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Akhtar MN, Singh A, Manjunath LE, Dey D, Kumar SD, Vasu K, Das A, Eswarappa SM. Hominini-specific regulation of the cell cycle by stop codon readthrough of FEM1B. J Cell Sci 2024; 137:jcs261921. [PMID: 39140134 DOI: 10.1242/jcs.261921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
FEM1B is a substrate-recognition component of the CRL2 E3 ubiquitin-protein ligase. This multi-protein complex targets specific proteins for ubiquitylation, which leads to their degradation. Here, we demonstrate the regulation of FEM1B expression by stop codon readthrough (SCR). In this process, translating ribosomes readthrough the stop codon of FEM1B to generate a C-terminally extended isoform that is highly unstable. A total of 81 nucleotides in the proximal 3'UTR of FEM1B constitute the necessary and sufficient cis-signal for SCR. Also, they encode the amino acid sequence responsible for the degradation of the SCR product. CRISPR-edited cells lacking this region, and therefore SCR of FEM1B, showed increased FEM1B expression. This in turn resulted in reduced expression of SLBP (a target of FEM1B-mediated degradation) and replication-dependent histones (target of SLBP for mRNA stability), causing cell cycle delay. Evolutionary analysis revealed that this phenomenon is specific to the genus Pan and Homo (Hominini). Overall, we show a relatively recently evolved SCR process that relieves the cell cycle from the negative regulation by FEM1B.
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Affiliation(s)
- Md Noor Akhtar
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Dhruba Dey
- Undergraduate Program, Indian Institute of Science, Bengaluru 560012, India
| | - Sangeetha Devi Kumar
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Arpan Das
- Undergraduate Program, Indian Institute of Science, Bengaluru 560012, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
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2
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Martin MV, Aguilar-Rosas S, Franke K, Pieterse M, Langelaar JV, Schreurs R, Bijlsma MF, Besselink MG, Koster J, Timens W, Khasraw M, Ashley DM, Keir ST, Ottensmeier CH, King EV, Verheij J, Waasdorp C, Valk PJM, Engels SAG, Oostenbach E, van Dinter JT, Hofman DA, Mok JY, van Esch WJE, Wilmink H, Monkhorst K, Verheul HMW, Poel D, Hiltermann TJN, Kempen LCLTV, Groen HJM, Aerts JGJV, Heesch SV, Löwenberg B, Plasterk R, Kloosterman WP. The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy. Cancer Immunol Res 2024; 12:759-778. [PMID: 38573707 DOI: 10.1158/2326-6066.cir-23-0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 09/22/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing of cancers to identify the collection of neo-open reading frame peptides (NOP) expressed in tumors. We termed this collection of NOPs the tumor framome. NOPs represent tumor-specific peptides that are different from wild-type proteins and may be strongly immunogenic. We describe a class of hidden NOPs that derive from structural genomic variants involving an upstream protein coding gene driving expression and translation of noncoding regions of the genome downstream of a rearrangement breakpoint, i.e., where no gene annotation or evidence for transcription exists. The entire collection of NOPs represents a vast number of possible neoantigens particularly in tumors with many structural genomic variants and a low number of missense mutations. We show that NOPs are immunogenic and epitopes derived from NOPs can bind to MHC class I molecules. Finally, we provide evidence for the presence of memory T cells specific for hidden NOPs in peripheral blood from a patient with lung cancer. This work highlights NOPs as a major source of possible neoantigens for personalized cancer immunotherapy and provides a rationale for analyzing the complete cancer genome and transcriptome as a basis for the detection of NOPs.
