PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The evolution of unique cranial traits in leporid lagomorphs
items: Superimposed vibration on suspended push-ups
items: Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries
items: Exogenous melatonin improves salt tolerance mainly by regulating the antioxidant system in cyanobacterium Nostoc flagelliforme
items: Spatial variation of parrotfish assemblages at oceanic islands in the western Caribbean: evidence of indirect effects of fishing?
items: Downregulated miRNA-491-3p accelerates colorectal cancer growth by increasing uMtCK expression
items: A pan-cancer analysis of the oncogenic role of ribonucleotide reductase subunit M2 in human tumors
items: A novel nomogram for anastomotic leakage after surgery for rectal cancer: a retrospective study
items: Assessing future shifts in habitat suitability and connectivity to old-growth forests to support the conservation of the endangered giant noctule
items: Investigating isoform switching in RHBDF2 and its role in neoplastic growth in breast cancer

The evolution of unique cranial traits in leporid lagomorphs
type: item
type: AcademicArticle
description: Background The leporid lagomorphs (rabbits and hares) are adapted to running and leaping (some more than others) and consequently have unique anatomical features that distinguish them from ochotonid lagomorphs (pikas) and from their rodent relatives. Two traits that have received some attention are fenestration of the lateral wall of the maxilla and facial tilting. These features are known to correlate with specialised locomotory form in that the faster running species will generally have fenestration that occupies the dorsal and the anteroventral surface of the maxillary corpus and a more acute facial tilt angle. Another feature is an intracranial joint that circumscribes the back of the skull, thought to facilitate skull mobility. This joint separates the anterior portion of the cranium (including the dentition, rostrum and orbit) from the posterior portion of the cranium (which encompasses the occipital and the auditory complex). Aside from the observation that the intracranial joint is absent in pikas (generalist locomotors) and appears more elaborate in genera with cursorial and saltatorial locomotory habits, the evolutionary history, biomechanical function and comparative anatomy of this feature in leporids lacks a comprehensive evaluation. Methodology The present work analysed the intracranial joint, facial tilting and lateral fenestration of the wall of the maxilla in the context of leporid evolutionary history using a Bayesian inference of phylogeny (18 genera, 23 species) and ancestral state reconstruction. These methods were used to gather information about the likelihood of the presence of these three traits in ancestral groups. Results Our phylogenetic analyses found it likely that the last common ancestor of living leporids had some facial tilting, but that the last common ancestor of all lagomorphs included in the dataset did not. We found that it was likely that the last common ancestor of living leporids had fenestration that occupies the dorsal, bu…
format: application/pdf
format: text/html
creator: Amber P. Wood-Bailey
creator: Philip G. Cox
creator: Alana C. Sharp
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.14414
publisher: PeerJ Inc.
rights: © 2022 Wood-Bailey et al.
abstract: Background The leporid lagomorphs (rabbits and hares) are adapted to running and leaping (some more than others) and consequently have unique anatomical features that distinguish them from ochotonid lagomorphs (pikas) and from their rodent relatives. Two traits that have received some attention are fenestration of the lateral wall of the maxilla and facial tilting. These features are known to correlate with specialised locomotory form in that the faster running species will generally have fenestration that occupies the dorsal and the anteroventral surface of the maxillary corpus and a more acute facial tilt angle. Another feature is an intracranial joint that circumscribes the back of the skull, thought to facilitate skull mobility. This joint separates the anterior portion of the cranium (including the dentition, rostrum and orbit) from the posterior portion of the cranium (which encompasses the occipital and the auditory complex). Aside from the observation that the intracranial joint is absent in pikas (generalist locomotors) and appears more elaborate in genera with cursorial and saltatorial locomotory habits, the evolutionary history, biomechanical function and comparative anatomy of this feature in leporids lacks a comprehensive evaluation. Methodology The present work analysed the intracranial joint, facial tilting and lateral fenestration of the wall of the maxilla in the context of leporid evolutionary history using a Bayesian inference of phylogeny (18 genera, 23 species) and ancestral state reconstruction. These methods were used to gather information about the likelihood of the presence of these three traits in ancestral groups. Results Our phylogenetic analyses found it likely that the last common ancestor of living leporids had some facial tilting, but that the last common ancestor of all lagomorphs included in the dataset did not. We found that it was likely that the last common ancestor of living leporids had fenestration that occupies the dorsal, bu…
bibliographic citation: Wood-Bailey et al. (2022) The evolution of unique cranial traits in leporid lagomorphs. PeerJ 10:e14414 https://doi.org/10.7717/peerj.14414
date submitted: 2022-05-16
date accepted: 2022-10-28
issued: 2022-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wood-Bailey
  given name: Amber P.
author list: Agent
  family name: Cox
  given name: Philip G.
author list: Agent
  family name: Sharp
  given name: Alana C.
doi: 10.7717/peerj.14414
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-29
copyright: © 2022 Wood-Bailey et al.
attribution name: Wood-Bailey et al.

