Biology subjects

Kim, C.

Publications and source records attributed to Kim, C..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

GENOMES UNCOUPLED1: an RNA-binding protein required for early PSII biogenesis

Genomes Uncoupled1 (GUN1), a nuclear-encoded chloroplast pentatricopeptide repeat (PPR) protein, serves as a master integrator of diverse retrograde signals, mediating chloroplast-to-nucleus retrograde signaling. Although PPR proteins primarily function in organelle RNA metabolism, a target RNA of GUN1 remained unknown. This study reveals that GUN1 recognizes psbD transcripts derived from a blue light-responsive promoter (BLRP), transcripts referred to as psbD BLRP. Overexpression of GUN1 significantly reduces the levels of psbD BLRP, whereas the loss of GUN1 leads to the accumulation of the putative target RNA. The in vitro RNA and in vivo genetic studies further demonstrate the critical role of the C-terminal small MutS-related (SMR) domain in stimulating psbD BLRP processing and PsbD (D2, a PSII core protein) synthesis. The GUN1-dependent psbD BLRP processing promotes PSII biogenesis during the early seedling development and de-etiolation phase. This finding underscores the role of GUN1 as an RNA-binding protein, highlighting the essential function of the SMR domain in processing the target RNA. SignificanceBiogenic retrograde signaling is essential in regulating chloroplast biogenesis, and it entails a nuclear-encoded chloroplast protein, Genomes Uncoupled1 (GUN1). Since its initial discovery in 1993, the gun1 mutant has been widely used to reveal the precise function of GUN1 in plastids as well as its downstream signaling components. Although GUN1 contains pentatricopeptide repeat motifs, it has been considered a non-canonical PPR protein because no one could demonstrate GUN1-RNA interaction in planta. However, through our computational analysis of PPR codes and subsequent biochemical studies, we were able to unravel its putative target RNA, namely psbD BLRP. Therefore, our finding may lead to a reevaluation of GUN1 research in the context of RNA metabolism and a revision of our current understanding of GUN1.

plant biology↗

bioRxiv2023

Fibronectin: a natural barrier against prion infection

A distinctive signature of the prion diseases is the accumulation of the pathogenic isoform of the prion protein, PrPSc, in the central nervous system of prion-affected humans and animals. PrPSc is also found in peripheral tissues, raising concerns about the potential transmission of pathogenic prions through human food supplies and posing a significant risk to public health. Although muscle tissues are considered to contain levels of low prion infectivity, it has been shown that myotubes in culture efficiently propagate PrPSc. Given the high consumption of muscle tissue, it is important to understand what factors could influence the establishment of a prion infection in muscle tissue. Here we used in vitro myotube cultures, differentiated from the C2C12 myoblast cell line (dC2C12), to identify factors affecting prion replication. A range of experimental conditions revealed that PrPSc is tightly associated with proteins found in the systemic extracellular matrix (ECM), mostly fibronectin (FN). The interaction of PrPSc with FN decreased prion infectivity, as determined by standard scrapie cell assay. Interestingly, the prion-resistant reserve cells in dC2C12 cultures displayed a FN-rich ECM while the prion-susceptible myotubes expressed FN at a low level. In agreement with the in vitro results, immunohistopathological analyses of tissues from sheep infected with natural scrapie demonstrated a prion susceptibility phenotype linked to an extracellular matrix with undetectable levels of FN. Conversely, PrPSc deposits were not observed in tissues expressing FN. These data indicate that extracellular FN may act as a natural barrier against prion replication and that the extracellular matrix composition may be a crucial feature determining prion tropism in different tissues. Author summaryPrion diseases are complex fatal neurodegenerative disorders caused by a misfolded form of the cellular protein PrPC (PrPSc). Due to the potential zoonotic transmission of these disorders through animal-based food intake, it is crucial to identify the tissues in which PrPSc can accumulate and what might influence its tropism. Animal muscle (or meat) and related food products are highly consumed, raising concern of the involvement of muscle cells in prion replication. Muscle tissue from prion-affected animals contains low levels of infectivity and PrPSc is mostly associated with nerve structures rather than myofibers, whereas C2C12 myotubes, a muscle-derived cell type, efficiently replicate prions in vitro and generate high levels of infectivity compared with other cell cultures. We demonstrate a fibronectin-mediated interference with prion infection in differentiated C2C12 cultures that correlates with the findings in tissues from naturally scrapie-infected animals. Our results suggest that extracellular matrix composition, specifically regarding the presence of fibronectin, might determine prion tropism and dissemination.

