genomics

Pioneering Genomics: How the Myxini Sequencing Redefines Our Evolutionary Tree

Posted by

0


An international consortium has sequenced the hagfish genome, filling a significant gap in vertebrate evolutionary research. This work, published in Nature Ecology & Evolution, enhances understanding of genome duplications in vertebrates and their impact on the evolution of major physiological structures. Credit: Universtiy of Malaga

Researchers have sequenced the hagfish genome, providing vital insights into vertebrate evolution and genome duplication history.

An international scientific team made up of more than 40 authors from seven different countries, led by the researcher at the University of Malaga Juan Pascual Anaya, has managed to sequence the first genome of the myxini – also known as ‘hagfish’ – the only large group of vertebrates for which there was no reference genome of any of its species yet.

This finding, published today (January 12) in the scientific journal Nature Ecology & Evolution, has allowed deciphering the evolutionary history of genome duplications – number of times a genome is completely duplicated – that occurred in the ancestors of vertebrates, a group that comprises the human beings.

“This study has important implications in the evolutionary and molecular field, as it helps us understand the changes in the genome that accompanied the origin of vertebrates and their most unique structures, such as the complex brain, the jaw, and the limbs,” explains the scientist of the Department of Animal Biology of the UMA Pascual Anaya, who has coordinated the research.

Thus, this study, which has taken almost a decade, has been carried out by an international consortium that includes more than 30 institutions from Spain, United Kingdom, Japan, China, Italy, Norway, and the United States, including the University of Tokyo, the Japan research institute RIKEN, the Chinese Academy of Science and the Centre for Genomic Regulation in Barcelona, among others.

To be more specific, for this study, the genome that has been sequenced is that of the Eptatretus burgeri, which lives in the Pacific, on the coasts of East Asia. To achieve this, the researchers generated data up to 400 times the size of its genome, using advanced techniques of chromosomal proximity and managing to assemble it at the chromosome level. Credit: Universtiy of Malaga

Ecological link

The myxini or ‘hagfish’ are a group of animals that inhabit deep ocean areas. Known for the amount of mucosa they release when they feel threatened – a focus of research of cosmetic companies – and, also, for their role as an ecological link in the seabed – since they are scavengers and are responsible for eliminating, among other things, the corpses of whales that end up at the bottom of the sea after dying.

Hitherto their genome had not been sequenced due to its complexity, since they are composed of a large number of microchromosomes, which, in turn, are composed of repetitive sequences. This is in addition to the difficulty of accessing biological material.

“Besides, these microchromosomes are lost during the development of the animal, so that only the genital organs maintain a whole genome,” says Juan Pascual Anaya.

An international team led by Juan Pascual Anaya has successfully sequenced the genome of the myxini (hagfish), a critical group of vertebrates previously lacking a reference genome. Credit: Universtiy of Malaga

Genome duplications

To be more specific, for this study, in collaboration with the Chinese Academy of Science, the genome that has been sequenced is that of the Eptatretus burgeri, which lives in the Pacific, on the coasts of East Asia. To achieve this, the researchers generated data up to 400 times the size of its genome, using advanced techniques – Hi-C – of chromosomal proximity and managing to assemble it at the chromosome level.

“This is important because it allowed us to compare, for example, the order of genes between this and the rest of vertebrates, including sharks and humans, and, thus, solve one of the most important open debates in genomic evolution: the number of genome duplications, and when these occurred during the origin of the different vertebrate lineages,” says the UMA scientist, who adds that thanks to this we now know that the common ancestor of all vertebrates derived from a species which genome was completely duplicated once.

Later, according to Pascual Anaya, the lineages that gave rise to modern mandibular and non-mandibular vertebrates separated, and each of these re-multiplied its genome independently: while the former, which include humans, duplicated it, the latter tripled it.

An international scientific team made up of more than 40 authors from seven different countries, led by the researcher at the University of Malaga Juan Pascual Anaya, has managed to sequence the first genome of the myxini, also known as ‘hagfish’, the only large group of vertebrates for which there was no reference genome of any of its species yet. Credit: Universtiy of Malaga

Evolutionary impact

An analysis of the functionality of genomes, based on extremely rare samples of myxini embryos, carried out in the prestigious laboratory of Professor Shigeru Kuratani of RIKEN; and a study on the possible impact of genome duplications on each vertebrate, developed together with the Professor at the University of Bristol and member of the Royal Society Phil Donoghue, complete this multidisciplinary research that is key to understanding the evolutionary history of vertebrates, since it provides perspectives on the genomic events that, probably, drove the appearance of important characteristics of vertebrates, such as brain structure, sensory organs or neural crest cells, among them, an increase in regulatory complexity, that is, a greater number of switches that turn genes on/off.

