Biomedical subjects

Qingfeng Yan

Publications and source records attributed to Qingfeng Yan.

13 recordsLinked to original sources

PubMed2025

Comprehensive discovery and functional characterization of the noncanonical proteome.

The systematic identification and functional characterization of noncanonical translation products, such as novel peptides, will facilitate the understanding of the human genome and provide new insights into cell biology. Here, we constructed a high-coverage peptide sequencing reference library with 11,668,944 open reading frames and employed an ultrafiltration tandem mass spectrometry assay to identify novel peptides. Through these methods, we discovered 8945 previously unannotated peptides from normal gastric tissues, gastric cancer tissues and cell lines, nearly half of which were derived from noncoding RNAs. Moreover, our CRISPR screening revealed that 1161 peptides are involved in tumor cell proliferation. The presence and physiological function of a subset of these peptides, selected based on screening scores, amino acid length, and various indicators, were verified through Flag-knockin and multiple other methods. To further characterize the potential regulatory mechanisms involved, we constructed a framework based on artificial intelligence structure prediction and peptide‒protein interaction network analysis for the top 100 candidates and revealed that these cancer-related peptides have diverse subcellular locations and participate in organelle-specific processes. Further investigation verified the interacting partners of pep1-nc-OLMALINC, pep5-nc-TRHDE-AS1, pep-nc-ZNF436-AS1 and pep2-nc-AC027045.3, and the functions of these peptides in mitochondrial complex assembly, energy metabolism, and cholesterol metabolism, respectively. We showed that pep5-nc-TRHDE-AS1 and pep2-nc-AC027045.3 had substantial impacts on tumor growth in xenograft models. Furthermore, the dysregulation of these four peptides is closely correlated with clinical prognosis. Taken together, our study provides a comprehensive characterization of the noncanonical proteome, and highlights critical roles of these previously unannotated peptides in cancer biology.

Humans↗

PubMed2006

Colloidal woodpile structure: three-dimensional photonic crystal with a dual periodicity.

With planar photolithography and self-assembly techniques, multilayer colloidal crystals with a woodpile structure were fabricated. They represent a new kind of photonic crystals, that is, three-dimensional (3D) photonic crystals with a dual periodicity; one comes from the face-centered cubic (fcc) structure within the colloidal crystal strips and the other one results from the periodic arrangement of the colloidal crystal strips.

Journal Article↗

PubMed2006

Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations.

The human mitochondrial 12S ribosomal RNA (rRNA) A1555G mutation has been associated with aminoglycoside-induced and nonsyndromic deafness in many families worldwide. Our previous investigation revealed that the A1555G mutation is a primary factor underlying the development of deafness but is not sufficient to produce a deafness phenotype. However, it has been proposed that nuclear-modifier genes modulate the phenotypic manifestation of the A1555G mutation. Here, we identified the nuclear-modifier gene TRMU, which encodes a highly conserved mitochondrial protein related to transfer RNA (tRNA) modification. Genotyping analysis of TRMU in 613 subjects from 1 Arab-Israeli kindred, 210 European (Italian pedigrees and Spanish pedigrees) families, and 31 Chinese pedigrees carrying the A1555G or the C1494T mutation revealed a missense mutation (G28T) altering an invariant amino acid residue (A10S) in the evolutionarily conserved N-terminal region of the TRMU protein. Interestingly, all 18 Arab-Israeli/Italian-Spanish matrilineal relatives carrying both the TRMU A10S and 12S rRNA A1555G mutations exhibited prelingual profound deafness. Functional analysis showed that this mutation did not affect importation of TRMU precursors into mitochondria. However, the homozygous A10S mutation leads to a marked failure in mitochondrial tRNA metabolisms, specifically reducing the steady-state levels of mitochondrial tRNA. As a consequence, these defects contribute to the impairment of mitochondrial-protein synthesis. Resultant biochemical defects aggravate the mitochondrial dysfunction associated with the A1555G mutation, exceeding the threshold for expressing the deafness phenotype. These findings indicate that the mutated TRMU, acting as a modifier factor, modulates the phenotypic manifestation of the deafness-associated 12S rRNA mutations.

Amino Acid Sequence↗

PubMed2006

From planar defect in opal to planar defect in inverse opal.