Superimposed vibration on suspended push-ups
type: item
type: AcademicArticle
description: Background Superimposition of vibration has been proposed in sports training using several devices and methods to enhance muscle activation and strength adaptations. Due to the popularity of suspension training, vibration systems have recently been developed to increase the effects of this training method. The present cross-sectional study aims to examine the effects of superimposing vibration on one of the most popular exercises in strength and conditioning programs: push-ups. Methods Twenty-eight physically active men and women executed push-ups in three suspended conditions (non-vibration, vibration at 25 Hz, and vibration at 40 Hz). OMNI-Res scale was registered, and surface electromyographic signals were measured for the activity of the right and left external oblique, anterior deltoid, triceps brachii, sternal, and clavicular heads of the pectoralis major. Results A linear mixed model indicated a significant fixed effect for vibration at 25 Hz and 40 Hz on muscle activity. Suspended push-ups with superimposed vibration (25 Hz and 40 Hz) showed a significant higher activity on left (25 Hz: p = 0.036, d = 0.34; 40 Hz: p = 0.003, d = 0.48) and right external oblique (25 Hz: p = 0.004, d = 0.36; 40 Hz: p = 0.000, d = 0.59), anterior deltoid (25 Hz: p = 0.032, d = 0.44; 40 Hz: p = 0.003, d = 0.64), and global activity (25 Hz: p = 0.000, d = 0.55; 40 Hz: p = 0.000, d = 0.83) compared to non-vibration condition. Moreover, OMNI-Res significant differences were found at 25 Hz (6.04 ± 0.32, p = 0.000 d = 4.03 CI = 3.27, 4.79) and 40 Hz (6.21 ± 0.36 p = 0.00 d = 4.29 CI = 3.49, 5.08) compared to the non-vibration condition (4.75 ± 0.32). Conclusion Superimposing vibration is a feasible strategy to enhance the muscle activity of suspended push-ups.
format: application/pdf
format: text/html
creator: Bernat Buscà
creator: Joan Aguilera-Castells
creator: Jordi Arboix-Alió
creator: Adrià Miró
creator: Azahara Fort-Vanmeerhaeghe
creator: Pol Huertas
creator: Javier Peña
subject: Anatomy and Physiology
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.14435
publisher: PeerJ Inc.
rights: © 2022 Buscà et al.
abstract: Background Superimposition of vibration has been proposed in sports training using several devices and methods to enhance muscle activation and strength adaptations. Due to the popularity of suspension training, vibration systems have recently been developed to increase the effects of this training method. The present cross-sectional study aims to examine the effects of superimposing vibration on one of the most popular exercises in strength and conditioning programs: push-ups. Methods Twenty-eight physically active men and women executed push-ups in three suspended conditions (non-vibration, vibration at 25 Hz, and vibration at 40 Hz). OMNI-Res scale was registered, and surface electromyographic signals were measured for the activity of the right and left external oblique, anterior deltoid, triceps brachii, sternal, and clavicular heads of the pectoralis major. Results A linear mixed model indicated a significant fixed effect for vibration at 25 Hz and 40 Hz on muscle activity. Suspended push-ups with superimposed vibration (25 Hz and 40 Hz) showed a significant higher activity on left (25 Hz: p = 0.036, d = 0.34; 40 Hz: p = 0.003, d = 0.48) and right external oblique (25 Hz: p = 0.004, d = 0.36; 40 Hz: p = 0.000, d = 0.59), anterior deltoid (25 Hz: p = 0.032, d = 0.44; 40 Hz: p = 0.003, d = 0.64), and global activity (25 Hz: p = 0.000, d = 0.55; 40 Hz: p = 0.000, d = 0.83) compared to non-vibration condition. Moreover, OMNI-Res significant differences were found at 25 Hz (6.04 ± 0.32, p = 0.000 d = 4.03 CI = 3.27, 4.79) and 40 Hz (6.21 ± 0.36 p = 0.00 d = 4.29 CI = 3.49, 5.08) compared to the non-vibration condition (4.75 ± 0.32). Conclusion Superimposing vibration is a feasible strategy to enhance the muscle activity of suspended push-ups.
bibliographic citation: Buscà et al. (2022) Superimposed vibration on suspended push-ups. PeerJ 10:e14435 https://doi.org/10.7717/peerj.14435
date submitted: 2022-08-01
date accepted: 2022-10-31
issued: 2022-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buscà
  given name: Bernat
author list: Agent
  family name: Aguilera-Castells
  given name: Joan
author list: Agent
  family name: Arboix-Alió
  given name: Jordi
author list: Agent
  family name: Miró
  given name: Adrià
author list: Agent
  family name: Fort-Vanmeerhaeghe
  given name: Azahara
author list: Agent
  family name: Huertas
  given name: Pol
author list: Agent
  family name: Peña
  given name: Javier
doi: 10.7717/peerj.14435
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-29
copyright: ©2022 Buscà et al.
attribution name: Buscà et al.

Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries
type: item
type: AcademicArticle
description: Background Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV). The objective of this study was to characterize the vaginal microbiomes across a more diverse intercontinental group of women (N = 151) of different ethnicities (African American, African Kenyan, Afro-Caribbean, Asian Indonesian and Caucasian German) using 16S rRNA gene sequence analysis to determine their structures and offer a comprehensive description of the non-Lactobacillus dominant CSTs and subtypes. Results In this study, the bacterial composition of the vaginal microbiomes differed significantly among the ethnic groups. Lactobacillus spp. (L. crispatus and L. iners) dominated the vaginal microbiomes in African American women (91.8%) compared to European (German, 42.4%), Asian (Indonesian, 45.0%), African (Kenyan, 34.4%) and Afro-Caribbean (26.1%) women. Expanding on CST classification, three subtypes of CST IV (CST IV-A, IV-B and IV-C) (N = 56, 37.1%) and four additional CSTs were described: CST VI Gardnerella vaginalis—dominant (N = 6, 21.8%); CST VII (Prevotella—dominant, N = 1, 0.66%); CST VIII (N = 9, 5.96%), resembling aerobic vaginitis, was differentiated by a high proportion of taxa such as Enterococcus, Streptococcus and Staphylococcus (relative abundance [RA] > 50%) and CST IX (N = 7, 4.64%) dominated by genera other than Lactobacillus, Gardnerella or Prevotella (e.g., Bifidobacterium breve and Anaerococcus vaginalis). Within the vaginal microbiomes, 32 “taxa with high pathogenic potential” (THPP) were identified. Collectively, THPP (mean RA ~5.24%) negatively correlated (rs = −0.68, p < 2.2e−16) with Lactobacillus species but not significantly with Gardnerella/Prevotella spp. combined (r = −0.13, p = 0.1). However, at the individual level, Mycoplasma hominis …
format: application/pdf
format: text/html
creator: Orville St. E. Roachford
creator: Angela T. Alleyne
creator: Karen E. Nelson
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
subject: Women’s Health
description: doi:10.7717/peerj.14449
publisher: PeerJ Inc.
