BMS Journal Club 2019-20

BMS Journal Club presentations are available via livestream and recorded video. UCSF MyAccess login is required.

**Note: the Safari web browser may not work correctly when trying to view video.**

**Due to COVID-19 social distancing, Journal Clubs were conducted by Zoom beginning 3/19/2020. Recorded videos can be found here: https://vimeo.com/user110104752**

September 5, 2019

Mary Helen Barcellos-Hoff (faculty)
"Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts"
10.1158/2159-8290.CD-19-0094 Published August 2019

Gokul Ramadoss (student)
"Careful Cas9 Cutting Cures Condemned Cochleas"
György et al. Allele-specific gene editing prevents deafness in a model of
dominant progressive hearing loss. Nat Med. 2019 Jul;25(7):1123-1130. doi:
10.1038/s41591-019-0500-9. Epub 2019 Jul 3.

Coaches: Aaron Tward and Bruce Conklin

September 12, 2019

Jeoung-Sook Shin (faculty)
"Role of protein crystallization in asthma"
Persson et al., 'Protein crystallization promotes type 2 immunity and is reversible by antibody treatment.' Science. 2019 May 24;364(6442). pii: eaaw4295. doi: 10.1126/science.aaw4295.

Raymond Dai (student)
"A dominant-negative effect drives selection of TP53 missense mutations in myeloid malignancies"
Boettcher, S. et al. (2019). A dominant-negative effect drives selection of TP53 missense mutations in myeloid malignancies. Science 365 (6453), 599-604. doi: 10.1126/science.aax3649
Coaches: Joe Costello and Kevin Shannon

September 19, 2019

Isha Jain (faculty)
"The Treasure Hunt for New Oxygen Sensors"
Masson et al., ‘Conserved N-terminal cysteine dioxygenases transduce responses to hypoxia in animals and plants.’ Science. 2019 Jul 5;365(6448):65-69. doi: 10.1126/science.aaw0112.

Yewande Alabi (student)
"Phase separation and nuclear protein quality control: How the nucleolus promotes nuclear protein maintenance under stress"
Frottin, F. et al. (2019). The nucleolus functions as a phase-separated protein quality control compartment. Science. doi: 10.1126/science.aaw9157
Coaches: Bill DeGrado and Aimee Kao

September 26, 2019

Stephen Floor (faculty)
"This is your brain on lipoic acid: small molecule control of phase separation and neurodegeneration."
Wheeler, R. et al. 'Small molecules for modulating protein driven liquid-liquid phase separation in treating neurodegenerative disease.' doi:10.1101/721001

Carlos Zuazo (student)
"Dreams From My Father: Neuronal Small RNAs Control Behavior Transgenerationally."
Posner et al. 'Neuronal Small RNAs Control Behavior Transgenerationally.' Cell 177, 1814–1826. June 13, 2019.
Coaches: Shaeri Mukherjee and Stephen Floor

October 3, 2019

Rohit Bose (faculty)
"Reversing oncogenic differentiation: can Humpty Dumpty be put together again?"
Walter et al., 'RB constrains lineage fidelity and multiple stages of tumour progression and metastasis' Nature volume 569, pages 423–427 (2019).

Kirsten Chen (student)
"An Emerging Panacea in Our Bodies - Microbiome"
Scheiman et al., 'Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism', Nature Medicine 25, 1104–1109 (2019)
Coaches: Katie Pollard and Peter Turnbaugh

October 10, 2019

Sophie Dumont (faculty)
"How mammalian oocytes build a spindle without centrosomes"
So et al., A liquid-like spindle domain promotes acentrosomal spindle assembly in mammalian oocytes. Science, Jun 28; 364. (2019).

Megan Montoya (student)
"Immune-suppressive tumor microenvironment leads to poor prognosis in Glioblastoma patients"
Alban et al., Global immune fingerprinting in glioblastoma patient peripheral blood reveals immune-suppression signatures associated with prognosis. JCI Insight. 2018;3(21):e122264
Coaches: Hideho Okada and Noriyuki Kasahara

October 17, 2019

Martin Kampmann (faculty)
"When the Powerhouse crumbles …"
Joshi et al (2019). Fragmented mitochondria released from microglia trigger A1 astrocytic response and propagate inflammatory neurodegeneration. Nature Neuroscience 22:1635.PMID: 31551592.

