Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.611416
Perla Pucci, Charlotte Barrett, Ricky Trigg, Jamie D. Matthews, Marcus Borenas, Michaela Schlederer, Leila Jahangiri, Lucy Hare, Christopher Steel, Emily James, Nina Prokoph, Lukas Kenner, Ruth Palmer, Bengt Hallberg, Amos Burke, Suzanne D Turner
Anaplastic Lymphoma Kinase inhibitors (ALK TKIs) are approved for the treatment of ALK-positive non-small cell lung cancer (NSCLC) and are in clinical trial for ALK-aberrant high-risk neuroblastoma (NB) patients, particularly loratinib. However, resistance to ALK inhibitors can occur in patients, via the activation of bypass-signalling pathways, and there is a need to identify these mechanisms as well as drugs that inhibit them to design therapeutic approaches that prevent resistance, and to treat ALK TKI relapsed/refractory disease. Using genome-wide CRISPR-Cas9 overexpression screens, we identified and validated FGFR2 as a desensitizer to lorlatinib in aberrant ALK-expressing high-risk NB. FGFR2 and FGFR2-associated pathways are up-regulated in lorlatinib-resistant NB cells. Moreover, high-throughput screens using a library of 1,430 FDA approved drugs identified kinase inhibitors including those targeting FGFR2 as efficacious in reducing the survival of lorlatinib resistant NB cells. Hence, the FGFR pathway was investigated as a therapeutic target applying the pan-FGFR inhibitor erdafitinib or the multi-kinase inhibitor ponatinib, resulting in reduced survival of lorlatinib-resitant cells in comparison to their lorlatinib-sensitive counterparts. Moreover, both FGFR inhibitors act synergistically with lorlatinib in vitro and in vivo, using patient-derived xenografts (PDXs) and genetically engineered models (GEMM) of ALK-expressing NB. FGFR2 mRNA expression also correlate with a poorer prognosis for NB patients, regardless of sub-type, suggesting that a broader range of patients may benefit from FGFR inhibitors. Overall, our data suggests that FGFR2 potentially plays roles in lorlatinib resistance in NB and that combined pharmacological inhibition of ALK and FGFR constitutes a therapeutic approach to treat high-risk NB.
{"title":"FGFR2 promotes resistance to ALK tyrosine kinase inhibitors and its inhibition acts synergistically with lorlatinib in the treatment of ALK-expressing neuroblastoma","authors":"Perla Pucci, Charlotte Barrett, Ricky Trigg, Jamie D. Matthews, Marcus Borenas, Michaela Schlederer, Leila Jahangiri, Lucy Hare, Christopher Steel, Emily James, Nina Prokoph, Lukas Kenner, Ruth Palmer, Bengt Hallberg, Amos Burke, Suzanne D Turner","doi":"10.1101/2024.09.05.611416","DOIUrl":"https://doi.org/10.1101/2024.09.05.611416","url":null,"abstract":"Anaplastic Lymphoma Kinase inhibitors (ALK TKIs) are approved for the treatment of ALK-positive non-small cell lung cancer (NSCLC) and are in clinical trial for ALK-aberrant high-risk neuroblastoma (NB) patients, particularly loratinib. However, resistance to ALK inhibitors can occur in patients, via the activation of bypass-signalling pathways, and there is a need to identify these mechanisms as well as drugs that inhibit them to design therapeutic approaches that prevent resistance, and to treat ALK TKI relapsed/refractory disease. Using genome-wide CRISPR-Cas9 overexpression screens, we identified and validated FGFR2 as a desensitizer to lorlatinib in aberrant ALK-expressing high-risk NB. FGFR2 and FGFR2-associated pathways are up-regulated in lorlatinib-resistant NB cells. Moreover, high-throughput screens using a library of 1,430 FDA approved drugs identified kinase inhibitors including those targeting FGFR2 as efficacious in reducing the survival of lorlatinib resistant NB cells. Hence, the FGFR pathway was investigated as a therapeutic target applying the pan-FGFR inhibitor erdafitinib or the multi-kinase inhibitor ponatinib, resulting in reduced survival of lorlatinib-resitant cells in comparison to their lorlatinib-sensitive counterparts. Moreover, both FGFR inhibitors act synergistically with lorlatinib in vitro and in vivo, using patient-derived xenografts (PDXs) and genetically engineered models (GEMM) of ALK-expressing NB. FGFR2 mRNA expression also correlate with a poorer prognosis for NB patients, regardless of sub-type, suggesting that a broader range of patients may benefit from FGFR inhibitors. Overall, our data suggests that FGFR2 potentially plays roles in lorlatinib resistance in NB and that combined pharmacological inhibition of ALK and FGFR constitutes a therapeutic approach to treat high-risk NB.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"58 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.08.611930
Purna A Joshi, Prashant Nuthalapati, Dibyo Maiti, Sharon Kwende, Subhajit Maity, Dun Ning
