Biomolecular Engineering Seminars

BME 280B Spring 2016

Biomedical Sciences Building room 200

Thursdays at noon

(abstracts below)

                 

March 31  

Dhanya Cheerambathur,Ludwig Institute for Cancer Research, UC San Diego:

“Kinetochore-microtubule interfaces during chromosome segregation and neuronal morphogenesis”

Host: Doug Kellogg, MCD

Note different time: 12.30 pm

 

April 7       

Luping Huang, Director of Business Development, Applied StemCell, Inc:

“Choosing the right genome editing technology for your animal and cell models:

CRISPR, TARGATT, and beyond.”

Host: Camilla Forsberg, BME

 

April 14     

Nathalie Scholler, Director, Cancer Immunology, SRI Biosciences, Menlo Park, CA:

“Mesothelin targeting for diagnostic, therapy and prevention of ovarian cancer”

Host: Phil Berman, BME

 

April 21     

Lucia Carbone, Assistant Professor, Oregon Health and Science University:

“Genomic earthquakes and LAVA flow: the gibbon has it all!”

Host: Ed Green, BME

 

April 28     No BME seminar. Please consider attending the UCSC STEM Postdoc Symposium,

                  Seymour Marine Center

 

May 5        TBD

 

May 12     

Patricia Ernst, Professor of Pediatrics, Blood Cancer & BMT Program, University of Colorado:

“Histone methyltransferases in hematopoiesis and leukemia”

Host: Camilla Forsberg, BME

 

May 19     

Shaheen Shabbir Sikandar, postdoctoral fellow, Michael Clarke lab, Stanford University:

“The LMO2 oncogene regulates breast cancer metastasis”

Host: Camilla Forsberg, BME

 

May 26     

Moritz Mall, postdoctoral fellow, Marius Wernig lab, Stanford University:

“Active transcriptional repression is required for neuronal cell fate induction”

Host: Camilla Forsberg, BME

 

June 2     

Gus Zeiner, co-founder and CSO at Chimera Bioengineering, South San Francisco:

“RNA-based gene regulation for chimeric antigen receptor therapeutics”

Host: Camilla Forsberg, BME

 

SEMINARS WITH ABSTRACTS:

April 7        Luping Huang, Director of Business Development, Applied StemCell, Inc:

“Choosing the right genome editing technology for your animal and cell models: CRISPR, TARGATT, and beyond.” Host: Camilla Forsberg, BME

Abstract: Genomic editing technology allows a gene of interest to be modified in the genome of a laboratory animal or cell line, and provides an extremely powerful tool to dissect the molecular mechanisms of disease. Genetically modified animal or cell models have been widely used in mimicking genetic disease, investigating pathology of the disease, and providing pre-clinical drug screening tools.  Applied StemCell is a leading company dedicated to develop innovative, proprietary precise genome editing and stem technologies. In this presentation, we will review the most advance gene editing technologies including CRISPR, TARGATTTM, transposons, zinc finger nucleases (ZFNs) and Tal effector nucleases (TALENs), and discuss their applications. These would help you identifying the right technologies to be used for your research purpose.

  

April 14      Nathalie Scholler, Director, Cancer Immunology, SRI Biosciences, Menlo Park, CA:   

                   “Mesothelin targeting for diagnostic, therapy and prevention of ovarian cancer”

                   Host: Phil Berman, BME

Abstract: Ovarian cancer remains the leading cause of gynecological cancer deaths and is mostly detected in late stages while chances of survival at 5 years are lower than 30%.  In contrast, patient survival is increased to more than 90% when the cancer is detected early. Thus the development of early detection and prevention strategies for this cancer has been our long-term focus. Mesothelin is a GPI-anchored glycoprotein that is evolutionary conserved and normally present on the epithelial layer of serous membranes. Mesothelin is also a tumor antigen overexpressed by ovarian, pancreas and lung carcinomas. The absence of obvious phenotype of mice genetically depleted of mesothelin indicated that it is a nonessential protein and suggested that mesothelin could be a suitable target for immunotherapy and prevention of cancer. We demonstrated that mesothelin is a serum biomarker for ovarian cancer and we generated the first mesothelin ELISA assay that is now commercialized as Mesomark^TM. Next, we engineered molecular targeting tools using yeast-display libraries of recombinant antibodies from naïve donors and ovarian cancer patients, as well as from mesothelin-immunized llama. We isolated anti-mesothelin single chain variable fragments (scFv) that we further biotinylated using site-specific, in vivo enzymatic modification in yeast (biobodies), as well as single domain antibodies (VHH or nanobodies). We have used the recombinant antibodies to detect mesothelin by bead-based assays with sera or by fluorescent imaging in vitro and in vivo. Anti-mesothelin scFv was also applied to the molecular engineering and preclinical validation of mesothelin-targeted CAR-T cells and recombinant immunotoxin. We are now developing novel strategies for ovarian cancer prevention and we will present data supporting the hypothesis that mesothelin-based vaccines could become part of the clinician arsenal against ovarian cancer. 

