Publications | Johns Hopkins Pathology

Barretts esophagus books 2

Research

Autopsy Pathology

Ho C, Salimian M, Hegert J, et al. Postmortem Assessment of Olfactory Tissue Degeneration and Microvasculopathy in Patients With COVID-19. JAMA Neurol. 2022;79(6):544–553.

Cardiovascular Pathology

Patil AH, Halushka MK. miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline. NAR Genom Bioinform. 2021 Sept;3(3):lqab068. PMID: 34308351

Clinical Chemistry

Chen SY, Lih TM, Li QK, Zhang H. Comparing Urinary Glycoproteins among Three Urogenital Cancers and Identifying Prostate Cancer-Specific Glycoproteins. ACS Omega. 2022 Mar;7(11):9172-80

Li QK, Lih TM, Wang Y, Hu Y, Höti N, Chan DW, Zhang H. Improving the detection of aggressive prostate cancer using immunohistochemical staining of protein marker panels. Am J Cancer Res 2022 Mar;12(3):1323-36

GI & Liver Pathology

Salimian KJ, Birkness-Gartman J, Waters KM. Review: The path(ology) from reflux oesophagitis to Barrett oesophagus to oesophageal adenocarcinoma. Pathology 2022 Mar;54(2):147-56

Kohi S, Macgregor-Das A, Dbouk M, Yoshida T, Chuidian M, Abe T, Borges M, Lennon AM, Shin EJ, Canto MI, Goggins M. Alterations in the duodenal fluid microbiome of patients with pancreatic cancer. Clin Gastroenterol Hepatol 2022 Feb;20(2):e196-e227

Kimura H, ... Wood LD, Eshleman JR, Hruban RH, Goggins MG, Klein AP; Familial PC Project, Roberts NJ. Functional CDKN2A assay identifies frequent deleterious alleles misclassified as variants of uncertain significance. Elife 2022 Jan;11:e71137

Lee JW, Zhang Y, Yoshizawa T, Argani P, Wood LD, Oshima K. Cancerization of ducts in hilar cholangiocarcinoma Virchows Arch. 2022 481:1-10

Gynecologic Pathology

Xing D, Miller K, Beierl K, Ronnett BM. Loss of p57 Expression in Conceptions Other Than Complete Hydatidiform Mole: A Case Series With Emphasis on the Etiology, Genetics, and Clinical Significance. Am J Surg Pathol 2022 Jan;46(1):18-32

Murdock TA, Xing D, ..., Hopkins MR, Askin F, Vang R. Bizarre Chorionic-type Trophoblast in Second-trimester and Third-trimester Placentas: Clinicopathologic Characterization of a Placental Pseudoneoplastic Lesion. Am J Surg Pathol 2022 Feb;46(2):258-67.

Feng PH, Wang X, Ferrall L, Wu TC, Hung CF. Control of Tumors by Antigen-Specific CD8+ T Cells through PDL1-Targeted Delivery of Antigenic Peptide. J Immunol Res. 2022 Jan;2022:9054569

Hematopathology

Borowitz MJ, Wood BL, Keeney M, Hedley BD. Measurable Residual Disease Detection in B-Acute Lymphoblastic Leukemia: The Children's Oncology Group (COG) Method. Curr Protoc 2022 Mar;2(3):e383

Immunology

Won T, Halushka MK, Rosenberg AZ, ..., Gilotra NA, Hooper JE, Pekosz A, Čiháková D. Endothelial thrombomodulin downregulation caused by hypoxia contributes to severe infiltration and coagulopathy in COVID-19 patient lungs. EBioMedicine 2022 Jan;75:103812

Won T, Gilotra NA, Wood MK, Hughes DM, Talor MV, Lovell J, Milstone AM, Steenbergen C, Čiháková D. Increased Interleukin 18-Dependent Immune Responses Are Associated With Myopericarditis After COVID-19 mRNA Vaccination. Front Immunol 2022 Feb;13:851620

Venkataraman T, ..., Spector T, Roederer M, Duggal P, Larman HB. Analysis of antibody binding specificities in twin and SNP-genotyped cohorts reveals that antiviral antibody epitope selection is a heritable trait. Immunity. 2022 Jan;55(1):174-84.e5

Sung BY, Lin YH, Kong Q, Shah PD, Glick Bieler J, Palmer S, Weinhold KJ, Chang HR, Huang H, Avery RK, Schneck J, Chiu YL. Wnt activation promotes memory T cell polyfunctionality via epigenetic regulator PRMT1. J Clin Invest. 2022 Jan;132(2):e140508

Monaco DR, ..., Anderson DE, Wijaya L, Tan K, Chia WN, Kammers K, Caturegli P, Waugh K, Roederer M, Petri M, Goldman DW, Rewers M, Wang LF, Larman HB. Deconvoluting virome-wide antibody epitope reactivity profiles. EBioMedicine. 2022 Jan; 75:103747

Informatics

Sidhom JW, Larman HB, Pardoll DM, Baras AS. DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires. Nat Commun. 2021 Mar;12(1):1605. PMID: 33707415

Medical Microbiology

White DAE, ..., Dashler G, Carroll KC, Mostafa HH, Rothman RE. Clinical Utility of the Signal-to-Cutoff Ratio of Reactive HIV Antigen/Antibody Screening Tests in Guiding Emergency Physician Management. J Acquir Immune Defic Syndr.2022 Mar;89(3):332-9

Simner PJ, ..., Rhoads D, Rolf R, She R, Souers RJ, Wojewoda C, Humphries RM. Raising the Bar: Improving Antimicrobial Resistance Detection by Clinical Laboratories by Ensuring Use of Current Breakpoints. Open Forum Infect Dis 2022 Feb;9(3):ofac007.

