Publications

2020
William E Allen, Han Altae-Tran, James Briggs, Xin Jin, Glen McGee, Rumya Raghavan, Andy Shi, Mireille Kamariza, Nicole Nova, Albert Pereta, Chris Danford, Amine Kamel, Patrik Gothe, Evrhet Milam, Jean Aurambault, Thorben Primke, Claire Li, Josh Inkenbrandt, Tuan Huynh, Evan Chen, Christina Lee, Michael Croatto, Helen Bentley, Wendy Lu, Robert Murray, Mark Travassos, John Openshaw, Brent Coull, Casey Greene, Ophir Shalem, Gary King, Ryan Probasco, David Cheng, Ben Silbermann, Feng Zhang, and Xihong Lin. 2020. “Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States.” medRxiv. Publisher's VersionAbstract
Despite social distancing and shelter-in-place policies, COVID-19 continues to spread in the United States. A lack of timely information about factors influencing COVID-19 spread and testing has hampered agile responses to the pandemic. We developed How We Feel, an extensible web and mobile application that aggregates self-reported survey responses, to fill gaps in the collection of COVID-19-related data. How We Feel collects longitudinal and geographically localized information on users’ health, behavior, and demographics. Here we report results from over 500,000 users in the United States from April 2, 2020 to May 12, 2020. We show that self- reported surveys can be used to build predictive models of COVID-19 test results, which may aid in identification of likely COVID-19 positive individuals. We find evidence among our users for asymptomatic or presymptomatic presentation, as well as for household and community exposure, occupation, and demographics being strong risk factors for COVID-19. We further reveal factors for which users have been SARS-CoV-2 PCR tested, as well as the temporal dynamics of self- reported symptoms and self-isolation behavior in positive and negative users. These results highlight the utility of collecting a diverse set of symptomatic, demographic, and behavioral self- reported data to fight the COVID-19 pandemic.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThe How We Feel Project is a non-profit corporation. Funding and in-kind donations for the How We Feel Project came from Ben and Divya Silbermann, Feng Zhang and Yufen Shi, Lore Harp McGovern, David Cheng, Ari Azhir, and Kyung H. Yoon, and the Bill & Melinda Gates Foundation. X.L. acknowledges support from Harvard University and NCI R35-CA197449-05. F.Z. is supported by the Howard Hughes Medical Institute, the McGovern Foundation, and James and Patricia Poitras and the Poitras Center.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The How We Feel application was approved as exempt by the Ethical & Independent Review Services LLP IRB (Study ID: 20049 - 01). The analysis of HWF data was also approved as exempt by Harvard University Longwood Medical Area IRB (Protocol #: IRB20-0514) and the Broad Institute of MIT and Harvard IRB (Protocol #: EX-1653). Informed consent was obtained from all users and the data were collected in de-identified form.All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesThis work used data from the How We Feel project (http://www.howwefeel.org/). The software used in analysis will be made available on Github upon final publication of the paper. Researchers with IRB approval to perform research involving human subjects can apply to obtain access to data used in the analysis.
2019
Xin Jin, Sean K Simmons, Amy X Guo, Ashwin S Shetty, Michelle Ko, Lan Nguyen, Elise B Robinson, Paul Oyler, Nathan Curry, Giulio Deangeli, Simona Lodato, Joshua Z Levin, Aviv Regev, Feng Zhang, and Paola Arlotta. 2019. “In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with Autism risk genes.” bioRxiv. bioRxiv PreprintAbstract
The thousands of disease risk genes and loci identified through human genetic studies far outstrip our current capacity to systematically study their functions. New experimental approaches are needed for functional investigations of large panels of genes in a biologically relevant context. Here, we developed a scalable genetic screen approach, in vivo Perturb-Seq, and applied this method to the functional evaluation of 35 autism spectrum disorder (ASD) de novo loss-of-function risk genes. Using CRISPR-Cas9, we introduced frameshift mutations in these risk genes in pools, within the developing brain in utero, and then performed single-cell RNA-Seq in the postnatal brain. We identified cell type-specific gene signatures from both neuronal and glial cell classes that are affected by genetic perturbations and pointed at elements of both convergent and divergent cellular effects across this cohort of ASD risk genes. In vivo Perturb-Seq pioneers a systems genetics approach to investigate at scale how diverse mutations affect cell types and states in the biologically relevant context of the developing organism.
2018
E. J. Dennis, M. Dobosiewicz, X. Jin, L. B. Duvall, P. S. Hartman, C. I. Bargmann, and L. B. Vosshall. 2018. “A natural variant and an engineered mutation in a GPCR promote DEET resistance in C. elegans.” Nature, 562, Pp. 119. BioRxiv Preprint
He Liu, Wenxing Yang, Taihong Wu, Fengyun Duan, Edward Soucy, Xin Jin, and Yun Zhang. 2018. “Cholinergic Sensorimotor Integration Regulates Olfactory Steering.” Neuron, 97, 2, Pp. 390 - 405.e3. Publisher's Version
2016
X. Jin, N. Pokala, and C. I. Bargmann. 2016. “Distinct circuits for the formation and retrieval of an imprinted olfactory memory.” Cell, 164, Pp. 632-43. Publisher's VersionAbstract

