood Pressure: A Trans-Ethnic Meta-Analysis.” Front Neurosci, 15, Pp. 678503.Abstract
    Growing research suggests that posttraumatic stress disorder (PTSD) may be a risk factor for poor cardiovascular health, and yet our understanding of who might be at greatest risk of adverse cardiovascular outcomes after trauma is limited. In this study, we conducted the first examination of the individual and synergistic contributions of PTSD symptoms and blood pressure genetics to continuous blood pressure levels. We harnessed the power of the Psychiatric Genomics Consortium-PTSD Physical Health Working Group and investigated these associations across 11 studies of 72,224 trauma-exposed individuals of European (n = 70,870) and African (n = 1,354) ancestry. Genetic contributions to blood pressure were modeled via polygenic scores (PGS) for systolic blood pressure (SBP) and diastolic blood pressure (DBP) that were derived from a prior trans-ethnic blood pressure genome-wide association study (GWAS). Results of trans-ethnic meta-analyses revealed significant main effects of the PGS on blood pressure levels [SBP: β = 2.83, standard error (SE) = 0.06, p < 1E-20; DBP: β = 1.32, SE = 0.04, p < 1E-20]. Significant main effects of PTSD symptoms were also detected for SBP and DBP in trans-ethnic meta-analyses, though there was significant heterogeneity in these results. When including data from the largest contributing study - United Kingdom Biobank - PTSD symptoms were negatively associated with SBP levels (β = -1.46, SE = 0.44, p = 9.8E-4) and positively associated with DBP levels (β = 0.70, SE = 0.26, p = 8.1E-3). However, when excluding the United Kingdom Biobank cohort in trans-ethnic meta-analyses, there was a nominally significant positive association between PTSD symptoms and SBP levels (β = 2.81, SE = 1.13, p = 0.01); no significant association was observed for DBP (β = 0.43, SE = 0.78, p = 0.58). Blood pressure PGS did not significantly moderate the associations between PTSD symptoms and blood pressure levels in meta-analyses. Additional research is needed to better understand the extent to which PTSD is associated with high blood pressure and how genetic as well as contextual factors may play a role in influencing cardiovascular risk.

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