A short duration of breastfeeding is a risk factor for the development of high-mortality, postpartum, triple-negative breast cancer. The intrinsic properties of cancer-initiating epithelial cells that persist following breastfeeding cessation and mammary gland remodeling are poorly understood. Previously, we showed that Platelet-Derived Growth Factor Receptor alpha (PDGFRα)-expressing stromal mammary adipocyte progenitors (MAPs) differentiate into epithelial luminal progenitors in the adult gland. In the current study, we demonstrate that MAP-derived luminal progenitors retain a mesenchymal transcriptomic signature. In an abrupt involution model that mimics a short breastfeeding duration, MAP-derived luminal progenitors persist and dominate luminal epithelia, undergoing transcriptomic alterations that signify a distinct ferrometabolic state linked to cancer. Concurrently, MAPs adopt an alternative interferon-mediated profibrotic and invasive stromal fate. Our work uncovers MAPs to be the primary cellular origin of a pathological stromal and epithelial microenvironment following abrupt involution, presenting a potential therapeutic target in postpartum breast cancer.
{"title":"Adipocyte progenitors are primary contributors to the disrupted epithelial niche that is sustained following abrupt mammary gland involution","authors":"Purna A Joshi, Prashant Nuthalapati, Dibyo Maiti, Sharon Kwende, Subhajit Maity, Dun Ning","doi":"10.1101/2024.09.08.611930","DOIUrl":"https://doi.org/10.1101/2024.09.08.611930","url":null,"abstract":"A short duration of breastfeeding is a risk factor for the development of high-mortality, postpartum, triple-negative breast cancer. The intrinsic properties of cancer-initiating epithelial cells that persist following breastfeeding cessation and mammary gland remodeling are poorly understood. Previously, we showed that Platelet-Derived Growth Factor Receptor alpha (PDGFRα)-expressing stromal mammary adipocyte progenitors (MAPs) differentiate into epithelial luminal progenitors in the adult gland. In the current study, we demonstrate that MAP-derived luminal progenitors retain a mesenchymal transcriptomic signature. In an abrupt involution model that mimics a short breastfeeding duration, MAP-derived luminal progenitors persist and dominate luminal epithelia, undergoing transcriptomic alterations that signify a distinct ferrometabolic state linked to cancer. Concurrently, MAPs adopt an alternative interferon-mediated profibrotic and invasive stromal fate. Our work uncovers MAPs to be the primary cellular origin of a pathological stromal and epithelial microenvironment following abrupt involution, presenting a potential therapeutic target in postpartum breast cancer.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.04.610994
George D Cresswell, Tasnim Chagtai, Reem Al-Saadi, Taryn D Treger, Gaganjit Madhan, Borbala Mifsud, Gordan Vujanic, Richard D Williams, Nicholas M Luscombe, Kathy Pritchard-Jones, William Mifsud
Understanding cancer evolution is fundamental to predicting cancer progression. However, the evolution of paediatric cancers is still under-researched. Large cohorts of patients are required to determine consistent evolutionary trajectories that shed light on key steps in cancer development and reveal underlying biology, especially in rare cancers. Additionally, well annotated clinical data is necessary for determining if evolutionary biomarkers are predictive of patient outcome. We performed detailed evolutionary analysis of 64 paediatric kidney cancers, including 60 Wilms tumours (WT), using DNA microarrays and, in a subset of 30 patients, a WT-specific targeted sequencing assay, to detect copy number alterations (CNA) and mutations, respectively. By analysing multiple tissue samples in the majority of cases we could detect mutation heterogeneity in each tumour. We reconstructed clones across the cohort and described their phylogenetic histories, in addition to detecting mirrored subclonal allelic imbalance. Our results highlight pervasive evidence of parallel evolution in WTs affecting CNAs, and CTNNB1 and TP53 mutations. Furthermore, we demonstrate that stromal-type WTs often evolve from a consistent series of events (WT1 mutation, 11p uniparental disomy and CTNNB1 mutation) and we suggest that 19q uniparental disomy is an important ancestral event in both epithelial and diffuse anaplastic WTs. Finally, we propose the total number of evolutionary CNA events as a prognostic biomarker in WTs for event-free survival, particularly in high-risk WT. Overall, this study sheds light on the evolution of the most common paediatric kidney cancer and links evolutionary analysis to fundamental clinical and biological questions in a large cohort of WTs. We conclude that histological subtypes of WT are often defined by consistent evolutionary sequences. We present evidence that a key marker of evolvability, namely CNA diversity measured phylogenetically across multiple tumour sites, is prognostic of patient outcome and should be considered for clinical use to detect the most aggressive blastemal and diffuse anaplastic type WTs.
