Major research accomplishments by Min Han prior to becoming a PI (1984-1991)

As a graduate student at UCLA under Michael Grunstein, his thesis work provided the first in vivo evidence for the fundamental role of histones and nucleosomes in regulating gene expression, which was credited as part of the “milestone discoveries” in gene expression by a panel of scientists assembled by Nature (nature.com/milestones/geneexpressions).  The research results were later also described in articles by the New York Times and Scientific American (Grunstein 1992; 267: 68-74).

As a postdoctoral fellow at Caltech under Paul Sternberg, his cloning and analysis of the C. elegans ras gene uncovered the fundamental function of this widely studied proto-oncogene in regulating animal development, impacting both signal transduction and developmental biology fields. The results of his two1990 papers, along with a paper from the Bob Horvitz lab (MIT), were considered landmark findings in the field that were commented by a Cell minireview and a Nature News & Views (Greenwald and Broach, Cell 1990; Bourne et al. 1990 Nature), as well as by AP news and other media outlets.

Major research accomplishments/contributions by the Han Lab (1991-2011)

Min has followed the research philosophy he learned from his mentors by encouraging his students and postdoctoral fellows to bravely pursue new important problems so that they have the opportunities to make novel findings and obtain new biological insights, even if it often means that the lab needs to move into new and unfamiliar research areas.

1.  Discovery and analysis of the roles of  >12 regulators of the RTK-RAS-MPK signaling pathway

The first important contribution the Han lab made was uncovering Raf as a critical factor downstream of Ras in early 1993 (Han et al.1993; collaborated with Andy Golden in Paul Sternberg’s lab where Min started the work on a raf mutation).  In the late 1980s and early 1990s, extensive efforts in the Ras signaling field were devoted to searching for Ras effectors. The genetic studies of Drosophila and C. elegans critically influenced the mammalian biochemical studies that determined Raf as a direct target (effector) of Ras.

Starting from the time the lab was established (1991), the Han lab has employed several genetic suppressor screens to search for new factors downstream of Ras in the RTK/Ras signaling pathway that controls developmental fate specification and cell proliferation in multi-cellular organisms. These efforts led to the isolation of a good number of mutations in more than12 genes that play conserved regulatory roles in this pathway. The genetic screen/mapping/position cloning/analysis effort not only determined roles of important known signaling molecules (such as MPK-1, MEK-2, SUR-6/phosphatase, CBP-1, PAR-1) in the Ras pathway but also lead to the discovery of a number of factors that were novel at the time [such as KSR (scaffold protein), SUR-8 (adaptor), SUR-2 (Mediator 23), SUR-5 (lipid modifier), and SUR-7 (Zn transporter)] (Wu and Han 1994; Wu et al. 1995; Sundaram and Han 1995; Singh and Han 1995; Sieburth et al. 1998; 1999; Gu and Han 1998; Yoder et al., 2004; Eastburn and Han 2005). The genetic studies that defined the critical roles of KSR, SUR-8 and SUR-2 in Ras signaling stimulated very extensive studies (including our own efforts) on the mammalian orthologs named after the initial genetic findings [KSR was named by parallel genetic studies in three worm/fly labs (Rubin, Horvitz and Han). The mammalian hSUR2 protein was later changed to MED-23 as part of a systematic renaming action. The first study on the mammalian SUR8 protein was carried out by our collaborative work with Kunliang Guan lab]. In addition, the studies on SUR-7 and PAR-1 led to an important insight into the functional relationship between KSR, RAF, MEK, PAR-1, as well as Zn++ transporters. Suppressor studies also revealed a rare allele of CBP-1 with hyperactive histone acetyl transferase activity. The sur-4 gene, defined by a spectacular dominant suppressor of activated Ras, is yet to be cloned and likely encodes another novel but important regulator, based on identities of genes in the mapped region.  The collection of published studies on these suppressor genes made a very large impact on both the field of signal transduction and development.

Of additional significance, the lab also determined that Ras is required for a limited number of cell fates and not for general proliferation in the worm (Yochem et al. 1997; Sundaram et al., 1996). We also pioneered the chemical/genetic analysis in C. elegans by testing the effects of two ras inhibitors (Hara and Han 1995).

