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At first, Xuebing Wu , PhD, was on track to pursue a research career in computer engineering. After taking a course by Dr. Yanda Li, a pioneer of bioinformatics, Dr. Wu’s interest quickly shifted and he soon got hooked on genomics research and computational biology.

Xuebing Wu, PhD
Xuebing Wu, PhD

“Around that time—2003 to 2004—the human genome project had just been completed, and there had been lots of enthusiasm about using computational approaches to decipher the human genome,” he said. “I was excited to dive into this field that seemed wide open for research possibilities.”

Dr. Wu joined Columbia University’s Department of Systems Biology in the fall of 2018, with a joint appointment in the Department of Medicine’s Cardiology Division . He also is a member of the Herbert Irving Comprehensive Cancer Center at NewYork-Presbyterian/Columbia and the Columbia Data Science Institute , and his lab straddles basic science and computational biology. Dr. Wu and collaborators often consider how their work can make an impact in novel therapeutics. 

At the center of his interests is understanding the fundamental principles of gene regulation in human cells through integrative genomics approaches. His previous work has uncovered important roles of RNA sequence and structure signals in controlling the expression and evolution of the mammalian genome. His lab currently studies RNA-centric gene regulation, focusing on mRNA structures and mRNA translation. Dr. Wu and his team are increasingly turning their attention to the development of genomic technologies such as the revolutionary CRISPR/Cas system and a high throughput analysis technology called massively parallel reporter assays (MPRA), as well as novel computational tools and deep learning models to study gene regulation at a global scale. 

Congenital diaphragmatic hernia (CDH) is a severe birth defect. For babies born with CDH, their diaphragms are not developed properly, with some or all parts of the abdominal organs pushed into the chest. The displacement of these critical organs can have a significant impact on how the lungs develop and grow. 

Dr. Yufeng Shen
Yufeng Shen, PhD, associate professor of systems biology

A recent study , led by Yufeng Shen , PhD, and Wendy Chung , MD, PhD, and their labs at Columbia University Irving Medical Center , investigated the genetic risk factors linked to CDH and analyzed data from whole genome sequencing and exome sequencing to determine novel mutations. The study also uncovered the link between CDH and additional developmental disorders. 

“Many babies with this birth defect also have lung hypoplasia or pulmonary hypertension and babies have difficulty breathing. Even with advanced care available, the mortality rate is still about 20 percent,” says Dr. Shen, associate professor of systems biology at Columbia, with a joint appointment in the Department of Biomedical Informatics

“One hypothesis is that the lung condition is not necessarily caused by the physical compression on the developing lungs in the chest,” explains Dr. Shen, “it can be caused by the same genetic defect that causes CDH. Finding those genes is absolutely necessary to improve care and develop effective treatment in the long run.”   

Scientists have been aiming to identify new risk genes in CDH—and other developmental disorders—with  the hope that with improved genetic diagnosis more tailored or long-term care for patients born with this defect could be provided, as well as potential targets for intervention down the road. 

 

PCF Challenge Award PIs
Principal investigators on the PCF Challenge Award grant, from left to right: Andrea Califano, Michael Shen and Charles Drake.

Columbia University Irving Medical Center experts in prostate cancer will lead a new team research project that tests a novel approach for personalized cancer treatment. 

The two-year project, funded by a $1 million Challenge Award from the Prostate Cancer Foundation (PCF) , combines cutting-edge techniques that include computational methods for targeted drug therapy, single-cell RNA sequencing and novel cancer immunotherapy. The combined approaches are behind a proof-of-concept clinical trial for patients with lethal metastatic prostate cancer.  

PCF Challenge Awards fund projects that bring together experts from a number of related fields to form a team focused on the creation of innovative, effective therapies for advanced prostate cancer. As part of Columbia’s grant, the new clinical trial will take place at the James J. Peters VA Medical Center (also known as the Bronx VA), a partner of Columbia University Irving Medical Center (CUIMC) and New York-Presbyterian .

