Deep scRNA sequencing reveals a broadly applicable Regeneration Classifier and implicates antioxidant response in corticospinal axon regeneration.

Despite substantial progress in understanding the biology of axon regeneration in the CNS, our ability to promote regeneration of the clinically important corticospinal tract (CST) after spinal cord injury remains limited. To understand regenerative heterogeneity, we conducted patch-based single-cell RNA sequencing on rare regenerating CST neurons at high depth following PTEN and SOCS3 deletion. Supervised classification with Garnett gave rise to a Regeneration Classifier, which can be broadly applied to predict the regenerative potential of diverse neuronal types across developmental stages or after injury. Network analyses highlighted the importance of antioxidant response and mitochondrial biogenesis. Conditional gene deletion validated a role for NFE2L2 (or NRF2), a master regulator of antioxidant response, in CST regeneration. Our data demonstrate a universal transcriptomic signature underlying the regenerative potential of vastly different neuronal populations and illustrate that deep sequencing of only hundreds of phenotypically identified neurons has the power to advance regenerative biology.

Probing regenerative heterogeneity of corticospinal neurons with scRNA-Seq.

The corticospinal tract (CST) is clinically important for the recovery of motor functions after spinal cord injury. Despite substantial progress in understanding the biology of axon regeneration in the central nervous system (CNS), our ability to promote CST regeneration remains limited. Even with molecular interventions, only a small proportion of CST axons regenerate1. Here we investigate this heterogeneity in the regenerative ability of corticospinal neurons following PTEN and SOCS3 deletion with patch-based single cell RNA sequencing (scRNA-Seq)2,3, which enables deep sequencing of rare regenerating neurons. Bioinformatic analyses highlighted the importance of antioxidant response and mitochondrial biogenesis along with protein translation. Conditional gene deletion validated a role for NFE2L2 (or NRF2), a master regulator of antioxidant response, in CST regeneration. Applying Garnett4, a supervised classification method, to our dataset gave rise to a Regenerating Classifier (RC), which, when applied to published scRNA-Seq data, generates cell type- and developmental stage-appropriate classifications. While embryonic brain, adult dorsal root ganglion and serotonergic neurons are classified as Regenerators, most neurons from adult brain and spinal cord are classified as Non-regenerators. Adult CNS neurons partially revert to a regenerative state soon after injury, which is accelerated by molecular interventions. Our data indicate the existence of universal transcriptomic signatures underlying the regenerative abilities of vastly different neuronal populations, and further illustrate that deep sequencing of only hundreds of phenotypically identified CST neurons has the power to reveal new insights into their regenerative biology.

Overexpressing eukaryotic elongation factor 1 alpha (eEF1A) proteins to promote corticospinal axon repair after injury.

Although protein synthesis is hypothesized to have a pivotal role in axonal repair after central nervous system (CNS) injury, the role of core components of the protein synthesis machinery has not been examined. Notably, some elongation factors possess non-canonical functions that may further impact axonal repair. Here, we examined whether overexpressing eukaryotic elongation factor 1 alpha (eEF1A) proteins enhances the collateral sprouting of corticospinal tract (CST) neurons after unilateral pyramidotomy, along with the underlying molecular mechanisms. We found that overexpressing eEF1A proteins in CST neurons increased the levels of pS6, an indicator for mTOR activity, but not pSTAT3 and pAKT levels, in neuronal somas. Strikingly, overexpressing eEF1A2 alone, but neither eEF1A1 alone nor both factors simultaneously, increased protein synthesis and actin rearrangement in CST neurons. While eEF1A1 overexpression only slightly enhanced CST sprouting after pyramidotomy, eEF1A2 overexpression substantially enhanced this sprouting. Surprisingly, co-overexpression of both eEF1A1 and eEF1A2 led to a sprouting phenotype similar to wild-type controls, suggesting an antagonistic effect of overexpressing both proteins. These data provide the first evidence that overexpressing a core component of the translation machinery, eEF1A2, enhances CST sprouting, likely by a combination of increased protein synthesis, mTOR signaling and actin cytoskeleton rearrangement.

A Critical Role for DLK and LZK in Axonal Repair in the Mammalian Spinal Cord.

