BMS Journal Club

2018-19 Journal Club Schedule

Dates: September 6, 2018 - June 6, 2019

Journal Club Chairs: Bruce Wang, MD and Tien Peng, MD
Day/Time: Thursdays, 12:00-1:00 p.m. except as noted
Location: N-225, Parnassus & videoconferenced to Room MH-1405, Mission Bay.
Links to the live stream and recorded video are in the sidebar.


**If you're watching the video stream at Mission Bay and would like to ask the speaker a question, send a DM via Twitter to @UCSF_BMS_JC and someone at Parnassus will ask your question for you.


See the BMS Journal Club Archives in the right sidebar for past journal club descriptions and recordings.


September 6, 2018

David Raleigh, PhD, MD (Faculty)
"Patch(ing) together the structure and function of the Hedgehog pathway"
Gong, X. et al. Sturctural basis for the recognition of Sonic Hedgehog by human Patched 1. Science 10.1126/science.aas8935. (2018).

Lauren McHenry (Student)
"Don't drink the Kool-Aid: Suppression of antitumor T cell immunity by the oncometabolite (R)-2-hydroxyglutarate."
Bunse, L., Pusch, S., Bunse, T., Sahm, F., Sanghvi, K., Friedrich, M., et al. (2018). Suppression of antitumor T cell immunity by the oncometabolite (R)-2-hydroxyglutarate. Nature Medicine, 1–25.
Coaches: William Weiss and Hidheo Okada


September 13, 2018

Elliott Sherr, MD, PhD (Faculty)
"Uncrossed wires of crowns and pyramids"
Marsh, A.P. et al. Mutations in DCC cause isolated agenesis of the corpus callosum with incomplete penetrance. Nature Genetics 49(4), 511-514. (2017).

Donovan Trinidad (Student)
Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding
Sibener, Leah V., et al. Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding. Cell 174(3), 672-687. (2018)
Coaches: Joel Ernst and Jason Cyster


September 20, 2018

James Rubenstein, MD, PhD (Faculty)
"Novel Role of S1P1 in Tumor Immune Escape"
Chongsathidkiet, P. et al. Sequestration of T cells in bone marrow in the setting of glioblastoma and other intracranial tumors. Nature Medicine 24, 1459-1468. (2018).

Rachel Nakagawa (Student)
"Run run as fast as you can, you can't catch me I'm a cancer cell: Disseminated cancer cells employ pericyte-like spreading for metastatic colonization"
Ekrem Emrah, E. et al. Pericyte-like spreading by disseminated cancer cells activates YAP and MRTF for metastatic colonization. Nature Cell Biology 20, 966-978. (2018).
Coaches: Zena Werb and Diane Barber


September 27, 2018

Martin Kampmann, PhD (Faculty)
"A wrinkle in time: RNA velocity of single cells"
La Manno, G. et al. RNA velocity of single cells. Nature 560, 494-498. (2018).

Naznin Jahan (Student)
"Epigenetic regulation of brain region-specific microglia clearance activity"
Ayata, P. et al. Epigenetic regulation of brain region-specific microglia clearance activity. Nature Neuroscience 21, 1049-1060. (2018).
Coaches: Eric Huang and Mercedes Paredes


October 4, 2018

Raymond Swanson, MD (Faculty)
"Superoxide to the Rescue!"
Hervera, A. Reactive Oxygen species regulate axonal regeneration through the release of exosomal NADPH oxidase 2 complexes into injured axons. Nat Cell Biol 20(3), 307-319. (2018).

Denise Allen (Student)
"When ROBOts Take Over Neurogenesis: Evolution of Cortical Neurogenesis in Amniotes Controlled by Robo Signaling Levels."
Cárdenas, A. et al. Evolution of Cortical Neurogenesis in Amniotes Controlled by Robo Signaling Levels. Cell 174, 590-606.e21. (2018).
Coaches: Tomasz Nowakowski and Alex Pollen


October 11, 2018

Andy Chang, PhD (Faculty)
"Plants fight back with a nervous system-like pathway"
Toyota, M. et al. Glutamate triggers long-distance, calcium-based plant defense signaling. Science 361(6407), 1112-1115. (2018).