Priscila Munoz Sandoval (student)
"Oh! That's where (T)hey went:"
Collins, N. et al. The Bone Marrow Protects and Optimizes Immunological Memory during Dietary Restriction. Cell (2019). doi:10.1016/j.cell.2019.07.049
Coaches: Mark Ansel & Jason Cyster

October 24, 2019

Andy Chang (faculty)
"What worms getting high can tell us about opioid signaling."
Wang et al., Genetic behavioral screen identifies an orphan anti-opioid system. Nature, Sep 20; 365(6459): 1267-1273 (2019).

Darwin Kwok (student)
"Connecting the Nodes Behind Gliomas: Electrical and synaptic integration of glioma into neural circuits."
Venkatesh et al. "Electrical and synaptic integration of glioma into neural circuits" Nature 573, 539-545 (September 18, 2019).
Coaches: David Raleigh and Erik Ullian

October 31, 2019

Elliott Sherr (faculty)
"A gene for you, a gene for me?"
J. Kim et al. Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease. October 24, 2019. N Engl J Med 2019; 381:1644-1652

Bahar Zirak (student)
"Tumor Heterogeneity and Immune Response in Melanoma"
Wolf et al. UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma. 2019, Cell 179, 219–235. 
Coaches: Melissa Reeves and Rohit Bose

November 7, 2019

Elphege Nora (faculty)
"The Energetics and Physiological Impact of Cohesin Extrusion."
Vian, Pękowska, Rao et al., The Energetics and Physiological Impact of Cohesin Extrusion. Cell 2018, May 17;173(5):1165-1178.e20.

November 14, 2019

Bjoern Schwer (faculty)
"To live longer, give your neurons some REST"
Zullo et al., Regulation of lifespan by neural excitation and REST. Nature, 574, pages 359–364 (2019).

Adam Wade-Vallance (student)
"There's just enough material here for a broadly-neutralizing vaccine."
Sangesland M et al. Encoded Affinity for Cognate Antigen Enables Vaccine Amplification of a Human Broadly Neutralizing Response against Influenza Virus. Immunity. 2019;51(4):735-49.
Coach: Chris Allen and Julie Zikherman

November 21, 2019

Valerie Weaver (faculty)
"Sometimes being fat is a good thing"
Dana Ishay-Ronen et al. Gain fat - Lose metastasis: Converting invasive breast cancer cells into adipocytes inhibits cancer metastasis. Cancer Cell 35, 17-32 2019

Nour Abdulhay (student)
"The Tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals."
Chavez et al., The Tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals. eLife 2019;8:e47682
Coaches: Noelle L'Etoile and Elphege Nora

January 9, 2020

David Solomon (faculty)
"Epigenomic-based classification of human cancer"
Capper D. et al. DNA methylation-based classification of central nervous system tumours. Nature. 2018 Mar 22;555(7697):469-474. doi: 10.1038/nature26000. Epub 2018 Mar 14.

Saumya Bollam (student)
"Divide and conquer: Inhibition of tumor growth by a novel engineered chimeric toxin that cleaves activated mutant and wild-type RAS"
Vidimar, V. et al. (2019). Inhibition of tumor growth by a novel engineered chimeric toxin that cleaves activated mutant and wild-type RAS. bioRxiv. doi: https://doi.org/10.1101/2019.12.17.880187
Coaches: Allan Balmain and Luke Gilbert 

January 16, 2020

David Raleigh (faculty)
“Pediatric Rhabdoid Tumors: Genomically boring, immunologically interesting, and (thankfully) really rare.”
Leruste A. et al. Clonally Expanded T Cells Reveal Immunogenicity of Rhabdoid Tumors. Cancer Cell. 2019 Dec 9;36(6):597-612.e8. doi: 10.1016/j.ccell.2019.10.008. Epub 2019 Nov 7.

Rhogerry Deshycka (student)    
"Prime Editing: 'Search-and-replace' genome editing with enhanced efficiency, precision and coverage"
Anzalone et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019) doi:10.1038/s41586-019-1711-4
Coaches: Stephen Floor and Luke Gilbert

January 23, 2020

Alejandro Sweet-Cordero (faculty)
"Bridging the gap: linking genomic instability to immunotherapy."
Zhang, H. et al. CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer.  Cancer Cell. 2020 Jan 13;37(1):37-54.e9. doi: 10.1016/j.ccell.2019.11.003. Epub 2019 Dec 26.

