BMS Journal Club

2021-22 Journal Club Schedule

Journal Club Chairs: Bruce Wang, MD and Tien Peng, MD
Day/Time: Thursdays, 12:00-1:00 p.m. except as noted
Location:In person at N-225 on the Parnassus campus, with a livestream/Zoom option as well. The Zoom link will be sent out with the email reminder sent to the BMS listservs. Please contact Demian Sainz if you are not already on one of our listservs.
Links to previous livestreams and recorded video are in the sidebar.

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

September 9, 2021

*Introduction to Journal Club with JC Chairs Bruce Wang and Tien Peng*

Dave Toczyski, Ph.D. (Faculty)
“Mitocytosis: Cells leave a trail of organellar jetsam” 
Jaio et al, “Mitocytosis, a migrasome-mediated mitochondrial quality-control process.” 2021 Cell May 27: 184(11):2896-2910.e13.

Joe Germino (Student)
"Expanding the throughput of single cell transcriptomics via combinatorial preindexing"
Datlinger, P., Rendeiro, A.F., Boenke, T. et al. Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing. Nat Methods18, 635–642 (2021).
Coaches: Vasilis Ntranos, Ph.D. and Jimmie Ye, Ph.D.

September 16, 2021

Elphege-Pierre Nora, Ph.D. (Facutly)
"Nonlinear control of transcription through enhancer-promoter interactions"
Jessica Zuin, Gregory Roth, Yinxiu Zhan, Julie Cramard, Josef Redolfi, Ewa Piskadlo, Pia Mach, Mariya Kryzhanovska, Gergely Tihanyi, Hubertus Kohler, View ORCID ProfilePeter Meister, Sebastien Smallwood, Luca Giorgetti


Gabi Reeder (Student)
"Painting the chromatin landscape for optimal CAR T cell function"
Seo, H., González-Avalos, E., Zhang, W. et al. BATF and IRF4 cooperate to counter exhaustion in tumor-infiltrating CAR T cells. Nat Immunol 22, 983–995 (2021).
Coaches: Justin Eyquem, Ph.D. and Rachel Rutishauser, M.D., Ph.D.


September 23, 2021

Shaeri Mukherjee, Ph.D. (Faculty)
"Traveling waves: how bacterial pathogens rewire host membranes"
Hsieh, Ting-Sung, Lopez, Victor A., Black, Miles H., et al. Science. 2021 May 28;372(6545):935-941.


Marilyn Steyert (Student)
"Could've had a V1: Vision is required for cell-type specification in the visual cortex"
Cheng, S., Butrus, S., Xu, V., Sagireddy, S., Tan, L., Shekhar, K., & Zipursky, S. L. (2021). Vision is Required for Cell Type Specification in the Visual Cortex. bioRxiv.
Coaches: Tomasz Nowakowski, Ph.D. and Michael Oldham, Ph.D.

October 21, 2021

Journal Club this week has been rescheduled so the community can attend the Chancellor’s State of the University Address.

January 6, 2022

Amy Chen (Student)
“Outsmarting the immune system: inactivation of the miRNA machinery protects tumor cells from T-cell mediated cytotoxicity"
Song, TY., Long, M., Zhao, HX. et al. Tumor evolution selectively inactivates the core microRNA machinery for immune evasion. Nat Commun 12, 7003 (2021)
Coaches: Melissa Reeves, PhD & Robert Blelloch, MD, PhD


Hanson Tam (Student)
"B cells unTEThered, lymphoma unleashed"
Shukla, V., Samaniego-Castruita, D., Dong, Z. et al. TET deficiency perturbs mature B cell homeostasis and promotes oncogenesis associated with accumulation of G-quadruplex and R-loop structures. Nat Immunol 23, 99–108 (2022).
Coaches: Jason Cyster, PhD & Mark Ansel, PhD

January 13, 2022

Holly Steininger (Student)
"Let Food be thy Medicine: Microbiota-Directed Food Intervention for Undernourished Children"
Chen, R. Y., Mostafa, I., Hibberd, M. C., Das, S., Mahfuz, M., Naila, N. N., ... & Gordon, J. I. (2021). A microbiota-directed food intervention for undernourished children. New England Journal of Medicine, 384(16), 1517-1528.
Coaches: Susan Lynch, PhD & Saul Villeda PhD


Meagan Olive (Student)
"Defense Against the Oxidative Arts: Mtb Resistance is More Than Magic"
Lien, K. A., Dinshaw, K., et al. (2021). A nanocompartment system contributes to defense against oxidative stress in Mycobacterium tuberculosis. eLife. doi: 10.7554/eLife.74358
Coaches: Sara Suliman, PhD & Maggie Feeney, MD

January 27, 2022

Leanne Jones (Faculty)
“Taking a shot at improving Healthspan”
Suda, M., Shimizu, I., Katsuumi, G. et al. Senolytic vaccination improves normal and pathological age-related phenotypes and increases lifespan in progeroid mice. Nat. Aging 1, 1117-1126 (2021).