rights: © 2022 Roachford et al.
abstract: Background Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV). The objective of this study was to characterize the vaginal microbiomes across a more diverse intercontinental group of women (N = 151) of different ethnicities (African American, African Kenyan, Afro-Caribbean, Asian Indonesian and Caucasian German) using 16S rRNA gene sequence analysis to determine their structures and offer a comprehensive description of the non-Lactobacillus dominant CSTs and subtypes. Results In this study, the bacterial composition of the vaginal microbiomes differed significantly among the ethnic groups. Lactobacillus spp. (L. crispatus and L. iners) dominated the vaginal microbiomes in African American women (91.8%) compared to European (German, 42.4%), Asian (Indonesian, 45.0%), African (Kenyan, 34.4%) and Afro-Caribbean (26.1%) women. Expanding on CST classification, three subtypes of CST IV (CST IV-A, IV-B and IV-C) (N = 56, 37.1%) and four additional CSTs were described: CST VI Gardnerella vaginalis—dominant (N = 6, 21.8%); CST VII (Prevotella—dominant, N = 1, 0.66%); CST VIII (N = 9, 5.96%), resembling aerobic vaginitis, was differentiated by a high proportion of taxa such as Enterococcus, Streptococcus and Staphylococcus (relative abundance [RA] > 50%) and CST IX (N = 7, 4.64%) dominated by genera other than Lactobacillus, Gardnerella or Prevotella (e.g., Bifidobacterium breve and Anaerococcus vaginalis). Within the vaginal microbiomes, 32 “taxa with high pathogenic potential” (THPP) were identified. Collectively, THPP (mean RA ~5.24%) negatively correlated (rs = −0.68, p < 2.2e−16) with Lactobacillus species but not significantly with Gardnerella/Prevotella spp. combined (r = −0.13, p = 0.1). However, at the individual level, Mycoplasma hominis …
bibliographic citation: Roachford et al. (2022) Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries. PeerJ 10:e14449 https://doi.org/10.7717/peerj.14449
date submitted: 2022-04-28
date accepted: 2022-11-01
issued: 2022-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roachford
  given name: Orville St. E.
author list: Agent
  family name: Alleyne
  given name: Angela T.
author list: Agent
  family name: Nelson
  given name: Karen E.
doi: 10.7717/peerj.14449
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-29
copyright: © 2022 Roachford et al.
attribution name: Roachford et al.

Exogenous melatonin improves salt tolerance mainly by regulating the antioxidant system in cyanobacterium Nostoc flagelliforme
type: item
type: AcademicArticle
description: Melatonin is a multifunctional nontoxic bio-stimulant or signaling molecule, generally distributing in different animal and plant organs for invigorating numerous physiological processes against abiotic stresses. In this study, we investigated the potential impact of melatonin on the cyanobacterium Nostoc flagelliforme when exposed to salt stress according to some biochemical and physiological parameters, such as relative electrolyte leakage, PSII activity, and photosynthetic pigments including chlorophyll a, phycocyanobilin, and phycoerythrobilin. We found that melatonin could also maintain K+ homeostasis in salt-stressed N. flagelliforme. These above results confirmed melatonin had multiple functions in hyperosmotic stress and ion stress caused by salinity. Notably, we observed melatonin could regulate the reactive oxygen species (ROS) signal and distinctly decrease the content of hydrogen peroxide and superoxide anion in salt-stressed cells, which were largely attributed to the increased antioxidant enzymes activities including catalase, superoxide dismutase, ascorbate peroxidase, and glutathione reductase. Finally, qRT-PCR analysis showed that melatonin stimulated the expression of antioxidant genes (NfCAT, NfSOD, and NfGR). In general, our findings demonstrate melatonin has beneficial effects on N. flagelliforme under salt stress by intensively regulating antioxidant system.
format: application/pdf
format: text/html
creator: Xiaolong Yuan
creator: Jing An
creator: Tao Zheng
creator: Wenjian Liu
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.14479
publisher: PeerJ Inc.
rights: © 2022 Yuan et al.