Evolution is not as random as previously thought, finds new study

Posted by

0


The coincident relationships of predictable genes and their predictors. The nodes are gene families, or groups of gene families with the same PAP, and the edges are coincidence relationships with the arrow pointing at the node whose presence is predicted by the other. Credit: Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2304934120

A new study has found that evolution is not as unpredictable as previously thought, which could allow scientists to explore which genes could be useful to tackle real-world issues such as antibiotic resistance, disease, and climate change.

The study, which is published in the Proceedings of the National Academy of Sciences (PNAS), challenges the long-standing belief about the unpredictability of evolution and has found that the evolutionary trajectory of a genome may be influenced by its evolutionary history, rather than determined by numerous factors and historical accidents.

The study was led by Professor James McInerney and Dr. Alan Beavan from the School of Life Sciences at the University of Nottingham, and Dr. Maria Rosa Domingo-Sananes from Nottingham Trent University.

“The implications of this research are nothing short of revolutionary,” said Professor McInerney, the lead author of the study. “By demonstrating that evolution is not as random as we once thought, we’ve opened the door to an array of possibilities in synthetic biology, medicine, and environmental science.”

The team carried out an analysis of the pangenome—the complete set of genes within a given species, to answer a critical question of whether evolution is predictable or whether the evolutionary paths of genomes are dependent on their history and so not predictable today.

Using a machine learning approach known as Random Forest, along with a dataset of 2,500 complete genomes from a single bacterial species, the team carried out several hundred thousand hours of computer processing to address the question.

After feeding the data into their high-performance computer, the team first made “gene families” from each of the gene of each genome.

“In this way, we could compare like-with-like across the genomes,” said Dr. Domingo-Sananes.

Once the families had been identified, the team analyzed the pattern of how these families were present in some genomes and absent in others.

“We found that some gene families never turned up in a genome when a particular other gene family was already there, and on other occasions, some genes were very much dependent on a different gene family being present.”

In effect, the researchers discovered an invisible ecosystem where genes can cooperate or can be in conflict with one another.

“These interactions between genes make aspects of evolution somewhat predictable and furthermore, we now have a tool that allows us to make those predictions,” adds Dr. Domingo-Sananes.

Dr. Beavan said, “From this work, we can begin to explore which genes ‘support’ an antibiotic resistance gene, for example. Therefore, if we are trying to eliminate antibiotic resistance, we can target not just the focal gene, but we can also target its supporting genes.

“We can use this approach to synthesize new kinds of genetic constructs that could be used to develop new drugs or vaccines. Knowing what we now know has opened the door to a whole host of other discoveries.”

The implications of the research are far-reaching and could lead to:

  • Novel Genome Design—allowing scientists to design synthetic genomes and providing a roadmap for the predictable manipulation of genetic material.
  • Combating Antibiotic Resistance—Understanding the dependencies between genes can help identify the ‘supporting cast’ of genes that make antibiotic resistance possible, paving the way for targeted treatments.
  • Climate Change Mitigation—Insights from the study could inform the design of microorganisms engineered to capture carbon or degrade pollutants, thereby contributing to efforts to combat climate change.
  • Medical Applications—The predictability of gene interactions could revolutionize personalized medicine by providing new metrics for disease risk and treatment efficacy.

A New FDA Approval Furthers the Role of Genomics in Cancer Care

Posted by

0


A recent drug approval by the Food and Drug Administration (FDA) marks another milestone in the treatment of cancer. The action by FDA expands the growing list of approved uses for the immune checkpoint inhibitor pembrolizumab (Keytruda).

In this case, it is now approved to treat some adults or children with advanced cancer, regardless of the type of cancer they have, if the patient’s tumor has a large number of genetic mutations—also called a tumor mutational burden-high (TMB-H) cancer. 

Because this is what is known as an accelerated approval, this new indication for pembrolizumab must be confirmed in additional studies. There also are a number of factors for oncologists to consider when deciding whether this treatment is a good option for their patients. I’ll return to those issues later. 

But from a broader perspective, this new approval represents a continued march toward the use of genomics to guide cancer treatment, including for children with cancer. 