{"title":"Subtype-specific Patterns of Evolution and Clinically Relevant Genomic Instability in Wilms Tumour","authors":"George D Cresswell, Tasnim Chagtai, Reem Al-Saadi, Taryn D Treger, Gaganjit Madhan, Borbala Mifsud, Gordan Vujanic, Richard D Williams, Nicholas M Luscombe, Kathy Pritchard-Jones, William Mifsud","doi":"10.1101/2024.09.04.610994","DOIUrl":"https://doi.org/10.1101/2024.09.04.610994","url":null,"abstract":"Understanding cancer evolution is fundamental to predicting cancer progression. However, the evolution of paediatric cancers is still under-researched. Large cohorts of patients are required to determine consistent evolutionary trajectories that shed light on key steps in cancer development and reveal underlying biology, especially in rare cancers. Additionally, well annotated clinical data is necessary for determining if evolutionary biomarkers are predictive of patient outcome. We performed detailed evolutionary analysis of 64 paediatric kidney cancers, including 60 Wilms tumours (WT), using DNA microarrays and, in a subset of 30 patients, a WT-specific targeted sequencing assay, to detect copy number alterations (CNA) and mutations, respectively. By analysing multiple tissue samples in the majority of cases we could detect mutation heterogeneity in each tumour. We reconstructed clones across the cohort and described their phylogenetic histories, in addition to detecting mirrored subclonal allelic imbalance. Our results highlight pervasive evidence of parallel evolution in WTs affecting CNAs, and <em>CTNNB1</em> and <em>TP53</em> mutations. Furthermore, we demonstrate that stromal-type WTs often evolve from a consistent series of events (<em>WT1</em> mutation, 11p uniparental disomy and <em>CTNNB1</em> mutation) and we suggest that 19q uniparental disomy is an important ancestral event in both epithelial and diffuse anaplastic WTs. Finally, we propose the total number of evolutionary CNA events as a prognostic biomarker in WTs for event-free survival, particularly in high-risk WT. Overall, this study sheds light on the evolution of the most common paediatric kidney cancer and links evolutionary analysis to fundamental clinical and biological questions in a large cohort of WTs. We conclude that histological subtypes of WT are often defined by consistent evolutionary sequences. We present evidence that a key marker of evolvability, namely CNA diversity measured phylogenetically across multiple tumour sites, is prognostic of patient outcome and should be considered for clinical use to detect the most aggressive blastemal and diffuse anaplastic type WTs.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.08.611923
Dhanusha A Nalawansha, Georgios Mazis, Gitte Husemoen, Kate S Ashton, Weixian Deng, Ryan P Wurz, Anh T Tran, Brian A Lanman, Jiansong Xie, Robert G Guenette, Shiqian Li, Christopher E Smith, Suresh Archunan, Manoj K Agnihotram, Arghya Sadhukhan, Rajiv Kapoor, Sajjan Koirala, Felipe De Sousa E Melo, Patrick Ryan Potts
Proximity-inducing modalities that co-opt cellular pathways offer new opportunities to regulate oncogenic drivers. Inspired by the success of proximity-based chimeras in both intracellular and extracellular target space, here we describe the development of LYsosome Membrane TArgeting Chimeras (LYMTACs) as a novel small molecule-based platform that functions intracellularly to modulate the membrane proteome. Conceptually, LYMTACs are heterobifunctional small molecules that co-opt short-lived lysosomal membrane proteins (LMPs) as effectors to deliver targets for lysosomal degradation. We demonstrate that a promiscuous kinase inhibitor-based LYMTAC selectively targets membrane proteins for lysosomal degradation via RNF152, a short-lived LMP. To extend these findings, we show that oncogenic, membrane-associated KRASG12D protein can be tethered to RNF152, inducing KRAS relocalization to the lysosomal membrane, inhibiting downstream phospho-ERK signaling, and leading to lysosomal degradation of KRASG12D in a LYMTAC-dependent manner. Notably, potent cell killing could be attributed to the multi-pharmacology displayed by LYMTACs, which differentiates the LYMTAC technology from existing modalities. Thus, LYMTACs represent a proximity-based therapeutic approach that promises to expand the target space for challenging membrane proteins through targeted protein relocalization and degradation.
