Bette Korber

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Bette Korber
Bette Korber with Zulu Basket.jpg
Korber with basket made for her by Zulu women at the orphanage she helped found
Alma mater California State University Long Beach, California Institute of Technology
Known fordesigning AIDS vaccines using HIV virus database
AwardsRichard Feynman Award for Innovation 2018, Thomson Reuters Corporation 100 most influential scientists of decade 2014, Ernest Orlando Lawrence Award 2004, Los Alamos National Laboratory fellow 2002, Distinguished Alumna of CSULB 2001, Elizabeth Glaser Scientist for pediatric AIDS 1997
Scientific career
Fields computational biology, molecular biology, population genetics, virology
Institutions Los Alamos National Laboratory, Santa Fe Institute
Thesis  (1988)
Doctoral advisor Leroy Hood, Iwona Stroynowski

Bette Korber is an American computational biologist focusing on the molecular biology and population genetics of the HIV virus that causes infection and eventually AIDS. She has contributed heavily to efforts to obtain an effective HIV vaccine. [1] She created a database at Los Alamos National Laboratory that has enabled her to design novel mosaic HIV vaccines, one of which is currently in human testing in Africa. [2] The database contains thousands of HIV genome sequences and related data. [2]

Contents

Korber is a scientist in theoretical biology and biophysics [1] at Los Alamos National Laboratory. She has received the Ernest Orlando Lawrence Award, the Department of Energy's highest award for scientific achievement. [3] She has also received several other awards including the Elizabeth Glaser Award for pediatric AIDS research [4] and the Richard Feynman Award for Innovation. [5]

Early life and education

Bette Korber grew up in Southern California. She earned her B.S. in chemistry in 1981 from California State University, Long Beach, where her father was a sociology professor, her mother graduated in nursing, and her sister graduated in journalism. [4] From 1981 to 1988, she was in the graduate program at the California Institute of Technology (Caltech), where she worked with Iwona Stroynowski in Leroy Hood's laboratory, [4] receiving her PhD in chemistry in 1988. [4] Her work focused on regulation of the expression of major histocompatibility complex type 1 genes, producing cell surface proteins that participate in the rejection of tissue transplants, by interferon induced by viral infections. [6] [7]

She then became a postdoctoral fellow with Myron Essex, working on the molecular epidemiology of the AIDS/HIV virus and HTLV-1, the human leukemia virus, at the Harvard School of Public Health until 1990. [8] There, Korber used polymerase chain reaction (PCR) to show both complete and deleted versions of viral genomes in leukemic cells. [9] Her work on these viral partial and complete genomes was influential and widely cited. [10] [11] [12] She became a visiting faculty member at the Santa Fe Institute in 1991, continuing in that position until 2011. [4]

Research

HIV release from infected cell HIV Release.jpg
HIV release from infected cell

Korber conducts her research at Los Alamos National Laboratory, where she began in 1990. [4] Her approach involves applying computational biology to the design of a vaccine against the HIV/AIDS virus. [13] She first became interested in HIV when a close friend of hers and her fiancé's at Caltech contracted one of the first cases of AIDS in Pasadena, California. [2] She said, "We learned a lot about HIV while he was sick. But there was no treatment for him and he died in 1991. I decided when I graduated from my PhD program that I wanted to work on HIV." [13] Several years later, looking back on this event, she described its effects: "I hate HIV ... I lost a couple friends to it. HIV kills in horrible ways. I think of what the epidemic has done to Africa and it motivates me." [13]

HIV database

Phylogenetic tree showing HIV compared to SIV HIV-SIV-phylogenetic-tree1.svg
Phylogenetic tree showing HIV compared to SIV

Korber oversees the HIV Database and Analysis Project at Los Alamos. [13] She and her team have built a global HIV database of more than 840,000 sequences from publications of the viral genome. [5] In addition, the database focuses on the small regions (called epitopes) within the virus that can be recognized by antibodies, and evaluates the evidence for the strength of each epitope in eliciting immune responses. There is also data on the immunological profiles of individuals resistant to HIV. [13] Korber and many other researchers have applied the data to devise possible treatments and vaccines against HIV. [5] Her work has resulted in design of vaccines now being tested in clinical trials. [4] [5]