abstract: Melatonin is a multifunctional nontoxic bio-stimulant or signaling molecule, generally distributing in different animal and plant organs for invigorating numerous physiological processes against abiotic stresses. In this study, we investigated the potential impact of melatonin on the cyanobacterium Nostoc flagelliforme when exposed to salt stress according to some biochemical and physiological parameters, such as relative electrolyte leakage, PSII activity, and photosynthetic pigments including chlorophyll a, phycocyanobilin, and phycoerythrobilin. We found that melatonin could also maintain K+ homeostasis in salt-stressed N. flagelliforme. These above results confirmed melatonin had multiple functions in hyperosmotic stress and ion stress caused by salinity. Notably, we observed melatonin could regulate the reactive oxygen species (ROS) signal and distinctly decrease the content of hydrogen peroxide and superoxide anion in salt-stressed cells, which were largely attributed to the increased antioxidant enzymes activities including catalase, superoxide dismutase, ascorbate peroxidase, and glutathione reductase. Finally, qRT-PCR analysis showed that melatonin stimulated the expression of antioxidant genes (NfCAT, NfSOD, and NfGR). In general, our findings demonstrate melatonin has beneficial effects on N. flagelliforme under salt stress by intensively regulating antioxidant system.
bibliographic citation: Yuan et al. (2022) Exogenous melatonin improves salt tolerance mainly by regulating the antioxidant system in cyanobacterium Nostoc flagelliforme. PeerJ 10:e14479 https://doi.org/10.7717/peerj.14479
date submitted: 2022-07-01
date accepted: 2022-11-07
issued: 2022-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Xiaolong
author list: Agent
  family name: An
  given name: Jing
author list: Agent
  family name: Zheng
  given name: Tao
author list: Agent
  family name: Liu
  given name: Wenjian
doi: 10.7717/peerj.14479
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-29
copyright: © 2022 Yuan et al.
attribution name: Yuan et al.

Spatial variation of parrotfish assemblages at oceanic islands in the western Caribbean: evidence of indirect effects of fishing?
type: item
type: AcademicArticle
description: Fish populations that bear considerable pressure levels tend to show a decline in the average size of individuals, with the small and unexploited species replacing the large and exploited ones. It is important to carry on with their characterization in areas where they are becoming an important source of food for local human populations. An example of such species are parrotfishes, whose responses to external factors such as fishing need to be understood and predicted. In this study, we used a diver-operated stereo-video to examine individual body size, sex ratios and proportion of species of the parrotfish assemblage and analyze them on a qualitative fishing pressure gradient at four oceanic islands in the Colombian Caribbean. We reported over 10,000 occurrences of eleven parrotfish species, of which we estimated the total length of over 90%, grouping them into three size categories (large, medium, and small). Our data showed a spatial variation of parrotfishes’ abundances, biomass, and individual body size. Observed differences are size-category-dependent throughout the qualitative fishing pressure. In general, the medium-bodied species had smaller sizes, lower abundances, and thus lower contribution to the total parrotfish biomass at the most heavily fished island. Unexpectedly, we found evidence of possible indirect effects over the small-bodied species Scarus iseri and Scarus taeniopterus with significantly greater abundances, and larger sizes of males of S. iseri, at the higher fishing pressure sites. Overall, our data highlights the extent of the spatial variation in the parrotfish communities at relatively short distances, and present new insights into the responses of parrotfish species on a spectrum of body sizes along a gradient of human pressure.
format: application/pdf
format: text/html
creator: Natalia Rivas
creator: Arturo Acero P.
creator: José Tavera
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Marine Biology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.14178
publisher: PeerJ Inc.
rights: © 2022 Rivas et al.
abstract: Fish populations that bear considerable pressure levels tend to show a decline in the average size of individuals, with the small and unexploited species replacing the large and exploited ones. It is important to carry on with their characterization in areas where they are becoming an important source of food for local human populations. An example of such species are parrotfishes, whose responses to external factors such as fishing need to be understood and predicted. In this study, we used a diver-operated stereo-video to examine individual body size, sex ratios and proportion of species of the parrotfish assemblage and analyze them on a qualitative fishing pressure gradient at four oceanic islands in the Colombian Caribbean. We reported over 10,000 occurrences of eleven parrotfish species, of which we estimated the total length of over 90%, grouping them into three size categories (large, medium, and small). Our data showed a spatial variation of parrotfishes’ abundances, biomass, and individual body size. Observed differences are size-category-dependent throughout the qualitative fishing pressure. In general, the medium-bodied species had smaller sizes, lower abundances, and thus lower contribution to the total parrotfish biomass at the most heavily fished island. Unexpectedly, we found evidence of possible indirect effects over the small-bodied species Scarus iseri and Scarus taeniopterus with significantly greater abundances, and larger sizes of males of S. iseri, at the higher fishing pressure sites. Overall, our data highlights the extent of the spatial variation in the parrotfish communities at relatively short distances, and present new insights into the responses of parrotfish species on a spectrum of body sizes along a gradient of human pressure.
bibliographic citation: Rivas et al. (2022) Spatial variation of parrotfish assemblages at oceanic islands in the western Caribbean: evidence of indirect effects of fishing?. PeerJ 10:e14178 https://doi.org/10.7717/peerj.14178
date submitted: 2022-05-26
date accepted: 2022-09-13
issued: 2022-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rivas
  given name: Natalia
author list: Agent
  family name: Acero P.
  given name: Arturo
author list: Agent
  family name: Tavera
  given name: José
doi: 10.7717/peerj.14178
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-28
copyright: © 2022 Rivas et al.
attribution name: Rivas et al.

