Varambally's Latest Cancer Research Featured in Nature Communications
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Written by Christina Crowe
Sooryanarayana Varambally, Ph.D., Professor, Molecular & Cellular Pathology, Director, Translational Oncologic Pathology Research, and his research team recently published an article in the journal Nature Communication featuring work they shared on their cancer data tool, UALCAN, "Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways." https://www.nature.com/articles/s41467-022-30342-3
UALCAN stands for University of Alabama Cancer Database, and is designed as an easy-to-use, interactive web portal to perform to in-depth analyses of TCGA gene expression data.
Following, Dr. Varambally explains the research highlighted in the article:
"In the current study published in Nature Communication, we systematically assessed pathway-level somatic alterations (by small mutation or copy number alteration) across tumors. In this study, along with our collaborator Dr. Chad Creighton from Baylor College of Medicine, lead author, we assembled a compendium dataset of mass-spectrometry-based proteomics data from 2002 primary tumors from 14 cancer types and 17 studies. We integrated proteomic data with other omics data to examine how somatic mutation affecting a given pathway shows up at the protein level. Further, the data were provided in UALCAN for cancer researchers and clinicians across the world."
Marques Awarded ASFA's Morrison Memorial Lecture Award
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Written by Christina Crowe
Marisa Marques, M.D., Professor and Medical Director, Transfusion Medicine, attended the American Society for Apheresis annual meeting in Philadelphia, PA, May 4-6, where she received the Francis S. Morrison, M.D., Memorial Lecture Award.
The Francis S. Morrison, M.D. Memorial Lecture is an annual keynote lecture created to keep alive and honor the memory of Francis S. Morrison, MD, a true pioneer in apheresis medicine and a leading apheresis professional. The first lecture was held at the ASFA Meeting in 2002. The award is bestowed upon a member of the Society who has made major contributions to the field of apheresis medicine and an apheresis professional who has made a lasting difference in the field, preferably at the national level.
The title of Marques' talk was, "How I Used The Tools That ASFA Gave Me To Give Back." UAB Pathology Blood Bank/Transfusion Medicine fellow, Dr. Sohaila Soltani (below, group photo, on right), attended the conference. Brooke Bartow, PGY1 (below, group photo, on left), presented a poster at the conference on, "The Evolution of an Apheresis Service: A Partnership with the Blood Bank to Serve the Underserved."
Department Celebrates Outgoing Residents and Fellows
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Written by Christina Crowe
The UAB Department of Pathology was thrilled to gather for an outgoing reception for our residents, fellows, and trainees on May 5. Department faculty, staff, fellows, and residents came together to celebrate at B&A Warehouse, near Railroad Park adjacent to downtown Birmingham, with dinner and an awards ceremony.
A welcome by Brandi McCleskey, M.D., Director of the Pathology Residency Program, was followed by announcements of this year’s Alpha Omega Alpha inductees: Denis Noubouossie, M.D., Ph.D., Michael Williams, M.D., Christine Pesoli, M.D., and Shuko Harada, M.D. AOA is a national honor medical society. Dr. McCleskey also recognized UAB Heersink School of Medicine graduating student, Hannah Cutshall, as the first Pathology Integrated Resident. This position is part of the unique Research and Clinical Experience for Pathology (RaCE4Path) program, which is a collaborative effort with the Physician Scientist Development Office.
McCleskey then acknowledged this year's outgoing chief resident for Education and Outreach, Oraine Snaith, M.D., and announced incoming chief in the same role, Geoffrey Herndon, D.O. Cristina Magi-Galluzzi, M.D., Ph.D., Division Director, Anatomic Pathology, presented a certificate to Raima Memon, M.D., outgoing AP chief resident, and announced incoming AP chief Sarah Anderson, D.O.. Vishnu Reddy, M.D., Division Director, Laboratory Medicine, presented a certificate to Denis Noubouossie, M.D., Ph.D., as Clinical Pathology outgoing chief, and recognized Sarah DePew, D.O., as incoming.
New Cancer Assay Provides Rapid Results and Reduces Needs for Repeat Biopsies
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Written by Christina Crowe
Genomic Diagnostics and Bioinformatics facultyinclude (left to right): Craig Mackinnon, M.D., Ph.D., Diana Morlote, M.D., Shuko Harada, M.D., director, Molecular Diagnostics Lab, and Yulong Fu, M.D., director, Medical Genomics Lab.
UAB Pathology and the Division of Genomic Diagnostics and Bioinformatics are pleased to announce a new, state-of-the-art Next Generation Sequencing (NGS) Cancer Assay, now available in the UAB Clinical Molecular Diagnostics Laboratory.
