BMS Journal Club 2017-18 (Fall 2017)

BMS Journal Club presentations are available via livestream and recorded video. You can access them via the links below. UCSF MyAccess login is required.

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September 7, 2017

Saul Villeda, PhD (Faculty)
"High as a Kite: Making the Old Brain Young Again?"
Bilkei-Gorzo, Andras et al. "A chronic low dose of Δ9-tetrahydrocannabinol (THC) restores cognitive function in old mice." Nature Medicine 23, 782–787 (2017).​

Alexis Krup (Student)
“The Crypt Keepers: a story of secret stem cells, as told by their chromatin”
Jadhav, Unmesh et al. “Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells.” Cell Stem Cell 21.1 (2016): 65–77.e5.
Coaches: Miguel Ramalho-Santos and Robert Blelloch

September 14, 2017

Joseph Shieh, MD, PhD (Faculty)
"Are we heterogeneous or homogeneous? Natural variation, mutation, and disease"
Florian Zink et al. "Clonal hematopoiesis, with and without candidate driver mutations, is common in the elderly." Blood , no. (2017): blood-2017-02-769869.​

Patrick Schupp (Student)
A Glioma miR-acle: miR128 drives Class Shift in Glioblastoma Stem-like Cells
Rooj, A. K. et al. MicroRNA-Mediated Dynamic Bidirectional Shift between the Subclasses of Glioblastoma Stem-like Cells. Cell Rep. 19, 2026–2032 (2017).
Coaches: Michael Oldham and Samuel Shelton

September 21, 2017

JJ Miranda, PhD (Faculty)
“Redefining viral infection during cancer”
Yogev O, Henderson S, Hayes MJ, Marelli SS, Ofir-Birin Y, Regev-Rudzki N, et al. (2017) Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs. PLoS Pathog 13(8): e1006524.

Jerika Barron (Student)
"Stop interferon’ with my synapses! IFN drives microglia-dependent synapse loss in CNS lupus"
Bialas, A. R. et al. Microglia-dependent synapse loss in type I interferon-mediated lupus. Nature 546, 539–543 (2017).
Coaches: Anna Molofsky and Susanna Rosi

September 28, 2017

Aaron Tward, MD, PhD (Faculty)
"The DRIVE to find Achilles’ heels of cancer: shRNA works great … if you have 100,000 of them."
Tsherniak A. et al. "Defining a Cancer Dependency Map." Cell, 170(3):564-576.e16. 2017.
McDonald E.R. et al. "Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening." Cell 170(3):577-592.e10. 2017.

Johnny Yu (student)
"Hi, my name is Cancer and I'm an exosome-oholic."
Nabet, B.Y. et al. "Exosome RNA Unshielding Couples Stromal Activation to Pattern Recognition Receptor Signaling in Cancer." Cell, Volume 170 (2), 352-366. 2017.
Coaches: Hani Goodarzi and Luke Gilbert

October 5, 2017

Laura van 't Veer, PhD (Faculty)
"Chemotherapy indices metastasis, ‘of mice to (wo-)men"
Karagiannis, George et al. “Neoadjuvant chemotherapy induces breast cancer metastasis through a TMEM-mediated mechanism.” Science Translation Medicine 05 Jul 2017: Vol. 9, Issue 397

Geil Merana (student)
"New Cell on the Block"
Wang S. et al. "Regulatory Innate Lymphoid Cells Control Innate Intestinal Inflammation." Cell 171 (1), 201-216. 2017 Aug 24.
Coaches: Tiffany Scharschmidt and Ari Molofsky

October 12, 2017

Raymond Swanson, MD (Faculty)
"Et tu, dopamine?"
Mor, D.E. et al. "Dopamine induces soluble α-synuclein oligomers and nigrostriatal degeneration." Nature Neuroscience (2017).

