Posts in category Immunology

Fighting HIV Evolution with an Evolved Therapeutic Agent: Phase I Dose Escalation Clinical Trial of a Potent Broadly Neutralizing Human Antibody

In previous commentaries (;;, I have discussed the critical role of extensive B-cell and immunoglobulin gene evolution in generating broadly neutralizing antibodies for HIV-1.  Of course, the unprecedented magnitude of antibody evolution necessary to achieve potent neutralization of a high percentage of HIV strains reflects the unprecedented evolutionary plasticity of HIV that originates in both high mutation and recombination rates for the HIV genome (Korber et al., 2001).  A new study by Caskey et al. (Nature, 2015) from the Nussenzweig Laboratory reports results for a first-in-human dose escalation phase I clinical trial of a human monoclonal antibody (mAb) specific for the HIV envelope (env) protein.


This mAb, 3BNC117, is specific for the CD4 binding site of the HIV envelope protein.  It neutralizes 195 out of 237 HIV-1 strains tested from 6 clades.  The average half-maximal inhibitory concentration of 0.08 ug/ml is a feasible concentration for a passively administered serum antibody.

Purified 3BNC117 was administered once to 17 HIV-1 infected patients and 12 healthy controls at one of 4 doses: 1, 3, 10, and 30 mg/kg.  Serum antibody concentrations were followed by both an ELISA using an anti-idiotypic antibody specific for the variable domains of 3BNC117 and an assay that measures neutralization activity.  The antibody serum half-life was approximately 17 days in uninfected recipients and 9 days in HIV-1-infected recipients.  More rapid clearance in the infected individuals was presumed by the authors to reflect clearance of antibody-antigen complexes, but they acknowledge the possibility of other unspecified mechanisms.

Assessment of serum viral titers revealed only minimal effects by 3BNC117 infused at 1 or 3 mg/kg.  However, the mAb at doses of 10 or 30 mg/kg was variably effective at reducing viral copies in the peripheral blood by from 0.8 to 2.5 log10.  The authors noted that the magnitude of the decrease in viral load was related to the starting viral load and the initial sensitivity of the viral population to neutralization by 3BNC117.  Substantial decrements in viral load were sustained throughout the observation period of 56 days only for individuals receiving 30 mg/kg of mAb.

Paired samples of virus from treated individuals taken seven days before the mAb infusion started and 28 days after the infusion were compared for neutralization sensitivity.  Even virus from some HIV-infected patients given 1 mg/kg of mAb showed decreases in sensitivity to neutralization suggestive of the selection of genetic escape variants by 3BNC117.  Decreases in sensitivity of comparable magnitude were seen for viruses from some but not other recipients of 3 or 10 mg/kg of mAb.  At 30 mg/kg of 3BNC117, only two of the five treated patients showed decreases in neutralization sensitivities of greater than five-fold.  The authors conclude that in only some HIV-infected individuals treated with 3BNC117 does virus evolve a high degree of resistance to neutralization.

Finally, the authors cloned and sequenced the envelope genes from paired plasma samples, taken before and 28 days after infusion, for ten patients from prior to and 28 days after administration of 3BNC117. The results reveal evidence for selection of escape variants in some but not other patients.  Evidence of selected amino acid substitutions correlated with greater decreases in neutralization sensitivity.  Some amino acids that were found at given positions only after treatment, suggestive of selection by the mAb, were at envelope positions known to be contacted by antibody while others were at sites not known to participate directly in contacting the antibody.  Most of these sites were near contact sites and could influence the interaction between envelope protein and 3BNC117.

Overall, the results suggest that passive transfer of a potent broadly HIV-neutralizing mAb can be safe, mediate reductions in viremia, and exert selective pressure on virus.  The evidence for selection in some but not other receipients of antibody infusion suggests, as the authors discuss, the use of combinations of potent broadly neutralizing mAbs or combinations of one or more mAbs with one or more anti-retroviral drugs.  Use of multiple therapeutic agents would be anticipated to constrain the evolutionary paths available to the virus.

Cocktails of mAbs or of mAbs and anti-retroviral drugs would also likely increase the number of patients who experience substantial therapeutic effects.  Much additional research will be required to optimize such regimens.


