Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder in which an RNA-binding protein, TDP-43, mislocalizes and pathologically accumulates from its normal nuclear locale to the cytosol. Given that the subcellular localization and expression of TDP-43 is tightly regulated, we posit that identifying novel interactors of wild-type and mutant TDP-43 could reveal insight into networks involved in regulating its localization, ultimately driving neurodegeneration in ALS. Using CRISPR/Cas9, our lab previously generated knock-in cell lines expressing GFP in the endogenous TARDBP locus (encoding for TDP-43) for both wildtype (WT) and an ALS-causing mutant (Q331K). We have shown that the Q331K mutation causes loss-of-function and mislocalization of TDP-43. I performed immunoprecipitation coupled to mass spectrometry (IP-MS) on this cell model to elucidate interactors of WT- and Q331K- TDP-43. Our data show that there is an overall loss of TDP-43 interactors in cells with the TDP-43Q331K mutation. By setting statistical cut-offs for significance, we identified 34 shared and 12 unique interactors of TDP-43WT. We used bioinformatic approaches to identify enriched pathways and literature searches to look for interactors relevant to TDP-43 and ALS pathobiology. Our shortlist of 14 candidates for validation included proteins involved in the nuclear mRNA export pathways, RNA binding proteins and proteins identified in other interactome studies and TDP-43 based screens. Using orthogonal approaches, we show evidence of robust interaction of four top hits (PABPC1, HNRNPC, DDX39b and ELAVL1) with TDP-43WT, and a significant decrease in the degree of interaction of HNRNPC, DDX39b and ELAVL1 with TDP-43Q331K. Importantly, this decrease in interaction was only observed at the endogenous level, highlighting the importance of maintaining the steady state levels of TDP-43 in the cell for these assays. We characterized the effects of knockdown and overexpression of these four hits using protein-specific overexpression constructs and shRNAs and observed a significant increase in TDP-43 nuclear localization upon knockdown of these four hits, suggesting that there is a functional effect associated with hit knockdown. Overexpression or knockdown of the top hits in a splicing assay did not identify significant changes in TDP-43’s splicing or RNA binding abilities, suggesting that these hits do not affect splicing function in our hit characterization studies. Using this novel experimental tool and unbiased screen, we identified alterations in TDP-43 protein-protein interactions in the context of ALS and have generated tools to characterize their roles in cellular functions using knockdown and overexpression approaches. Together with the knock-in cells, these tools will allow us to gain insight into pathways involved in driving neurodegeneration, in the context of ALS.

