Biopharmconsortium Blog

Expert commentary from Haberman Associates biotechnology and pharmaceutical consulting.

Posts filed under: Drug discovery

Can adoptive cellular immunotherapy successfully treat metastatic gastrointestinal cancers?


Dr. Steven Rosenberg

Dr. Steven Rosenberg

On September 6, 2014, we published an article on this blog announcing the publication of our book-length report, Cancer Immunotherapy: Immune Checkpoint Inhibitors, Cancer Vaccines, and Adoptive T-cell Therapies, by Cambridge Healthtech Institute (CHI).

In that article, we cited the example of the case of a woman with metastatic cholangiocarcinoma (bile-duct cancer), which typically kills the patient in a matter of months. The patient, Melinda Bachini, was treated via adoptive immunotherapy with autologous tumor-infiltrating T cells (TILs) resulting in survival over a period of several years, with a good quality of life.

Our report includes a full discussion of that case, as of the date of the May 2014 publication of a report in Science by Steven A. Rosenberg, M.D., Ph.D. and his colleagues at the National Cancer Institute (NCI). Ms. Bachini’s story was also covered in a May 2014 New York Times article.

Now comes the publication, in Science on December 2015, of an update from the Rosenberg group on their clinical studies of TIL-based immunotherapy of metastatic gastrointestinal cancers. This article discusses the results of TIL treatment of ten patients with a variety of gastrointestinal cancers, including cancers of the bile duct, the colon or rectum, the esophagus, and the pancreas. The case of Ms. Bachini (“patient number 3737”) was included.

Ms. Bachini, a paramedic and a married mother of six children, and a volunteer with the Cholangiocarcinoma Foundation, was 41 years old when first diagnosed with cancer. She remains alive today—a five-year survivor—at age 46.

The Foundation produced a video, dated March 13, 2015, in which Ms. Bachini gives her “patient perspective”. This video includes her story “from the beginning”—from diagnosis through surgery and chemotherapy, and continuing with adoptive immunotherapy at the NCI under Dr. Rosenberg. Although her tumors continue to shrink and she remains alive, she still is considered to have “Stage 4” (metastatic) cancer. Ms. Bachini is a remarkable woman.

The Cholangiocarcinoma Foundation has also produced an on-demand webinar (dated October 21, 2014) on the adoptive cellular therapy trial in patients with various types of metastatic gastrointestinal cancers, led by Drs. Eric Tran and Steven Rosenberg. Ms. Bachini is also a presenter on that webinar. The December 2015 Science article is an updated version of the results of this trial.

The trial, a Phase 2 clinical study (NCT01174121) remains ongoing, and is recruiting new patients.

The particular focus of Dr. Tran’s and Dr. Rosenberg’s study in TIL treatment of gastrointestinal cancers is whether TILs derived from these tumors include T-cell subpopulations that target specific somatic mutations expressed by the cancers, and whether these subpopulations might be harnessed to successfully treat patients with these cancers. Of the ten patients who were the focus of the December 2015 publication, only Ms. Bachini had a successful treatment. In the case of Ms. Bachini, she received a second infusion of TILs that were enriched for CD4+ T cells that targeted a unique mutation in a protein known as ERBB2IP. It was this second treatment that resulted in the successful knockdown of her tumors, which continues to this day.

Despite the lack of similar successes in the treatment of the other nine patients, the researchers found that TILs from eight of these patients contained CD4+ and/or CD8+ T cells that recognized one to three somatic mutations in the patient’s own tumors. Notably, CD8+ TILs isolated from a colon cancer tumor of one patient (patient number 3995) recognized a mutation in KRAS known as KRAS G12D. This mutation results in an amino acid substitution at position 12 in KRAS, from glycine (G) to aspartic acid (D). KRAS G12D is a driver mutation that is involved in causation of many human cancers.

Although two other patients (numbers 4032 and 4069, with colon and pancreatic cancer, respectively) had tumors that expressed KRAS G12D, the researchers did not detect TILs that recognized the KRAS mutation in these patients. The researchers concluded that KRAS G12D was not immunogenic in these patients. The TILs from patient 3995 were CD8+ T cells that recognized KRAS G12D in the context of the human leukocyte antigen (HLA) allele HLA-C*08:02. [As with all T cells, TILs express T-cell receptors (TCRs) that recognize a specific antigenic peptide bound to a particular major histocompatibility complex (MHC) molecule—this is referred to as “MHC restriction”.] The two patients for whom KRAS G12D was not immunogenic did not express the HLA-C*08:02 allele.

The results seen with KRAS G12D-expressing tumor suggest the possibility of constructing genetically-engineered CD8+ T cells that express a TCR that is reactive with the KRAS mutation in the context of the HLA-C*08:02 allele. The KRAS G12D driver mutation is expressed in about 45% of pancreatic adenocarcinomas, 13% of colorectal cancers, and at lower frequencies in other cancers, and the HLA-C*08:02 allele is expressed by approximately 8% and 11% of white and black people, respectively, in the U.S. Thus, in the U.S. alone, thousands of patients per year with metastatic gastrointestinal cancers would potentially be eligible for immunotherapy with this KRASG12D-reactive T cell.

Although only Ms. Bachini (“patient number 3737”) was a long-term survivor, the researchers were able to treat three other patients with enriched populations of TILs targeting predominantly one mutated tumor antigen. Patient 4069 experienced a transient regression of multiple lung metastases of his pancreatic adenocarcinoma, but patients 4007 and 4032 had no objective response. Whereas 23% of circulating T cells at one month after treatment were adoptively transferred mutation-specific TILs in the case of Ms. Bachini, the other three patients treated with enriched populations of mutation-specific TILs showed no or minimal persistence. The researchers concluded that they will need to develop strategies designed to enhance the potency and persistence of adoptively transferred mutation-specific TILs. Nevertheless, the researchers concluded that nearly all patients with advanced gastrointestinal cancers harbor tumor mutation-specific TILs. This finding may serve as the basis for developing personalized adoptive cellular therapies and/or vaccines that can effectively target common epithelial cancers.


Dr. Rosenberg pioneered the study and development of adoptive cellular immunotherapy, beginning in the 1980s. Most studies with TIL-based adoptive immunotherapy have been in advanced melanoma. Adoptive cellular immunotherapy is the most effective approach to inducing complete durable regressions in patients with metastatic melanoma.

As we discussed in our cancer immunotherapy report, melanoma tumors have many more somatic mutations (about 200 nonsynonymous mutations per tumor) than most types of cancer. This appears to be due to the role of a potent immunogen—ultraviolet light—in the pathogenesis of melanoma. The large number of somatic mutations in melanomas results in the infiltration of these tumors by TILs that target the mutations. As discussed in our report, Dr. Rosenberg and his colleagues cultured TIL cell lines that addressed specific immunodominant mutations in patients’ melanomas. Treatment with these cell lines in several cases resulted in durable complete remissions of the patients’ cancers.

Dr. Rosenberg and his colleagues used the same strategy employed in identification of TIL cell lines that targeted specific mutations in melanomas to carry out the study in gastrointestinal cancers, as discussed in our report. However, the small number of somatic mutations and of endogenous TILs in gastrointestinal cancers and in most other epithelial cancers has made studies in these cancers more difficult than studies in melanoma.

in addition, the susceptibility of melanoma to treatment with checkpoint inhibitors such as the PD-1 blockers pembrolizumab (Merck’s Keytruda) and nivolumab (Bristol-Myers Squibb’s Opdivo) correlates with the large number of somatic mutations in this type of cancer. As we discussed in our December 15, 2014 article on this blog, immune checkpoint inhibitors work by reactivating endogenous tumor-infiltrating T cells (TILs). In the case of melanoma, these endogenous TILs target the numerous somatic mutations found in these cancers, and—as suggested by Dr. Rosenberg’s studies with cultured TIL cell lines—those endogenous TILs that target immunodominant mutations can induce durable compete remissions. As discussed in our December 15, 2014 blog article, the three major types of immuno-oncology treatments—immune checkpoint inhibitors, cancer vaccines, and adoptive T-cell therapies, work via related mechanisms.

In 2015, researchers showed that other types of cancers that have numerous somatic mutations are especially susceptible to checkpoint inhibitor treatment. These include, for example, non-small cell lung cancers (NSCLCs) that have mutational signatures that indicate that the cancers were caused by smoking, and cancers that have mutations in genes involved in DNA repair. (Mutations in genes involved in DNA repair pathways result in the generation of numerous additional mutations.)

Moreover, as discussed in our December 15, 2014 blog article, cancer immunotherapy researchers have been expanding the types of tumors that can be treated with checkpoint inhibitors. Genentech/Roche’s PD-L1 inhibitor that was discussed in that article, MPDL3280A, is now called atezolizumab. The clinical trials of atezolizumab discussed in that article and in our report have continued to progress. In a pivotal Phase 2 study in locally advanced or metastatic urothelial bladder cancer (UBC), atezolizumab shrank tumors in 27 percent of people whose disease had medium and high levels of PD-L1 expression and had worsened after initial treatment with platinum chemotherapy. These responses were found to be durable. According to Genentech, these results may represent the first major treatment advance in advanced UBC in nearly 30 years. Atezolizumab also gave positive results in Phase 2 clinical trials in patients with NSCLC that expresses medium to high levels of PD-L1.

Meanwhile, NewLink Genetics (Ames, IA) has entered Phase 3 clinical trials in pancreatic cancer with its HyperAcute cellular immunotherapy vaccine therapy. A Phase 2 trial of the company’s HyperAcute cellular immunotherapy algenpantucel-L in combination with chemotherapy and chemoradiotherapy in resected pancreatic cancer (clinical trial number NCT00569387) appears to be promising.

Dr. Rosenberg’s studies of TIL therapies of gastrointestinal cancers represent another approach to moving immuno-oncology treatments beyond melanoma, based on mutation-specific targeting. The types of cancers that form the focus of these studies—gastrointestinal epithelial cancers—have proven difficult to treat. Moreover, several of them are among the most common of cancers. The researchers and patients involved in these and other immuno-oncology studies are heroes, and oncologists appear to be making measured progress against cancers that have been until recently considered untreatable.