Extent of Tumor Evolution as Assessed by Numbers of Nonsynonymous Somatic Mutations Correlates with the Effectiveness of Anti-Checkpoint Therapy

It would be hard to identify an approach to cancer treatment that has received more attention recently than anti-checkpoint therapy (Pollack, 2015).  This strategy for eliminating tumor cells is based on interfering with one or another pathway that inhibits the initial activation or functions of T cells, such as CD8+ cytotoxic T cells (CTL).  Activated tumor-specific CTL can directly kill their targets.  However, if copies of the T-cell surface molecule, PD-1, are bound by their physiological ligands on tumor cells, either PD-L1 or PD-L2, or other cells the ability of the T cell to perform its functions is substantially reduced.  A report published in Science (2015) by Rizvi et al. last month addresses the question of whether tumor mutation burden correlates with response to anti-checkpoint therapy for non-small cell lung cancer (NSCLC).


Chromosomal Catastrophe (Chromothripsis) Causing Curative Clonal Conquest

Last month, Murphy and colleagues (Cell, 2015) published a fascinating report about a patient with an immunodeficiency syndrome that underwent spontaneous resolution.  The mechanism for this remarkable outcome points to the importance of somatic cell selection and evolution in the origins, pathogenesis, and most dramatically in this case, elimination of disease. READ MORE »

Putting the Kill in “Shock and Kill”: Overcoming Evolutionary Obstacles to HIV Cure

According to estimates by the World Health Organization, in 2013 on the order of 35 million people were infected with HIV worldwide (  Globally, about 1.5 million people are believed to have died from AIDS-related diseases in that year.  Substantial, although perhaps not insurmountable, obstacles to the development of a highly effective vaccine for HIV-1 have increased interest in curative strategies.  A key challenge to cure strategies is that infected people harbor a latent reservoir of infected CD4+ memory T cells that do not express significant amounts of viral proteins.  The paucity of viral proteins in these cells makes it more difficult to identify infected cells and eradicate them.  A new study (Deng et al., 2015) in Nature from Robert Siliciano’s lab at Johns Hopkins identifies an additional difficulty faced by one of the currently popular approaches to curative therapy but also, more optimistically, suggests a way to overcome this challenge. READ MORE »

Cellular ‘Gold’: Competition for Iron as the Cause of Reciprocal Positive Selection of Host and Pathogen Iron-Binding Proteins

Iron is a critical metal for essential cellular processes, such as respiration, in both human and microbial cells.  Thus, in the context of infection, iron is a high-value cellular commodity and an evolutionist might reasonably expect a metallic tug-of-war between host and pathogen iron-binding proteins or other iron-binding molecules (siderophores).  This speculation is impressively supported in a paper published this month (Barber and Elde, 2014).  These authors provide strong evidence for positive selection affecting several sites in host (transferrin, Tf) and pathogen (transferrin binding protein A) iron-binding proteins based on a combination of genetic, structural, and functional experimental methods. READ MORE »

Epistasis in Adaptive versus Stochastic Evolution of the Influenza A Virus Nucleoprotein Gene

Epistasis refers to the influence of one genomic mutation or variant on the phenotypic effects of another mutation or variant.  Based on available evidence and theory, this phenomenon has a major influence on evolutionary trajectories for organisms of all sorts.  The role of epistasis has been studied primarily in the context of adaptive evolutionary change.  In a recent paper (2014), Gong and Bloom attempt to determine the relative frequencies of epistatic interactions in adaptive versus stochastic evolution, i.e. evolution driven by selection as opposed to evolution resulting from random processes without a significant selective ‘pressure.’  Gong and Bloom perform this comparison by analyzing homologous nucleoprotein (NP) genes in human and swine influenza A viruses.  The authors argue that the human viruses are subject to substantially more intense selection than the swine viruses since domestic swine are much shorter lived and their viruses are not as likely to be subjected to immune memory responses. READ MORE »

An Evolutionary Link between Cancer and Scleroderma: Somatic Cell Variation and Selection

Geneticists have recognized for some time that many genes exhibit pleiotropy, meaning that one mutation can manifest in two or more distinguishable phenotypic effects. In a fascinating study recently published in Science [2014 Jan 10;343(6167):152-7. doi:10.1126/science.1246886], Joseph et al. offer evidence for an example of pleiotropy in which the distinct phenotypic effects associated with mutation of the POLR3A gene, which encodes a subunit (RPC1) of RNA polymerase III, are associated with two different diseases: one or another form of cancer and an autoimmune disease (scleroderma). READ MORE »

Fever: how does it work?