biochemistry↗

bioRxiv2023

Spatiotemporal molecular dynamics of the developing human thalamus

The thalamus plays a central coordinating role in the brain. Thalamic neurons are organized into spatially-distinct nuclei, but the molecular architecture of thalamic development is poorly understood, especially in humans. To begin to delineate the molecular trajectories of cell fate specification and organization in the developing human thalamus, we used single cell and multiplexed spatial transcriptomics. Here we show that molecularly-defined thalamic neurons differentiate in the second trimester of human development, and that these neurons organize into spatially and molecularly distinct nuclei. We identify major subtypes of glutamatergic neuron subtypes that are differentially enriched in anatomically distinct nuclei. In addition, we identify six subtypes of GABAergic neurons that are shared and distinct across thalamic nuclei. One-Sentence SummarySingle cell and spatial profiling of the developing thalamus in the first and second trimester yields molecular mechanisms of thalamic nuclei development.

neuroscience↗

bioRxiv2023

Macrophages sense ECM mechanics and growth factor availability through cytoskeletal remodeling to regulate their tissue repair program

Tissue resident macrophages play important roles in tissue homeostasis and repair. However, how macrophages monitor and maintain tissue integrity is not well understood. The extracellular matrix (ECM) is a key structural and organizational component of all tissues. Here, we find that macrophages sense the mechanical properties of the ECM in order to regulate a specific tissue repair program. We show that macrophage mechanosensing is mediated by cytoskeletal remodeling and can be performed in three-dimensional environments through a non-canonical, integrin-independent mechanism analogous to amoeboid migration. We find that these cytoskeletal dynamics also integrate biochemical signaling by CSF1 and ultimately regulate chromatin accessibility to control the mechanosensitive gene expression program. This study suggests a distinct mode of ECM mechanosensing and growth factor signaling through which macrophages may regulate tissue repair and fibrosis.

immunology↗

bioRxiv2023

Neurophysiological correlates of Somatosensory tinnitus modulation

Tinnitus is the subjective perception of a sound in absence of corresponding external acoustic stimuli. Research highlights the influence of the sensorimotor system on tinnitus perception. Associated neuronal processes, however, are insufficiently understood and it remains unclear how and at which hierarchical level the sensorimotor system interacts with the tinnitus-processing auditory system. We therefore asked 23 patients suffering from chronic tinnitus (11 males) to perform specific exercises, aimed at relaxing or tensing the jaw area, which temporarily modulated tinnitus perception. Associated neuronal processes were assessed using Magnetencephalography. Results show that chronic tinnitus patients experienced their tinnitus as weaker and less annoying after completion of relaxing compared to tensing exercises. Furthermore, (1) sensorimotor alpha power and alpha-band connectivity directed from the somatosensory to the auditory cortex increased, and (2) gamma power in the auditory cortex, reduced, which (3) related to reduced tinnitus annoyance perception on a trial-by-trial basis in the relaxed state. No effects were revealed for 23 control participants without tinnitus (6 males) performing the same experiment. We conclude that the increase in directed alpha-band connectivity from somatosensory to auditory cortex is most likely reflecting the transmission of inhibition from somatosensory to auditory cortex during relaxation, where concurrently tinnitus-related gamma power reduces. We suggest that revealed neuronal processes are transferable to other tinnitus modulating systems beyond the sensorimotor one that are e.g. involved in attentional or emotional tinnitus modulation and provide deeper mechanistic insights into how and through which channels phantom sound perception might be modulated on a neuronal level. Significance StatementTinnitus describes the perception of auditory phantom sounds. Research suggests that the sensorimotor system impacts on tinnitus perception, associated neuronal mechanisms, however, have remained unclear. Here, chronic tinnitus patients performed exercises with the jaw temporarily reducing (versus increasing) tinnitus perception. Tinnitus reduction was accompanied by an increase of alpha-band connectivity directed from the somatosensory to the auditory cortex and gamma power reduction in the auditory cortex. We suggest that the increase in alpha-band connectivity, when tinnitus is reduced, reflects the transmission of inhibition from somatosensory to auditory cortex, where, in parallel, probably tinnitus related, gamma power reduces. The findings have important implications both for the understanding of phantom sound perception and, more generally, of top-down modulation in healthy and impaired cognition.