As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

“Our Promise to Nicholas”, Batten disease, and gene therapy


Wayland MA Source:

Wayland MA Source:

Russell’s Garden Center, on Route 20, a family-owned business established in 1876, is a unique Wayland MA institution. When you shop at Russell’s and approach the check-out counter with your plants, flowers, or other purchases, you will see a donation box for a rare-disease charity called “Our Promise to Nicholas Foundation”.

This charity is named for Nicholas R. Dainiak, a Bedford MA boy who died on his 11th birthday in 2014, after “a courageous six year battle with Batten’s disease”. The primary mission of the foundation is to raise funds and create partnerships aimed at promoting awareness, providing education, and developing translational research in Batten disease.

One of the events that the Foundation sponsors in order to raise funds and awareness is the John Tanner Memorial 5-K Run and Walk, which this year took place on October 4, 2015 in Wayland. This event memorializes both Nicholas and John Tanner. John Tanner was a competitive runner who devoted all of his races over 5 years to raising awareness about Nicholas and Batten disease. He was also a long-time employee of Russell’s Garden Center—hence the Russell’s and Wayland connection to the Foundation. John Tanner died unexpectedly while running the NYC half marathon in the spring of 2013.

Batten disease

Batten disease is a very rare, fatal, autosomal recessive neurodegenerative disorder that usually begins in childhood. Juvenile Batten disease is one of a group of disorders known as neuronal ceroid lipofuscinoses (NCLs). NCLs may be caused by one of over 400 different mutations. They affect the nervous system with vision loss, seizures, movement disorders, slow learning, altered thought processes, and cognitive decline.

Although Batten disease was originally used to describe only the juvenile form of NCL the term “Batten disease” is now widely used to refer to all forms of NCL, including adult-onset disease. Juvenile NCL, the most prevalent form of Batten disease, has been linked to mutations in the CLN3 gene. Late infantile NCL has been linked to mutations in NCL2.

Batten disease is a type of lysosomal storage disease. The CLN3 gene codes for a protein called battenin, which is found principally in lysosomes and in endosomes. The protein’s function is currently unknown. The CLN2 gene codes for a lysosomal enzyme called tripeptidyl peptidase 1 (TPP1), which is an acid protease.

Mutations in CLN2, CLN3, and other Batten disease genes result in the accumulation of lipofuscins in the tissues of the body. Lipofuscins are lipoproteins that form autofluorescent ceroid (i.e., waxy) deposits throughout the body of Batten disease patients.  Lipopfuscin deposits can sometimes be detected visually in the back of the eye. As the disease progresses, the deposits in the retina appear more pronounced, and ophthalmologists see circular bands of different shades of pink and orange in the patient’s optic nerve and retina. Ceroid lipofuscins are a hallmark of Batten disease, and appear to cause disease symptoms.

Juvenile Batten disease has an estimated incidence between 0.5 – 8 per 100,000 live births, with an average of 1.2. Despite its rarity, juvenile Batten disease appears to be the most common form of pediatric neurodegenerative disease. In addition to Batten disease patients, there are approximately 440,000 asymptomatic people in the United States who are carriers of juvenile Batten disease who have one copy of a mutated version of the CLN3 gene.

As with other rare diseases, a typical Batten disease patient may visit 8 physicians and receives 2 to 3 misdiagnoses before being correctly diagnosed. This may take many years. In the case of Nicholas, he had several misdiagnoses and mis-treatments over the early course of his disease, from age 4 to age 5. It was a ophthalmologist who finally correctly diagnosed Nicholas with Batten disease.

Relationship between Batten disease and more common neurodegenerative diseases

The written material next to the donation box for “Our Promise to Nicholas” in Russell’s Garden Center claims that study of Batten disease may lead to a greater understanding of such neurodegenerative diseases of aging as Alzheimer’s and Parkinson’s disease. Some of the symptoms and consequences of Batten disease resemble those of Alzheimer’s and Parkinson’s. Nevertheless, Batten disease is classified as a lysosomal storage disease, while Alzheimer’s and Parkinson’s are thought to be caused via other mechanisms.

However, some researchers see common mechanisms in the pathobiology of neurodegenerative lysosomal storage diseases such as Batten and of other neurodegenerative diseases such as Alzheimer’s and Parkinson’s. Specifically, these include impairment of autophagy and increase in cytoplasmic protein aggregation. For example, some researchers have found relationships between mutations in the Alzheimer’s disease-related protein presenilin 1 and lysosomal dysfunction.

Since clinical trials of drugs for Alzheimer’s disease have so far been unsuccessful, study of alternative mechanisms for the pathogenesis of Alzheimer’s may be useful in developing new ways of addressing drug discovery for this devastating and all-too-common disease.

Discovery and development of gene therapies for Batten disease

The “Our Promise to Nicholas” website has a page entitled “Where your donations go”. According to that Web page, Nicholas’ disease was caused by a splice mutation in CLN2, which blocked production of TPP1. This is the most common mutation in children with the late infantile subtype of Batten Disease.

The same Web page discusses a gene therapy program led by Beverly Davidson, Ph.D. (then at the University of Iowa, Iowa City, IA), which had been supported by Our Promise To Nicholas Foundation. As of April 2014, Dr. Davidson joined the Children’s Hospital of Philadelphia (CHOP). At that time, Dr. Davidson became the director of CHOP’s Center for Cellular and Molecular Therapeutics. She has also continued her research on gene therapy for neurodegenerative diseases, including Batten disease, other neurologic lysosomal storage disorders, Huntington’s and Alzheimer’s diseases, and others.

While at Iowa, and continuing at CHOP, Dr. Davidson and her colleagues were investigating the use of adeno-associated virus (AAV) vectors carrying a functional TPP1 gene in treatment of late infantile Batten disease in animal models.

On November 11, 2015, Spark Therapeutics (Philadelphia, PA) announced that its first gene therapy program targeting a central nervous system (CNS) disease will target late infantile Batten disease. In that press release, it also announced that a report published in the 11 November issue of Science Translational Medicine provides preclinical proof of principle for Spark’s gene therapy, known as SPK-TPP1. The preclinical study, in a naturally occurring dog model, was led by Dr. Davidson at CHOP.

The study demonstrated the potential of a one-time administration of SPK-TPP1 to delay onset and progression of Batten disease in the dog model. SPK-TPP1 consists of Spark’s AAV2 vector carrying a functional TPP1 gene. The preclinical study showed that one-time administration of SPK-TPP1 to the ependymal cells of the brain ventricular system produced steady expression of the enzyme in the cerebrospinal fluid, and throughout the CNS. It also resulted in delayed onset of clinical symptoms and disease progression, protection from cognitive decline and extension of lifespan, as compared to untreated controls.

Based on these results, Spark plans to initiate Investigational New Drug Application (IND)-enabling studies in 2015.

Our November 2015 book-length report, Gene Therapy: Moving Toward Commercialization (published by Cambridge Healthtech Institute), contains a discussion of gene therapy vectors, including AAV. It also highlights Spark Therapeutics as a leader in AAV-based gene therapy and in gene-therapy treatments for retinal diseases. Spark’s technology platform had been developed over a 20-year period at CHOP.

As also discussed in our November 16, 2015 article on this blog, Spark has recently completed a Phase 3 pivotal trial of SPK-RPE65, a gene therapy for treatment of inherited retinal diseases (IRDs) caused by mutations in the gene for RPE65. SPK-TPP1 uses the same AAV2 vector as SPK-RPE65, and will utilize the same manufacturing processes. AAV2 has a neural tropism. Since the retina is an extension of the brain, researchers can utilize AAV2 vectors to target both tissues.


On the Web page “Where your donations go”, Dr. Davidson says that funding from “family foundations such as Our Promise to Nicholas Foundation” has provided much needed support. Their donations have allowed cutting-edge research to be conducted in a timely manner, rather than months or years after researchers develop the ideas for these studies. Moreover, interacting with Batten disease families is especially motivating, and the advisory role of scientists who review grant proposals for family foundations is valuable as well.

Our Promise to Nicholas is far from the only Batten disease “family foundation”. Other families of patients with juvenile and adult-onset Batten disease have formed foundations to fund research and awareness. For example, there are Nathan’s Battle Foundation and the Batten Disease Support and Research Association (BDSRA). Our Promise to Nicholas participated in the 2015 BDSRA Annual Conference, and worked together with other Batten disease family foundations to provide nursing care and childcare for the event. Thus when Dr. Davidson refers to “family foundations”, she is referring to several such organizations.

Dr. Davidson also pointed out that grant funding from the National Institutes of Health (NIH) has dramatically decreased in recent years due to Federal budget constraints. This has especially affected research on rare diseases such as Batten disease. Dr. Davidson believes that “family foundation support is being increasingly relied upon to fill a growing void in NIH funding”.

Funding of Dr. Davidson’s research by Our Promise to Nicholas Foundation and other family foundations has resulted in a gene therapy R&D program that has been adopted by one of the world’s leading gene therapy companies, Spark Therapeutics. Spark (in collaboration with Dr. Davidson’s group at CHOP) is taking its Batten disease program into the clinic, and intends to commercialize SPK-TPP1. Spark is also using its Batten disease program as the basis for its larger neurodegenerative disease program. Thus Our Promise to Nicholas Foundation has much to be proud of.


As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Gene editing technology used to treat infant with leukemia


Baby_Face Source:

Baby_Face Source:

In November 2015, the use of gene editing technology to treat an 11-month-old child with leukemia was reported in news articles in Nature and in Science. Because of the human-interest value of this story, it was also reported in Time magazine and in the New York Times.

Data from this first-in-humans clinical use of the therapy will be presented at the 57th American Society of Hematology (ASH) Annual Meeting in Orlando, FL in early December 2015.

The young patient was treated with a complex cellular immunotherapy regimen developed by Cellectis (Paris, France and New York, NY). Cellectis’ platform involves production of allogeneic (rather than autologous) chimeric antigen receptor (CAR) T-cells to create an “off-the-shelf solution” to cellular immunotherapy for cancer, potentially simplifying manufacturing and standardization of therapies.