{"title":"LYMTACs: Chimeric Small Molecules Repurpose Lysosomal Membrane Proteins for Target Protein Relocalization and Degradation","authors":"Dhanusha A Nalawansha, Georgios Mazis, Gitte Husemoen, Kate S Ashton, Weixian Deng, Ryan P Wurz, Anh T Tran, Brian A Lanman, Jiansong Xie, Robert G Guenette, Shiqian Li, Christopher E Smith, Suresh Archunan, Manoj K Agnihotram, Arghya Sadhukhan, Rajiv Kapoor, Sajjan Koirala, Felipe De Sousa E Melo, Patrick Ryan Potts","doi":"10.1101/2024.09.08.611923","DOIUrl":"https://doi.org/10.1101/2024.09.08.611923","url":null,"abstract":"Proximity-inducing modalities that co-opt cellular pathways offer new opportunities to regulate oncogenic drivers. Inspired by the success of proximity-based chimeras in both intracellular and extracellular target space, here we describe the development of LYsosome Membrane TArgeting Chimeras (LYMTACs) as a novel small molecule-based platform that functions intracellularly to modulate the membrane proteome. Conceptually, LYMTACs are heterobifunctional small molecules that co-opt short-lived lysosomal membrane proteins (LMPs) as effectors to deliver targets for lysosomal degradation. We demonstrate that a promiscuous kinase inhibitor-based LYMTAC selectively targets membrane proteins for lysosomal degradation via RNF152, a short-lived LMP. To extend these findings, we show that oncogenic, membrane-associated KRASG12D protein can be tethered to RNF152, inducing KRAS relocalization to the lysosomal membrane, inhibiting downstream phospho-ERK signaling, and leading to lysosomal degradation of KRASG12D in a LYMTAC-dependent manner. Notably, potent cell killing could be attributed to the multi-pharmacology displayed by LYMTACs, which differentiates the LYMTAC technology from existing modalities. Thus, LYMTACs represent a proximity-based therapeutic approach that promises to expand the target space for challenging membrane proteins through targeted protein relocalization and degradation.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.611373
Ben Nicholas, Alistair Bailey, Katy J McCann, Peter Johnson, Tim Elliott, Christian Ottensmeier, Paul Skipp
Non-small cell lung cancer (NSCLC) is frequently diagnosed at an advanced stage and has poor survival. NSCLC subtypes require different treatment regimes, hence there are extensive efforts to find more precise and non-invasive differential diagnostics tools. Complementing these efforts, we examined two NSCLC subtypes for differences that may inform treatment options and identify potential novel therapeutic pathways. Here we present a comparative analysis of transcriptomic and proteomic expression in tumours from a cohort of 22 NSCLC patients: 8 squamous cell carcinoma (LUSC), 14 adenocarcinoma (LUAD). We examined differential gene and differential protein expression between LUSC and LUAD, and between NSCLC subtypes and either PBMCs or normal adjacent lung tissue (NAT). We found that both NSCLC subtypes shared common differences in gene expression to PBMC relating to developmental and structural changes, and common protein expression differences to NAT relating to protein translation and RNA related processing and splicing. Between NSCLC subtypes we found differential gene expression relating to cell differentiation for LUSC and cellular structure and immune response regulation for LUAD. Differential protein expression between NSCLC subtypes related to extracellular structure for LUSC and metabolic processes, including glucose metabolism for LUAD. Many of our observations of differentially expressed genes and proteins between NSCLC subtypes support and inform existing observations, aiding both basic and clinical research seeking to identify subtype biomarkers or druggable targets.
