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A Global Look at Cancer Genomes

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Cancer Genomics

Cancer is a disease of the genome. It can be driven by many different types of DNA misspellings and rearrangements, which can cause cells to grow uncontrollably. While the first oncogenes with the potential to cause cancer were discovered more than 35 years ago, it’s been a long slog to catalog the universe of these potential DNA contributors to malignancy, let alone explore how they might inform diagnosis and treatment. So, I’m thrilled that an international team has completed the most comprehensive study to date of the entire genomes—the complete sets of DNA—of 38 different types of cancer.

Among the team’s most important discoveries is that the vast majority of tumors—about 95 percent—contained at least one identifiable spelling change in their genomes that appeared to drive the cancer [1]. That’s significantly higher than the level of “driver mutations” found in past studies that analyzed only a tumor’s exome, the small fraction of the genome that codes for proteins. Because many cancer drugs are designed to target specific proteins affected by driver mutations, the new findings indicate it may be worthwhile, perhaps even life-saving in many cases, to sequence the entire tumor genomes of a great many more people with cancer.

The latest findings, detailed in an impressive collection of 23 papers published in Nature and its affiliated journals, come from the international Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. Also known as the Pan-Cancer Project for short, it builds on earlier efforts to characterize the genomes of many cancer types, including NIH’s The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC).

In these latest studies, a team including more than 1,300 researchers from around the world analyzed the complete genomes of more than 2,600 cancer samples. Those samples included tumors of the brain, skin, esophagus, liver, and more, along with matched healthy cells taken from the same individuals.

In each of the resulting new studies, teams of researchers dug deep into various aspects of the cancer DNA findings to make a series of important inferences and discoveries. Here are a few intriguing highlights:

• The average cancer genome was found to contain not just one driver mutation, but four or five.

• About 13 percent of those driver mutations were found in so-called non-coding DNA, portions of the genome that don’t code for proteins [2].

• The mutations arose within about 100 different molecular processes, as indicated by their unique patterns or “mutational signatures.” [3,4].

• Some of those signatures are associated with known cancer causes, including aberrant DNA repair and exposure to known carcinogens, such as tobacco smoke or UV light. Interestingly, many others are as-yet unexplained, suggesting there’s more to learn with potentially important implications for cancer prevention and drug development.

• A comprehensive analysis of 47 million genetic changes pieced together the chronology of cancer-causing mutations. This work revealed that many driver mutations occur years, if not decades, prior to a cancer’s diagnosis, a discovery with potentially important implications for early cancer detection [5].

The findings represent a big step toward cataloging all the major cancer-causing mutations with important implications for the future of precision cancer care. And yet, the fact that the drivers in 5 percent of cancers continue to remain mysterious (though they do have RNA abnormalities) comes as a reminder that there’s still a lot more work to do. The challenging next steps include connecting the cancer genome data to treatments and building meaningful predictors of patient outcomes.

To help in these endeavors, the Pan-Cancer Project has made all of its data and analytic tools available to the research community. As researchers at NIH and around the world continue to detail the diverse genetic drivers of cancer and the molecular processes that contribute to them, there is hope that these findings and others will ultimately vanquish, or at least rein in, this Emperor of All Maladies.

References:

[1] Pan-Cancer analysis of whole genomes. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Nature. 2020 Feb;578(7793):82-93.

[2] Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Rheinbay E et al; PCAWG Consortium. Nature. 2020 Feb;578(7793):102-111.

[3] The repertoire of mutational signatures in human cancer. Alexandrov LB et al; PCAWG Consortium. Nature. 2020 Feb;578(7793):94-101.

[4] Patterns of somatic structural variation in human cancer genomes. Li Y et al; PCAWG Consortium. Nature. 2020 Feb;578(7793):112-121.

[5] The evolutionary history of 2,658 cancers. Gerstung M, Jolly C, Leshchiner I, Dentro SC et al; PCAWG Consortium. Nature. 2020 Feb;578(7793):122-128.

Links:

The Genetics of Cancer (National Cancer Institute/NIH)

Precision Medicine in Cancer Treatment (NCI)

ICGC/TCGA Pan-Cancer Project

The Cancer Genome Atlas Program (NIH)

NCI and the Precision Medicine Initiative (NCI)

NIH Support: National Cancer Institute, National Human Genome Research Institute


Widening Gap in U.S. Life Expectancy

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Map of life expectancies

Caption: Life expectancy at birth by county, 2014. Life expectancy into 80s (blue), 70s (green, yellow, orange), 60s (red).

