• Alexander “Craig” Mackinnon Jr., M.D., Ph.D., is the inaugural director of the Division of Genomics Diagnostics and Bioinformatics in the Department of Pathology, School of Medicine at the University of Alabama at Birmingham. Mackinnon leads ongoing efforts to establish the Genomic Diagnostic Laboratory (GDL) at UAB and advance testing capabilities at UAB to promote precision medicine.

    Dr. Mackinnon is a physician-scientist whose areas of expertise are Anatomical Pathology (AP) and Molecular Genetic Pathology (MGP). He is trained and board certified by the American Board of Pathology in the disciplines of Molecular Genetic Pathology and Anatomical Pathology.

    His professional activities include leadership, clinical, and administrative roles serving as the Medical Director of CLIA certified and CAP accredited molecular diagnostics laboratories, training Pathology residents and fellows, and performing service devoted towards advancing institutional-level commitments, such as committee work and collaborations with funded researchers in the role of co-investigator or core lab director.

    Mackinnon is a member of the College of American Pathologists and the American Society of Clinical Pathology, where he served on the Molecular Pathology Section, Pathologist Recertification Individualized Self-Assessment Examination Committee.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2023 Epithelioid and Clear Cell Solitary Fibrous Tumors: Clinicopathologic, Immunohistochemical, and Molecular Genetic Study of 13 CasesAmerican Journal of Surgical Pathology.  47:259-269. 2023
    2023 Oral and Inhaled Fosamprenavir Reverses Pepsin-Induced Damage in a Laryngopharyngeal Reflux Mouse Model 2023
    2022 Desmoplastic Adamantinoma-like Thymic Carcinoma: Clinicopathologic, Immunohistochemical, and Molecular Study of 5 CasesAmerican Journal of Surgical Pathology.  46:1722-1731. 2022
    2022 Performance of Idylla KRAS assay on extracted DNA and de-stained cytology smears: Can we rescue small sample?Annals of Diagnostic Pathology.  60. 2022
    2022 The diagnostic utility of RNA-based fusion panel testing ordered by pathologists in challenging casesAnnals of Diagnostic Pathology.  60. 2022
    2022 Thyroid Oncocytic (Hürthle Cell) Nodules With Longitudinal Nuclear Grooves.Archives of Pathology and Laboratory Medicine2022
    2022 Utility of Single-Gene Testing in Cancer SpecimensClinics in Laboratory Medicine.  42:385-394. 2022
    2022 Solid Thyroid Follicular Nodules with Longitudinal Nuclear Grooves: Clinicopathologic, Immunohistochemical, and Molecular Genetic Study of 18 CasesArchives of Pathology and Laboratory Medicine.  146:984-993. 2022
    2022 Atypical thymomas with squamoid and spindle cell features: clinicopathologic, immunohistochemical and molecular genetic study of 120 cases with long-term follow-upModern Pathology.  35:875-894. 2022
    2022 Epithelioid osteoblastoma. Clinicopathologic and immunohistochemical study of 17 casesHuman Pathology.  125:68-78. 2022
    2022 Lymphocyte-Rich Spindle Cell Thymoma: Clinicopathologic, Immunohistochemical, Ultrastructural and Molecular Genetic Study of 80 CasesAmerican Journal of Surgical Pathology.  46:603-616. 2022
    2022 New Approaches and Strategies for Proficiency Testing for Next-Generation Sequencing-Based Oncology AssaysAmerican Journal of Clinical Pathology.  157:478-479. 2022
    2022 Immature Chondroid Choristoma: Clinicopathologic, Immunohistochemical, and Molecular Study of an Unusual Benign Skin TumorAmerican Journal of Dermatopathology.  44:148-151. 2022
    2022 Molecular pathology of thymoma and thymic carcinoma 2022