It reinforces the idea that, as a routine matter, oncologists should be discussing tumor genomic testing (or biomarker testing) with their patients with advanced cancer, in particular those for whom there are no effective standard-of-care treatments. This applies to testing not only for biomarkers like TMB that might predict response to immunotherapies, but also for genetic biomarkers that identify those who might benefit from a specific targeted cancer treatment.  

This type of biomarker testing has helped patients with many types of cancers, even hard-to-treat cancers such as brain and pancreatic, by identifying therapies that might be more effective and less toxic for them. But it’s important to note that biomarker testing has important limitations and, clearly, there are many patients who do not benefit from this testing.  

This new approval for pembrolizumab marks the fourth time that FDA has approved a drug to be used in a “tissue-agnostic” manner—that is, for any cancer type—based solely on the results of biomarker testing. Given that there are now many approved cancer therapies whose use requires genomic biomarker testing (via what are known as “companion diagnostics”), I believe that genomic biomarker testing should be strongly considered for all patients with advanced cancers for which no known effective treatments currently exist.

Given this increasing role of genomic biomarker testing in cancer care, it is important to note that many patients do not benefit from molecularly targeted treatments because they are never offered that testing.  

For example, a recent review in lung cancer, where genomic testing is particularly critical for selecting the most appropriate treatments, found that 10%–40% of patients are not being tested for molecular alterations that predict response to FDA-approved therapies, even though such testing is recommended by clinical guidelines. 

This lack of biomarker testing, which can lead to the use of treatments with the potential to markedly improve how long patients live, is concerning. At NCI, we’re particularly worried about the possibility that less genomic biomarker testing in patients from underserved populations could further exacerbate existing cancer-related health disparities.

Learning about Cancer and Tumor Mutational Burden

Having a TMB-H tumor is not a guarantee that pembrolizumab will be effective, but it is an opportunity, based on a robust evidence base that was developed in part by NCI-supported research and investigators.

It’s also important to note that this is not the first tissue-agnostic FDA approval for pembrolizumab. In May 2017, it was approved to treat any cancer that has specific genetic alterations that affect a cell’s ability to repair damaged DNA, known as microsatellite instability high (MSI-H) tumors. MSI-H and TMB-H are related, with most MSI-H tumors also showing increased TMB. The converse, however, is not true—that is, many TMB-H tumors are not MSI-H. 

Moreover, MSI status does not necessarily need to be established through extensive tumor genomic testing, whereas TMB status generally does. So having a drug approval based on TMB is important, because it is more common in tumors than MSI-H, and thus should promote far greater adoption of tumor genomic testing.

Cancer cells that are MSI-H or TMB-H tend to produce a large number of mutant proteins, which are then often displayed on the cells’ surface as “neoantigens.” Since normal cells do not display such mutant proteins, the production of neoantigens can be a signal that draws the immune system’s attention. That, in turn, can increase the likelihood that treatments like pembrolizumab, which strengthen the anti-tumor immune response, will help immune cells kill those tumors.

In the clinical trial on which FDA based this new approval, called KEYNOTE-158, nearly 30% of patients with TMB-H tumors had a response to treatment—meaning they experienced at least 30% reduction in the size of their tumors—including some whose tumors disappeared completely. In contrast, only 6% of patients who were not TMB-H exhibited a response to pembrolizumab. In half of the participants who responded to the treatment, their tumors did not begin to grow again for at least 2 years!

Although patients on KEYNOTE-158 were not randomly assigned to an alternative therapy or placebo, these types of sustained treatment responses among patients with solid tumors are extremely rare with standard chemotherapies. 

In addition, most participants in KEYNOTE-158 had received numerous other therapies and had no remaining treatment options known to be effective against their cancers. That’s an important point, because FDA’s new approval applies only to people with advanced cancer without any other standard treatment options. 

In general, tumors in children and young adults with cancer do not have a large number of mutations and are therefore less likely to be TMB-H. But some tumors that arise in children are TMB-H, and this approval now means that such young patients have a new, potentially meaningful treatment option available to them as well.

Contribution of Genomics Research

The role of NCI-supported research in helping to identify TMB as a biomarker of immunotherapy response is particularly gratifying. 

For example, although TMB did not even exist as a concept at the time that The Cancer Genome Atlas (TCGA) was launched, researchers used TCGA data to perform wide-scale analyses of the relationship between tumor mutation numbers and immunotherapy response in the first place. The finding is another example of how building large, high-quality, and diverse sets of research data and making them publicly available can yield unexpected insights that lead to meaningful advances in treatment.