We have discussed CAR T-cell therapies on this blog, and—in more detail—in two book-length reports published by Cambridge Healthtech Institute (CHI). These are our 2014 Cancer Immunotherapy report, and our new November 2015 report, Gene Therapy: Moving Toward Commercialization.

CAR T-cell therapies directed against the B-cell antigen CD19, being developed by Novartis/University of Pennsylvania, Juno Therapeutics, and Kite Pharma, have demonstrated impressive clinical results against B-cell leukemias and lymphomas. However, in order to avoid immune incompatibility, CAR T-cell must be constructed and manufactured using autologous T-cells derived from the patient to be treated. This is an expensive and laborious process. Hence the rationale for allogeneic CAR T-cell therapy.

Cellectis uses gene editing in construction of its allogeneic CAR T-cells. Specifically, the company first modifies T-cells from healthy donors with an anti-CD19 CAR gene construct, similar to the methods used by other companies that are developing anti-CD19 CAR cellular immunotherapies. Cellectis then uses gene editing based on transcription activator-like effector nucleases (TALENS) to disrupt expression of the T-cells’ TCR (T-cell receptor) genes. It is the TCRs of the transplanted T cells that recognize the patient’s own cells as foreign, and thus attack them. Cellectis also uses TALENS gene editing to disrupt expression of a gene for another cell-surface protein, CD52. CD52 is present on mature lymphocytes, and is the target of the monoclonal antibody drug alemtuzumab (Genzyme’s Lemtrada). Researchers can then use alemtuzumab to prevent host-mediated rejection of the HLA mismatched CAR19 T cells. Cellectis’ “Talen engineered universal CAR19 T cells” can thus in principle be used to treat any patient with B-ALL (B-cell acute lymphoblastic leukemia), instead of autologous anti-CD19 CAR T-cells.

The treatment of the young patient, Layla Richards of London, was on a compassionate use basis. She had refractory relapsed B-ALL, and was expected to die shortly. Meanwhile, Cellectis had a universal CAR19 (UCART19) cell bank in the same hospital in which Layla was being treated. The cell bank had been characterized in detail, in preparation for submission for regulatory approval and Phase 1 testing.

Prior to administration of the UCART19 cells, the patient received lymphodepleting chemotherapy (including administration of alemtuzumab). After getting the UCART19 cells in June 2015 (near her first birthday), Layla went into remission, and has no trace of leukemia. After about three months she had a bone marrow transplant to help her immune system recover, and is now at home. However the follow-up period since her treatment has only been 5 months. Therefore, Layla’s doctors do not yet know how durable the remission will be. The key question is how long the UCART19 cells can survive in the body and prevent recurrence of leukemia.

Gene editing companies and their technologies discussed in our November 2015 report

Our November 2015 gene therapy report includes a chapter (Chapter 8) that focuses on gene-editing technologies and on companies that are developing therapies based on these technologies. The gene-editing technology that has been getting the most attention from the scientific and financial communities is known as CRISPR/Cas9. The other two technologies discussed in Chapter 8 are TALENS and zinc-finger nucleases (ZFN). The basic principle of these gene-editing technologies is that a “molecular scissors” makes a specific double-strand break in a deleterious DNA sequence. This break is either repaired in such a way as to disrupt the gene by forming deletions or mutations, or—if a suitable donor DNA is provided—the deleterious gene is replaced with a desired, functional gene sequence.

Gene-editing specialty companies discussed in our report based on CRISPR/Cas9 technology include Editas Medicine (Cambridge, MA) (which also utilizes TALENS), Intellia Therapeutics (Cambridge MA), CRISPR Therapeutics (Basel, Switzerland; Stevenage, U.K.; and Cambridge MA), and Caribou Biosciences (Berkeley, CA). Sangamo BioSciences (Richmond, CA), which is also discussed in our report, is a pioneer in ZFN technology.

Despite the predominant focus on CRISPR/Cas9 technology and companies in the biotechnology and venture capital communities, the first clinical studies involving gene editing have used Sangamo’s ZFN technology. These studies are in the field of HIV/AIDS. They involve ex vivo treatment of HIV-infected patients’ T-cells with a specific ZFN-based vector, in order to render the patients resistant to further manifestations of the disease.

Meanwhile, Editas has developed a vector designed to enable the company to move its CRISPR/Cas9 technology into the clinic. Editas’ first clinical program will be a potential treatment for a form of the genetically-driven retinal disease, Leber congenital amaurosis (LCA). (This is a different form of LCA than the one being targeted by Spark Therapeutics, which we discussed in our November 16, 2015 article on this blog).

bluebird bio (Cambridge, MA) is also pursuing a gene-editing technology program based on homing endonucleases and MegaTAL enzymes. This research and preclinical-stage program came to bluebird via its 2014 acquisition of Precision Genome Engineering Inc. (Seattle WA).

Cellectis is not the only company that is combining CAR T-cell therapies with gene-editing technology. In May 2015, Editas formed a collaboration with Juno Therapeutics to pursue research programs that combine Editas’ genome editing technologies with Juno’s CAR and TCR T-cell technologies.


Despite the great deal of excitement about gene-editing technologies and companies (especially CRISPR/Cas9) these are early days for development of therapies based on these technologies. Despite the almost miraculous results in the treatment of Layla Richards, it is only one case, and the follow-up period has been short. Nevertheless, this one case may open the way for this therapy to be used in other “desperate situations” where there is no time, or it is not possible, to use a patient’s own T cells. And researchers are already speculating that a similar technique may be used to treat people with other blood cancers, and eventually people with solid tumors.

For more information on our November 2105 gene therapy report, or to order it, see the CHI Insight Pharma Reports website.


As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Gene Therapy Report Published By CHI Insight Pharma Reports


Adeno-associated virus, a common gene therapy vector. Source:

Adeno-associated virus, a common gene therapy vector. Source:

On November 6, 2015, Cambridge Healthtech Institute (CHI) announced the publication of a new book-length report, Gene Therapy: Moving Toward Commercialization, by Allan B. Haberman, Ph.D.

As demonstrated by several late-breaking news items that appeared as our report was in the process of publication, gene therapy is a “hot”, fast-moving field. For example:

On October 5, 2015, Spark Therapeutics (Philadelphia, PA) announced positive top-line results from the Phase 3 pivotal trial of SPK-RPE65, a gene therapy for treatment of inherited retinal diseases (IRDs) caused by mutations in the gene for RPE65. This trial met its primary endpoint, and there were no serious adverse events related to treatment with the therapy. In results presented at a scientific meeting later in October, SPK-RPE65 was found to give durable improvements in vision over a three-year period.

SPK-RPE65 is not only Spark’s most advanced gene therapy in development, but is the most advanced gene therapy for retinal disease of any company. It is covered in our report.

bluebird’s LentiGlobin BB305—including the company’s strategy for commercializing this product—is also discussed in our report. In bluebird’s November 5, 2015 presentation at the American Society of Hematology (ASH) Annual Meeting, it was revealed that in Phase 1/2 clinical trials, LentiGlobin BB305 rendered the few sickle-cell disease patients in the trials transfusion-free and hospitalization-free for at least six months. Among patients with severe beta-thalassemia, all except for those with the β0/β0 genotype were rendered transfusion-free for at least 90 days, with a median of 287 days transfusion-free. Two of the β0/β0 patients (who made no hemoglobin at baseline) received a single transfusion post-discharge, and the third β0/β0 patient remains transfusion-dependent.

The stock market had focused on the negative results with the β0/β0 patients, and thus bluebird stock lost over 20% of its value after the ASH abstracts were released. However, the β0/β0 patients represent only one-third of the beta-thalassemia market, and sickle-cell disease is a larger market than beta-thalassemia. Thus, provided further clinical trials are positive, LentiGlobin BB305 can still be a successful product. bluebird is increasing the number of patients who will be enrolled in the trial from eight to 20, so more data should be forthcoming in 2016.

In corporate gene therapy news, Spark Therapeutics recently opened a new satellite office in the Boston area, joining Boston-area gene therapy companies bluebird bio, Dimension Therapeutics, and Voyager Therapeutics. All are discussed in our report. Spark and bluebird are public companies, and Dimension and Voyager recently went public. In addition, uniQure, the company that developed the first approved gene therapy product, opened a Lexington MA office and manufacturing facility in 2013. Boston has thus become Gene Therapy Central. As discussed in our report, Boston is also the most important center for companies that focus on gene editing, based on CRISPR/Cas9 technology.

These and other recent news articles and scientific publications attest to the progress of gene therapy, which only a few years ago was considered to be a “premature technology”.

Our gene therapy report looks at how researchers have been working to overcome critical barriers to development of safe and efficacious gene therapy, from 1990 to 2015. It then focuses on clinical-stage gene therapy programs that are aimed at commercialization, and the companies that are carrying out these programs. A major theme of the report is whether gene therapy can attain near-term commercial success, and what hurdles still need to be overcome.

Topics covered in the report:

  • Development of improved vectors (integrating and non-integrating vectors)
  • Gene therapy for ophthalmological diseases
  • Gene therapy for hemophilias and other rare diseases
  • Gene therapy for more common diseases (e.g., Parkinson’s disease, osteoarthritis, and heart failure)
  • Companies whose central technology platform involves ex vivo gene therapy
  • Gene editing technology
  • Outlook for gene therapy
  • Outlook for eight gene therapy products expected to reach the market before 2020

The report also includes:

  • An exclusive interview with Sam Wadsworth, Ph.D., the Chief Scientific Officer of Dimension Therapeutics and former Head of Gene Therapy R&D at Genzyme
  • The results and an analysis of a survey of individuals working in gene therapy, conducted by Insight Pharma Reports in conjunction with this report.
  • Companies profiled: uniQure, Spark Therapeutics, GenSight, Dimension Therapeutics, Voyager Therapeutics, Oxford BioMedica, bluebird, Juno Therapeutics, Kite Pharma, Editas, and others.

Our report is designed to enable you to understand current and future developments in gene therapy. It is also designed to inform the decisions of leaders in companies and in academic groups that are working in gene therapy R&D and in development of gene therapy enabling technologies.

