Multi-Omics Data Analysis

Introduction

The Multi-Omics Data Analysis Core (MODAC) provides cutting-edge bioinformatics and multi-omics analysis and advanced data visualization for both translational and fundamental scientific research. Our expertise spans bulk and single-cell transcriptomics and epigenomics, spatial transcriptomics, targeted and unbiased metabolomics, lipidomics, and proteomics, as well as integrative multi-omics bioinformatics. We support other ATC Omics Cores, ensuring meticulous data processing and quality control. Additionally, MODAC offers training programs in bulk and single-cell analysis of data generated by ATC Omics cores and assists with grant applications and educational initiatives to all the researchers within and outside BCM.

Overview

The Multi-Omics Data Analysis group assists with analysis of data generated by the major technology platforms of the CPRIT Core Facility, including mass spectrometry (MS) metabolomics, MS-based proteomics and reverse phase protein array (RPPA) proteomics. In addition, we accept and processes high-throughput sequencing data including:

Coding and noncoding transcriptomics: RNA-Seq, smallRNA-Seq
Single cell transcriptomics scRNA-Seq
Cistrome: ChIP-Seq, Reduced Representation Bisulfite Sequencing (RRBS), and Whole Genome Bisulfite Sequencing (WGBS)
Genomics: Whole Genome Sequencing (WGS) or Whole Exome sequencing (WES)

Using a consistent data work-flow, we assist with Primary/Tier 1 data analysis in close collaboration with the Core Facility leadership. Additionally, we provide as independent support services Integrative/Tier 2 analysis for multiple omics data to lead to systems biology level insight, and also to generate robust testable hypotheses. Integrative analysis can be further performed using data sets from national and international projects, such as The Cancer Genome Atlas (TCGA), Encode, the NIH Epigenomic Roadmap, International Human Epigenome Consortium (IHEC), The Metabolomics Workbench, as well as data sets from scientific community repositories such as the NIH Gene Expression Omnibus (GEO) and NIH Short Read Archive (SRA).

References (Core Supported Publications)

Grimm SL, Karki M, Blum KA, Bertocchio JP, He R, Tripathi DN, Zacharias NM, Lebenthal JM, Sheth RA, Rao P, Genovese G, Lu Z, Bast RC, Ingram DR, Lazcano R, Wani KM, Wang WL, Lazar AJ, Tannir NM, Walker CL, Coarfa C, Msaouel P. CA-125 as a Biomarker in Renal Medullary Carcinoma: Integrated Molecular Profiling, Functional Characterization, and Prospective Clinical Validation. Clin Cancer Res. 2025 Mar 17;31(6):1057-1068. doi: 10.1158/1078-0432.CCR-24-3324. PMID: 39836407; PMCID: PMC11913570.

Grimm SL, Talley T, Jangid RK, Koirala A, Castillo MB, Gunaratne PH, Coarfa C, Walker CL. Transcriptomic and epigenomic signatures distinguish high- and low-risk endotypes for liver tumor development. Environ Mol Mutagen. 2024 Nov;65(9):351-359. doi: 10.1002/em.22639. Epub 2024 Nov 26. PMID: 39588573.

Patel TD, Grimm SL, Kanchi RS, Gandhi T, Koirala A, Yustein JT, Coarfa C. Identification of an early survival prognostic gene signature for localized osteosarcoma patients. Sci Rep. 2024 Mar 27;14(1):7327. doi: 10.1038/s41598-024-57527-8. PMID: 38538763; PMCID: PMC10973371.

Ahn S, Park JH, Grimm SL, Piyarathna DWB, Samanta T, Putluri V, Mezquita D, Fuqua SAW, Putluri N, Coarfa C, Kaipparettu BA. Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer. Cancer Res. 2024 Jan 16;84(2):291-304. doi: 10.1158/0008-5472.CAN-23-0184. PMID: 37906431; PMCID: PMC10842725.

Padilla J, Osman NM, Bissig-Choisat B, Grimm SL, Qin X, Major AM, Yang L, Lopez-Terrada D, Coarfa C, Li F, Bissig KD, Moore DD, Fu L. Circadian dysfunction induces NAFLD-related human liver cancer in a mouse model. J Hepatol. 2024 Feb;80(2):282-292. doi: 10.1016/j.jhep.2023.10.018. Epub 2023 Oct 27. PMID: 37890720; PMCID: PMC10929560.