Grace Hernandez (Student)
"Highway to H(C)ell: Nanotubular highways transfer mitochondria from T-cells to cancer cells"
Saha, T., Dash, C., Jayabalan, R. et al. Intercellular nanotubes mediate mitochondrial trafficking between cancer and immune cells. Nat. Nanotechnol. (2021). 
Coaches: Rushika Perera, PhD & Emily Goldberg, PhD

February 3, 2022

Demi Sandel (Student)
"Targeting epigenetic programs to evade exhaustion"
Prinzing, Brooke et al. “Deleting DNMT3A in CAR T cells prevents exhaustion and enhances antitumor activity.” Science translational medicine,(2021).
Coaches: Rachel Rutishauser, MD, PhD & Matt Spitzer, PhD


Laura Dwyer (Student)
"Biochem 101: MTHFD2's role in T cell fate, function, and metabolism"
Sugiura, A., Andrejeva, G., Voss, K., Heintzman, D.R., Xu, X., Madden, M.Z., Ye, X., Beier, K.L., Chowdhury, N.U., Wolf, M.M., et al. (2022). MTHFD2 is a metabolic checkpoint controlling effector and regulatory T cell fate and function. Immunity 55, 65-81.e9.
Coaches: Alexis Combes, PhD & Joanna Halkias, MD

February 17, 2022

Laine Goudy (Student)
"A new role for Roquin in anti-tumor immunity"
Zhao H, Liu Y, Wang L, Jin G, Zhao X, Xu J, et al. Genome-wide fitness gene identification reveals Roquin as a potent suppressor of CD8 T cell expansion and anti-tumor immunity. Cell Reports. 2021 Dec;37(10):110083.
Coaches: Luke Gilbert, PhD & Justin Eyquem, PhD


Rhea Misra (Student)
"No time to die: Anti-aging benefits of intermittent Time Restricted Feeding are due to circadian autophagy"
Ulgherait, M., Midoun, A.M., Park, S.J. et al. Circadian autophagy drives iTRF-mediated longevity. Nature 598, 353–358 (2021). 
Coaches: Qili Liu, PhD & Leanne Jones, PhD

February 24, 2022

Cuyler Luck (Student)
"Go to sleep! Inducing dormancy to suppress metastasis"
Khalil, BD et al. "An NR2F1-specific agonist suppresses metastasis by inducing cancer cell dormancy." Journal of Experimental Medicine, 2021
Coaches: Rushika Perera, PhD & Jeff Bush, PhD


Kyle Jacobs (Student)
"It takes guts: using engineered hydrogels to model intestinal crypt and villi morphogenesis"
Gjorevski, N., Nikolaev, M., Brown, T. E., Mitrofanova, O., Brandenberg, N., DelRio, F. W., Yavitt, F. M., Liberali, P., Anseth, K. S., & Lutolf, M. P. (2022). Tissue geometry drives deterministic organoid patterning. Science, 375(6576). 
Coaches: Matt Kutys, PhD & Todd Nystul, PhD

March 3, 2022

Owen Jiang (Student)
"Friends or enemies? Distinct metabolic programs dictate pro- or anti-tumor function of gamma delta T cells"
Lopes, N., McIntyre, C., Martin, S. et al. Distinct metabolic programs established in the thymus control effector functions of γδ T cell subsets in tumor microenvironments. Nat Immunol 22, 179–192 (2021).
Coaches: Emily Goldberg, PhD & Sagar Bapat, MD, PhD


Juliana Sucharov Costa (Student)
"Stranger Danger: the potential role of Th17 cells in Lewy body dementia"
Gate D, Tapp E, Leventhal O, et al. CD4+ T cells contribute to neurodegeneration in Lewy body dementia. Science. 2021;374(6569):868-874. doi:10.1126/science.abf7266
Coaches: Michael Waterfield, MD, PhD & Eric Huang, MD, PhD

March 10, 2022

Mary Clare Beytagh (Student)
"Tick tock: Fbl drives the developmental clock in neural stem cells"
Wu, Q., Shichino, Y., Abe, T. et al. Selective translation of epigenetic modifiers affects the temporal pattern and differentiation of neural stem cells. Nat Commun 13, 470 (2022).
Coaches: David Raleigh, MD, PhD & Joanna Phillips, MD, PhD


Nav Lally (Student)
"Science is an Art: Patterned Presentation of Mitophagy in Mitochondrial Myopathy"
Mito, T., Vincent, A. E., Faitg, J., Taylor, R. W., Khan, N. A., McWilliams, T. G., & Suomalainen, A. (2022). Mosaic dysfunction of mitophagy in mitochondrial muscle disease. Cell metabolism, 34(2), 197–208.e5.
Coaches: Aparna Lakkaraju, PhD & Matthew Kutys, PhD

