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College of Medicine: Department of Biochemistry and Molecular Biology

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November 2021 Publications

Members of the Miller lab

CYP2C9 and 3A4 play opposing roles in bioactivation and detoxification of diphenylamine NSAIDs.
Schleiff MA, Crosby S, Blue M, Schleiff BM, Boysen G, Miller GP.
Biochem Pharmacol. 2021

Members of the Byrd lab

A structural feature of Dda helicase which enhances displacement of streptavidin and trp repressor from DNA.
Byrd AK, Malone EG, Hazeslip L, Zafar MK, Harrison DK, Thompson MD, Gao J, Perumal SK, Marecki JC, Raney KD.
Protein Sci. 2021

Members of the Kendrick Lab

Clinical implications of loss of bone marrow minimal residual disease negativity in multiple myeloma.
Mohan M, Kendrick S, Szabo A, Yarlagadda NK, Atwal D, Pandey Y, Roy AM, Parikh R, Lopez J, Thanendrarajan S, Schinke C, Alapat D, Sawyer JR, Tian E, Tricot G, van Rhee F, Zangari M.
Blood Adv. 2021

Dr. Michael Birrer

Utilization of a 3-D tissue engineered model to investigate the effects of perfusion on gynecologic cancer biology.
Martinez A, Buckley MS, Scalise CB, Wang D, Katre AA, Birrer MJ, Berry JL, Arend RC.
J Tissue Eng. 2021

Risk stratification after recurrence of human papillomavirus (HPV)-related and non-HPV-related oropharyngeal cancer: A secondary analysis of NRG Oncology RTOG 0129 and 0522.
Bigelow EO, Harris J, Fakhry C, Gillison ML, Nguyen-Tân PF, Rosenthal DI, Frank SJ, Nair SG, Bahig H, Ridge JA, Caudell J, Donaldson C, Clifford BT, Shenouda G, Birrer MJ, Chen Y, Le QT.
Head Neck. 2021

Milk Formula Diet Alters Bacterial and Host Protein Profile in Comparison to Human Milk Diet in Neonatal Piglet Model.
Rosa F, Zybailov BL, Glazko GV, Rahmatallah Y, Byrum S, Mackintosh SG, Bowlin AK, Yeruva L.
Nutrients. 2021

Popular Paper

Duah Alkam

An article by Dr. Duah Alkam, Assistant Staff Scientist in the Department of Biochemistry and Molecular Biology working in the Bioinformatics core, and colleagues has been one of the most popular articles in the journal Microbial Genomics this fall. The article – the journal’s third most read in both October and November – was part of her thesis project for her Ph.D. in the Graduate Program in Interdisciplinary Biomedical Sciences, which she completed earlier this year. As a graduate student, she worked with Dr. Mark Smeltzer, Professor of Microbiology and Immunology, and Dr. David Ussery, Professor of Biomedical Informatics. Great job!

Bethany Paxton Wins at AR-INBRE

AR-INBRE conference

Bethany Paxton

Bethany Paxton won won 1st place in Biological Sciences at the 2021 AR-INBRE meeting. Bethany worked in Robert Eoff’s lab on their NSF-funded project investigating the role of human Rev1 in G4 replication. This was her first scientific conference. Great job Bethany!

October 2021 Publications

Duah Alkam

Is amplification bias consequential in transposon sequencing (TnSeq) assays? A case study with a Staphylococcus aureus TnSeq library subjected to PCR-based and amplification-free enrichment methods.
Alkam D, Wongsurawat T, Nookaew I, Richardson AR, Ussery D, Smeltzer MS, Jenjaroenpun P.
Microb Genom.

Dr. Michael Birrer

A highly annotated database of genes associated with platinum resistance in cancer.
Huang D, Savage SR, Calinawan AP, Lin C, Zhang B, Wang P, Starr TK, Birrer MJ, Paulovich AG.
Oncogene.