For more information on the report, or to order it, see the CHI Insight Pharma Reports website.


As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Our New Year’s 2015 article: Notable researchers and breakthrough research of 2014


Pre-1917 Russian Happy Christmas and Happy New Year card

Pre-1917 Russian Happy Christmas and Happy New Year card

As is their customary practice, both Nature and Science ran end-of-year specials. The Nature special (in their 18 December issue) is entitled “365 days: Nature’s 10. Ten people who mattered this year.” The Science special (in their 19 December issue) is entitled, as usual “2014 Breakthrough of the Year.” As is also usual, there is a section for “Runners Up” to the year’s “Breakthrough”.

From the point of view of a consulting group—and a blog—that focuses on effective drug discovery and development strategies, we were disappointed with both end-of-year specials. Most of the material in these articles was irrelevant to our concerns.

Science chose the Rosetta/Philae comet-chasing mission as the “Breakthrough of the Year”, and its “runners up” included several robotics and space-technology items, as well as new “letters” to the DNA “alphabet” that don’t code for anything.

Nature also focused on comet chasers, robot makers, and space technologists, as well as cosmologist and mathematicians, and a fundraising gimmick—“the ice-bucket challenge”. Moreover, Nature was much too restrictive in titling its article “Ten people who mattered”. Every human being matters!

Nevertheless, these two special sections do contain a few gems that are both relevant to effective drug discovery and development, and are worthy of highlighting as “notable researchers of 2014” and “breakthrough research of 2014”. We discuss these in the remainder of this article.

Suzanne Topalian, M.D.

Suzanne Topalian is one of the researchers profiled in “Nature’s 10”. She is a long-time cancer immunotherapy clinical researcher who began her career in 1985 in the laboratory of cancer immunotherapy pioneer Steven Rosenberg at the National Cancer Institute (Bethesda MD). In the early days of the field, when cancer immunotherapy was scientifically premature, there was a great deal of skepticism that these types of treatments would even work. However, both Dr. Rosenberg and Dr. Topalian persevered in their research.

In 2006, Dr. Topalian moved to Johns Hopkins University (Baltimore, MD) to help launch clinical trials of Medarex/Bristol-Myers Squibb/Ono’s nivolumab, a PD-1 inhibitor. As noted in the Nature article, her work “led to a landmark publication in 2012 showing that nivolumab produced dramatic responses not only in some people with advanced melanoma but also in those with lung cancer [specifically, non–small-cell lung cancer, NSCLC].” We also discussed that publication on the Biopharmconsortium Blog, and in our recently published book-length Insight Pharma Report, Cancer Immunotherapy: immune checkpoint inhibitors, cancer vaccines, and adoptive T-cell therapies. Our report also includes discussions of Dr. Rosenberg’s more recent work in cellular immunotherapy.

As discussed in our report, nivolumab was approved in Japan as Ono’s Opdivo in July 2014 for treatment of unresectable melanoma, and a competitive PD-1 inhibitor, pembrolizumab (Merck’s Keytruda) was approved in the United States for advanced melanoma on September 5, 2014. More recently, on December 22, 2014, the FDA also approved nivolumab (BMS’ Opdivo) for advanced melanoma in the U.S. There are thus now two FDA-approved PD-1 inhibitors [in addition to the CTLA-4 inhibitor ipilimumab (BMS’ Yervoy)] available for treatment of advanced melanoma in the U.S.

Meanwhile, researchers continue to test both nivolumab and pembrolizumab for treatment of NSCLC and other cancers. And some analysts project that both of these agents are likely to be approved by the FDA for treatment of various populations of patients with NSCLC before the middle of 2015. Researchers are also testing combination therapies that include nivolumab or pembrolizumab in various cancers. And clinical trials of Genentech/Roche’s PD-L1 blocking agent MPDL3280A are also in progress.

Science’s 2013 Breakthrough of the Year was cancer immunotherapy, as we highlighted in our New Year’s 2014 blog article. Science could not make cancer immunotherapy the Breakthrough of the Year for 2014, too. Thus it chose to give physical scientists a turn in the limelight by highlighting the comet-chasing mission instead. Nevertheless, 2014 was the year in which cancer immunotherapy demonstrated its maturity by the regulatory approval of the two most advanced checkpoint inhibitor agents, pembrolizumab and nivolumab.

Implications for patients with terminal cancers

The clinically-promising results of cancer immunotherapy in a wide variety of cancers, coupled with the very large numbers of clinical trials in progress in this area, has also changed the situation for patients who have terminal cancers. Researchers who are conducting clinical trials of immunotherapies for these cancers are actively recruiting patients, of whom there are limited numbers at any one time. For example, there are now numerous clinical trials—mainly of immunotherapies—in pancreatic cancer, and most of these trials are recruiting patients. There are also active clinical trials of promising immunotherapies in the brain tumor glioblastoma. These are only two of many examples.

Recently, a 29-year-old woman with terminal glioblastoma ended her life using Oregon’s physician-assisted suicide law. Prior to her suicide, she became an advocate for “terminally ill patients who want to end their own lives”. We, however, are advocating that patients with glioblastoma and other types of terminal cancer for which there are promising immunotherapies seek out clinical trials that are actively recruiting patients. There is the possibility that some of these patients will receive treatments that will result in regression of their tumors or long-term remissions. (See, for example, the case highlighted in our September 16, 2014 blog article. There are many other such cases.) And it is highly likely that patients who participate in these trials will help researchers to learn how to better treat cancers that are now considered “incurable” or “terminal”, and thus help patients who contract these diseases in the future. From our point of view, that is a lot better than taking one’s own life via assisted suicide, and/or becoming an euthanasia advocate.

Masayo Takahashi, M.D., Ph.D.

Another researcher profiled in “Nature’s 10” is Masayo Takahashi, an ophthalmologist at the RIKEN Center for Developmental Biology (CDB) in Kobe, Japan who has been carrying out pioneering human stem cell clinical studies. We also discussed Dr. Takahashi’s research in our March 14, 2013 article on this blog.

At the time of our article, Dr. Takahashi and her colleagues planned to submit an application to the Japanese health ministry for a clinical study of induced pluripotent stem cell (iPS)-derived cells, which would constitute the first human study of such cells. They planned to treat approximately six people with severe age-related macular degeneration (AMD). The researchers planned to take an upper arm skin sample the size of a peppercorn, and transform the cells from this sample into iPS cells by using specific proteins. They were then to add other factors to induce differentiation of the iPS cells into retinal cells. Then a small sheet of these retinal cells were to be placed under the damaged area of the retina, where they were expected to grow and repair the damaged retinal pigment epithelium (RPE). Although the researchers would like to demonstrate efficacy of this treatment, the main focus of the initial studies was to be on safety.

According to the “Nature’s 10” article, such an autologous iPS-derived implant was transplanted into the back of a the damaged retina of one patient in September 2014. This patient, a woman in her 70s, had already lost most of her vision, and the treatment is unlikely to restore it. However, Dr. Takahashi and her colleagues are determining whether the transplant is safe and prevents further retinal deterioration. So far, everything has gone smoothly, and the transplant appears to have retained its integrity. However, the researchers will not reveal whether the study has been a success until a year after the transplantation.

The “Nature’s 10” article discusses how this technology might be moved forward into clinical use if the initial study is successful. It also discusses how Dr. Takahashi has been carrying her research forward in the face of a major setback that has plagued stem cell research at the CDB in 2014, as the result of the withdrawal of two once highly-regarded papers and the suicide of one of their authors.

Generation of insulin-producing human pancreatic β cells from embryonic stem (ES) cells or iPS

Another stem cell-related item, which was covered in Science’s end-of-2014 “Runners Up” article, concerned the in vitro generation of human pancreatic β cells from embryonic stem (ES) cells or iPS. For over a decade, researchers have been attempting to accomplish this feat, in order to have access to autologous β cells to treat type 1 diabetes, in which an autoimmune attack destroys a patient’s own β cells. In vitro generated β cells might also be used to screen for drugs that can improve β cell function, survival, and/or proliferation in patients with type 2 diabetes.

As reported in the Science article, two research groups—one led by Douglas A. Melton, Ph.D. (Harvard Stem Cell Institute, Cambridge, MA), and the other by Alireza Rezania, Ph.D. at BetaLogics Venture, a division of Janssen Research & Development, LLC.–developed protocols to produce unlimited quantities of β cells, in the first case from IPS cells, and in the other from ES cells.

However, in order to use the β cells to treat type 1 diabetes patients, researchers need to develop means (for example, some type of encapsulation) to protect the cells from the autoimmune reaction that killed patients’ own natural β cells in the first place. For example, Dr. Melton is collaborating with the laboratory of Daniel Anderson, Ph.D. (MIT Koch Institute for Integrative Cancer Research). Dr. Anderson and his colleagues have developed a chemically modified alginate that can be used to coat and protects clusters of β cells, thus forming artificial islets. Dr. Melton estimates that such implants would be about the size of a credit card.

The 2014 Boston biotech IPO boom

Meanwhile, the Boston area biotechnology community has seen a boom in young companies holding their initial public offerings (IPOs). 17 such companies were listed in a December 24 article in the Boston Business Journal. Among these companies are three that have been covered in the Biopharmconsortium Blog—Zafgen, Dicerna, and Sage Therapeutics.

We hope that 2015 will see at least the level of key discoveries, drug approvals, and financings seen in 2014.

As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

The Genentech/NewLink alliance, the IDO/TDO pathway, and targeting metabolism for immuno-oncology

Indoleamine 2,3-dioxygenase 1

Indoleamine 2,3-dioxygenase 1

On October 20, 2014, New Link Genetics Corporation (Ames, IA) announced that it had entered into an exclusive worldwide license agreement with Genentech/Roche for the development of NLG919, an IDO (indoleamine-pyrrole 2,3-dioxygenase) inhibitor under development by NewLink. The two companies also initiated a research collaboration for the discovery of next generation IDO/TDO (tryptophan-2,3-dioxygenase) inhibitors.