 

April 21      Lucia Carbone Assistant Professor, Oregon Health and Science University: “Genomic

                  earthquakes and LAVA flow: the gibbon has it all!” Host: Ed Green, BME

Abstract: Gibbons are small Asian apes heavily threatened by extinction. They carry many distinctive traits that set them apart from their close relatives, human and the great apes, including brachiation (i.e. locomotion mainly using their upper limbs), pair bonding, and duet singing to advertise their territory. Their most striking trait, however, is the unusually high number of chromosomal rearrangements. There are four gibbon genera (Nomascus, Hoolock, Hylobates, and Symphalangus) that split from each other only 5 million years ago and each of them carries a distinct karyotype with chromosome numbers ranging from 38 to 52. This exceptional accelerated karyotype evolution makes gibbons an ideal model to study chromosome evolution and mechanism of genome instability. Together with geographical changes occurring in their territory, the abundance of chromosomal rearrangements was responsible for an “instantaneous” radiation of the gibbon genera and the higher number of species (n=19) found in the gibbon family. We discovered that a gibbon specific retrotransposon, the LAVA element, inserted in genes involved in chromosome segregation, suggesting that  in these species chromosome fragility might have been triggered by mis-segregation during meiosis. This phenomenon has recently been characterized in cancer genomes and embryo development, highlighting an analogy between mechanisms underlying genome instability during species evolution and disease.

 

May 12      Patricia Ernst, Professor of Pediatrics, Blood Cancer & BMT Program, University of

                  Colorado: “Histone methyltransferases in hematopoiesis and leukemia” Host: Camilla Forsberg, BME

Abstract: MLL1 chromosomal translocations occur frequently in infant leukemia and in adult therapy-induced leukemia. Due to the poor prognosis of MLL-rearranged (MLLr) leukemia, significant effort has gone into developing targeted therapeutics to inhibit MLL-fusion proteins (FPs), which are expressed from the most common MLL1 rearrangements. The remaining wild-type MLL1 allele is typically preserved in MLL-FP leukemia blasts, suggesting functional importance of the wild-type MLL1 protein. In addition, published studies suggest that the recruitment or activity of MLL-FPs may depend on the activity of the remaining MLL1 allele. Since MLL1 encodes a protein with histone methyltransferase (HMT) activity, compounds that inhibit HMT activity are under development. However, MLL-FPs lack the HMT domain and our recent studies demonstrate that MLL-AF9-driven leukemogenesis progresses normally in cells genetically engineered to lack the HMT domain. Furthermore, the existence of patient-derived cell lines (e.g. ML2) in which the entire wild-type MLL1 locus has been lost calls into question the role of MLL1 in MLL-FP-initiated leukemia. These conflicting observations prompted us to carefully revisit the role of wild-type MLL1 in MLL-FP-initiated leukemia using genetic models. To directly address whether endogenous MLL1 plays any role in facilitating transformation by MLL-FPs, we employed conditional mutagenesis to delete Mll1 or a critical cofactor, Menin (Men1), in the context of ongoing acute myelogenous leukemia (AML) initiated by either MLL-AF9 or MLL-AF6. Men1 encodes a protein that directs chromatin targeting of both wild-type MLL1 and MLL-FP complexes. Surprisingly, we find that Mll1 is dispensable for MLL-AF9- and MLL-AF6-mediated AML progression in vitro or in vivo. In contrast, deletion of Men1 significantly impairs leukemia progression both in vivo and in vitro, as others have observed. Furthermore, the lack of requirement for endogenous Mll1 was confirmed using two distinct Mll1 conditional knockout alleles. Upon Mll1 deletion few gene expression changes occurred, and MLL-AF9 fusion targets were absolutely unaffected by Mll1 deletion. This result contrasted with striking gene expression changes, cell cycle arrest and ultimately death of AML blasts that occurred upon deletion of Men1. To understand the lack of impact of MLL1 loss, we co-deleted both Mll1 and the related methyltransferase Mll2 in MLL-AF9 initiated AML. Co-deletion had a significant impact on AML growth and survival, but this was surprisingly not due to redundancy between the Mll genes as genome wide data indicated they regulate largely distinct sets of genes, and largely not MLL-AF9 direct targets. MLL2, but not MLL1 loss led to a global reduction in H3K4me3 and me2 in MLL-AF9 leukemia cells. Overall, our data demonstrate that endogenous MLL1 is not required for maintaining leukemogenesis in MLL-FP-initiated leukemia and argue against the utility of drugs that exclusively target the wild-type MLL1 protein complex in the treatment of MLLr leukemia. However, inhibition of both related methyltransferases may significantly impair leukemia survival.