Napoli M, Deshpande AA, Chakravarti D, Rajapakshe K, Gunaratne PH, Coarfa C, Flores ER. Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses. Cancer Res Commun. 2024 Feb 1;4(2):264-278. doi: 10.1158/2767-9764.CRC-23-0358. PMID: 38165157; PMCID: PMC10832605.

Thaiparambil J, Dong J, Grimm SL, Perera D, Ambati CSR, Putluri V, Robertson MJ, Patel TD, Mistretta B, Gunaratne PH, Kim MP, Yustein JT, Putluri N, Coarfa C, El-Zein R. Integrative metabolomics and transcriptomics analysis reveals novel therapeutic vulnerabilities in lung cancer. Cancer Med. 2023 Jan;12(1):584-596. doi: 10.1002/cam4.4933. Epub 2022 Jun 8. PMID: 35676822; PMCID: PMC9844651.

Single cell RNA-Seq
Li L, Coarfa C, Yuan Y, Abu-Taha I, Wang X, Song J, Zeng Y, Chen X, Koirala A, Grimm SL, Kamler M, McClendon LK, Tallquist M, Nattel S, Dobrev D, Li N. Fibroblast-Restricted Inflammasome Activation Promotes Atrial Fibrillation and Heart Failure With Diastolic Dysfunction. JACC Basic Transl Sci. 2025 Apr 16:101244. doi: 10.1016/j.jacbts.2025.02.004. Epub ahead of print. PMID: 40243956.

Bomidi C, Zeng XL, Poplaski V, Coarfa C, Estes MK, Blutt SE. Using Human Intestinal Organoids to Understand the Small Intestine Epithelium at the Single Cell Transcriptional Level. J Vis Exp. 2024 Jun 28;(208):10.3791/66749. doi: 10.3791/66749. PMID: 39007612; PMCID: PMC11987515.

Bulk RNA-Seq
Emig AA, Hansen M, Grimm S, Coarfa C, Lord ND, Williams MK. Temporal dynamics of BMP/Nodal ratio drive tissue-specific gastrulation morphogenesis. Development. 2025 May 1;152(9):dev202931. doi: 10.1242/dev.202931. Epub 2025 May 1. PMID: 39651654; PMCID: PMC12070064.

Adeniyi-Ipadeola GO, Hankins JD, Kambal A, Zeng X-L, Patil K, Poplaski V, Bomidi C, Nguyen-Phuc H, Grimm SL, Coarfa C, Stossi F, Crawford SE, Blutt SE, Speer AL, Estes MK, Ramani S. Infant and adult human intestinal enteroids are morphologically and functionally distinct. mBio. 2024 Aug 14;15(8):e0131624. doi: 10.1128/mbio.01316-24. Epub 2024 Jul 2. PMID: 38953637; PMCID: PMC11323560.

Joshi CS, Salazar AM, Wang C, Ligon MM, Chappidi RR, Fashemi BE, Felder PA, Mora A, Grimm SL, Coarfa C, Mysorekar IU. D-Mannose reduces cellular senescence and NLRP3/GasderminD/IL-1β-driven pyroptotic uroepithelial cell shedding in the murine bladder. Dev Cell. 2024 Jan 8;59(1):33-47.e5. doi: 10.1016/j.devcel.2023.11.017. Epub 2023 Dec 14. PMID: 38101412; PMCID: PMC10872954.

Grimm SL, Reddick S, Dong X, Leek C, Wang AX, Gutierrez MC, Hartig SM, Moorthy B, Coarfa C, Lingappan K. Loss of microRNA-30a and sex-specific effects on the neonatal hyperoxic lung injury. Biol Sex Differ. 2023 Aug 8;14(1):50. doi: 10.1186/s13293-023-00535-6. PMID: 37553579; PMCID: PMC10408139.

Nirala BK, Patel TD, Kurenbekova L, Shuck R, Dasgupta A, Rainusso N, Coarfa C, Yustein JT. MYC regulates CSF1 expression via microRNA 17/20a to modulate tumor-associated macrophages in osteosarcoma. JCI Insight. 2023 Jul 10;8(13):e164947. doi: 10.1172/jci.insight.164947. PMID: 37279073; PMCID: PMC10371352.

