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Genomics in the Journals: Dec 5, 2013

NEW YORK (GenomeWeb News) – In a study (pdf) in press in eLife, a Harvard University-led team presented findings from their research on mice missing a dozen-and-a-half different long, non-coding RNAs, or lncRNAs.

In an effort to explore the functions of and requirements for lncRNAs from the long, intergenic non-coding RNA, or lincRNA variety, the researchers developed 18 knockout mouse strains, each lacking a different lincRNA.

For mice from five of the resulting strains, they found that this genetic tinkering led to death shortly before or after birth in all or some mice and/or growth defects in others, highlighting the potential functional importance of the non-protein-coding molecules produced from these regions of the genome.

For example, a closer look at the often-lethal defects associated with the absence of a lncRNA called Fendrr revealed problems affecting the development of mouse lung, gut, and heart systems, while unusual patterns in the neocortex of mouse brains turned up in a mouse strain lacking a lncRNA known as linc-Brn1b.

"This study demonstrates that lncRNAs play critical roles in vivo and provides a framework and impetus for future larger scale functional investigation into the roles of lncRNA molecules," Harvard's John Rinn, senior author on the study, and his colleagues wrote.


A Nature Genetics study described a handful of loci that appear to be linked to elevated risk of chronic lymphocytic leukemia, or CLL, in individuals of European ancestry.

Researchers from the Institute of Cancer Research in Sutton and other centers in the UK and Sweden started by doing a genome-wide association study involving 1,271 individuals with CLL and more than 2,500 unaffected controls. From there, they folded in existing data from a past GWAS of CLL for a meta-analysis on 1,739 cases and 5,199 controls. Suspicious SNPs found in those stages of the study were subsequently verified using data for another 1,144 individuals with CLL and 3,151 without.

Along with associations for variants at 22 loci implicated in CLL risk in the past, the team's search led to previously undetected sites on chromosomes 3, 4, 6, and 7 harboring SNPs with significant CLL associations. Several other spots in the genome showed more tenuous ties to CLL.

The study's authors pointed out that "additional studies will be required to decipher the functional basis of these risk loci," but noted that "the proximity of several of the loci to genes having a role at telomeres suggests a plausible mechanism of biological relevance."


A new Science study suggests the chronic autoimmune condition scleroderma, which causes connective tissue thickening, may sometimes stem from individuals' immune response to cancer — particularly tumors containing mutations to the POLR3A gene.

Researchers from Johns Hopkins University used targeted gene sequencing to test tumor and normal samples from scleroderma patients, focusing on genes coding for three of the proteins that tend to be targeted by autoantibodies in those with scleroderma.

Past studies suggested scleroderma patients who produce autoantibodies that target RPC1, a protein encoded by POLR3A, are at increased risk of cancer. But based on the mutation patterns they saw in tumors from individuals with scleroderma — together with findings from follow-up experiments on patient blood, immune cell, and antibody samples — the investigators found clues that genetic changes within cancers could create circumstances that produce scleroderma.

The team compared POLR3A sequences in matched tumor and matched normal samples from eight RPC1 antibody-positive individuals with scleroderma who had been diagnosed with cancer shortly before or after developing scleroderma. Six of those individuals had tumors containing POLR3A mutations.

Such findings hint that individuals' immune systems may start recognizing unusual forms of RBC1 produced by tumors containing POLR3A mutations. That, in turn, could cause scleroderma if the immune system begins attacking versions of the protein found in non-cancerous tissues.

Alterations in POLR3A were absent in tumors from another eight individuals with scleroderma who did not produce antibodies targeting the RPC1 protein, the study authors reported, noting that cancer often appeared many years later in that group.

"Our study results could change the way many physicians evaluate and eventually treat autoimmune diseases like scleroderma," co-corresponding author Antony Rosen, director of rheumatology and vice dean of research at Johns Hopkins University, said in a statement. "Current treatment strategies that are focused on dampening down the immune response in scleroderma could instead be replaced by strategies aimed at finding, diagnosing and treating the underlying cancer."

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.