{"title":"Comparative analysis of transcriptomic and proteomic expression between two non-small cell lung cancer subtypes","authors":"Ben Nicholas, Alistair Bailey, Katy J McCann, Peter Johnson, Tim Elliott, Christian Ottensmeier, Paul Skipp","doi":"10.1101/2024.09.05.611373","DOIUrl":"https://doi.org/10.1101/2024.09.05.611373","url":null,"abstract":"Non-small cell lung cancer (NSCLC) is frequently diagnosed at an advanced stage and has poor survival. NSCLC subtypes require different treatment regimes, hence there are extensive efforts to find more precise and non-invasive differential diagnostics tools. Complementing these efforts, we examined two NSCLC subtypes for differences that may inform treatment options and identify potential novel therapeutic pathways. Here we present a comparative analysis of transcriptomic and proteomic expression in tumours from a cohort of 22 NSCLC patients: 8 squamous cell carcinoma (LUSC), 14 adenocarcinoma (LUAD). We examined differential gene and differential protein expression between LUSC and LUAD, and between NSCLC subtypes and either PBMCs or normal adjacent lung tissue (NAT). We found that both NSCLC subtypes shared common differences in gene expression to PBMC relating to developmental and structural changes, and common protein expression differences to NAT relating to protein translation and RNA related processing and splicing. Between NSCLC subtypes we found differential gene expression relating to cell differentiation for LUSC and cellular structure and immune response regulation for LUAD. Differential protein expression between NSCLC subtypes related to extracellular structure for LUSC and metabolic processes, including glucose metabolism for LUAD. Many of our observations of differentially expressed genes and proteins between NSCLC subtypes support and inform existing observations, aiding both basic and clinical research seeking to identify subtype biomarkers or druggable targets.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.1101/2024.09.09.612071
Daniel KC Lee, Ryan Loke, Jonathan TS Chow, Martino Marco Gabra, Leonardo Salmena
Phosphoinositides (PIs) are minor but essential phospholipids that play crucial roles in cellular signaling pathways, membrane dynamics, and the regulation of various cellular processes. We developed and utilized a novel PI-focused CRISPR gRNA library to perform negative-selection and positive-selection screens in PANC-1 and OCI-AML2 cells, models of pancreatic ductal adenocarcinoma (PDAC) and acute myeloid leukemia (AML), respectively. Through these screens, we identified 28 essential genes in PANC-1, 84 essential genes in OCI-AML2, and 28 regulators of colony formation in OCI-AML2. Our results using this small and focused library uncovered false negatives and subtle effects that may be missed in genome-wide approaches, while enabling adaptation to different screening conditions. Overall, our results uncovered previously uncharacterized essential genes in PDAC and AML that can be leveraged as therapeutic targets and biomarkers. We also demonstrate that focused libraries offer a more efficient and targeted approach to uncovering critical genetic determinants of cancer progression.
{"title":"Phosphoinositide-focused CRISPR screen identifies novel genetic vulnerabilities in PDAC and AML cells","authors":"Daniel KC Lee, Ryan Loke, Jonathan TS Chow, Martino Marco Gabra, Leonardo Salmena","doi":"10.1101/2024.09.09.612071","DOIUrl":"https://doi.org/10.1101/2024.09.09.612071","url":null,"abstract":"Phosphoinositides (PIs) are minor but essential phospholipids that play crucial roles in cellular signaling pathways, membrane dynamics, and the regulation of various cellular processes. We developed and utilized a novel PI-focused CRISPR gRNA library to perform negative-selection and positive-selection screens in PANC-1 and OCI-AML2 cells, models of pancreatic ductal adenocarcinoma (PDAC) and acute myeloid leukemia (AML), respectively. Through these screens, we identified 28 essential genes in PANC-1, 84 essential genes in OCI-AML2, and 28 regulators of colony formation in OCI-AML2. Our results using this small and focused library uncovered false negatives and subtle effects that may be missed in genome-wide approaches, while enabling adaptation to different screening conditions. Overall, our results uncovered previously uncharacterized essential genes in PDAC and AML that can be leveraged as therapeutic targets and biomarkers. We also demonstrate that focused libraries offer a more efficient and targeted approach to uncovering critical genetic determinants of cancer progression.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.1101/2024.09.09.611411
Thomas R.W. Oliver, Andrew R.J. Lawson, Henry Lee-Six, Anna Tollit, Hynchul Jung, Yvette Hooks, Rashesh Sanghvi, Matthew D. Young, Timothy M. Butler, Pantelis Nicola, Taryn D. Treger, G.A. Amos Burke, Kristian Aquilina, Ulrike Lobel, Isidro Cortes-Ciriano, Darren Hargrave, Mette Jorgensen, Flora A. Jessop, Tim H.H. Coorens, Adrienne M. Flanagan, Kieren Allinson, Inigo Martincorena, Thomas S. Jacques, Sam Behjati
Cancer predisposition syndromes mediated by recessive cancer genes generate tumours via somatic variants (second hits) in the unaffected allele. Second hits may or may not be sufficient for neoplastic transformation. Here, we performed whole genome and exome sequencing on 479 tissue biopsies from a child with neurofibromatosis type 1, a multi-system cancer-predisposing syndrome mediated by constitutive monoallelic NF1 inactivation. We identified multiple independent NF1 driver variants in histologically normal tissues, but not in 610 biopsies from two non-predisposed children. We corroborated this finding using targeted duplex sequencing, including a further nine adults with the same syndrome. Overall, truncating NF1 mutations were under positive selection in normal tissues from individuals with neurofibromatosis type 1. We demonstrate that normal tissues in neurofibromatosis type 1 commonly harbour second hits in NF1, the extent and pattern of which may underpin the syndrome's cancer phenotype.