Americans are living longer than ever before, thanks in large part to NIH-supported research. But a new, heavily publicized study shows that recent gains in longevity aren’t being enjoyed equally in all corners of the United States. In fact, depending on where you live in this great country, life expectancy can vary more than 20 years—a surprisingly wide gap that has widened significantly in recent decades.

Researchers attribute this disturbing gap to a variety of social and economic influences, as well as differences in modifiable behavioral and lifestyle factors, such as obesity, inactivity, and tobacco use. The findings serve as a sobering reminder that, despite the considerable progress made possible by biomedical science, more research is needed to figure out better ways of addressing health disparities and improving life expectancy for all Americans.

In the new study published in JAMA Internal Medicine, a research team, partially funded by NIH, found that the average American baby born in 2014 can expect to live to about age 79 [1]. That’s up from a national average of about 73 in 1980 and around 68 in 1950. However, babies born in 2014 in remote Oglala Lakota County, SD, home to the Pine Ridge Indian Reservation, can expect to live only about 66 years. That’s in stark contrast to a child born about 400 miles away in Summit County, CO, where life expectancy at birth now exceeds age 86.


Are E-cigarettes Leading More Kids to Smoke?

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Cigarettes vs. E-Cigarettes

Thinkstock\MilknCoffee

Today, thanks to decades of educational efforts about the serious health consequences of inhaled tobacco, fewer young people than ever smoke cigarettes in the United States. So, it’s interesting that a growing of number of middle and high school kids are using e-cigarettes—electronic devices that vaporize flavored liquid that generally contains nicotine.

E-cigarettes come with their own health risks, including lung inflammation, asthma, and respiratory infections. But their supporters argue that “vaping,” as it’s often called, might provide an option that would help young people steer clear of traditional cigarettes and the attendant future risks of lung cancer, emphysema, heart disease, and other serious health conditions. Now, a new NIH-funded study finds that this is—pardon the pun—mostly a pipe dream.

Analyzing the self-reported smoking behaviors of thousands of schoolkids nationwide, researchers found no evidence that the availability of e-cigarettes has served to accelerate the decline in youth smoking. In fact, the researchers concluded the opposite: the popularity of e-cigarettes has led more kids—not fewer—to get hooked on nicotine, which meets all criteria for being an addictive substance.


Largest Study Yet Shows Mother’s Smoking Changes Baby’s Epigenome

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Pregnant woman smoking

Credit: Daniel Berehulak/Getty Images

Despite years of public health campaigns warning of the dangers of smoking when pregnant, many women are unaware of the risk or find themselves unable to quit. As a result, far too many babies are still being exposed in the womb to toxins that enter their mothers’ bloodstreams when they inhale cigarette smoke. Among the many infant and child health problems that have been linked to maternal smoking are premature birth, low birth weight, asthma, reduced lung function, sudden infant death syndrome (SIDS), and cleft lip and/or palate.

Now, a large international study involving NIH-supported researchers provides a biological mechanism that may explain how exposure to cigarette toxins during fetal development can produce these health problems [1]. That evidence centers on the impact of the toxins on the epigenome of the infant’s body tissues. The epigenome refers to chemical modifications of DNA (particularly methylation of cytosines), as well as proteins that bind to DNA and affect its function. The genome of an individual is the same in all cells of their body, but the epigenome determines whether genes are turned on or off in particular cells. The study found significant differences between the epigenetic patterns of babies born to women who smoked during pregnancy and those born to non-smokers, with many of the differences affecting genes known to play key roles in the development of the lungs, face, and nervous system.


Eradicating Ebola: In U.S. Biomedical Research, We Trust

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BSL-4 environment

Caption: Researcher inside a biosafety level 4 laboratory, which provides the necessary precautions for working with the Ebola virus.
Credit: National Institute of Allergy and Infectious Diseases, NIH

Updated August 28, 2014: Today, the National Institutes of Health (NIH) announced plans to begin initial human testing of an investigational vaccine to prevent Ebola virus disease. Testing of the vaccine, co-developed by NIH’s National Institute of Allergy and Infectious Diseases (NIAID) and GlaxoSmithKline, will begin next week at the NIH Clinical Center in Bethesda, MD.

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As the outbreak of Ebola Virus Disease continues to spread in West Africa, now affecting four countries in the region, I am reminded how fragile life is—and how important NIH’s role is in protecting it.

NIH research has helped us understand how Ebola initially infects people and how it spreads from person to person. Preventing this spread is currently our greatest defense in fighting it. Through research, we know that the Ebola virus is transmitted through direct contact with bodily fluids and is not transmitted through the air like the flu. We also know the symptoms of Ebola and the period during which they can appear. This knowledge has informed how we manage the disease. We know that the virus can be contained and eradicated with early identification, isolation, strict infection control, and meticulous medical care.


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