INTRODUÇÃO: A proteína TDP-43 (Transactive DNA-binding protein 43) é o principal agregado proteico anormal verificado em casos de Degeneração Lobar Frontotemporal (DLFT) e Esclerose Lateral Amiotrófica (ELA). Apesar dos avanços na área, o papel da TDP-43 no envelhecimento normal ainda é pouco compreendido. A falta de indivíduos controles em estudos de associação clinicopatológica com tecido cerebral humano é resultado do alto custo da prática de autópsia mundialmente. O que é um diferencial do Brasil, onde essa prática é obrigatória em casos de morte natural sem causa definida. O Banco de Encéfalos Humanos do Grupo de Estudos em Envelhecimento Cerebral (BEHGEEC) possui grande número de encéfalos de sujeitos sem déficit cognitivo com alta miscigenação étnica e variação de graus de escolaridade. O que possibilita estudos mais aprofundados sobre envelhecimento cerebral humano não-patológico. OBJETIVOS: (1) investigar de maneira sistemática a distribuição dos achados neuropatológicos da TDP-43 no envelhecimento humano normal; (2) caracterizar a distribuição dessa proteína em diferentes áreas encefálicas; (3) explorar associação de características, clínicas, sociodemográficas ou neuropatológicas com o aparecimento das inclusões de TDP-43. MÉTODOS: Foram incluídos participantes com idade acima de 50 anos e classificados clinicamente e anatomopatologicamente como normais. Reação imunoistoquímica contra a conformação anormal da TDP-43 foi realizada em três regiões cerebrais de interesse córtex temporal, amígdala e hipocampo. RESULTADOS: Os agregados de TDP-43 estavam presentes em 10,5% dos indivíduos estudados (n=323). A região mais frequentemente acometida foi a amígdala (85,3% dos casos). O acúmulo de TDP-43 foi associado à idade e raça (p=0,002). Análise de regressão logística demonstrou que indivíduos da raça asiática possuem maior chance de apresentar os agregados de TDP-43 do que caucasianos, independente dos fatores gênero, idade, estágio de Braak para emaranhados neurofibrilares e escolaridade (odds ratio=3,5: intervalo de confiança: 1,41-8,69, p=0,007). CONCLUSÕES: Os resultados sugerem que o acúmulo anormal de TDP-43 aumenta com o avanço da idade e que a amígdala é a região cerebral mais susceptível ao acúmulo desse tipo de inclusão. Como os idosos estudados são cognitivamente normais, sugerimos que indivíduos asiáticos estão protegidos contra os efeitos deletérios da proteína TDP-43 no cérebro. Futuros estudos de associação clinicopatológica e genética em populações de diferentes raças poderão contribuir para identificação de possíveis fatores de proteção contra a expressão clínica dos achados da proteína TDP-43 / BACKGROUND: Transactive DNA-binding protein 43 (TDP-43) is the major abnormal aggregate present in Frontotemporal Lobar Degeneration (FTLD) and Amyotrophic Lateral Slcerosis (ALS). Although all the efforts in research in this field, the role played by TDP-43 in normal aging is still unknown. The lack of normal controls in studies focusing on clinicopathological associations is a result of the high cost of autopsy practice worldwide. In Brazil, autopsy is mandatory by law in cases without a certificate. The Brain Bank of the Brazilian Aging Study Group (BBBASG) comprises a large number of cognitively normal elderly subjects highly ethnically admixtured and with broad education attainment. This allow us to further study the non-pathological process of the human aging brain. GOALS: (1) sistematically investigate the distrubution of neuropathological findings of TDP-43 in the normal human brain; (2) characterize the distribution of theses findings in different brain regions; (3) explore clinical, sociodemographics or neuropathological variables that could be associated with TDP-43 inclusion outcome. METHODS: We included participants over 50 years old previously classified cognitively and neuropathologically as normals. Imunnohistochemistry against abnormal form of TDP-43 was performed in three brain regions: temporal cortex, hippocampal formation and amygdala. RESULTS: TDP-43 aggregates were present in 10,5% of the study subjects (n=323). Amygdala was the most frequently affected brain region (85.3% of the cases). TDP-43 accumulation was associated with age at death and race (p=0.002). Logistic regression analysis showed that asians older adults have higher odds of presenting TDP-43 inclusions than caucasians, regardless of gender, age, Braak stage for neurofibrilarly tangles and education attainment (OD=3.5, CI: 1.41-8.69, p=0.007). CONCLUSIONS: Our results suggest that TDP-43 abnormal accumulation increases along aging process and the amygdala is the brain region most susceptible to these alterations. Because we studied cognitively normal elderlies, we suggest that Asians older adults are protected against deleterious effects of TDP-43 in the brain. Future clinicopathological and genetic studies in populations dwelling in different ethnical backgrounds may identify possible protecting factors against the clinical expression of TDP-43 neuropathological findings

