BMS Journal Club

2017-18 Journal Club Schedule

Dates: September 2017-June 2018

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.


January 11, 2018

Kamir Hiam (Student)
"How to Prepare for the Plague: A Systems Biologist’s Guide to Immunity"
Kadoki, M. et al. Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues. Cell, 171 (2), 398 - 413. (2017).
Coaches: Matthew Spitzer and Mark Ansel

Mission Bay videoconference: MH-1405


January 18, 2018

Elise Wolf (Student)
"Keeping transposons in LINE"
Liu, N. et al. Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Nature, 553, 228-232. (2018).
Coaches: Jason Cyster and Hiten Madhani

Sara Sunshine (Student)
"Scrambled Eggs: When Adaptations Alter Vaccine Efficacy"
Zost, S.J. et al. Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies elicited by egg-adapted vaccine strains. Proceedings of the National Academy of Sciences of the United States of America, 114 (47), 12578-12583. (2017).
Coaches: Shomyseh Sanjabi and Alan Frankel

Mission Bay videoconference: MH-1405


January 25, 2018

*Note: BMS Interview Day, Journal Club takes place at 5:00pm.

Diane Barber (Faculty)

"YAP YAP YAP - p53 and Hippo signaling converse for pancreatic cancer"
Mello, S. et al. A p53 Super-tumor Suppressor Reveals a Tumor Suppressive p53-Ptpn14-Yap Axis in Pancreatic Cancer. Cancer Cell 32, 460-473. (2017).​

Breanna Allen (Student)
"How the Macrophage Got Sued"
Özge, C. et al. Myeloid Cell-Derived Reactive Oxygen Species Induce Epithelial Mutagenesis. Cancer Cell, 32, 869–883. (2017).
Coaches: Matthew Spitzer and Lewis Lanier

Mission Bay videoconference: MH-1405


February 8, 2018

*Note: BMS Interview Day, Journal Club takes place at 5:00pm.

Kole Roybal (Faculty)

"Remote Control of Tumor Growth by the Bone Marrow"
Engblom, et al. Osteoblasts remotely supply lung tumors with cancer-promoting SiglecFhigh neutrophils. Science 358, 1147 (2017).​

Ramiro Patino (Student)
"Look what a surface made me (bacteria) do"
Hug I.,  Deshpande S., Sprecher K.S., Pfohl T., & Jenal, U. Second messenger-mediated tactile response by a bacterial rotary motor. Science, 358 (6362), 531-534. (2017).
Coaches: Joanne Engel and Oren Rosenberg

Mission Bay videoconference: MH-1405


February 15, 2018

Jiapei Chen (Student)
"When Radial Glial Fibers give Rad Guidance"
Jinnou, H. et al. Radial Glial Fibers Promote Neuronal Migration and Functional Recovery after Neonatal Brain Injury. Cell Stem Cell, 22(1), 128–137.e9. (2018).
Coaches: Adam Ferguson and Eric Huang

Devan Diwanji (Student)
"The Force Awakens (Nuclear Transport): Molecular mechanical stability and transmitted forces regulate YAP nuclear entry"
Elosegui-Artola, A. et al. Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores. Cell 171, 1397–1410.e14. (2017).
Coaches: Valerie Weaver and Natalia Jura

Mission Bay videoconference: MH-1405


February 22, 2018

Camille Simoneau (Student)
"Safety in mTOR: A genetic basis for protection against Zika"
Caires-Juniors, L.C. et al. Discordant congenital Zika syndrome twins show differential in vitro viral susceptibility of neural progenitor cells. Nature Communications, 9(475). (2018).
Coaches: Melanie Ott and Faranak Fattahi

Austin Hsu (Student)
"N.T. the N-Terminus"
Lehmann, L. et al. A Proteolytic Fragment of Histone Deacetylase 4 Protects the Heart from Failure by Regulating the Hexosamine Biosynthetic Pathway. Nature Medicine 24, 62–72. (2018).
Coaches: Saptarsi Haldar and Guo Huang

Mission Bay videoconference: MH-1405


March 1, 2018

Camillia Azimi (Student)
"Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism"
Mao, K. et al.  Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism. Nature, 554, 255–259. (2018).
Coaches: Ari Molofsky and Mark Ansel

Cassandra Burnett (Student)
"Engineering next generation CAR T-cells through intracellular domain modification"
Kagoya, Y. et al. A novel chimeric antigen receptor containing a JAK-STAT signaling domain mediates superior antitumor effects. Nature medicine, epub. (2018).
Coaches: Kole Roybal and Michael Rosenblum

Mission Bay videoconference: MH-1405


March 8, 2018

Karen Chan (Student)
"A Breath of Fresh Air: How Viral Infection Can Reshape the Lung Microenvironment"
Machiels, B. et al. A gammaherpesvirus provides protection against allergic asthma by inducing the replacement of resident alveolar macrophages with regulatory monocytes. Nature Immunology 18 (12): 1310-1320. (2017).
Coaches: Chris Allen and Erin Gordon

