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Regulators of mesenchymal GBM subtype

An example of tumor oncotecture. Transcription factors involved in the activation of mesenchymal glioblastoma subtype are shown in purple. Together, they comprise a tightly knit tumor checkpoint, controlling 74% of the genes in the mesenchymal signature of high-grade glioma. CEBP (both β and δ subunits) and STAT3 regulate the other three transcription factors in the tumour checkpoint, synergistically regulating the state of mesenchymal GBM cells. (Image: Nature Reviews Cancer)

In a detailed Perspective article published in Nature Reviews Cancer, Department of Systems Biology chair Andrea Califano and research scientist Mariano Alvarez (DarwinHealth) summarize more than a decade of work to propose the existence of a universal, tumor independent “oncotecture” that consistently defines cancer at the molecular level. Their findings, they argue, indicate that identifying and targeting highly conserved, essential proteins called master regulators — instead of the widely diverse genetic and epigenetic alterations that initiate cancer and have been the focus of much cancer research — could offer an effective way to classify and treat disease.

As coverage of the paper in The Economist reports:

ONE of the most important medical insights of recent decades is that cancers are triggered by genetic mutations. Cashing that insight in clinically, to improve treatments, has, however, been hard. A recent study of 2,600 patients at the M.D. Anderson Cancer Centre in Houston, Texas, showed that genetic analysis permitted only 6.4% of those suffering to be paired with a drug aimed specifically at the mutation deemed responsible. The reason is that there are only a few common cancer-triggering mutations, and drugs to deal with them. Other triggering mutations are numerous, but rare—so rare that no treatment is known nor, given the economics of drug discovery, is one likely to be sought. 

Facts such as these have led many cancer biologists to question how useful the gene-led approach to understanding and treating cancer actually is. And some have gone further than mere questioning. One such is Andrea Califano of Columbia University, in New York. He observes that, regardless of the triggering mutation, the pattern of gene expression—and associated protein activity—that sustains a tumour is, for a given type of cancer, almost identical from patient to patient. That insight provides the starting-point for a different approach to looking for targets for drug development. In principle, it should be simpler to interfere with the small number of proteins that direct a cancer cell’s behaviour than with the myriad ways in which that cancer can be triggered in the first place. (Read full article.)

Papers

Each year, participants in the ISCB/RECOMB Conference on Regulatory and Systems Genomics select publications over the past year that they consider to have made the most significant contributions to the field. During the most recent conference, held in Philadelphia on November 15-18, 2015, the top 10 papers were announced. Among those selected were four involving Columbia University Department of Systems Biology investigators. 

cQTLs modify TF binding

Cofactors work with transcription factors (TFs) to enable efficient transcription of a TF's target gene. The Bussemaker Lab showed that genetic alterations in the cofactor gene (cQTLs) change the nature of this interaction, affecting the connectivity between the TF and its target gene. This, combined with other factors called aQTLs that affect the availability of the TF in the nucleus, can lead to downstream changes in gene expression.

When different people receive the same drug, they often respond to it in different ways — what is highly effective in one patient can often have no benefit or even cause dangerous side effects in another. From the perspective of systems biology, this is because variants in a person’s genetic code lead to differences in the networks of genes, RNA, transcription factors (TFs), and other proteins that implement the drug’s effects inside the cell. These multilayered networks are much too complex to observe directly, and so systems biologists have been developing computational methods to infer how subtle differences in the genome sequence produce these effects. Ultimately, the hope is that this knowledge could improve scientists’ ability to identify drugs that would be most effective in specific patients, an approach called precision medicine.

In a paper published in the Proceedings of the National Academy of Sciences, a team of Columbia University researchers led by Harmen Bussemaker proposes a novel approach for discovering some critical components of this molecular machinery. Using statistical methods to analyze biological data in a new way, the researchers identified genetic alterations they call connectivity quantitative trait loci (cQTLs), a class of variants in transcription cofactors that affect the connections between specific TFs and their gene targets.

Yaniv Erlich
Yaniv Erlich. Photo: Jared Leeds.

A new article published online in Nature Genetics reports that short tandem repeats, a class of genetic alterations in which short motifs of nucleotide base pairs occur multiple times in a row, play a role in modulating gene expression. Leading the study was Yaniv Erlich, an assistant professor in the Columbia University Department of Computer Science and core member of the New York Genome Center who recently joined the Center for Computational Biology and Bioinformatics.