INTRODUÇÃO: A proteína TDP-43 (Transactive DNA-binding protein 43) é o principal agregado proteico anormal verificado em casos de Degeneração Lobar Frontotemporal (DLFT) e Esclerose Lateral Amiotrófica (ELA). Apesar dos avanços na área, o papel da TDP-43 no envelhecimento normal ainda é pouco compreendido. A falta de indivíduos controles em estudos de associação clinicopatológica com tecido cerebral humano é resultado do alto custo da prática de autópsia mundialmente. O que é um diferencial do Brasil, onde essa prática é obrigatória em casos de morte natural sem causa definida. O Banco de Encéfalos Humanos do Grupo de Estudos em Envelhecimento Cerebral (BEHGEEC) possui grande número de encéfalos de sujeitos sem déficit cognitivo com alta miscigenação étnica e variação de graus de escolaridade. O que possibilita estudos mais aprofundados sobre envelhecimento cerebral humano não-patológico. OBJETIVOS: (1) investigar de maneira sistemática a distribuição dos achados neuropatológicos da TDP-43 no envelhecimento humano normal; (2) caracterizar a distribuição dessa proteína em diferentes áreas encefálicas; (3) explorar associação de características, clínicas, sociodemográficas ou neuropatológicas com o aparecimento das inclusões de TDP-43. MÉTODOS: Foram incluídos participantes com idade acima de 50 anos e classificados clinicamente e anatomopatologicamente como normais. Reação imunoistoquímica contra a conformação anormal da TDP-43 foi realizada em três regiões cerebrais de interesse córtex temporal, amígdala e hipocampo. RESULTADOS: Os agregados de TDP-43 estavam presentes em 10,5% dos indivíduos estudados (n=323). A região mais frequentemente acometida foi a amígdala (85,3% dos casos). O acúmulo de TDP-43 foi associado à idade e raça (p=0,002). Análise de regressão logística demonstrou que indivíduos da raça asiática possuem maior chance de apresentar os agregados de TDP-43 do que caucasianos, independente dos fatores gênero, idade, estágio de Braak para emaranhados neurofibrilares e escolaridade (odds ratio=3,5: intervalo de confiança: 1,41-8,69, p=0,007). CONCLUSÕES: Os resultados sugerem que o acúmulo anormal de TDP-43 aumenta com o avanço da idade e que a amígdala é a região cerebral mais susceptível ao acúmulo desse tipo de inclusão. Como os idosos estudados são cognitivamente normais, sugerimos que indivíduos asiáticos estão protegidos contra os efeitos deletérios da proteína TDP-43 no cérebro. Futuros estudos de associação clinicopatológica e genética em populações de diferentes raças poderão contribuir para identificação de possíveis fatores de proteção contra a expressão clínica dos achados da proteína TDP-43 / BACKGROUND: Transactive DNA-binding protein 43 (TDP-43) is the major abnormal aggregate present in Frontotemporal Lobar Degeneration (FTLD) and Amyotrophic Lateral Slcerosis (ALS). Although all the efforts in research in this field, the role played by TDP-43 in normal aging is still unknown. The lack of normal controls in studies focusing on clinicopathological associations is a result of the high cost of autopsy practice worldwide. In Brazil, autopsy is mandatory by law in cases without a certificate. The Brain Bank of the Brazilian Aging Study Group (BBBASG) comprises a large number of cognitively normal elderly subjects highly ethnically admixtured and with broad education attainment. This allow us to further study the non-pathological process of the human aging brain. GOALS: (1) sistematically investigate the distrubution of neuropathological findings of TDP-43 in the normal human brain; (2) characterize the distribution of theses findings in different brain regions; (3) explore clinical, sociodemographics or neuropathological variables that could be associated with TDP-43 inclusion outcome. METHODS: We included participants over 50 years old previously classified cognitively and neuropathologically as normals. Imunnohistochemistry against abnormal form of TDP-43 was performed in three brain regions: temporal cortex, hippocampal formation and amygdala. RESULTS: TDP-43 aggregates were present in 10,5% of the study subjects (n=323). Amygdala was the most frequently affected brain region (85.3% of the cases). TDP-43 accumulation was associated with age at death and race (p=0.002). Logistic regression analysis showed that asians older adults have higher odds of presenting TDP-43 inclusions than caucasians, regardless of gender, age, Braak stage for neurofibrilarly tangles and education attainment (OD=3.5, CI: 1.41-8.69, p=0.007). CONCLUSIONS: Our results suggest that TDP-43 abnormal accumulation increases along aging process and the amygdala is the brain region most susceptible to these alterations. Because we studied cognitively normal elderlies, we suggest that Asians older adults are protected against deleterious effects of TDP-43 in the brain. Future clinicopathological and genetic studies in populations dwelling in different ethnical backgrounds may identify possible protecting factors against the clinical expression of TDP-43 neuropathological findings