Under the terms of the agreement, NewLink will receive an upfront payment of $150 million, and may receive up to over $1 billion in milestone payments, as well as royalties on any sales of drugs developed under the agreement. Genentech will also provide research funding to NewLink in support of the collaboration. Other details of the agreement are outlined in NewLink’s October 20, 2014 press release.

The target of NewLink’s iDO/TDO program, and of its collaboration with Genentech, is cancer immunotherapy. As we discussed in our September 2014 report, Cancer Immunotherapy: Immune Checkpoint Inhibitors, Cancer Vaccines, and Adoptive T-cell Therapies (published by Cambridge Healthtech Institute), Genentech is developing the PD-L1 inhibitor MPDL3280A, which is in Phase 2 trials in renal cell carcinoma and urothelial bladder cancer, and in Phase 1 trials in several other types of cancer. PD-L1 inhibitors such as MPDL3280A constitute an alternative means to PD-1 inhibitors of blocking The PD-1/PD-L1 immune checkpoint pathway.

Two PD-1 inhibitors, pembrolizumab (Merck’s Keytruda) and nivolumab (Medarex/Bristol-Myers Squibb’s Opdivo) are in a more advanced stage of development than MPDL3280A and other PD-L1 inhibitors. The FDA approved pembrolizumab for treatment of advanced melanoma in September 2014, and nivolumab was approved in Japan in July 2014, also for treatment of advanced melanoma.

MPDL3280A, pembrolizumab, and nivolumab are monoclonal antibody (MAb) drugs. Another MAb immune checkpoint inhibitor, ipilimumab (Medarex/BMS’s Yervoy) was approved for treatment of advanced melanoma in 2011. Ipilimumab, which was the first checkpoint inhibitor to gain regulatory approval, targets CTLA-4.

As summarized in the October 20, 2014 New Link press release, IDO pathway inhibitors constitute another class of immune checkpoint inhibitors. However, they are small-molecule drugs. The IDO pathway is active in many types of cancer both within tumor cells and within antigen presenting cells (APCs) in tumor draining lymph nodes. This pathway can suppress T-cell activation within tumors, and also promote peripheral tolerance to tumor associated antigens. Via both of these mechanisms, the IDO pathway may enable the survival, growth, invasion and metastasis of malignant cells by preventing their recognition and destruction by the immune system.

As also summarized in this press release, NewLink has several active IDO inhibitor discovery and development programs, and has also discovered novel tryptophan-2,3-dioxygenase (TDO) inhibitors. As with IDO, TDO is expressed in a significant proportion of human tumors, and also functions in immunosuppression. TDO inhibitors are thus potential anti-cancer compounds that might be used alone or in combination with IDO inhibitors.

The kynurenine pathway and its role in tumor immunity and in neurodegenerative diseases

IDO and TDO are enzymes that catalyze the first and rate-limiting step of tryptophan catabolism through the kynurenine pathway (KP). The resulting depletion of tryptophan, an essential amino acid, inhibits T-cell proliferation. Moreover, the tryptophan metabolite kynurenine can induce development of immunosuppressive regulatory T cells (Tregs), as well as causing apoptosis of effector T cells, especially Th1 cells.

A 2014 review by Joanne Lysaght Ph.D. and her colleagues on the role of metabolic pathways in tumor immunity, and the potential to target these pathways in cancer immunotherapy also highlights the role of IDO and kynurenine in upregulation of Tregs and in the phenomenon of T-cell exhaustion, in which T cells chronically exposed to antigen become inactivated or anergic.

In our cancer immunotherapy report, we discuss the role of Tregs and T-cell exhaustion in immune suppression in tumors, and the role of anti-PD-1 agents in overcoming these immune blockades. Targeting the IDO and TDO-mediated tryptophan degradation pathway may thus complement the use of anti-PD-1 (and/or anti-PD-L1) MAb drugs, and potentially lead to the development of combination therapies.

We have discussed the kynurenine pathway of tryptophan catabolism in another context in our July 11, 2011 article on this blog. This article discusses the potential role of kynurenine pathway metabolites in such neurodegenerative diseases as Alzheimer’s disease (AD) and Huntington’s disease (HD).

As discussed in that article, HD and AD patients have elevated levels of two metabolites in the KP–quinolinic acid (QUIN) and 3-hydroxykynurenine (3-HK)–in their blood and brains. Both of these metabolites have been implicated in pathophysiological processes in the brain. In contrast, kynurenic acid (KYNA), which is formed in a side arm of the KP by conversion of kynurenine by the enzyme kynurenine aminotransferase, appears to be neuroprotective.

Researchers have been targeting kynurenine 3-monooxygenase (KMO) in order to induce a more favorable ratio of KYNA to QUIN. As a result, they have discovered a drug candidate, JM6. They proposed to first conduct clinical trials in HD, since the cause of HD is much better understood than for AD, and disease progression in placebo controls is better characterized than for AD. Moreover, clinical trials in AD are notoriously long and expensive.

A 2014 review of targets for future clinical trials in HD lists JM6 as a “current priority preclinical therapeutic targets in Huntington’s disease”. It also contains an updated discussion of the mechanism of action of JM6.

NewLink’s IDO inhibitor development program

NewLink presented progress posters on its IDO inhibitor development program at the American Society for Clinical Oncology (ASCO) 2014 annual meeting. These described trials in progress, which did not yet have any results. As described in these presentations, NewLink’s most advanced IDO inhibitor, indoximod is in:

  • a Phase 1/2 clinical trial in combination with ipilimumab in advanced melanoma
  • a Phase 1/2 study in combination with the alkylating agent temozolomide (Merck’s Temodar) in primary malignant brain tumors
  • a Phase 2 study in combination with the antimitotic agent docetaxel (Sanofi’s Taxotere) in metastatic breast cancer
  • a Phase 2 study in which indoximod is given subsequent to the anticancer vaccine sipuleucel-T (Dendreon’s Provenge) in metastatic castration-resistant prostate cancer.

The company also presented a progress poster on a first-in-humans Phase 1 study of NLG919, in solid tumors. NLG919, the focus of NewLink’s alliance with Genentech, is the second product candidate from NewLink’s IDO pathway inhibitor technology platform.

The major theme of NewLink’s ASCO meeting presentations is thus the development of the company’s IDO inhibitors as elements of combination immuno-oncology therapies with MAb immune checkpoint inhibitors, cancer vaccines, and cytotoxic chemotherapies.

In this connection, NewLink also hosted a panel discussion on combination therapies entitled “Points to Consider in Future Cancer Treatment: Chemotherapy, Checkpoint Inhibitors and Novel Synergistic Combinations” at the ASCO meeting. The collaboration of NewLink with Genentech will provide the opportunity for the two companies to test combinations of IDO inhibitors with Genentech’s PD-L1 inhibitor MPDL3280A.

Might targeting T-cell metabolism be used to enhance cancer immunotherapy?

In their 2014 review, Dr. Lysaght and her colleagues outline changes in metabolism as T-cells become activated, and differences in metabolism between various T-cell subsets (e.g., effector T cells, Tregs, exhausted or anergic T cells, and memory T cells). These researchers propose devising means to modulate T-cell metabolism in order to enhance anti-tumor immunity. However more research needs to be done in order to make such approaches a reality. In the meantime, development of IDO and TDO inhibitors is already in the clinic, providing the possibility of a metabolic approach to cancer immunotherapy.


As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or an initial one-to-one consultation on an issue that is key to your company’s success, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Obesity therapeutics update

Obesity, 12th century Japan.

Obesity, 12th century Japan.

The Biopharmconsortium Blog has over the years included numerous articles about obesity, and the attempts of researchers and companies to develop treatments for this disease.

Obesity, which has historically been considered the result of “lack of willpower” or other behavioral issues, was recognized as a disease by the American Medical Association in June 2013. This followed many years of genetic, molecular biology, and physiological studies that revealed the pathobiological basis of obesity. Nevertheless, many people—including many doctors, patients, and nutritionists—persist in the believing the older view of obesity. This continues to fuel an extremely lucrative diet industry, even thought most—if not all—attempts at dieting eventually fail.

However, researchers and companies have continued in their efforts to develop approved therapies for obesity. We have followed the results of companies that had come close to obtaining FDA approval for three central nervous system (CNS)-acting antiobesity agents in 2010—only to encounter opposition due to safety concerns. However, two of their agents were approved in 2012. Now the third one was approved in September 2014.

Orexigen/Takeda’s Contrave approved by the FDA

On September 11, 2014, Orexigen Therapeutics (La Jolla, CA) and its partner, Takeda, announced that the FDA had approved their antiobesity agent, Contrave (naltrexone HCI and bupropion HCI) extended-release tablets as an adjunct to diet and exercise for chronic weight management in obese adults [body mass index (BMI) of 30 kg/m2 or greater], and in overweight adults (BMI of 27 kg/m2 or greater) who have at least one weight-related comorbid condition (e.g, high cholesterol, Type 2 diabetes, or hypertension).

However, the FDA requires Contrave’s label to carry a boxed warning of increased risk of suicidal thoughts and other psychiatric issues. The label also warns that “The effect of Contrave on cardiovascular morbidity and mortality has not been established.” Orexigen is also required to conduct several post-marketing studies, including studies in pediatric patients, and assessment of the effects of long-term treatment with Contrave on the incidence of major adverse cardiovascular (CV) events in overweight and obese subjects with CV disease or multiple CV risk factors.

The September 2014 approval of Contrave followed the February 2011 issuance by the FDA of a Complete Response Letter requiring extensive clinical studies before Contrave could be approved. In 2010 the FDA had also rejected the applications of two other preregistration antiobesity drugs—Vivus’ Qnexa and Arena Therapeutics’ lorcaserin (Lorqess). Also in 2010, the then-marketed antiobesity drug sibutramine (Abbott’s Meridia) was withdrawn from the market at the FDA’s request.

Concern about long-term safety was the major consideration in all of these cases.

Nevertheless, lorcaserin (rebranded as Belviq) was approved in June 2012, and Qsymia (formerly known as Qnexa) was approved in July 2012.