neuroscience↗

bioRxiv2023

Deep speech-to-text models capture the neural basis of spontaneous speech in everyday conversations

Humans effortlessly use the continuous acoustics of speech to communicate rich linguistic meaning during everyday conversations. In this study, we leverage 100 hours (half a million words) of spontaneous open-ended conversations and concurrent high-quality neural activity recorded using electrocorticography (ECoG) to decipher the neural basis of real-world speech production and comprehension. Employing a deep multimodal speech-to-text model named Whisper, we develop encoding models capable of accurately predicting neural responses to both acoustic and semantic aspects of speech. Our encoding models achieved high accuracy in predicting neural responses in hundreds of thousands of words across many hours of left-out recordings. We uncover a distributed cortical hierarchy for speech and language processing, with sensory and motor regions encoding acoustic features of speech and higher-level language areas encoding syntactic and semantic information. Many electrodes--including those in both perceptual and motor areas--display mixed selectivity for both speech and linguistic features. Notably, our encoding model reveals a temporal progression from language-to-speech encoding before word onset during speech production and from speech-to-language encoding following word articulation during speech comprehension. This study offers a comprehensive account of the unfolding neural responses during fully natural, unbounded daily conversations. By leveraging a multimodal deep speech recognition model, we highlight the power of deep learning for unraveling the neural mechanisms of language processing in real-world contexts.

neuroscience↗

bioRxiv2023

Decreasing alpha flow releases task-specific processing paths

Directing and maintaining attention toward relevant information and away from non-relevant information is a critical competence of higher-order nervous systems. Here, we used directed connectivity to investigate how the human brain prioritizes appropriate processing paths when participants are performing a behavioral task requiring attention in the visual or the auditory modality. We show that the efficient transfer of information relevant for the task is mediated by a region- and task-specific decrease of alpha band connectivity from parietal and, in case a motor response is required, motor cortex to the relevant sensory cortices. Further, alpha-band connectivity modulations reliably predict alpha power modulations in the task-related sensory cortices, particularly where the task-irrelevant cortex is inhibited via local alpha power increases. We suggest that the task- and region-specific modulation of alpha-band connectivity in the present study is a basic neuronal mechanism orchestrating the allocation of task-relevant neuronal resources related to and possibly underlying the previously reported sensory alpha power modulations in association with the allocation of competing attentional resources.

neuroscience↗

bioRxiv2023

Albumin-binding recombinant human IL-18BP ameliorates macrophage activation syndrome and atopic dermatitis via direct IL-18 inactivation

Given the clinical success of cytokine blockade in managing diverse inflammatory human conditions, this approach could be exploited for numerous refractory or uncontrolled inflammatory conditions by identifying novel targets for functional blockade. IL-18, a pro-inflammatory cytokine, is relatively underestimated as a therapeutic target, despite accumulated evidence indicating the unique roles of IL-18 in acute and chronic inflammatory conditions, such as macrophage activation syndrome. Herein, we designed a new form of IL-18 blockade, i.e., APB-R3, a long-acting recombinant human IL-18BP linked to human albumin-binding Fab fragment, SL335, for extending half-life. We then explored the pharmacokinetics and pharmacodynamics of APB-R3. In addition to an extended serum half-life, APB-R3 alleviates liver inflammation and splenomegaly in a model of the macrophage activation syndrome induced in IL-18BP knockout mice. Moreover, APB-R3 substantially controlled skin inflammation in a model of atopic dermatitis. Thus, we report APB-R3 as a new potent IL-18 blocking agent that could be applied to treat IL-18-mediated inflammatory diseases.