Authors

Raman spectroscopy and machine learning reveals early tumor microenvironmental changes induced by immunotherapy.
Paidi SK, Troncoso JR, Raj P, Monterroso Diaz P, Ivers JD, Lee DE, Avaritt NL, Gies AJ, Quick CM, Byrum SD, Tackett AJ, Rajaram N, Barman I.
Cancer Res.

Robert Eoff, Ph.D.

Biobanked Glioblastoma Patient-Derived Organoids as a Precision Medicine Model to Study Inhibition of Invasion.
Darrigues E, Zhao EH, De Loose A, Lee MP, Borrelli MJ, Eoff RL, Galileo DS, Penthala NR, Crooks PA, Rodriguez A.
Int J Mol Sci.

UAMS Cancer Researcher Brian Koss, Ph.D., Is First in State to Earn Prestigious NIH Director’s Award

Koss award

Brian Koss

Brian Koss, Ph.D., a researcher with the UAMS Winthrop P. Rockefeller Cancer Institute, is the state’s first recipient of the prestigious National Institutes of Health (NIH) Director’s Early Independence Award.

By Yavonda Chase

 | LITTLE ROCK — Brian Koss, Ph.D., a researcher with the UAMS Winthrop P. Rockefeller Cancer Institute, is the state’s first recipient of the prestigious National Institutes of Health (NIH) Director’s Early Independence Award.

Part of the High-Risk, High-Reward Research program, the Early Independence Award supports outstanding junior scientists with the intellect, scientific creativity, drive and maturity to bypass the traditional postdoctoral training period to launch independent research careers.

Koss joins an elite group of only 13 2021 NIH Director’s Early Independence Award recipients in the U.S. from such institutions as Stanford, Harvard, Johns Hopkins, Mount Sinai, Vanderbilt and Columbia. He will receive a five-year, nearly $1.9 million grant to fund his highly specialized cancer research at UAMS.

“This award provides a tremendous opportunity to expand my research on immune-based therapies for cancer,” said Koss. “I plan to use the Early Independence Award to build a team of researchers who will be crucial for establishing an innovative and collaborative research laboratory.”

In addition to being the first Arkansan to receive the award, Koss is only the second recipient from an NIH-designated Institutional Development Award (IDeA) state, a group of 23 states plus Puerto Rico that have historically received lower research funding.

“The NIH Director’s Early Independence Award is one of the most prestigious awards given by the NIH to the most promising young scientists across the country,” said Michael Birrer, M.D., Ph.D., UAMS vice chancellor and director of the Winthrop P. Rockefeller Cancer Institute. “Dr. Koss’ research will be a key supporting component of taking the Cancer Institute to NCI designation in the near future.”

“We are thrilled that Dr. Koss is Arkansas’ first recipient of this prestigious and transformative award,” said Susan Smyth, M.D., Ph.D., executive vice chancellor of UAMS and dean of the College of Medicine. “All of us at UAMS look forward to watching Dr. Koss’ ingenuity and hard work lead to meaningful advances in the understanding of the immune response to cancer, and potentially to effective new treatments for cancer patients.”

“This award demonstrates how exceptionally promising the NIH considers Dr. Koss, and how confident the NIH is in the supportive environment at UAMS and the Winthrop P. Rockefeller Cancer Institute,” Smyth said. “Dr. Koss has superb mentors in the Cancer Institute and College of Medicine.”

Unique to Koss’ research is the use of proteomics — powerful computing tools that help make sense of enormous amounts of biological data. This includes creating functional maps of cells and other techniques that lead to better understanding of the molecular pathways in cancer and other diseases. UAMS is home to the NIH’s only national proteomics resource, the IDeA National Resource for Quantitative Proteomics. Koss will use proteomics to study protein turnover rates on a massive scale.

“Dr. Koss performed his graduate work in my laboratory, building a program that focused on how the environment in solid tumors creates unique challenges for immunotherapies,” said Alan Tackett, Ph.D., deputy director of the Winthrop P. Rockefeller Cancer Institute and one of Koss’ mentors. “He will now translate his graduate work to build an independent research program at the Cancer Institute, focusing on how to better understand and engineer the immune system to recognize and eliminate tumors from the body.”