Daphne Superville (student)
"Kicking out the comp53tition: p53 mutant cells outcompeted in normal esophagus by redox manipulation"
Fernandez-Antoran, David, et al. “Outcompeting P53-Mutant Cells in the Normal Esophagus by Redox Manipulation.” Cell Stem Cell, vol. 25, no. 3, 2019, pp. 329–41, doi:10.1016/j.stem.2019.06.011.
Coaches: Melissa Reeves and Mary Helen Barcellos-Hoff

January 30, 2020

Diana Laird (faculty)
"The early worm gets the H3K4me3: larval oxidation state determines lifelong resilience via SET1/MLL histone methyltransferases"
Bazopoulou, D. et al. Developmental ROS individualizes organismal stress resistance and lifespan. Nature. 2019 Dec;576(7786):301-305. doi: 10.1038/s41586-019-1814-y. Epub 2019 Dec 4.

Brian Woo (student)
"Functional Enhancers Shape Extrachromosomal Oncogene Amplifications"
Morton, A. et al. Functional Enhancers Shape Extrachromosomal Oncogene Amplifications. Cell (2019). doi.org/10.1016/j.cell.2019.10.039
Coaches: Elphege Nora and Ross Okimoto

 

February 6, 2020

Alex Marson (faculty)
"Designing better immunotherapy with CRISPR"
Wei et al. Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy. Nature volume 576, pages471–476(2019).

Julie Garcia (student)    
"Oops…we cured cancer??? Genome Wide CRISPR Cas-9 Screening Reveals Ubiquitous T Cell Cancer Targeting via the monomorphic MHC-class I related MR1 protein"
Crowther MD, Dolton G, Legut M, et al. Genome-wide CRISPR-Cas9 screening reveals ubiquitous T cell cancer targeting via the monomorphic MHC class I-related protein MR1. Nat Immunol. January 2020. doi:10.1038/s41590-019-0578-8
Coaches: Kole Roybal and Justin Eyquem

February 13, 2020

Ed Hsiao (faculty)
"The smoking gun: detecting mutational load in lungs of smokers and ex-smokers"
Yoshida, K., Gowers, K.H.C., Lee-Six, H. et al. Tobacco smoking and somatic mutations in human bronchial epithelium. Nature (2020). https://doi.org/10.1038/s41586-020-1961-1

Nick Mroz (student)
"(VEGF-)C-ing glioblastoma antigens: VEGF-C-driven meningeal lymphatic drainage enables immunosurveillance of brain tumors."
Song, E., Mao, T., Dong, H. et al. VEGF-C-driven lymphatic drainage enables immunosurveillance of brain tumours. Nature (2020). https://doi.org/10.1038/s41586-019-1912-x
Coaches: TBD

February 20, 2020

Abby Buchwalter (faculty)
"Thanks for the lifespan, mom: transgenerational inheritance of longevity through chromatin modifications"
Lee et al. Repressive H3K9me2 protects lifespan against the transgenerational burden of COMPASS activity in C. elegans. eLife 2019;8:e48498, doi: 10.7554/eLife.48498

Vikas Daggubati (student)
"Toxoplasma gondii: It's a BFD"
Waldman, B. S. et al. Identification of a Master Regulator of Differentiation in Toxoplasma. Cell 180, 359–372.e16 (2020).
Coaches: David Raleigh and Seemay Chou

February 27, 2020

Yashodara Abeykoon (student)
"Hominini-Specific Regulation of CBLN2 Increases Prefrontal Synaptogenesis"
Hominini-Specific Regulation of CBLN2 Increases Prefrontal Synaptogenesis. Mikihito Shibata, Kartik Pattabiraman, Sydney K. Muchnik, and Nenad Sestan. bioRxiv.
Coaches: Alex Pollen and Anita Sil

Than Kyaw (student)
"Preventing Dysbiosis of the Neonatal Mouse Intestinal Microbiome Protects Against Late-Onset Sepsis"
Singer, J.R., Blosser, E.G., Zindl, C.L. et al. Preventing dysbiosis of the neonatal mouse intestinal microbiome protects against late-onset sepsis. Nat Med 25, 1772–1782 (2019). https://doi.org/10.1038/s41591-019-0640-y
Coaches: Peter Turnbaugh and Suzanne Noble

March 5, 2020

Oscar Yip (student)
"Autonomous Movement of RNA Granules in Neurons Prevents Axon Degeneration"
Segal, R. A., Seo, H. S., Adelmant, G., Walensky, L., Marto, J. A., Dhe-Paganon, S., ... & Rose, L. (2020). Fast transport of RNA granules by direct interactions with KIF5A/KLC1 motors prevents axon degeneration. BioRxiv.
Coaches: Stephen Floor and Abby Buchwalter