In addition, NCI has had a sustained and successful partnership with Foundation Medicine, the company that developed FoundationOne CDx, the test used to identify patients with TMB-H tumors for this approval. NCI-supported researchers made important contributions to the development of the technologies used by this test. 

As should be expected, though, this is an extremely complicated area of research. Even with the best tests, measuring TMB and deciding what that measurement means for individual patients—in particular, estimating their likelihood of response to immunotherapy—is far from straightforward.

So NCI has been working on other fronts to make further advancements that build on the use of TMB, MSI, and other biomarkers to help guide treatment decisions. For example, NCI has partnered with Friends of Cancer Research and several other organizations on the TMB Harmonization ProjectExit Disclaimer, which is working to standardize how mutational burden is measured in tumors using different technologies and approaches. This project will help to ensure that TMB is used in the most effective manner possible to guide decisions about patient care.

NCI is also supporting research through the Cancer MoonshotSM on the impact of TMB and other biomarkers on how patients respond to immunotherapy. That effort is being carried out by researchers who are part of the Moonshot-funded Cancer Immune Monitoring and Analysis CentersExit Disclaimer and through a large public–private partnership called the PACT initiativeExit Disclaimer.

Good News, But More To Learn

This new approval is exciting, and it will have an immediate impact on patient care. However, it’s important to stress that TMB status is just one piece of information about a tumor. Its relevance to treatment may depend on a number of factors, including a patient’s physical ability and willingness to tolerate further treatment. 

In KEYNOTE-158, most patients with TMB-H tumors didn’t benefit from pembrolizumab, and a small percentage of patients whose tumors had a low TMB did respond to treatment. This suggests we still have more to learn in order to predict who will respond to immunotherapy drugs.

There is evidence, for example, that the extent of TMB required to improve the likelihood of responding to immunotherapy may vary from cancer to cancer. Information such as whether cancer type influences treatment response is important, because no cancer treatment comes without side effects, including financial toxicity. 

Larger studies of pembrolizumab, which are required by FDA as part of an accelerated approval, and other research being supported by NCI can hopefully provide answers to these questions. Those answers can then help patients and their doctors have informed discussions and engage in a true process of shared decision making. For patients with advanced cancer and their families, such discussions are vital.

Especially during these hectic times, one can become cynical. But as I’ve said previously, NCI is committed to addressing the challenges of the COVID-19 pandemic while also supporting the research required to address the most pressing needs for those with cancer and heralding important progress. The expanding role and value of immunotherapy as a cancer treatment is good news for patients, and that’s something I think is worth celebrating.

Spatial CRISPR Genomics of Tumor Microenvironments

Posted by

0


A new spatial functional genomics technology developed by scientists at the Icahn School of Medicine at Mount Sinai, New York, makes it possible to discover genes that regulate cell-extrinsic functions at an unprecedented scale and at single-cell resolution. The technology, called Perturb-map, employs a genetic barcode to mark cancer cells, normal neighboring cells, and components of the tumor microenvironment without removing them from the tissue, thereby preserving spatial architecture.

The authors apply their new platform to knockout different genes in parallel in a mouse model of lung cancer to understand their impact on the growth, cellular architecture, and immune composition of tumors. The team also combines Perturb-map and spatial transcriptomics to analyze CRISPR-edited tumors.

These findings were published on March 14, 2022, in the journal Cell, in an article titled “Spatial CRISPR genomics identifies regulators of the tumor microenvironment.”

Brian Brown, PhD, professor of genetics and genomic sciences at the Icahn School of Medicine at Mount Sinai and the senior author of the study, said, “The paper establishes a new technology that is going to help accelerate the discovery of genes and gene functions that serve to control many different aspects of tumor biology, such as tumor morphology, metastasis, and immunity. For the cancer immunology field, and for the tumor microenvironment field, there are lots of genetic screens that will be made possible that weren’t before.”

Probing beyond the cell

Brown’s team was inspired by the need to identify genes that (1) control extracellular processes that protect cancer cells and (2) that cannot be probed well through existing CRISPR screens, which are best suited to study processes within cells such as genetic mechanisms of cell proliferation, protein expression, and drug resistance.

