Alakesh Bera PhD

Education

1999 B.Sc. (Chemistry) – University of Calcutta, Kolkata, India
2001 M.Sc. (Chemistry) – University of Calcutta, Kolkata, India
2006 Ph.D. (Biochemistry) – Université d'Orléans, Orléans, France
2008 Post-Doc (Viral Oncology) - Johns Hopkins University, Baltimore, USA
2009 Post-Doc (Molecular Medicine) - Texas A & M University, College Station, USA

Biography

Biography:
Dr. Alakesh Bera is a tenure-track Assistant Professor in the Department of Anesthesiology at the Uniformed Services University of the Health Sciences (USUHS). As the Director of the Malignant Hyperthermia Core Facility, his research focuses on mutational analysis of the Ryanodine Receptor (RYR1) gene, investigating its role in malignant hyperthermia (MH) susceptibility, cancer association, and neuromuscular dysfunction. With over 17 years of experience in biochemistry, biophysics, structural biology, drug discovery and translational oncology, Dr. Bera has made significant contributions to understanding protein dynamics and their implications in various diseases. His current research involves the development of advanced organoid models using CRISPR/Cas9 technology to study RYR1 mutations and their effects on muscle function and anesthetic response. Dr. Bera has previously worked at premier institutions such as the National Institutes of Health (NIH), Johns Hopkins University, and the University of Texas.

Current Projects:
Leading a DoD-USUHS -funded project on RYR1 mutational analysis and organoid model development (~ $600K funding); Start-up funding.
Developed methodologies for CRISPR/Cas9 gene editing and advanced imaging for studying neuromuscular dysfunctions.
Collaborative projects to discover the early stage TBI biomarkers.
Cancer immunotherapy and identification of serum biomarkers for various cancers.

Positions and Employment:
2024 – Present Assistant Professor (Tenure-Track), Uniformed Services University, Bethesda.
2021 – 2024 Research Scientist, Clinical Research Center, NCI/NIH, Bethesda, MD.
2019 – 2021 Assistant Professor (Adjunct), Department of APG, Uniformed Services University (USU), Bethesda
2016 – 2020 Sr. Scientist. Henry M Jackson Foundation (HJF)/USU, Bethesda, MD.
2015 – 2016 Faculty Member (Research Associate), Oncology Department, Johns Hopkins University, Baltimore.
2009 – 2015 Co-Investigator/Postdoc Fellow, Audie L. Murphy VA Hospital, U. of Texas HSC, San Antonio.

Awards and Honors:
2020 Keynote speaker. ICMR2020, India
2020 Keynote speaker: Cancer and Covid-19, AACR special meeting
2019 Invited foreign reviewer member for French research funding (over €500K funding on
Prion research) society ANSES: Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail. http://www.anses.fr
2010-12 CPTIR Research Grant. State of Texas. $100,000 FY. 2010-2012 Title: Chemo-resistance pathways in pancreatic cancer.
2003- 06 Doctoral fellowship, from Scientific Council of ‘Indo-French Collaboration for the Advancement of Scientific Research’ (CEFIPRA)
2001 CSIR-UGC (NET) Highest research fellowship offered by Govt. of India
1993 – 99 National Scholarship for higher studies: Award offered by Govt. of India

Other Experience and Professional Memberships
2006 – 2008 Member, Biophysical Society
2006 – 2009 Member, Indian Association for Animal Production (IAAP)
2010 – Present Member, American Association for the Advancement of Science (AAAS)
2013 – Present Active Member, American Association for Cancer Research (AACR)

Publications:
Dr. Bera has authored over 50 peer-reviewed publications, including groundbreaking studies on cancer system biology, biomarkers, drug discovery and immunotherapy, infectious disease, and Neurodegenerations.

Representative Bibliography:
For a complete list of Dr. Bera’s publications, visit his Google Scholar profile.
Complete List of Published Work in My Bibliography: Google Scholar: https://scholar.google.com/citations?user=UHtP60YAAAAJ&hl=en

PATENT:
Levin, Noam; Rosenberg, Steven A.; Kim, Peter; Lowery, Frank; Parkhurst, Maria R.; Bera, Alakesh. T CELL RECEPTORS TARGETING RAS WITH G12D, G12R, OR G12V MUTATION. Patent filed (2023); NCI/NIH ref: HHS E-132-2023-0-US-01