Thus there are now three CNS-targeting weight-loss drugs on the U.S. market—all of which are “adjuncts to diet and exercise”, all of which work by suppressing appetite, and all of which have safety concerns that require post-marketing studies. Moreover, at least two of these drugs have levels of efficacy less than might be desired. For example, in one trial of Contrave, significant weight loss — defined as the loss of at least 5% of body weight — was achieved by 42% of Contrave-treated subjects, and 17% of subjects in the placebo group. The FDA says that patients taking Contrave should be evaluated after 12 weeks of treatment. Those who have failed to lose at least 5% of their body weight should discontinue Contrave.

Lorcaserin is the least efficacious of these drugs. Qsymia is the most efficacious, with 66.7% of patients on high-dose Qsymia losing at least 5% of body weight, as compared to 17.3% for placebo. The average weight loss in that trial was 10.9% of body weight with high-dose Qsymia and 1.2% with placebo.

A drop in weight of as little as 5% can have positive effects on risk of obesity’s comorbidities (e.g., insulin resistance, diabetes, high blood pressure, dyslipidemia, cardiovascular disease). Nevertheless, all three of these drugs are aids in management of obesity, rather than effective treatments. Moreover, their potential adverse effects are significant. It must be remembered that it was adverse effects that resulted in the withdrawal from the market of several antiobesity drugs (including sibutramine), and prevented the approval of any obesity drugs at all in 2010.

The FDA’s approval of these three drugs indicates that the agency is more willing to make antiobesity drugs available to patients than it has been previously, even in the face of continuing concerns about long-term safety. Rather than rejecting these drugs, the FDA is handling its concerns about safety via post-marketing studies, and restricted distribution of the drugs.

Liraglutide for treatment of obesity?

Meanwhile, Novo Nordisk is awaiting the FDA’s decision on the approval of its high-dose formulation of liraglutide (Saxenda) for treatment of obesity. An FDA advisory board recommended approval of the agent on September 11, 2014. The drug has an October 20 PDUFA date. The advisory board vote was based on Phase 3 results, which indicated that liraglutide produced an average 8% weight loss in obese subjects, when combined with diet and exercise. 69% of prediabetic obese individuals who were treated with liraglutide also showed no signs of prediabetes after 56 weeks, as compared to 33% for the placebo group.

We have discussed the potential use of liraglutide in treatment of obesity on this blog. A lower-dose formulation of this agent, under the trade name of Victoza, is already approved for treatment of type 2 diabetes. Liraglutide is a recombinant protein drug. It is a member of a class of drugs called incretin mimetics. An incretin is a gastrointestinal hormone that triggers an increase in insulin secretion by the pancreas, and also reduces gastric emptying. The latter effect slows nutrient release into the bloodstream and appears to increase satiety and thus reduce food intake. The major physiological incretin is glucagon-like peptide 1 (GLP-1), and incretin-mimetic drugs are peptides with homology to GLP-1 that have a longer half-life in the bloodstream than does GLP-1.

Although liraglutide does not act in the CNS, its major mechanisms of action in treatment of obesity appears to be—like CNS drugs—appetite control. Moreover, clinical trial results indicate that liraglutide is more of an aid in management of obesity than an effective treatment. Nevertheless, liraglutide’s antidiabetic effects and lack of CNS adverse effects constitute potential advantages over CNS-acting antiobesity drugs.

Sales of approved antiobesity drugs have been struggling

Despite the excitement over the approval of antiobesity drugs after so many roadblocks, sales of these drugs have fallen short of estimates. Estimates for Qsymia sales have fallen to $141 million in 2016 from the $1.2 billion projection for 2016 when the drug was approved in 2012. Eisai estimates that Belviq will generate $118 million in sales. Producers and marketers of these two drugs hope that the approval of Contrave will drive patient acceptance of all three CNS-targeting antiobesity drugs. At least one analyst projects that Contrave may achieve $740 million in sales in 2018.

If it is approved, Saxenda may have a sales advantage over the CNS-targeting drugs, since the low-dose formulation, Victoza for type 2 diabetes, is an established drug, with relationships with doctors and insurers already in place. Analysts project that liraglutide (branded as Saxenda) will generate $556 million in weight-loss sales in 2018, in addition to $3.2 billion for the antidiabetic low-dose formulation, Victoza.

A big factor in the level of sales of antiobesity drugs has been insurance reimbursement. It is estimated that some 50 percent of people with private insurance receive at least some coverage for diet drugs. However, insurers tend to classify Qsymia and Belviq as third-tier medications, requiring large patient co-payments. Moreover, Medicare and Medicaid do not pay for the drugs. Analysts hope that the approval of Contrave will result in expanded insurer coverage.

Obesity specialist company Zafgen continues to make progress

The vast majority of efforts to develop antiobesity drugs—over several decades—have been aimed at targeting the CNS. However, obesity is a complex metabolic disease that involves communication between numerous organs and tissues, notably adipose tissue (white, brown, and beige fat), skeletal muscle, the liver, the pancreas, the brain (especially the hypothalamus), the digestive system, and the endocrine system. The pathophysiology of obesity is also related to that of other major metabolic diseases, especially type 2 diabetes.

The mechanistic basis of obesity is not well understood, even though breakthroughs in understanding aspects of this disease have occurred in recent years. Thus there is great need for continuing basic research, and for novel programs aimed at development of breakthrough treatments for obesity based on non-CNS pathways.

One company that has been active in this area is Zafgen (Cambridge, MA), which we have been following on this blog. On June 24, 2014, Zafgen announced the closing of its Initial Public Offering. Zafgen is thus a young company pursuing an alternative approach to antiobesity drug discovery and development that has been able to go public.

In our May 23, 2012 article on this blog, we discussed Zafgen’s lead drug candidate, beloranib (ZGN-433). Beloranib is a methionine aminopeptidase 2 (MetAP2) inhibitor, which exerts an antiobesity effect by downregulating signal transduction pathways in the liver that are involved in the biosynthesis of fat. Animals or humans treated with beloranib oxidize fat to form ketone bodies, which can be used as energy or are excreted from the body. The result is breakdown of fat cells and weight loss. Obese individuals do not usually have the ability to form ketone bodies.

On June 22, 2013, Zafgen announced the interim results of an ongoing double blind placebo-controlled Phase 2 study of beloranib in a group of obese men and women. These results were presented in a poster session at the American Diabetes Association’s 73rd Scientific Sessions in Chicago on June 23, 2013.

Subjects had a mean age of 40.3 years, a mean weight of 101.2 kg (223.1 lbs.), and a mean BMI of 37.9 kg/m2 at the beginning of the study. 38 subjects receiving 12 weeks of treatment in the full trial were randomized to one of three doses of subcutaneous beloranib vs. placebo. The subjects were counseled not to change their usual diet and exercise patterns—this protocol thus differed from trials of the agents discussed earlier in this article. The interim analysis was of results from the first 19 subjects who completed 12 weeks of treatment.

Beloranib appeared safe and showed dose responsive weight loss. After 12 weeks, subjects on 0.6 mg, 1.2 mg, or 2.4 mg of beloranib lost an average of 3.8, 6.1 and 9.9 kg, respectively (8.4, 13.4, and 21.8 lbs.), versus 1.8 kg (4.0 lbs.) for placebo; these results were statistically significant. In addition, beloranib treated subjects showed improvements versus placebo in CV risk factors including levels of triglycerides, LDL cholesterol and C-reactive protein. Sensation of hunger also was reduced significantly.

Subcutaneous beloranib treatment over 12 weeks was generally well-tolerated. There were no major adverse events or deaths.

If later clinical trials confirm these interim Phase 2 clinical results, beloranib may have significant advantages over the three approved CNS-targeting drugs and over Saxenda, because of beloranib’s apparent benign adverse-effect profile, and major effects on weight and fat loss, even in the absence of diet and exercise advice. However, beloranib is years away from reaching the market for treatment of severe obesity with no known genetic causation.

Zafgen is attempting to develop beloranib not only as a superior alternative to “diet drugs”, but also as an alternative to bariatric surgery. In order to obtain approval for that indication, beloranib must (in late-stage, long-term clinical trials) demonstrate both the degree of weight loss and the positive metabolic effects seen in severely obese patients treated via bariatric surgery.

In addition to developing beloranib for severe obesity, Zafgen is developing this drug for treatment of the rare genetic disease Prader-Willi syndrome (PWS). Patients with PWS exhibit such symptoms as low muscle mass, short stature, incomplete sexual development, cognitive disabilities, and a chronic feeling of hunger that can result in life-threatening obesity. PWS is the most common genetic cause of life-threatening obesity. Many children with PWS become morbidly obese before age 5.

In January 2013, the FDA granted Zafgen orphan designation to treat PWS with beloranib. On July 10, 2014, the European Commission also granted orphan drug designation for beloranib for this indication. These regulatory actions were based on the initial results of Zafgen’s Phase 2a clinical trial of beloranib in PWS. This trial showed improvements in hunger-related behaviors and body composition, including reductions in body fat and preservation of lean body mass.

On October 1, 2014, Zafgen announced that it had begun a randomized, double-blind, placebo-controlled Phase 3 clinical trial of beloranib in obese adolescents and adults with PWS (clinical trial number NCT02179151). The company is also testing beloranib in Phase 2 trials in obesity due to hypothalamic injury, and is in preclinical studies with a second-generation MetAP2 inhibitor for treatment of general obesity.

Energesis Pharmaceuticals

The Biopharmconsortium Blog has also been following an earlier-stage company, Energesis Pharmaceuticals (Cambridge, MA), whose approach to developing antiobesity therapeutics is based on targeting brown fat. On June 19, 2014, FierceBiotech and Energesis announced that Janssen Pharmaceuticals and Johnson & Johnson Innovation had entered into a collaboration with Energesis, aimed at identifying agents that stimulate the formation of new brown fat in order to treat metabolic diseases.


The antiobesity drug field, which in 2010 was the domain of a “pall of gloom”, is now populated by three approved CNS-targeting drugs, perhaps to be soon joined by Saxenda. These drugs promise to give patients and physicians a new set of tools to aid in the management of obesity. However, the history of the CNS-targeting obesity drug field is littered with tales of the withdrawal of drug after drug due to unacceptable adverse effects. Moreover, the market—and especially payers—have not yet fully accepted the new antiobesity agents.