A Mountain Home native, Koss completed his undergraduate degree in biology at Hendrix College in Conway, where he got his first exposure to undergraduate research. Cancer became real to Koss when he worked as a research technician at St. Jude Children’s Hospital in Memphis after college. He returned to Arkansas in 2015 to begin graduate studies at UAMS and earned a Ph.D. in 2020.

In 2021, the National Institutes of Health awarded 106 grants through its High-Risk, High-Reward Research (HRHR) program. Examples of supported research include understanding how long-term memory might be encoded in the shape of folded DNA in our neurons, mining data from unconventional sources to reveal social determinants of suicide, establishing new paradigms to address the functional consequences of health disparities in drug development and looking at the impact of high school and collegiate athlete injuries on long-term health. The 106 awards total approximately $329 million over five years, pending available funds. Koss’ award is funded by NIH Grant DP5-OD031863.

September 2021 publications

Members of the Chambers lab

Phosphoproteomics Provides Novel Insights into the Response of Primary Acute Lymphoblastic Leukemia Cells to Microtubule Depolymerization in G1 Phase of the Cell Cycle.
Delgado M, Washam CL, Urbaniak A, Heflin B, Storey AJ, Lan RS, Mackintosh SG, Tackett AJ, Byrum SD, Chambers TC.
ACS Omega. 2021

Alicja Urbaniak

Characterization of cannabinoid receptors expressed in Ewing sarcoma TC-71 and A-673 cells as potential targets for anti-cancer drug development.
Shoeib AM, Yarbrough AL, Ford BM, Franks LN, Urbaniak A, Hensley LL, Benson LN, Mu S, Radominska-Pandya A, Prather PL.
Life Sci. 2021

Marie Burdine

DNA-PKcs kinase activity stabilizes the transcription factor Egr1 in activated immune cells.
Waldrip ZJ, Burdine L, Harrison DK, Azevedo-Pouly AC, Storey AJ, Moffett OG, Mackintosh SG, Burdine MS.
J Biol Chem. 2021

Authors

A NSD3-targeted PROTAC suppresses NSD3 and cMyc oncogenic nodes in cancer cells.
Xu C, Meng F, Park KS, Storey AJ, Gong W, Tsai YH, Gibson E, Byrum SD, Li D, Edmondson RD, Mackintosh SG, Vedadi M, Cai L, Tackett AJ, Kaniskan HÜ, Jin J, Wang GG.
Cell Chem Biol. 2021

Congratulations to our Ph.D. candidates

Welcome Dr. Rahman

Rahman family
Mohammad Rahman at his Ph.D. graduation ceremony in Nagoya University, Japan with his wife and son in traditional Japanese dress.

Mohamad Rahman, Ph.D., joined the Department of Biochemistry and Molecular Biology as an Assistant Professor in August 2021. Find out more about him with this Q&A.

  • Where are you from and what do you miss most? I am from Bangladesh. I miss my childhood. I wish I could go back to my middle school and meet my friends.
  • Fun fact about yourself. I wanted to serve as a fighter pilot in the Bangladesh Air Force (BAF). I was rejected during my enrolment as a cadet in the BAF due to my compromised eye power. Then I became a biologist. Now I feel fortunate for my rejection from the BAF, which allowed me to explore the fascinating mysteries and fun of biology.
  • What is your favorite place you’ve lived? I completed my undergraduate education in Bangladesh. I moved to Nagoya in Japan for my Ph.D., and stayed there for six years. Then I moved to New York, and stayed there six years more for my Postdoctoral training, prior to my moving in Little Rock. So far, Nagoya is the most favorite place I have ever lived.
  • What place you would like to visit? I would like to visit Melbourne.
  • Do you like to cook? What is your favorite recipe? I love to cook. I enjoy cooking South Asian cuisines. My favorite recipe is Mutton Biryani.
  • What is your favorite food? I love hot and spicy foods. My most favorite food is Mutton Biryani.
  • What is your favorite sport? My favorite sport is cricket.
  • What is your favorite movie? My favorite movie is “3 Idiots”, Directed by RajKumar Hirani.
  • What is your favorite song or band/singer? My favorite band is Little River Band (LRB) in Bangladesh.
  • Name something on your bucket list? A family trip to Europe
  • Do you have any hobbies outside of work? I love to watch movies