We demonstrate a facile method of fabricating opal and inverse opal structures with a planar defect. A single layer of silica beads was embedded into polystyrene opals by combining an inward-growing self-assembly method with spin-coating technique. After the infiltration of silica followed by the removal of the polystyrene beads by calcination, an inverted structure was obtained. The silica beads were connected together by the infiltrated silica, thus a solid silica phase with the silica beads as a planar defect embedded in the inverse silica opal was obtained. The thickness of the defect layer can be adjusted by changing the size of the silica beads. Scanning electron microscope images showed the good quality of the crystal and the uniformity of the defect layer. Optical transmission spectra indicated the existence of a defect state induced by the defect layer in both the opal and inverse opal structures. High-cost techniques such as lithography and chemical vapor deposition are not involved in the fabrication of inverse opals with planar defects.

Journal Article↗

PubMed2006

Human TRMU encoding the mitochondrial 5-methylaminomethyl-2-thiouridylate-methyltransferase is a putative nuclear modifier gene for the phenotypic expression of the deafness-associated 12S rRNA mutations.

Nuclear modifier genes have been proposed to modulate the phenotypic manifestation of human mitochondrial 12S rRNA A1491G mutation associated with deafness in many families world-wide. Here we identified and characterized the putative nuclear modifier gene TRMU encoding a highly conserved mitochondrial protein related to tRNA modification. A 1937bp TRMU cDNA has been isolated and the genomic organization of TRMU has been elucidated. The human TRMU gene containing 11 exons encodes a 421 residue protein with a strong homology to the TRMU-like proteins of bacteria and other homologs. TRMU is ubiquitously expressed in various tissues, but abundantly in tissues with high metabolic rates including heart, liver, kidney, and brain. Immunofluorescence analysis of human 143B cells expressing TRMU-GFP fusion protein demonstrated that the human Trmu localizes and functions in mitochondrion. Furthermore, we show that in families with the deafness-associated 12S rRNA A1491G mutation there is highly suggestive linkage and linkage disequilibrium between microsatellite markers adjacent to TRMU and the presence of deafness. These observations suggest that human TRMU may modulate the phenotypic manifestation of the deafness-associated mitochondrial 12S rRNA mutations.

Base Sequence↗

PubMed2006

Nanosphere lithography from template-directed colloidal sphere assemblies.

Conventional nanosphere lithography holds the drawbacks of lacking precise control over the shape and architecture of the resultant nanostructures. In this work, nanoimprinting lithography was used to construct various desired patterns on a polymer film coated on a silicon substrate. The patterns were then used as templates to direct the self-assembly of silica colloidal spheres, forming colloidal assemblies with well-controlled sizes, shapes, and structures. Subsequent nanosphere lithography using template-directed colloidal sphere assemblies resulted in complex nanostructures that can not be obtained using the conventional nanosphere lithography method.

Colloids↗

PubMed2005

Mutations in MTO2 related to tRNA modification impair mitochondrial gene expression and protein synthesis in the presence of a paromomycin resistance mutation in mitochondrial 15 S rRNA.

Nuclear gene(s) have been shown to modulate the phenotypic expression of mitochondrial DNA mutations. We report here the identification and characterization of the yeast nuclear gene MTO2 encoding an evolutionarily conserved protein involved in mitochondrial tRNA modification. Interestingly, mto2 null mutants expressed a respiratory-deficient phenotype when coexisting with the C1409G mutation of mitochondrial 15 S rRNA at the very conservative site for human deafness-associated 12 S rRNA A1491G and C1409T mutations. Furthermore, the overall rate of mitochondrial translation was markedly reduced in a yeast mto2 strain in the wild type mitochondrial background, whereas mitochondrial protein synthesis was almost abolished in a yeast mto2 strain carrying the C1409G allele. The other interesting feature of mto2 mutants is the defective expression of mitochondrial genes, especially CYTB and COX1, but only when coexisting with the C1409G allele. These data strongly indicate that a product of MTO2 functionally interacts with the decoding region of 15 S rRNA, particularly at the site of the C1409G or A1491G mutation. In addition, we showed that yeast and human Mto2p localize in mitochondria. The isolated human MTO2 cDNA can partially restore the respiratory-deficient phenotype of yeast mto2 cells carrying the C1409G mutation. These functional conservations imply that human MTO2 may act as a modifier gene, modulating the phenotypic expression of the deafness-associated A1491G or C1409T mutation in mitochondrial 12 S rRNA.