immunology↗

bioRxiv2023

Targeting Transferrin Receptor to Transport Antisense Oligonucleotides Across the Blood-Brain Barrier

Antisense oligonucleotides (ASO) are promising therapies for neurological disorders, though they are unable to cross the blood-brain barrier (BBB) and must be delivered directly to the central nervous system (CNS). Here, we use a human transferrin receptor (TfR)-binding molecule to transport ASO across the BBB in mice and non-human primates, termed oligonucleotide transport vehicle (OTV). Systemically delivered OTV drives significant, cumulative, and sustained knockdown of the ASO target across multiple CNS regions and all major cell types. Further, systemic OTV delivery enables more uniform ASO biodistribution and knockdown compared to two other clinically relevant ASO delivery routes: a standard, high affinity TfR antibody, or direct ASO delivery to the CSF. Together, our data support systemically delivered OTV as a potential therapeutic platform for neurological disorders. One-Sentence SummarySystemically dosed OTV delivered via TfR1 targeting shows widespread and cumulative target knockdown in the mouse and NHP CNS.

neuroscience↗

bioRxiv2023

Characterization of Tryptophan Oxidation Affecting D1 Degradation by FtsH in the Photosystem II Quality Control of Chloroplasts

Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH. Competing Interest StatementThe authors have no conflict of interest, financial or otherwise, in relation to this study Impact StatementOxidative modification of Tryptophan residues in the reaction center protein D1 may be a key to drive the Photosystem II repair, likely enhancing accessibility of FtsH protease to D1.

plant biology↗

bioRxiv2023

A biophysical framework for double-drugging kinases

Orthosteric inhibition of kinases has been challenging due to the conserved active site architecture of kinases and emergence of resistance mutants. Simultaneous inhibition of distant orthosteric and allosteric sites, which we refer to as "double-drugging", has recently been shown to be effective in overcoming drug resistance. However, detailed biophysical characterization of the cooperative nature between orthosteric and allosteric modulators has not been undertaken. Here, we provide a quantitative framework for double-drugging of kinases employing isothermal titration calorimetry, Forster resonance energy transfer, coupled-enzyme assays, and X-ray crystallography. We discern positive and negative cooperativity for Aurora A kinase (AurA) and Abelson kinase (Abl) with different combinations of orthosteric and allosteric modulators. We find that a conformational equilibrium shift is the main principle governing this cooperative effect. Notably, for both kinases, we find a synergistic decrease of the required orthosteric and allosteric drug dosages when used in combination to inhibit kinase activities to clinically relevant inhibition levels. X-ray crystal structures of the doubledrugged kinase complexes reveal the molecular principles underlying the cooperative nature of double-drugging AurA and Abl with orthosteric and allosteric inhibitors. Finally, we observe the first fully-closed conformation of Abl when bound to a pair of positively cooperative orthosteric and allosteric modulators, shedding light onto the puzzling abnormality of previously solved closed Abl structures. Collectively, our data provide mechanistic and structural insights into rational design and evaluation of doubledrugging strategies.

biochemistry↗

bioRxiv2023

Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf genetic affiliations and their taxonomic implications, we sequenced and analysed the genomes of a historical Korean wolf dated to the beginning of the 20th century, and a captive wolf originally located at the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find the Korean wolf has similar diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is more genetically similar to wolves from the Tibetan Plateau, hence, Korean wolf conservation programs might not benefit from the inclusion of this specimen.