Downregulated miRNA-491-3p accelerates colorectal cancer growth by increasing uMtCK expression
type: item
type: AcademicArticle
description: Colorectal carcinoma (CRC) is the second most frequent cancer worldwide. MiR-491-3p, a tumor-suppressive microRNA (miRNA, miR), has been revealed to be abnormally expressed in CRC tissues. Meanwhile, up-regulated ubiquitous mitochondrial creatine kinase (uMtCK) contributes to CRC cell proliferation. Here we aim to explore whether aberrant miR-491-3p expression promotes CRC progression through regulating uMtCK. To this end, miR-491-3p and uMtCK levels were assessed in CRC tissues using quantitative real-time PCR (qRT-PCR). The biological roles of miR-491-3p and uMtCK in regulating CRC growth were evaluated using colony formation assay and mouse Xenograft tumour model. We found that miR-491-3p expression was decreased in CRC tissues compared with matched para-cancerous tissues, whereas uMtCK expression was increased. Functionally, miR-491-3p overexpression repressed SW480 cell growth, whereas miR-491-3p depletion accelerated SW620 cell proliferation and growth. Inversely, uMtCK positively regulated CRC cell proliferation. Mechanistically, miR-491-3p post-transcriptionally downregulated uMtCK expression by binding to 3’-UTR of uMtCK. Consequently, restoring uMtCK expression markedly eliminated the role of miR-491-3p in suppressing CRC growth. Collectively, miR-491-3p functions as a tumour suppressor gene by repressing uMtCK, and may be a potential target for CRC treatment.
format: application/pdf
format: text/html
creator: Xingkui Tang
creator: Yukun Lin
creator: Jialin He
creator: Xijun Luo
creator: Junjie Liang
creator: Xianjun Zhu
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.14285
publisher: PeerJ Inc.
rights: © 2022 Tang et al.
abstract: Colorectal carcinoma (CRC) is the second most frequent cancer worldwide. MiR-491-3p, a tumor-suppressive microRNA (miRNA, miR), has been revealed to be abnormally expressed in CRC tissues. Meanwhile, up-regulated ubiquitous mitochondrial creatine kinase (uMtCK) contributes to CRC cell proliferation. Here we aim to explore whether aberrant miR-491-3p expression promotes CRC progression through regulating uMtCK. To this end, miR-491-3p and uMtCK levels were assessed in CRC tissues using quantitative real-time PCR (qRT-PCR). The biological roles of miR-491-3p and uMtCK in regulating CRC growth were evaluated using colony formation assay and mouse Xenograft tumour model. We found that miR-491-3p expression was decreased in CRC tissues compared with matched para-cancerous tissues, whereas uMtCK expression was increased. Functionally, miR-491-3p overexpression repressed SW480 cell growth, whereas miR-491-3p depletion accelerated SW620 cell proliferation and growth. Inversely, uMtCK positively regulated CRC cell proliferation. Mechanistically, miR-491-3p post-transcriptionally downregulated uMtCK expression by binding to 3’-UTR of uMtCK. Consequently, restoring uMtCK expression markedly eliminated the role of miR-491-3p in suppressing CRC growth. Collectively, miR-491-3p functions as a tumour suppressor gene by repressing uMtCK, and may be a potential target for CRC treatment.
bibliographic citation: Tang et al. (2022) Downregulated miRNA-491-3p accelerates colorectal cancer growth by increasing uMtCK expression. PeerJ 10:e14285 https://doi.org/10.7717/peerj.14285
date submitted: 2022-06-17
date accepted: 2022-10-02
issued: 2022-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Xingkui
author list: Agent
  family name: Lin
  given name: Yukun
author list: Agent
  family name: He
  given name: Jialin
author list: Agent
  family name: Luo
  given name: Xijun
author list: Agent
  family name: Liang
  given name: Junjie
author list: Agent
  family name: Zhu
  given name: Xianjun
doi: 10.7717/peerj.14285
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-28
copyright: ©2022 Tang et al.
attribution name: Tang et al.

A pan-cancer analysis of the oncogenic role of ribonucleotide reductase subunit M2 in human tumors
type: item
type: AcademicArticle
description: Background Recent studies have identified ribonucleotide reductase subunit M2 (RRM2) as a putative promoter of tumors. However, no systematic analysis of its carcinogenicity has been conducted. Methods The potential functions of RRM2 in various tumor types were investigated using data from the Genotype-Tissue Expression (GTEx), the Clinical Proteomic Tumor Analysis Consortium (CPTAC), the Cancer Genome Atlas (TCGA), the Human Protein Atlas (HPA), cBioPortal, GEPIA, String, and Gene Set Enrichment Analysis (GSEA). We analyzed the difference in mRNA and protein expression, pathological stage, survival, mutation, tumor microenvironment (TME), and immune cell infiltration in relation to RRM2. Meanwhile, using TCGA and the Tumor Immune Estimation Resource 2 (TIMER 2), the associations between RRM2 expression, immune infiltration, and immune-related genes were assessed. Additionally, CCK-8, Edu and RT-PCR assays were used to validate that RRM2 acts as an oncogene in liver cancer cells and its association with HBx. A cohort of liver hepatocellular carcinoma (LIHC) patients (n=154) from Huashan Hospital was analyzed for the expression of RRM2 and the association between RRM2 and immune infiltration. Results Using the GTEx and TCGA databases, we discovered that 28 tumors expressed RRM2 at significantly higher levels than the corresponding normal tissues. Increased RRM2 expression may be predictive of a poor overall survival (OS) in patients with seven different cancers. GO, KEGG, and GSEA analyses revealed that the biological process of RRM2 was associated with the regulation of carcinogenic processes and immune pathways in a variety of tumor types. The expression of RRM2 was highly correlated with maker genes involved in immune activation and immunosuppression, immune checkpoints, DNA mismatch repair system (MMR), and the infiltration levels of Tregs and macrophages (TAMs), suggesting that the carcinogenic effect of RRM2 may be achieved by regulating immune related genes. M…