{"title":"Cancer-independent, second somatic NF1 mutation of normal tissues in neurofibromatosis type 1","authors":"Thomas R.W. Oliver, Andrew R.J. Lawson, Henry Lee-Six, Anna Tollit, Hynchul Jung, Yvette Hooks, Rashesh Sanghvi, Matthew D. Young, Timothy M. Butler, Pantelis Nicola, Taryn D. Treger, G.A. Amos Burke, Kristian Aquilina, Ulrike Lobel, Isidro Cortes-Ciriano, Darren Hargrave, Mette Jorgensen, Flora A. Jessop, Tim H.H. Coorens, Adrienne M. Flanagan, Kieren Allinson, Inigo Martincorena, Thomas S. Jacques, Sam Behjati","doi":"10.1101/2024.09.09.611411","DOIUrl":"https://doi.org/10.1101/2024.09.09.611411","url":null,"abstract":"Cancer predisposition syndromes mediated by recessive cancer genes generate tumours via somatic variants (second hits) in the unaffected allele. Second hits may or may not be sufficient for neoplastic transformation. Here, we performed whole genome and exome sequencing on 479 tissue biopsies from a child with neurofibromatosis type 1, a multi-system cancer-predisposing syndrome mediated by constitutive monoallelic NF1 inactivation. We identified multiple independent NF1 driver variants in histologically normal tissues, but not in 610 biopsies from two non-predisposed children. We corroborated this finding using targeted duplex sequencing, including a further nine adults with the same syndrome. Overall, truncating NF1 mutations were under positive selection in normal tissues from individuals with neurofibromatosis type 1. We demonstrate that normal tissues in neurofibromatosis type 1 commonly harbour second hits in NF1, the extent and pattern of which may underpin the syndrome's cancer phenotype.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"71 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.1101/2024.08.23.609447
Courtney Clark, Amir Barzegar Behrooz, Simone C Da Silva Rosa, Jaodi Jacobs, Xiaohui Weng, Abhay Srivastava, Rui Vitorino, Sudharsan Rao Ande, Amir Ravandi, Sanjiv Dhingra, Stevan Pecic, Donald Miller, Shahla Shojaei, Saeid Ghavami
Temozolomide (TMZ) resistance in glioblastoma (GB) poses a significant therapeutic challenge. We developed a TMZ-resistant (TMZ-R) U251 GB model, revealing distinct differences in cell viability, apoptosis, autophagy, and lipid metabolism between TMZ-R and non-resistant (TMZ-NR) cells. TMZ-NR cells exhibited heightened sensitivity to TMZ-induced apoptosis, while TMZ-R cells-maintained viability. Autophagy flux was completely inhibited in TMZ-R cells, indicated by LC3βII and SQSTM1 accumulation. BCL2L13, which showed higher expression in TMZ-R cells, demonstrated increased interaction with Ceramide Synthase 6 (CerS6) and reduced interaction with Ceramide Synthase 2 (CerS2) in TMZ-NR cells. BCL2L13 knockdown (KD) disrupted autophagy flux, decreasing autophagosome accumulation in TMZ-R cells while increasing it in TMZ-NR cells. These changes contributed to altered ceramide profiles, where TMZ-R cells displayed elevated levels of Cer 16:0, 18:0, 20:0, 22:0, 24:0, and 24:1. Our findings highlight BCL2L13 and altered ceramide metabolism as potential therapeutic targets to overcome TMZ resistance in GB.