As readers of this blog well know, we favor approaches to treatment of obesity and its comorbidities based on targeting somatic physiological pathways that appear to be at the heart of the causation of obesity, not just the CNS. The progress of Zafgen in addressing a set of these pathways is very encouraging. However, these results must be confirmed by Phase 3 clinical trials.


As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Cancer Immunotherapy Report Published By CHI Insight Pharma Reports

T cells attached to tumor cell. Source: MSKCC.

T cells attached to tumor cell. Source: MSKCC.


On September 9, 2014, Cambridge Healthtech Institute’s (CHI’s) Insight Pharma Reports announced the publication of a new book-length report, Cancer Immunotherapy: Immune Checkpoint Inhibitors, Cancer Vaccines, and Adoptive T-cell Therapies, by Allan B. Haberman, Ph.D.

As attested by the torrent of recent news, cancer immunotherapy is a “hot”, fast-moving field. For example:

  • On September 5, 2014, the FDA granted accelerated approval to the PD-1 inhibitor pembrolizumab (Merck’s Keytruda, also known as MK-3475) for treatment of advanced melanoma. This approval was granted nearly two months ahead of the agency’s own deadline. Pembrolizumab is the first PD-1 inhibitor to reach the U.S. market.
  • On May 8, 2014, the New York Times published an article about a woman in her 40’s who was treated with adoptive immunotherapy with autologous T cells to treat her cancer, metastatic cholangiocarcinoma (bile-duct cancer). This deadly cancer typically kills the patient in a matter of months. However, as a result of this treatment, the patient lived for over 2 years, with good quality of life, and is still alive today.

These and other recent news articles and scientific publications attest to the rapid progress of cancer immunotherapy, a field that only a few years ago was considered to be impracticable.

Our report focuses on the three principal types of therapeutics that have become the major focuses of research and development in immuno-oncology in recent years:

  • Checkpoint inhibitors
  • Therapeutic anticancer vaccines
  • Adoptive cellular immunotherapy

The discussions of these three types of therapeutics are coupled with an in-depth introduction and history as well as data for market outlook.

Also featured in this report are exclusive interviews with the following leaders in cancer immunotherapy:

  • Adil Daud, MD, Clinical Professor, Department of Medicine (Hematology/Oncology), University of California at San Francisco (UCSF); Director, Melanoma Clinical Research, UCSF Helen Diller Family Comprehensive Cancer Center.
  • Matthew Lehman, Chief Executive Officer, Prima BioMed (a therapeutic cancer vaccine company with headquarters in Sydney, Australia).
  • Marcela Maus, MD, PhD, Director of Translational Medicine and Early Clinical Development, Translational Research Program, Abramson Cancer Center, University of Pennsylvania in Philadelphia.

The report also includes the results and an analysis of a survey of individuals working in immuno-oncology R&D, conducted by Insight Pharma Reports in conjunction with this report. The survey focuses on market outlook, and portrays industry opinions and perspectives.

Our report is an in-depth discussion of cancer immunotherapy, an important new modality of cancer treatment that may be used to treat as many as 60% of cases of advanced cancer by the late 2010s/early 2020s. It includes updated information from the 2014 ASCO (American Society of Clinical Oncology) and AACR (American Association for Cancer Research) meetings. The report is designed to enable you to understand current and future developments in immuno-oncology. It is also designed to inform the decisions of leaders in companies and in academic groups that are working in areas that relate to cancer R&D and treatment.

For more information on Cancer Immunotherapy: Immune Checkpoint Inhibitors, Cancer Vaccines, and Adoptive T-cell Therapies, or to order it, see the Insight Pharma Reports website.


As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Forma Therapeutics’ expanded R&D collaboration with Celgene


Ubiquitin pathway. Source: Rogerdodd, English language Wikipedia

Ubiquitin pathway. Source: Rogerdodd, English language Wikipedia

On April 1, 2014, Forma Therapeutics (Watertown MA) announced that it had entered into an expanded strategic collaboration with Celgene (Summit, NJ).

Under the new agreement, Forma has received an upfront cash payment of $225 million. The initial collaboration between the two companies under the new agreement will be for 3 1⁄2 years. Celgene will also have the option to enter into up to two additional collaborations with terms of two years each for additional payments totaling approximately $375 million. Depending on the success of the collaborations and if Celgene elects to enter all three collaborations, the combined duration of the three collaborations may be at least 7 1⁄2 years.

Under the terms of the new agreement, Forma will control projects from the research stage through Phase 1 clinical trials. For programs selected for licensing, Celgene will take over clinical development from Phase 2 to commercialization. Forma will retain U.S. rights to these products, and Celgene will have the rights to the products outside of the U.S. For products not licensed to Celgene, FORMA will maintain worldwide rights.

During the term of the third collaboration, Celgene will have the exclusive option to acquire Forma, including the U.S. rights to all licensed programs, and worldwide rights to other wholly owned programs within Forma at that time.

The April 2013 agreement between Forma and Celgene

The new collaboration between Forma and Celgene builds on an earlier agreement between the two companies. On April 29, 2013, the two companies entered into a collaboration aimed at discovery, development, and commercialization of drug candidates to modulate targets involved in protein homeostasis.

Protein homeostasis, also known as proteostasis, involves a tightly regulated network of pathways controlling the biogenesis, folding, transport and degradation of proteins. The ubiquitin pathway (illustrated in the figure above) is one of these pathways. We recently discussed how the ubiquitin pathway is involved in the mechanism of action of thalidomide and lenalidomide (Celgene’s Thalomid and Revlimid).

Targeting protein homeostasis has application to discovery and development of drugs for oncology, neurodegenerative disease, and other disorders. However, the April 2013 Forma/Celgene agreement focused on cancer. Under that agreement, Forma received an undisclosed upfront payment. Upon licensing of preclinical drug candidates by Celgene, Forma was to be eligible to receive up to $200 million in research and early development payments. FORMA was also to be eligible to receive $315 million in potential payments based upon development, regulatory and sales objectives for the first ex-U.S. license, as well as  up to a maximum of $430 million per program for further licensed products, in addition to post-sales royalties.

On October 8, 2013, Forma announced that it had successfully met the undisclosed first objective under its April 2013 strategic collaboration agreement with Celgene. This triggered an undisclosed payment to Forma. Progress in the April 2013 collaboration was an important basis for Celgene’s decision to enter into a new, broader collaboration with Forma a year later.

The scope of the new April 2014 Forma/Celgene collaboration

Unlike the April 2013 agreement, the April 2014 agreement between Forma and Celgene is not limited to protein homeostasis, or to oncology. The goal of the new collaboration is to “comprehensively evaluate emerging target families for which Forma’s platform has exceptional strength” over “broad areas of chemistry and biology”.  The expanded collaboration will thus involve discovery and development of compounds to address a broad range of target families and of therapeutic areas.

According to Celgene’s Thomas Daniel, M.D. (President, Global Research and Early Development), Celgene’s motivation for signing the new agreement is based not only on the early success of the existing Forma/Celgene collaboration, but also on “emerging evidence of the power of Forma’s platform to generate unique chemical matter across important emerging target families”.

According to Forma’s President and CEO, Steven Tregay, Ph.D., the new collaboration with Cegene enables Forma to maintain its autonomy in defining its research strategy and conducting discovery through early clinical development. It also aligns Forma with Celgene’s key strengths in hematology and in inflammatory diseases.

Forma Therapeutics in Haberman Associates publications

We have been following Forma on the the Biopharmconsortium Blog since July 2011. At that time, I was a speaker at Hanson Wade’s World Drug Targets Summit (Cambridge, MA). At that meeting, Mark Tebbe, Ph.D. (then Vice President, Medicinal and Computational Chemistry at Forma) was also a speaker. At the conference, Dr. Tebbe discussed FORMA’s technology platforms, which are designed to be enabling technologies for discovery of small-molecule drugs to address challenging targets such as protein-protein interactions (PPIs).

In particular, Dr. Tebbe discussed Forma’s Computational Solvent Mapping (CS-Mapping) platform, which enables company researchers to interrogate PPIs in intracellular environments, to define hot spots on the protein surfaces that might constitute targets for small-molecule drugs. FORMA has been combining CS-Mapping technology with its chemistry technologies (e.g., structure guided drug discovery, diversity orientated synthesis) for use in drug discovery.

We also discussed Forma’s earlier fundraising successes as of January 2012, and cited Forma as a “built to last” research-stage platform company in an interview for Chemical & Engineering News (C&EN).

Finally, we discussed Forma and its technology platform in our book-length report, Advances in the Discovery of Protein-Protein Interaction Modulators, published by Informa’s Scrip Insights in 2012. (See also our April 25, 2012 blog article.)

In our report, we discussed Forma as a company that employs “second-generation technologies” for the discovery of small-molecule PPI modulators. This refers to a suite of technologies designed to overcome the hurdles that stand in the way of the accelerated and systematic discovery and development of PPI modulators. Such technologies are necessary to make targeting of PPIs a viable field.

Forma’s website now has a brief explanation of its drug discovery engine, as it is applied to targeting PPIs. This includes links to web pages describing:

Our 2012 book-length report discusses technologies of these types, as applied to discovery of PPI modulators, in greater detail than the Forma website.

According to Dr. Daniel: “Progress in our existing [protein homeostasis] collaboration, coupled with emerging evidence of the power of FORMA’s platform to generate unique chemical matter across important emerging target families” led Celgene to enter into its new, expanded collaboration with Forma in April 2014. This suggests that Celgene is especially impressed by Forma’s chemistry and chemical biology platforms. it also suggests that chemistry technology platforms developed to address PPIs may be applicable to areas of drug discovery beyond PPIs as well.

Concluding remarks

Despite the enthusiasm for Forma and its drug discovery engine shown by Celgene, Forma’s other partners, and various industry experts, it must be remembered that Forma is still a research-stage company. The company has not one lone drug candidate in the clinic, let alone achieving proof-of-concept in humans. It is clinical proof-of-concept, followed by Phase 3 success and approval and marketing of the resulting drugs, that is the “proof of the pudding” of a company’s drug discovery and development efforts.

