BMS Journal Club 2019-20

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

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**Due to COVID-19 social distancing, Journal Clubs were conducted by Zoom beginning 3/19/2020. Recorded videos can be found here: https://bmsintranet.ucsf.edu/journal-club-video-archive**

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 n ucleolus 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

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
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