    2022 Spindle Cell Sarcoma of the Uterus Harboring MEIS1::NCOA1 Fusion Gene and Mimicking Endometrial Stromal SarcomaInternational Journal of Surgical Pathology2022
    2021 Diagnostic utility of one-stop fusion gene panel to detect TFE3/TFEB gene rearrangement and amplification in renal cell carcinomasModern Pathology.  34:2055-2063. 2021
    2021 The Interpretation of Sequence Variants in Myeloid NeoplasmsAmerican Journal of Clinical Pathology.  156:728-748. 2021
    2021 Expression patterns for Bcl-2, EMA, β-catenin, E-cadherin, PAX8, and MIB1 in thymomasModern Pathology.  34:1831-1838. 2021
    2021 TFEB rearranged renal cell carcinoma. A clinicopathologic and molecular study of 13 cases. Tumors harboring MALAT1-TFEB, ACTB-TFEB, and the novel NEAT1-TFEB translocations constantly express PDL1Modern Pathology.  34:842-850. 2021
    2020 Myxoinflammatory fibroblastic sarcoma: an immunohistochemical and molecular genetic study of 73 casesModern Pathology.  33:2520-2533. 2020
    2020 P38g MAPK Is essential for aerobic glycolysis and pancreatic tumorigenesisCancer Research.  80:3251-3264. 2020
    2020 Increased SPARC expression is associated with neoadjuvant therapy in resectable pancreatic ductal adenocarcinomaPractical Laboratory Medicine.  21. 2020
    2020 Comparison of tissue molecular biomarker testing turnaround times and concordance between standard of care and the biocartis idylla platform in patients with colorectal cancerAmerican Journal of Clinical Pathology.  154:266-276. 2020
    2019 Esophageal pepsin and proton pump synthesis in barrett's esophagus and esophageal adenocarcinoma 2019
    2019 Antibiotic modulation of mucins in otitis media; should this change our approach to watchful waiting?International Journal of Pediatric Otorhinolaryngology.  125:134-140. 2019
    2019 Evaluation, Validation, and Implementation of the Idylla System as Rapid Molecular Testing for Precision Medicine 2019
    2019 MDM2 amplification and immunohistochemical expression in sarcomatoid renal cell carcinomaHuman Pathology.  87:28-36. 2019
    2019 Tubulopapillary adrenocortical adenoma in a patient with familial adenomatous polyposis: a morphologic, ultrastructural, and molecular studyHuman Pathology.  87:51-56. 2019
    2019 A serum-induced transcriptome and serum cytokine signature obtained at diagnosis correlates with the development of early pancreatic ductal adenocarcinoma metastasisCancer Epidemiology, Biomarkers and Prevention.  28:680-689. 2019
    2019 Antibiotic modulation of mucins in otitis media; should this change our approach to watchful waiting?International Journal of Pediatric Otorhinolaryngology.  2687-2695. 2019
    2019 The Development and Characterization of Estrogen Receptor Beta Agonists to Treat Cognitive Decline in Post‐Menopausal Women 2019
    2019 Proliferative potential and resistance to immune checkpoint blockade in lung cancer patientsJournal for ImmunoTherapy of Cancer.  7. 2019
    2019 Next generation sequencing of PD-L1 for predicting response to immune checkpoint inhibitorsJournal for ImmunoTherapy of Cancer.  7. 2019
    2018 Expression of PD-L1/PD-1 in lymphoepithelioma-like carcinoma of the thymusModern Pathology.  31:1801-1806. 2018
    2018 Immunogenomic Landscape Contributes to Hyperprogressive Disease after Anti-PD-1 Immunotherapy for CanceriScience.  9:258-277. 2018
    2018 A Phase II Clinical Trial of Molecular Profiled Neoadjuvant Therapy for Localized Pancreatic Ductal AdenocarcinomaAnnals of Surgery.  268:610-619. 2018
