Research Overview

Collagen is the major component of extracellular matrix (ECM) and the most abundant protein in mammals, playing a critical role in tissue homeostasis and cell signaling. Its functions are regulated by collagen-modifying enzymes that catalyze the post-translational modifications of collagen. Our group seeks to study how collagen-modifying enzymes (e.g., lysyl hydroxylase 2 or LH2) influence matrix homeostasis and signaling in health and diseases, such as cancer, fibrosis and connective tissue diseases. Our projects build on several decades of work in the connective tissue disease field that has identified a 4-step reactions of collagen lysine modifications critical for creating a collagen rich matrix to regulate cell behaviors. Our goal is to gain structural insights into the key collagen-modifying enzymes, to define the specific roles of collagen post-translational modifications in matrix assembly and signaling, and to ultimately use these insights to develop antagonists (e.g. LH2 antagonist) and control the biomechanical and biochemical properties of diseased stroma in cancer, fibrosis and connective tissue diseases. Since LH2 driven fibrosis and tumor stiffening are a general barrier for drug delivery to multiple cancer types, LH2 antagonists may act synergistically with the current paradigm of cancer treatments, such as chemotherapy, immunotherapy and targeted therapy. These insights will also help design tailor-made collagens for bioengineering purposes and inform fibrotic diseases, regeneration, aging and connective tissues diseases. Our long-term goal is to determine how extracellular matrices and matricellular proteins influence matrix remodeling and diseases.

HPC Cluster Based Projects

Compare Mimivirus genome to human

We and others have shown that Mimivirus genome encodes 1262 open reading frames, including collagen like proteins and a close homology of human lysyl hydroxylases (>40% amino acid sequence identity), and mimiviral lysyl hydroxylase modifies human collagen. Since Mimivirus is an opportunistic pneumonia pathogen, these findings suggest collagen post-translational modification crosstalk may happen during mimivirus’s infection cycle. Thus, it is interesting to look at to what extent human and Mimivirus share the ECM genes (>300 for human). Toward this end, we seek to perform a genome wide search of Mimiviral gene homologs in human genome.

ECM gene expression atlas

The expression pattern of ECM and ECM modifying enzyme genes regulates the composition and post-translational modifications of ECM to influence cell behaviors. Thus, gaining insights into the expression pattern of ECM and ECM modifying enzyme genes may help inform how cell behaviors are regulated in biology and diseases. Toward this end, we would like to mine the single cell sequencing databases and perform ECM and ECM modifying enzyme gene expression analyses to generate an ECM gene expression atlas for many tissues, such as heart, bone and brain.

Personnel:

Dr. Houfu Guo, PI

Dr. Jeong seon Kim, Postdoc

Ms. Tingfei Chen, Technician

Mr. Stephen Richards, Temp Tech

Computational Methods:

Data acquisition: Download raw and/or processed bulk and/or single cell RNA and/or DNA sequencing data from public data repositories such as Sequence Read Archive (SRA), GEO, cBioPortal, Single Cell Portal from Broad Institute et. al.

Bioinformatics workflows: Raw sequencing reads quality control, low quality reads filtering/adaptor trimming, genomic/transcriptomic alignment, quantification/isoform identification, somatic/germline SNP/INDEL/structural variation identification et. al.

Statistical and functional analyses: Differential expression, functional annotation/prediction, correlation/pathway/network analysis, sequence similarity analysis, classification/biomarker identification.

Software:

NCBI BLAST, GSEA, SRA Toolkit, FastQC, fastp, Bowtie2, BWA, TopHat2, STAR, RSEM, Cufflinks, Samtools, bedtools, VCFtools, VarScan2, GATK, Mutect2, ANNOVAR, Oncotator, R and Python packages.

Current analysis involves NCBI BLAST. We will request for the installation of other tools when encountered.

Collaborators:

Wendy Wu

Publications:

D Raoult, S Audic, C Robert, C Abergel, P Renesto, H Ogata, BL Scola, M Suzan, J Claverie. The 1.2-megabase genome sequence of Mimivirus. Science, 2004 Nov; 306(5700): 1344-50.

H Guo, C Tsai, M Terajima, X Tan, P Banerjee, MD Miller, X Liu, J Yu, J Byemerwa, S Alvarado, TS Kaoud, KN Dalby, N Bota-Rabassedas, Y Chen, M Yamauchi, JA Tainer, GN Phillips, Jr., JM Kurie. Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+–binding. Nature Communications, 2018 Feb; 9(1): 512.

Grants:

NIH/NCI R00CA225633 Determining structural features of a collagen lysyl hydroxylase that promotes lung cancer metastasis. Hou-Fu Guo, Ph.D. 09/11/20-08/31/23 $734,16

UK new lab startup funds