The Oncomine Precision Assay (OPA) uses a streamlined workflow to analyze both DNA and RNA extracted from formalin fixed, paraffin embedded (FFPE) solid tumor tissues. Important features of OPA are the ability to test small tissue samples (e.g., biopsies), and very fast turnaround time (e.g. 3-5 days upon receipt in the molecular lab). OPA detects single nucleotide variants (SNVs), insertions and deletions (INDELs), copy number variations (CNVs), and gene fusions in actionable, cancer-related genes.
“UAB was one of the first academic medical centers to gain access to this instrument—the Ion Torrent Genexus—and implement it,” says Alexander “Craig” Mackinnon, Jr., M.D., Ph.D., Division Director. “It represents the latest technology for in-house, next generation sequencing using amplicon-based targeted sequencing.”
Collaborative Article on Health Disparities Wins Impact Award
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Written by Christina Crowe
A 2021 article written by a collaborative team of UAB researchers has been awarded the American Journal of Physiology-Heart and Circulatory Physiology's 2022 Impact Award. "Racial and socioeconomic disparity associates with differences in cardiac DNA methylation among men with end-stage heart failure," authored by Mark Pepin, M.D., Ph.D., Humboldt postdoctoral fellow at the Institute for Experimental Cardiology at Heidelberg University; Bertha Hidalgo, Ph.D., M.P.H., Associate Professor, School of Public Health; Adam Wende, Ph.D., Associate Professor, UAB Pathology, and Selwyn Vickers, M.D., Office of the Dean and Senior Vice President for Medicine, UAB Heersink School of Medicine, received the honor.
The AJP-Heart and Circ Impact Award is based on the Altmetric Score for the article (241) and the total online article usage (2,800+ abstract/full text/PDF downloads). The article was picked up by eight news outlets, including UAB News, and tweeted over 250 times. In addition, the episode “Racial & Socioeconomic Determinants of the Cardiac Epigenome” of the The AJP-Heart and Circ Podcast about the work has been downloaded over 350 times.
This is the fourth year for this award, which was announced at the American Physiological Society Cardiovascular Section Banquet at Experimental Biology 2022 in Philadelphia, PA.
Dean Vickers interviewed Wende about the study on his podcast, "The Checkup."
Other UAB collaborators on the article include, Chae-Myeong Ha, Luke A. Potter and Sayan Bakshi, Division of Molecular and Cellular Pathology, UAB Department of Pathology; Joseph P. Barchue, Ayman Haj Asaad, Steven M. Pogwizd and Salpy V. Pamboukian, Division of Cardiovascular Disease, UAB Department of Medicine,
The study, of end-stage heart-failure patients, found that cytosine-p-guanine, or CpG, methylation of the DNA in the heart has a bimodal distribution among the patients, and that race — African American versus Caucasian — was the sole variable in patient records that explained the difference. A subsequent look at the census tracts where the patients lived showed that the African American subjects lived in neighborhoods with more racial diversity and poverty, suggesting that the underlying variable may be a socioeconomic difference.
Resident Nouboussie's RISE Scores Among Highest in Nation
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Written by Christina Crowe
UAB Pathology Resident Denis Nouboussie Fondjie, M.D., Ph.D., PGY3, previous chief resident, Clinical Pathology, learned recently that he scored among the highest in the nation of the Resident In-Service Examination, or RISE. Fondjie scored in the greater than 99th percentile on the Clinical Pathology component of the exam as compared to other PGY3s nationally taking the test.
The RISE is required of all residents as an annual assessment of their medical knowledge and help them (and the program) track their progress throughout their training. This examination is a standardized way to assist trainees when preparing for their careers and future board examinations. Although it is not used to determine academic progression for individual residents, overall performance on this examination is helpful to the program when assessing the medical knowledge competency for each resident as well as the value of our curriculum.
Fondjie will be sitting for his American Board of Pathology Clinical Pathology examination this spring, and starting a fellowship in Transfusion Medicine at University of North Carolina. Of note, Denis also had a submission accepted for this year's Academy of Clinical Laboratory Physicians and Scientists annual meeting that has also been awarded the Paul E. Strandjord Young Investigator Award as one of the top 20 scoring abstracts.
"Denis’s scores on this exam are truly impressive, and come as little surprise to those of us who have worked with him for the past three years at UAB Pathology," says Brandi McCleskey, M.D., Pathology Residency Training Program Director. "His professionalism, expertise, and dedication to clinical pathology are among the reasons he was selected to serve as chief resident. He has been a pleasure to have as a trainee and colleague, and we congratulate him on this achievement."
Benson, Reilly, Litovsky Awarded USCAP Stout Award
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Written by Christina Crowe
A multi-institutional paper on COVID autopsies published in Archives of Pathology and Laboratory Medicine was awarded the United States and Canadian Academy of Pathologists' L.Clark Jr. and Elaine F. Stout Award for best Anatomic Pathology paper in 2022.