format: application/pdf
format: text/html
creator: Yaqun Li
creator: Wenhuan Fu
creator: Zikai Geng
creator: Yun Song
creator: Xionggang Yang
creator: Tianye He
creator: Jian Wu
creator: Bin Wang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.14432
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Recent studies have identified ribonucleotide reductase subunit M2 (RRM2) as a putative promoter of tumors. However, no systematic analysis of its carcinogenicity has been conducted. Methods The potential functions of RRM2 in various tumor types were investigated using data from the Genotype-Tissue Expression (GTEx), the Clinical Proteomic Tumor Analysis Consortium (CPTAC), the Cancer Genome Atlas (TCGA), the Human Protein Atlas (HPA), cBioPortal, GEPIA, String, and Gene Set Enrichment Analysis (GSEA). We analyzed the difference in mRNA and protein expression, pathological stage, survival, mutation, tumor microenvironment (TME), and immune cell infiltration in relation to RRM2. Meanwhile, using TCGA and the Tumor Immune Estimation Resource 2 (TIMER 2), the associations between RRM2 expression, immune infiltration, and immune-related genes were assessed. Additionally, CCK-8, Edu and RT-PCR assays were used to validate that RRM2 acts as an oncogene in liver cancer cells and its association with HBx. A cohort of liver hepatocellular carcinoma (LIHC) patients (n=154) from Huashan Hospital was analyzed for the expression of RRM2 and the association between RRM2 and immune infiltration. Results Using the GTEx and TCGA databases, we discovered that 28 tumors expressed RRM2 at significantly higher levels than the corresponding normal tissues. Increased RRM2 expression may be predictive of a poor overall survival (OS) in patients with seven different cancers. GO, KEGG, and GSEA analyses revealed that the biological process of RRM2 was associated with the regulation of carcinogenic processes and immune pathways in a variety of tumor types. The expression of RRM2 was highly correlated with maker genes involved in immune activation and immunosuppression, immune checkpoints, DNA mismatch repair system (MMR), and the infiltration levels of Tregs and macrophages (TAMs), suggesting that the carcinogenic effect of RRM2 may be achieved by regulating immune related genes. M…
bibliographic citation: Li et al. (2022) A pan-cancer analysis of the oncogenic role of ribonucleotide reductase subunit M2 in human tumors. PeerJ 10:e14432 https://doi.org/10.7717/peerj.14432
date submitted: 2022-07-11
date accepted: 2022-10-31
issued: 2022-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yaqun
author list: Agent
  family name: Fu
  given name: Wenhuan
author list: Agent
  family name: Geng
  given name: Zikai
author list: Agent
  family name: Song
  given name: Yun
author list: Agent
  family name: Yang
  given name: Xionggang
author list: Agent
  family name: He
  given name: Tianye
author list: Agent
  family name: Wu
  given name: Jian
author list: Agent
  family name: Wang
  given name: Bin
doi: 10.7717/peerj.14432
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-28
copyright: ©2022 Li et al.
attribution name: Li et al.

A novel nomogram for anastomotic leakage after surgery for rectal cancer: a retrospective study
type: item
type: AcademicArticle
description: Background Anastomotic leakage remains one of the most common serious complications after rectal cancer surgery. How to predict its occurrence and prevent it remains largely elusive. Objective This study aimed to identify the risk factors of anastomotic leakage and construct a nomogram for predicting postoperative anastomotic leakage in patients with rectal cancer. Methods The data of 406 patients with rectal cancer after gastrointestinal surgery in the Third Affiliated Hospital of Sun Yat-sen University from January 2011 to May 2020 were collected (243 in the training set and 163 in the testing set). Logistic regression was applied to determine the risk factors of postoperative anastomotic leakage of rectal cancer, and a nomogram prediction model was thus established. Predictive performance of the nomogram was evaluated by C-index and area under the receiver-operating characteristic (ROC) curve. Results Logistic regression analysis showed that preoperative bowel obstruction (odds ratio [OR] = 12.846, 95% confidence interval CI [1.441–114.54], p = 0.022) and early first defecation after surgery (OR = 0.501, 95% CI [0.31–0.812], p = 0.005) were independent risk factors, which could be used to develop a nomogram to predict the occurrence of anastomotic leakage accurately. The evaluation of the prediction model shows that the C-index value of the model was 0.955, the area under the ROC curve (AUC) of the training set was 0.820, and the testing set was 0.747, whereas the optimal cut-off point based on the nomogram score was 174.6. Conclusion This nomogram had a good prediction ability for postoperative anastomotic leakage in patients with rectal cancer. It can provide a reference for perioperative treatment and the selection of surgical methods to promote individualized and accurate treatment.