PUBLICATIONS:
FIELD OF IMMUNOLOGY AND IMMUNOTHERAPY (NCI/NIH; DR. ROSENBERG’S GROUP)
1. Levin N, Kim SP,………Bera A, Robbins PF, Goff SL, Rosenberg SA. Neoantigen-specific stimulation of tumor-infiltrating lymphocytes enables effective TCR isolation and expansion while preserving stemlike memory phenotypes. Journal for Immunotherapy of Cancer, 2024, 12 (5)
2. Parkhurst M, Goff SL, Lowery FJ, Beyer RK, H Halas, PF Robbins.. Bera A, … Rosenberg SA. Adoptive transfer of personalized neoantigen-reactive TCR-transduced T cells in metastatic colorectal cancer: phase 2 trial interim results. Nature Medicine, 2024, 30 (9), 2586-2595
3. Yoseph R, Krishna S, ………Bera A…. Robbins PF, Rosenberg SA. Phenotypic Signatures of Circulating Neoantigen-Reactive CD8+ T Cells in Patients with Metastatic Cancers. Cancer Cell, 2023 41 (12), 2154-2165. e5.
4. Chatani. P, Lowery. F, Parikh, N,….. Bera, A, Krishna, S, Rosenberg, SA. Cell Surface Marker-Based Capture of Neoantigen-Reactive CD8+ T Cell Receptors from Metastatic Tumor Digests. Journal for ImmunoTherapy of Cancer, 2023, 11(5): e006264.
5. Kim SP, Vale NR, Bera A, Robbins PF, Goff SL, Rosenberg SA. Adoptive Cellular Therapy with Autologous Tumor-Infiltrating Lymphocytes and T-cell Receptor–Engineered T Cells Targeting Common p53 Neoantigens in Human Solid Tumors. Cancer Immunol. Res. 10 (8),2022, 932-946.

VIRUS/ MICROBIAL RESEARCH INCLUDING COVID-19
1. H-H Yang , CA Simpson, M Srivastava, A Bera.. JT Lee. Biodiversity of the Bacterial and Fungal Microbiome and Associated Inflammatory Cytokine Profile in Chronic Rhinosinusitis. International Forum of Allergy & Rhinology 2024 (in press).
2. H Caohuy, O Eidelman, T Chen, S Liu, Q Yang, A Bera, NI Walton et al. Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Scientific reports, 2021, 11 (1), 22195
3. A Bera, E Russ, S Radhakrishnan, H Hu, COLCD Shriver, M Srivastava. Inflammatory biomarkers: Breast cancer survival and possible role in COVID-19 associated comorbidity. Cancer Research, 2023, 83 (7_S), 807-807
4. A Bera, E Russ, D Chatterjee, J Karaian, M Subramanian, S Chatterjee.. et. al. A prediction of prostate cancer deaths spiking by SARS-CoV-2 infection. Clinical Cancer Research 26 (18_S), 2020, S01-03-S01-03
5. A Bera, EM Perkins, Zhu J, Zhu H, Desai P. DNA binding and condensation properties of the herpes simplex virus type 1 triplex protein VP19C. PLoS One. 2014; 9(8): e104640.
6. BW Henson, N Johnson, A Bera, Okoye ME, Desai KV, Desai PJ. Expression of the HSV-1 capsid protein VP19C in Escherichia coli: a single amino acid change overcomes an expression block of the full-length polypeptide. Protein expression and purification. 2011;77(1):80-5.