2. Established the concept of universal pairing of SUN-KASH proteins at the nuclear envelope and uncovered their roles in multiple nucleus-involved cellular events in both C. elegans and mice

Through genetic and molecular analysis of three genes involved in nuclear migration and anchorage, the Han lab made breakthrough findings regarding nuclear envelope proteins that mediate nucleus-related cellular functions. The 1999 paper by Malone et al., collaborated with R. Horvitz’s group, defined the SUN gene family after cloning the unc-84 gene and identifying the first two mammalian SUN proteins. The 2001 and 2002 papers (Starr et al.; Starr and Han) defined the KASH domain and proposed the concept of the “universal” KASH-SUN pairing at the NE. These published findings ignited a wave of studies on these proteins that have now become a popular research area.

The Han lab, including researchers at both the University of Colorado and Fudan University, also took the leading role in studying the fundamental functions of these complexes in mice and made seminal/breakthrough findings that significantly advanced our knowledge in four areas: (1) uncovered the mechanism of synaptic and non-synaptic nuclear anchorage in mammalian muscle fibers (Grady et al. 2005, collaboration with J. Sanes lab; Zhang et al. 2007; Lei et al. 2009); (2) determined how telomeres of homologous chromosomes are anchored to the nuclear envelope for chromosome pairing and recombination during meiosis in animals (Ding et al. 2007); (3) uncovered the mechanism by which SUN-KASH complexes function in neuronal migration and neurogenesis in the brain cortex and retina, and provided critical insights about the mechanism (Zhang et al. 2009; Yu et al. 2011); and (4) uncovered the function of SUN proteins in mitotic cell proliferation (unpublished).

3. Discovery of the essential role of GW182 family proteins in miRISCs and development of novel biochemical methods to systematically analyze in vivo miRNA-target interactions under different physiological conditions

The Han lab first identified and reported the essential roles of GW182 family proteins in miRNA-mediated gene silencing in July 2005 (Ding et al. 2005), after a 5-year effort that began with a genetic screen. In this paper, we provided genetic evidence for the critical role of AIN-1/GW182 in miRNA function, determined the interaction of AIN-1 with Ago proteins and miRNAs, and revealed the role of AIN-1 in transporting miRISCs to P bodies known to be the site for RNA degradation. The lab later found AIN-2 as the second GW182 protein that shares functions with AIN-1. By high throughput analysis of the AIN-1 and AIN-2 containing complex, the lab showed both proteins associated with all miRNAs and interact with miRNA-specific Ago proteins (Zhang et al. 2007).

The researchers in the lab then pioneered a novel biochemical approach to systematically identify and analyze the miRNA-target interaction network under true physiological conditions. The method was established based on the finding that the levels of known miRNA targets correlate with the levels of corresponding miRNAs in the AIN-IP, indicating that the AIN-containing RISCs are legitimate miRNA effector complexes. Using the AIN-IP method, the students identified more than 4000 mRNAs that are likely targets of about 122 miRNAs in C. elegans (Zhang et al. 2007). These data led to the development of a new miRNA target prediction program by Victor Ambros lab (Hamell et al. 2008, collaboration with us and the Ding Ye lab). To identify the interaction network under specific physiological conditions, the lab developed methods to carry out stage- and tissue-specific IPs. These innovative approaches gained important insights regarding miRNA-mediated gene regulation during development and during animals’ response to stress conditions (Zhang et al. 2009, collaborated with Victor Ambros lab; Kudlow et al, unpublished). These studies support the idea that most of the individual miRNA-target interactions do not play an instructive role in regulating animal development or other physiological functions; rather, the majority of miRNAs act to maintain proper levels of gene expression, often counter to the activities of transcriptional induction of inducible genes, through a complex miRNA-target interaction network.