Yu X, Li W, Liu H, Wang X, Coarfa C, Cheng C, Yu X, Zeng Z, Cao Y, Young KH, Li Y. PD-L1 translocation to the plasma membrane enables tumor immune evasion through MIB2 ubiquitination. J Clin Invest. 2023 Feb 1;133(3):e160456. doi: 10.1172/JCI160456. PMID: 36719382; PMCID: PMC9888393.

Xu Y, Zhang L, Thaiparambil J, Mai S, Perera DN, Zhang J, Pan PY, Coarfa C, Ramos K, Chen SH, El-Zein R. Patients with Lung Cancer of Different Racial Backgrounds Harbor Distinct Immune Cell Profiles. Cancer Res Commun. 2022 Aug 29;2(8):884-893. doi: 10.1158/2767-9764.CRC-22-0057. PMID: 36923308; PMCID: PMC10010305.

smallRNA-Seq
Kosten TR, Koirala A, Nielsen DA, Domingo CB, Thomas YT, Gunaratne PH, Coarfa C. Plasma microRNAs to Select Optimal Patients for Antibody Production from Anti-Addiction Vaccines. Vaccines (Basel). 2025 Feb 13;13(2):181. doi: 10.3390/vaccines13020181. PMID: 40006728; PMCID: PMC11860428.

Gunasekara CJ, MacKay H, Scott CA, Li S, Laritsky E, Baker MS, Grimm SL, Jun G, Li Y, Chen R, Wiemels JL, Coarfa C, Waterland RA. Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control. Genome Biol. 2023 Jan 12;24(1):2. doi: 10.1186/s13059-022-02827-3. PMID: 36631879; PMCID: PMC9835319.

Li Y, Yadollahi P, Essien FN, Putluri V, Ambati CSR, Kami Reddy KR, Kamal AHM, Putluri N, Abdurrahman LM, Ruiz Echartea ME, Ernste KJ, Trivedi AJ, Vazquez-Perez J, Hudson WH, Decker WK, Patel R, Osman AA, Kheradmand F, Lai SY, Myers JN, Skinner HD, Coarfa C, Lee K, Jain A, Malovannaya A, Frederick MJ, Sandulache VC. Tobacco smoke exposure is a driver of altered oxidative stress response and immunity in head and neck cancer. J Transl Med. 2025 Apr 5;23(1):403. doi: 10.1186/s12967-025-06258-z. PMID: 40188338; PMCID: PMC11971752.

Powell H, Coarfa C, Ruiz-Echartea E, Grimm SL, Najjar O, Yu B, Olivares L, Scheurer ME, Ballantyne C, Alsarraj A, Salem EM, Thrift AP, El Serag HB, Kaochar S. Differences in Prediagnostic Serum Metabolomic and Lipidomic Profiles Between Cirrhosis Patients with and without Incident Hepatocellular Carcinoma. J Hepatocell Carcinoma. 2024 Sep 7;11:1699-1712. doi: 10.2147/JHC.S474010. PMID: 39263690; PMCID: PMC11389719.

Bacha F, El-Ayash H, Mohamad M, Sharma S, Puyau M, Kanchi R, Coarfa C. Distinct Amino Acid Profile Characterizes Youth With or at Risk for Type 2 Diabetes. Diabetes. 2024 Apr 1;73(4):628-636. doi: 10.2337/db23-0375. PMID: 38215171.

Zhang L, Hsu JI, Braekeleer ED, Chen CW, Patel TD, Martell AG, Guzman AG, Wohlan K, Waldvogel SM, Uryu H, Tovy A, Callen E, Murdaugh RL, Richard R, Jansen S, Vissers L, de Vries BBA, Nussenzweig A, Huang S, Coarfa C, Anastas J, Takahashi K, Vassiliou G, Goodell MA. SOD1 is a synthetic-lethal target in PPM1D-mutant leukemia cells. Elife. 2024 Jun 18;12:RP91611. doi: 10.7554/eLife.91611. PMID: 38896450; PMCID: PMC11186636.

Grimm SL, Stading RE, Robertson MJ, Gandhi T, Fu C, Jiang W, Xia G, Lingappan K, Coarfa C, Moorthy B. Loss of cytochrome P450 (CYP)1B1 mitigates hyperoxia response in adult mouse lung by reprogramming metabolism and translation. Redox Biol. 2023 Aug;64:102790. doi: 10.1016/j.redox.2023.102790. Epub 2023 Jun 16. PMID: 37348155; PMCID: PMC10271936.