    2018 Poorly differentiated nonkeratinizing squamous cell carcinoma of the thymus: Clinicopathologic and molecular genetic study of 25 casesAmerican Journal of Surgical Pathology.  42:1224-1236. 2018
    2018 Tubulo-papillary adrenocortical adenoma in a patient with familial adenomatous polyposis: A morphologic, ultrastructural and molecular study.Annals of Surgery.  610-619. 2018
    2018 Bronchiolar Adenoma: Expansion of the Concept of Ciliated Muconodular Papillary Tumors With Proposal for Revised Terminology Based on Morphologic, Immunophenotypic, and Genomic Analysis of 25 Cases.American Journal of Surgical Pathology.  42:1010-1026. 2018
    2018 Bronchiolar adenomaAmerican Journal of Surgical Pathology.  42:1010-1026. 2018
    2018 A-C Estrogens as Potent and Selective Estrogen Receptor-Beta Agonists (SERBAs) to Enhance Memory Consolidation under Low-Estrogen ConditionsJournal of Medicinal Chemistry.  61:4720-4738. 2018
    2018 Cerebellar Pleomorphic Xanthoastrocytoma in a Patient with Neurofibromatosis Type 1- Molecular Study and Review of the Literature.Human Pathology: Case Reports.  11:38-42. 2018
    2018 Cerebellar pleomorphic xanthoastrocytoma in a patient with neurofibromatosis type 1 – Molecular study and review of literatureHuman Pathology: Case Reports.  11:39-42. 2018
    2018 Optimized b -value selection for the discrimination of prostate cancer grades, including the cribriform pattern, using diffusion weighted imagingJournal of Medical Imaging.  5. 2018
    2018 Overexpression of the VRK1 kinase, which is associated with breast cancer, induces a mesenchymal to epithelial transition in mammary epithelial cells.PLoS One.  13:e0203397. 2018
    2017 Immune Check Point Inhibition in Sarcomatoid Renal Cell Carcinoma: A New Treatment ParadigmClinical Genitourinary Cancer.  15:e897-e901. 2017
    2017 Association of gel-forming mucins and aquaporin gene expression with hearing loss, effusion viscosity, and inflammation in otitis media with effusionJAMA Otolaryngology-Head and Neck Surgery.  143:810-817. 2017
    2017 Evaluation of CD43 expression in non-hematopoietic malignanciesAnnals of Diagnostic Pathology.  29:23-27. 2017
    2017 Cancer cell chemokines direct chemotaxis of activated stellate cells in pancreatic ductal adenocarcinomaLaboratory Investigation.  97:302-317. 2017
    2016 Abstract A21: Chemokine directed migration of activated stellate cells in pancreatic ductal adenocarcinomaCancer Research.  76:a21-a21. 2016
    2016 Correlation of SMAD4 Expression in Pretreatment Cytologic Specimens and Postneoadjuvant Treatment Surgical Specimens in Patients With Pancreatic Cancer 2016
    2016 Association of microRNA 146 with middle ear hyperplasia in pediatric otitis mediaInternational Journal of Pediatric Otorhinolaryngology.  88:104-108. 2016
    2016 A single center's approach to discriminating donor versus host origin of renal neoplasia in the allograft kidneyAnnals of Diagnostic Pathology.  23:32-34. 2016
    2016 Erratum: The tumor-suppressive small GTPase DiRas1 binds the noncanonical guanine nucleotide exchange factor SmgGDS and antagonizes SmgGDS interactions with oncogenic small GTPases (Journal of Biological Chemistry (2016) 291 (6534-6545))Journal of Biological Chemistry.  291:10948. 2016
    2016 Desmoplastic melanoma: An updated immunohistochemical analysis of 40 cases with a proposal for an additional panel of stains for diagnosisJournal of Cutaneous Pathology.  43:313-323. 2016
    2016 The tumor-suppressive small GTPase DiRas1 binds the noncanonical guanine nucleotide exchange factor SmgGDS and antagonizes SmgGDS interactions with oncogenic small GTPasesJournal of Biological Chemistry.  291:6534-6545. 2016