A careful reading of the review of fever in “Fever: Friend or Foe?”, reveals the embarrassing deficiency in medical science’s understanding of how fever, much less anorexia, functions in infection. Since fever (as well as anorexia and other components of the acute-phase response) is induced by our own cytokines, it is virtually axiomatic that fever has been more beneficial than harmful on an evolutionary scale (since otherwise the response would have been deleted). As a “fan” of fever, I’ve compiled a list of six potential benefits of fever, each of which is found in the literature and has a reasonable experimental or theoretical basis (and each likely has some degree of correctness). Note that the first four are based on fever being a heat stressor. Have a look and then see my take on it.

Fever may work by:
1) directly harming pathogens,*
2) inducing apoptosis of infected cells (and neoplastic cells),
3) inducing host’s heat shock proteins to protect host cells during infection,
4) inducing heat shock proteins in pathogens—extracellular heat shock proteins activate immune responses as “danger signals”,
5) increasing efficacy of immune responses since they work better at slightly elevated temperatures,*
6) turning down the immune response by causing apoptosis of neutrophils and lymphocytes. READ MORE »

Teaching the Relevance of Evolution to Understanding Immune Recognition

Last month, I completed teaching a graduate course for the tenth time.  After several years (in the early 1990’s) of thinking about launching a new alternate-year seminar course and then planning it, I began teaching PATH 480 in the fall of 1994.  The original name of the course, maintained through the first seven times I taught it, was: “Immunology, Evolution and Logic.”  Beginning in 2009, another faculty member, Derek Abbott, joined me in teaching the course, and the title was revised to: “Logical Dissection of Biomedical Investigations.”  In my portion of the course, I retained an emphasis on the relevance of logic and evolutionary principles to thinking about immune recognition and immune functioning more generally.  I focused class sessions on concepts and underlying assumptions critical to experimental investigations as well as on experimental design and data interpretation in articles reporting studies pertaining to immune recognition. Dr. Abbott has focused his portion of the course on the practical cognitive skills involved in reviewing papers and grant proposals pertaining primarily to innate immune signaling. READ MORE »

Boundary-Breaking Evolution via B Lymphocyte Clonal Selection in Response to HIV-1

A central focus of recent research aimed at developing a vaccine for HIV-1 is the identification of potent broadly-neutralizing antibodies (bNAbs).  Due to work from several laboratories, many such antibodies have now been identified, produced in quantity as monoclonal antibodies, and characterized with respect to key properties such as epitope specificity, affinity for the corresponding HIV-1 epitope, and neutralizing activity against many strains of varying susceptibility to antibody-mediated inactivation (important examples of these publications are: Scheid et al., 2009; Walker et al., 2009; Wu et al., 2010; Walker et al., 2011; Huang et al., 2012).  These successes notwithstanding, the scale of the challenge facing the vaccine developers is clarified by the following facts: 1) potent bNAbs only develop in 10-30% of infected individuals, 2) it typically takes between two and three or four years after initial infection for these antibodies to appear in the blood of these individuals, and 3) antibodies with the desired attributes often have extraordinary numbers of somatic mutations in the variable domains that mediate binding to the HIV-1 antigen (Klein et al., 2013a).   A study (Klein et al., 2013b) published earlier this year from the laboratory of Michel Nussenzweig both illuminates one possible factor accounting for the impressive length of time and number of mutations associated with the generation of potent bNAbs and provides an extraordinary example of the power of intense selection to confound expectations arising from previously observed associations.  In this instance, the undermined expectations related to the well-established functional correlates of hypervariable and framework regions within antibody variable domains. READ MORE »

The Case for Applying Negative Selection to Thoughts on Clonal Selection by Prospect Magazine’s Number One 2013 “World Thinker”

