HMS-CSSA Lightning Talks

Hongli Hu, Ph.D.

Current Position:

Instructor

Program in Cellular and Molecular Medicine at Boston Children's Hospital

Department of Pediatrics, Harvard Medical School

Biography:

Dr. Hu received his Ph.D. degree with Dr. Daming Gao from the Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, and studied cancer cell signaling pathways and cell metabolism. As a postdoctoral fellow with Dr. Frederick W. Alt at Boston Children’s Hospital, he widened his research focus on basic immunity study - V(D)J recombination in B cell development. Dr. Hu is working on the mechanism study that explains the fundamental role of cohesin-mediated loop extrusion in Igh and Igk V(D)J recombination. His research aim is to explain the possible mechanisms that antibody heavy and light chain utilize to organize their gene segments together to produce various kinds of antibodies. His long-term goal is to optimize animal models and develop new immunotherapies. His study is supported by Irvington Postdoc Fellowship from Cancer Research Institute (CRI).

Talk title: 

Molecular Basis for Differential Igk versus Igh V(D)J Joining Mechanisms.

Abstract: 

In developing B cells, V(D)J recombination assembles exons encoding IgH and Igκ variable regions from hundreds of gene segments clustered across Igh and Igk loci. V, D and J gene segments are flanked by conserved recombination signal sequences (RSSs) that target RAG endonuclease. RAG orchestrates Igh V(D)J recombination upon capturing a JH-RSS within the JH-RSS-based recombination centre (RC). JH-RSS orientation programmes RAG to scan upstream D- and VH-containing chromatin that is presented in a linear manner by cohesin-mediated loop extrusion. During Igh scanning, RAG robustly utilizes only D-RSSs or VH-RSSs in convergent (deletional) orientation with JH-RSSs. However, for Vκ-to-Jκ joining, RAG utilizes Vκ-RSSs from deletional- and inversional-oriented clusters, inconsistent with linear scanning. Here we characterize the Vκ-to-Jκ joining mechanism. Igk undergoes robust primary and secondary rearrangements, which confounds scanning assays. We therefore engineered cells to undergo only primary Vκ-to-Jκ rearrangements and found that RAG scanning from the primary Jκ-RC terminates just 8 kb upstream within the CTCF-site-based Sis element. Whereas Sis and the Jκ-RC barely interacted with the Vκ locus, the CTCF-site-based Cer element 4 kb upstream of Sis interacted with various loop extrusion impediments across the locus. Similar to VH locus inversion, DJH inversion abrogated VH-to-DJH joining; yet Vκ locus or Jκ inversion allowed robust Vκ-to-Jκ joining. Together, these experiments implicated loop extrusion in bringing Vκ segments near Cer for short-range diffusion-mediated capture by RC-based RAG. To identify key mechanistic elements for diffusional V(D)J recombination in Igk versus Igh, we assayed Vκ-to-JH and D-to-Jκ rearrangements in hybrid Igh–Igk loci generated by targeted chromosomal translocations, and pinpointed remarkably strong Vκ and Jκ RSSs. Indeed, RSS replacements in hybrid or normal Igk and Igh loci confirmed the ability of Igk-RSSs to promote robust diffusional joining compared with Igh-RSSs. We propose that Igk evolved strong RSSs to mediate diffusional Vκ-to-Jκ joining, whereas Igh evolved weaker RSSs requisite for modulating VH joining by RAG-scanning impediments.

Highlighted publications:

(*denotes co-first authors, #Corresponding authors)

1. Zhang Y*, Li X*, Ba Z, Lou J, Gaertner K.E, Zhu T, Lin X, Ye Y, Alt F.W#, Hu H*#.Molecular basis for differential Igk versus Igh V(D)J joining mechanisms. Nature 2024 (*Co-first authors; #Corresponding authors)

2. Zhang Y#, Zhang X, Dai H-Q, Hu H and Alt FW#. The role of chromatin loop extrusion in antibody diversification. Nat Rev Immunol 2022 

3. Dai HQ*#, Hu H*, Lou J, Ye AY, Ba Z, Zhang X, Zhang Y, Zhao L, Yoon HS, Chapdelaine-Williams AM, Kyritsis N, Chen H, Johnson K, Lin S, Conte A, Casellas R, Lee CS#, Alt FW#. Loop extrusion mediates physiological Igh locus contraction for RAG scanning. Nature 2021 (*Co-first authors)

4. Zhang Y, Zhang X, Ba Z, Liang Z, Dring EW, Hu H, Lou J, Kyritsis N, Zurita J, Shamim MS, Presser Aiden A, Lieberman Aiden E, Alt FW#. The fundamental role of chromatin loop extrusion in physiological V(D)J recombination. Nature 2019

Yangyang Zhu, Ph.D.