As an article in Columbia Engineering explains, the findings reveal a new class of genome regulation.

The Department of Systems Biology and Center for Computational Biology and Bioinformatics are pleased to announce that three Columbia University faculty members have recently joined our community. Kam Leong, the Samuel Y. Sheng Professor of Biomedical Engineering at Columbia University, is now an interdisciplinary faculty member in the Department of Systems Biology. In addition, Yaniv Erlich and Guy Sella are now members of the Center for Computational Biology and Bioinformatics (C2B2). Their addition to the Department and to C2B2 will bring new expertise that will benefit our research and education activities, incorporating perspectives from fields such as nanotechnology, bioinformatics, and evolutionary genomics.

Breast cancer cells

A histological slide of cancerous breast tissue. The pink "riverways" are normal connective tissue while areas stained blue are cancer cells. (Source: National Cancer Institute)

Investigators at Columbia University Medical Center and the Icahn School of Medicine at Mount Sinai have discovered a molecular signaling mechanism that drives a specific type of highly aggressive breast cancer. As reported in a paper in Genes & Development, a team led by Jose Silva and Andrea Califano determined that the gene STAT3 is a master regulator of breast tumors lacking hormone receptors but testing positive for human epidermal growth receptor 2 (HR-/HER2+). The researchers also characterized a pathway including IL-6, JAK2, STAT3, and S100A8/9 — genes already known to play important roles within the immune response — as being essential for the survival of HR-/HER2+ cancer cells. Additional tests showed that disrupting this pathway severely limits the ability of these cells to survive.

These findings are particularly exciting because the pathway the researchers identified contains multiple targets for which known FDA-approved drugs exist. The paper reports that when these drugs were tested in disease models, the cancer cells showed a dramatic response, suggesting promising strategies for the treatment of the HR-/HER2+ cancer subtype. A clinical trial is now underway to investigate the effects of these approaches in humans.

Saeed TavazoieSaeed Tavazoie, a professor in the Columbia University Department of Systems Biology, has been named a recipient of a 2015 National Institutes of Health Transformative Research Award. The grant will support research to develop state-of-the-art experimental and computational methods for comprehensively mapping and modeling all pairwise molecular interactions inside cells. 

The Transformative Research Award is a part of the NIH Common Fund’s High-Risk, High-Reward Research program, which provides critical funding to scientists it recognizes as being exceptionally creative and who propose particularly innovative approaches to solving key problems in biomedical research. The Transformative Research Award is designed to support projects that use methods and perspectives that are unconventional and untested, but show great potential to create or overturn fundamental paradigms.

Alex Lachmann
Alex Lachmann during his presentation to the RNA-Seq "boot camp."

In June 2015, the Columbia University Department of Systems Biology held a five-part lecture series focusing on advanced applications of RNA-Seq in biological research. The talks covered topics such as the use of RNA-Seq for studying heterogeneity among single cells, RNA-Seq experimental design, statistical approaches for analyzing RNA-Seq data, and the utilization of RNA-Seq for the prediction of molecular interaction networks. The speakers and organizers have compiled a list of lecture notes and study materials for those wishing to learn more. Click on the links below for more information.

We are pleased to announce that Columbia University Medical Center professors Oliver Hobert, Richard Mann, and Rodney Rothstein have been named to interdisciplinary appointments in the Department of Systems Biology. The addition of this new expertise will expand the breadth of science currently being explored in the Department, enhance educational opportunities for students, facilitate new collaborations, and promote the integration of systems biology perspectives and methods into research being conducted elsewhere in the university.

Differential decay rates in MDA-LM2 vs. MDA cells

The presence of the structural RNA stability element (sSRE) family of mRNA elements distinguishes transcript stability in metastatic MDA-LM2 breast cancer cell lines from that seen in its parental MDA cell line. Each bin contains differential decay rate measurements for roughly 350 transcripts. From left (more stable in MDA) to right (more stable in MDA-LM2), sRSE-carrying transcripts were enriched among those destabilized in MDA-LM2 cells. The TEISER algorithm collectively depicts sSREs as a generic stem-loop with blue and red circles marking nucleotides with low and high GC content, respectively. Also included are mutual information (MI) values and their associated z-scores. 

