Ras is mutated in up to 30% of cancers, including 90% of pancreatic ductal adenocarcinomas, causing it to be constitutively GTP-bound, and leading to activation of downstream effectors that promote a ...tumorigenic phenotype. As targeting Ras directly is difficult, there is a significant effort to understand the downstream biological processes that underlie its protumorigenic activity. Here, we show that expression of oncogenic Ras or direct activation of the MAPK pathway leads to increased mitochondrial fragmentation and that blocking this phenotype, through knockdown of the mitochondrial fission-mediating GTPase Drp1, inhibits tumor growth. This fission is driven by Erk2-mediated phosphorylation of Drp1 on Serine 616, and both this phosphorylation and mitochondrial fragmentation are increased in human pancreatic cancer. Finally, this phosphorylation is required for Ras-associated mitochondrial fission, and its inhibition is sufficient to block xenograft growth. Collectively, these data suggest mitochondrial fission may be a target for treating MAPK-driven malignancies.
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•Drp1 is required for xenograft growth•MAPK promotes mitochondrial fragmentation through Drp1•Erk2 phosphorylates Drp1 to promote mitochondrial fission•Drp1 S616 phosphorylation is required for mitochondrial fission and tumor growth
Mitochondrial function is important for the growth of tumors driven by oncogenic Ras or the MAPK pathway. Kashatus et al. demonstrate that activation of these pathways leads to Mek-dependent phosphorylation of the GTPase Drp1 and subsequent mitochondrial fragmentation. They further demonstrate that inhibition of Drp1 or its phosphorylation blocks tumor growth.
In recent years, it has been proposed that unrealistic requirements for academics and medical doctors to publish in scientific journals, combined with monetary publication rewards, have led to forms ...of contract cheating offered by organizations known as paper mills. Paper mills are alleged to offer products ranging from research data through to ghostwritten fraudulent or fabricated manuscripts and submission services. While paper mill operations remain poorly understood, it seems likely that paper mills need to balance product quantity and quality, such that they produce or contribute to large numbers of manuscripts that will be accepted for publication. Producing manuscripts at scale may be facilitated by the use of manuscript templates, which could give rise to shared features such as textual and organizational similarities, the description of highly generic study hypotheses and experimental approaches, digital images that show evidence of manipulation and/or reuse, and/or errors affecting verifiable experimental reagents. Based on these features, we propose practical steps that editors, journal staff, and peer reviewers can take to recognize and respond to research manuscripts and publications that may have been produced with undeclared assistance from paper mills.
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and ...difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Although biobanks can support research across geographic and governance boundaries, biomedical researchers consistently describe preferences for either collaborating with local biobanks or ...establishing their own biobanks. This article summarizes the potential research impacts of local biobank use and suggests how descriptions of biospecimen provenance can be improved in research publications.
Nucleotide sequence reagents are verifiable experimental reagents in biomedical publications, because their sequence identities can be independently verified and compared with associated text ...descriptors. We have previously reported that incorrectly identified nucleotide sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud. Because of the throughput limitations of manual verification of nucleotide sequences, we developed a semi-automated fact checking tool, Seek & Blastn, to verify the targeting or non-targeting status of published nucleotide sequence reagents. From previously described and unknown corpora of 48 and 155 publications, respectively, Seek & Blastn correctly extracted 304/342 (88.9%) and 1066/1522 (70.0%) nucleotide sequences and a predicted targeting/ non-targeting status. Seek & Blastn correctly predicted the targeting/ non-targeting status of 293/304 (96.4%) and 988/1066 (92.7%) of the correctly extracted nucleotide sequences. A total of 38/39 (97.4%) or 31/79 (39.2%) Seek & Blastn predictions of incorrect nucleotide sequence reagent use were correct in the two literature corpora. Combined Seek & Blastn and manual analyses identified a list of 91 misidentified nucleotide sequence reagents, which could be built upon through future studies. In summary, incorrect nucleotide sequence reagents represent an under-recognized source of error within the biomedical literature, and fact checking tools such as Seek & Blastn may help to identify papers and manuscripts affected by these errors.
Human gene research studies that describe wrongly identified nucleotide sequence reagents have been mostly identified in journals of low to moderate impact factor, where unreliable findings could be ...considered to have limited influence on future research. This study examined whether papers describing wrongly identified nucleotide sequences are also published in high-impact-factor cancer research journals. We manually verified nucleotide sequence identities in original
Molecular Cancer
articles published in 2014, 2016, 2018, and 2020, including nucleotide sequence reagents that were claimed to target circRNAs. Using keywords identified in some 2018 and 2020
Molecular Cancer
papers, we also verified nucleotide sequence identities in 2020
Oncogene
papers that studied miRNA(s) and/or circRNA(s). Overall, 3.8% (251/6647) and 4.0% (47/1165) nucleotide sequences that were verified in
Molecular Cancer
and
Oncogene
papers, respectively, were found to be wrongly identified. Wrongly identified nucleotide sequences were distributed across 18% (91/500) original
Molecular Cancer
papers, including 38% (31/82)
Molecular Cancer
papers from 2020, and 40% (21/52) selected
Oncogene
papers from 2020. Original papers with wrongly identified nucleotide sequences were therefore unexpectedly frequent in two high-impact-factor cancer research journals, highlighting the risks of employing journal impact factors or citations as proxies for research quality.