Current position: 

Postdoctoral fellow

Harvard Medical School

Biography:

Dr. Yangyang Zhu earned her B.S. degree in Biology at Shandong University in 2014. She went on to earn her Ph.D. in Biology (Immunology direction) at Tsinghua University in 2019. Her Ph.D. work studied the role of E3 ligase VHL in follicular helper T cells and humoral responses. Currently, Dr. Zhu is a postdoctoral fellow at Harvard Medical School, studying neuro-immune interactions in the gut. This involves the establishment of a chemogenetic-based neuronal activation system, by which she discovered that nociceptors regulate gut regulatory T cells via CGRP-Ramp1 axis, connecting pain signaling with Treg cells. Dr. Zhu commits to expand our understanding on gut neuro-immune crosstalk and shed light on IBD therapeutics.

Talk title:

A chemogenetic screen reveals that Trpv1-expressing neurons control regulatory T cells in the gut

Abstract: 

Neuroimmune crosstalk participates in intestinal tissue homeostasis and host defense. However, the matrix of interactions between arrays of molecularly defined neuron subsets and of immunocyte lineages remains unclear. We used a chemogenetic approach to activate eight distinct neuronal subsets, assessing effects by deep immunophenotyping, microbiome profiling, and immunocyte transcriptomics in intestinal organs. Distinct immune perturbations followed neuronal activation: Nitrergic neurons regulated T helper 17 (TH17)–like cells, and cholinergic neurons regulated neutrophils. Nociceptor neurons, expressing Trpv1, elicited the broadest immunomodulation, inducing changes in innate lymphocytes, macrophages, and RORg+ regulatory T (Treg) cells. Neuroanatomical, genetic, and pharmacological follow-up showed that Trpv1+ neurons in dorsal root ganglia decreased Treg cell numbers via the neuropeptide calcitonin gene-related peptide (CGRP). Given the role of these neurons in nociception, these data potentially link pain signaling with gut Treg cell function.

Highlighted publications:

1. Yangyang Zhu*, Kimberly Meerschaert*, Silvia Galvan-Pena, Na-Ryum Bin, Daping Yang, Himanish Basu, Ryo Kawamoto, Amre Shalaby, Stephen Liberles, Daine Mathis, Christophe Benoist# and Isaac Chiu# (2024).  A chemogenetic screen reveals that Trpv1-expressing neurons control regulatory T cells in the gut. Science 385, eadk1679. (* Co-first author, # Co-corresponding author).

2. Silvia Galván-Peña, Yangyang Zhu, Bola S Hanna, Diane Mathis, Christophe Benoist (2024). A dynamic atlas of immunocyte migration from the gut. Sci Immunol 9, eadi0672.

3. Deepshika Ramanan, Alvin Pratama, Yangyang Zhu, Olivia Venezia, Martina Sassone-Corsi, Kaitavjeet Chowdhary, Silvia Galván-Peña, Esen Sefik, Chrysothemis Brown, Adélaïde Gélineau, Diane Mathis, Christophe Benoist (2023). T regulatory cells in the face of the intestinal microbiota. Nat Rev Immunol 23, 749-762.

4. Juliette Leon, Daniel A Michelson, Judith Olejnik, Kaitavjeet Chowdhary, Hyung Suk Oh, Adam J Hume, Silvia Galván-Peña, Yangyang Zhu, Felicia Chen, Brinda Vijaykumar, Liang Yang, Elena Crestani, Lael M Yonker, David M Knipe, Elke Mühlberger, Christophe Benoist (2022). A virus-specific monocyte inflammatory phenotype is induced by SARS-CoV-2 at the immune-epithelial interface. Proc Natl Acad Sci U S A 119.

5. Yangyang Zhu, Yanxia Zhao, Le Zou, Danfeng Zhang, Daisuke Aki, Yun-Cai Liu (2019). The E3 ligase VHL promotes follicular helper T cell differentiation via glycolytic-epigenetic control. J Exp Med 216, 1664-1681.

6. Yangyang Zhu, Le Zou, Yun-Cai Liu (2016). T follicular helper cells, T follicular regulatory cells and autoimmunity. Int Immunol 28, 173-179.