UAB Pathology faculty authors include Paul Benson, M.D., Associate Professor; Stephanie Reilly, M.D., Associate Professor (retired), and Silvio Litovsky, M.D., Professor. Benson is director of the Autopsy Section, taking over for Litovsky in the role in 2020.
The paper, titled, "A Postmortem Portrait of the Coronavirus Disease 2019 (COVID-19) Pandemic: A Large Multi-institutional Autopsy Survey Study," was published in the May 2021 issue of Archives.
UAB Pathology Labs Focus on Sustainability with Green Labs Certification
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Written by Hannah Weems
UAB is the state of Alabama’s largest employer, supporting one of every 31 jobs statewide, with an annual impact of more than $7 billion. UAB is also an R1 Institution, ranked 20th nationally in NIH funding. In turn, UAB is also the largest electricity consumer in the state and generates more than 2,000 tons of landfill waste annually, according to UAB Sustainability. A portion of this waste comes from the necessary work of UAB’s nearly 2,000 laboratories, but researchers have the ability to reduce this impact by becoming certified in UAB’s Green Labs Program.
The goal of the Green Labs Program is to reduce the use of energy, water, material goods, and hazardous chemicals in UAB labs without compromising research integrity or safety. The program provides tips for better sustainability within labs and a recycling service to pick up nontoxic batteries, Styrofoam, paper, plastic, aluminum, and other reusable materials. Active since November 2016, it now has more than 130 participating labs across campus.
5-Year Retrospective: Dr. Netto at the Helm
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Five years ago in late 2016, George J. Netto, M.D., accepted the role of Robert and Ruth Anderson Endowed Chair, UAB Department of Pathology. This would be his first position at the chair level, having previously served as director of surgical pathology molecular diagnostics at Johns Hopkins Hospital for five years.
Netto made a big leap from Baltimore to Birmingham to join the team at UAB. A native of Damascus, Syria, his path to pathology chair has been filled with many challenges and opportunities- even a global pandemic- that require ongoing adaptation and a steadfast vision for a constantly improving operation.
Today Netto runs UAB Pathology with a team of more than 300 faculty, trainees, and staff members from his office in the West Pavilion of UAB Hospital. The department is one of the largest academic pathology departments in the country.
It was word of mouth and reputation about UAB Pathology that first interested Netto in the open chair position, he recalls.
Pathology Employees to be Recognized in Annual Service Awards
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In April, six of our colleagues will be recognized for their years of service working at UAB and the Department of Pathology.
The UAB Service Awards proudly honors those employees who have made a significant career commitment to the University of Alabama at Birmingham. The program is designed to recognize and express appreciation to employees at each five-year milestone who have completed five or more years of service to UAB. More than 1,200 UAB employees will be honored at the annual service awards and those with more than 20 years of service will be honored by the university on April 11 at the Hilton Birmingham at UAB. Click here to meet the 2022 Service Award Recipients with 20 or more years of service.
How T cell-derived interleukin-22 promotes antibacterial defense of colonic crypts
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Casey Weaver, M.D. Photography: Amanda MabryIntestinal epithelial cells line the inner wall of the gut, creating a barrier to dangerous bacteria like enteropathogenic E. coli that seek to attach and efface that barrier, causing diarrhea. Such pathogens pose significant risks to human health and cause infant death in developing countries.
In a study published in the journal Immunity, Carlene L. Zindl, Ph.D., and Casey T. Weaver, M.D., of the University of Alabama at Birmingham Department of Pathology show how two types of immune cells — one a part of the innate immune system and the other a part of the adaptive immune system — play distinct and indispensable roles to defend that barrier.
“In this study, we define a nonredundant role for interleukin-22-producing T cells in antibacterial defense of colonic crypts,” Weaver said. “Our findings address a central, unresolved issue regarding the coordination of innate and adaptive immunity and specialization of innate lymphoid cells, or ILCs, and CD4 T cells. Since the discovery of ILC subsets and appreciation of their functional parallel with T cell subsets, it has been unclear what functions are unique to each immune cell population.”
Molecular and Cellular Pathology Welcomes New Faculty in April
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On April 12, 2022, the Department of Pathology welcomes a new faculty member to the Division of Molecular and Cellular Pathology, directed by Ralph Sanderson, Ph.D.
Steve Lim, Ph.D., joins the Department as Associate Professor, Molecular and Cellular Pathology. Dr. Lim joins us from the University of South Alabama, where he served as Associate Professor.
Division of Women's Health Welcomes New Faculty in April
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On April 1, 2022, the Department of Pathology welcomes a new faculty member to the Division of Women’s Health.