Memories formed early in life are particularly stable and influential, representing privileged experiences that shape enduring behaviors. We show that exposing newly hatched C. elegans to pathogenic bacteria results in persistent aversion to those bacterial odors, whereas adult exposure generates only transient aversive memory. Long-lasting imprinted aversion has a critical period in the first larval stage and is specific to the experienced pathogen. Distinct groups of neurons are required during formation (AIB, RIM) and retrieval (AIY, RIA) of the imprinted memory. RIM synthesizes the neuromodulator tyramine, which is required in the L1 stage for learning. AIY memory retrieval neurons sense tyramine via the SER-2 receptor, which is essential for imprinted, but not for adult-learned, aversion. Odor responses in several neurons, most notably RIA, are altered in imprinted animals. These findings provide insight into neuronal substrates of different forms of memory, and lay a foundation for further understanding of early learning.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. El Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann. 2016. “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging.” Biomed Opt Express, 7, Pp. 855-69. Publisher's VersionAbstract

Multifocus microscopy (MFM) allows high-resolution instantaneous three-dimensional (3D) imaging and has been applied to study biological specimens ranging from single molecules inside cells nuclei to entire embryos. We here describe pattern designs and nanofabrication methods for diffractive optics that optimize the light-efficiency of the central optical component of MFM: the diffractive multifocus grating (MFG). We also implement a "precise color" MFM layout with MFGs tailored to individual fluorophores in separate optical arms. The reported advancements enable faster and brighter volumetric time-lapse imaging of biological samples. In live microscopy applications, photon budget is a critical parameter and light-efficiency must be optimized to obtain the fastest possible frame rate while minimizing photodamage. We provide comprehensive descriptions and code for designing diffractive optical devices, and a detailed methods description for nanofabrication of devices. Theoretical efficiencies of reported designs is approximately 90% and we have obtained efficiencies of > 80% in MFGs of our own manufacture. We demonstrate the performance of a multi-phase MFG in 3D functional neuronal imaging in living C. elegans.

2011
J. Z. Long, M. LaCava, X. Jin, and B. F. Cravatt. 2011. “An anatomical and temporal portrait of physiological substrates for fatty acid amide hydrolase.” J Lipid Res, 52, Pp. 337-44. Publisher's VersionAbstract

Fatty acid amide hydrolase (FAAH) regulates amidated lipid transmitters, including the endocannabinoid anandamide and its N-acyl ethanolamine (NAE) congeners and transient receptor potential channel agonists N-acyl taurines (NATs). Using both the FAAH inhibitor PF-3845 and FAAH(-/-) mice, we present a global analysis of changes in NAE and NAT metabolism caused by FAAH disruption in central and peripheral tissues. Elevations in anandamide (and other NAEs) were tissue dependent, with the most dramatic changes occurring in brain, testis, and liver of PF-3845-treated or FAAH(-/-) mice. Polyunsaturated NATs accumulated to very high amounts in the liver, kidney, and plasma of these animals. The NAT profile in brain tissue was markedly different and punctuated by significant increases in long-chain NATs found exclusively in FAAH(-/-), but not in PF-3845-treated animals. Suspecting that this difference might reflect a slow pathway for NAT biosynthesis, we treated mice chronically with PF-3845 for 6 days and observed robust elevations in brain NATs. These studies, taken together, define the anatomical and temporal features of FAAH-mediated NAE and NAT metabolism, which are complemented and probably influenced by kinetically distinguishable biosynthetic pathways that produce these lipids in vivo.