Irene Chen (Student)
"Stay Cultured: Gut Microbes Influence Efficacy of Immunotherapy"
Routy, B. et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359 (6371), 91-97. (2018).
Coaches: Lewis Lanier and Peter Turnbaugh

Mission Bay videoconference: MH-1405


March 15, 2018

Tyler Fair (Student)
Not a Gag: The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer
Pastuzyn, E. D. et al. The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer. Cell 172, 275–288.e18 (2018).
Coaches: Alex Pollen and Tomasz Nowakowski

Kristoffer Leon (Student)
"Maybe the Anti-Vaxxers are Right: How Dengue Vaccination can Enhance Disease"
Wang, T. T. et al. IgG antibodies to dengue enhanced for FcγRIIIA binding determine disease severity. Science 355, 395-398. (2017).
Coaches: Melanie Ott and Shomyseh Sanjabi

Mission Bay videoconference: MH-1405


March 22, 2018

Antonia Gallman (Student)
"NK Cells Recruit cDC1s to Tumors for Cancer Immune Control"
Böttcher, J. P. et al. NK Cells Stimulate Recruitment of cDC1 into the Tumor Microenvironment Promoting Cancer Immune Control. Cell, 172(5), 1022–1028.e14. (2018).
Coaches: Jason Cyster and Lewis Lanier

Mission Bay videoconference: MH-1405


March 29, 2018

Ian Boothby (Student)
"A simple Wnt circuit for maintaining stem cells in the lung"
Nabhn, A. et al. Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells. Science online pre-publication. (2018).
Coaches: Tien Peng and Zena Werb

Paul Wei (Student)
"Carpe Dentatum: Seize the Dentate"
Bui, A.D. et al. Dentate gyrus mossy cells control spontaneous convulsive seizures and spatial memory. Science. 359, 787-790. (2018).
Coaches: Jeanne Paz and Kevin Yackle

Mission Bay videoconference: MH-1405


April 5, 2018

Isobel Hawes (Student)
"Time heals all wounds: Circadian actin dynamics drive rhythmic fibroblast mobilization during wound healing."
Hoyle, N.P. et al. Circadian actin dynamics drive rythmic fibroblast mobilization during wound healing Sci. Transl. Med. 9, eaal2774. (2017).
Coaches: Diane Barber and Stephen Fancy

Kun Leng (Student)
"The epigenome gets old and forgets too"
Nativio, R. et al. Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease. Nature neuroscience. epub. (2018).
Coaches: Eric Huang and Bassem Al-Sady

Mission Bay videoconference: MH-1405


April 12, 2018

Elizabeth Hwang (Student)
"CRISPR Clue: discovering the source of dipeptide-repeat-protein neurotoxicity"
Kramer, N. J. et al. CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity. Nature Genetics. (2018).
Coaches: Daniel Lim and Martin Kampmann

David Shin (Student)
"Raiders of the Lost Arx: Searching for Lost Phenotypes After Deleting Ultraconserved Enhancers"
Dickel, D.E. et al. Ultraconserved Enhancers are Required for Normal Development. Cell 172(3): 491-499.e15 (2018).
Coaches: Nadav Ahituv, Yin Shen, and Alex Pollen

Mission Bay videoconference: MH-1405


April 19, 2018

Naznin Jahan (Student)
"Pericyte degeneration causes white matter dysfunction in the mouse central nervous system"
Montagne, A. et al. Pericyte degeneration causes white matter dysfunction in the mouse central nervous system. Nature Medicine 24, 326-337. (2018).
Coaches: Eric Huang and Dena Dubal

Kyle Kisor (Student)
"New approaches to treating K-RAS mutant cancers: Targeting the Riff c-Raf"
Sanclemente, M. et al. c-RAF Ablation Induces Regression of Advanced Kras/Trp 53 Mutant Lung Adenocarcinomas by a Mechanism Independent of MAPK Signaling. Cancer Cell, 33(2), 217-228. (2018).
Coaches: Diane Barber and Melissa Reeves

Mission Bay videoconference: MH-1405


April 26, 2018

Emmy Li (Student)
"There's more to the story: C9ORF72 haploinsufficiency can lead to neurodegeneration in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD"
Shi. Y. et al. “Haploinsufficiency Leads to Neurodegeneration in C9ORF72 ALS/FTD Human Induced Motor Neurons” Nature Medicine 24(3), 313–325. (2018).
Coaches: Martin Kampmann and Alex Pollen

Nicholas Stevers (Student)
"KRAS dimerization: Understanding the MEKanism of wild-type driven insensitivity"
Ambrogio, C. et al. KRAS Dimerization Impacts MEK Inhibitor Sensitivity and Oncogenic Activity of Mutant KRAS. Cell, 172(4), 857-868. (2018).
Coaches: Alejandro Sweet-Cordero and Allan Balmain

