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Colorectal Cancer and Inflammatory Bowel Disease: Molecular Mechanisms and Metabolic Pathways

Xue Lab, The University of New Mexico

Dr. Xiang Xue’s lab at the University of New Mexico focuses on understanding the molecular mechanisms underlying inflammatory bowel disease (IBD) and colorectal cancer (CRC). His research integrates cell line and enteroid cultures, mouse models, patient tissues, and a wide array of molecular and biochemical methodologies to uncover critical pathways that drive disease progression.

This fellowship will provide hands-on training and theoretical insights into key research areas, including:

The Role of Micronutrients in Cancer Cell Growth – How essential nutrients regulate tumor progression.
Mitochondrial Metabolism and Cancer – The impact of metabolic reprogramming on tumor survival.
Stress-Activated Pathways in Cancer Metabolism – Understanding cellular stress responses in tumor growth.
Hypoxia Signaling in Intestinal Inflammation and CRC – The influence of HIF pathways on disease progression.
Nutrient Homeostasis, Inflammation, and Cancer – How metabolic imbalance links to chronic inflammation and cancer initiation.

Participants will gain expertise in iron metabolism, hypoxia biology, oxidative stress, and mitochondrial dysfunction, using state-of-the-art techniques such as organoid culture, metabolomics, CRISPR gene editing, and advanced imaging to explore novel therapeutic strategies for gastrointestinal diseases.

Main Areas of Interest

Iron Metabolism & Nutrient Regulation in CRC & IBD

How iron homeostasis, micronutrients, and metabolic pathways drive cancer progression and inflammation.
Role of DMT1, hepcidin, and transferrin receptor in colon tumorigenesis.
Link between nutrient metabolism and immune response in IBD.

Hypoxia & Inflammatory Signaling in CRC & IBD

Role of Hypoxia-Inducible Factors (HIF-1α, HIF-2α) in gut inflammation and tumor growth.
How oxygen deprivation in the gut microenvironment affects IBD severity and CRC progression.
Targeting hypoxia pathways for therapeutic interventions in gastrointestinal diseases.

Mitochondrial Dysfunction & Oxidative Stress in CRC & IBD

How mitochondrial stress and mitophagy (PINK1, Sestrin2) regulate tumorigenesis.
Reactive oxygen species (ROS) & inflammation in CRC and IBD.
Exploring mitochondrial-targeted therapies for colorectal cancer treatment.

Immune System & Microbiome in CRC & IBD

Role of immune cells (T-cells, macrophages, neutrophils) and cytokines in colitis and cancer progression.
Influence of gut microbiome dysbiosis on CRC and IBD pathogenesis.
Using immune modulation & microbiome-based therapies for disease management.

Translational Research & Therapeutic Strategies

Developing targeted therapies against iron metabolism and hypoxia pathways.
Role of drug screening and repurposing in CRC & IBD treatment.
Application of organoid models & patient-derived tissues for personalized medicine.

Specialties

Oncology

Cancer

Gastroenterology

Techniques You Will Learn

Techniques You Can Learn

Participants will gain experience with the following molecular, cellular, and computational techniques:

Molecular Biology & Gene Regulation

qPCR, Western Blot, Immunohistochemistry (IHC), ELISA
CRISPR-Cas9 gene editing
RNA sequencing (RNA-seq) & transcriptomics

Hypoxia & Oxidative Stress Assays

HIF activation assays
ROS detection (DCFDA staining)
Seahorse metabolic flux analysis

Cell & Organoid Models for CRC & IBD

2D and 3D enteroid and colonoid cultures
In vitro tumor spheroids & organoid drug screening

Animal Models & In Vivo Research

Mouse models for CRC & IBD (colitis, DSS, AOM models)
Iron metabolism studies in mice

Microbiome & Immunology Assays

Flow cytometry for immune profiling
Cytokine multiplex assays
Gut microbiome sequencing (16S rRNA analysis)

Curriculum

Can be customized based on the visiting scientist needs

12-Week General Fellowship Curriculum

Week 1: Orientation & Access

The program begins with an orientation session, where participants will gain access to research facilities, lab protocols, and safety guidelines. They will be introduced to the research team, their mentorship structure, and available resources, including databases, lab equipment, and experimental models used in colorectal cancer (CRC) and inflammatory bowel disease (IBD) research.