X. Jin, C. Uttamapinant, and A. Y. Ting. 2011. “Synthesis of 7-aminocoumarin by Buchwald-Hartwig cross coupling for specific protein labeling in living cells.” Chembiochem, 12, Pp. 65-70. Publisher's VersionAbstract

We report the synthesis of a pH-insensitive blue fluorophore, 7-aminocoumarin, by using palladium- catalyzed Buchwald–Hartwig cross coupling. 7-Aminocoumarin can be used to tag recombinant proteins on the cell surface and inside living cells through PRIME (probe incorporation mediated by enzymes), and unlike 7-hydroxycoumarin, can be visualized in acidic organelles such as endosomes.

2010
J. Z. Long, X. Jin, A. Adibekian, W. Li, and B. F. Cravatt. 2010. “Characterization of tunable piperidine and piperazine carbamates as inhibitors of endocannabinoid hydrolases.” J Med Chem, 53, Pp. 1830-42. Publisher's VersionAbstract

Monoacylglycerol lipase (MAGL) and fatty acid amide hydrolase (FAAH) are two enzymes from the serine hydrolase superfamily that degrade the endocannabinoids 2-arachidonoylglycerol and anandamide, respectively. We have recently discovered that MAGL and FAAH are both inhibited by carbamates bearing an N-piperidine/piperazine group. Piperidine/piperazine carbamates show excellent in vivo activity, raising brain endocannabinoid levels and producing CB1-dependent behavioral effects in mice, suggesting that they represent a promising class of inhibitors for studying the endogenous functions of MAGL and FAAH. Herein, we disclose a full account of the syntheses, structure-activity relationships, and inhibitory activities of piperidine/piperazine carbamates against members of the serine hydrolase family. These scaffolds can be tuned for MAGL-selective or dual MAGL-FAAH inhibition by the attachment of an appropriately substituted bisarylcarbinol or aryloxybenzyl moiety, respectively, on the piperidine/piperazine ring. Modifications to the piperidine/piperazine ring ablated inhibitory activity, suggesting a strict requirement for a six-membered ring to maintain potency.

2009
J. Z. Long, D. K. Nomura, R. E. Vann, D. M. Walentiny, L. Booker, X. Jin, J. J. Burston, L. J. Sim-Selley, A. H. Lichtman, J. L. Wiley, and B. F. Cravatt. 2009. “Dual blockade of FAAH and MAGL identifies behavioral processes regulated by endocannabinoid crosstalk in vivo.” Proc Natl Acad Sci U S A, 106, Pp. 20270-5. Publisher's VersionAbstract

Delta(9)-tetrahydrocannabinol (THC), the psychoactive component of marijuana, and other direct cannabinoid receptor (CB1) agonists produce a number of neurobehavioral effects in mammals that range from the beneficial (analgesia) to the untoward (abuse potential). Why, however, this full spectrum of activities is not observed upon pharmacological inhibition or genetic deletion of either fatty acid amide hydrolase (FAAH) or monoacylglycerol lipase (MAGL), enzymes that regulate the two major endocannabinoids anandamide (AEA) and 2-arachidonoylglycerol (2-AG), respectively, has remained unclear. Here, we describe a selective and efficacious dual FAAH/MAGL inhibitor, JZL195, and show that this agent exhibits broad activity in the tetrad test for CB1 agonism, causing analgesia, hypomotilty, and catalepsy. Comparison of JZL195 to specific FAAH and MAGL inhibitors identified behavioral processes that were regulated by a single endocannabinoid pathway (e.g., hypomotility by the 2-AG/MAGL pathway) and, interestingly, those where disruption of both FAAH and MAGL produced additive effects that were reversed by a CB1 antagonist. Falling into this latter category was drug discrimination behavior, where dual FAAH/MAGL blockade, but not disruption of either FAAH or MAGL alone, produced THC-like responses that were reversed by a CB1 antagonist. These data indicate that AEA and 2-AG signaling pathways interact to regulate specific behavioral processes in vivo, including those relevant to drug abuse, thus providing a potential mechanistic basis for the distinct pharmacological profiles of direct CB1 agonists and inhibitors of individual endocannabinoid degradative enzymes.