The limited ability for axonal repair after spinal cord injury underlies long-term functional impairment. Dual leucine-zipper kinase [DLK; MAP kinase kinase kinase 12; MAP3K12] is an evolutionarily conserved MAP3K implicated in neuronal injury signaling from Caenorhabditis elegans to mammals. However, whether DLK or its close homolog leucine zipper kinase (LZK; MAP3K13) regulates axonal repair in the mammalian spinal cord remains unknown. Here, we assess the role of endogenous DLK and LZK in the regeneration and compensatory sprouting of corticospinal tract (CST) axons in mice of both sexes with genetic analyses in a regeneration competent background provided by PTEN deletion. We found that inducible neuronal deletion of both DLK and LZK, but not either kinase alone, abolishes PTEN deletion-induced regeneration and sprouting of CST axons, and reduces naturally-occurring axon sprouting after injury. Thus, DLK/LZK-mediated injury signaling operates not only in injured neurons to regulate regeneration, but also unexpectedly in uninjured neurons to regulate sprouting. Deleting DLK and LZK does not interfere with PTEN/mTOR signaling, indicating that injury signaling and regenerative competence are independently controlled. Together with our previous study implicating LZK in astrocytic reactivity and scar formation, these data illustrate the multicellular function of this pair of MAP3Ks in both neurons and glia in the injury response of the mammalian spinal cord.SIGNIFICANCE STATEMENT Functional recovery after spinal cord injury is limited because of a lack of axonal repair in the mammalian CNS. Dual leucine-zipper kinase (DLK) and leucine zipper kinase (LZK) are two closely related protein kinases that have emerged as regulators of neuronal responses to injury. However, their role in axonal repair in the mammalian spinal cord has not been described. Here, we show that DLK and LZK together play critical roles in axonal repair in the mammalian spinal cord, validating them as potential targets to promote repair and recovery after spinal cord injury. In addition to regulating axonal regeneration from injured neurons, both kinases also regulate compensatory axonal growth from uninjured neurons, indicating a more pervasive role in CNS repair than originally anticipated.

Visualizing APP and BACE-1 approximation in neurons yields insight into the amyloidogenic pathway.

Cleavage of amyloid precursor protein (APP) by BACE-1 (ß-site APP cleaving enzyme-1) is the rate-limiting step in amyloid-ß (Aß) production and a neuropathologic hallmark of Alzheimer's disease; thus, physical approximation of this substrate-enzyme pair is a crucial event with broad biological and therapeutic implications. Despite much research, neuronal locales of APP and BACE-1 convergence and APP cleavage remain unclear. Here we report an optical assay, based on fluorescence complementation, for visualizing in cellulo APP-BACE-1 interactions as a simple on/off signal. Combining this with other assays tracking the fate of internalized APP in hippocampal neurons, we found that APP and BACE-1 interacted in both biosynthetic and endocytic compartments, particularly along recycling microdomains such as dendritic spines and presynaptic boutons. In axons, APP and BACE-1 were cotransported, and they also interacted during transit. Finally, our assay revealed that the Alzheimer's disease-protective 'Icelandic' mutation greatly attenuates APP-BACE-1 interactions, suggesting a mechanistic basis for protection. Collectively, the data challenge canonical models and provide concrete insights into long-standing controversies in the field.

Impact of age on treatment trends and clinical outcome in patients with metastatic renal cell carcinoma.

OBJECTIVES: Clinical outcomes in older adults with metastatic renal cell carcinoma (mRCC) are poorly understood, particularly in the era of targeted therapies. We characterize survival and relevant treatment-related variables in a modern series. MATERIALS AND METHODS: From an institutional database including 562 patients with RCC, a total of 219 patients with metastatic disease were identified for the current analysis. Survival was assessed in four age-based cohorts: (1) age<55, (2) age 55­64, (3) age 65­74, and(4) age≥75. The number of lines of therapy rendered was collected for each patient, and the reason for treatment discontinuation was characterized. RESULTS: Of the 219 patients assessed, median age was 58 (range, 26­87), and most patients had clear cell histology (82%) and prior nephrectomy (70.9%). The majority of patients were characterized as intermediate-risk (53%) by MSKCC criteria. Median survival in patients age≥75 was 12.5 months, as compared to 26.4 months for patients age<75 (P=0.003). Patients age≥75 received fewer lines of systemic therapy as compared to other age-based subsets, and more frequently discontinued therapies due to toxicity. CONCLUSIONS: Older adults represent a unique subpopulation of patients with mRCC, with distinct clinical outcomes. Further research is warranted to better understand the safety and tolerability of current therapies for mRCC in this group.

Clinical outcome in patients receiving systemic therapy for metastatic sarcomatoid renal cell carcinoma: a retrospective analysis.