HIV vaccine design

Creating a vaccine against HIV has been challenging because the virus mutates rapidly, creating multiple variants that may not be recognized by immune system components specific to the original infecting virus. [2] The most variable region is the surface of the virus, but there is also some variation of the internal proteins involved in virus replication, which may be attacked by the cellular immunity system or T cell responses. [14] A recent approach that Korber and collaborators have taken is to design mosaic antigens. [2] Korber developed a novel mosaic HIV vaccine that may slow or prevent HIV infection; this is currently in human testing in Africa. [2] The goal of the mosaic antigen vaccine is to protect the vaccinated person against the great variety of HIV variants encountered. [2]

Since the proteins of HIV vary so greatly, mosaic test proteins are designed to represent the most common forms of HIV-1 virus that can be recognized by antibodies or cellular immune responses (epitopes). [15] In 2009, Korber described the process: "I create sort of little Frankenstein proteins that look and feel like HIV proteins but they don't exist in nature." [16]

Several of the major variations are included in each molecule of protein, thus producing a variant protein antigen that probably does not exist in the wild virus population but should cross-react with variants that do exist. [15] Korber has taken two different approaches to designing such antigens. Her group has developed a computer algorithm to choose epitopes to combine into a mosaic molecule for the mosaic antigens. [17] In 2009, she described a designed mosaic protein this way: "People didn't know if it would fold properly, if it would be antigenic, or if it would have the same sites that recognized by killer T cells". They found that the newly designed antigens did fold properly and acted as a strong antigen, and were recognized by the cytotoxic T cells (killer cells). [16] Also, Korber and her collaborators have developed a graphical analysis called Epigraph that can generate promising antigens with a mixture of epitopes. [17] Korber explains that the approach of designing a protein via computer, combining bits of known proteins that provoke immune responses, had never been tried. She says, "Even after it worked, it was hard to convince people that this novel thing could be a vaccine because it hadn't been done before". [2]

In collaboration with Dan Barouch, a professor at Harvard Medical School, some of these antigens have been tested in monkeys as possible vaccines. With one series of tests, Barouch checked a number of possible ways to deliver the virus genes and chose to use the common cold virus as a vehicle. [2] The tested mosaic vaccine routinely slowed monkey infection with the closely related Simian Immunodeficiency Virus (SIV), and for 66 percent of monkeys exposed multiple times, no infection resulted. [2] Next, in collaboration with the National Institutes of Health, Janssen Pharmaceutical Companies (a division of Johnson & Johnson), and the Bill and Melinda Gates Foundation, the researchers tested a mosaic vaccine for safety in human subjects; it passed that test too. [2] In 2017, the group of collaborators announced a human efficiency test with that same mosaic protein preparation, vaccinating 2,600 women in Sub Saharan Africa, who will be examined for several years to show how efficiently, if at all, the virus interferes with infection. [2] Korber cautioned that effectiveness of this strategy in monkeys is not a guarantee that a human vaccine will work. [2]

In recognition of her research, Korber received the 2018 Feynman Award for Innovation, the first woman at Los Alamos National Laboratory to receive one. [18] She recalled that at Caltech when few women were there, she took a class with physicist Richard Feynman and became friends with him. She said, "At a time when kindness seemed rare, I really appreciated his generous spirit and encouragement. I think he would have been pleased about this award". [5]

Dating the HIV-1 virus

In the history of HIV/AIDS virus with regard to when and where HIV originated, Edward Hooper had postulated in a best-selling book called The River: A Journey to the Source of HIV and AIDS in 1999 [19] that HIV could have jumped from chimpanzees to humans because of an accidental contamination by chimpanzee SIV of the oral polio vaccine (CHAT) used in Africa in the 1950s. [20] Korber and her colleagues employed the Los Alamos National Laboratory database's genomic data to calculate when the HIV sequence evolution began, using a model of evolution based on the mutation rate of HIV strains and assuming that variable was the same on all branches of the evolutionary tree. In 2000 they published an estimate of approximately 1930 for the origin of the human immunodeficiency virus. [21] Their research was covered widely as establishing a new date for the origin of the human virus, discrediting the oral polio virus theory, and therefore refuting concerns about using oral polio vaccine (OPV). [22] [23] [24] [25] [26] These two concepts of the origin of this virus plus other related theories continued to compete for scientific credibility. [20] [21] [27]