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Affiliation(s)
| | | | - Katka Franke
- CureVac Netherlands B.V., Amsterdam, the Netherlands
| | - Mark Pieterse
- CureVac Netherlands B.V., Amsterdam, the Netherlands
| | | | | | - Maarten F Bijlsma
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Marc G Besselink
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Surgery, Amsterdam, the Netherlands
| | - Jan Koster
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University, Medical Center Groningen, the Netherlands
| | - Mustafa Khasraw
- Duke University Medical Center, Duke University, Durham, North Carolina
| | - David M Ashley
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University, Durham, North Carolina
| | - Stephen T Keir
- Duke University Medical Center, Duke University, Durham, North Carolina
| | - Christian H Ottensmeier
- Liverpool Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool and Clatterbridge Cancer Center NHS Foundation Trust, Liverpool, UK
| | - Emma V King
- Department of Otorhinolaryngology, Head and Neck Surgery, Poole Hospital, Poole, UK
| | - Joanne Verheij
- Amsterdam UMC, location University of Amsterdam, Department of Pathology, Amsterdam, the Netherlands
| | - Cynthia Waasdorp
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sem A G Engels
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ellen Oostenbach
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jip T van Dinter
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Damon A Hofman
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Juk Yee Mok
- Sanquin Reagents, Sanquin, Amsterdam, the Netherlands
| | | | - Hanneke Wilmink
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Medical Oncology, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dennis Poel
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the, Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Léon C L T van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University, Medical Center Groningen, the Netherlands
- University of Antwerp, Antwerp University Hospital, Edegem, Belgium
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | | | | | - Bob Löwenberg
- CureVac Netherlands B.V., Amsterdam, the Netherlands
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3
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Zuo C, Liu Y, Wang Y, Wang Z, Ma H, Wang F, Qiao Y. Underlying effect of SMAD4 gene polymorphism on risk prediction of papillary thyroid carcinoma in Chinese population. Heliyon 2024; 10:e28824. [PMID: 38596142 PMCID: PMC11002234 DOI: 10.1016/j.heliyon.2024.e28824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024] Open
Abstract
Objective This research intends to explore how variations in the SMAD4 gene impact papillary thyroid carcinoma (PTC) among patients in China. Methods The rs10502913 and rs12968012 polymorphisms were genotyped in 405 subjects using SNP-scan high-throughput technology. Differential mRNA expression of SMAD4 was analyzed using data from TCGA and GSE33630, and protein level expression differences were analyzed using immunohistochemistry. Results The results showed that SMAD4 mRNA expression was lower in thyroid cancer (THCA) tissues than in normal tissues. Immunohistochemical results showed that the expression level of SMAD4 in normal tissue, thyroid papillary carcinoma tissue and poorly differentiated tissue was significantly different. We found that SMAD4 mismatch variants (rs10502913 and rs12968012) were associated with PTC susceptibility. Specifically, the SMAD4-rs10502913 genotypes (GA and AA) showed a notable correlation with a lower likelihood of PTC in comprehensive and segmented studies (genotype GA: OR (95% CI) = 0.270 (0.077-0.950), p = 0.041; genotype AA: OR (95% CI) = 0.103 (0.025-0.416), p = 0.001). We categorized the immunohistochemical results according to genotype and found that rs10502913-GG protein level was expressed at the lowest level, and both GA and AA were higher than GG (GG vs. AA, P < 0.05), and rs12968012-CG protein level was expressed at the lowest level, and both GG and CC were higher than CG (GG vs. CG, P < 0.01). Conclusion Two missense variants of SMAD4 (rs10502913 and rs12968012) are associated with reduced risk of papillary thyroid carcinoma, possibly by reducing protein expression leading to susceptibility to papillary thyroid carcinoma.
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Affiliation(s)
- Chao Zuo
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Yi Liu
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Yu Wang
- Department of Geriatrics, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Ziqiang Wang
- Research Center of Clinical Laboratory Science, Bengbu Medical College, Bengbu Anhui, China
| | - Hongyu Ma
- Department of Clinical Medicine, Bengbu Medical College, Bengbu, Anhui China
| | - Feng Wang
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Yongchao Qiao
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
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4
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Mirzaei G. Constructing gene similarity networks using co-occurrence probabilities. BMC Genomics 2023; 24:697. [PMID: 37990157 PMCID: PMC10662556 DOI: 10.1186/s12864-023-09780-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023] Open
Abstract
Gene similarity networks play important role in unraveling the intricate associations within diverse cancer types. Conventionally, gauging the similarity between genes has been approached through experimental methodologies involving chemical and molecular analyses, or through the lens of mathematical techniques. However, in our work, we have pioneered a distinctive mathematical framework, one rooted in the co-occurrence of attribute values and single point mutations, thereby establishing a novel approach for quantifying the dissimilarity or similarity among genes. Central to our approach is the recognition of mutations as key players in the evolutionary trajectory of cancer. Anchored in this understanding, our methodology hinges on the consideration of two categorical attributes: mutation type and nucleotide change. These attributes are pivotal, as they encapsulate the critical variations that can precipitate substantial changes in gene behavior and ultimately influence disease progression. Our study takes on the challenge of formulating similarity measures that are intrinsic to genes' categorical data. Taking into account the co-occurrence probability of attribute values within single point mutations, our innovative mathematical approach surpasses the boundaries of conventional methods. We thereby provide a robust and comprehensive means to assess gene similarity and take a significant step forward in refining the tools available for uncovering the subtle yet impactful associations within the complex realm of gene interactions in cancer.
