Programs of the Colorectal Cancer Research Center

Programs of the Colorectal Cancer Research Center


The Colorectal Cancer Research Center has a number of wide-ranging programs focused on a range of topics and areas of expertise.

Precision Pathology

Within the Colorectal Cancer Research Center, the pathology section works closely with radiology and surgery and strives to bring pathology to high levels of precision.

Three major innovative “precision pathology” endeavors are ongoing:

  • Wholemount pathology for rectal cancer resection specimens: Specimens are thinly sliced into cross-sections and put into wholemount paraffin blocks and glass slides, which are then digitized. With this technique, the entire tumor is captured, along with the area around the tumor and the nearby lymph nodes. The samples are topographically oriented, offering complete and site-specific pathology data. These cross-sections are also aligned with MRI images for precision pathology-MRI correlation.
  • Lymph node mapping for complete mesocolic excision: This technique improves the informative value of pathology for colonic cancer resection specimens.
  • Efforts focused on the appendix and peritoneum tackle two related categories of challenging malignancies: appendiceal tumors and peritoneal tumors. We have ongoing work in which we systematically explore institutional data from surgery, radiology, and pathology (including molecular pathology) to develop clinically informative classification systems and to identify prognostic variables.

    Precision pathology initiatives are led by Jinru Shia, MD, and Efsevia Vakiani, MD, PhD.


The Colorectal Cancer Research Center performs comprehensive research banking of serial tissue and blood samples. These samples are collected from people with colorectal cancer as well as people at high risk for developing colorectal cancer.

Rapid triaging, banking, freezing, storage, aliquoting, and retrieving of research specimens ensures the timely and complete collection of critical specimens for research. In collaboration with MSK’s Precision Pathology Biobanking Center, computational tools are used for specimen ordering and tracking.

Biobanking initiatives are led by Martin Weiser, MD, and Efsevia Vakiani, MD, PhD


In collaboration with the Departments of Radiology and Pathology at MSK, radiologists within the Colorectal Cancer Research Center are conducting research aimed learning more about how colon and rectal cancers behave. To carry out this research, a team led by Marc Gollub, MD, and Iva Petkovska, MD, is conducting robust co-registration studies that include MRI data and whole-mount pathological rectal specimens.

The goals of this research are the following: 

  • To more fully determine the accuracy of MRI observations related to tumor margins, lymph nodes, tumor deposits, extramural venous invasion, and mucin-containing tumors
  • To study tumor biology and the tumor microenvironment — with the goals of fortifying our understanding of tumor diffusion restriction and bolstering the reliability of our artificial intelligence radiomic models that are created for tumor response assessment.

With this unique and uncommon co-registration, we have been able to refine our knowledge of the limitations of tumor margin assessments using MRI and to better understand potential biomarkers of poor outcomes, such as residual extramural vascular invasion after treatment.

Precision Modeling

The Colorectal Cancer Research Center is developing an infrastructure to seamlessly generate organoids from any person with colorectal cancer treated at MSK. With the goal of generating heterogeneous, representative, patient-specific models of colon and rectal cancers, this project has the following aims:

  • To genetically and pharmacologically manipulate organoids in order to characterize disease mechanisms in detail
  • To facilitate co-clinical trials. This means applying the same treatments to organoids and to patients participating in clinical trials
  • To establish an infrastructure for prospective studies that will assess the use of organoids for predicting which tumors will respond to or resist certain treatments

This initiative is led by J. Joshua Smith, MD, PhD, and Karuna Ganesh, MD, PhD.

Computational Biology

The computational biology initiative within the Colorectal Cancer Research Center has several objectives. These are:

  • To use genomic characterization to study untreated tumors and treatment-induced changes, with the goal of developing new approaches to enhance tumor response
  • To use multimodal data integration to enhance ways to detect rectal cancer’s response to neoadjuvant therapy and to develop ways to better predict those responses
  • To integrate multimodal data as a way to enhance prediction of which patient will have a complete response and to find ways to detect those responses

This initiative is led by Francisco Sanchez-Vega, PhD.

Young Onset

The Young-Onset Colorectal and Gastrointestinal Cancer Center was established with the following goals:

  • to meet the specific needs of people with young-onset colorectal cancer (CRC) and other gastrointestinal (GI) cancers
  • to identify the cause or causes of the increased incidence seen in the younger population
  • to raise public awareness of MSK’s resources for treatment of young-onset CRC and GI cancers

The Center has set the following specific objectives:

  • Establish an integrated clinical program for addressing the clinical and psychosocial needs of younger people with CRC and GI cancers, from diagnosis through survivorship
  • Expand MSK’s colorectal clinical database and biospecimen repository (including tissue, blood, and stool)
  • Strengthen research efforts aimed at understanding the genetic and epigenetic factors contributing to young-onset CRC and GI cancers

The Young-Onset Colorectal and Gastrointestinal Cancer Center is led by Andrea Cercek, MD, and Robin Mendelsohn, MD. For more information click here.

Patient-Reported Outcomes

For people receiving colorectal cancer care atMSK, the Colorectal Service in the Department of Surgery is leading efforts to incorporate patient-reported outcome measures (PROMs) into standard practice. These efforts are spearheaded by Emmanouil Pappou, MD, PhD, and Julio Garcia-Aguilar, MD, PhD, who are leading research in the development and implementation of electronic PROMs.

These measures help to advance clinical care using a patient-centered approach and to help the service fulfill the mission of performing cutting-edge research in patient-reported outcomes (PROs).

The Colorectal Service currently provides a comprehensive assessment of PROs by using PROMs throughout a person’s entire course of treatment. This includes measuring PROs during preoperative assessment, postoperative recovery, post-discharge recovery, and long-term follow up in the clinic.

Through close, multidisciplinary collaborations with clinicians including nursing staff, patient educators, statisticians, and website developers, this team has developed a concise, comprehensive PROM to evaluate a patient’s well-being. This includes bowel, sexual, and urinary function and the ability to work and enjoy life.

We have combined internationally validated tools to assess both function (bowel/urinary/sexual) and the impact of each function on an individual’s quality of life. We have also pioneered the incorporation of patient priorities into our Colorectal Scorecard, to better understand each individual’s priorities during treatment.

Future efforts will concentrate on establishing a specialized clinic to assess long-term symptoms and side effects in people undergoing treatment for colorectal cancer, including chemotherapy, radiation therapy, and surgery. These efforts will also focus on interventions to treat related bowel, urinary, and sexual dysfunctions.