March 17, 2022

Min Joo Kim (Student)
"The power of E on microglial dynamics" 
Serrano-Pozo, A., Li, Z., Noori, A., Nguyen, H. N., Mezlini, A., Li, L., ... & Das, S. (2021). Effect of APOE alleles on the glial transcriptome in normal aging and Alzheimer’s disease. Nature Aging, 1(10), 919-931.
Coaches: Carlo Condello, PhD & Ryan Corces, PhD


Xian Liu (Student)
"Fuel Anti-Tumor Immune Response, Bacteria Return to the Arena"
Canale FP et al. "Metabolic modulation of tumours with engineered bacteria for immunotherapy" Nature. 2021 Oct;598(7882):662-666
Coaches: Peter Turnbaugh, PhD & Lewis Lanier, PhD

March 24, 2022

Matt Arvedson (Student)
“Do these Tregs make me look fat? Adipose Tregs are composed of distinct subsets that contribute to age and obesity related metabolic disorders”
Li, Y., Lu, Y., Lin, SH. et al. Insulin signaling establishes a developmental trajectory of adipose regulatory T cells. Nat Immunol 22, 1175–1185 (2021).
Coaches: Sagar Bapat, MD, PhD & Ari Molofsky, MD, PhD

Caroline Whitty (Student)
“Neo Evidence for a Lung-Brain Axis”
Hosang, L. et al. The lung microbiome regulates brain autoimmunity. Nature (2022).
Coaches: Peter Turnbaugh, PhD & Ari Molofsky, MD, PhD

May 5, 2022

Letitia Yang (Student)
"Defining your identity - the T follicular helper cell's journey in the germinal center"
Yeh, C.-H., Finney, J., Okada, T., Kurosaki, T., & Kelsoe, G. (2022). Primary germinal center-resident T follicular helper cells are a physiologically distinct subset of CXCR5hiPD-1hi T follicular helper cells. Immunity, 55(2).
Coaches: Julie Zikherman, MD & Tiffany Scharschmidt, MD 

Kaylee Wedderburn-Pugh (Student)
“Bears, Beets, Battlestar Galactica?: working to define the BBB, through the lens of pericyte-to-endothelial signaling”
Ayloo, S., Lazo, C. G., Sun, S., Zhang, W., Cui, B., & Gu, C. (2022). Pericyte-to-endothelial cell signaling via vitronectin-integrin regulates blood-CNS barrier. Neuron, S0896-6273(22)00184-2. Advance online publication.
Coaches: Andrew Yang, PhD & Betsy Crouch, MD, PhD

May 12, 2022

Lexi Schneider (Student)
"Micro(glia) or Macro(phages)? The Economics of Brain Immunity"
Sailor, K. A. et al. Hematopoietic stem cell transplantation chemotherapy causes microglia senescence and peripheral macrophage engraftment in the brain. Nat Med 28, 517–527 (2022).
Coaches: Andrew Yang, PhD & Ari Molofsky, MD, PhD

Charlotte Wang (Student)
"CD8+ T cells KIR+bing CD4+ T cells: 
KIR+CD8+ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19"
Li, Jing et al. “KIR+CD8+ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19.” Science (New York, N.Y.), eabi9591. 8 Mar. 2022, doi:10.1126/science.abi9591
Coaches: Rachel Rutishauser, MD, PhD & Qizhi Tang, PhD

May 19, 2022

Tori Tran (Student)
"The CAMPaign to eRAdicate Acne: A new role for preadipocytes in C. acnes infection"
O'Neill AM, Liggins MC, Seidman JS, et al. Antimicrobial production by perifollicular dermal preadipocytes is essential to the pathophysiology of acne. Sci Transl Med. 2022;14(632):eabh1478. doi:10.1126/scitranslmed.abh1478
Coaches: Tiffany Scharschmidt, MD & Roberto Ricardo-Gonzales, MD, PhD


Rita Loudermilk (Student)
"DUBing over biology: Engineering deubiquitinases for targeted protein stabilization."
Henning, N.J., Boike, L., Spradlin, J.N. et al. Deubiquitinase-targeting chimeras for targeted protein stabilization. Nat Chem Biol 18, 412–421 (2022).
Coaches: Jim Wells, PhD & Seth Shipman, PhD

June 2, 2022

Max Pass (Student)
"You can trust the locals: FOLR2+ tissue resident macrophages associate with anti-tumor immunity"
Nalio Ramos, R. et al. Tissue-resident FOLR2+ macrophages associate with CD8+ T cell infiltration in human breast cancer. Cell 185, 1189-1207.e25 (2022).
Coaches: Max Krummel, PhD and Jeroen Roose, PhD


Jingwen Ding (Student)
Breuss, M.W., Yang, X., Schlachetzki, J.C.M. et al. Somatic mosaicism reveals clonal distributions of neocortical development. Nature (2022).

Coaches: Daniel Lim, MD, PhD & Mercedes Paredes, MD, PhD

June 9, 2022

Evan Semenza (Student)


William Xie (Student)

June 16, 2022

TBD (Faculty)


Jun Hyung Sin (Student)