{"title":"BCL2L13 Influences Autophagy and Ceramide Metabolism without Affecting Temozolomide Resistance in Glioblastoma","authors":"Courtney Clark, Amir Barzegar Behrooz, Simone C Da Silva Rosa, Jaodi Jacobs, Xiaohui Weng, Abhay Srivastava, Rui Vitorino, Sudharsan Rao Ande, Amir Ravandi, Sanjiv Dhingra, Stevan Pecic, Donald Miller, Shahla Shojaei, Saeid Ghavami","doi":"10.1101/2024.08.23.609447","DOIUrl":"https://doi.org/10.1101/2024.08.23.609447","url":null,"abstract":"Temozolomide (TMZ) resistance in glioblastoma (GB) poses a significant therapeutic challenge. We developed a TMZ-resistant (TMZ-R) U251 GB model, revealing distinct differences in cell viability, apoptosis, autophagy, and lipid metabolism between TMZ-R and non-resistant (TMZ-NR) cells. TMZ-NR cells exhibited heightened sensitivity to TMZ-induced apoptosis, while TMZ-R cells-maintained viability. Autophagy flux was completely inhibited in TMZ-R cells, indicated by LC3βII and SQSTM1 accumulation. BCL2L13, which showed higher expression in TMZ-R cells, demonstrated increased interaction with Ceramide Synthase 6 (CerS6) and reduced interaction with Ceramide Synthase 2 (CerS2) in TMZ-NR cells. BCL2L13 knockdown (KD) disrupted autophagy flux, decreasing autophagosome accumulation in TMZ-R cells while increasing it in TMZ-NR cells. These changes contributed to altered ceramide profiles, where TMZ-R cells displayed elevated levels of Cer 16:0, 18:0, 20:0, 22:0, 24:0, and 24:1. Our findings highlight BCL2L13 and altered ceramide metabolism as potential therapeutic targets to overcome TMZ resistance in GB.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.1101/2024.09.08.611557
Yi Yang, Dan Zhao, Ji Luo, Ling Lin, Yuxiang Lin, Baozhen Shan, Hongxu Chen, Liang Qiao
Intact glycopeptide characterization by mass spectrometry has proven a versatile tool for site-specific glycoproteomics analysis and biomarker screening. Here, we present a method using the ZenoTOF instrument with optimized fragmentation for intact glycopeptide identification and demonstrate its ability to analyze large-cohort glycoproteomes. From 124 clinical serum samples of breast cancer, non-cancerous diseases, and non-disease controls, a total of 6901 unique site-specific glycans on 807 glycosites of proteins were detected. Much more differences of glycoproteome were observed in breast diseases than the proteome. By employing machine learning, 15 site-specific glycans were determined as potential glyco-signatures in detecting breast cancer. The results demonstrate that our method provides a powerful tool in glycoproteomic analyses for biomarker discovery studies.
{"title":"Quantitative site-specific glycoproteomics by ZenoTOF reveals glyco-signatures for breast cancer diagnosis","authors":"Yi Yang, Dan Zhao, Ji Luo, Ling Lin, Yuxiang Lin, Baozhen Shan, Hongxu Chen, Liang Qiao","doi":"10.1101/2024.09.08.611557","DOIUrl":"https://doi.org/10.1101/2024.09.08.611557","url":null,"abstract":"Intact glycopeptide characterization by mass spectrometry has proven a versatile tool for site-specific glycoproteomics analysis and biomarker screening. Here, we present a method using the ZenoTOF instrument with optimized fragmentation for intact glycopeptide identification and demonstrate its ability to analyze large-cohort glycoproteomes. From 124 clinical serum samples of breast cancer, non-cancerous diseases, and non-disease controls, a total of 6901 unique site-specific glycans on 807 glycosites of proteins were detected. Much more differences of glycoproteome were observed in breast diseases than the proteome. By employing machine learning, 15 site-specific glycans were determined as potential glyco-signatures in detecting breast cancer. The results demonstrate that our method provides a powerful tool in glycoproteomic analyses for biomarker discovery studies.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"58 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.1101/2024.09.09.611245
Mariah Joy Berner, Heather K. Beasley, Zer Vue, Audra Lane, Larry Vang, Mokryun Lily Baek, Andrea G Marshall, Mason Killion, Faben Zeleke, Bryanna Shao, Dominque Parker, Autumn Peterson, Julie Sterling Rhoades, Estevao Scudese, Lacey E Dobrolecki, Michael T Lewis, Antentor Hinton, Gloria V Echeverria