Mission Bay videoconference: MH-1405


May 3, 2018

Tara McIntyre (Student)
"Profiling follicular T cells in HIV infection"
Wendel, B.S. et al. The receptor repertoire and functional profile of follicular T cells in HIV-infected lymph nodes. Science Immunology, 3(22), eaan8884. (2018).
Coaches: Nadia Roan and Matt Spitzer

Catherine Tan (Student)
"The secrets of DNA loops revealed on camera: Real-time imaging of DNA loop extrusion by condensin"
Ganji, M. et al. Real-time imaging of DNA loop extrusion by condensin. Science, epub. (2018).
Coaches: Fred Chang and Stephen Floor

Mission Bay videoconference: MH-1405


May 10, 2018

Rachel Nakagawa (Student)
"Wrong-side out: Colorectal tumor spheres with inverted polarity drive peritoneal metastasis"
Zajac, O. et al. Tumor spheres with inverted polarity drive the formation of peritoneal metastases in patients with hypermethylated colorectal carcinomas. Nature Cell Biology. 20, 296-306. (2018).
Coaches: Diane Barber and Jeff Bush

Jennifer Umhoefer (Student)
"A global transcriptional network connecting noncoding mutations to changes in tumor gene expression."
Zhang, W. et al. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nature Genetics 50, 613-620. (2018).
Coaches: Robert Blelloch and Joseph Costello

Mission Bay videoconference: MH-1405


May 17, 2018

Maxine Nelson (Student)
"Dopamine-dependent toxic cascade and Parkinson's Disease"
Burbulla, L.F. et al. Dopamine oxidation mediates mitochondrial and lysosomal dysfunction in Parkinson's disease. Science 357(6357), 1255-1261. (2017).
Coaches: Martin Kampmann and Anita Sil

Kevin Wilkins (Student)
"Lost in Translation: how an untranslated 5’ extended mRNA isoform regulates kinetochore inactivation"
Chia, M. et al. Transcription of a 5’ extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter. eLife. 2017;6:e27420.
Coaches: Stephen Floor and Alex Pollen

Mission Bay videoconference: MH-1405


May 24, 2018

Lindsey Pieper (Student)
"When Friends Become Enemies: Tumorigenic Bacterial Biofilm Formation in Patients with Familial Adenomatous Polyposis"
Dejea, C. M. et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359(6375), 592–597 (2018).
Coaches: Peter Turnbaugh and Matthew Spitzer

Fauna Yarza (Student)
"Watch out, fellas: Male-killing toxin in a bacterial symbiont of Drosophila"
Harumoto, T. & Lemaitre, B. Male-killing toxin in a bacterial symbiont of Drosophila. Nature. (2018).
Coaches: Seemay Chou and Melanie Ott

Mission Bay videoconference: MH-1405


May 31, 2018

Yuhao Wang (Student)
"An EPIC1 Story of IncRNA, Myc, and Tumor Progression"
Wang, Z. et al. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer Cell 33 (4), 706-720.e9. (2018).
Coaches: Michael McManus and Eric Collisson

Ryan Ziffra (Student)
Open Your Mind: The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis.
de la Torre-Ubieta, L., Stein, J. L., Won, H., Opland, C. K., Liang, D., Lu, D., & Geschwind, D. H. The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis. Cell 172(1–2), 289–295.e18. (2018).
Coaches: Tomasz Nowakowski and Nadav Ahituv

Mission Bay videoconference: MH-1405


June 7, 2018

Donovan Trinidad (Student)
"Using CRISPR-Cas13 as a Viral Diagnostic Tool"
Myhrvold, C. et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science 360(6387), 444-448. (2018).
Coaches: Oren Rosenberg and Melanie Ott

Denise Allen (Student)
"Even RNA is Mettling in Neurogenesis: Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation"
Yoon, K.-J. et al. Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation. Cell 171, 877-889.e17. (2017).
Coaches: Tomasz Nowakowski and Stephen Floor

Mission Bay videoconference: MH-1405


June 14, 2018

Katharine Yu (Student)
"MERGE-ing big data with drug screening to improve molecular marker predictions"
Lee, S. I. et al. A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia. Nature Communications 9(42): 1-13. (2018).
Coaches: Aaron Diaz and Catherine Smith

Nikolai Zapero (Student)
"You are what you don't eat? How the fasting intestine spurs regenerative capacity through fatty acid oxidation"
Mihaylova, M. et al. Fasting Activates Fatty Acid Oxidation to Enhance Intestinal Stem Cell Function during Homeostasis and Aging. Cell Stem Cell 22, 769-778.e4. (2018).
Coaches: Andrew Brack and Barbara Panning

Mission Bay videoconference: MH-1405