Irek Habrylo (student)
"Sex drives Tregs in fat"
Vasanthakumar et al. Sex-specific adipose tissue imprinting of regulatory T cells. Nature (2020), 26 Feb 2020. https://doi.org/10.1038/s41586-020-2040-3.
Coaches: Michael Rosenblum and Tiffany Scharschmidt

March 12, 2020

Nebat Ali (student)
"Get a load of this: Selective loading and processing of prespacers for precise CRISPR adaptation"
Kim, S., Loeff, L., Colombo, S. et al. Selective loading and processing of prespacers for precise CRISPR adaptation. Nature (2020).
Coaches: Anita Sil and Aaron Tward
In person attendance is open to registered students only.  We encourage the rest of the community to attend virtually.

March 19, 2020

Alyssa Indart (student)
"Fc Receptors expressed on CD8+ T cells"
Morris, A., Farley, C., Pinelli, D., et al. Signaling through the Inhibitory Fc Receptor FcyRIIB Induces CD8+ T cell Apoptosis to Limit T cell Immunity. Immunity. 52, 136-150.(2020). https://www.ncbi.nlm.nih.gov/pubmed/31940267
Coaches: Shomyseh Sanjabi and Robert Raffai

Jackson Gardner (student)
"Catch me outside (the cell), how bout dat"
Matthew D. Keller, Krystal L. Ching, Feng-Xia Liang, Avantika Dhabaria, Kayan Tam, Beatrix M. Ueberheide, Derya Unutmaz, Victor J. Torres & Ken Cadwell. Decoy exosomes provide protection against bacterial toxins. Nature. 2020 Mar 4. doi: 10.1038/s41586-020-2066-6.
Coaches: Tiffany Scharschmidt and Robert Blelloch

View the recording here: https://vimeo.com/399188836

March 26, 2020

Rachel DeBarge (student)
"The Devil’s in the Details"
Flies, A. S. et al. A novel system to map protein interactions reveals evolutionarily conserved immune evasion pathways on transmissible cancers. bioRxiv 831404 (2019). doi:10.1101/831404 
Coaches: Matthew Spitzer and Rohit Bose

Ben Wheeler (student)
"Latent Plasticity of Effector-like Exhausted CD8 T cells contributes to memory responses"
Latent Plasticity of Effector-like Exhausted CD8 T cells contributes to memory responses
Saravanan Raju, Yu Xia, Bence Daniel, Kathryn E. Yost, Elliot Bradshaw, Elena Tonc, Daniel J. Verbaro, Ansuman T. Satpathy, Takeshi Egawa
bioRxiv 2020.02.22.960278; doi: https://doi.org/10.1101/2020.02.22.960278

Coaches: Mark Ansel and Michael Waterfield
View the recording here: https://vimeo.com/401115080 

April 2, 2020

Jacqueline Yee (student)
"Metabolic Adaption in Intratumoral Tregs"
Wang, H., Franco, F., Tsui, Y. et al. CD36-mediated metabolic adaptation supports regulatory T cell survival and function in tumors. Nat Immunol 21, 298–308 (2020). https://doi.org/10.1038/s41590-019-0589-5
Coaches: Justin Eyquem and Isha Jain

Anthony Chang (student)
"Do we control bacteria or do bacteria control us?"
James, K.R., Gomes, T., Elmentaite, R. et al. Distinct microbial and immune niches of the human colon. Nat Immunol 21, 343–353 (2020). https://doi.org/10.1038/s41590-020-0602-z
Coaches: Tiffany Scharschmidt and Ari Molofsky
View the recording here: https://vimeo.com/403462298 

April 9, 2020

Cambria Chou-Freed (student)
"Protective Protein Reshuffling in C9orf72 Hexanucleotide Repeat Expansion Disease"
Ortega, J. A., Daley, E. L., Kour, S., Samani, M., Tellez, L., Smith, H. S., … Kiskinis, E. (2019). Nucleocytoplasmic Proteomic Analysis Uncovers eRF1 and Nonsense Mediated Decay as Modifiers of ALS C9orf72 Toxicity. doi: 10.1101/677419
Coaches: Martin Kampmann and Stephen Floor

Jessica Wang (student)
"MHCII on cDC1s is required for cross-tolerization of CD8+ T cells"
Wohn C, Le Guen V, Voluzan O, Fiore F, Henri S, Malissen B. Absence of MHC class II on cDC1 dendritic cells triggers fatal autoimmunity to a cross-presented self-antigen. Sci Immunol. 2020 Vol. 5, Issue 45, eaba1896 DOI: 10.1126/sciimmunol.aba1896
Coaches: James Gardner and Tiffany Scharschmidt
View the recording here: https://vimeo.com/405996090 