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Affiliation(s)
- Golrokh Mirzaei
- Department of Computer Science and Engineering, The Ohio State University, Marion, USA.
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5
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Komatsu S, Ohno H, Saito H. Target-dependent RNA polymerase as universal platform for gene expression control in response to intracellular molecules. Nat Commun 2023; 14:7256. [PMID: 37978180 PMCID: PMC10656481 DOI: 10.1038/s41467-023-42802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023] Open
Abstract
Controlling gene expression in response to specific molecules is an essential technique for regulating cellular functions. However, current platforms with transcription and translation regulators have a limited number of detectable molecules to induce gene expression. Here to address these issues, we present a Target-dependent RNA polymerase (TdRNAP) that can induce RNA transcription in response to the intracellular target specifically recognized by single antibody. By substituting the fused antibody, we demonstrate that TdRNAPs respond to a wide variety of molecules, including peptides, proteins, RNA, and small molecules, and produce desired transcripts in human cells. Furthermore, we show that multiple TdRNAPs can construct orthogonal and multilayer genetic circuits. Finally, we apply TdRNAP to achieve cell-specific genome editing that is autonomously triggered by detecting the target gene product. TdRNAP can expand the molecular variety for controlling gene expression and provide the genetic toolbox for bioengineering and future therapeutic applications.
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Affiliation(s)
- Shodai Komatsu
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hirohisa Ohno
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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6
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Keyan KS, Salim S, Gowda S, Abdelrahman D, Amir SS, Islam Z, Vargas C, Bengoechea-Alonso MT, Alwa A, Dahal S, Kolatkar PR, Da'as S, Torrisani J, Ericsson J, Mohammad F, Khan OM. Control of TGFβ signalling by ubiquitination independent function of E3 ubiquitin ligase TRIP12. Cell Death Dis 2023; 14:692. [PMID: 37863914 PMCID: PMC10589240 DOI: 10.1038/s41419-023-06215-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023]
Abstract
Transforming growth factor β (TGFβ) pathway is a master regulator of cell proliferation, differentiation, and death. Deregulation of TGFβ signalling is well established in several human diseases including autoimmune disorders and cancer. Thus, understanding molecular pathways governing TGFβ signalling may help better understand the underlying causes of some of those conditions. Here, we show that a HECT domain E3 ubiquitin ligase TRIP12 controls TGFβ signalling in multiple models. Interestingly, TRIP12 control of TGFβ signalling is completely independent of its E3 ubiquitin ligase activity. Instead, TRIP12 recruits SMURF2 to SMAD4, which is most likely responsible for inhibitory monoubiquitination of SMAD4, since SMAD4 monoubiquitination and its interaction with SMURF2 were dramatically downregulated in TRIP12-/- cells. Additionally, genetic inhibition of TRIP12 in human and murine cells leads to robust activation of TGFβ signalling which was rescued by re-introducing wildtype TRIP12 or a catalytically inactive C1959A mutant. Importantly, TRIP12 control of TGFβ signalling is evolutionary conserved. Indeed, genetic inhibition of Drosophila TRIP12 orthologue, ctrip, in gut leads to a reduced number of intestinal stem cells which was compensated by the increase in differentiated enteroendocrine cells. These effects were completely normalised in Drosophila strain where ctrip was co-inhibited together with Drosophila SMAD4 orthologue, Medea. Similarly, in murine 3D intestinal organoids, CRISPR/Cas9 mediated genetic targeting of Trip12 enhances TGFβ mediated proliferation arrest and cell death. Finally, CRISPR/Cas9 mediated genetic targeting of TRIP12 in MDA-MB-231 breast cancer cells enhances the TGFβ induced migratory capacity of these cells which was rescued to the wildtype level by re-introducing wildtype TRIP12. Our work establishes TRIP12 as an evolutionary conserved modulator of TGFβ signalling in health and disease.