PCF is recognized as the leading philanthropic organization for prostate cancer research. For the team at Columbia’s Herbert Irving Comprehensive Cancer Center (HICCC ), receiving a Challenge Award from the foundation was more than just an exciting achievement. It underscores CUIMC’s continued commitment to strengthen and expand its expertise in prostate cancer research and care through investments in faculty recruitment, enhanced emphases on bolstering basic science research and clinical trials centered on the disease and direct engagement with PCF. 

 

Cory Abate-Shen
Cory Abate-Shen, PhD

Cory Abate-Shen , PhD, who is known for her leading work in the development of innovative mouse models for translational research in prostate and bladder cancers, has been elected a fellow of the American Association for the Advancement of Science (AAAS) . The AAAS is honoring Dr. Abate-Shen for her work in mouse models to better understand how basic cellular mechanisms are co-opted in cancer and for her contributions to the field of cancer biology. 

She joins a class of 416 new fellows, including two additional Columbia University faculty members, Drs. Richard Axel and Upmanu Lall, who also were elected today to the prestigious group. 

Dr. Abate-Shen, the Michael and Stella Chernow Professor of Urologic Sciences at Columbia University Irving Medical Center (CUIMC) , holds joint appointments in the Departments of Systems Biology , Medicine and Pathology & Cell Biology , and is a member and former interim director of the Herbert Irving Comprehensive Cancer Center (HICCC) . An internationally recognized leader in genitourinary malignancies, Dr. Abate-Shen is particularly interested in advancing our understanding of the mechanisms and modeling of prostate and bladder tumors. An innovator in the generation of novel mouse models for these cancers, her work has led to the discovery of new biomarkers for early detection, as well as key advances in cancer prevention and treatment. Dr. Abate-Shen has been the recipient of numerous awards, including a Sinsheimer Scholar Award, an NSF Young Investigator Award, a Bladder Cancer Advocacy Network Innovator Award and the Women in Cell Biology Junior Award from the American Society for Cell Biology. Currently, she is an American Cancer Society Research Professor, the first to be awarded at CUIMC. 

Faculty

Xuebing Wu

Assistant Professor of Medical Sciences (in Medicine and in Systems Biology)

Assistant Professor of Medical Sciences (in Medicine and in Systems Biology)

A research team from Columbia University Irving Medical Center has received a 2018 PCF Challenge Award from the Prostate Cancer Foundation (PCF) to advance prostate cancer research. The interdisciplinary team at Columbia includes leading experts in systems biology, cancer research and medicine from Columbia’s Department of Systems Biology and the Herbert Irving Comprehensive Cancer Center (HICCC)

Announced today, PCF is awarding more than $5.5 million in funding to a total of six teams to conduct research with the highest potential for accelerating new and improved treatments for advanced prostate cancer. PCF is one of the largest non-governmental organizations dedicated solely to funding prostate cancer research, and its annual Challenge Awards are highly coveted in the scientific and medical fields. 

In the United States, prostate cancer is the most common non-skin cancer, and 1 out of every 9 men in the U.S. will be diagnosed with the disease in his lifetime. To date, treatment of the most aggressive forms of prostate cancer represents a clinical challenge. After treatment failure with anti-androgen drugs, which are part of the standard of care for advanced metastatic prostate cancer, only few current therapeutic options remain and the impact on patient survival is limited. Indeed, the field needs major innovative, out-of-the-box approaches to new therapies to combat advanced prostate cancer. 

Organoids bladder cancer

Organoids created from the bladder cancers of patients mimic the characteristics of each patient’s tumor and may be used in the future to identify the best treatment for each patient. Images: Michael Shen

Columbia University Irving Medical Center (CUIMC) and NewYork-Presbyterian researchers have created patient-specific bladder cancer organoids that mimic many of the characteristics of actual tumors. As reported by CUIMC, the use of organoids, tiny 3-D spheres derived from a patient’s own tumor, may be useful in the future to guide treatment of patients.

The study was published April 5 in the online edition of Cell.

Faculty

Nicholas Tatonetti

Associate Professor of Biomedical Informatics (in Systems Biology and in Medicine)

Associate Professor of Biomedical Informatics (in Systems Biology and in Medicine)

Faculty

Michael Shen

Professor, Departments of Medicine, Genetics & Development, Urology, and Systems Biology

Professor, Departments of Medicine, Genetics & Development, Urology, and Systems Biology