evolutionary biology↗

bioRxiv2023

FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

Cellular exposure to free fatty acids (FFA) is implicated in the pathogenesis of obesity-associated diseases. However, studies to date have assumed that a few select FFAs are representative of broad structural categories, and there are no scalable approaches to comprehensively assess the biological processes induced by exposure to diverse FFAs circulating in human plasma. Furthermore, assessing how these FFA- mediated processes interact with genetic risk for disease remains elusive. Here we report the design and implementation of FALCON (Fatty Acid Library for Comprehensive ONtologies) as an unbiased, scalable and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids (MUFAs) with a distinct lipidomic profile associated with decreased membrane fluidity. Furthermore, we developed a new approach to prioritize genes that reflect the combined effects of exposure to harmful FFAs and genetic risk for type 2 diabetes (T2D). Importantly, we found that c-MAF inducing protein (CMIP) protects cells from exposure to FFAs by modulating Akt signaling and we validated the role of CMIP in human pancreatic beta cells. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism. HighlightsO_LIFALCON (Fatty Acid Library for Comprehensive ONtologies) enables multimodal profiling of 61 free fatty acids (FFAs) to reveal 5 FFA clusters with distinct biological effects C_LIO_LIFALCON is applicable to many and diverse cell types C_LIO_LIA subset of monounsaturated FAs (MUFAs) equally or more toxic than canonical lipotoxic saturated FAs (SFAs) leads to decreased membrane fluidity C_LIO_LINew approach prioritizes genes that represent the combined effects of environmental (FFA) exposure and genetic risk for disease C_LIO_LIC-Maf inducing protein (CMIP) is identified as a suppressor of FFA-induced lipotoxicity via Akt-mediated signaling C_LI

cell biology↗

bioRxiv2023

Human Bone Marrow Plasma Cell Atlas: Maturation and Survival Pathways Unraveled by Single Cell Analyses

Human bone marrow (BM) plasma cells are heterogeneous, ranging from newly arrived antibody-secreting cells (ASC) to long-lived plasma cells (LLPC). We provide single cell transcriptional resolution of 17,347 BM ASC from 5 healthy adults. Fifteen clusters were identified ranging from newly minted ASC (cluster 1) expressing MKI67 and high MHC Class II that progressed to late clusters 5-8 through intermediate clusters 2-4. Additional clusters included early and late IgM-predominant ASC of likely extra-follicular origin; IFN-responsive; and high mitochondrial activity ASC. Late ASCs were distinguished by differences in G2M checkpoints, MTOR signaling, distinct metabolic pathways, CD38 expression, and utilization of TNF-receptor superfamily members. They mature through two distinct paths differentiated by the degree of TNF signaling through NFKB. This study provides the first single cell resolution atlas and molecular roadmap of LLPC maturation, thereby providing insight into differentiation trajectories and molecular regulation of these essential processes in the human BM microniche. This information enables investigation of the origin of protective and pathogenic antibodies in multiple diseases and development of new strategies targeted to the enhancement or depletion of the corresponding ASC. One Sentence Summary: The single cell transcriptomic atlas of human bone marrow plasma cell heterogeneity shows maturation of class-switched early and late subsets, specific IgM and Interferon-driven clusters, and unique heterogeneity of the late subsets which encompass the long-lived plasma cells.

immunology↗

bioRxiv2022

Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups

We present 4,157 whole-genome sequences (Korea4K) coupled with 107 health check-up parameters as the largest whole genomic resource of Koreans. Korea4K provides 45,537,252 variants and encompasses most of the common and rare variants in Koreans. We identified 1,356 new geno-phenotype associations which were not found by the previous Korea1K dataset. Phenomics analyses revealed 24 genetic correlations, 1,131 pleiotropic variants, and 127 causal relationships from Mendelian randomization. Moreover, the Korea4K imputation reference panel showed a superior imputation performance to Korea1K. Collectively, Korea4K provides the most extensive genomic and phenomic data resources for discovering clinically relevant novel genome-phenome associations in Koreans.

genomics↗

bioRxiv2022

An improved reference of the grapevine genome supports reasserting the origin of the PN40024 highly-homozygous genotype