Week 2: Review of Basics

Participants will conduct an in-depth literature review on CRC and IBD pathogenesis, focusing on key molecular pathways, recent advances, and unresolved research questions. They will analyze landmark studies, discuss research gaps, and attend expert-led sessions on nutrient metabolism, hypoxia signaling, and immune responses in gastrointestinal diseases.

Week 3: Techniques Training - Molecular Biology

This week will focus on essential molecular biology techniques used in CRC and IBD research. Participants will learn qPCR, Western Blot, and ELISA for gene and protein expression analysis. Additionally, they will receive training in CRISPR-Cas9 gene editing and RNA sequencing (RNA-seq) for transcriptomic studies.

Week 4: Techniques Training - Cell & Organoid Culture

Participants will gain hands-on experience with in vitro models, including 2D cell culture and 3D organoid models for CRC and IBD. They will learn to establish, maintain, and characterize enteroids and colonoids derived from patient samples and mouse models. Drug screening and gene expression studies using organoids will also be introduced.

Week 5: Techniques Training - Metabolic & Hypoxia Studies

This week will focus on hypoxia and metabolic regulation in CRC and IBD. Participants will study hypoxia-inducible factors (HIF-1α and HIF-2α) and learn techniques such as hypoxia chamber experiments, Seahorse metabolic flux analysis, and ROS detection (DCFDA staining). The impact of mitochondrial stress on tumor growth will also be explored.

Week 6: Techniques Training - Animal Models

Participants will be introduced to preclinical models used in CRC and IBD research, including the DSS colitis model and AOM-induced colorectal cancer model in mice. They will learn how to assess inflammation, tumor progression, and tissue pathology through histological staining and biomarker analysis.

Week 7: Techniques Training - Microbiome & Immunology

This week will explore the role of the gut microbiome and immune system in CRC and IBD. Participants will perform gut microbiome sequencing (16S rRNA analysis) to identify bacterial dysbiosis in disease models. They will also learn flow cytometry for immune profiling, focusing on how immune cells such as T-cells, macrophages, and neutrophils contribute to inflammation and tumorigenesis.

Week 8: Experimental Design & Hypothesis Building

With a solid foundation in lab techniques, participants will begin designing their research projects. They will define a hypothesis related to CRC or IBD, develop an experimental plan, and select appropriate methodologies. Mentors will provide feedback on study design, feasibility, and clinical relevance.

Week 9: Data Collection & Analysis

Participants will conduct experiments based on their proposed research projects. They will collect and analyze data using bioinformatics tools, statistical software, and imaging techniques. They will learn best practices for data interpretation, reproducibility, and troubleshooting experimental challenges.

Week 10: Translation to Clinical Research

This week will focus on bridging basic science to clinical applications. Participants will explore personalized medicine approaches, the potential of organoid models for drug screening, and the use of targeted therapies for CRC and IBD. Case studies and discussions with clinical researchers will provide insight into translating research findings into therapeutic strategies.

Week 11: Final Research Presentation & Peer Review

Participants will prepare and present their research findings in a formal seminar. They will receive constructive feedback from faculty and peers, refining their results for potential publication. Emphasis will be placed on scientific communication, manuscript preparation, and effective research dissemination.

Week 12: Future Applications & Career Development

The fellowship concludes with a session on career development, focusing on grant writing, publishing, networking, and transitioning to independent research. Participants will discuss funding opportunities, postdoctoral positions, and industry collaborations, preparing them for the next stage of their scientific careers.

Accommodation

Try airbnb.com

Fees and Program Logistics

This program has the following durations available:

Duration	Fee
6 weeks	$1,813.00
12 weeks	$3,250.00

This program allows Merit Applications. This program allows merit-based applications for virtual and onsite clinical and research programs. If you are successfully awarded under this category, Trialect or the host mentor will cover the tuition fee only. All applications will be evaluated based on merit. Due to the high level of competition, the chances of being selected under the merit category are quite limited.

Who Can Apply

Life Sciences and Health care

Host Details

Host Name: Xiang Xue

Affiliation: Xue Lab, The University of New Mexico

Address: MSC 08 4670, Fitz Hall 259, 915 Camino de Salud NE, Albuquerque, NM 87131

Website URL: https://sites.google.com/site/xiangxueus/home?authuser=0

Disclaimer:It is mandatory that all applicants carry workplace liability insurance, e.g., https://www.protrip-world-liability.com (Erasmus students use this package and typically costs around 5 € per month - please check) in addition to health insurance when you join any of the onsite Trialect partnered fellowships.

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