OBJECTIVES: Sarcomatoid metastatic renal cell carcinoma (mRCC) represents an aggressive subset of disease, and a definitive therapeutic strategy is lacking. We seek to define outcomes associated with systemic therapy (including immunotherapy, cytotoxic therapy, and targeted agents) for sarcomatoid mRCC, with attention to novel prognostic schema. MATERIALS AND METHODS: From an institutional database including 270 patients with mRCC, we identified 34 patients with documented sarcomatoid features. Within this cohort, we assessed 21 patients who received systemic therapy. Survival was assessed in the overall cohort and in subgroups divided by clinicopathologic characteristics, including the extent of sarcomatoid features, Memorial Sloan-Kettering Cancer Center (MSKCC) risk criteria, Heng criteria, and the nature of systemic therapy rendered. RESULTS: Of the 21 patients assessed, 2 patients received chemotherapy, 7 patients received immunotherapy, and 12 patients received targeted agents as their first line treatment. Median overall survival (OS) in the overall cohort was 18.0 months (95% CI 6.9-22.0). By MSKCC criteria, patients with poor-risk disease had a median OS of 4.7 months, compared with 20.1 months for patients with intermediate-risk disease [hazard ratio (HR) 0.02, 95%CI 0.003-0.15; P = 0.0001]. A similar difference in median OS was seen poor- and intermediate-risk groups when stratifying by Heng criteria (HR 0.17, 95%CI 0.001-0.12). There was no significant difference in survival in patients with sarcomatoid predominant disease vs. nonpredominant disease (HR 0.62, 95%CI 0.23-1.65; P = 0.34), nor was there a difference amongst patients who received targeted therapies vs. nontargeted therapies (HR 1.0, 95%CI 0.61-1.40; P = 0.36). CONCLUSIONS: Compared with previous series and prospective trials assessing patients with sarcomatoid mRCC, the observed survival was prolonged. Although both Heng and MSKCC risk scores may be useful in determining prognosis, further studies are needed to identify relevant biomarkers and define the optimal therapeutic strategy for this disease.

Quality of life in patients with metastatic renal cell carcinoma: assessment of long-term survivors.

BACKGROUND: An emerging literature describes the potential for long-term survival with targeted agents, but the health-related quality of life (HR-QOL) in patients who receive chronic therapy with these agents is poorly defined. METHODS: From an institutional database including 562 patients with renal cell carcinoma (RCC), patients were identified who (1) were alive 3 years beyond initiation of systemic therapy for metastatic renal cell carcinoma (mRCC) and (2) received a targeted therapy as a component of their treatment. European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire-Core 36 (QLQ-C30) and Functional Assessment of Cancer Therapy-Kidney Symptom Index (FKSI-15) questionnaires were administered by telephone survey. Data from questionnaires were compared with historical estimates derived from pivotal studies evaluating targeted agents. RESULTS: A total of 38 patients met eligibility criteria for the study, and 28 patients participated in the telephone survey. Most were male patients and had clear cell histologic type (75% for both). All patients had either good- or intermediate-risk disease by Heng criteria. The mean QLQ-C30 Global QOL score in the present cohort was higher than the mean score among patients evaluated at baseline in the phase III evaluations of pazopanib (73.5 vs. 65.8; P = .07) and everolimus (73.5 vs. 61.0; P = .007). The FKSI-15 score in the present cohort was similar to the mean score among patients evaluated at baseline in the phase III evaluation of sunitinib (45.1 and 46.5, respectively; P = .41). CONCLUSION: In this small pilot study, long-term survivors with mRCC who received targeted therapies appear to have an HR-QOL comparable to that of patients who participated in relevant phase III studies. Given the many emerging treatment options for mRCC, the HR-QOL of long-term survivors warrants greater attention.

Paclitaxel-based high-dose chemotherapy with autologous stem cell rescue for relapsed germ cell tumor: clinical outcome and quality of life in long-term survivors.

BACKGROUND: High-dose chemotherapy (HDCT) is a viable and potentially curative approach for patients with relapsed or refractory germ cell tumors (GCTs). However, no comparative data exist to define the optimal chemotherapeutic strategy, and little is known about the quality of life (QOL) of long-term survivors. Herein we attempt to characterize the QOL in long-term survivors who received high-dose paclitaxel, etoposide, carboplatin, and ifosfamide (TECTIC). PATIENTS AND METHODS: Details of the TECTIC regimen and clinical outcomes for the initial 33 patients have been reported. In the present study, we report the clinical data for 15 additional patients. Using the European Organization for the Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire-Core 30 (QLQ-C30) and the Functional Assessment of Cancer Therapy-Taxane (FACT-T) questionnaires, we surveyed all patients who survived at least 4 years after HDCT. RESULTS: Forty-eight patients were enrolled and 46 patients received protocol therapy. For all 48 patients, the median progression-free survival (PFS) and overall survival (OS) were 11.8 months (range, 5.8-not reached) and 21.7 months (range, 12.7-not reached), respectively. Seventeen patients were progression free at a median of 123.2 months (51.6-170.2 months), and 6 patients remain alive after progression with a median OS of 68.8 months (47.6-147.1 months). Of the 23 surviving patients, 18 were accessible and consented to telephone interviews. Compared with historical cohorts, survivors had a higher global health scale score (87.04 vs. 75.62; P = .02) but a lower physical functioning score (68.89 vs. 92.66; P = .0001) by the QLQ-C30 scale. CONCLUSIONS: HDCT with the TECTIC regimen produces durable remissions in patients with relapsed or refractory GCTs with acceptable QOL in long-term survivors.