Brown said, “The spatial information is lost in these [pooled CRISPR] screens. If a particular gene knockout altered the local environment of the cell, for example, by changing the vasculature or by recruiting more T cells, this information is lost because we never see what was outside the cancer cells.”

Perturb-map
Perturb-map combines CRISPR pools, multiplex imaging, and spatial transcriptomics. Dhainaut et al. Cell 2022; 185(7): 1223–1239. e20.

The Perturb-map platform images cancer cells and normal cells in and around the tumor, as well as extracellular molecules like mucins. “We are also able to screen entire classes of genes, for example, genes for cytokines and chemokines, that can’t be screened with existing pooled screens because they operate outside the cell. This is because we don’t have to disrupt the cells from their environment to study how a particular gene knockout altered its local environment,” Brown explained.

A new barcode

Perturb-map detects CRISPR-mediated gene knockouts in tissues using Pro-Code technology that was developed in Brown’s lab and published in a 2018 Cell paper. The platform uses multiplex imaging where tissues are stained with antibodies that detect the barcodes called ‘Pro-Codes.’

“We used Pro-Codes to mark cells carrying different CRISPR guide RNAs. We adopted multiplex imaging techniques—which enable >10 different proteins to be detected on a single tissue section with single-cell resolution—to detect 120 Pro-Code-expressing cancer cells,” Brown said.

This approach allows the spatial resolution of hundreds of tumor lesions with different gene knockouts in situ. Combined with spatial transcriptomics, the platform can determine the molecular state of tumor lesions with different gene knockouts.

For the current study, the investigators created a new set of Pro-Codes with a different scaffold protein that is not membrane-bound but moves into the nucleus. New Pro-Codes, together with a digital pipeline for registering images and segmenting cells, upgraded image analysis in this study.

Spatial mapping of Pro-Code/CRISPR lung tumor lesions.
Spatial mapping of Pro-Code/CRISPR lung tumor lesions.

Lung tumor immunity

Through the application of Perturb-map in animal models, the researchers uncovered insights into lung tumor immunity that could help develop new immunotherapies. Specifically, the authors found loss of SOC1 increased the growth of lung tumors, accompanied by a paradoxical increase in the infiltration of T cells into tumors. They resolved the conundrum by probing further to uncover that SOCS1 knockout leads to a simultaneous increase in PD-L1 on cancer cells that incapacitates T cells that enter the tumor.

Brian Brown, PhD
Brian Brown, PhD, professor of genetics and genomic sciences at the Icahn School of Medicine at Mount Sinai, is the senior author of the study.

“When we treated SOCS1 knockout tumors with a drug that blocks PD-L1, the tumors shrank more than controls,” Brown said. This mechanistic insight could pave the way for pairing PD1/PD-L1 blockade with SOCS1 inhibition as a more effective immunotherapeutic strategy.

In parallel experiments, the investigators found that on cancer cells, the loss of the receptor of a multifunctional cytokine called “transforming growth factor beta”, changed the tumor microenvironment into a slimy mucus-filled pool dotted with fibrous cells that prevented the entry of T cells. The genetic perturbation indicated loss of the Tgfbr2 receptor gene increased the availability of the cytokine that suppresses immune response in the tumor microenvironment.

Next steps

In future studies, Brown’s team intends to diversify to probe tumor immunity in other types of cancer including ovarian, pancreatic, and breast cancers. In these different tumors, the focus of the team continues to be understanding the genes that tumors use to subvert the immune system. In addition to probing cancer cells, the team is applying Perturb-map to study genes that control the biology of immune cells.

Brown’s team has deposited the Pro-Code constructs at Addgene to make them widely available. “We’re looking forward to what others will do with the technology,”
Brown said.

Applications of this new platform could accelerate the discovery of new targets for better cancer therapies.

Lung Ca and Ethnicity: Why Genomics Needs to Step Up

Posted by

0


Research reveals insufficient samples from racial minorities to detect moderately common genomic alterations

The current ethnic demography of the U.S. gives truth to the melting pot metaphor: 61.3% white, 17.8% Hispanic, 13.3% black, 5.7% Asian, and 1.5% Native peoples. Cancer researchers have begun evaluating this demographic breakdown against the available genomic data for carcinomas.

For instance, there’s The Cancer Genome Atlas (TCGA), a collaboration between the National Cancer Institute and the National Human Genome Research Institute (NHGRI) to create multi-dimensional maps of the key genomic changes in 33 types of cancer.