format: application/pdf
format: text/html
creator: Tingzhen Li
creator: Jianglong Huang
creator: Purun Lei
creator: Xiaofeng Yang
creator: Zehong Chen
creator: Peng Chen
creator: Jiancheng Zhai
creator: Xuefeng Guo
creator: Hongbo Wei
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.14437
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Anastomotic leakage remains one of the most common serious complications after rectal cancer surgery. How to predict its occurrence and prevent it remains largely elusive. Objective This study aimed to identify the risk factors of anastomotic leakage and construct a nomogram for predicting postoperative anastomotic leakage in patients with rectal cancer. Methods The data of 406 patients with rectal cancer after gastrointestinal surgery in the Third Affiliated Hospital of Sun Yat-sen University from January 2011 to May 2020 were collected (243 in the training set and 163 in the testing set). Logistic regression was applied to determine the risk factors of postoperative anastomotic leakage of rectal cancer, and a nomogram prediction model was thus established. Predictive performance of the nomogram was evaluated by C-index and area under the receiver-operating characteristic (ROC) curve. Results Logistic regression analysis showed that preoperative bowel obstruction (odds ratio [OR] = 12.846, 95% confidence interval CI [1.441–114.54], p = 0.022) and early first defecation after surgery (OR = 0.501, 95% CI [0.31–0.812], p = 0.005) were independent risk factors, which could be used to develop a nomogram to predict the occurrence of anastomotic leakage accurately. The evaluation of the prediction model shows that the C-index value of the model was 0.955, the area under the ROC curve (AUC) of the training set was 0.820, and the testing set was 0.747, whereas the optimal cut-off point based on the nomogram score was 174.6. Conclusion This nomogram had a good prediction ability for postoperative anastomotic leakage in patients with rectal cancer. It can provide a reference for perioperative treatment and the selection of surgical methods to promote individualized and accurate treatment.
bibliographic citation: Li et al. (2022) A novel nomogram for anastomotic leakage after surgery for rectal cancer: a retrospective study. PeerJ 10:e14437 https://doi.org/10.7717/peerj.14437
date submitted: 2022-08-29
date accepted: 2022-10-31
issued: 2022-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Tingzhen
author list: Agent
  family name: Huang
  given name: Jianglong
author list: Agent
  family name: Lei
  given name: Purun
author list: Agent
  family name: Yang
  given name: Xiaofeng
author list: Agent
  family name: Chen
  given name: Zehong
author list: Agent
  family name: Chen
  given name: Peng
author list: Agent
  family name: Zhai
  given name: Jiancheng
author list: Agent
  family name: Guo
  given name: Xuefeng
author list: Agent
  family name: Wei
  given name: Hongbo
doi: 10.7717/peerj.14437
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-28
copyright: ©2022 Li et al.
attribution name: Li et al.

Assessing future shifts in habitat suitability and connectivity to old-growth forests to support the conservation of the endangered giant noctule
type: item
type: AcademicArticle
description: Background Suitable climate and availability of habitats for roosting, foraging, and dispersing are critical for the long-term persistence of bat species. The giant noctule (Nyctalus lasiopterus) represents one of the lesser-known European bats, especially regarding the environmental factors which shape its distribution. Methodology We integrated climate-based ecological niche models with information about topography and rivers’ network to model weighted suitability for N. lasiopterus in the western Palearctic. The weighted suitability map was then used to estimate connectivity among the distinct occurrence localities of N. lasiopterus, as well as from these latter towards European old-growth forests, under current conditions and different combinations of future timeframes (2030, 2050, 2070) and shared socioeconomic pathways (SSPs 3.70 and 5.85). Results Current weighted suitability is highest in Andalusia, northern Iberia, southwestern France, peninsular Italy, coastal Balkans and Anatolia, with dispersed suitable patches elsewhere. A north-eastward shift of weighted suitability emerges in the considered future scenarios, especially under SSP 5.85. The major current ecological corridors for N. lasiopterus are predicted within a ‘belt’ connecting northern Spain and southwestern France, as well as in the Italian Alps. However, following changes in weighted suitability, connectivity would increase in central-eastern Europe in the future. The bioclimatic niche of the western N. lasiopterus populations does not overlap with those of the central and eastern ones, and it only overlaps with climatic conditions characterizing old-growth forests in western Europe. Conclusions The outcomes of our analyses would help in designing specific conservation measures for the distinct groups of giant noctule populations, favoring the possibility of range expansion and movement towards forested habitats.
format: application/pdf
format: text/html
creator: Mattia Iannella
creator: Urbana Masciulli
creator: Francesco Cerasoli
creator: Michele Di Musciano
creator: Maurizio Biondi
subject: Biogeography
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.14446
publisher: PeerJ Inc.
rights: © 2022 Iannella et al.
abstract: Background Suitable climate and availability of habitats for roosting, foraging, and dispersing are critical for the long-term persistence of bat species. The giant noctule (Nyctalus lasiopterus) represents one of the lesser-known European bats, especially regarding the environmental factors which shape its distribution. Methodology We integrated climate-based ecological niche models with information about topography and rivers’ network to model weighted suitability for N. lasiopterus in the western Palearctic. The weighted suitability map was then used to estimate connectivity among the distinct occurrence localities of N. lasiopterus, as well as from these latter towards European old-growth forests, under current conditions and different combinations of future timeframes (2030, 2050, 2070) and shared socioeconomic pathways (SSPs 3.70 and 5.85). Results Current weighted suitability is highest in Andalusia, northern Iberia, southwestern France, peninsular Italy, coastal Balkans and Anatolia, with dispersed suitable patches elsewhere. A north-eastward shift of weighted suitability emerges in the considered future scenarios, especially under SSP 5.85. The major current ecological corridors for N. lasiopterus are predicted within a ‘belt’ connecting northern Spain and southwestern France, as well as in the Italian Alps. However, following changes in weighted suitability, connectivity would increase in central-eastern Europe in the future. The bioclimatic niche of the western N. lasiopterus populations does not overlap with those of the central and eastern ones, and it only overlaps with climatic conditions characterizing old-growth forests in western Europe. Conclusions The outcomes of our analyses would help in designing specific conservation measures for the distinct groups of giant noctule populations, favoring the possibility of range expansion and movement towards forested habitats.