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Affiliation(s)
- Kripa S Keyan
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Safa Salim
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Swetha Gowda
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Syeda Sakina Amir
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Zeyaul Islam
- Qatar Biomedical Research Institute, Doha, Qatar
| | - Claire Vargas
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | | | - Amira Alwa
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Subrat Dahal
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Sahar Da'as
- Department of Research, Sidra Medicine, Doha, Qatar
| | - Jerome Torrisani
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Johan Ericsson
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Farhan Mohammad
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Omar M Khan
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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7
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Müller MBD, Kasturi P, Jayaraj GG, Hartl FU. Mechanisms of readthrough mitigation reveal principles of GCN1-mediated translational quality control. Cell 2023:S0092-8674(23)00587-1. [PMID: 37339632 PMCID: PMC10364623 DOI: 10.1016/j.cell.2023.05.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023]
Abstract
Readthrough into the 3' untranslated region (3' UTR) of the mRNA results in the production of aberrant proteins. Metazoans efficiently clear readthrough proteins, but the underlying mechanisms remain unknown. Here, we show in Caenorhabditis elegans and mammalian cells that readthrough proteins are targeted by a coupled, two-level quality control pathway involving the BAG6 chaperone complex and the ribosome-collision-sensing protein GCN1. Readthrough proteins with hydrophobic C-terminal extensions (CTEs) are recognized by SGTA-BAG6 and ubiquitylated by RNF126 for proteasomal degradation. Additionally, cotranslational mRNA decay initiated by GCN1 and CCR4/NOT limits the accumulation of readthrough products. Unexpectedly, selective ribosome profiling uncovered a general role of GCN1 in regulating translation dynamics when ribosomes collide at nonoptimal codons, enriched in 3' UTRs, transmembrane proteins, and collagens. GCN1 dysfunction increasingly perturbs these protein classes during aging, resulting in mRNA and proteome imbalance. Our results define GCN1 as a key factor acting during translation in maintaining protein homeostasis.
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Affiliation(s)
- Martin B D Müller
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Prasad Kasturi
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Gopal G Jayaraj
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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8
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Kesner JS, Chen Z, Shi P, Aparicio AO, Murphy MR, Guo Y, Trehan A, Lipponen JE, Recinos Y, Myeku N, Wu X. Noncoding translation mitigation. Nature 2023; 617:395-402. [PMID: 37046090 PMCID: PMC10560126 DOI: 10.1038/s41586-023-05946-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/13/2023] [Indexed: 04/14/2023]
Abstract
Translation is pervasive outside of canonical coding regions, occurring in long noncoding RNAs, canonical untranslated regions and introns1-4, especially in ageing4-6, neurodegeneration5,7 and cancer8-10. Notably, the majority of tumour-specific antigens are results of noncoding translation11-13. Although the resulting polypeptides are often nonfunctional, translation of noncoding regions is nonetheless necessary for the birth of new coding sequences14,15. The mechanisms underlying the surveillance of translation in diverse noncoding regions and how escaped polypeptides evolve new functions remain unclear10,16-19. Functional polypeptides derived from annotated noncoding sequences often localize to membranes20,21. Here we integrate massively parallel analyses of more than 10,000 human genomic sequences and millions of random sequences with genome-wide CRISPR screens, accompanied by in-depth genetic and biochemical characterizations. Our results show that the intrinsic nucleotide bias in the noncoding genome and in the genetic code frequently results in polypeptides with a hydrophobic C-terminal tail, which is captured by the ribosome-associated BAG6 membrane protein triage complex for either proteasomal degradation or membrane targeting. By contrast, canonical proteins have evolved to deplete C-terminal hydrophobic residues. Our results reveal a fail-safe mechanism for the surveillance of unwanted translation from diverse noncoding regions and suggest a possible biochemical route for the preferential membrane localization of newly evolved proteins.