The genome sequence assembly of the diploid and highly homozygous V. vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements of the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, despite the PN40024 genome is nearly homozygous, it still contains various heterozygous regions. Taking the opportunity of the improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences and considering that several Vitis sp. genomes have recently been assembled with these approaches, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased. The number of scaffolds decreased from 2,059 to 640 and the number of N bases was reduced by 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the amount of unplaced scaffolds were reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation to date of 35,230 genes. Finally, we demonstrate that PN40024 resulted from selfings of cv. Helfensteiner (cross of cv. Pinot noir and Schiava grossa) instead of a single Pinot noir. These advances will help maintaining the PN40024 genome as a gold-standard reference also contributing in the eventual elaboration of the grapevine pangenome.

genomics↗

bioRxiv2022

Frequent first-trimester pregnancy loss in rhesus macaques infected with African-lineage Zika virus

In the 2016 Zika virus (ZIKV) pandemic, a previously unrecognized risk of birth defects surfaced in babies whose mothers were infected with Asian-lineage ZIKV during pregnancy. Less is known about the impacts of gestational African-lineage ZIKV infections. Given high human immunodeficiency virus (HIV) burdens in regions where African-lineage ZIKV circulates, we evaluated whether pregnant rhesus macaques infected with simian immunodeficiency virus (SIV) have a higher risk of African-lineage ZIKV-associated birth defects. Remarkably, in both SIV+ and SIV-animals, ZIKV infection early in the first trimester caused a high incidence (78%) of spontaneous pregnancy loss within 20 days. These findings suggest a significant risk for early pregnancy loss associated with African-lineage ZIKV infection and provide the first consistent ZIKV-associated phenotype in macaques for testing medical countermeasures.

microbiology↗

bioRxiv2022

Induced Degradation of Lineage-specific Oncoproteins Drives the Selective PARP1 Inhibitor Toxicity in Small Cell Lung Cancer

A subset of small cell lung cancer (SCLC) shows clinically relevant response to PARP1 inhibitors (PARPi). However, BRCA1/2 mutations are not commonly found in SCLC, and the underlying mechanism(s) of PARPi sensitivity in SCLC is poorly understood. We performed quantitative proteomic analyses and identified proteomic changes that signify PARPi responses in a large panel of molecularly annotated patient-derived SCLC lines. We found that the toxicity of PARPi in SCLC could be explained, at least in part, by the PARPi-induced degradation of key lineage-specific oncoproteins including ASCL1, NEUROD1, POU2F3, KDM4A, and KDM5B. Importantly, the degradation of these SCLC lineage-specific oncoproteins could also be induced by commonly used chemotherapeutic agents. Biochemical experiments showed that PARPi-induced activation of E3 ligases (e.g., HUWE1 and RNF8) mediated the ubiquitin-proteasome system (UPS)-dependent degradation of these oncoproteins. Interestingly, although PARPi resulted in a general DNA damage response in SCLC cells, this signal is sensed by different SCLC cell lines to generate a cell-specific response. The dissection of the cell-specific oncoprotein degradation response led to the identification of potentially predictive biomarkers for PARPi in SCLC. The combination of PARPi and agents targeting these pathways led to dramatically improved cytotoxicity in SCLC. PARPi-induced degradation of lineage-specific oncoproteins therefore represents a novel mechanism to explain the efficacy of PARPi in tumors without BRCA1/2 mutations. HighlightsO_LIQuantitative mass spectrometric analysis identifies proteomic changes associated with PARPi treatment in a large panel of SCLC cell lines. C_LIO_LIPARPi leads to the degradation of lineage-specific oncoproteins (e.g., ASCL1 and KDM4A) via the DNA damage responsive E3 ubiquitin ligases (e.g., HUWE1 and RNF8). C_LIO_LIA combination of PARPi and agents targeting the lineage-specific oncoproteins offers a more complete and durable therapeutic response in SCLC, compared to PARPi alone. C_LIO_LIExpression of lineage-specific oncoproteins and the associated ubiquitination machinery are predictive biomarkers for PARPi-induced cytotoxicity in SCLC. C_LI

cancer biology↗