More than 11,000 cancer patients have contributed biospecimens for genomic sequencing and analysis to TCGA, with upwards of 500 samples analyzed for each tumor type, including lung cancer. These large datasets are needed to provide statistical power to produce a comprehensive genomic profile of each cancer. A large sample size is also necessary to provide the power to detect mutations against the background rate.

“TCGA project has uncovered numerous uncommon subtypes and mutations across multiple cancer types, and these results are being used to develop new therapies and ultimately improve outcomes for patients with cancer,” noted Joseph Osborne, MD, PhD, of Memorial Sloan Kettering Cancer Center in New York City, and colleagues.

But there is a weakness of the data used to study cancer genomics, and that’s an imbalance in the representation of the various ethnic groups.

Alex Adjei, MD, PhD, editor-in-chief of the Journal of Thoracic Oncology, noted: “The genomic revolution has led to the sequencing of lung cancer specimens in large consortia such as TCGA in the United States, that have provided useful genomic information to drive therapeutic as well as other research in lung cancer. However, tumors from under-represented minorities in the United States such as blacks and Hispanics were under-represented in these samples. This has meant that the mutational profiles of lung cancer from these populations are not accurately documented.”

Researchers have tackled this disparity by taking a closer look at how databases like TCGA and others can increase the sample size to better represent the population. As Osborne’s group remarked, “Without adequate representation of racial minorities within massive sequencing efforts, healthcare disparities may inadvertently be increased, because race-specific mutational patterns are unable to be appreciated.”

‘Avoid Widening the Gap’

“It is probable, but poorly understood, that ethnic diversity is related to the pathogenesis of cancer, and may have an impact on the generalizability of findings from TCGA to racial minorities,” Osborne et al continued. “Despite the important benefits that continue to be gained from genomic sequencing, dedicated efforts are needed to avoid widening the already pervasive gap in healthcare disparities.”

The team reviewed ethnic data in TCGA from 5,729 samples in 10 of the 33 available tumor types, including lung adenocarcinoma and lung squamous cell carcinoma. They used the estimated median somatic mutational frequency for each tumor type by racial ethnicity to calculate the samples needed beyond TCGA to detect a 5% and 10% mutational frequency over the background somatic mutation frequency.

For patients of white ethnicity, TCGA is very powerful, the authors said. All tumor types from white patients contained enough samples to detect a 10% mutational frequency. Of the 5,729 samples analyzed by the team 77% (4,389) came from white patients — an overrepresentation of white patients compared with their percentage of the U.S. population, they pointed out.

“This is in contrast to all other racial ethnicities, for which group-specific mutations with 10% frequency would be detectable only for black patients with breast cancer. Group-specific mutations with 5% frequency would be undetectable in any racial minority, but detectable in white patients for all cancer types except lung (adenocarcinoma and squamous cell carcinoma) and colon cancer.”

The median somatic mutation frequency (per Mb) was 8.1 for lung adenocarcinoma and 9.9 for lung squamous cell carcinoma.

Black ethnicity comprised 12% (660) of patients, Asian were 3% (173), Hispanic made up 3% (149), and less than 0.5% combined were from Native Peoples of the 5,729 TCGA samples analyzed.

“As we demonstrate, despite the approximately proportional relative sample size of many demographic minorities within TCGA when compared with the U.S. population, the absolute sample size of these minorities is inadequate to capture even relatively common somatic mutations that are specific to those groups,” the authors wrote. “Still, TCGA can be commended for their enrollment of racial minorities that has been far more successful than many clinical trial efforts.”

The investigators cited non-small cell lung cancer (NSCLC) and the epidermal growth factor receptor (EGFR) mutation as an example of a carcinoma where ethnicity-specific data made a difference. The phase III ISEL trial failed to show a benefit of treatment with gefitinib (Iressa) in a predominantly white cohort. But there was a significant overall survival benefit in Asian patients.

“These observations are explained by the PIONEER study, a multinational epidemiologic prospective study that demonstrated that EGFR mutations are present in 51.4% of stage IIIB or IV lung adenocarcinomas among Asian patients, in contrast to approximately 20% in white and African-American patients,” the researchers said. “Given the potential for disparate tumor biology by race, we must critically evaluate the generalizability of new discoveries to all patients.”

NSCLC and Hispanics

Giuseppe Giaccone, MD, PhD, co-leader of the Experimental Therapeutics Program at the Lombardi Comprehensive Cancer Center of Georgetown University Medical Center in Washington, D.C., and colleagues sought to narrow the Hispanic cancer genomic knowledge gap by assessing EGFR mutations (exons 18-21) among NSCLC patients at seven institutions in the U.S. and Latin America.