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Affiliation(s)
- Jordan S Kesner
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ziheng Chen
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Peiguo Shi
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alexis O Aparicio
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael R Murphy
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yang Guo
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aditi Trehan
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jessica E Lipponen
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yocelyn Recinos
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natura Myeku
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Xuebing Wu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
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9
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Bauer AH, Basta DW, Hornick JL, Dong F. Loss of function SMAD4 nonstop mutations in human cancer. Histopathology 2023; 82:1098-1104. [PMID: 36740808 DOI: 10.1111/his.14880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
BACKGROUND SMAD4 is a tumour suppressor gene that is mutated in a variety of cancers. SMAD4 nonstop mutations, which convert stop codons to sense codons that extend transcription, have been identified in genomic databases but have not been characterised in human pathology samples. The frequency of SMAD4 nonstop mutations and the consequences of nonstop mutations on SMAD4 protein expression are unknown. METHODS We retrospectively analysed our cancer sequencing database of 38,002 tumour specimens and evaluated the spectrum of SMAD4 mutations. SMAD4 protein expression was evaluated by immunohistochemistry in tumours with SMAD4 nonstop mutations. RESULTS In total, 1956 SMAD4 mutations were identified in 1822 tumours. SMAD4 mutations were most common in tumours of the gastrointestinal tract and included nonsense variants (n = 344), frameshift indels (n = 258), splice site variants (n = 104), and missense variants at codon R361 (n = 245). In a subset of cases with immunohistochemistry, SMAD4 expression was lost in 23 of 25 tumours (92%) with protein truncating variants and in 7 of 27 tumours (26%) with missense variants. Four cases harboured SMAD4 nonstop mutations. SMAD4 nonstop mutations were identified in two pancreatic adenocarcinomas, one colonic adenocarcinoma, and one non-small cell lung carcinoma. Immunohistochemistry demonstrated loss of SMAD4 protein expression in each of the four tumours with SMAD4 nonstop mutations. CONCLUSION SMAD4 nonstop mutations are associated with loss of SMAD4 protein expression in multiple tumour types. SMAD4 nonstop mutations should be clinically interpreted as pathogenic loss of function alterations when identified in cancer sequencing panels.
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Affiliation(s)
- Anna H Bauer
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,University of Missouri School of Medicine, Columbia, MO, USA
| | - David W Basta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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10
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Ghosh A, Myacheva K, Riester M, Schmidt C, Diederichs S. Chimeric oligonucleotides combining guide RNA and single-stranded DNA repair template effectively induce precision gene editing. RNA Biol 2021; 19:588-593. [PMID: 35465826 PMCID: PMC9128553 DOI: 10.1080/15476286.2022.2067713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 10/30/2022] Open
Abstract
The ability to precisely alter the genome holds immense potential for molecular biology, medicine and biotechnology. The development of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) into a genomic editing tool has vastly simplified genome engineering. Here, we explored the use of chemically synthesized chimeric oligonucleotides encoding a target-specific crRNA (CRISPR RNA) fused to a single-stranded DNA repair template for RNP-mediated precision genome editing. By generating three clinically relevant oncogenic driver mutations, two non-stop extension mutations, an FGFRi resistance mutation and a single nucleotide change, we demonstrate the ability of chimeric oligos to form RNPs and direct Cas9 to effectively induce genome editing. Further, we demonstrate that the polarity of the chimeric oligos is crucial: only chimeric oligos with the single-stranded DNA repair template fused to the 3'-end of the crRNA are functional for accurate editing, while templates fused to the 5'-end are ineffective. We also find that chimeras can perform editing with both symmetric and asymmetric single-stranded DNA repair templates. Depending on the target locus, the editing efficiency using chimeric RNPs is similar to or less than the efficiency of editing using the bipartite standard RNPs. Our results indicate that chimeric RNPs comprising RNA-DNA oligos formed from fusing the crRNA and DNA repair templates can successfully induce precise edits. While chimeric RNPs do not display an advantage over standard RNPs, they nonetheless represent a viable approach for one-molecule precision genome editing.
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Affiliation(s)
- Avantika Ghosh
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Freiburg, Germany
| | - Ksenia Myacheva
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Freiburg, Germany
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marisa Riester
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Freiburg, Germany
| | - Carla Schmidt
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Freiburg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Freiburg, Germany
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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11
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The HOXB13 variant X285K is associated with clinical significance and early age at diagnosis in African American prostate cancer patients. Br J Cancer 2021; 126:791-796. [PMID: 34799695 DOI: 10.1038/s41416-021-01622-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 10/21/2021] [Accepted: 10/29/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Recently, a novel HOXB13 variant (X285K) was observed in men of African descent with prostate cancer (PCa) in Martinique. Little is known about this or other variants in HOXB13 which may play a role in PCa susceptibility in African-American (AA) men. METHODS We sequenced HOXB13 in an AA population of 1048 men undergoing surgical treatment for PCa at Johns Hopkins Hospital. RESULTS Seven non-synonymous germline variants were observed in the patient population. While six of these variants were seen only once, X285K was found in eight patients. In a case-case analysis, we find that carriers of this latter variant are at increased risk of clinically significant PCa (1.2% carrier rate in Gleason Score ≥7 PCa vs. 0% in Gleason Score <7 PCa, odds ratio, OR = inf; 95% Confidence Interval, 95%CI:1.05-inf, P = 0.028), as well as PCa with early age at diagnosis (2.4% carrier rate in patients <50 year vs. 0.5% carrier rate in patients ≥50 year, OR = 5.25, 95% CI:1.00-28.52, P = 0.03). CONCLUSIONS While this variant is rare in the AA population (~0.2% MAF), its ancestry-specific occurrence and apparent preferential association with risk for the more aggressive disease at an early age emphasizes its translational potential as an important, novel PCa susceptibility marker in the high-risk AA population.