Gene expression analysis has become a widely used method for identifying interactions between genes within regulatory networks. If fluctuations in the expression levels of two genes consistently shift in parallel over time, the logic goes, it is reasonable to hypothesize that they are regulated by the same factors. However, such analyses have typically focused on steady-state gene expression, and have not accounted for modifications that messenger RNAs (mRNAs) can undergo during the time between their transcription from DNA and their translation into proteins. Researchers now understand that certain stem loop structures in mRNAs make it possible for proteins to bind to them, often causing RNA degradation and subsequently modulating protein synthesis. From the perspective of systems biology, this can have implications for the activity of entire regulatory networks, and recent studies have even suggested that aberrations in mRNA stability can play a role in disease initiation and progression.

In a new paper published in the journal Nature, Department of Systems Biology Professor Saeed Tavazoie and collaborators at the Rockefeller University describe a new computational and experimental approach for identifying post-transcriptional modifications and investigating their effects in biological systems. In a study of metastatic breast cancer, they determined that when the protein TARBP2 binds to a specific structural element in mRNA transcripts, it increases the likelihood that cancer cells will become invasive and spread. Interestingly, they also found that TARBP2 causes metastasis by binding transcripts of two genes — amyloid precursor protein (APP) and zinc finger protein 395 (ZNF395) — that have previously been implicated in Alzheimer’s disease and Huntington’s disease, respectively. Although the nature of this intersection between the regulatory networks underlying cancer and neurodegenerative diseases is unclear, the finding raises a tantalizing question about whether these very different disorders might be linked at some basic biological level.

Saeed Tavazoie

One of the defining features of systems biology has been its integration of computational and experimental methods for probing networks of molecular interactions. The research of Saeed Tavazoie, a professor in the Columbia University Department of Systems Biology, has been emblematic of this approach. After undergraduate studies in physics, he became fascinated by the processes that govern gene expression, particularly in understanding how gene expression is regulated by information encoded in the genome. Since then, his multidisciplinary approach to research has generated important insights into the principles that orchestrate genome regulation, as well as a number of novel algorithms and technologies for exploring this complex landscape.

In this conversation, Dr. Tavazoie discusses his research in the areas of gene transcription, post-transcriptional regulation, and molecular evolution, as well as some innovative technologies and experimental methods his lab has developed.

Barry Honig

When Columbia University founded the Center for Multiscale Analysis of Genomic and Cellular Networks (MAGNet) in 2005, one of its goals was to integrate the methods of structural biology with those of systems biology. Considering protein structure within the context of computational models of cellular networks, researchers hoped, would not only improve the predictive value of their models by giving another layer of evidence, but also lead to new types of predictions that could not be made using other methods.

In a new paper published in Nature magazine, Barry Honig, Andrea Califano, and other members of the Columbia Initiative in Systems Biology, including first authors Qiangfeng Cliff Zhang and Donald Petrey, report that this goal has now been realized. For the first time, the researchers have shown that information about protein structure can be used to make predictions about protein-protein interactions on a genome-wide scale. Their approach capitalizes on innovative techniques in computational structural biology that the Honig lab has developed over the last 15 years, culminating in the development of a new algorithm called Predicting Protein-Protein Interactions (PrePPI). In this interview, Honig describes the evolution of this new approach, and what it could mean for the future of systems biology.

An extensive microRNA-mediated network of RNA-RNA interactions

Genome-wide inference of sponge modulators identified a miR-program mediated post-transcriptional regulatory (mPR) network including ~248,000 interactions.

For decades, scientists have thought that the primary role of messenger RNA (mRNA) is to shuttle information from the DNA to the ribosomes, the sites of protein synthesis. However, new studies now suggest that the mRNA of one gene can control, and be controlled by, the mRNA of other genes via a large pool of microRNA molecules, with dozens to hundreds of genes working together in complex self-regulating sub-networks.

Transcriptional Network for Mesenchymal Transformation of Brain Tumors

The mesenchymal signature of high-grade gliomas is controlled by six transcription factors. TFs involved in activation of MGES targets are shown in pink, those involved in repression are in purple.

High-grade gliomas, such as glioblastoma, are incurable partly because the tumor cells are widely disseminated throughout the brain. This capacity for invasive growth has been associated with the expression of genes more commonly transcribed in mesenchymal cells. In work published in the journal Nature, Antonio Iavarone, Andrea Califano, and colleagues have identified a small transcription factor network that is responsible for the mesenchymal behavior of glioma cells.