Since it was established in October 1991, the Han lab has developed and engaged in dynamic research programs in the field of cell and developmental biology, with an emphasis on addressing important questions in relatively unexplored areas so that the findings have the potential to be seminal and paradigm shifting. The lab encourages postdocs and students to follow their own ideas during their research, as a number of them have done quite successfully.
Major research accomplishments (1991-2013)
We have followed the research philosophy, adopted by many leading genetic labs, to bravely pursue new important problems so that we may have better opportunities to make novel discoveries and obtain new biological insights. This often means that the lab needs to move into diverse and unfamiliar research areas.
1. Discovered and analyzed the roles of 12+ regulators of the highly-conserved 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 80s and early 90s, extensive efforts in the Ras signaling field were devoted to searching for Ras effectors. The genetic studies done in Drosophila and C. elegans critically influenced the mammalian biochemical studies that determined Raf as a direct target (effector) of Ras.
From the start in 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’s 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 suppression of activated Ras, was later identified to encode CNK. 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 the 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 DNA damage response during mitotic cell proliferation that provided mechanistic insight into the pathology of H-G Progeria Syndrome and Emery-Dreifuss muscular dystrophy (Lei et al. 2012).
3. Discovered the essential role of GW182 family proteins in miRISCs and developed biochemical and genetic methods to systematically analyze the in vivo miRNA-target interactions for different physiological functions
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).
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, 2012; Than et al, 2013). For example, the mapping of gut-specific miRNA-target interactions led to the finding that ~17 miRNAs repressed ~100 pathogen-responsive genes in the gut to prevent their toxic effects (Kudow et al. 2012).
Adding combinatory genetic tools, we have effectively uncovered important roles of these “non-essential” miRNAs in stress responses and development. For example, we found multiple miRNAs in the gut and neurons play critical roles in promoting two types of starvation-induced responses (Zhang et al. 2011; Than et al. 2013). 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. Discovered the mechanisms by which specific fatty acid and lipid variants critically impact cell signaling pathways to regulate animal development and behaviors
In one specific example, we showed that ACS family enzymes critically regulate the incorporation of mmBCFAs into specific phospholipids (PLs) in the somatic gonad so that proper PL composition is achieved in the zygote (Kniazeva et al. 2012). Imbalance of mmBCFA-containing PL compromises IP3 signaling leading to dramatic disruption of membrane dynamics. Understanding how different FAs are channeled into different high-order lipids, and how the lipid composition impacts animal growth and development, is one of the focuses of the lab.
In the early 2000s, propelled by our prior analysis of human macular degeneration that revealed a role for a fatty acid (FA) elongase, the Han lab made a bold move into the wide-open field of lipid functional analysis. Fatty acids (FAs) are highly variable in their structures and these variations greatly contribute to the vast diversity in lipid structures. Despite sporadic reports linking FA variants with human diseases and animal development, their functional specificities are poorly studied in general, and we know little about the mechanisms by which these variants contribute to the lipid composition in specific tissues for cellular events under physiological conditions. Combining genetics with biochemistry, including mass spectrometry, we uncovered spectacular impacts of monomethyl branched-chain fatty acids (mmBCFAs) on cell signaling and development.
Our 2004 paper (Kniazeva et al.) described the first significant functional analysis of the obscure mmBCFAs of the worm, and the striking essential functions of FAs 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 shutdown the entire postembryonic developmental program in response to depletion of mmBCFAs, and the role of a P-type ATPase in this specific function (Kniazeva et al. 2008; Seamen et al. 2009). Further study led to a series of papers and our current project that focuses on a lipid-TORC1 signaling pathway (see current research).
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 the 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. Starvation-induced stress response
How animals coordinate gene expression in response to starvation is an outstanding problem closely linked to aging, obesity, and cancer. Newly hatched Caenorhabditis elegans respond to food deprivation by halting development and promoting long-term survival (L1 diapause), thereby providing an excellent model to study starvation response. Through a genetic search, we have discovered many factors including tumor suppressor Rb and ceramide that critically promote survival during L1 diapause and likely do so by regulating the expression of genes in both insulin-IGF-1 signaling (IIS)-dependent and -independent pathways (Cui et al. 2013; 2017). Global gene expression analyses suggested that Rb maintains the “starvation-induced transcriptome” and represses the “re-feeding induced transcriptome”, including the repression of many pathogen/toxin/oxidative stress-inducible and metabolic genes, as well as the activation of mitochondrial respiratory chain genes. Importantly, the majority of genes dysregulated in starved L1 Rb(-) animals were not found to be dysregulated in fed conditions. Our studies suggest a link between functions of tumor suppressors and starvation survival. These results may provide mechanistic insights into why cancer cells are often hypersensitive to starvation treatment.
7. 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).