Neurodegenerative Erkrankungen (NDs) wie Alzheimer (AD), Parkinson (PD), und amyotrophe lateral Sklerose (ALS) sind Hirnerkrankungen, die durch unlösliche Proteinaggregate in Neuronen oder im Extrazellularraum charakterisiert sind. In dieser Arbeit habe ich für verschiede bekannte und vorhergesagte neurodegenerative Krankheitsproteine (NDPs) Proteininteraktionsnetzwerke erstellt, um mögliche gemeinsame Krankheitsmechanismen genauer zu studieren. Mit Hilfe eines automatisierten Hefe-Zwei-Hybrid-Systems (Y2H) konnte ich 18.663 Protein-Protein-Interaktionen (PPIs) für 449 wildtyp und 22 mutierte Proteine identifizieren. Eine genaue funktionelle Analyse der Interaktionspartner von korrespondierenden wildtyp und mutierten Proteinen ergab deutliche Unterschiede zum einen im Fall von allen untersuchten Proteinen und insbesondere im Fall vom ALS Krankheitsprotein TDP-43. Die identifizierten PPIs wurden außerdem verwendet um krankheitsspezifische Netzwerke zu erstellen und um Proteine zu identifizieren, die mit mehreren NDPs verbunden sind. Ich habe auf diese Weise vier Proteine (APP, IQSEC1, ZNF179 und ZMAT2) gefunden, die mit bekannten NDPs with Huntingtin, TDP-43, Parkin und Ataxin-1 interagieren und so fünf verschiedene NDs miteinander verbinden. Die Reduktion der mRNA Expression von IQSEC1, ZNF179 oder ZMAT2 mit Hilfe von siRNA führte zu einer Verstärkung von pathogenen Mechanismen wie der Aggregation von mutiertem Huntingtin und TDP-43 sowie der Hyperphosphorylierung des Proteins Tau. Außerdem habe ich 22 Proteine entdeckt, die die Aggregation von TDP-43 deutlich verändern und außerdem Mitglieder in sieben vorhergesagten Proteinkomplexen sind. Die Proteinkomplexe habe ich durch Kombination von Interaktionsdaten und Daten eines siRNA Screenings vorhergesagt. Zusätzlich habe ich herausgefunden, dass die Proteine eines vorhergesagten Komplexes, nämlich HDAC1, pRB, HP1, BRG1 und c-MYC, die Aggregation von TDP-43 durch Veränderung von dessen Genexpression beeinflussen. / Neurodegenerative diseases (NDs) such as Alzheimer’s disease (AD), Parkinson’s disease (PD) or amyotrophic lateral sclerosis (ALS) are progressive brain disorders characterized by the accumulation of insoluble protein aggregates in neuronal cells or the extracellular space of patient brains. To elucidate potential common pathological mechanisms in different NDs, I created comprehensive interaction networks for various known and predicted neurodegenerative disease proteins (NDPs). I identified 18,663 protein-protein interactions (PPIs) for 449 bioinformatically selected wild-type target proteins and 22 mutant variants of 11 known NDPs by using an automated yeast two-hybrid (Y2H) system. The functional analysis of the interaction partners of corresponding wild-type and mutant NDPs revealed strong differences in the case of all 11 NDPs and especially for the ALS protein TDP-43. The identified PPIs were used to generate networks for individual NDs such as AD or PD and to identify proteins that are connected to multiple NDPs. For example, I found that five neurodegenerative diseases are connected by four proteins (APP, ZMAT2, ZNF179 and IQSEC1) that link known NDPs such as huntingtin, TDP-43, parkin, ataxin-1 and SOD1. Analysis of publicly available gene expression data suggested that the mRNA expression of the four proteins is abnormally altered in brains of ND patients. Moreover, the knock-down of IQSEC1, ZNF179 or ZMAT2 aggravates pathogenic disease mechanisms such as aggregation of mutant huntingtin or TDP-43 as well as hyperphosphorylation of tau. Additionally, I identified 22 modifiers of TDP-43 aggregation, which are members in 7 protein complexes. These complexes were predicted based on combined data from PPI as well as siRNA screenings. Finally, I found that the proteins HDAC1, pRB, HP1, BRG1 and c-MYC, which form one of the predicted complexes, influence TDP-43 aggregation by altering its mRNA expression.

Amyotrophic Lateral Sclerosis (ALS) is an incurable late onset neurodegenerative disorder characterised by the specific loss of motor neurones (MNs). It has been recently demonstrated that Transactive response DNA-binding protein (TDP-43) is the dominant disease protein in both ALS and a sub-group of frontotemporal lobar degeneration (FTLDTDP). Moreover, the identification of TARDBP mutations in familial ALS confirms a mechanistic link between the observed mis-accumulation of TDP-43 and neurodegeneration but also provides an opportunity to establish an in vitro platform to model these diseases, based on patient-derived induced pluripotent stem cells (iPSCs). This study presents the optimization of an iPSC-based platform to study the consequences of TDP-43 M337V mutation in human functional populations of MNs and astrocytes in isolation as well as in co-culture. To develop this platform, two protocols to differentiate patient-derived iPSCs into functional MNs and astrocytes were first optimized, and the obtained cellular populations were then used to characterize the behaviour of mutant TDP-43 and its effect on the different cell types. This study show that it is possible to use iPSC-based platforms to recapitulate in vitro key aspects of TDP-43 proteinopathies such as MN cell autonomous toxicity and TDP-43 accumulation, but they can also be used to highlight previously unrecognised disease specific mechanisms and to test novel therapeutic approaches. Moreover, by performing co-culture experiments it was possible to evaluate the effects of M337V astrocytes on the survival of wild-type and M337V TDP-43 motor neurons, showing that mutant TDP-43 astrocytes do not adversely affect survival of co-cultured neurons. This iPSC-based platform represents an in vitro model to study both the effect of somatic mutations on isolated patient-specific cultures, but also to investigate cellular autonomy and neurodegeneration in the context of TDP-43 proteinopathies.