Alleles↗

PubMed2005

Inward-growing self-assembly of colloidal crystal films on horizontal substrates.

Colloidal crystal films have been fabricated on solid substrates with a horizontal deposition method. Scanning electron microscope images showed that the colloidal crystal films exhibit ordered face-centered cubic structures in large domains. Optical measurements demonstrated the presence of photonic band gap along the crystallographic [111] direction. The fabrication method described in this paper allows one to rapidly fabricate colloidal crystal films of different thicknesses, which can be controlled by varying colloidal suspension concentration or volume. In addition, the method also works well for growing colloidal crystal films on a hydrophilic solid substrate with a rough surface. Furthermore, the fabrication of colloidal crystal heterostructures has been demonstrated. An inward-growing mechanism responsible for self-assembly of colloidal spheres on horizontal substrates has been proposed to interpret the observed experimental results.

Colloids↗

PubMed2005

Functional characterization of the mitochondrial 12S rRNA C1494T mutation associated with aminoglycoside-induced and non-syndromic hearing loss.

In this study, we report the biochemical characterization of the deafness-associated mitochondrial 12S rRNA C1494T mutation using 27 cybrid cell lines constructed by transferring mitochondria from 9 lymphoblastoid cell lines derived from a Chinese family into human mitochondrial DNA (mtDNA)-less (rho degrees) cells. Six cybrids derived from two asymptomatic members, and nine cybrids derived from three symptomatic members of the Chinese family carrying the C1494T mutation exhibited approximately 38 and 43% decrease in the rate of mitochondrial protein labeling, respectively, compared with twelve cybrids derived from four Chinese control individuals. These defects are apparently a primary contributor to significant reductions in the rate of overall respiratory capacity or the rate of malate/glutamate promoted respiration, or succinate/G3P-promoted respiration, or TMPD/ascorbate-promoted respiration in mutant cybrid cell lines derived from either symptomatic or asymptomatic individuals. Furthermore, the very significant/nearly identical increase in the ratio of doubling times in DMDM medium in the presence/absence of high concentration of paromomycin was observed in symptomatic or asymptomatic cybrid cell lines carrying the C1494T mutation as compared with the average rate in control cell lines. These observations provide the direct biochemical evidences that the C1494T mutation is a pathogenic mtDNA mutation associated with aminoglycoside-induced and non-syndromic hearing loss. In addition, these data provide the first biochemical evidence that nuclear background plays a critical role in the phenotypic manifestation of non-syndromic hearing loss and aminoglycoside toxicity associated with the C1494T mutation.

Cell Growth Processes↗

PubMed2004

Genomic organization, expression, and subcellular localization of mouse mitochondrial seryl-tRNA synthetase.

We report here the identification and characterization of the mouse mitochondrial seryl-tRNA synthetase (mtSerRS). The genomic organization of mouse mtSerRS has been elucidated. The mouse mtSerRS gene containing 16 exons encodes a 519 residue protein with a strong homology to the mitochondria-like seryl-tRNA synthetase of bacteria, yeast, and other homologs. The mouse mtSerRS is ubiquitously expressed in various tissues, but more abundantly in tissues with high metabolic rates including heart and liver. Surprisingly, this gene, unlike other nuclear genes encoding mitochondrial proteins, exhibited a low expression in skeletal muscle and brain. Furthermore, immunofluorescence analysis of NIH3T3 cells expressing the mtSerRS-GFP fusion protein demonstrated that the mouse mtSerRS localizes in mitochondrion. These observations suggest that the mouse mtSerRS is an evolutionarily conserved protein involved in aminoacylation. Thus, it may play a role in the fidelity in mitochondrial translation and pathogenesis of deafness-associated mutations in the mitochondrial tRNA(Ser(UCN)).

Animals↗

PubMed2004

Biochemical characterization of the mitochondrial tRNASer(UCN) T7511C mutation associated with nonsyndromic deafness.