August 2021 Publications

Ryan lab

Targeting Rearranged during Transfection in Cancer: A Perspective on Small-Molecule Inhibitors and Their Clinical Development.
Saha D, Ryan KR, Lakkaniga NR, Acharya B, Garcia NG, Smith EL, Frett B.
J Med Chem. 2021

Michael Wang

Discovery of imidazo[1,2-a]pyridine-thiophene derivatives as FLT3 and FLT3 mutants inhibitors for acute myeloid leukemia through structure-based optimization of an NEK2 inhibitor.
Zhang L, Lakkaniga NR, Bharate JB, Mcconnell N, Wang X, Kharbanda A, Leung Y-K, Frett B, Sha NP, Li H-Y.
Eru J Med Chem. 2021

Dr. Michael Birrer

Chemotherapy with or without avelumab followed by avelumab maintenance versus chemotherapy alone in patients with previously untreated epithelial ovarian cancer (JAVELIN Ovarian 100): an open-label, randomised, phase 3 trial.
Monk BJ, Colombo N, Oza AM, Fujiwara K, Birrer MJ, Randall L, Poddubskaya EV, Scambia G, Shparyk YV, Lim MC, Bhoola SM, Sohn J, Yonemori K, Stewart RA, Zhang X, Perkins Smith J, Linn C, Ledermann JA.
Lancet Oncol. 2021

July 2021 Publications

Miller lab

4-Methyl-1,2,3-Triazoles as N-Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity.
Cui H, Carlson AS, Schleiff MA, Divakaran A, Johnson JA, Buchholz CR, Zahid H, Vail NR, Shi K, Aihara H, Harki DA, Miller GP, Topczewski JJ, Pomerantz WCK.
J Med Chem. 2021

Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort.
Datta A, Flynn NR, Barnette DA, Woeltje KF, Miller GP, Swamidass SJ.
PLoS Comput Biol. 2021

Bioactivation of Isoxazole-Containing Bromodomain and Extra-Terminal Domain (BET) Inhibitors.
Flynn NR, Ward MD, Schleiff MA, Laurin CMC, Farmer R, Conway SJ, Boysen G, Swamidass SJ, Miller GP.
Metabolites. 2021

Members of the Raney lab

G-quadruplex DNA inhibits unwinding activity but promotes liquid-liquid phase separation by the DEAD-box helicase Ded1p.
Gao J, Gao Z, Putnam AA, Byrd AK, Venus SL, Marecki JC, Edwards AD, Lowe HM, Jankowsky E, Raney KD.
Chem Commun (Camb). 2021 Jul

Dr. Michael Birrer

Sequential Phase II clinical trials evaluating CRLX101 as monotherapy and in combination with bevacizumab in recurrent ovarian cancer.
Krasner CN, Campos SM, Young CL, Chadda KR, Lee H, Birrer MJ, Horowitz NS, Konstantinopoulos PA, D’Ascanio AM, Matulonis UA, Penson RT. Gynecol Oncol. 2021

Effects of Slide Storage on Detection of Molecular Markers by IHC and FISH in Endometrial Cancer Tissues From a Clinical Trial: An NRG Oncology/GOG Pilot Study.
Grushko TA, Filiaci VL, Montag AG, Apushkin M, Gomez MJ, Monovich L, Ramirez NC, Schwab C, Kesterson JP, Seward SM, Method MW, Olopade OI, Fleming GF, Birrer MJ.
Appl Immunohistochem Mol Morphol. 2021