Mitochondria, which are hubs of metabolism and signaling, play an important role in tumorigenesis, therapeutic resistance, and metastasis in many cancer types. Various laboratory models of cancer demonstrate the extraordinary dynamics of mitochondrial structure, but little is known about the role of mitochondrial structure in resistance to anticancer therapy. We previously demonstrated the importance of mitochondrial structure and oxidative phosphorylation in the survival of chemotherapy-refractory triple negative breast cancer (TNBC) cells. As TNBC is a highly aggressive breast cancer subtype with few targeted therapy options, conventional chemotherapies remain the backbone of early TNBC treatment. Unfortunately, approximately 45% of TNBC patients retain a substantial tumor burden following chemotherapy, associated with abysmal prognoses. Using an orthotopic patient-derived xenograft mouse model of human TNBC, we compared mitochondrial structures between treatment-naive tumors and residual tumors after conventional chemotherapeutics were administered singly or in combination. We reconstructed 1,750 mitochondria in three dimensions from serial block-face scanning electron micrographs, providing unprecedented insights into the complexity and intra-tumoral heterogeneity of mitochondria in human TNBC. Following exposure to carboplatin or docetaxel given individually, residual tumor mitochondria exhibited significant increases in mitochondrial complexity index, area, volume, perimeter, width, and length relative to treatment-naive tumor mitochondria. In contrast, residual tumors exposed to those chemotherapies given in combination exhibited diminished mitochondrial structure changes. Further, we document extensive intra-tumoral heterogeneity of mitochondrial shape, especially in the absence of treatment. These results demonstrate the potential for structure-based monitoring of chemotherapeutic responses and reveal potential molecular mechanisms that underlie chemotherapeutic resistance in TNBC.
{"title":"Three-dimensional analysis of mitochondria in a patient-derived xenograft model of triple negative breast cancer reveals mitochondrial network remodeling following chemotherapy treatments","authors":"Mariah Joy Berner, Heather K. Beasley, Zer Vue, Audra Lane, Larry Vang, Mokryun Lily Baek, Andrea G Marshall, Mason Killion, Faben Zeleke, Bryanna Shao, Dominque Parker, Autumn Peterson, Julie Sterling Rhoades, Estevao Scudese, Lacey E Dobrolecki, Michael T Lewis, Antentor Hinton, Gloria V Echeverria","doi":"10.1101/2024.09.09.611245","DOIUrl":"https://doi.org/10.1101/2024.09.09.611245","url":null,"abstract":"Mitochondria, which are hubs of metabolism and signaling, play an important role in tumorigenesis, therapeutic resistance, and metastasis in many cancer types. Various laboratory models of cancer demonstrate the extraordinary dynamics of mitochondrial structure, but little is known about the role of mitochondrial structure in resistance to anticancer therapy. We previously demonstrated the importance of mitochondrial structure and oxidative phosphorylation in the survival of chemotherapy-refractory triple negative breast cancer (TNBC) cells. As TNBC is a highly aggressive breast cancer subtype with few targeted therapy options, conventional chemotherapies remain the backbone of early TNBC treatment. Unfortunately, approximately 45% of TNBC patients retain a substantial tumor burden following chemotherapy, associated with abysmal prognoses. Using an orthotopic patient-derived xenograft mouse model of human TNBC, we compared mitochondrial structures between treatment-naive tumors and residual tumors after conventional chemotherapeutics were administered singly or in combination. We reconstructed 1,750 mitochondria in three dimensions from serial block-face scanning electron micrographs, providing unprecedented insights into the complexity and intra-tumoral heterogeneity of mitochondria in human TNBC. Following exposure to carboplatin or docetaxel given individually, residual tumor mitochondria exhibited significant increases in mitochondrial complexity index, area, volume, perimeter, width, and length relative to treatment-naive tumor mitochondria. In contrast, residual tumors exposed to those chemotherapies given in combination exhibited diminished mitochondrial structure changes. Further, we document extensive intra-tumoral heterogeneity of mitochondrial shape, especially in the absence of treatment. These results demonstrate the potential for structure-based monitoring of chemotherapeutic responses and reveal potential molecular mechanisms that underlie chemotherapeutic resistance in TNBC.","PeriodicalId":501233,"journal":{"name":"bioRxiv - Cancer Biology","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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