Catherine Tan (Student)
"Cancer nuclei should relax: Too much tension promotes DNA damage"
Xi, Y. et. Al. Nuclear rupture at sites of high curvature compromises retention of DNA repair factors. Journal of Cell Biology, epub. (2018).
Coaches: Todd Nystul and Jay Debnath


October 18, 2018

Stephen Floor, PhD (Faculty)
"One of these things is not like the other: Heritable variation in gene expression in clonal cell populations"
Shaffer, S.M. et al. Memory sequencing reveals heritable single cell gene expression programs assoicated with distinct cellular behaviors. bioRxiv, epub. (2018).

Casey Burnett (Student)
"Exosomal PD-L1 contributes to immunosuppression and is associated with anti-PD-1 response"
Chen, G. et al. Exosomal PD-L1 contributes to immunosuppression and is associated with anti-PD-1 response. Nature 560, 382-386. (2018).
Coaches: Matt Spitzer and Melissa Reeves


October 25, 2018

David Solomon, MD, PhD (Faculty)
"Cohesin is awesome and also functions as a critical regulator of chromatin architecture"
Rao, S.S.P. et al. Cohesin loss eliminates all loop domains. Cell 171(2), 305-320. (2017).

Lindsey Pieper (Student)
"Resistance is Futile: A Gut Bacterium-Derived Metabolite Mediates  Colonization Resistance to Salmonella Infection"
Jacobson, A. et al. A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection. Cell Host Microbe 24, 296–307.e7. (2018).
Coaches: Joanne Engel and Peter Turnbaugh


November 1, 2018

Sophie Dumont, PhD (Faculty)
"Chromosome segregation fidelity: The tissue context matters"
Knouse, K.A., Lopez K.E., Bachofner, M. and A. Amon. Chromosome Segregation Fidelity in Epithelia Requires Tissue Architecture. Cell 175 (1), 200-211. (2018).

Kevin Wilkins (Student)
"It Takes Two to Translate: co-translational assembly of protein complexes in eukaryotes"
Shiber, A. et al. Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome profiling. Nature 561, 268-272. (2018).
Coaches: Stephen Floor and Martin Kampmann


November 8, 2018

Xianhua Piao, MD, PhD (Faculty)
"Nature vs Nurture: How Ontogeny and Environment Shape Microglial Identity"
Bennett, F.C. et al. A combination of ontogeny and CNS environment establishes microglial identity. Nueron 98(6), 1170-1183.e8. (2018).

Yuhao Wang (Student)
"Notch an Advantage for Cancer: How Notch3 and β-catenin regulate persistence in lung cancer cells"
Arasada, R.R. et al. Notch3-dependent β-catenin signaling mediates EGFR TKI drug persistence in EGFR mutant NSCLC. Nature Communications 9(3198): 1-16.(2018).
Coaches: Michael McManus and Eric Collisson


November 15, 2018

Maxence Nachury, PhD (Faculty)
"Microtubule dynamics: no longer just at the ends"
Vemu, A. Severing enzymes amplify microtubule arrays through lattice GTP-tubulin incorporation. Science 361(6404), eaau1504. (2018).

Camillia Azimi (Student)
"Are you in or are you out? Unique pattern of neutrophil migration and function during tumor progression"
Patel, S. et al. Unique pattern of neutrophil migration and function during tumor progression. Nature Immunology 19, 1236–1247. (2018).
Coaches: Kole Roybal and Melissa Reeves


November 29, 2018

Isha Jain, PhD (Faculty)
"Contracting Spleens and Evolutionary Adaptations to Deep Diving"
Ilardo, M.A. et al. Physiological and genetic adaptations to diving in sea nomads. Cell 173(3), 569-580. (2018).

Isobel Hawes (Student)
"Antigen-specific antibody Fc glycosylation enhances humoral immunity via the recruitment of complement"
Lofano, G. et al. Antigen-specific antibody Fc glycosylation enhances humoral immunity via the recruitment of complement. Science Immunology 3, eaat7796. (2018).
Coaches: Michael Wilson and Satish Pillai


December 6, 2018

Edward Hsiao, MD, PhD (Faculty)
"Ow, that hurts! How cell interactions contribute to abnormal wound healing and tissue fibrosis"
Shook, B.A. et al. Myofibroblast proliferation and heterogeneity are supported by macrophages during skin repair. Science 362(6417), eaar2971. (2018).