4. Identification of novel, but important, developmental functions associated with specific fatty acid and lipid variants

In 2002, the Han lab made a bold move into the wide-open field of functional analysis of lipid molecules. Fatty acid (FA) variants (>100) are very diverse in their structures and their levels are strictly maintained in a given organism, but little is known about the functional consequences of these variations, nor how animals achieve proper lipid composition in their membranes during development. For example, in analyzing the functions of phospholipids, the focus has commonly centered on the difference in the phospholipid head group, while few have paid attention to the role of variation in length and other aspects of the two side chains. Functional analysis of these variants in live animals is technically challenging since there is no linear relationship between the genome and lipid molecules. In the late 1990s/early 2000s, our lab was involved in a human genetics study of macular dystrophy initiated by a visiting MD (several publications by Kniazeva et al. and Zhang et al). The identification of a mutation in a human FA elongase led to a growing interest among our lab members in investigating the fundamental problem using C. elegans genetics (Kniazeva et al, 2002).

The 2004 paper (Kniazeva et al.) described the first significant functional analysis of the obscure mono-methyl branched chain fatty acids (mmBCFAs) of the worm, and the striking essential functions of fatty acids during development surprised many lipid experts. The pioneering work received exceptionally high remarks by the Faculty of 1000. The lab later reported further findings about how animals shut down the entire postembryonic developmental program in response to depletion of mmBCFA and the role of a P-type ATPase in this specific function (Kniazeva et al. 2008; Seamen et al., 2009).  More recently, the lab has made a major advancement in understanding the impact that proper fatty acid and lipid composition has on animal development, and the mechanism by which healthy lipid composition is achieved in the zygote.

5. Tackling the problem of “genetic redundancy by structurally unrelated genes”, roles of tumor suppressor genes in development

Genetic redundancy associated with structurally unrelated genes is a common phenomenon and an impediment to the functional dissection of a genome. Over the years, the lab has tackled this problem by doing combinational genetics. Most significantly, in 2002 and 2006, we reported two systematic approaches to identify many “hidden” developmental functions and “redundant” genes associated with two well-known tumor suppressor genes, Rb and Pten (Fay et al. 2002; Suzuki and Han 2006). At least one of these approaches could be applied to analyzing functions of any given gene with no obvious KO phenotypes. Other lab members have since used the methods to tackle “genetic redundancy” with other genes.

The lab has also made important contributions to understanding the mechanism underlying the negative regulation on RTK/Ras signaling provided by a large number of SynMuv genes divided into two redundant pathways. In a particular effort (Cui et al. 2006 Dev Cell, collaborated with Greenwald and Sternberg labs), we made a breakthrough finding on the problem by showing that the SynMuvA and SynMuvB gene classes redundantly repress transcription of the lin-3/EGF gene in the hypodermis to prevent ectopic vulval induction. This result underscored the importance of preventing inappropriate cell signaling during development, and suggested that de-repression of growth factors may be the mechanism by which tumor suppressor genes such as Rb can have cell non-autonomous effects.  Other efforts led to the identification of multiple chromatin-remodeling complexes involved in maintaining gene expression for precise developmental decisions (e.g., Chen and Han 2001 Dev; 2001 Curr Biol; Cui et al. 2006 PLoS Genetics).

6. Other research accomplishments

In the past 20 years, the lab has also gained significant insights in addressing other cell and developmental biology problems. These include the identifications of the role of LRP-1 as the steroid receptor at major epidermis (Yochem et al. 1999), several novel factors involved in morphogenesis (Hanna-Rose and Han 1999; 2000), roles of small GTPase ARL2, nuclear receptor NHR-25, RhoGEF, several cell adhesion molecules and a novel peptidase in cell migration, fusion and/or cytokinesis (Antoshechkin and Han 2002; Chen et al. 2004; Morita et al. 2005; Tucker et al. 2008), the role of a human disease gene homolog in maintaining the functional and structural integrity of the sensory organs (Tucker et al. 2005), the roles of cyclin E, a dynein protein and two cohesion molecules in mitosis and meiosis during C. elegans’ development (Fay and Han 2000; Yoder et al. 2001; Wang et al, 2003), and several factors in transcription termination/3’ formation (Cui et al. 2009, collaboration with T Blumenthal lab). The lab also developed a GFP-based mosaic analysis method (Yochem et al. 1998).