Currently, I am on vacation near the beach in South Carolina.  Consequently, I have opted for a topic that is bit different than the majority of my monthly commentaries in that it focuses not on a recent original report but instead on a conceptual point made in a book over thirty years ago.  Nevertheless, after a somewhat less strictly scientific diversion I will come to the central idea at issue, which is arguably the premier exemplar of the relevance of evolutionary principles to the operation of the immune system on short time scales, by which I refer to the concept of clonal selection.  But first, we make a foray into the world of magazine publishing and the niche within that domain focusing on the arguably more intellectual readers. READ MORE »

The Power of Graur to Explode ENCODE Using Incision and Derision

The consortium of investigators known as ENCODE (ENCyclopedia Of DNA Elements) published, with much publicity, a series of about thirty papers last fall purporting to “identify all functional elements in the human genome sequence” (  Dan Graur, an evolutionary geneticist at the University of Houston, and his associates have published a paper in Genome Biology and Evolution (2013; online) challenging the assertion by the ENCODE investigators that 80.4% of the human genome can be considered functional (Nature, 2012).  Graur’s critique of the ENCODE claim is grounded in evolutionary principles. READ MORE »

A Possible Evolutionary Explanation for the Frequency of CCR5Δ32

In 1996, Dean et al. (Science), demonstrated that a loss-of-function allele (CCR5Δ32) encoding a version of the chemokine receptor, CCR5, confers very substantial resistance to infection with HIV-1 in the homozygous state and slows progression in the heterozygous state.  Given the relatively recent origin of HIV-1, this finding raised the question of what source of selection could account for the frequency, approximately 0.08 among Caucasians according to Dean et al., of this allele.  A recent paper (Alonzo et al., 2013) offers new information on a relationship between CCR5 and a different pathogen that might offer insight into the evolutionary trajectory of CCR5Δ32.

The new study presents compelling evidence that leukotoxin ED (LukED), one of a family of bi-component exotoxins produced by Staphylococcus aureus, can bind to CCR5 and thereby cause cell death.  LukED consistently produces substantially more cytotoxicity for CCR5+ than CCR5 cell lines of several types.  Ligands for CCR5, including the drug, maraviroc, which is approved for clinical treatment of HIV-1 infection, significantly inhibit both the binding of LukED to cells and the magnitude of associated cytotoxicity.  LukED also binds to and kills CCR5+ primarycells, such as human memory T cells, macrophages, and dendritic cells. READ MORE »

Influenza A Virus: Is Virulence Attributable to Virulence Factors?

Influenza A viruses continue to be of enormous interest to biomedical researchers and clinicians alike.  In addition to the annual influenza epidemics, which have been inferred to cause substantial excess mortality, there is the ever-present threat of a global pandemic due to several features of influenza virus biology.  A high mutation rate associated with a segmented negative-sense RNA genome that facilitates recombination confers on these orthomyxoviruses a prodigious ability to evolve in ways that confound and evade the human immune system.  The ability of influenza viruses to infect domesticated mammals, such as pigs, as well as birds, both wild and domesticated, provides additional opportunities for the virus to try out new genetic combinations and to disseminate around the globe by means both dependent and independent of human travel.

A recent paper by Jagger et al. (Science 2012) reveals that influenza A viruses are also, not surprisingly, capable of exploiting rather subtle and ingenious genetic “tricks” to maximize the value of every base pair in a total of a mere 13.5 kilobases of genome.  These authors have discovered a new influenza gene product, PA-X, that represents a fusion protein incorporating 191 amino-terminal amino acids of the well-known RNA-dependent RNA polymerase (PA) protein and another carboxy-terminal 61 amino acids of a protein from a reading frame shifted by one nucleotide downstream.  They present evidence from multiple experiments suggesting that the frameshift is related to a highly conserved codon that is rarely employed in mammalian and avian genomes and therefore interacts with a cognate tRNA of relatively low concentration in the cytosol.  The longer-than-average wait for this tRNA to be recruited to the ribosome makes a frameshift mutation more probable. READ MORE »