Simner PJ, ..., Quan J, Walker GT, Jacobs MR, Rhoads D. Multicenter Evaluation of the Acuitas ® AMR Gene Panel for Detection of an Extended Panel of Antimicrobial Resistance Genes among Bacterial Isolates. J Clin Microbiol 2022 Mar;60(3):e0209821.

Armstrong DT, ..., Parrish N. Clinical Validation of the Xpert MTB/RIF Test for Identification of the Mycobacterium tuberculosis Complex in Acid-Fast Bacillus Smear-Positive MGIT Broth Cultures. J Clin Microbiol 2022 Feb;60(2):e0216421

Molecular Pathology

Lin MT, Zheng G, Rodriguez E, Tseng LH, Parini V, Xian R, Zou Y, Gocke CD, Eshleman JR. Double PIK3CA Alterations and Parallel Evolution in Colorectal Cancers. Am J Clin Pathol 2022 Feb ;157(2):244-51

Lin JH, Chen S, Pallavajjala A, Guedes LB, Lotan TL, Bacher JW, Eshleman JR. Validation of Long Mononucleotide Repeat Markers for Detection of Microsatellite Instability. J Mol Diagn 2022 Feb;24(2):144-57

Fischer CG, Eshleman JR, Gocke CD, Lin MT, Xian RR, et al. Artificial intelligence-assisted serial analysis of clinical cancer genomics data identifies changing treatment recommendations and therapeutic targets. Clin Cancer Res. 2022 Jun;28(11):2361-72.

Neuropathology

Nauen DW, Troncoso JC. Amyloid-beta is present in human lymph nodes and greatly enriched in those of the cervical region. Alzheimers Dement 2022 Feb;18(2):205-10.

Britson KA, Ling JP, ..., Mammen AL, Villalta SA, Larman HB, Wong PC, Lloyd TE. Loss of TDP-43 function and rimmed vacuoles persist after T cell depletion in a xenograft model of sporadic inclusion body myositis. Sci Transl Med 2022 Jan;14(628):eabi9196

Surgical Pathology

Xu J, Wang Y, Li Z, Tian Y, Li Z, Lu A, Hsu CY, Negri S, Tang C, Tower RJ, Morris C, James AW. PDGFRα reporter activity identifies periosteal progenitor cells critical for bone formation and fracture repair. Bone Res. 2022 Jan;10(1):7

Xu J, Li Z, Tower RJ, Negri S, Wang Y, Meyers CA, Sono T, Qin Q, Lu A, Xing X, McCarthy EF, Clemens TL, James AW. NGF-p75 signaling coordinates skeletal cell migration during bone repair. Sci Adv. 2022 Mar;8(11):eabl5716

Liang A*, Baraban E*, Myers KS, Mullen LA, Panigrahi B, Oluyemi E, Cimino-Mathews A, Ambinder EB. Developing Asymmetries without Sonographic Correlate at Digital Breast Tomosynthesis. Radiology 2022 Mar;302(3):525-32

Jagannathan G, White MJ, Xian RR, Emens LA, Cimino-Mathews A. A New Landscape of Testing and Therapeutics in Metastatic Breast Cancer. Surg Pathol Clin 2022 Mar;15(1):105-20

Birkness-Gartman JE, Oshima K. Review: Liver pathology in pregnancy. Pathol Int 2022 Jan;72(1):1-13.

Assarzadegan N, Brooks E, Voltaggio L. HPV-driven anal neoplasia: review and recent developments. Pathology 2022 Mar;54(2):184-94.

Argani P, Mehra R. Renal cell carcinoma associated with tuberous sclerosis complex (TSC)/mammalian target of rapamycin (MTOR) genetic alterations. Mod Pathol 2022 Mar;35(3):296-7.

Baraban E, Ding CC, ..., Dobs A, Ketheeswaran S, Liang F, Epstein JI. Prostate Cancer in Male-to-Female Transgender Individuals: Histopathologic Findings and Association With Gender-affirming Hormonal Therapy. Am J Surg Pathol. 2022 Dec 1;46(12):1650-8.

Transfusion Medicine

Redd AD, Bloch EM, ..., Fehlings M, Quinn TC, Tobian AAR. Minimal Crossover between Mutations Associated with Omicron Variant of SARS-CoV-2 and CD8+ T-Cell Epitopes Identified in COVID-19 Convalescent Individuals. mBio 2022 Mar;13(2):e0361721.