    2016 Dysregulation of WNT5A/ROR2 signaling characterizes the progression of barrett-associated esophageal adenocarcinomaMolecular Cancer Research.  14:647-659. 2016
    2015 Comparing gene expression data from formalin-fixed, paraffin embedded tissues and qPCR with that from snap-frozen tissue and microarrays for modeling outcomes of patients with ovarian carcinomaBMC Clinical Pathology.  15. 2015
    2015 Role of Immunohistochemistry in the Diagnosis of Sebaceous Carcinoma: A Clinicopathologic and Immunohistochemical StudyAmerican Journal of Dermatopathology.  37:809-821. 2015
    2015 Genomic variations in plasma cell free DNA differentiate early stage lung cancers from normal controlsLung Cancer.  90:78-84. 2015
    2015 Granulomatous and lymphocytic interstitial lung disease: A spectrum of pulmonary histopathologic lesions in common variable immunodeficiency - Histologic and immunohistochemical analyses of 16 casesHuman Pathology.  46:1306-1314. 2015
    2015 Sa1883 High Levels of Dickkopf-1 in Blood Serum and Esophageal Tissue Are Associated With Severe Inflammation and Cellular Senescence in Human Reflux-EsophagitisGastroenterology.  148:s-346. 2015
    2015 Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genomeHuman Molecular Genetics.  24:154-166. 2015
    2015 Spindle cell atypical fibroxanthoma: Myofibroblastic differentiation represents a diagnostic pitfall in this variant of AFXAmerican Journal of Dermatopathology.  37:509-516. 2015
    2015 Wnt/β-Catenin Signaling Activation beyond Robust Nuclear β-Catenin Accumulation in Nondysplastic Barrett's Esophagus: Regulation via Dickkopf-1Neoplasia.  17:598-611. 2015
    2014 Depletion of M2-like tumor-associated macrophages delays cutaneous T-cell lymphoma development in vivoJournal of Investigative Dermatology.  134:2814-2822. 2014
    2014 Tu1657 CXCL12 Suppresses Pancreatic Cancer by Regulating Tumor Cell Growth, Migration, and Metastatic HomingGastroenterology.  146:s-811. 2014
    2014 Dickkopf-1, the Wnt antagonist, is induced by acidic pH and mediates epithelial cellular senescence in human reflux esophagitis 2014
    2014 CXCL12 chemokine expression suppresses human pancreatic cancer growth and metastasisPLoS One.  9. 2014
    2014 Antral atrophy, intestinal metaplasia, and preneoplastic markers in Mexican children with Helicobacter pylori-positive and Helicobacter pylori-negative gastritisAnnals of Diagnostic Pathology.  18:129-135. 2014
    2014 Cribriform adenocarcinoma of the lung: Clinicopathologic, immunohistochemical, and molecular analysis of 15 cases of a distinctive morphologic subtype of lung adenocarcinomaModern Pathology.  27:1063-1072. 2014
    2014 The SmgGDS splice variant SmgGDS-558 is a key promoter of tumor growth and rhoa signaling in breast cancerMolecular Cancer Research.  12:130-142. 2014
    2013 Tracking in anatomic pathologyArchives of Pathology and Laboratory Medicine.  137:1798-1810. 2013
    2013 Mitochondria-targeted vitamin E analogs inhibit breast cancer cell energy metabolism and promote cell deathBMC Cancer.  13. 2013
    2013 Extracolonic gastrointestinal tract morphologic findings in a case of pseudomembranous collagenous colitisAnnals of Diagnostic Pathology.  17:291-294. 2013
    2013 Mo1867 Wnt/β-Catenin Signaling in Non-Dysplastic Barrett's Esophagus: Activation Beyond Robust Nuclear β-CateninGastroenterology.  144:s-678-s-679. 2013
    2013 Tu1842 The Biological Role of Dickkopf-1 (DKK1) in Human Reflux-EsophagitisGastroenterology.  144:s-860-s-861. 2013
    2013 Use of combination chemotherapy for treatment of granulomatous and lymphocytic interstitial lung disease (GLILD) in patients with common variable immunodeficiency (CVID)Journal of Clinical Immunology.  33:30-39. 2013