An Ecological and Evolutionary Perspective on Gastrointestinal Health

There have been claims that variations in the composition of the intestinal flora influence individual health going back at least to the early years of the 1900s.  Late in his career, Ilya Mechnikov, co-receipient of the Nobel Prize for Physiology or Medicine in 1908 (along with Paul Ehrlich) and a pioneer in the study of what we now call innate immune mechanisms, promoted a diet based on fermented milk containing live bacterial cultures of lactobacilli (i.e., yogurt) (1).  Mechnikov apparently believed that the bacteria in the yogurt would compete with bacterial species that he thought were, on balance, harmful to human health.  In other words, Mechnikov recognized the potential relevance of gastrointestinal ecology to human health a century ago. READ MORE »

Humoral Immune Responses to HIV-1: Fighting Evolution with Evolution

Among the most pressing global public health problems at present is the AIDS epidemic.  While it is clear that chemotherapy and behavioral interventions have much to offer in limiting the spread of infections by the causative virus, HIV-1, interest in developing a vaccine remains strong.  Immunization would potentially provide a relatively cost-effective and scalable approach to minimizing the incidence of new infections on a global scale.

However, HIV-1 presents numerous challenges to would-be vaccine developers.  There are many different lineages of HIV-1 viruses with different clades dominating in different geographic regions of the world.  Even in a single infected patient, HIV-1 continues to generate many variants.  Astonishingly, according to Korber et al. (2001), “The diversity of influenza sequences world-wide in any given year appears to be roughly comparable to the diversity of HIV sequences found within a single infected individual at one time point ….  The virion surface protein, gp120, which is critically involved in infecting host cells and is a major target for protective antibodies, contains regions that are especially variable in amino acid sequence.

In addition to the serious challenge of eliciting an immune response, of whatever sort, that can effectively provide immunity to the many viral variants in circulation, it remains unclear what types of immune responses are essential for providing a high level of protection against infection or disease.  Some investigators are focsed on eliciting strong cell-mediated immune response.  Others are devoting their efforts to generating humoral responses including potent and broadly-neutralizing antibodies.  There are several recent and interesting reports pertaining to this latter effort. READ MORE »

Evolutionary and Ecological Factors in Influenza A Virus Spread

In the May 26 (2011) issue of Nature, Vijaykrishna et al. address patterns of evolution and transmission exhibited by swine influenza A viruses (SwIV) isolated from pigs beings slaughtered in Hong Kong between May 1998 and January 2010.  Although the focus of the study is on viruses that circulate in swine, this study is relevant to human medicine and public health because these viruses can serve as the ancestors of viruses that infect people.  READ MORE »

History of the Immunological Thread in the Fabric of Evolutionary Medicine

In his essay (2011) on the history of Darwinian (or evolutionary) medicine, Jonathan Fuller describes potentially relevant interests and insights that preceded the famous paper by Nesse and Williams (1991) that is widely regarded as having catalyzed the resurgence of interest in applying evolutionary concepts and principles to medicine.  For example, the author describes aspects of Aristotle’s biological thinking as well as elements of the medical concepts of Hippocrates that anticipated some features of evolutionary medicine while possibly also impeding full acceptance of the evolutionary perspective on medical phenomena.  Fuller also mentions the writings of individuals such as A. C. Allison and Paul Ewald relating to infectious disease as relevant examples of pre-1991 applications of evolutionary thinking to medically-relevant problems.

There is, however, another medical field with a relatively long history (going back at least a century) of applying evolutionary principles and concepts to understanding phenomena of interest, immunology (Silverstein, 2003), which Fuller mentions only in passing. READ MORE »

A Genomic Perspective on Pathogen Adaptation to Antibiotics and Vaccines

Among human pathogens, Streptococcus pneumoniae holds an especially prominent place in the history of biomedical investigation.  Griffith (1928) described the transforming principle, a soluble substance released by dead, virulent pneumococci that could render living avirulent pneumococci able to effectively kill a mouse.  Oswald Avery’s commitment to curing pneumococcal pneumonia ( led him and his collaborators to determine that the pneumococcal transforming principle was DNA (Avery et al., 1944).  It was also Avery’s and his collaborators’ work on pneumococci that provided some of the first insights into the chemical nature of most bacterial capsules. READ MORE »

Contributions and suggestions welcome

Please email