White JL, Patel EU, Grabowski MK, Petersen MR, Gaydos CA, Quinn TC, Tobian AAR. Trends and Correlates of Age-Disparate Sexual Partnerships in the United States: The National Health and Nutrition Examination Surveys. Sex Transm Dis. 2022 Jan;49(1):e17-e21.

Patel EU, Zhu X, Quinn TC, Tobian AAR. Public Knowledge and Attitudes Toward Clinical Trials in the COVID-19 Era. Am J Prev Med 2022 Mar;62(3):469-71.

Patel EU, Genberg BL, Zhu X, Krawczyk N, Mehta SH, Tobian AAR. HIV and Hepatitis C Virus Testing and Treatment Services in Specialty Treatment Facilities That Offer Medication for Opioid Use Disorder in the US. JAMA 2022 Feb;327(8):776-7.

Patel EU, Bloch EM, Tobian AAR. Editorial commentary: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Serosurveillance in Blood Donor Populations. J Infect Dis. 2022 Jan ;225(1):1-4.

Klein EY, Zhu X, Petersen M, Patel EU, Cosgrove SE, Tobian AAR. Methicillin-Resistant and Methicillin-Sensitive Staphylococcus aureus Hospitalizations: National Inpatient Sample, 2016-2019. Open Forum Infect Dis 2022 Jan;9(1):ofab585.

Fowler MG, ..., Familiar I, Taha T, Boivin MJ; PROMISE-NEURODEV study team. Growth deficits in antiretroviral and HIV exposed uninfected versus unexposed children in Malawi and Uganda persist through 60 months-of-age. AIDS 2022 Mar;36(4):573-82.

Durand CM, Florman S, Motter JD, …, Tobian AAR, Segev DL; HOPE in Action Investigators. HOPE in action: A prospective multicenter pilot study of liver transplantation from donors with HIV to recipients with HIV. Am J Transplant. 2022 Mar;22(3):853-64.

Bloch EM, Day JR, Krause PJ, Kjemtrup A, O'Brien SF, Tobian AAR, Goel R. Epidemiology of Hospitalized Patients with Babesiosis, United States, 2010-2016. Emerg Infect Dis. 2022 Feb;28(2):354–62.

Sullivan D, Gebo KA, Shoman S, Bloch EM, …, Casadevall A*, Tobian AAR*, Hanley D* (*Shared Senior Authors). Early outpatient COVID-19 treatment trial with convalescent plasma. N Engl J Med. 2022 May;386(18):1700-11.

Urologic/Kidney Pathology

Sfanos KS. Comment: Immune cell infiltrates and prognosis in localized prostate cancer. J Pathol. 2022 Feb;256(2):135-8

Russell DH, Epstein JI. Intraductal Adenocarcinoma of the Prostate With Cribriform or Papillary Ductal Morphology: Rare Biopsy Cases Lacking Associated Invasive High-grade Carcinoma. Am J Surg Pathol 2022 Feb;46(2):233-40

Maynard JP, ..., Mummert L, Ali T, Kempski R, Carter AM, Sosa RY, Peiffer LB, Joshu CE, Lotan TL, De Marzo AM, Sfanos KS. P2X4 purinergic receptors offer a therapeutic target for aggressive prostate cancer. J Pathol 2022 Feb;256(2):149-63

Jones CB, White JR, Ernst SE, Sfanos KS, Peiffer LB. Incorporation of Data From Multiple Hypervariable Regions when Analyzing Bacterial 16S rRNA Gene Sequencing Data. Front Genet 2022 Mar;13:799615

Geetha D, Attarwala N, Zhang C, Kant S, Antiochos B, Seo P, Le A. Serum and urinary metabolites discriminate disease activity in ANCA associated glomerulonephritis in a pilot study. J Nephrol 2022 Mar;35(2):657-63

Nelson WG, Brawley OW, Isaacs WB, Platz EA, Yegnasubramanian S, Sfanos KS, Lotan TL, De Marzo AM. Review: Health inequity drives disease biology to create disparities in prostate cancer outcomes. J Clin Invest 2022 Feb;132(3):e155031

Angajala A, Raymond H, ..., R, Karanam B, Kahn AG, Bedi D, Davis M, Tan M, Dean-Colomb W, Yates C. MicroRNAs within the Basal-like signature of Quadruple Negative Breast Cancer impact overall survival in African Americans. Sci Rep 2022 Dec;12(1):22178

Asrani K, Woo J, Mendes AA, ..., Murali S, Liu HB, Salles DC, Lam B, Argani P, Lotan TL. An mTORC1-mediated negative feedback loop constrains amino acid-induced FLCN-Rag activation in renal cells with TSC2 loss. Nat Commun 2022 Nov 10;13(1):6808.

Ozbek B, Ertunc O, Erickson A, Vidal ID, Gomes-Alexandre C, Guner G, Hicks JL, Jones T, Taube JM, Sfanos KS, Yegnasubramanian S, De Marzo AM. Multiplex immunohistochemical phenotyping of T cells in primary prostate cancer. Prostate. 2022 May;82(6):706-22.