SYSTEM BIOLOGY, DRUG DISCOVERY AND BIOMARKERS: PROSTATE, LUNG, BREAST AND PANCREATIC CANCERS
1. Bera A, Radhakrishnan S, Puthillathu N, Subramanian M, N Gana, E Russ, ... M Srivastava. Role of Annexin 7 (ANXA7) as a tumor suppressor and a regulator of drug resistance in thyroid cancer. International Journal of Molecular Sciences. 2024, 25 (23), 13217
2. Bera A, Chatterjee D, Hester J, Srivastava M. Integrated In Silico Analysis of Proteogenomic and Drug Targets for Pancreatic Cancer Survival. Methods in Molecular Biology, 2023, vol 2660, pp. 273–282
3. Srivastava M, Bera A, Eidelman O, Tran MB, Jozwik C et al. A Dominant-Negative Mutant of ANXA7 Impairs Calcium Signaling and Enhances the Proliferation of Prostate Cancer Cells by Downregulating the IP3 Receptor and the PI3K/mTOR Pathway. Int. J. of Molecular Sciences, 2023, 24 (10), 8818
4. Rosario OD, Suresh K, Kallem M, Singh G, …. Jiang H, D’Alessio F, Srivastava M, Bera A, Shimoda LA,… and Damarla M. MK2 non-enzymatically promotes nuclear translocation of caspase-3 and resultant apoptosis. Am. J. of Physiol.-Lung Cell. and Mol. Physiol. 2023. 324 (5), L700-L711.
5. Suresh K, Rosario OD, …Kallem M, Singh G, .. Srivastava M, Bera A, Shimoda LA, … et. al. Tumor MK2 transcript levels are associated with improved response to chemo-therapy and patient survival in NSCLC. Physiologic Genomics, 2023, 55 (4), 168-178.
6. Bera A, Russ E, Karaian J, Landa A, Radhakrishnan S, Subramanian M, Hueman M, Pollard HB, Hu H, Shriver CD and Srivastava M. Circulating cell-free DNA in serum as a marker for the early detection of tumor recurrence in breast cancer patients. Cancer Diagnosis & Prognosis, 2022, 2 (3), 285
7. Ahn J, Park S, Zuniga B, Bera A,.. Vitamin D in Prostate Cancer. Vitam Horm. 2016; 100:321-55.
8. Bera A, Leighton XM, Pollard H, Srivastava M. Cyclin E and FGF8 are downstream cell growth regulators in distinct tumor suppressor effects of ANXA7 in hormone-resistant cancer cells of breast versus prostate origin. Trends Cancer Res. 2018; 13:55-62.
9. Leighton X#, Bera A#, Eidelman O, Bubendorf L, Zellweger T, Banerjee J, Gelmann EP, Pollard HB, Srivastava M. Tissue microarray analysis delineate potential prognostic role of Annexin A7 in prostate cancer progression. PLoS One. 2018 Oct 15;13(10):e0205837.
10. Leighton X#, Bera A#, Eidelman O, et al. High ANXA7 Potentiates Eucalyptol Toxicity in Hormonerefractory Prostate Cancer. Anticancer Res. 2018 ;38(7):3831- 3842. #equal contributions
11. Natarajan M, Konopinski R, Krishnan M, Roman L, Bera A, Hongying Z, et al. Inhibitor- κB kinase attenuates Hsp90-dependent endothelial nitric oxide synthase function in vascular endothelial cells. Am J Physiol- Cell Physiol. 2015 Apr 15;308 (8):C673-83.
12. Bera A, …..Freeman JW. A miRNA signature of chemoresistant mesenchymal phenotype identifies novel molecular targets associated with advanced pancreatic cancer. PLoS One. 2014;9(9):e106343.
13. Bera A et al. Oncogenic K-Ras and loss of Smad4 mediate invasion by activating an EGFR/NF-κB Axis that induces expression of MMP9 and uPA in PDAC. PLoS One. 2013;8(12):e82282.

NEURODEGENERATION AND PRION
1. Bera A and Biring S. A Sequence-Dependent DNA Condensation Induced by Prion Protein. J Nucleic Acids. 2018: 9581021.
2. Bera A and Biring S. A quantitative characterization of interaction between prion protein with nucleic acids. Biochem and Biophy Repts, 2018, vol. 14, pp. 114–124.
3. Bera A and Nandi PK. Nucleic acid induced unfolding of recombinant prion protein globular fragment is pH dependent. Protein Sci. 2014 Dec; 23(12):1780-8.
4. Bera A, Roche AC, Nandi PK. Bending and unwinding of nucleic acid by prion protein. Biochemistry. 2007 Feb 6; 46 (5):1320-8.
5. Bera A and Nandi PK. Biological polyamines inhibit nucleic-acid-induced polymerisation of prion protein. Arch Virol. 2007; 152 (4):655-68.
6. Nandi PK, Bera A, Sizaret PY. Osmolyte trimethylamine N-oxide converts recombinant alpha-helical prion protein to its soluble beta-structured form at high temperature. J Mol Biol. 2006 Sep 29; 362(4):810-20

Representative Bibliography

Bera A and Biring S. A quantitative characterization of interaction between prion protein with nucleic acids. Biochem and Biophy Repts, 2018, vol. 14, pp. 114–124.

Bera A, Roche AC, Nandi PK. Bending and unwinding of nucleic acid by prion protein. Biochemistry. 2007 Feb 6; 46 (5):1320-8.

Bera A, …..Freeman JW. A miRNA signature of chemoresistant mesenchymal phenotype identifies novel molecular targets associated with advanced pancreatic cancer. PLoS One. 2014;9(9):e106343. 13.

Bera A et al. Oncogenic K-Ras and loss of Smad4 mediate invasion by activating an EGFR/NF-κB Axis that induces expression of MMP9 and uPA in PDAC. PLoS One. 2013;8(12):e82282.

Bera A, Radhakrishnan S, Puthillathu N, M Subramanian.... M Srivastava. Role of Annexin 7 (ANXA7) as a tumor suppressor and a regulator of drug resistance in thyroid cancer. Int. J. of Molecular Sciences. 2024, 25 (23), 13217

Parkhurst M, Goff SL, Lowery FJ, Beyer RK, Halas H, Robbins PF.. Bera A, … Rosenberg SA. Adoptive transfer of personalized neoantigen-reactive TCR-transduced T cells in metastatic colorectal cancer: phase 2 trial interim results. Nature Medicine, 2024, 30 (9), 2586-2595

Yoseph R, Krishna S, ………Bera A…. Robbins PF, Rosenberg SA. Phenotypic Signatures of Circulating Neoantigen-Reactive CD8+ T Cells in Patients with Metastatic Cancers. Cancer Cell, 2023 41 (12), 2154-2165. e5.