April 16, 2020

Brandon Desousa (student)
"Uncovering a metabolic death poem upon cellular seppuku"
Medina, C. B. et al. Metabolites released from apoptotic cells act as tissue messengers. Nature 1–6 (2020) doi:10.1038/s41586-020-2121-3.
Coaches: Isha Jain and Guo Huang

Nicole Tsai (student)
"Determining Differences in Retinal Ganglion Cell Subtype Survival after Injury Using Single-Cell RNA Sequencing"
Tran, N. M. et al. Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes. Neuron 104, 1039-1055 e1012, doi:10.1016/j.neuron.2019.11.006 (2019).
Coaches: Xin Duan and Tomasz Nowakowski
View the recording here: https://vimeo.com/408618520

April 23, 2020

Mariko Foecke (student)
"Avoiding stress keeps you looking young: sympathetic nerve hyperactivation depletes melanocyte stem cells"
Zhang, B., Ma, S., Rachmin, I. et al. Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells. Nature 577, 676–681 (2020). https://doi-org.ucsf.idm.oclc.org/10.1038/s41586-020-1935-3
Coaches: Faranak Fattahi and Saul Villeda

Sonia Scaria (student)
"Leu-sening the need for Leucine"
Leucine Signals to mTORC1 via Its Metabolite Acetyl-Coenzyme A. Son SM et al. Cell Metabolism, 29: 192-201 (2019).
Coaches: Isha Jain and Aaron Tward
View the recording here: https://vimeo.com/411469442 

April 30, 2020

Sophia Guldberg (student)
"Keep Calm and Carry on, Mom: Effects of Perinatal Stress on Long-Term CD8 T cell Immunity"
Hong, J. Y., Lim, J., Carvalho, F., Cho, J. Y., Vaidyanathan, B., Yu, S., . . . Medzhitov, R. (2020). Long-Term Programming of CD8 T Cell Immunity by Perinatal Exposure to Glucocorticoids. Cell, 180(5), 847-861.e815. doi:https://doi.org/10.1016/j.cell.2020.02.018
Coaches: Diana Laird and Matthew Spitzer

Dianne Laboy Cintrón (student)
"The Sound of Silence: Systematic identification of silencers in human cells"
Pang, B., Snyder, M.P. Systematic identification of silencers in human cells. Nature Genetics 52(3), 254–263 (2020). https://doi.org/10.1038/s41588-020-0578-5
Coaches: Nadav Ahituv and Elphege Nora
View the recording here: https://vimeo.com/413751322

May 7, 2020

Zach Howard (student)
"My"cough"bacterium tuberculosis: bacterial factors induce coughing during Mtb infection"
Ruhl CR, Pasko BL, Khan HS, et al. Mycobacterium tuberculosis Sulfolipid-1 Activates Nociceptive Neurons and Induces Cough. Cell. 2020;181(2):293–305.e11. doi:10.1016/j.cell.2020.02.026.
Coaches: Joel Ernst and Melanie Ott
Erin Huiting (student)
"Archaeal viruses are cool too: Discovery of viral anti-CRISPR enzyme that rapidly degrades cyclic oligoadenylate"
Athukoralage, J.S., McMahon, S.A., Zhang, C. et al. An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature 577, 572–575 (2020). https://doi.org/10.1038/s41586-019-1909-5
Coaches: Joe Bondy-Denomy and Anita Sil
View the recording here: https://vimeo.com/416101503 

May 14, 2020

Niko Eng (student)
"Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations."
Fulco, C.P., Nasser, J., Jones, T.R. et al. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations. Nat Genet 51, 1664–1669 (2019). https://doi.org/10.1038/s41588-019-0538-0
Coaches: Yin Shen and Joseph Costello
Matt Ryan (student)
"YAPity YAP Don’t Grow Back: Targeting YAP-mediated Dormancy in EGFR-Mutant Non-Small Cell Lung Cancer"
Kurppa KJ, Liu Y, To C, Zhang T, Fan M, Vajdi A, Knelson EH, Xie Y, Lim K, Cejas P, et al. Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway. Cancer Cell (2020) 37:104-122.e12. doi:10.1016/j.ccell.2019.12.006
Coaches: Rohit Bose and Michael McManus
View the recording here: https://vimeo.com/418640199