We await the achievement of such clinical milestones by Forma Therapeutics.

From a business strategy point of view, we have discussed Forma’s efforts to build a stand-alone, independent company for the long term in this blog and elsewhere. Now Forma has entered into an agreement with Celgene that might—in around 7-10 years—result in Forma’s acquisition. This would seem to contradict Forma’s “built to last” strategy.

However, in the business environment that has prevailed over the past several years, several established independent biotech companies, notably Genentech and Genzyme, have been acquired by larger companies. Even several Big Pharmas (e.g., Schering-Plough and Wyeth) have been acquired.

Nevertheless, we do not know what the business environment in the biotech/pharma industry will be like in 7-10 years, despite the efforts of strategists to predict it. And Celgene might forgo its option to acquire Forma, for any number of reasons. So the outlook for Forma’s status as an independent or an acquired company (which also depends on its success in developing drugs) is uncertain.


As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to  your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.

Neandertals, diabetes, and drug discovery

Neanderthal Family

Neanderthal Family

In our 2010 end-of-year blog article entitled “2010: Breakthroughs, Newsmakers, And Deals Of The Year”, we proposed an alternative nominee for the life science breakthrough of the year: the determination of the sequence of approximately two-thirds of the Neandertal genome by Svante Pääbo (Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany.) and his colleagues. We stated that this momentous achievement was “of great cultural significance, since it indicates that Neandertals contributed some 1-4 percent of the genome sequences of non-African present-day humans.” (This figure is now thought to be 1.5 to 2.1 percent.)

However, we also said that we had not blogged on this work “simply because it [had] nothing to do with drug discovery and development.” We then further stated that “perhaps someday, for example, some of the products of genes that are found in present-day humans but not in Neandertals could emerge as potential drug targets…researchers [had] begun studying some of these gene products in cell culture systems.”

Now, as of early 2014, one of the genes identified via sequencing Neandertal genomes has been implicated in a novel pathway involved in type 2 diabetes in present-day humans. However, rather than being a modern human gene not present in Neandertals, it is a haplotype that introgressed into modern humans via admixture with Neandertals.

The study that identified this gene initially had no connection with Neandertal genome studies at all. I was published by the SIGMA (Slim Initiative in Genomic Medicine for the Americas) Type 2 Diabetes Consortium in the 6 February 2014 issue of Nature. SIGMA is a joint U.S.-Mexico project funded by the Carlos Slim Foundation. It focuses on several important diseases that have particular relevance to public health in Mexico and Latin America, including type 2 diabetes and cancer. Type 2 diabetes has approximately twice the prevalence in Mexican and other Latin American populations, as compared to U.S. non-Hispanic whites.

The researchers performed a genome-wide association study (GWAS), in which they analyzed 9.2 million single nucleotide polymorphisms (SNPs) in each of 8,214 Mexicans and other Latin Americans, including 3,848 with type 2 diabetes and 4,366 non-diabetic controls. As a result of that analysis, the researchers replicated the identification of haplotypes previously associated with type 2 diabetes. They also identified a novel locus associated with type 2 diabetes at genome-wide significance.  This locus spans the genes that encode the solute carrier proteins SLC16A11 and SLC16A13. The risk haplotype carries four amino acid substitutions, all in SLC16A11.  It is present at approximately 50% frequency in Native American individuals and around 10% in East Asians, but is rare in Europeans and Africans.

Each copy of the risk newly-identified haplotype is associated with an approximately 20% increased risk of type 2 diabetes. The haplotype would thus be expected to contribute to the higher burden of type 2 diabetes in Mexican and Latin American populations. Mutations in SLC16A11 had never before been associated with type 2 diabetes. SLC16A11 thus represents a novel type 2 diabetes pathway.

The Neandertal connection

The researchers noted that the sequence of the risk haplotype is highly divergent, with an estimated time to the most recent common ancestor of both the novel haplotype and a European haplotype of 799,000 years. This is long before modern humans migrated from Africa into Eurasia. Moreover, the novel haplotype is not found in Africans and is rare in European populations. The researchers therefore hypothesized that the novel haplotype entered modern human populations via admixture with Neandertals.

At the time that this research was being conducted, the variant was not seen in published Neandertal (or Denisovan) genome sequences. However, with the help of Svante Pääbo, the researchers obtained access to a then-unpublished full-length Neandertal genome sequence from a Central Asian specimen. The Central Asian Neandertal genome sequence was homozygous across 5 killobases for the risk haplotype including all four missense SNPs in SLC16A11 . Over a span of 73 kb, the Neandertal sequence is nearly identical to that of individuals from the 1000 Genomes Project who are homozygous for the risk haplotype. The full-length Central Asian Neandertal genome has recently been published.

Moreover, the genetic length of the 73-kb risk haplotype is longer than would be expected if it had undergone recombination for the approximately 9,000 generations since the split with Neandertals. This is consistent with the hypothesis that the risk haplotype is not only similar to the Neandertal sequence, but was probably introduced into modern humans relatively recently through archaic admixture. Although this particular Neandertal-derived haplotype is common in the Americas, Native Americans and Latin Americans have the same proportion of Neandertal ancestry genome-wide as other Eurasian-derived populations. In general, although non-African populations have about the same percentage of Neandertal genes, different populations have different complements of genes derived from Neandertals.

Functional studies of SLC16A11

Although the risk haploype encodes four missense mutations in a single gene, the gene for SLC16A11, there is no formal genetic proof that SLC16A11 is responsible for increased risk of type 2 diabetes. Therefore, the researchers performed preliminary functional studies of SLC16A11.

Via immunofluorescence studies, the researchers found that SLC16A11 was expressed in the liver, the salivary glands and the thyroid. When the gene for SLC16A11 was introduced into HeLa cells, SLC16A1 was found to localize in the endoplasmic reticulum, but not in the plasma membrane, Golgi apparatus, or mitochondria. Other SLC16 family members show distinct intracellular localization pattern within the membranous structures of the cell.

SLC16A11, and other SLC16 family members, are solute carrier transporters (SLCs). We discussed SLCs and their role in transporting small-molecule nutrients and drugs across the blood-brain barrier in our 2009 book-length report, Blood-Brain Barrier: Bridging Options for Drug Discovery and Development, published by Cambridge Healthtech Institute. We also discussed SLCs in a 2009 article entitled “Strategies to Overcome Blood-Brain Barrier” in Genetic Engineering and Biotechnology News.

SLC16 family proteins are monocaboxylate transporters, which transport such compounds as lactate, pyruvate and ketone bodies, as well as thyroid hormone and aromatic amino acids, across biological membranes. As of 2008, of the 14 known members of this family, eight (including SLC16A11) had unknown functions.

The SIGMA researchers expressed SLC16A11 (or control proteins) in HeLa cells, and looked for changes in intracellular concentrations of approximately 300 polar and lipid metabolites. Expression of SLC16A11 resulted in substantial increases in intracellular triacylglycerol (triglyceride) levels, with smaller increases in intracellular diacylglycerols, and decreases in lysophosphatidylcholine, cholesteryl esters, and sphingomyelin. Since triglyceride synthesis occurs in the endoplasmic reticulum of hepatocytes, the researchers hypothesized that SLC16A11 may have a role in hepatic lipid metabolism.

Moreover, serum levels of triglycerides and accumulation of intracellular lipids are associated with insulin resistance, the metabolic syndrome, and the risk of developing type 2 diabetes. Thus, although further functional studies of SLC16A11 are needed, the researchers hypothesize that the novel risk allele for type 2 diabetes that they identified may exert its pro-diabetic effect by altering lipid metabolism in the liver.


This study, a GWAS in Mexican and other Latin American samples, is an illustration of how genetic mapping studies in understudied populations may identify previously undiscovered aspects of disease pathogenesis.

The risk gene identified in this study, SLC16A11, has not previously been associated with type 2 diabetes. It thus potentially represents a novel diabetes pathway, which might yield new targets for drug discovery. This new pathway might be important in type 2 diabetes not only in Native Americans and Latin Americans, but in other populations as well, even in those that lack mutations in SLC16A11.

The study initially had nothing to do with Neandertal genetics. However, the researchers noted unusual population genetics features of the risk haplotype that they identified, which led them to identify this haplotype as having entered modern human populations via introgression from Neandertals. Via the initial introgression, natural selection and/or genetic drift, the haplotype became fixed in Native Americans and some East Asians, but not in other Eurasian-derived populations such as Europeans and Euro-Americans.

It is extremely unlikely that either Neandertals, or Native Americans and Latin Americans in pre-modern times, had type 2 diabetes. However, modern diets, perhaps in concert with other risk genes, produced type 2 diabetes in carriers of the mutant SLC16A11 gene. The well-know case of the Pima Indians indicates that change from native diets and high levels of physical activity to processed foods and a more “Western” lifestyle is the major cause of the high levels of type 2 diabetes and obesity in this genetically-predisposed population. (It is not known, however, whether SLC16A11 is a factor in Pima Indians.)

As for studies of the Neandertal genome, John Hawks, Ph.D. (University of Wisconsin), an anthropologist who has been active in studies of the genetics of Neandertals and of Upper Paleolithic modern humans, believes that studies of the genomes of these ancient peoples may have relevance for the biology of present-day humans. [I took a Massive Open Online Course (MOOC) led by Dr. Hawks, entitled “Human Evolution: Past and Future” between late January and early March, 2014.]

Other researchers who study ancient genomes generally agree. As indicated by the SIGMA diabetes study, both genes for modern humans that were not present in Neandertals, and genes introgressed from Neandertals into modern humans may be relevant to modern human biology—and perhaps eventually to drug discovery.


As the producers of this blog, and as consultants to the biotechnology and pharmaceutical industry, Haberman Associates would like to hear from you. If you are in a biotech or pharmaceutical company, and would like a 15-20-minute, no-obligation telephone discussion of issues raised by this or other blog articles, or of other issues that are important to your company, please contact us by phone or e-mail. We also welcome your comments on this or any other article on this blog.