    2012 Certification in molecular pathology in the united states: An update from the association for molecular pathology training and education committee 2012
    2012 Disseminated Nocardia farcinica: Literature review and fatal outcome in an immunocompetent patientSurgical Infections.  13:163-170. 2012
    2012 Mitochondria-targeted drugs synergize with 2-deoxyglucose to trigger breast cancer cell deathCancer Research.  72:2634-2644. 2012
    2012 Abstract 1210: Tetraspanin CD63 interacts with extranuclear estrogen receptor alpha and regulates non-genomic signaling pathways in breast cancerCancer Research.  72:1210-1210. 2012
    2012 Preface 2012
    2011 SmgGDS splice variants: Potential novel targets for breast cancer therapeutics.Journal of Clinical Oncology.  29:225-225. 2011
    2011 Erratum: Cardiac-specific transcription factor genes Smad4 and Gata4 cooperatively regulate cardiac valve development (Proceedings of the National Academy of Sciences of the United States of America (2011) 108 (4006-4011) DOI:10.1073/pnas.1019025108) 2011
    2011 Cardiac-specific transcription factor genes Smad4 and Gata4 cooperatively regulate cardiac valve development 2011
    2011 Paxillin expression and amplification in early lung lesions of high-risk patients, lung adenocarcinoma and metastatic disease 2011
    2010 Ets1 is required for proper migration and differentiation of the cardiac neural crest 2010
    2010 Identification of histologically distinct conventional adenomas that arise predominately in patients with sessile serrated adenomasAmerican Journal of Surgical Pathology.  34:355-363. 2010
    2009 Update in neoplastic lung diseases and mesothelioma (Archives of Pathology and Laboratory Medicine (2009) 133, 7, (1106-1115))Archives of Pathology and Laboratory Medicine.  133:1733. 2009
    2009 Molecular biology underlying the clinical heterogeneity of prostate cancer: An updateArchives of Pathology and Laboratory Medicine.  133:1033-1040. 2009
    2009 Recent developments in the pathology of renal tumors: Morphology and molecular characteristics of select entitiesArchives of Pathology and Laboratory Medicine.  133:1026-1032. 2009
    2009 Update in neoplastic lung diseases and mesotheliomaArchives of Pathology and Laboratory Medicine.  133:1106-1115. 2009
    2009 Update in nonneoplastic lung diseasesArchives of Pathology and Laboratory Medicine.  133:1096-1105. 2009
    2008 Expression and mutational analysis of MET in human solid cancers 2008
    2008 Paxillin is a target for somatic mutations in lung cancer: Implications for cell growth and invasionCancer Research.  68:132-142. 2008
    2002 C. elegans PAT-4/ILK functions as an adaptor protein within integrin adhesion complexesCurrent Biology.  12:787-797. 2002
    1997 Development of a coupled VanA/VanX assay: Screening for inhibitors of glycopeptide resistanceSLAS Discovery.  2:241-247. 1997
    1996 High throughput screen for inhibitors of bacterial DNA topoisomerase I using the scintillation proximity assaySLAS Discovery.  1:135-143. 1996


    Year Title Altmetric
    2012 Pediatric Neoplasia: Advances in Molecular Pathology and Translational Medicine 2012


    Year Title Altmetric
    2020 Synovial Sarcoma 2020
    2010 Lung and pleura.  217-280. 2010
    2010 4 Lung and Pleura.  217-280. 2010
    2009 Lung and pleura.  217-280. 2009

    Research Overview

  • Dr. Mackinnon's research interests include the molecular pathology of solid tumors and quantitative immunohistochemistry.
  • Full Name

  • Alexander Mackinnon