In 2008, Worobey and collaborators used a computer modeling approach similar to Korber's but with a relaxed evolutionary model and two older samples, collected earlier than any genomes included in Korber's study, and found an origin date for HIV of approximately 1900. [28]

COVID-19

As the COVID-19 pandemic unfolded, Korber and her Los Alamos colleagues devised computational strategies that look for evolutionary changes in genes that encode the Spike proteins that stud the SARS-CoV-2 coronavirus and give it its crown-like appearance. [29] Her strategies can examine millions of global genomes stored by GISAID, and it flags mutations that vary from the original Wuhan sequence by at least a minimum specified threshold amount. [30] Using this strategy, she and colleagues identified a particular Spike mutation, Aspartic acid (Asp) to Glycine (Gly) at position 614 (D614G), that was gaining prevalence across the globe since February 2020. [31] This finding, which was controversial at first, [32] was validated by multiple other groups who showed that the D614G mutation was shown to improve the efficiency of replication and transmission of SARS-CoV-2, [33] and this mutation, as of June 2020, has become part of all globally prevalent SARS-CoV-2 strains. As of September 28, 2021, she and her group continue to analyze GISAID data for novel variants, [34] [29] and she continues to be an active member of the NIH TRACE Working Group, [35] whose objective is to "provide actionable intelligence on SARS-CoV-2 variants through genomic surveillance, data sharing and curation, and standardized in vitro assessments of therapeutics against novel strains."

Personal life

Korber married James Theiler in 1988. [13] They have two sons. [13]

Out of her concern for the impact of AIDS on those with few financial resources, Korber contributed $50,000 from her EO Lawrence Award to help establish, along with family and friends, an AIDS orphanage in South Africa, working through Nurturing Orphans of AIDS for Humanity (NOAH). [13] She has joined the Board of NOAH. [36] She also contributed to the distribution of Earth Boxes of maintenance-free portable gardens to orphanages, clinics, and schools in Africa. [13]

Awards and honors

Other work

In 2019, Korber led a series of lectures called Frontiers in Science that focused on her work designing a vaccine against HIV. [42]

Selected publications

Related Research Articles

<span class="mw-page-title-main">HIV</span> Human retrovirus, cause of AIDS

The human immunodeficiency viruses (HIV) are two species of Lentivirus that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immune system allows life-threatening opportunistic infections and cancers to thrive. Without treatment, the average survival time after infection with HIV is estimated to be 9 to 11 years, depending on the HIV subtype.

<span class="mw-page-title-main">HIV vaccine development</span> In-progress vaccinations that may prevent or treat HIV infections

An HIV vaccine is a potential vaccine that could be either a preventive vaccine or a therapeutic vaccine, which means it would either protect individuals from being infected with HIV or treat HIV-infected individuals.

<i>Simian immunodeficiency virus</i> Species of retrovirus

Simian immunodeficiency virus (SIV) is a species of retrovirus that cause persistent infections in at least 45 species of non-human primates. Based on analysis of strains found in four species of monkeys from Bioko Island, which was isolated from the mainland by rising sea levels about 11,000 years ago, it has been concluded that SIV has been present in monkeys and apes for at least 32,000 years, and probably much longer.

<i>Adenoviridae</i> Family of viruses

Adenoviruses are medium-sized, nonenveloped viruses with an icosahedral nucleocapsid containing a double-stranded DNA genome. Their name derives from their initial isolation from human adenoids in 1953.

<span class="mw-page-title-main">SV40</span> Species of virus

SV40 is an abbreviation for simian vacuolating virus 40 or simian virus 40, a polyomavirus that is found in both monkeys and humans. Like other polyomaviruses, SV40 is a DNA virus that sometimes causes tumors in animals, but most often persists as a latent infection. SV40 has been widely studied as a model eukaryotic virus, leading to many early discoveries in eukaryotic DNA replication and transcription.