 

May 19      Shaheen Shabbir Sikandar, postdoctoral fellow, Michael Clarke lab, Stanford University: “The LMO2 oncogene regulates breast cancer metastasis.”Host: Camilla Forsberg, BME

Abstract: Recent evidence suggests that expression of genes related to epithelial mesenchymal

transition (EMT) in breast cancer cells regulate metastases and chemoresistance. However, a normal

counterpart of these cells in the mammary gland is largely unknown. Using S100a4/FSP1, a gene

whose expression is induced with EMT, we demonstrate that less than 1% of epithelial cells in the

normal mammary gland are S100a4+. These cells are present in both luminal and basal lineages.

Lineage traced S100a4+ basal cells can transplant in vivo, have long term reconstitution ability and

are bipotent. Single cell gene expression analysis of S100a4+ cells shows that they express

significantly higher levels of EMT associated genes such as Zeb1 and Zeb2. In addition, we identify

LMO2, a T-cell leukemia oncogene to be expressed in S100a4+ cells. Lineage tracing for Lmo2,

indicates that Lmo2+ cells contribute to luminal and basal lineages of the mammary gland network

during development. Furthermore, in humans LMO2 is expressed in basal cells in the normal

mammary gland and in breast cancer cells. Knockdown studies in patient derived xenografts show

that a decrease in LMO2 specifically reduces lung metastasis while increased expression of LMO2

enhances metastasis-seeding ability. RNA-seq analysis shows that LMO2 regulates genes previously

implicated in metastasis such as VCAM1, CKIT, STC2 and TMEM45A.  Taken together, we

demonstrate that in the normal mammary gland, a subset of cells express genes associated with EMT

and have regenerative capacity in vivo. Moreover, we identify LMO2 as a novel player in the

metastasis that can serve as a therapeutic target in the future.

 

May 26      Moritz Mall, postdoctoral fellow, Marius Wernig lab, Stanford University:

                “Active transcriptional repression is required for neuronal cell fate induction”

                Host: Camilla Forsberg, BME

Abstract: Induction of cell identity demands activation of lineage specific transcriptional programs and shut down of several existing and alternative programs. Studying the neuronal reprogramming factor Myt1l we found that it mediates active and sequence-specific repression mechanisms to generally suppress many unrelated lineage programs. Thereby Myt1l enables efficient neuronal fate induction and might be involved in neuronal stability during development and disease. One Sentence Summary: A neuron-restricted zinc finger transcription factor represses non-neuronal programs to enable proper lineage specification. Speaker Bio: Dr. Moritz Mall is a postdoctoral fellow in the laboratory of Prof. Marius Wernig at the Institute of Stem Cell Biology and Regenerative Medicine at Stanford University. After studying biochemistry and molecular biology at the LMU in Munich and the ETH in Zurich he received his Ph.D. from the EMBL in Heidelberg for his mechanistic studies on mitotic cell division. Dr. Mall’s current research focus is on the mechanisms of cell fate determination during reprogramming, development and disease.

 

June 2      Gus Zeiner, co-founder and CSO at Chimera Bioengineering, South San Francisco:

                  “RNA-based gene regulation for chimeric antigen receptor therapeutics” Host: Camilla

                  Forsberg, BME

Abstract: By the time a person is talking to their oncologist, cancer has evaded their immune system. Chimeric antigen receptor (CAR) technology is a modern blend of synthetic biology and personalized medicine that shows clinical promise at reversing this immune evasion. CARs hotwire patient-derived T-cells, redirecting them to find and kill tumor cells that are decorated with a defined target antigen. A key limitation of CAR technology is immune toxicity, which is a consequence of their potency. Toxicity currently limits the disease application horizon of CARs to a handful of liquid tumors. To solve CAR toxicity problems, Chimera Bioengineering builds modular, tunable, genetically encoded gene regulatory switches for CARs. Our gene regulatory switches respond to bio-orthogonal small molecule ligands, and can be customized to respond to a variety of distinct ligand inputs. Our long-term goal is to tune CAR therapies to maximize their therapeutic window, and to expand the application horizon of CAR therapies to include all cancers.

 

 

 

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