We report here the biochemical characterization of the deafness-associated mitochondrial tRNA(Ser(UCN)) T7511C mutation, in conjunction with homoplasmic ND1 T3308C and tRNA(Ala) T5655C mutations using cybrids constructed by transferring mitochondria from lymphoblastoid cell lines derived from an African family into human mtDNA-less (rho degrees ) cells. Three cybrids derived from an affected matrilineal relative carrying the homoplasmic T7511C mutation, exhibited approximately 75% decrease in the tRNA(Ser(UCN)) level, compared with three control cybrids. This amount of reduction in the tRNA(Ser(UCN)) level is below a proposed threshold to support a normal rate of mitochondrial protein synthesis in lymphoblastoid cell lines. This defect is likely a primary contributor to approximately 52% reduction in the rate of mitochondrial protein synthesis and marked defects in respiration and growth properties in galactose-containing medium. Interestingly, the T5655C mutation produces approximately 50% reduction in the tRNA(Ala) level in mutant cells. Strikingly, the T3308C mutation causes a significant decrease both in the amount of ND1 mRNA and co-transcribed tRNA(Leu(UUR)) in mutant cells. Thus, mitochondrial dysfunctions caused by the T5655C and T3308C mutations may modulate the phenotypic manifestation of the T7511C mutation. These observations imply that a combination of the T7511C mutation with two mtDNA mutations accounts for the high penetrance of deafness in this family.

Africa↗

PubMed2004

Identification and characterization of mouse TRMU gene encoding the mitochondrial 5-methylaminomethyl-2-thiouridylate-methyltransferase.

The nucleotide modification in tRNA plays a pivotal role in the fidelity of translational process. The mutated mitochondrial tRNA (mt tRNA) associated with human diseases often exhibited a defect in nucleotide modification at wobble position of anticodons. Recently, the product of trmU, 5-methylaminomethyl-2-thiouridylate-methyltransferase, has been shown to be one component of enzyme complex for the biosynthesis of mnm5s2U in the wobble position of the bacterial tRNAs. Here we report the identification and characterization of mouse TRMU homolog. A 1532 bp TRMU cDNA has been isolated and the genomic organization of TRMU has been elucidated. The mouse TRMU gene containing 11 exons encodes a 417 residue protein with a strong homology to the TRMU-like proteins of bacteria and other homologs related to tRNA modification. The mouse TRMU is ubiquitously expressed in various tissues, but abundantly in tissues with high metabolic rates including heart, liver and brain. Furthermore, immunofluorescence analysis of NIH3T3 cells expressing TRMU-GFP fusion protein demonstrated that the mouse Trmu localizes in mitochondria. These observations suggest that the mouse TRMU is a structural and functional homolog of bacterial TrmU, thereby playing a role in the mt tRNA modification and protein synthesis.

3T3 Cells↗

PubMed2003

Maternally inherited aminoglycoside-induced and nonsyndromic deafness is associated with the novel C1494T mutation in the mitochondrial 12S rRNA gene in a large Chinese family.

We report here the characterization of a large Chinese family with maternally transmitted aminoglycoside-induced and nonsyndromic deafness. In the absence of aminoglycosides, some matrilineal relatives in this family exhibited late-onset/progressive deafness, with a wide range of severity and age at onset. Notably, the average age at onset of deafness has changed from 55 years (generation II) to 10 years (generation IV). Clinical data reveal that the administration of aminoglycosides can induce or worsen deafness in matrilineal relatives. The age at the time of drug administration appears to be correlated with the severity of hearing loss experienced by affected individuals. Sequence analysis of mitochondrial DNA in this pedigree identified a homoplasmic C-to-T transition at position 1494 (C1494T) in the 12S rRNA gene. The C1494T mutation is expected to form a novel U1494-1555A base pair, which is in the same position as the C1494-1555G pair created by the deafness-associated A1555G mutation, at the highly conserved A site of 12S rRNA. Exposure to a high concentration of paromomycin or neomycin caused a variable but significant average increase in doubling time in lymphoblastoid cell lines derived from four symptomatic and two asymptomatic individuals in this family carrying the C1494T mutation when compared to four control cell lines. Furthermore, a significant decrease in the rate of total oxygen consumption was observed in the mutant cell lines. Thus, our data strongly support the idea that the A site of mitochondrial 12S rRNA is the primary target for aminoglycoside-induced deafness. These results also strongly suggest that the nuclear background plays a role in the aminoglycoside ototoxicity and in the development of the deafness phenotype associated with the C1494T mutation in the mitochondrial 12S rRNA gene.

Adult↗