Valeria Dal Zotto, M.D., joins the Department as Assistant Professor, Women’s Health. Dr. Dal Zotto was previously a Clinical Assistant Professor in the Department of Pathology and Laboratory Medicine at East Carolina University in Greenville, North Carolina.
USCAP Conference 2022 a Success
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The United States and Canadian Academy of Pathology (USCAP) hosted its 111th annual meeting March 19-24, 2022 at the Los Angeles Convention Center in Los Angeles, California, where members of UAB Pathology represented the Department in full force to present various topics of research. This year's meeting was held both in-person and online.
UAB Pathology Welcomes 2022-23 Residents on Match Day
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We are thrilled to announce the successful completion of this year's residency match program where we filled all seven of our open positions for 2022-23. Please join us in welcoming the following individuals to our team:
UAB Pathology at USCAP 2022
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The United States and Canadian Academy of Pathology (USCAP) hosts its annual meeting in person and virtually this year, March 19-24, 2022, in Los Angeles, California.
The department will participate in the conference in a variety of ways, from the Fellowship Fair on Sunday March 20, to a reception on Monday, March 21, and many poster and platform presentations throughout the nearly weeklong conference, UAB Pathology will be represented in force.
Department Publishes Pathology in Focus, Volume 4
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We are delighted to announce the publication of our latest annual volume of Pathology in Focus.
Each year, the magazine allows for a chance to highlight our accolades. This year, we highlight the first five years of leadership by George Netto, M.D., Robert and Ruth Anderson Endowed Chair, and include a personal history of his educational and professional background. Our content continues to cover recent clinical, educational and research activities, and successes of the UAB Department of Pathology. This year, we highlight awards and accolades from around the department, and cover our wellness and Diversity, Equity and Inclusion initiatives. Our cover features Isam-Eldin-Eltoum, M.D., M.B.A., Vice Chair for Quality and Patient Safety, in a photo taken during our department-wide shoot last fall.
UAB Pathology Plays Key Role in First of Its Kind Pig-to-Human Kidney Transplant
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On Thursday, January 20, 2022, the University of Alabama at Birmingham Marnix E. Heersink School of Medicine announced the first peer-reviewed research outlining the successful transplant of genetically modified, clinical-grade pig kidneys into a brain-dead human individual, replacing the recipient’s native kidneys. The study is a promising step toward prospective clinical trials of kidney transplant from pigs to living humans, to address the worldwide organ shortage crisis.
The team at UAB Pathology was excited to play a crucial role in this groundbreaking study by providing details of pathological findings on diagnostic biopsies throughout the procedure.
Welcoming Dr. Varma to the Women's Health Division
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On March 1, 2022, the UAB Department of Pathology welcomed Kavita Varma, M.D., DNB, as assistant professor in the newly established Division of Women’s Health.
Varma joins the department after having worked as a staff pathologist at Laboratory Corporation of America (LabCorp) in Birmingham for the past four years. Prior to that position, she was a clinical instructor of breast and gynecologic pathology in Magee Women’s Hospital, University of Pittsburgh Medical Center.
She completed a residency in anatomic and clinical pathology at the Department of Pathology and Lab medicine, Henry Ford Hospital, Detroit, MI. Prior to that, she worked as a research assistant and clinical observer at the Washington University School of St. Louis’s Department Pathology. Before coming to the U.S., Dr. Varma worked as a research assistant and resident in India, where she completed her medical training.
Varma’s research interests include ovarian and endometrial cancers, their pathogenesis and progression at histological and molecular level. She has several dozen peer-reviewed publications and abstracts, in addition to many poster presentations at pathology conferences in the US and India. Varma is a member of the United States and Canadian Academy of Pathologists, American Society for Clinical Pathology, College of American Pathologists, and the Indian Association of Pathologists and Microbiologists.
Please join us in welcoming Dr. Varma to our faculty and pathology team.
A Career of Practicing Compassionate Care
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By Christina Crowe
For more than 45 years, Thurman Richardson has worked with the recently departed, serving as a liaison between the doctors and nurses who cared for them in their last moments of life, and their families.
Richardson, Technical Director for the UAB Autopsy Service and the Office of Decedent Affairs, is one of UAB Medicine’s longest serving employees, and some might say has one of the most unique jobs in the health system. He refers to what he does as, “practicing compassionate care.”
A pathology assistant by training, Richardson has served in an administrative role since 1989, and has worked at UAB Pathology with the autopsy service since his days as a student at UAB.
Richardson was an undergrad at Lawson College who needed money to pay for tuition. Some friends who worked in the department as morgue attendants got him a job doing the same. Rather than being deterred by death, Richardson found it fascinating, he says, using an analogy of batteries powering toys.
“Toys run out of batteries,” he says. “I used to look at human beings living 70 or 90 years without a battery and think, ‘how does that work?’ I wanted to know how a human being could keep functioning for so long.”