In recent years, it has been proposed that unrealistic requirements for academics and medical doctors to publish in scientific journals, combined with monetary publication rewards, have led to forms ...of contract cheating offered by organizations known as paper mills. Paper mills are alleged to offer products ranging from research data through to ghostwritten fraudulent or fabricated manuscripts and submission services. While paper mill operations remain poorly understood, it seems likely that paper mills need to balance product quantity and quality, such that they produce or contribute to large numbers of manuscripts that will be accepted for publication. Producing manuscripts at scale may be facilitated by the use of manuscript templates, which could give rise to shared features such as textual and organizational similarities, the description of highly generic study hypotheses and experimental approaches, digital images that show evidence of manipulation and/or reuse, and/or errors affecting verifiable experimental reagents. Based on these features, we propose practical steps that editors, journal staff, and peer reviewers can take to recognize and respond to research manuscripts and publications that may have been produced with undeclared assistance from paper mills.
For decades, neuroscientists have used enriched preparations of synaptic particles called synaptosomes to study synapse function. However, the interpretation of corresponding data is problematic as ...synaptosome preparations contain multiple types of synapses and non‐synaptic neuronal and glial contaminants. We established a novel Fluorescence Activated Synaptosome Sorting (FASS) method that substantially improves conventional synaptosome enrichment protocols and enables high‐resolution biochemical analyses of specific synapse subpopulations. Employing knock‐in mice with fluorescent glutamatergic synapses, we show that FASS isolates intact ultrapure synaptosomes composed of a resealed presynaptic terminal and a postsynaptic density as assessed by light and electron microscopy. FASS synaptosomes contain bona fide glutamatergic synapse proteins but are almost devoid of other synapse types and extrasynaptic or glial contaminants. We identified 163 enriched proteins in FASS samples, of which FXYD6 and Tpd52 were validated as new synaptic proteins. FASS purification thus enables high‐resolution biochemical analyses of specific synapse subpopulations in health and disease.
Synopsis
This study describes the establishment, validation, and application of a new fluorescence‐activated sorting method ‐ Fluorescence Activated Synaptosome Sorting or FASS ‐ that allows for purification of glutamatergic synaptosomes from knock‐in mutant mice expressing the fluorescent synaptic marker protein VGLUT1‐Venus.
Fluorescence Activated Synaptosome Sorting from samples of VGLUT1‐Venus knock‐in mice enriches glutamatergic synaptosomes to near homogeneity.
Glutamatergic synaptosomes purified by Fluorescence Activated Synaptosome Sorting contain bona fide glutamatergic synapse proteins but lack other synapse types and glia cell contaminants.
Proteomic analysis of glutamatergic synaptosomes purified by Fluorescence Activated Synaptosome Sorting allows for identifying and cataloguing known and novel components of glutamatergic synapses.
Proteomic analysis of glutamatergic synaptosomes purified by Fluorescence Activated Synaptosome Sorting identified FXYD6 and Tpd52 as novel components of glutamatergic synapses.
A novel Fluorescence Activated Synaptosome Sorting (FASS) approach allows for high‐resolution biochemical analyses of specific synapse subpopulations and identification of 163 proteins that are specifically enriched in FASS‐sorted synaptosomes.
Human gene research generates new biology insights with translational potential, yet few studies have considered the health of the human gene literature. The accessibility of human genes for targeted ...research, combined with unreasonable publication pressures and recent developments in scholarly publishing, may have created a market for low-quality or fraudulent human gene research articles, including articles produced by contract cheating organizations known as paper mills. This review summarises the evidence that paper mills contribute to the human gene research literature at scale and outlines why targeted gene research may be particularly vulnerable to systematic research fraud. To raise awareness of targeted gene research from paper mills, we highlight features of problematic manuscripts and publications that can be detected by gene researchers and/or journal staff. As improved awareness and detection could drive the further evolution of paper mill-supported publications, we also propose changes to academic publishing to more effectively deter and correct problematic publications at scale. In summary, the threat of paper mill-supported gene research highlights the need for all researchers to approach the literature with a more critical mindset, and demand publications that are underpinned by plausible research justifications, rigorous experiments and fully transparent reporting.
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