<span class="mw-page-title-main">Original antigenic sin</span> Immune phenomenon

Original antigenic sin, also known as antigenic imprinting, the Hoskins effect, immunological imprinting, or primary addiction is the propensity of the immune system to preferentially use immunological memory based on a previous infection when a second slightly different version of that foreign pathogen is encountered. This leaves the immune system "trapped" by the first response it has made to each antigen, and unable to mount potentially more effective responses during subsequent infections. Antibodies or T-cells induced during infections with the first variant of the pathogen are subject to repertoire freeze, a form of original antigenic sin.

The genome and proteins of HIV (human immunodeficiency virus) have been the subject of extensive research since the discovery of the virus in 1983. "In the search for the causative agent, it was initially believed that the virus was a form of the Human T-cell leukemia virus (HTLV), which was known at the time to affect the human immune system and cause certain leukemias. However, researchers at the Pasteur Institute in Paris isolated a previously unknown and genetically distinct retrovirus in patients with AIDS which was later named HIV." Each virion comprises a viral envelope and associated matrix enclosing a capsid, which itself encloses two copies of the single-stranded RNA genome and several enzymes. The discovery of the virus itself occurred two years following the report of the first major cases of AIDS-associated illnesses.

<span class="mw-page-title-main">DC-SIGN</span> Protein-coding gene in the species Homo sapiens

DC-SIGN also known as CD209 is a protein which in humans is encoded by the CD209 gene.

<span class="mw-page-title-main">Envelope glycoprotein GP120</span> Glycoprotein exposed on the surface of the HIV virus

Envelope glycoprotein GP120 is a glycoprotein exposed on the surface of the HIV envelope. It was discovered by Professors Tun-Hou Lee and Myron "Max" Essex of the Harvard School of Public Health in 1984. The 120 in its name comes from its molecular weight of 120 kDa. Gp120 is essential for virus entry into cells as it plays a vital role in attachment to specific cell surface receptors. These receptors are DC-SIGN, Heparan Sulfate Proteoglycan and a specific interaction with the CD4 receptor, particularly on helper T-cells. Binding to CD4 induces the start of a cascade of conformational changes in gp120 and gp41 that lead to the fusion of the viral membrane with the host cell membrane. Binding to CD4 is mainly electrostatic although there are van der Waals interactions and hydrogen bonds.

A T-cell vaccine is a vaccine designed to induce protective T-cells.

<span class="mw-page-title-main">Tetherin</span> Mammalian protein found in Homo sapiens

Tetherin, also known as bone marrow stromal antigen 2, is a lipid raft associated protein that in humans is encoded by the BST2 gene. In addition, tetherin has been designated as CD317. This protein is constitutively expressed in mature B cells, plasma cells and plasmacytoid dendritic cells, and in many other cells, it is only expressed as a response to stimuli from IFN pathway.

<span class="mw-page-title-main">Virus</span> Infectious agent that replicates in cells

A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 11,000 of the millions of virus species have been described in detail. The study of viruses is known as virology, a subspeciality of microbiology.

Tat (HIV)

In molecular biology, Tat is a protein that is encoded for by the tat gene in HIV-1. Tat is a regulatory protein that drastically enhances the efficiency of viral transcription. Tat stands for "Trans-Activator of Transcription". The protein consists of between 86 and 101 amino acids depending on the subtype. Tat vastly increases the level of transcription of the HIV dsDNA. Before Tat is present, a small number of RNA transcripts will be made, which allow the Tat protein to be produced. Tat then binds to cellular factors and mediates their phosphorylation, resulting in increased transcription of all HIV genes, providing a positive feedback cycle. This in turn allows HIV to have an explosive response once a threshold amount of Tat is produced, a useful tool for defeating the body's response.

A subunit vaccine is a vaccine that contains purified parts of the pathogen that are antigenic, or necessary to elicit a protective immune response. Subunit vaccine can be made from dissembled viral particles in cell culture or recombinant DNA expression, in which case it is a recombinant subunit vaccine.

A neutralizing antibody (NAb) is an antibody that defends a cell from a pathogen or infectious particle by neutralizing any effect it has biologically. Neutralization renders the particle no longer infectious or pathogenic. Neutralizing antibodies are part of the humoral response of the adaptive immune system against viruses, bacteria and microbial toxin. By binding specifically to surface structures (antigen) on an infectious particle, neutralizing antibodies prevent the particle from interacting with its host cells it might infect and destroy.

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References

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