Katerina Popova (Student)
"Don't get antsy...CRISPR-engineered ants are already here!"
Hua, Y. et al. An Engineered orco Mutation Produces Aberrant Social Behavior and Defective Neural Development in Ants. Cell 170(4), 736-747, 10 Aug 2017.
Coaches: Stephen Floor and Luke Gilbert

October 19, 2017

Arun Wiita, MD, PhD (Faculty)
"It's ok to judge a tumor by its cover"
Bosse KR et al. Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma. Cancer Cell (2017) 32:295.​

Anthony Venida (Student)
"The Sidekick Tale of an Immune Checkpoint Regulator: CMTM6 is to PD-L1 as Robin is to Batman"
Burr, Marian L. et al. "CMTM6 Maintains the Expression of PD-LI and Regulates Anti-Tumor Immunity." Nature 549, 101-105 (2017).
Coaches: Rushika Perera and Matthew Spitzer

October 26, 2017

Aditi Bhargava, PhD (Faculty)
"Sex or Gender: Scoop on COUP-TFII"
Zhao, F. et al. "Elimination of the male reproductive tract in the femal embryo is promoted by COUP-TFII in mice." Science, 357, 6352, 717-720. 18 Aug 2017.​

Karen Wong (Student)
"Most wanted: missing sequences in the reference genome"
Kehr B. et al. “Diversity in non-repetitive human sequences not found in the reference genome.” Nature genetics. 49, 588-593. 2017 Feb 27.
Coaches: Joseph Shieh and Marina Sirota

November 2, 2017

Seemay Chou, PhD (Faculty)
"Controlled destruction: how predatory microbes navigate prey cells"
Kuru, E. et al. Fluorescent D-amino-acids reveal bi-cellular cell wall modifications important for Bdellovibrio bacteriovorus predation. Nature Microbiology doi:10.1038/s41564-017-0029-y. epub 3 Oct 2017.

Jeremy Williams (Student)
"Don't take the STING out of treatment: How the cGAS pathway can drive abscopal response to cancer therapy."
Harding, S. M., Benci, J. L., Irianto, J., Discher, D. E., Minn, A. J., & Greenberg, R. A. (2017). Mitotic progression following DNA damage enables pattern recognition within micronuclei. Nature Publishing Group, 548(7668), 466–470.
Coaches: Stephen Floor and Andrei Goga

November 9, 2017

Stephen Floor, PhD (Faculty)
Title: "To PB or not to PB: Condensed Granules of RNA Regulons"
Hubstenberger, A. et al. "P-Body Purification Reveals the Condensation of Repressed mRNA Regulons" Molecular Cell 68, 1-14 (2017).

Elma Frias (Student)
"Hungry Hungry Astrocytes"
Morizawa, Yosuke M. et al. “Reactive Astrocytes Function as Phagocytes after Brain Ischemia via ABCA1-Mediated Pathway.” Nature Communications 8 (2017): 28.
Coaches: Susanna Rosi and TBA

November 16, 2017

Rushika Perera, PhD (Faculty)
"Quality over quantity wins!"
Balachandran, V.P. et al. Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer. Nature, doi:10.1038/nature24462. epub Nov 8, 2017.​

Nicholas Gentry (Student)
"A further step in uncovering the molecular basis of memory"
Mews, P. et al. Acetyl-CoA synthetase regulates histone acetylation and hippocampal memory. Nature 546, 381-386. (2017).
Coaches: Bassem Al-Sady and Daniel Lim

November 30, 2017

Andy Chang, PhD (Faculty)
"Who needs oxygen when you have fructose"
Park, TJ. et al. Fructose-driven glycolysis supports anoxia resistance in the naked mole-rat. Science. 2017 Apr 21;356(6335):307-311.​

Jeanmarie Gonzalez (Student)
"Bad intestines: oral bacteria driving inflammation in the gut"
Atarashi, K. et al. Ectopic colonization of oral bacteria in the intestine drives Th1 cell induction and inflammation. Science. 358, 6361, 359-365. 20 October 2017.
Coaches: Tiffany Scharschmidt and Peter Turnbaugh

December 7, 2017

Diana Laird, PhD (Faculty)
"When sex is negative and cancer is positive"
Martincorena, I. et al. Universal Patters of Selection in Cancer and Somatic Tissues. Cell 171, 1029-1041. (2017).

Didi Zhu (Student)
Turn Up for What? ILC2s Turn Up for Neuromedin U
Cardoso V. et al. Neuronal regulation of type 2 innate lymphoid cells via neuromedin U. Nature 549: 277-281 (2017).
Coaches: Ari Molofsky and Mark Ansel

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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