Maxine Nelson (Student)
"Zombie Apocalypse: Senescent Cells Lead to Neurodegeneration"
Bussian, T. J. et al. Clearance of senescent glial cells prevents tau-dependent pathology and cognitive decline. Nature 562, 578–582. (2018).
Coaches: Eric Huang and Lea Grinberg


January 17, 2019

Ryan Ziffra (Student)
"Buzz or Breakthrough?: Cerebral Organoids as a Model for Human Cortical Development"
Amiri, A. et al. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science (80- ). 2018;362(6420):eaat6720.
Coaches: Nadav Ahituv and Tomasz Nowakowski


January 24, 2019

Matthew Spitzer (Faculty)
“The mutants in us all”
Martincorena, et al. Somatic mutant clones colonize the human esophagus with age. Science (2018).

Nicholas Stevers (Student)
"Straight outta SVZ: Determining the anatomical and cellular origins of Glioblastoma."
Lee, J. H., et al. Human glioblastoma arises from subventricular zone cells with low-level driver mutations. Nature 560, 243-247 (2018).
Coaches: Joseph Costello and Joanna Phillips


January 31, 2019

Nour Abdulhay (Student)
"JARID2 Functions as a Tumor Suppressor in Myeloid Neoplasms by Repressing Self-Renewal in Hematopoietic Progenitor Cells"
Celik, H. et al. JARID2 Functions as a Tumor Suppressor in Myeloid Neoplasms by Repressing Self-Renewal in Hematopoietic Progenitor Cells. Cancer Cell. 34(5):741-756.
Coaches: Alex Pollen and Luke Gilbert

Emmy Li (Student)
"Reversal of ApoE4-induced recycling block as a novel prevention approach for Alzheimer’s disease"
Xian, Xunde, et al. Reversal of ApoE4-induced recycling block as a novel prevention approach for Alzheimer’s disease. eLife 2018;7:e40048
Coaches: Yadong Huang and Martin Kampmann


February 7, 2019

Joel Ernst (Faculty)
"How does the Mosquito Microbiome Modulate Misery?"
Wu, Pa, et al. “A Gut Commensal Bacterium Promotes Mosquito Permissiveness to Arboviruses.” Cell Host & Microbe, 2018 Nov 28. pii: S1931-3128(18)30561-4. doi: 10.1016/j.chom.2018.11.004.

Fauna Yarza (Student)
"What a drag: Vibrio cholerae motility exerts drag force to impede attack by the bacterial predator Bdellovibrio bacteriovorus"
Duncan MC et al. Vibrio cholerae motility exerts drag force to impede attack by the bacterial predator Bdellovibrio bacteriovorus, Nature Communications 9:4757.
Coaches: Seemay Chou and Peter Turnbaugh


February 14, 2019

Tyler Fair (Student)
"Just add more gRNAs:  Mapping Gene Regulation via Multiplexed Cellular Genetic Screens"
Gasperini, M. et al. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. 2019, Cell 176, 1–14
Coaches: Luke Gilbert and Vijay Ramani

Irene Chen (Student)
"MDMA Turning Up the PDA: A Conserved Role for Serotonergic Neurotransmission in Mediating Social Behavior in Octopus"
Edsinger, Eric & Dölen, Gül. (2018). A Conserved Role for Serotonergic Neurotransmission in Mediating Social Behavior in Octopus. Current Biology. 28. 10.1016/j.cub.2018.07.061.
Coaches: Melanie Ott and Josh Woolley


February 21, 2019

Jennifer Umhoefer (Student)
"Immune genes are primed for robutranscription by proximal long noncoding RNAs located in nuclear compartments"
Fanucchi, S. et al. Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments. Nature Genetics 51: 138-150 (2019).
Coaches: Abigail Buchwalter, Stephen Floor

Donovan Trinidad (Student)
"How Am I Supposed to Infect with No Air?: Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition"
Litvak, Litvak, Y., Mon, Nguyen, H., Chanthavixay, G., Liou, M., ... Bäumler, Y. (2019). Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition. Cell Host and Microbe, 25(1), 128-139.e5.
Coaches: Peter Turnbaugh, Suzanne Noble


February 28, 2019

Cody Mowery (student)
Akkaya, B. et al. Regulatory T cells mediate specific suppression by depleting peptide–MHC class II from dendritic cells. Nature Immunology 20, 218–231 (2019).
Coaches: Qizhi Tang and Michael Rosenblum

 

Iowis Zhu (student)
“A Crucial Catch: Catch and Slip Bonds in T-cell Thymic Selection”
Hong, Jinsung, et al. A TCR mechanotransduction signaling loop induces negative selection in the thymus. Nature Immunology. 19:1379-1390. (2018)
Coaches: Kole Roybal and Ron Vale

 