The causes of Amyotrophic Lateral Sclerosis (ALS), a fatal neurodegenerative disease that results in skeletal muscle paralysis, remain unclear. However, a nuclear DNA and RNA binding protein called TAR DNA binding protein 43 (TDP-43) has emerged as a critical marker of ALS pathology. A previous drug screen conducted in the Zarnescu laboratory showed that anti-diabetic drugs can rescue lethality in a fruit fly model of ALS based on TDP-43. These results suggested that the insulin signaling pathway might be altered in motor neurons in a TDP-43 dependent manner. Therefore, we hypothesized that the insulin pathway is interacting with TDP-43 in vivo and may be contributing to TDP-43neurotoxicity. Using genetic interaction approaches in flies we found that TDP-43dependent locomotor defects are sensitive to the levels of insulin receptor activity. In addition, genetic interaction data suggest that Akt is hyperactivated in motor neurons expressing TDP-43, possibly as a compensatory mechanism to enable survival. Finally, upregulating protein synthesis through S6K and 4EBP appears to have beneficial effects. These findings support our hypothesis and provide insights into potential therapeutic strategies to help treat this devastating disease.

abstract: Alzheimer’s Disease (AD) and Frontotemporal Dementia (FTD) are the leading causes of early onset dementia. There are currently no ways to slow down progression, to prevent or cure AD and FTD. Both AD and FTD share a lot of the symptoms and pathology. Initial symptoms such as confusion, memory loss, mood swings and behavioral changes are common in both these dementia subtypes. Neurofibrillary tau tangles and intraneuronal aggregates of TAR DNA Binding Protein 43 (TDP-43) are also observed in both AD and FTD. Hence, FTD cases are often misdiagnosed as AD due to a lack of accurate diagnostics. Prior to the formation of tau tangles and TDP-43 aggregates, tau and TDP-43 exist as intermediate protein variants which correlate with cognitive decline and progression of these neurodegenerative diseases. Effective diagnostic and therapeutic agents would selectively recognize these toxic, disease-specific variants. Antibodies or antibody fragments such as single chain antibody variable domain fragments (scFvs), with their diverse binding capabilities, can aid in developing reagents that can selectively bind these protein variants. A combination of phage display library and Atomic Force Microscopy (AFM)-based panning was employed to identify antibody fragments against immunoprecipitated tau and immunoprecipitated TDP-43 from human postmortem AD and FTD brain tissue respectively. Five anti-TDP scFvs and five anti-tau scFvs were selected for characterization by Enzyme Linked Immunosorbent Assays (ELISAs) and Immunohistochemistry (IHC). The panel of scFvs, together, were able to identify distinct protein variants present in AD but not in FTD, and vice versa. Generating protein variant profiles for individuals, using the panel of scFvs, aids in developing targeted diagnostic and therapeutic plans, gearing towards personalized medicine. / Dissertation/Thesis / Doctoral Dissertation Neuroscience 2018

TAR DNA binding protein of 43 kDa (TDP-43) has been implicated in the pathogenesis of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Pathologically misfolded and aggregated forms of TDP-43 are found in cytoplasmic inclusion bodies of affected neurons in these diseases. The mechanism by which TDP-43 misfolding causes disease is not well understood. We postulate that the aggregation process plays a major role in pathogenesis, and we hypothesize that oligonucleotide ligands of TDP-43 can stabilize the native functional state of the protein and ameliorate aggregation of this aggregation-prone protein. Using recombinant TDP-43 we were able to examine the extent to which various oligonucleotide molecules affects its aggregation in vitro. We have found that certain natural sequence and de novo designed oligonucleotides bind TDP-43 and prevent its natural tendency to aggregate. The clinical and therapeutic implications of these findings are discussed.

TAR DNA binding protein of 43 kDa (TDP-43) has been implicated in the pathogenesis of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Pathologically misfolded and aggregated forms of TDP-43 are found in cytoplasmic inclusion bodies of affected neurons in these diseases. The mechanism by which TDP-43 misfolding causes disease is not well understood. We postulate that the aggregation process plays a major role in pathogenesis, and we hypothesize that oligonucleotide ligands of TDP-43 can stabilize the native functional state of the protein and ameliorate aggregation of this aggregation-prone protein. Using recombinant TDP-43 we were able to examine the extent to which various oligonucleotide molecules affects its aggregation in vitro. We have found that certain natural sequence and de novo designed oligonucleotides bind TDP-43 and prevent its natural tendency to aggregate. The clinical and therapeutic implications of these findings are discussed.

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