Samples were obtained from 642 patients; 75% (480) of the samples had EGFR mutation analysis successfully performed. The ethnic breakdown of the samples was:

  • 66% (318) non-Latino whites
  • 19% (90) Latino
  • 7% (35) non-Latino Asians
  • 6% (30) non-Latino blacks
  • 2% other races/ethnicities

EGFR mutations were found in 23% (21) of the Latino cohort, with varying frequencies according to the country of origin. Latinos from Peru demonstrated the highest frequency at 37%, followed by the U.S. at 23%, Mexico at 18%, Venezuela at 10%, and Bolivia at 8%.

The researchers found a significant difference in the frequency of EGFR mutations among the different racial and ethnic subgroups analyzed (P < 0.001), with non-Latino Asians having the highest frequency at 57%, followed by Latinos at 23%, non-Latino whites at 19%, and non-Latino blacks at 10%. Patients from Peru had an overall higher frequency of mutations (37%) than all other Latinos (17%), but this difference exhibited only a trend toward significance (P = 0.058).

There were two significant study limitations, the authors said: First, Latino patient enrollment in the U.S. was low (30 patients, 7%) despite a study protocol specifically targeted toward Latino enrollment. In addition, although several large Latin American cancer centers participated, they also had low Latino enrollment.

“This problem highlights the significant difficulties of research collaborations with developing countries in which resource constraints, logistic, and legal challenges may significantly affect enrollment,” the authors stated.

Second, the study did not account for the significant racial and genetic differences within the Latino population. The authors did not collect information on race in the Latino population, nor did they perform genetic ancestry analyses or germline ancestry informative markers that could characterize genetic origin within admixed populations.

“It is possible that we may have primarily sampled a subset of Latino patients with NSCLC, such as the Latino white population. Because this population is similar, in terms of genetic ancestry, to the non-Latino white population in the U.S., this may have obscured a potential difference in EGFR mutation frequency between the two groups.”

The authors acknowledged that Latinos with Native peoples ancestry are of special interest, given that they represent the majority population in Mexico, Central America, and parts of South America (such as Peru), and Latinos from these geographic areas comprise the largest subgroup of Latinos in the U.S.

Citing the high frequency (37%) of EGFR mutations found in Peru, the investigators said they believe this may be an indication there may be a higher EGFR mutation frequency among Latinos defined by a high Native Peoples ancestry. Or, it may be related to a sampling of the Peruvian population of Chinese and Japanese descent, which is among the largest in Latin America.

“Although we did not observe a difference in the frequency of EGFR mutations between Latinos and non-Latinos, our results should be interpreted with caution, given the significant limitations of the study,” the researchers wrote.

Latino Lung Registry

In an effort to address the lack of genomic data from Hispanic/Latino patients with lung cancer, the Latino Lung Cancer Registry was recently established. It is a multinational effort among the University of South Florida in Tampa; Ponce Health Sciences University in Ponce, Puerto Rico; and Universidad Peruana Cayetano Heredia in Lima, Peru.

The registry currently has NSCLC tumor samples from 163 Hispanic/Latino patients. The ethnic background of the Hispanic/Latino patients in the registry is reported as 67% European, 21% Native peoples, and 12% African. Patients are clustered into ancestral groups on the basis of ancestry informative marker analyses.

In another study, Nicholas Gimbrone, of Lee Moffitt Cancer Center and Research Institute in Tampa, FL, and colleagues from the Latino Lung Cancer Registry performed targeted exome sequencing of the registry samples to determine how ethnicity may affect the genetic aberrations found in NSCLC. The mutation frequencies were compared with those in a similar cohort of non-Hispanic white (NHW) patients. The adenocarcinomas (120) in the Hispanic/Latino group had EGFR mutations in 31% versus 17% in the NHW group (P<0.001).

“Our data suggest that the increase in EGFR mutations within our [Hispanic/Latino] cohort is driven by females, with 48% having EGFR mutations,” the authors wrote.

In addition, they said, the data suggests that relative to European ancestry, Native peoples ancestry correlates with low rates of tumor protein p53 (TP53) and serine/threonine kinase 11 (STK11) mutations and high rates of EGFR mutations and that African ancestry correlates to low rates of KRAS mutations.