7. Yafei Yin, Pixi Yan, Jinlong Lu, Guang Song, Yangyang Zhu, Zhaohui Li, Yi Zhao, Bin Shen, Xingxu Huang, Heng Zhu, Stuart H Orkin, Xiaohua Shen (2015). Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation. Cell Stem Cell 16, 504-516.

Yuanli Zhen, Ph.D.

Current position: 

Instructor in Medicine, 

Harvard Medical School, 

Department of Cancer Center, Massachusetts General Hospital

Biography:

Dr. Zhen received her Ph.D. degree at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences in Beijing, studying molecular mechanisms underlying the pathogenesis of human diseases with patient samples and mouse models. Dr. Zhen’s long-term interest is to improve molecular-targeted cancer therapy. With this, she has done a series of translational studies focusing on molecular targets and the mechanisms of action of molecular-targeted anti-tumor drugs in UT Southwestern Medical Center and HMS/MGH. Her recent work has provided new strategies to improve FGFR-targeted therapy by studying genetically activated FGFR2 signaling in cholangiocarcinoma.

Talk title:

Genetically activated FGFR2 signaling in intrahepatic cholangiocarcinoma

Abstract: 

FGFR2 is activated by gene fusions and other genomic alterations across a wide range of malignancies, including most commonly in cholangiocarcinoma (CCA, bile duct cancer). Patients with FGFR2+ CCA benefit from treatment with FGFR inhibitors (FGFRi), although the depth and duration of response need improvement. By studying our newly established patient-derived tumor models, we found the FGFR inhibitors only lead to cell growth arrest, but not cell death. To overcome the limitation, we performed high-throughput combination drug screens to identify strategies that potentiate FGFR inhibitors to induce cell death. We found that combining EGFR inhibitors with FGFR inhibitors leads to cell death (FGFR inhibition induces activation of EGFR signaling to maintain cell viability) and overcomes the resistance of FGFR inhibitors in cell lines and preclinical models, which has led to the opening of a clinical trial. Furthermore, to better understand the biology of FGFR2 signaling in cholangiocarcinoma, I conducted integrative multi-omic (transcriptomics, metabolomics, and phosphoproteomics) analysis of multiple patient-derived models and have defined that the NF-kB-dependent glycolysis is the major oncogenic mechanism downstream of FGFR2 signaling in cholangiocarcinoma. Conversely, FGFR inhibition blocks glycolysis while inciting adaptive changes, including switching fuel source utilization, favoring fatty acid oxidation, and increasing mitochondrial fusion and autophagy. Accordingly, FGFR inhibitor efficacy is potentiated by combined mitochondrial targeting, an effect enhanced in xenograft models by diet intervention (intermittent fasting). In summary, we have provided therapeutic strategies from the signaling transduction and metabolic aspects of view to potentiate FGFR-targeted therapy in cholangiocarcinoma. 

Highlighted publications: 

(#denotes co-first authors)

1. Zhen, Y., Liu, K., Shi, L., et al. FGFR inhibition blocks NF-ĸB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma. Nature Communications. 15 (1), 1-17, 2024.

2. Li, P.#, Zhen, Y.#, Kim, C.#, et al. Nimbolide Targets RNF114 to Induce the Trapping of PARP1 and Synthetic Lethality in BRCA-mutated Cancer. Science Advances. 9, eadg7752 (2023). 

3. Wu, Q.#, Zhen, Y.#, Shi, L., Vu, P., et al. EGFR Inhibition Potentiates FGFR Inhibitor Therapy and Overcomes Resistance in FGFR2 Fusion–Positive Cholangiocarcinoma. Cancer Discovery. (2022) 12 (5): 1378–1395. 

4. Zhen, Y., Zhang, Y., Yu, Y. A Cell-Line-Specific Atlas of PARP-Mediated Protein Asp/Glu-ADP-Ribosylation in Breast Cancer. Cell Reports. 2017; 21(8):2326-2337

5. Zhen, Y., Li, W. Selective impairment of autophagosome-lysosome fusion in buff mice with VPS33A (D251E) mutation. Autophagy. 2015; 11(9):1608-22.

6. Wang, L#., He, F#., Bu, J#., Zhen, Y#., Liu, X., Du, W., Dong, J., Cooney, J.D., Dubey, S.K., Shi, Y., et al. ABCB6 mutations cause ocular coloboma. American Journal of Human Genetics. 2012, 90, 40-48. 

We are looking for speakers on a permanent basis. Sign up to present: 

https://docs.google.com/forms/d/1I5cJunp0VZ3gM8rSKHoCvEhFjtmdSBJ3_nCwUUNrYZY/edit 

(或点击阅读原文报名主讲)