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12
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Pal J, Becker AC, Dhamija S, Seiler J, Abdelkarim M, Sharma Y, Behr J, Meng C, Ludwig C, Kuster B, Diederichs S. Systematic analysis of migration factors by MigExpress identifies essential cell migration control genes in non-small cell lung cancer. Mol Oncol 2021; 15:1797-1817. [PMID: 33934493 PMCID: PMC8253088 DOI: 10.1002/1878-0261.12973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 11/07/2022] Open
Abstract
Cell migration is an essential process in health and in disease, including cancer metastasis. A comprehensive inventory of migration factors is nonetheless lacking-in part due to the difficulty in assessing migration using high-throughput technologies. Hence, there are currently very few screens that systematically reveal factors controlling cell migration. Here, we introduce MigExpress as a platform for the 'identification of Migration control genes by differential Expression'. MigExpress exploits the combination of in-depth molecular profiling and the robust quantitative analysis of migration capacity in a broad panel of samples and identifies migration-associated genes by their differential expression in slow- versus fast-migrating cells. We applied MigExpress to investigate non-small cell lung cancer (NSCLC), which is the most frequent cause of cancer mortality mainly due to metastasis. In 54 NSCLC cell lines, we comprehensively determined mRNA and protein expression. Correlating the transcriptome and proteome profiles with the quantified migration properties led to the discovery and validation of FLNC, DSE, CPA4, TUBB6, and BICC1 as migration control factors in NSCLC cells, which were also negatively correlated with patient survival. Notably, FLNC was the least expressed filamin in NSCLC, but the only one controlling cell migration and correlating with patient survival and metastatic disease stage. In our study, we present MigExpress as a new method for the systematic analysis of migration factors and provide a comprehensive resource of transcriptomic and proteomic data of NSCLC cell lines related to cell migration.
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Affiliation(s)
- Jagriti Pal
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany
| | - Andrea C Becker
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany
| | - Sonam Dhamija
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany.,Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Jeanette Seiler
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mahmoud Abdelkarim
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany
| | - Yogita Sharma
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany
| | - Jürgen Behr
- Leibniz Institute for Food Systems, Technical University of Munich, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany.,Chair of Proteomics and Bioanalytics, DKTK Partner Site Munich, Freising, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK) - Partner Site Freiburg, Germany.,Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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13
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Jorge GL, Balbuena TS. Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140594. [PMID: 33385527 DOI: 10.1016/j.bbapap.2020.140594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
Eucalyptus species are widely used in the forestry industry, and a significant increase in the number of sequences available in database repositories has been observed for these species. In proteomics, a protein is identified by correlating the theoretical fragmentation spectrum derived from genomic/transcriptomic data against the experimental fragmentation mass spectrum acquired from large-scale analysis of protein mixtures. Proteogenomics is an alternative approach that can identify novel proteins encoded by regions previously considered as non-coding. This study aimed to confidently identify and confirm the existence of previously unknown protein-coding sequences in the Eucalyptus grandis genome. To this end, we used a modified spectral correlation strategy and a dedicated de novo peptide sequencing pipeline. Upon the strategy used here, we confidently identified 41 novel peptide forms and six peptides containing at least one single amino acid substitution. The most representative genomic class of novel peptides was identified as originating from alternative reading frames. In contrast, no clear single amino acid substitution pattern was identified. Validation of the identifications was carried out using a parallel reaction monitoring approach that provided further mass spectrometry support for the existence of the novel peptide sequences. Data are available via ProteomeXchange with identifier PXD022110.
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Affiliation(s)
- Gabriel Lemes Jorge
- Sao Paulo State University, Department of Technology, Jaboticabal, Sao Paulo, Brazil.
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