Cox AR, Masschelin PM, Saha PK, Felix JB, Sharp R, Lian Z, Xia Y, Chernis N, Bader DA, Kim KH, Li X, Yoshino J, Li X, Li G, Sun Z, Wu H, Coarfa C, Moore DD, Klein S, Sun K, Hartig SM. The rheumatoid arthritis drug auranofin lowers leptin levels and exerts antidiabetic effects in obese mice. Cell Metab. 2022 Dec 6;34(12):1932-1946.e7. doi: 10.1016/j.cmet.2022.09.019. Epub 2022 Oct 14. PMID: 36243005; PMCID: PMC9742315.

Chacon-Alberty L, Kanchi RS, Ye S, Hochman-Mendez C, Daoud D, Coarfa C, Li M, Grimm SL, Baz M, Rosas I, Loor G. Plasma protein biomarkers for primary graft dysfunction after lung transplantation: a single-center cohort analysis. Sci Rep. 2022 Sep 27;12(1):16137. doi: 10.1038/s41598-022-20085-y. PMID: 36167867; PMCID: PMC9515157.

Carrero Longlax S, Koster KJ, Kamat AM, Lozano M, Lerner SP, Hannigan R, Nishiguchi T, Abhimanyu, Sheikh D, Ladki M, Portillo A, Koirala A, Patel TD, Spieler Z, Benjamin AB, Lebedev M, Ofili TU, Hutchison RW, Udeani G, Opperman LA, Neal G, Mandalakas AM, Netea MG, Arditi M, Avalos P, Grimm SL, Coarfa C, Cirillo JD, DiNardo AR. BCG-Induced DNA Methylation Changes Improve Coronavirus Disease 2019 Vaccine Immunity Without Decreasing the Risk for Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Open Forum Infect Dis. 2025 Jan 16;12(1):ofaf007. doi: 10.1093/ofid/ofaf007. PMID: 39872813; PMCID: PMC11770274.

Abhimanyu, Longlax SC, Nishiguchi T, Ladki M, Sheikh D, Martinez AL, Mace EM, Grimm SL, Caldwell T, Portillo Varela A, Sekhar RV, Mandalakas AM, Mlotshwa M, Ginidza S, Cirillo JD, Wallis RS, Netea MG, van Crevel R, Coarfa C, DiNardo AR. TCA metabolism regulates DNA hypermethylation in LPS and Mycobacterium tuberculosis-induced immune tolerance. Proc Natl Acad Sci U S A. 2024 Oct 8;121(41):e2404841121. doi: 10.1073/pnas.2404841121. Epub 2024 Sep 30. PMID: 39348545; PMCID: PMC11474056.

Chang WJ, Baker MS, Laritsky E, Gunasekara CJ, Maduranga U, Galliou JC, McFadden JW, Waltemyer JR, Berggren-Thomas B, Tate BN, Zhang H, Rosen BD, Van Tassell CP, Liu GE, Coarfa C, Ren YA, Waterland RA. Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. Genome Biol. 2024 Jul 15;25(1):185. doi: 10.1186/s13059-024-03307-6. PMID: 39004763; PMCID: PMC11247883.

Berchuck JE, Adib E, Abou Alaiwi S, Dash AK, Shin JN, Lowder D, McColl C, Castro P, Carelli R, Benedetti E, Deng J, Robertson M, Baca SC, Bell C, McClure HM, El Zarif T, Davidsohn MP, Lakshminarayanan G, Rizwan K, Skapura DG, Grimm SL, Davis CM, Ehli EA, Kelleher KM, Seo JH, Mitsiades N, Coarfa C, Pomerantz MM, Loda M, Ittmann M, Freedman ML, Kaochar S. The Prostate Cancer Androgen Receptor Cistrome in African American Men Associates with Upregulation of Lipid Metabolism and Immune Response. Cancer Res. 2022 Aug 16;82(16):2848-2859. doi: 10.1158/0008-5472.CAN-21-3552. PMID: 35731919; PMCID: PMC9379363.

Basil P, Robertson MJ, Bingman WE 3rd, Dash AK, Krause WC, Shafi AA, Piyarathna B, Coarfa C, Weigel NL. Cistrome and transcriptome analysis identifies unique androgen receptor (AR) and AR-V7 splice variant chromatin binding and transcriptional activities. Sci Rep. 2022 Mar 30;12(1):5351. doi: 10.1038/s41598-022-09371-x. PMID: 35354884; PMCID: PMC8969163.