“This observation may point to a connection to a genetic component from Asia-Pacific migration, because it is known that the EGFR mutation rate is high among Asian patients,” the authors stated.

Study limitations were the various tissue sources and sequencing technologies utilized by the participating institutions; the incomplete clinical data for several samples; and the lack of age, tumor stage, and outcome data for all patients. “Substantial variation in the distribution of sex, smoking history, and ancestry is evident between the three Latino cohorts included in the registry, indicating the potential complexity in untangling the factors contributing to driver mutation frequencies,” stated Ann Schwartz, PhD, and Donovan Watza, both from the Barbara Ann Karmanos Cancer Institute in Detroit, in an accompanying editorial.

They noted that the formation of the Latino Lung Cancer Registry represents progress in addressing the dearth of genomic cancer data in the Hispanic/Latino population, but cautioned that additional funding, enrollment, and data collection will be necessary for this registry to reach maturity.

The First Book To Be Encoded in DNA.

Posted by

0


Two Harvard scientists have produced 70 billion copies of a book in DNA code –and it’s smaller than the size of your thumbnail.
Despite the fact there are 70 billion copies of it in existence, very few people have actually read the book Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves in DNA, by George Church and Ed Regis. The reason? It is written in the basic building blocks of life: Deoxyribonucleic acid, or DNA.

Church, along with his colleague Sriram Kosuri, both molecular geneticists from the Wyss Institute for Biomedical Engineering at Harvard, used the book to demonstrate a breakthrough in DNA data storage. By copying the 53,000 word book (alongside 11 jpeg images and a computer program) they’ve managed to squeeze a thousand times more data than ever previously encoded into strands of DNA, as reported in the August 17 issue of the journal Science. (To give you some idea of how much information we’re talking about, 70 billion copies is more than three times the total number of copies for the next 200 most popular books in the world combined.)

Part of DNA’s genius is just how conspicuously small it is: so dense and energy efficient that one gram of the stuff can hold 455 billion gigabytes. Four grams could in theory hold ever scrap of data the entire world produces in a year. Couple this with a theoretical lifespan of 3.5 billion years and you have a revolution in data storage, with wide ranging implications for the amount of information we could record and store.

Don’t expect your library to transform from paperbacks to vials of DNA anytime soon though. “It took a decade to work out the next generation of reading and writing of DNA – I’ve been working on reading for 38 years, and writing since the 90s,” Church tells TIME.

The actual work of encoding the book into DNA and then decoding it and copying it only took a couple weeks. “I did it with my own two hands!” says Dr. Church, “which is very rare to have that kind of time to spend doing something like this.” Church and Kosuri took a computer file of Regenesis and converted it into binary code — strings of ones and zeroes. They then translated that code into the basic building blocks of DNA. “The 1s stand for adenine (A) or cytosine (C) and the zero for guanine (G) and thymine (T),” says Kosuri.  Using a computer program, this translation was simple.

While the future implications and applications are not yet clear, the DNA storage industry is moving at an incredible speed. “Classical electronic technology is moving forward something like 1.5 fold per year,” says Dr. Church, “whereas reading and writing DNA is improving roughly ten fold per year. We’ve already had a million-fold improvement in the past few years, which is shocking.”

Given that the genomics field has attracted its fair share of criticism — witness, for example, the firestorm that greeted biologist Craig Venter and his colleagues when they created the first synthetic cell in 2010 — there are ethical questions to address. Dr. Church and co-author Ed Regis have decided not to include a DNA insert of the book with the actual paper copy when it comes out in October because of this sensitivity.

“We’re always trying to think proactively about the ethical, social and economic implications in this line of work,” says Dr. Church. He explains that the risks are relatively small, but both he and Dr. Kosuri mention that if it is possible to encode a book using DNA encode, it is also theoretically possible to encode a virus–though this would be a far-fetched scenario.

“The chances that something bad will come out of this is so small,” says Dr. Kosuri. “If someone really nefarious wanted to make a virus they would have to use a much larger chunk of DNA to encode function.”

Why make 70 billion copies of the book? “Oh that was a bit of fun,” says Dr. Church. “We calculated the total copies of the top 200 books of all time, including A Tale of Two Cities and the Bible and so on, and they add up to about 20 billion. We figured we needed to go well beyond that.”

Source: Time

 
Read more: http://newsfeed.time.com/2012/08/20/the-first-book-to-be-encoded-in-dna/#ixzz246tbt1He