March 7, 2019

Marissa Chou (Student)
"Eos inphil-tration: DPP4 inhibition enhances anti-tumor response"
Hollande, C. et al. Inhibition of the dipeptidyl peptidase DPP4 (CD26) reveals IL-33-dependent eosinophil-mediated control of tumor growth. Nature Immunology 20, 257–264 (2019).
Coaches: Jason Cyster and Ari Molofsky

Darwin Kwok (Student)
"Sizing Up Senescence: Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence"
Neurohr et al., 2019, Cell 176, 1083–1097 February 21, 2019 ª 2019 The Author(s). Published by Elsevier Inc.
Coaches: Fred Chang and Andrew Brack


March 14, 2019

Adam Wade-Vallance (Student)
“Shaping of infant B cell receptor repertoires by environmental factors and infectious disease”
Nielsen SCA et. al. Shaping of infant B cell receptor repertoires by environmental factors and infectious disease. Sci Transl Med. 2019 Feb 27;11(481).
Coaches: Jason Cyster and Chris Allen

Alyssa Indart (Student)
"On pi day, we enjoy pie flavor diversity; why not also Treg TCR repertoire diversity”
Ahmadzadeh,M. et al. Tumor-infiltrating human CD4+ regulatory T cells display a distinct TCR epertoire and exhibit tumor and neoantigen reactivity. Science Immunology. 4,eaa04310 (2019)
Coaches: Arthur Weiss and Joanna Phillips


March 21, 2019

Kyle Kisor (Student)
"Targeting Wnt/β-catenin pathway driven colorectal cancer via Bcl9/9l"
David Gay et al. Loss of BCL9/9l suppresses Wnt driven tumourigenesis in models that recapitulate human cancer. Nature Communications 10:723. (2019)
Coaches: Diane Barber and Todd Nystul

Jiapei Chen (Student)
"Deciphering the microglia transcriptome"
Li, Q. et al. Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing. Neuron 101, 207-223. (2019).
Coaches: Eric Huang and Tomasz Nowakowski


March 28, 2019

Tara McIntyre (Student)
"Oxygen: The Puppet Master?"
Chakraborty et al. Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate. Science 363, 1217–1222 (2019).
Coaches: Mark Ansel and Dan Lim

Karen Chan (Student)
"Considerations for CRISPR-Cas9 Therapies: Identification of preexisting adaptive immunity to Cas9 proteins in humans"
Charlesworth, C et al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nature Medicine 25, 242-248 (2019).
Coaches: Chris Allen and Joseph Bondy-Denomy


April 4, 2019

Abrar Choudhury (Student)
"The Devil is in the Details"
Kosack, L., Wingelhofer, B., Popa, A., Orlova, A., Agerer, B., Vilagos, B., Majek, P., Parapatics, K., Lercher, A., Ringler, A., et al. (2019). The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease. Cancer Cell 35, 125-139.
Coaches: David Raleigh and William Weiss

Marci Rosenberg (Student)
"Stay off the lawn! Herbicide enhances astrocyte pathogenicity via activation of the unfolded protein response"
Wheeler, Michael A. et al. (2019) Environmental control of astrocyte pathogenic activities in CNS inflammation. Cell 176, 581-596.. doi:    10.1016/j.cell.2018.12.012
Coaches: Anna Molofsky and Martin Kampmann


April 25, 2019

Gokul Ramadoss (Student)
"C/G-to-T/A base editor Tauses siAnifiTant Aenome-wide off-tarAet effeTts"
Zuo, E. et al. (2019). Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science. doi:10.1126/science.aav9973
Coaches: Bruce Conklin and Luke Gilbert


Saumya Bollam (Student)
"PTEN doesn't need that phospho-helmet!: Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair"
Ma, J. et al. (2019). Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell. doi: 10.1016/j.ccell.2019.01.020
Coaches: Russ Pieper and Joanna Phillips


May 2, 2019

Benjamin Wheeler (Student)
"Estradiol-ing in on HIV Latency: Estrogen receptor-1 is a key regulator of HIV-1 latency that imparts gender sex-specific restrictions on the latent reservoir"
Estrogen receptor-1 is a key regulator of HIV-1 latency that imparts gender-specific restrictions on the latent reservoir
Biswajit Das, Curtis Dobrowolski, Benjamin Luttge, Saba Valadkhan, Nicolas Chomont, Rowena Johnston, Peter Bacchetti, Rebecca Hoh, Monica Gandhi, Steven G. Deeks, Eileen Scully, Jonathan Karn
Proceedings of the National Academy of Sciences Aug 2018, 115 (33) E7795-E7804; DOI: 10.1073/pnas.1803468115