bibliographic citation: Iannella et al. (2022) Assessing future shifts in habitat suitability and connectivity to old-growth forests to support the conservation of the endangered giant noctule. PeerJ 10:e14446 https://doi.org/10.7717/peerj.14446
date submitted: 2022-07-13
date accepted: 2022-11-01
issued: 2022-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Iannella
  given name: Mattia
author list: Agent
  family name: Masciulli
  given name: Urbana
author list: Agent
  family name: Cerasoli
  given name: Francesco
author list: Agent
  family name: Di Musciano
  given name: Michele
author list: Agent
  family name: Biondi
  given name: Maurizio
doi: 10.7717/peerj.14446
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-28
copyright: © 2022 Iannella et al.
attribution name: Iannella et al.

Investigating isoform switching in RHBDF2 and its role in neoplastic growth in breast cancer
type: item
type: AcademicArticle
description: Background Breast cancer is the second leading cause of cancer-related deaths globally, and its prevalence rates are increasing daily. In the past, studies predicting therapeutic drug targets for cancer therapy focused on the assumption that one gene is responsible for producing one protein. Therefore, there is always an immense need to find promising and novel anti-cancer drug targets. Furthermore, proteases have an integral role in cell proliferation and growth because the proteolysis mechanism is an irreversible process that aids in regulating cellular growth during tumorigenesis. Therefore, an inactive rhomboid protease known as iRhom2 encoded by the gene RHBDF2 can be considered an important target for cancer treatment. Speculatively, previous studies on gene expression analysis of RHBDF2 showed heterogenous behaviour during tumorigenesis. Consistent with this, several studies have reported the antagonistic role of iRhom2 in tumorigenesis, i.e., either they are involved in negative regulation of EGFR ligands via the ERAD pathway or positively regulate EGFR ligands via the EGFR signalling pathway. Additionally, different opinions suggest iRhom2 mediated cleavage of EGFR ligands takes place TACE dependently or TACE independently. However, reconciling these seemingly opposing roles is still unclear and might be attributed to more than one transcript isoform of iRhom2. Methods To observe the differences at isoform resolution, the current strategy identified isoform switching in RHBDF2 via differential transcript usage using RNA-seq data during breast cancer initiation and progression. Furthermore, interacting partners were found via correlation and enriched to explain their antagonistic role. Results Isoform switching was observed at DCIS, grade 2 and grade 3, from canonical to the cub isoform. Neither EGFR nor ERAD was found enriched. However, pathways leading to TACE-dependent EGFR signalling pathways were more observant, specifically MAPK signalling pathways, GP…
format: application/pdf
format: text/html
creator: Mehar Masood
creator: Madahiah Bint E Masood
creator: Noor Us Subah
creator: Maria Shabbir
creator: Rehan Zafar Paracha
creator: Mehak Rafiq
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.14124
publisher: PeerJ Inc.
rights: © 2022 Masood et al.
abstract: Background Breast cancer is the second leading cause of cancer-related deaths globally, and its prevalence rates are increasing daily. In the past, studies predicting therapeutic drug targets for cancer therapy focused on the assumption that one gene is responsible for producing one protein. Therefore, there is always an immense need to find promising and novel anti-cancer drug targets. Furthermore, proteases have an integral role in cell proliferation and growth because the proteolysis mechanism is an irreversible process that aids in regulating cellular growth during tumorigenesis. Therefore, an inactive rhomboid protease known as iRhom2 encoded by the gene RHBDF2 can be considered an important target for cancer treatment. Speculatively, previous studies on gene expression analysis of RHBDF2 showed heterogenous behaviour during tumorigenesis. Consistent with this, several studies have reported the antagonistic role of iRhom2 in tumorigenesis, i.e., either they are involved in negative regulation of EGFR ligands via the ERAD pathway or positively regulate EGFR ligands via the EGFR signalling pathway. Additionally, different opinions suggest iRhom2 mediated cleavage of EGFR ligands takes place TACE dependently or TACE independently. However, reconciling these seemingly opposing roles is still unclear and might be attributed to more than one transcript isoform of iRhom2. Methods To observe the differences at isoform resolution, the current strategy identified isoform switching in RHBDF2 via differential transcript usage using RNA-seq data during breast cancer initiation and progression. Furthermore, interacting partners were found via correlation and enriched to explain their antagonistic role. Results Isoform switching was observed at DCIS, grade 2 and grade 3, from canonical to the cub isoform. Neither EGFR nor ERAD was found enriched. However, pathways leading to TACE-dependent EGFR signalling pathways were more observant, specifically MAPK signalling pathways, GP…
bibliographic citation: Masood et al. (2022) Investigating isoform switching in RHBDF2 and its role in neoplastic growth in breast cancer. PeerJ 10:e14124 https://doi.org/10.7717/peerj.14124
date submitted: 2022-01-21
date accepted: 2022-09-06
issued: 2022-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Masood
  given name: Mehar
author list: Agent
  family name: Masood
  given name: Madahiah Bint E
author list: Agent
  family name: Us Subah
  given name: Noor
author list: Agent
  family name: Shabbir
  given name: Maria
author list: Agent
  family name: Paracha
  given name: Rehan Zafar
author list: Agent
  family name: Rafiq
  given name: Mehak
doi: 10.7717/peerj.14124
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-25
copyright: ©2022 Masood et al.
attribution name: Masood et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359