Coaches:Nadia Roan and Jason Cyster

Nick Mroz (Student)
"An Unexpected Source of IL-2: ILC3-derived Interleukin-2 Supports Intestinal Tregs and Gut Homeostasis"
Zhou, Lei et al. Innate lymphoid cells support regulatory T cells in the intestine through interleukin-2. Nature (2019). doi: 10.1038/s41586-019-1082-x
Coaches: Ari Molofsky and Michael Rosenblum


May 9, 2019

Rachel DeBarge (Student)
"Efficiency is just intelligent laziness: How migrating immune cells choose the path of least resistance"
Renkawitz, J. et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature (2019). doi:10.1038/s41586-019-1087-5
Coaches: Matt Spitzer and Max Krummel

Julie Cole (Student)
"
CAR T Cell-Driven Trogocytosis: Another Mechanism of Tumor Escape?"
Hamieh M, Dobrin A, Cabriolu A, et al. CAR T cell trogocytosis and cooperative killing regulate tumour antigen escape. Nature. doi:10.1038/s41586-019-1054-1
Coaches: Kole Roybal and Matthew Spitzer


May 16, 2019

Megan Montoya (Student)
"Genomic Instability causes Female-Biased Embryonic Death"
McNairn, AJ, Chuang, C, Bloom JC, Wallace MD, & Schimenti JC. (2019). Female-biased embryonic death from inflammation induced by genomic instability. Nature. 567: 105-108.
Coaches: Adrian Erlebacher and Scott Kogan

Brian Woo (Student)
"Lesser of two evils": Pol θ Error-Prone Replication Protects against Skin Cancers
Yoon, J. H., McArthur, M. J., Park, J., Basu, D., Wakamiya, M., Prakash, L., & Prakash, S. (2019). Error-Prone Replication through UV Lesions by DNA Polymerase θ Protects against Skin Cancers. Cell, 176(6), 1295-1309.e1215. doi:10.1016/j.cell.2019.01.023
Coaches: Hani Goodarzi and Vijay Ramani
 


May 23, 2019

Carlos Zuazo (Student)
"Into the belly of the beast:  TGFβ/BMP immune signaling alters C. elegans gut microbiota"
Berg M et al. TGFβ/BMP immune signaling affects abundance and function of C. elegans gut commensals. Nature Communications 10, Article number: 604 (2019).
Coaches: Dengke Ma and Kaveh Ashrafi

Yewande Alabi (Student)
“Aging and the nucleolus: How CBX4 counteracts cellular senescence via maintenance of nucleolar homeostasis”
Ren, X. et al. Maintenance of Nucleolar Homeostasis by CBX4 Alleviates Senescence and Osteoarthritis. Cell Reports. 2019 Mar 26;26(13):3643-3656.e7. doi: 10.1016/j.celrep.2019.02.088.
Coaches: Abigail Buchwalter and Barbara Panning


May 30, 2019

Bahar Zirak (Student)
"TAMs send their regards: HIF-1a stabilizing lncRNA from TAMs regulates aerobic glycolysis of breast cancer cells."
Chen, F. et al. Extracellular vesicle-packaged HIF-1α-stabilizing lncRNA from tumour-associated macrophages regulates aerobic glycolysis of breast cancer cells. Nature Cell Biology. 2019. doi: 10.1038/s41556-019-0299-0
Coaches: Hani Goodarzi and Isha Jain

Niko Eng (Student)
"Visualizing DNA folding and RNA in embryos at single-cell resolution
Visualizing DNA folding and RNA in embryos at single-cell resolution, Nature 568, 49-54 (2019), Leslie J. Mateo, Sedona E. Murphy... Carly A. Walker, Alistair N. Boettiger
Coaches: Yin Shen and Elphege Nora


June 6, 2019

Jackson Gardner (Student)
TBA

Priscila Munoz Sandoval (Student)
"Bugs in your lungs: Dysregulated Lung Commensal Bacteria Promote Pulmonary Fibrosis"
Yang D, Chen X, Wang J, Lou Q, Lou Y, Li L, et al. Dysregulated Lung Commensal Bacteria Drive Interleukin-17B Production to Promote Pulmonary Fibrosis through Their Outer Membrane Vesicles. Immunity. 2019;50(3):692-706.e7
Coaches: Tiffany Scharschmidt and Anthony Shum